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GSE233985/metadata.tsv

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+sample_id	group	time	batch	original_sample_id	study_id	organism	tissue	specimen	cell_type	treatment	age	src_batch	platform	assay	source_file	title_short	sample_description	instrument	strain	characteristics	condition
+HSCaged1	control	>80 weeks old	1	RNA-Seq - HSC - aged control 1	GSE233985	Mus musculus	Bone marrow	Bone marrow	Hemtopoietic stem cells	control	>80 weeks old	1	GPL21626	RNA-Seq	GSE233985_series_matrix.txt.gz	RNA-Seq - HSC - aged control 1	HSCaged1	NextSeq 550	C57BL/6	tissue=Bone marrow; strain=C57BL/6; cell type=Hemtopoietic stem cells; age=>80 weeks old; treatment=control; sequencing batch=1	aged_control
+HSCaged2	control	>80 weeks old	2	RNA-Seq - HSC - aged control 2	GSE233985	Mus musculus	Bone marrow	Bone marrow	Hemtopoietic stem cells	control	>80 weeks old	2	GPL21626	RNA-Seq	GSE233985_series_matrix.txt.gz	RNA-Seq - HSC - aged control 2	HSCaged2	NextSeq 550	C57BL/6	tissue=Bone marrow; strain=C57BL/6; cell type=Hemtopoietic stem cells; age=>80 weeks old; treatment=control; sequencing batch=2	aged_control
+HSCaged3	control	>80 weeks old	3	RNA-Seq - HSC - aged control 3	GSE233985	Mus musculus	Bone marrow	Bone marrow	Hemtopoietic stem cells	control	>80 weeks old	3	GPL21626	RNA-Seq	GSE233985_series_matrix.txt.gz	RNA-Seq - HSC - aged control 3	HSCaged3	NextSeq 550	C57BL/6	tissue=Bone marrow; strain=C57BL/6; cell type=Hemtopoietic stem cells; age=>80 weeks old; treatment=control; sequencing batch=3	aged_control
+HSCrhoai1	RhoA-inhibitor (Ri) treatment	>80 weeks old	1	RNA-Seq - HSC - aged + RhoA-inhibitor (Ri) 1	GSE233985	Mus musculus	Bone marrow	Bone marrow	Hemtopoietic stem cells	RhoA-inhibitor (Ri) treatment	>80 weeks old	1	GPL21626	RNA-Seq	GSE233985_series_matrix.txt.gz	RNA-Seq - HSC - aged + RhoA-inhibitor (Ri) 1	HSCrhoai1	NextSeq 550	C57BL/6	tissue=Bone marrow; strain=C57BL/6; cell type=Hemtopoietic stem cells; age=>80 weeks old; treatment=RhoA-inhibitor (Ri) treatment; sequencing batch=1	aged_Ri
+HSCrhoai2	RhoA-inhibitor (Ri) treatment	>80 weeks old	2	RNA-Seq - HSC - aged + RhoA-inhibitor (Ri) 2	GSE233985	Mus musculus	Bone marrow	Bone marrow	Hemtopoietic stem cells	RhoA-inhibitor (Ri) treatment	>80 weeks old	2	GPL21626	RNA-Seq	GSE233985_series_matrix.txt.gz	RNA-Seq - HSC - aged + RhoA-inhibitor (Ri) 2	HSCrhoai2	NextSeq 550	C57BL/6	tissue=Bone marrow; strain=C57BL/6; cell type=Hemtopoietic stem cells; age=>80 weeks old; treatment=RhoA-inhibitor (Ri) treatment; sequencing batch=2	aged_Ri
+HSCrhoai3	RhoA-inhibitor (Ri) treatment	>80 weeks old	2	RNA-Seq - HSC - aged + RhoA-inhibitor (Ri) 3	GSE233985	Mus musculus	Bone marrow	Bone marrow	Hemtopoietic stem cells	RhoA-inhibitor (Ri) treatment	>80 weeks old	2	GPL21626	RNA-Seq	GSE233985_series_matrix.txt.gz	RNA-Seq - HSC - aged + RhoA-inhibitor (Ri) 3	HSCrhoai3	NextSeq 550	C57BL/6	tissue=Bone marrow; strain=C57BL/6; cell type=Hemtopoietic stem cells; age=>80 weeks old; treatment=RhoA-inhibitor (Ri) treatment; sequencing batch=2	aged_Ri
+HSCyoung1	control	10-16 weeks old	1+3	RNA-Seq - HSC - young control 1	GSE233985	Mus musculus	Bone marrow	Bone marrow	Hemtopoietic stem cells	control	10-16 weeks old	1+3	GPL21626	RNA-Seq	GSE233985_series_matrix.txt.gz	RNA-Seq - HSC - young control 1	HSCyoung1	NextSeq 550	C57BL/6	tissue=Bone marrow; strain=C57BL/6; cell type=Hemtopoietic stem cells; age=10-16 weeks old; treatment=control; sequencing batch=1+3	young_control
+HSCyoung2	control	10-16 weeks old	2	RNA-Seq - HSC - young control 2	GSE233985	Mus musculus	Bone marrow	Bone marrow	Hemtopoietic stem cells	control	10-16 weeks old	2	GPL21626	RNA-Seq	GSE233985_series_matrix.txt.gz	RNA-Seq - HSC - young control 2	HSCyoung2	NextSeq 550	C57BL/6	tissue=Bone marrow; strain=C57BL/6; cell type=Hemtopoietic stem cells; age=10-16 weeks old; treatment=control; sequencing batch=2	young_control
+HSCyoung3	control	10-16 weeks old	3	RNA-Seq - HSC - young control 3	GSE233985	Mus musculus	Bone marrow	Bone marrow	Hemtopoietic stem cells	control	10-16 weeks old	3	GPL21626	RNA-Seq	GSE233985_series_matrix.txt.gz	RNA-Seq - HSC - young control 3	HSCyoung3	NextSeq 550	C57BL/6	tissue=Bone marrow; strain=C57BL/6; cell type=Hemtopoietic stem cells; age=10-16 weeks old; treatment=control; sequencing batch=3	young_control

GSE233985/study_description.txt

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+We studied long-term hematopoietic stem cells (LT-HSCs) sorted from the bone marrow of young (10-16 weeks old) and aged (>80 weeks old) C57BL/6 mice and cultured ex vivo for 16 hours; the RhoA inhibitor Rhosin (Ri, 100 µM) was added to aged cells only. The three conditions, three samples each, are in the `condition` column: young_control (young cells without Ri), aged_control (aged cells without Ri) and aged_Ri (aged cells with Ri). The `group` column, copied in `treatment`, records only whether Ri was added, so its control level pools young and aged cells. The `time` column, copied in `age`, holds the donor age, not a sampling time: all samples were collected at the end of the 16-hour culture, so there is no time variable.
+
+Each sample is one cultured population of sorted LT-HSCs and one library; there are no technical replicates. No mouse or sort identifiers are recorded, and no record links an aged control to a particular Ri-treated sample; the numbers 1 to 3 in the sample names only count the samples within each condition. The GEO records also carry a code labelled 'sequencing batch', copied into `batch` and `src_batch` (1, 2, 3, and '1+3' for one young sample), with no explanation beyond that label. We cannot tell what the codes, including '1+3', correspond to in practice, and the expression data show no clear grouping by them, so the batch structure of these samples is unknown to us. No other variable matters to us; the remaining columns are annotations or constant.
+
+These are bulk RNA-seq data from SMART-Seq v4 low-input libraries. The matrix holds gene-level read-pair counts from featureCounts for protein-coding genes; multi-mapping reads were counted fractionally, so the counts have been rounded to whole numbers.
+
+Our question is which genes are differentially expressed in aged LT-HSCs treated with the RhoA inhibitor (aged_Ri) compared with untreated aged LT-HSCs (aged_control). Only the six samples with `condition` aged_control or aged_Ri are part of this question; the young_control samples are not.

GSE244440/metadata.tsv

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+sample_id	group	original_sample_id	study_id	organism	tissue	specimen	cell_type	timepoint	platform	assay	source_file	title_short	sample_description	instrument	differentiation	characteristics
+SC1_0	Day0	SC1_Day0	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day0	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC1_Day0	SC1_0	Illumina NovaSeq 6000	Differentiation SC1	tissue=Brain; time point=Day0; cell type=igNeurons; differentiation=Differentiation SC1
+SC2_0	Day0	SC2_Day0	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day0	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC2_Day0	SC2_0	Illumina NovaSeq 6000	Differentiation SC2	tissue=Brain; time point=Day0; cell type=igNeurons; differentiation=Differentiation SC2
+SC3_0	Day0	SC3_Day0	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day0	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC3_Day0	SC3_0	Illumina NovaSeq 6000	Differentiation SC3	tissue=Brain; time point=Day0; cell type=igNeurons; differentiation=Differentiation SC3
+SC1_9	Day9	SC1_Day9	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day9	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC1_Day9	SC1_9	Illumina NovaSeq 6000	Differentiation SC1	tissue=Brain; time point=Day9; cell type=igNeurons; differentiation=Differentiation SC1
+SC2_9	Day9	SC2_Day9	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day9	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC2_Day9	SC2_9	Illumina NovaSeq 6000	Differentiation SC2	tissue=Brain; time point=Day9; cell type=igNeurons; differentiation=Differentiation SC2
+SC3_9	Day9	SC3_Day9	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day9	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC3_Day9	SC3_9	Illumina NovaSeq 6000	Differentiation SC3	tissue=Brain; time point=Day9; cell type=igNeurons; differentiation=Differentiation SC3
+SC1_15	Day15	SC1_Day15	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day15	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC1_Day15	SC1_15	Illumina NovaSeq 6000	Differentiation SC1	tissue=Brain; time point=Day15; cell type=igNeurons; differentiation=Differentiation SC1
+SC2_15	Day15	SC2_Day15	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day15	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC2_Day15	SC2_15	Illumina NovaSeq 6000	Differentiation SC2	tissue=Brain; time point=Day15; cell type=igNeurons; differentiation=Differentiation SC2
+SC3_15	Day15	SC3_Day15	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day15	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC3_Day15	SC3_15	Illumina NovaSeq 6000	Differentiation SC3	tissue=Brain; time point=Day15; cell type=igNeurons; differentiation=Differentiation SC3
+SC1_21	Day21	SC1_Day21	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day21	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC1_Day21	SC1_21	Illumina NovaSeq 6000	Differentiation SC1	tissue=Brain; time point=Day21; cell type=igNeurons; differentiation=Differentiation SC1
+SC2_21	Day21	SC2_Day21	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day21	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC2_Day21	SC2_21	Illumina NovaSeq 6000	Differentiation SC2	tissue=Brain; time point=Day21; cell type=igNeurons; differentiation=Differentiation SC2
+SC3_21	Day21	SC3_Day21	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day21	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC3_Day21	SC3_21	Illumina NovaSeq 6000	Differentiation SC3	tissue=Brain; time point=Day21; cell type=igNeurons; differentiation=Differentiation SC3
+SC1_27	Day27	SC1_Day27	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day27	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC1_Day27	SC1_27	Illumina NovaSeq 6000	Differentiation SC1	tissue=Brain; time point=Day27; cell type=igNeurons; differentiation=Differentiation SC1
+SC2_27	Day27	SC2_Day27	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day27	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC2_Day27	SC2_27	Illumina NovaSeq 6000	Differentiation SC2	tissue=Brain; time point=Day27; cell type=igNeurons; differentiation=Differentiation SC2
+SC3_27	Day27	SC3_Day27	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day27	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC3_Day27	SC3_27	Illumina NovaSeq 6000	Differentiation SC3	tissue=Brain; time point=Day27; cell type=igNeurons; differentiation=Differentiation SC3
+SC1_33	Day33	SC1_Day33	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day33	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC1_Day33	SC1_33	Illumina NovaSeq 6000	Differentiation SC1	tissue=Brain; time point=Day33; cell type=igNeurons; differentiation=Differentiation SC1
+SC2_33	Day33	SC2_Day33	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day33	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC2_Day33	SC2_33	Illumina NovaSeq 6000	Differentiation SC2	tissue=Brain; time point=Day33; cell type=igNeurons; differentiation=Differentiation SC2
+SC3_33	Day33	SC3_Day33	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day33	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC3_Day33	SC3_33	Illumina NovaSeq 6000	Differentiation SC3	tissue=Brain; time point=Day33; cell type=igNeurons; differentiation=Differentiation SC3
+SC1_40	Day40	SC1_Day40	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day40	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC1_Day40	SC1_40	Illumina NovaSeq 6000	Differentiation SC1	tissue=Brain; time point=Day40; cell type=igNeurons; differentiation=Differentiation SC1
+SC2_40	Day40	SC2_Day40	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day40	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC2_Day40	SC2_40	Illumina NovaSeq 6000	Differentiation SC2	tissue=Brain; time point=Day40; cell type=igNeurons; differentiation=Differentiation SC2
+SC3_40	Day40	SC3_Day40	GSE244440	Homo sapiens	Brain	Brain	igNeurons	Day40	GPL24676	RNA-Seq	GSE244440_series_matrix.txt.gz	SC3_Day40	SC3_40	Illumina NovaSeq 6000	Differentiation SC3	tissue=Brain; time point=Day40; cell type=igNeurons; differentiation=Differentiation SC3

GSE244440/study_description.txt

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+We differentiated human iPSCs into excitatory cortical-like neurons (igNeurons) by NGN2 induction and followed them over time. We ran three independent differentiations, recorded in the `differentiation` column as Differentiation SC1, Differentiation SC2 and Differentiation SC3, and took one RNA sample from each on days 0, 9, 15, 21, 27, 33 and 40, 21 samples in total. The day of differentiation is in the `timepoint` column (Day0, Day9, Day15, Day21, Day27, Day33, Day40); the `group` column repeats the same labels. Day0 is the undifferentiated iPSC stage, and Day9 to Day40 cover neuronal maturation. There are no treatment or control groups: this is a pure time course.
+
+Because every differentiation was sampled on every day, the samples of one differentiation are related: they come from the same starting cells and the same induction and form one series over time. Each sample was sequenced once, so there are no technical replicates. We have no record of processing or sequencing batches, and no other variable we think matters; the remaining columns are GEO annotations.
+
+The data are ribosomal-RNA-depleted bulk total RNA-seq, quantified with featureCounts as raw gene-level read counts for Ensembl genes.
+
+Our question is which genes change in expression over neuronal maturation, looking at the overall change across Day9, Day15, Day21, Day27, Day33 and Day40, with Day9 as the baseline. Only the samples whose `timepoint` is one of these six days are part of this question; the Day0 iPSC samples are not.

GSE267256/metadata.tsv

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+sample_id	group	original_sample_id	study_id	organism	tissue	specimen	cell_type	treatment	platform	assay	source_file	title_short	sample_description	instrument	strain	genotype	characteristics	geo_gsm	geo_title
+GFP_1dpiCF_1_S1_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI Replicate 1	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI Replicate 1	GFP_1dpiCF_1_S1_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263035	Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI Replicate 1
+GFP_1dpiCF_2_S2_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI Replicate 2	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI Replicate 2	GFP_1dpiCF_2_S2_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263036	Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI Replicate 2
+GFP_1dpiCF_3_S3_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI Replicate 3	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI Replicate 3	GFP_1dpiCF_3_S3_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263037	Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI Replicate 3
+GFP_2dpiCF_1_S4_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI Replicate 1	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI Replicate 1	GFP_2dpiCF_1_S4_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263038	Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI Replicate 1
+GFP_2dpiCF_2_S5_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI Replicate 2	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI Replicate 2	GFP_2dpiCF_2_S5_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263039	Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI Replicate 2
+GFP_2dpiCF_3_S6_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI Replicate 3	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI Replicate 3	GFP_2dpiCF_3_S6_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263040	Col1a1 GFP+ Cardiac Fibroblasts 2 days after MI Replicate 3
+3dpi_1	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 1	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 1	3dpi_1	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263031	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 1
+3dpi_2	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 2	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 2	3dpi_2	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263032	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 2
+3dpi_3	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 3	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 3	3dpi_3	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263033	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 3
+3dpi_4	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 4	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 4	3dpi_4	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263034	Col1a1 GFP+ Cardiac Fibroblasts 3 days after MI Replicate 4
+GFP_4dpiCF_1_S7_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI Replicate 1	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI Replicate 1	GFP_4dpiCF_1_S7_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263041	Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI Replicate 1
+GFP_4dpiCF_2_S8_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI Replicate 2	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI Replicate 2	GFP_4dpiCF_2_S8_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263042	Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI Replicate 2
+GFP_4dpiCF_3_S9_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI Replicate 3	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI Replicate 3	GFP_4dpiCF_3_S9_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263043	Col1a1 GFP+ Cardiac Fibroblasts 4 days after MI Replicate 3
+GFP_5dpiCF_1_S10_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 5 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 5 days after MI Replicate 3	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 5 days after MI Replicate 3	GFP_5dpiCF_1_S10_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263044	Col1a1 GFP+ Cardiac Fibroblasts 5 days after MI Replicate 3
+GFP_6dpiCF_1_S11_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI Replicate 1	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI Replicate 1	GFP_6dpiCF_1_S11_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263045	Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI Replicate 1
+GFP_6dpiCF_2_S12_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI Replicate 2	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI Replicate 2	GFP_6dpiCF_2_S12_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263046	Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI Replicate 2
+GFP_6dpiCF_3_S13_R1_001	Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI	Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI Replicate 3	GSE267256	Mus musculus	Heart	Heart	Col1a1-GFP+ cells	myocardial infarction	GPL19057	RNA-Seq	GSE267256_series_matrix.txt.gz	Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI Replicate 3	GFP_6dpiCF_3_S13_R1_001	Illumina NextSeq 500	C57BL/6	Collagen1a1-GFP+	tissue=Heart; cell type=Col1a1-GFP+ cells; strain=C57BL/6; genotype=Collagen1a1-GFP+; treatment=myocardial infarction	GSM8263047	Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI Replicate 3

GSE267256/study_description.txt

@@ -0,0 +1,7 @@
+We studied mouse cardiac fibroblasts in the first days after myocardial infarction (MI). Col1a1-GFP reporter mice (C57BL/6 background, 8-10 weeks old) received an MI by permanent ligation of the left anterior descending coronary artery, and their hearts were harvested 1, 2, 3, 4, 5 or 6 days later; from each harvest we FACS-sorted Col1a1-GFP+ CD31- CD45- cardiac fibroblasts. The six harvest days are the groups we compare. They are recorded in the `group` column, from 'Col1a1 GFP+ Cardiac Fibroblasts 1 days after MI' to 'Col1a1 GFP+ Cardiac Fibroblasts 6 days after MI', with 3, 3, 4, 3, 1 and 3 samples for days 1 to 6 (17 in all). The day appears only inside these labels; there is no separate time column. All mice had an MI, and there is no healthy or sham group.
+
+Mice are killed at harvest, so each sample is a separately sorted cell population and no mouse appears at two harvest days; whether a sample came from one heart or from several pooled hearts is not recorded. Each library was sequenced once, so there are no technical replicates. The MARS-seq library pools and sequencing runs were not recorded, so we have no batch information. Mouse IDs and sex are not recorded either, and no other variable matters to us; the remaining columns are constant annotations or sample names.
+
+The data are bulk RNA-seq made with the MARS-seq protocol. The matrix holds raw gene-level read counts from featureCounts, one row per Ensembl gene ID (mm10).
+
+Our question is which genes differ in expression among the six harvest days: an overall difference anywhere among the six `group` levels, with day 1 as the baseline, rather than a comparison of two particular days. All 17 samples, including the single day-5 sample, are part of this question.

GSE273740/metadata.tsv

@@ -0,0 +1,7 @@
+sample_id	group	organism	tissue	platform	assay	study_id
+Con_1	control_Klf4wt	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273740
+Con_2	control_Klf4wt	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273740
+Con_3	control_Klf4wt	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273740
+Mut_1	Klf4_alphaKO	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273740
+Mut_2	Klf4_alphaKO	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273740
+Mut_3	Klf4_alphaKO	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273740

GSE273740/study_description.txt

@@ -0,0 +1,7 @@
+We studied whole pancreatic islets from 5-week-old mice in which Klf4 was knocked out in the alpha-cell lineage. The `group` column holds the genotype: Klf4_alphaKO are Klf4fl/fl;Gcg-iCre knockout mice (samples Mut_1 to Mut_3) and control_Klf4wt are Klf4+/+;Gcg-iCre mice that carry only the Cre (samples Con_1 to Con_3). The islets were not sorted, so each sample contains all islet cell types. All islets were collected at the same age, so there is no time variable.
+
+Each sample is a separate whole-islet RNA preparation sequenced as one library, and there are no technical replicates. There is no record of repeated sampling of a mouse, pooling of mice or litter pairing; the numbers in the sample names only count the samples within each genotype. No islet-isolation, library or sequencing batch is recorded, so we have no batch information. The sex of the mice is not recorded, and no other variable matters to us; the remaining columns are constant annotations.
+
+The data are bulk poly(A) mRNA-seq (Tecan Universal Plus mRNA-seq). The matrix holds raw gene-level read counts from featureCounts (mm10), one row per gene.
+
+Our question is which genes are differentially expressed in Klf4 alpha-cell knockout islets (Klf4_alphaKO) compared with Cre-only control islets (control_Klf4wt), using all six samples.

GSE273742/metadata.tsv

@@ -0,0 +1,9 @@
+sample_id	group	organism	tissue	platform	assay	study_id	batch
+beta_control_1	empty_vector_control	Mus musculus	Min6	GPL24247	RNA-Seq	GSE273742	batch_1
+beta_control_2	empty_vector_control	Mus musculus	Min6	GPL24247	RNA-Seq	GSE273742	batch_1
+beta_control_3	empty_vector_control	Mus musculus	Min6	GPL24247	RNA-Seq	GSE273742	batch_2
+beta_control_4	empty_vector_control	Mus musculus	Min6	GPL24247	RNA-Seq	GSE273742	batch_2
+beta_overexpression_1	Klf4_overexpression	Mus musculus	Min6	GPL24247	RNA-Seq	GSE273742	batch_1
+beta_overexpression_2	Klf4_overexpression	Mus musculus	Min6	GPL24247	RNA-Seq	GSE273742	batch_1
+beta_overexpression_3	Klf4_overexpression	Mus musculus	Min6	GPL24247	RNA-Seq	GSE273742	batch_2
+beta_overexpression_4	Klf4_overexpression	Mus musculus	Min6	GPL24247	RNA-Seq	GSE273742	batch_2

GSE273742/study_description.txt

@@ -0,0 +1,7 @@
+We transfected the mouse pancreatic beta-cell line MIN6 with either a Klf4 overexpression plasmid (pGloMyc-Klf4) or the empty pcDNA3 vector as a control, and harvested the cells 48 hours after transfection. The `group` column holds the condition: Klf4_overexpression or empty_vector_control, four cultures each. All samples were harvested at the same time, so there is no time variable.
+
+Each sample is a separate transfected culture sequenced as one library; no culture was measured twice, so there are no technical replicates. According to the GEO sample records, the samples were processed in two batches, recorded in the `batch` column: batch_1 holds replicates 1 and 2 of each condition and batch_2 holds replicates 3 and 4 (the number at the end of each sample name), so each batch contains two cultures of each condition. There is no record that a particular control culture was matched to a particular overexpression culture within a batch. No other variable matters to us; the remaining columns are constant annotations.
+
+The data are bulk poly(A) mRNA-seq (Tecan Universal Plus mRNA-seq). The matrix holds raw gene-level read counts from featureCounts (mm10).
+
+Our question is which genes are differentially expressed in Klf4-overexpressing MIN6 cells (Klf4_overexpression) compared with empty-vector control cells (empty_vector_control), using all eight samples.

GSE273744/metadata.tsv

@@ -0,0 +1,8 @@
+sample_id	group	organism	tissue	platform	assay	study_id
+Con_1	control_Nkx22wt	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273744
+Con_2	control_Nkx22wt	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273744
+Con_3	control_Nkx22wt	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273744
+Con_4	control_Nkx22wt	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273744
+Mut_1	Nkx2.2_alphaKO	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273744
+Mut_2	Nkx2.2_alphaKO	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273744
+Mut_4	Nkx2.2_alphaKO	Mus musculus	pancreatic islets	GPL34328	RNA-Seq	GSE273744

GSE273744/study_description.txt

@@ -0,0 +1,7 @@
+We studied alpha-cell-lineage cells sorted from the pancreatic islets of 5-week-old mice. The `group` column holds the genotype: Nkx2.2_alphaKO are alpha-cell-specific Nkx2.2 knockouts (Nkx2.2fl/fl;Gcg-iCre;Rosa26:tdTomato) and control_Nkx22wt are Gcg-iCre controls (Nkx2.2+/+;Gcg-iCre;Rosa26:tdTomato). From both genotypes we collected the tdTomato-positive cells by FACS. There are four control libraries (Con_1 to Con_4) and three knockout libraries, named Mut_1, Mut_2 and Mut_4; there is no Mut_3 in the files. All mice were sampled at the same age, so there is no time variable.
+
+Each sample is one library of sorted cells, and there are no technical replicates. Whether a library comes from one mouse or from cells pooled from several mice is not recorded, but no mouse is recorded as contributing to more than one library; the numbers in the sample names only count the libraries within each genotype, and there is no record of litters or pairing. Sort, library and sequencing batches are not recorded, so we have no batch information. Sex is not recorded, and no other variable matters to us; the remaining columns are constant annotations.
+
+The data are low-input bulk total RNA-seq (SMARTer Stranded Total RNA-Seq Pico v2). The matrix holds raw gene-level read counts from featureCounts after STAR alignment to mm10.
+
+Our question is which genes are differentially expressed in sorted alpha-cell-lineage cells of Nkx2.2 knockout mice (Nkx2.2_alphaKO) compared with Gcg-iCre controls (control_Nkx22wt), using all seven libraries.

GSE275234/metadata.tsv

@@ -0,0 +1,7 @@
+sample_id	group	original_sample_id	study_id	organism	tissue	specimen	cell_type	treatment	platform	assay	source_file	title_short	sample_description	instrument	genotype	characteristics
+EP-NC-1	wild type	control,replicate 1	GSE275234	Homo sapiens	thyroid	thyroid	Htoris-3.1	Etoposide treatment for 12 hours	GPL29480	RNA-Seq	GSE275234_series_matrix.txt.gz	control	EP_NC_1	DNBSEQ-T7	wild type	tissue=thyroid; cell line=Htoris-3.1; cell type=normal thyroid cell line; genotype=wild type; treatment=Etoposide treatment for 12 hours
+EP-NC-2	wild type	control,replicate 2	GSE275234	Homo sapiens	thyroid	thyroid	Htoris-3.1	Etoposide treatment for 12 hours	GPL29480	RNA-Seq	GSE275234_series_matrix.txt.gz	control	EP_NC_2	DNBSEQ-T7	wild type	tissue=thyroid; cell line=Htoris-3.1; cell type=normal thyroid cell line; genotype=wild type; treatment=Etoposide treatment for 12 hours
+EP-NC-3	wild type	control,replicate 3	GSE275234	Homo sapiens	thyroid	thyroid	Htoris-3.1	Etoposide treatment for 12 hours	GPL29480	RNA-Seq	GSE275234_series_matrix.txt.gz	control	EP_NC_3	DNBSEQ-T7	wild type	tissue=thyroid; cell line=Htoris-3.1; cell type=normal thyroid cell line; genotype=wild type; treatment=Etoposide treatment for 12 hours
+EP-Sg-1	BMAL1 knock out	sgRNA Bmal1,replicate 1	GSE275234	Homo sapiens	thyroid	thyroid	Htoris-3.1	Etoposide treatment for 12 hours	GPL29480	RNA-Seq	GSE275234_series_matrix.txt.gz	sgRNA Bmal1	EP_sg_1	DNBSEQ-T7	BMAL1 knock out	tissue=thyroid; cell line=Htoris-3.1; cell type=normal thyroid cell line; genotype=BMAL1 knock out; treatment=Etoposide treatment for 12 hours
+EP-Sg-2	BMAL1 knock out	sgRNA Bmal1,replicate 2	GSE275234	Homo sapiens	thyroid	thyroid	Htoris-3.1	Etoposide treatment for 12 hours	GPL29480	RNA-Seq	GSE275234_series_matrix.txt.gz	sgRNA Bmal1	EP_sg_2	DNBSEQ-T7	BMAL1 knock out	tissue=thyroid; cell line=Htoris-3.1; cell type=normal thyroid cell line; genotype=BMAL1 knock out; treatment=Etoposide treatment for 12 hours
+EP-Sg-3	BMAL1 knock out	sgRNA Bmal1,replicate 3	GSE275234	Homo sapiens	thyroid	thyroid	Htoris-3.1	Etoposide treatment for 12 hours	GPL29480	RNA-Seq	GSE275234_series_matrix.txt.gz	sgRNA Bmal1	EP_sg_3	DNBSEQ-T7	BMAL1 knock out	tissue=thyroid; cell line=Htoris-3.1; cell type=normal thyroid cell line; genotype=BMAL1 knock out; treatment=Etoposide treatment for 12 hours

GSE275234/study_description.txt

@@ -0,0 +1,7 @@
+We used the human normal thyroid cell line Htoris-3.1 and knocked out BMAL1 with CRISPR-Cas9, selecting single clones. The `group` column, repeated in `genotype`, holds the genotype: BMAL1 knock out (samples EP-Sg-1 to EP-Sg-3) or wild type, the control cells (samples EP-NC-1 to EP-NC-3), three cultures each. All six cultures were treated with etoposide before RNA was collected; the `treatment` column gives 'Etoposide treatment for 12 hours' for every sample. There is no untreated group, and all samples were collected at the same point, so there is no time variable.
+
+Each sample is a separate culture sequenced as one library, no two libraries are recorded as coming from the same culture, and there are no technical replicates. Both groups carry the numbers 1 to 3 at the end of their sample names, but these only count the cultures within each group: there is no record that same-numbered knockout and control cultures were grown, treated or sequenced together, and same-numbered cultures are no more alike in expression than other combinations. We have no record of processing or sequencing batches, and no other variable matters to us; the remaining columns are GEO annotations.
+
+The data are bulk RNA-seq (DNBSEQ-T7, paired-end reads). The matrix holds raw gene-level read counts after alignment to hg38; most rows are gene symbols, the others Ensembl IDs or novel loci named MSTRG.
+
+Our question is which genes are differentially expressed in BMAL1 knockout cells (BMAL1 knock out) compared with control cells (wild type) after etoposide treatment, using all six samples.

GSE278237/metadata.tsv

@@ -0,0 +1,7 @@
+sample_id	group	organism	tissue	platform	assay	study_id	original_sample_id	specimen	cell_type	treatment	source_file	title_short	sample_description	instrument	genotype	characteristics
+count.DMS114_1	WT	Homo sapiens	DMS114	GPL24676	RNA-Seq	GSE278237	DMS114 cells, control, rep1	DMS114	DMS114	WT	GSE278237_series_matrix.txt.gz	DMS114 cells	DMS114_1	Illumina NovaSeq 6000	non-NE(SCLC-YAP1)	cell line=DMS114; cell type=SCLC cells; genotype=non-NE(SCLC-YAP1); treatment=WT
+count.DMS114_2	WT	Homo sapiens	DMS114	GPL24676	RNA-Seq	GSE278237	DMS114 cells, control, rep2	DMS114	DMS114	WT	GSE278237_series_matrix.txt.gz	DMS114 cells	DMS114_2	Illumina NovaSeq 6000	non-NE(SCLC-YAP1)	cell line=DMS114; cell type=SCLC cells; genotype=non-NE(SCLC-YAP1); treatment=WT
+count.DMS114_3	WT	Homo sapiens	DMS114	GPL24676	RNA-Seq	GSE278237	DMS114 cells, control, rep3	DMS114	DMS114	WT	GSE278237_series_matrix.txt.gz	DMS114 cells	DMS114_3	Illumina NovaSeq 6000	non-NE(SCLC-YAP1)	cell line=DMS114; cell type=SCLC cells; genotype=non-NE(SCLC-YAP1); treatment=WT
+count.DMS114_Tre_1	treated with 200 mM trehalose for 12 hours	Homo sapiens	DMS114	GPL24676	RNA-Seq	GSE278237	DMS114 cells,treated with 200 mM trehalose, rep1	DMS114	DMS114	treated with 200 mM trehalose for 12 hours	GSE278237_series_matrix.txt.gz	DMS114 cells	DMS114_Tre_1	Illumina NovaSeq 6000	non-NE(SCLC-YAP1)	cell line=DMS114; cell type=SCLC cells; genotype=non-NE(SCLC-YAP1); treatment=treated with 200 mM trehalose for 12 hours
+count.DMS114_Tre_2	treated with 200 mM trehalose for 12 hours	Homo sapiens	DMS114	GPL24676	RNA-Seq	GSE278237	DMS114 cells,treated with 200 mM trehalose, rep2	DMS114	DMS114	treated with 200 mM trehalose for 12 hours	GSE278237_series_matrix.txt.gz	DMS114 cells	DMS114_Tre_2	Illumina NovaSeq 6000	non-NE(SCLC-YAP1)	cell line=DMS114; cell type=SCLC cells; genotype=non-NE(SCLC-YAP1); treatment=treated with 200 mM trehalose for 12 hours
+count.DMS114_Tre_3	treated with 200 mM trehalose for 12 hours	Homo sapiens	DMS114	GPL24676	RNA-Seq	GSE278237	DMS114 cells,treated with 200 mM trehalose, rep3	DMS114	DMS114	treated with 200 mM trehalose for 12 hours	GSE278237_series_matrix.txt.gz	DMS114 cells	DMS114_Tre_3	Illumina NovaSeq 6000	non-NE(SCLC-YAP1)	cell line=DMS114; cell type=SCLC cells; genotype=non-NE(SCLC-YAP1); treatment=treated with 200 mM trehalose for 12 hours

GSE278237/study_description.txt

@@ -0,0 +1,7 @@
+We treated the human small cell lung cancer cell line DMS114, a non-neuroendocrine line of the SCLC-YAP1 subtype, with the autophagy activator trehalose in vitro. The `group` column, repeated in `treatment`, holds the condition: 'treated with 200 mM trehalose for 12 hours' or 'WT', which here means untreated control cultures, not a genotype; there are three cultures of each. There is a single dose and a single time point, so there is no time variable.
+
+Each sample is one culture sequenced as one library, no two libraries are recorded as coming from the same culture, and there are no technical replicates. The GEO series title calls the comparison 'paired', but no record says what this refers to, and the numbers 1 to 3 at the end of the sample names only count the cultures within each condition: nothing links a control culture to a particular treated culture, and same-numbered cultures are no more alike in expression than other combinations. We have no record of processing or sequencing batches, and no other variable matters to us; the remaining columns are GEO annotations.
+
+The data are bulk poly(A) RNA-seq (stranded, paired-end reads). The matrix holds raw gene-level integer read counts, one row per Ensembl gene ID (hg38).
+
+Our question is which genes are differentially expressed in trehalose-treated DMS114 cells ('treated with 200 mM trehalose for 12 hours') compared with untreated control cells ('WT'), using all six samples.

GSE278238/metadata.tsv

@@ -0,0 +1,7 @@
+sample_id	group	organism	tissue	platform	assay	study_id	original_sample_id	specimen	cell_type	treatment	source_file	title_short	sample_description	instrument	genotype	characteristics
+count.H1092_1	treated with 5 μL DMSO for 24 hours	Homo sapiens	H1092	GPL24676	RNA-Seq	GSE278238	H1092 cells,treated with 5 μL DMSO, rep1	H1092	H1092	treated with 5 μL DMSO for 24 hours	GSE278238_series_matrix.txt.gz	H1092 cells	H1092_1	Illumina NovaSeq 6000	NE(SCLC-ASCL1)	cell line=H1092; cell type=SCLC cells; genotype=NE(SCLC-ASCL1); treatment=treated with 5 μL DMSO for 24 hours
+count.H1092_2	treated with 5 μL DMSO for 24 hours	Homo sapiens	H1092	GPL24676	RNA-Seq	GSE278238	H1092 cells,treated with 5 μL DMSO, rep2	H1092	H1092	treated with 5 μL DMSO for 24 hours	GSE278238_series_matrix.txt.gz	H1092 cells	H1092_2	Illumina NovaSeq 6000	NE(SCLC-ASCL1)	cell line=H1092; cell type=SCLC cells; genotype=NE(SCLC-ASCL1); treatment=treated with 5 μL DMSO for 24 hours
+count.H1092_3	treated with 5 μL DMSO for 24 hours	Homo sapiens	H1092	GPL24676	RNA-Seq	GSE278238	H1092 cells,treated with 5 μL DMSO, rep3	H1092	H1092	treated with 5 μL DMSO for 24 hours	GSE278238_series_matrix.txt.gz	H1092 cells	H1092_3	Illumina NovaSeq 6000	NE(SCLC-ASCL1)	cell line=H1092; cell type=SCLC cells; genotype=NE(SCLC-ASCL1); treatment=treated with 5 μL DMSO for 24 hours
+count.H1092_Baf_1	treated with 2 μM BafA1 for 24 hours	Homo sapiens	H1092	GPL24676	RNA-Seq	GSE278238	H1092 cells,treated with 2 μM BafA1, rep1	H1092	H1092	treated with 2 μM BafA1 for 24 hours	GSE278238_series_matrix.txt.gz	H1092 cells	H1092_Baf_1	Illumina NovaSeq 6000	NE(SCLC-ASCL1)	cell line=H1092; cell type=SCLC cells; genotype=NE(SCLC-ASCL1); treatment=treated with 2 μM BafA1 for 24 hours
+count.H1092_Baf_2	treated with 2 μM BafA1 for 24 hours	Homo sapiens	H1092	GPL24676	RNA-Seq	GSE278238	H1092 cells,treated with 2 μM BafA1, rep2	H1092	H1092	treated with 2 μM BafA1 for 24 hours	GSE278238_series_matrix.txt.gz	H1092 cells	H1092_Baf_2	Illumina NovaSeq 6000	NE(SCLC-ASCL1)	cell line=H1092; cell type=SCLC cells; genotype=NE(SCLC-ASCL1); treatment=treated with 2 μM BafA1 for 24 hours
+count.H1092_Baf_3	treated with 2 μM BafA1 for 24 hours	Homo sapiens	H1092	GPL24676	RNA-Seq	GSE278238	H1092 cells,treated with 2 μM BafA1, rep3	H1092	H1092	treated with 2 μM BafA1 for 24 hours	GSE278238_series_matrix.txt.gz	H1092 cells	H1092_Baf_3	Illumina NovaSeq 6000	NE(SCLC-ASCL1)	cell line=H1092; cell type=SCLC cells; genotype=NE(SCLC-ASCL1); treatment=treated with 2 μM BafA1 for 24 hours

GSE278238/study_description.txt

@@ -0,0 +1,7 @@
+We treated the human small cell lung cancer cell line H1092, a neuroendocrine line of the SCLC-ASCL1 subtype, with the autophagy inhibitor bafilomycin A1 (BafA1) in vitro. The `group` column, repeated in `treatment`, holds the condition: 'treated with 2 μM BafA1 for 24 hours' or 'treated with 5 μL DMSO for 24 hours', the solvent control; there are three cultures of each. All cultures were harvested at the end of the 24-hour treatment, so there is no time variable.
+
+Each sample is one culture sequenced as one library, no two libraries are recorded as coming from the same culture, and there are no technical replicates. The GEO series title calls the comparison 'paired', but no record says what this refers to, and the numbers 1 to 3 at the end of the sample names only count the cultures within each condition: nothing links a DMSO culture to a particular BafA1 culture, and same-numbered cultures are no more alike in expression than other combinations. We have no record of processing or sequencing batches, and no other variable matters to us; the remaining columns are GEO annotations.
+
+The data are bulk poly(A) RNA-seq (stranded, paired-end reads). The matrix holds raw gene-level integer read counts, one row per Ensembl gene ID (hg38).
+
+Our question is which genes are differentially expressed in BafA1-treated H1092 cells ('treated with 2 μM BafA1 for 24 hours') compared with DMSO-treated control cells ('treated with 5 μL DMSO for 24 hours'), using all six samples.

GSE296350/metadata.tsv

@@ -0,0 +1,6 @@
+sample_id	group	original_sample_id	study_id	organism	tissue	specimen	cell_type	treatment	platform	assay	source_file	title_short	sample_description	instrument	characteristics	geo_treatment	geo_gsm	geo_title
+Mouse_RNAseq_Fli1KO_Rep1	Fli1 KO	Mouse RNAseq Fli1 KO, Rep1	GSE296350	Mus musculus	NK cells	NK cells	NK cells	Fli1 KO	GPL24247	RNA-Seq	GSE296350_series_matrix.txt.gz	Mouse RNAseq Fli1 KO	Library name: Mouse_RNAseq_Fli1KO_Rep1	Illumina NovaSeq 6000	cell type=NK cells; treatment=Fli1 KO	Fli1 KO	GSM8968968	Mouse RNAseq Fli1 KO, Rep1
+Mouse_RNAseq_Fli1KO_Rep2	Fli1 KO	Mouse RNAseq Fli1 KO, Rep2	GSE296350	Mus musculus	NK cells	NK cells	NK cells	Fli1 KO	GPL24247	RNA-Seq	GSE296350_series_matrix.txt.gz	Mouse RNAseq Fli1 KO	Library name: Mouse_RNAseq_Fli1KO_Rep2	Illumina NovaSeq 6000	cell type=NK cells; treatment=Fli1 KO	Fli1 KO	GSM8968969	Mouse RNAseq Fli1 KO, Rep2
+Mouse_RNAseq_Fli1KO_Rep3	Fli1 KO	Mouse RNAseq Fli1 KO, Rep3	GSE296350	Mus musculus	NK cells	NK cells	NK cells	Fli1 KO	GPL24247	RNA-Seq	GSE296350_series_matrix.txt.gz	Mouse RNAseq Fli1 KO	Library name: Mouse_RNAseq_Fli1KO_Rep3	Illumina NovaSeq 6000	cell type=NK cells; treatment=Fli1 KO	Fli1 KO	GSM8968970	Mouse RNAseq Fli1 KO, Rep3
+Mouse_RNAseq_NTC_Rep1	NTC	Mouse RNAseq NTC, Rep1	GSE296350	Mus musculus	NK cells	NK cells	NK cells	NTC	GPL24247	RNA-Seq	GSE296350_series_matrix.txt.gz	Mouse RNAseq NTC	Library name: Mouse_RNAseq_NTC_Rep1	Illumina NovaSeq 6000	cell type=NK cells; treatment=NTC	NTC	GSM8968971	Mouse RNAseq NTC, Rep1
+Mouse_RNAseq_NTC_Rep2	NTC	Mouse RNAseq NTC, Rep2	GSE296350	Mus musculus	NK cells	NK cells	NK cells	NTC	GPL24247	RNA-Seq	GSE296350_series_matrix.txt.gz	Mouse RNAseq NTC	Library name: Mouse_RNAseq_NTC_Rep2	Illumina NovaSeq 6000	cell type=NK cells; treatment=NTC	NTC	GSM8968972	Mouse RNAseq NTC, Rep2

GSE296350/study_description.txt

@@ -0,0 +1,7 @@
+We studied mouse splenic NK cells after CRISPR editing with either a Fli1-targeting guide (Fli1 knockout) or a control guide (NTC). The `group` column, repeated in `treatment` and `geo_treatment`, holds the condition: Fli1 KO (three libraries) or NTC (two libraries). All cells were harvested at a single time point after editing, so there is no time variable.
+
+Each library is one edited bulk NK-cell population, and there are no technical replicates. Donor mice are not recorded, and whether a library came from one spleen or from several pooled spleens is not stated. The sample names number the libraries within each condition (Fli1 KO Rep1 to Rep3, NTC Rep1 and Rep2), but there is no record that same-numbered knockout and control libraries share a donor or an editing run, and the third knockout library has no control with its number. We have no record of processing or sequencing batches, and no other variable matters to us; the remaining columns are GEO annotations.
+
+The data are bulk total RNA-seq (Illumina RNA Prep with Enrichment). The matrix holds raw gene-level read counts after STAR alignment to mm10, one row per Ensembl gene ID.
+
+Our question is which genes are differentially expressed in Fli1 knockout NK cells (Fli1 KO) compared with control-guide NK cells (NTC), using all five libraries.

GSE296351/metadata.tsv

@@ -0,0 +1,7 @@
+sample_id	group	original_sample_id	study_id	organism	tissue	specimen	cell_type	treatment	platform	assay	source_file	title_short	sample_description	instrument	characteristics	replicate
+Human_RNAseq_FLI1KO_Rep1	FLI1 KO	Human RNAseq FLI1 KO, Rep1	GSE296351	Homo sapiens	NK cells	NK cells	NK cells	FLI1 KO	GPL34281	RNA-Seq	GSE296351_series_matrix.txt.gz	Human RNAseq FLI1 KO	Library name: Human_RNAseq_FLI1KO_Rep1	Illumina NovaSeq X	cell type=NK cells; treatment=FLI1 KO	Rep1
+Human_RNAseq_FLI1KO_Rep2	FLI1 KO	Human RNAseq FLI1 KO, Rep2	GSE296351	Homo sapiens	NK cells	NK cells	NK cells	FLI1 KO	GPL34281	RNA-Seq	GSE296351_series_matrix.txt.gz	Human RNAseq FLI1 KO	Library name: Human_RNAseq_FLI1KO_Rep2	Illumina NovaSeq X	cell type=NK cells; treatment=FLI1 KO	Rep2
+Human_RNAseq_FLI1KO_Rep3	FLI1 KO	Human RNAseq FLI1 KO, Rep3	GSE296351	Homo sapiens	NK cells	NK cells	NK cells	FLI1 KO	GPL34281	RNA-Seq	GSE296351_series_matrix.txt.gz	Human RNAseq FLI1 KO	Library name: Human_RNAseq_FLI1KO_Rep3	Illumina NovaSeq X	cell type=NK cells; treatment=FLI1 KO	Rep3
+Human_RNAseq_NTC_Rep1	NTC	Human RNAseq NTC, Rep1	GSE296351	Homo sapiens	NK cells	NK cells	NK cells	NTC	GPL34281	RNA-Seq	GSE296351_series_matrix.txt.gz	Human RNAseq NTC	Library name: Human_RNAseq_NTC_Rep1	Illumina NovaSeq X	cell type=NK cells; treatment=NTC	Rep1
+Human_RNAseq_NTC_Rep2	NTC	Human RNAseq NTC, Rep2	GSE296351	Homo sapiens	NK cells	NK cells	NK cells	NTC	GPL34281	RNA-Seq	GSE296351_series_matrix.txt.gz	Human RNAseq NTC	Library name: Human_RNAseq_NTC_Rep2	Illumina NovaSeq X	cell type=NK cells; treatment=NTC	Rep2
+Human_RNAseq_NTC_Rep3	NTC	Human RNAseq NTC, Rep3	GSE296351	Homo sapiens	NK cells	NK cells	NK cells	NTC	GPL34281	RNA-Seq	GSE296351_series_matrix.txt.gz	Human RNAseq NTC	Library name: Human_RNAseq_NTC_Rep3	Illumina NovaSeq X	cell type=NK cells; treatment=NTC	Rep3

GSE296351/study_description.txt

@@ -0,0 +1,7 @@
+We edited primary human NK cells by CRISPR with either a FLI1-targeting guide (FLI1 knockout) or a non-targeting control guide (NTC) and harvested them at a single time point after editing, so there is no time variable. The `group` column, repeated in `treatment`, holds the condition: FLI1 KO or NTC, three libraries each.
+
+Within each condition the libraries are numbered Rep1, Rep2 and Rep3, recorded in the `replicate` column. The FLI1 KO and NTC libraries that share a replicate number form a matched pair from the same NK-cell source, either the same donor or the same experiment (the records do not say which), so each replicate contributes one knockout and one control library. Each such pair is more alike in expression than libraries of the same condition with different numbers. Each library is one edited NK-cell culture, and there are no technical replicates. We have no record of processing or sequencing batches, and no other variable matters to us; the remaining columns are GEO annotations.
+
+The data are bulk RNA-seq (Illumina RNA Prep with Enrichment libraries from total RNA), aligned with STAR to hg38. The matrix holds raw gene-level read counts, one row per Ensembl gene ID.
+
+Our question is which genes are differentially expressed in FLI1 knockout NK cells (FLI1 KO) compared with NTC control cells (NTC), using all six libraries.

GSE303503/metadata.tsv

@@ -0,0 +1,11 @@
+sample_id	group	original_sample_id	study_id	organism	tissue	specimen	treatment	platform	assay	source_file	title_short	sample_description	instrument	characteristics	geo_gsm	geo_title
+KOEIC_0384	Mouse tumor, EZH2knockout	Mouse tumor, EZH2knockout, biol rep1	GSE303503	Mus musculus	Mouse mammary gland tumors	Mouse mammary gland tumors	Doxycycline induced at age 8-12weeks until tumor reach endpoint	GPL24247	RNA-Seq	GSE303503_series_matrix.txt.gz	Mouse tumor	Library name: KOEIC_0384	Illumina NovaSeq 6000	tissue=Mouse mammary gland tumors; treatment=Doxycycline induced at age 8-12weeks until tumor reach endpoint	GSM9128166	Mouse tumor, EZH2knockout, biol rep1
+KOEIC_0729	Mouse tumor, EZH2knockout	Mouse tumor, EZH2knockout, biol rep2	GSE303503	Mus musculus	Mouse mammary gland tumors	Mouse mammary gland tumors	Doxycycline induced at age 8-12weeks until tumor reach endpoint	GPL24247	RNA-Seq	GSE303503_series_matrix.txt.gz	Mouse tumor	Library name: KOEIC_0729	Illumina NovaSeq 6000	tissue=Mouse mammary gland tumors; treatment=Doxycycline induced at age 8-12weeks until tumor reach endpoint	GSM9128167	Mouse tumor, EZH2knockout, biol rep2
+KOEIC_0794	Mouse tumor, EZH2knockout	Mouse tumor, EZH2knockout, biol rep3	GSE303503	Mus musculus	Mouse mammary gland tumors	Mouse mammary gland tumors	Doxycycline induced at age 8-12weeks until tumor reach endpoint	GPL24247	RNA-Seq	GSE303503_series_matrix.txt.gz	Mouse tumor	Library name: KOEIC_0794	Illumina NovaSeq 6000	tissue=Mouse mammary gland tumors; treatment=Doxycycline induced at age 8-12weeks until tumor reach endpoint	GSM9128168	Mouse tumor, EZH2knockout, biol rep3
+KOEIC_4331	Mouse tumor, EZH2knockout	Mouse tumor, EZH2knockout, biol rep4	GSE303503	Mus musculus	Mouse mammary gland tumors	Mouse mammary gland tumors	Doxycycline induced at age 8-12weeks until tumor reach endpoint	GPL24247	RNA-Seq	GSE303503_series_matrix.txt.gz	Mouse tumor	Library name: KOEIC_4331	Illumina NovaSeq 6000	tissue=Mouse mammary gland tumors; treatment=Doxycycline induced at age 8-12weeks until tumor reach endpoint	GSM9128169	Mouse tumor, EZH2knockout, biol rep4
+KOEIC_4970	Mouse tumor, EZH2knockout	Mouse tumor, EZH2knockout, biol rep5	GSE303503	Mus musculus	Mouse mammary gland tumors	Mouse mammary gland tumors	Doxycycline induced at age 8-12weeks until tumor reach endpoint	GPL24247	RNA-Seq	GSE303503_series_matrix.txt.gz	Mouse tumor	Library name: KOEIC_4970	Illumina NovaSeq 6000	tissue=Mouse mammary gland tumors; treatment=Doxycycline induced at age 8-12weeks until tumor reach endpoint	GSM9128170	Mouse tumor, EZH2knockout, biol rep5
+WTEIC_434	Mouse tumor, EZH2wildtype	Mouse tumor, EZH2wildtype, biol rep4	GSE303503	Mus musculus	Mouse mammary gland tumors	Mouse mammary gland tumors	Doxycycline induced at age 8-12weeks until tumor reach endpoint	GPL24247	RNA-Seq	GSE303503_series_matrix.txt.gz	Mouse tumor	Library name: WTEIC_434	Illumina NovaSeq 6000	tissue=Mouse mammary gland tumors; treatment=Doxycycline induced at age 8-12weeks until tumor reach endpoint	GSM9128174	Mouse tumor, EZH2wildtype, biol rep4
+WTEIC_2883	Mouse tumor, EZH2wildtype	Mouse tumor, EZH2wildtype, biol rep1	GSE303503	Mus musculus	Mouse mammary gland tumors	Mouse mammary gland tumors	Doxycycline induced at age 8-12weeks until tumor reach endpoint	GPL24247	RNA-Seq	GSE303503_series_matrix.txt.gz	Mouse tumor	Library name: WTEIC_2883	Illumina NovaSeq 6000	tissue=Mouse mammary gland tumors; treatment=Doxycycline induced at age 8-12weeks until tumor reach endpoint	GSM9128171	Mouse tumor, EZH2wildtype, biol rep1
+WTEIC_2943	Mouse tumor, EZH2wildtype	Mouse tumor, EZH2wildtype, biol rep2	GSE303503	Mus musculus	Mouse mammary gland tumors	Mouse mammary gland tumors	Doxycycline induced at age 8-12weeks until tumor reach endpoint	GPL24247	RNA-Seq	GSE303503_series_matrix.txt.gz	Mouse tumor	Library name: WTEIC_2943	Illumina NovaSeq 6000	tissue=Mouse mammary gland tumors; treatment=Doxycycline induced at age 8-12weeks until tumor reach endpoint	GSM9128172	Mouse tumor, EZH2wildtype, biol rep2
+WTEIC_3321	Mouse tumor, EZH2wildtype	Mouse tumor, EZH2wildtype, biol rep3	GSE303503	Mus musculus	Mouse mammary gland tumors	Mouse mammary gland tumors	Doxycycline induced at age 8-12weeks until tumor reach endpoint	GPL24247	RNA-Seq	GSE303503_series_matrix.txt.gz	Mouse tumor	Library name: WTEIC_3321	Illumina NovaSeq 6000	tissue=Mouse mammary gland tumors; treatment=Doxycycline induced at age 8-12weeks until tumor reach endpoint	GSM9128173	Mouse tumor, EZH2wildtype, biol rep3
+WTEIC_4432	Mouse tumor, EZH2wildtype	Mouse tumor, EZH2wildtype, biol rep5	GSE303503	Mus musculus	Mouse mammary gland tumors	Mouse mammary gland tumors	Doxycycline induced at age 8-12weeks until tumor reach endpoint	GPL24247	RNA-Seq	GSE303503_series_matrix.txt.gz	Mouse tumor	Library name: WTEIC_4432	Illumina NovaSeq 6000	tissue=Mouse mammary gland tumors; treatment=Doxycycline induced at age 8-12weeks until tumor reach endpoint	GSM9128175	Mouse tumor, EZH2wildtype, biol rep5

GSE303503/study_description.txt

@@ -0,0 +1,7 @@
+We studied endpoint mammary tumors from a genetically engineered mouse line (EIC) in which doxycycline induces HER2 together with Cre in the mammary epithelium, crossed with a conditional Ezh2 strain. In Ezh2 fl/fl mice, Ezh2 is deleted in the Cre-expressing tumor epithelium; Ezh2 wild-type (wt/wt) mice keep Ezh2 and are the controls. All mice received doxycycline from 8-12 weeks of age until their tumors reached the humane endpoint (the constant `treatment` column), and every tumor was harvested at that endpoint, so there is no time variable.
+
+The genotype is in the `group` column: "Mouse tumor, EZH2knockout" marks tumors of Ezh2 fl/fl mice and "Mouse tumor, EZH2wildtype" marks tumors of Ezh2 wild-type mice, five tumors each. Each sample is one endpoint tumor, and the ten tumors come from ten different mice, so the samples are independent and no two come from the same animal. The replicate numbers 1 to 5 in `original_sample_id` and `geo_title` only count the tumors within each genotype; a knockout and a wild-type tumor with the same number are unrelated. Each tumor was sequenced once, so there are no technical replicates.
+
+We have no record of processing or sequencing batches, and no other variable we consider relevant; the remaining columns are GEO annotations that are the same for all samples or only name the libraries. The data are bulk RNA-seq of RNA from snap-frozen tumor tissue, given as raw gene-level read counts (one row per gene symbol).
+
+Our question is which genes are differentially expressed in Ezh2 knockout tumors ("Mouse tumor, EZH2knockout") compared with Ezh2 wild-type tumors ("Mouse tumor, EZH2wildtype").

GSE304598_c1/metadata.tsv

@@ -0,0 +1,34 @@
+sample_id	group	time	batch	original_sample_id	study_id	organism	tissue	specimen	cell_type	treatment	timepoint	src_batch	platform	assay	source_file	title_short	sample_description	instrument	genotype	characteristics
+J0_1	iPSc	day 0	2	iPSc_rep1	GSE304598	Homo sapiens	iPSc	iPSc	LON71 iPSc		day 0	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_rep1	Library name: J0_1	Illumina NovaSeq 6000	WT	tissue=iPSc; cell line=LON71 iPSc; cell type=iPSc; genotype=WT; timepoint=day 0; batch=2
+J0_2	iPSc	day 0	2	iPSc_rep2	GSE304598	Homo sapiens	iPSc	iPSc	LON71 iPSc		day 0	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_rep2	Library name: J0_2	Illumina NovaSeq 6000	WT	tissue=iPSc; cell line=LON71 iPSc; cell type=iPSc; genotype=WT; timepoint=day 0; batch=2
+J0_3	iPSc	day 0	2	iPSc_rep3	GSE304598	Homo sapiens	iPSc	iPSc	LON71 iPSc		day 0	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_rep3	Library name: J0_3	Illumina NovaSeq 6000	WT	tissue=iPSc; cell line=LON71 iPSc; cell type=iPSc; genotype=WT; timepoint=day 0; batch=2
+J1_1	iPSc-to-TEP	day 1	2	iPSc_to_TEP_J1_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 1	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J1_rep1	Library name: J1_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 1; batch=2
+J2_1	iPSc-to-TEP	day 2	2	iPSc_to_TEP_J2_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 2	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J2_rep1	Library name: J2_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 2; batch=2
+J3_1	iPSc-to-TEP	day 3	2	iPSc_to_TEP_J3_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 3	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J3_rep1	Library name: J3_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 3; batch=2
+J3_2	iPSc-to-TEP	day 3	2	iPSc_to_TEP_J3_rep2	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 3	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J3_rep2	Library name: J3_2	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 3; batch=2
+J3_3	iPSc-to-TEP	day 3	2	iPSc_to_TEP_J3_rep3	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 3	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J3_rep3	Library name: J3_3	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 3; batch=2
+J3_4	iPSc-to-TEP	day 3	2	iPSc_to_TEP_J3_rep4	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 3	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J3_rep4	Library name: J3_4	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 3; batch=2
+J7_1	iPSc-to-TEP	day 7	1	iPSc_to_TEP_J7_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 7	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J7_rep1	Library name: J7_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 7; batch=1
+J7_2	iPSc-to-TEP	day 7	1	iPSc_to_TEP_J7_rep2	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 7	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J7_rep2	Library name: J7_2	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 7; batch=1
+J7_3	iPSc-to-TEP	day 7	1	iPSc_to_TEP_J7_rep3	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 7	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J7_rep3	Library name: J7_3	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 7; batch=1
+J7_4	iPSc-to-TEP	day 7	1	iPSc_to_TEP_J7_rep4	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 7	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J7_rep4	Library name: J7_4	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 7; batch=1
+J7_5	iPSc-to-TEP	day 7	1	iPSc_to_TEP_J7_rep5	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 7	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J7_rep5	Library name: J7_5	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 7; batch=1
+J9_1	iPSc-to-TEP	day 9	1	iPSc_to_TEP_J9_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 9	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J9_rep1	Library name: J9_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 9; batch=1
+J9_2	iPSc-to-TEP	day 9	1	iPSc_to_TEP_J9_rep2	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 9	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J9_rep2	Library name: J9_2	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 9; batch=1
+J9_3	iPSc-to-TEP	day 9	1	iPSc_to_TEP_J9_rep3	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 9	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J9_rep3	Library name: J9_3	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 9; batch=1
+J9_4	iPSc-to-TEP	day 9	1	iPSc_to_TEP_J9_rep4	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 9	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J9_rep4	Library name: J9_4	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 9; batch=1
+J9_5	iPSc-to-TEP	day 9	1	iPSc_to_TEP_J9_rep5	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 9	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J9_rep5	Library name: J9_5	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 9; batch=1
+J9_6	iPSc-to-TEP	day 9	2	iPSc_to_TEP_J9_rep6	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 9	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J9_rep6	Library name: J9_6	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 9; batch=2
+J10_1	iPSc-to-TEP	day 10	2	iPSc_to_TEP_J10_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 10	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J10_rep1	Library name: J10_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 10; batch=2
+J10_2	iPSc-to-TEP	day 10	2	iPSc_to_TEP_J10_rep2	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 10	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J10_rep2	Library name: J10_2	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 10; batch=2
+J10_3	iPSc-to-TEP	day 10	2	iPSc_to_TEP_J10_rep3	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 10	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J10_rep3	Library name: J10_3	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 10; batch=2
+J10_4	iPSc-to-TEP	day 10	2	iPSc_to_TEP_J10_rep4	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 10	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J10_rep4	Library name: J10_4	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 10; batch=2
+J14_1	iPSc-to-TEP	day 14	2	iPSc_to_TEP_J14_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 14	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J14_rep1	Library name: J14_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 14; batch=2
+J14_2	iPSc-to-TEP	day 14	3	iPSc_to_TEP_J14_rep2	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 14	3	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J14_rep2	Library name: J14_2	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 14; batch=3
+J15_1	iPSc-to-TEP	day 15	2	iPSc_to_TEP_J15_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 15	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J15_rep1	Library name: J15_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 15; batch=2
+J17_1	iPSc-to-TEP	day 17	3	iPSc_to_TEP_J17_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 17	3	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J17_rep1	Library name: J17_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 17; batch=3
+J22_1	iPSc-to-TEP	day 22	2	iPSc_to_TEP_J22_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 22	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J22_rep1	Library name: J22_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 22; batch=2
+TEC_1	Thymus		2	TEC_rep1	GSE304598	Homo sapiens	Thymus	Thymus	primary TEC			2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	TEC_rep1	Library name: TEC_1	Illumina NovaSeq 6000	WT	tissue=Thymus; cell type=primary TEC; genotype=WT; batch=2
+TEC_2	Thymus		2	TEC_rep2	GSE304598	Homo sapiens	Thymus	Thymus	primary TEC			2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	TEC_rep2	Library name: TEC_2	Illumina NovaSeq 6000	WT	tissue=Thymus; cell type=primary TEC; genotype=WT; batch=2
+TEC_3	Thymus		2	TEC_rep3	GSE304598	Homo sapiens	Thymus	Thymus	primary TEC			2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	TEC_rep3	Library name: TEC_3	Illumina NovaSeq 6000	WT	tissue=Thymus; cell type=primary TEC; genotype=WT; batch=2
+TEC_4	Thymus		2	TEC_rep4	GSE304598	Homo sapiens	Thymus	Thymus	primary TEC			2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	TEC_rep4	Library name: TEC_4	Illumina NovaSeq 6000	WT	tissue=Thymus; cell type=primary TEC; genotype=WT; batch=2

GSE304598_c1/study_description.txt

@@ -0,0 +1,7 @@
+We differentiated the human iPSC line LON71 toward thymic epithelial progenitors (TEPs) with an iPSC-to-TEP protocol and harvested cells on days 0, 1, 2, 3, 7, 9, 10, 14, 15, 17 and 22 (1 to 6 samples per day, 29 in all). The harvest day is in the `time` column (the `timepoint` column repeats it); day 0 is the undifferentiated iPSC stage before induction, and the other days count from induction. Four primary pediatric thymic epithelial cell (TEC) samples were added for comparison; their `time` is empty. The `group` column only separates iPSCs (iPSc), differentiating cells (iPSc-to-TEP) and TECs (Thymus).
+
+Each LON71 sample is one harvest of cultures on one day, with its own RNA sample and library, and no technical replicates are recorded. All LON71 samples come from this one cell line, but no column identifies a differentiation or culture, and as far as we know no two samples come from the same culture.
+
+GEO gives every sample a batch number (`batch`, repeated in `src_batch`: 1, 2 or 3) without saying what it stands for. All samples of days 0, 3 and 10 have batch 2, so there is no batch variable among the samples of this question, and we have no other record of processing batches. We have no other variable we consider relevant either; the remaining columns are GEO annotations. The data are bulk 3′ RNA-seq (3′ DGE-seq), given as raw UMI counts per gene (RefSeq genes); two batch 3 samples, from days 14 and 17, have no counts for 3,827 genes.
+
+For this question the harvest days are the groups we compare, not a time trend, so there is no separate time variable. We want to find the genes that are differentially expressed at day 3 of the differentiation compared with day 0, the undifferentiated iPSCs, using the samples of days 0, 3 and 10 ("day 0", "day 3" and "day 10" in `time`: 3, 4 and 4 samples). The other days and the TEC samples are not part of this question.

GSE304598_c2/metadata.tsv

@@ -0,0 +1,34 @@
+sample_id	group	time	batch	original_sample_id	study_id	organism	tissue	specimen	cell_type	treatment	timepoint	src_batch	platform	assay	source_file	title_short	sample_description	instrument	genotype	characteristics
+J0_1	iPSc	day 0	2	iPSc_rep1	GSE304598	Homo sapiens	iPSc	iPSc	LON71 iPSc		day 0	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_rep1	Library name: J0_1	Illumina NovaSeq 6000	WT	tissue=iPSc; cell line=LON71 iPSc; cell type=iPSc; genotype=WT; timepoint=day 0; batch=2
+J0_2	iPSc	day 0	2	iPSc_rep2	GSE304598	Homo sapiens	iPSc	iPSc	LON71 iPSc		day 0	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_rep2	Library name: J0_2	Illumina NovaSeq 6000	WT	tissue=iPSc; cell line=LON71 iPSc; cell type=iPSc; genotype=WT; timepoint=day 0; batch=2
+J0_3	iPSc	day 0	2	iPSc_rep3	GSE304598	Homo sapiens	iPSc	iPSc	LON71 iPSc		day 0	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_rep3	Library name: J0_3	Illumina NovaSeq 6000	WT	tissue=iPSc; cell line=LON71 iPSc; cell type=iPSc; genotype=WT; timepoint=day 0; batch=2
+J1_1	iPSc-to-TEP	day 1	2	iPSc_to_TEP_J1_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 1	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J1_rep1	Library name: J1_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 1; batch=2
+J2_1	iPSc-to-TEP	day 2	2	iPSc_to_TEP_J2_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 2	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J2_rep1	Library name: J2_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 2; batch=2
+J3_1	iPSc-to-TEP	day 3	2	iPSc_to_TEP_J3_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 3	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J3_rep1	Library name: J3_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 3; batch=2
+J3_2	iPSc-to-TEP	day 3	2	iPSc_to_TEP_J3_rep2	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 3	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J3_rep2	Library name: J3_2	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 3; batch=2
+J3_3	iPSc-to-TEP	day 3	2	iPSc_to_TEP_J3_rep3	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 3	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J3_rep3	Library name: J3_3	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 3; batch=2
+J3_4	iPSc-to-TEP	day 3	2	iPSc_to_TEP_J3_rep4	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 3	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J3_rep4	Library name: J3_4	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 3; batch=2
+J7_1	iPSc-to-TEP	day 7	1	iPSc_to_TEP_J7_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 7	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J7_rep1	Library name: J7_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 7; batch=1
+J7_2	iPSc-to-TEP	day 7	1	iPSc_to_TEP_J7_rep2	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 7	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J7_rep2	Library name: J7_2	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 7; batch=1
+J7_3	iPSc-to-TEP	day 7	1	iPSc_to_TEP_J7_rep3	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 7	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J7_rep3	Library name: J7_3	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 7; batch=1
+J7_4	iPSc-to-TEP	day 7	1	iPSc_to_TEP_J7_rep4	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 7	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J7_rep4	Library name: J7_4	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 7; batch=1
+J7_5	iPSc-to-TEP	day 7	1	iPSc_to_TEP_J7_rep5	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 7	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J7_rep5	Library name: J7_5	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 7; batch=1
+J9_1	iPSc-to-TEP	day 9	1	iPSc_to_TEP_J9_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 9	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J9_rep1	Library name: J9_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 9; batch=1
+J9_2	iPSc-to-TEP	day 9	1	iPSc_to_TEP_J9_rep2	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 9	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J9_rep2	Library name: J9_2	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 9; batch=1
+J9_3	iPSc-to-TEP	day 9	1	iPSc_to_TEP_J9_rep3	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 9	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J9_rep3	Library name: J9_3	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 9; batch=1
+J9_4	iPSc-to-TEP	day 9	1	iPSc_to_TEP_J9_rep4	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 9	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J9_rep4	Library name: J9_4	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 9; batch=1
+J9_5	iPSc-to-TEP	day 9	1	iPSc_to_TEP_J9_rep5	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 9	1	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J9_rep5	Library name: J9_5	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 9; batch=1
+J9_6	iPSc-to-TEP	day 9	2	iPSc_to_TEP_J9_rep6	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 9	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J9_rep6	Library name: J9_6	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 9; batch=2
+J10_1	iPSc-to-TEP	day 10	2	iPSc_to_TEP_J10_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 10	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J10_rep1	Library name: J10_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 10; batch=2
+J10_2	iPSc-to-TEP	day 10	2	iPSc_to_TEP_J10_rep2	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 10	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J10_rep2	Library name: J10_2	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 10; batch=2
+J10_3	iPSc-to-TEP	day 10	2	iPSc_to_TEP_J10_rep3	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 10	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J10_rep3	Library name: J10_3	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 10; batch=2
+J10_4	iPSc-to-TEP	day 10	2	iPSc_to_TEP_J10_rep4	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 10	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J10_rep4	Library name: J10_4	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 10; batch=2
+J14_1	iPSc-to-TEP	day 14	2	iPSc_to_TEP_J14_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 14	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J14_rep1	Library name: J14_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 14; batch=2
+J14_2	iPSc-to-TEP	day 14	3	iPSc_to_TEP_J14_rep2	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 14	3	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J14_rep2	Library name: J14_2	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 14; batch=3
+J15_1	iPSc-to-TEP	day 15	2	iPSc_to_TEP_J15_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 15	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J15_rep1	Library name: J15_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 15; batch=2
+J17_1	iPSc-to-TEP	day 17	3	iPSc_to_TEP_J17_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 17	3	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J17_rep1	Library name: J17_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 17; batch=3
+J22_1	iPSc-to-TEP	day 22	2	iPSc_to_TEP_J22_rep1	GSE304598	Homo sapiens	iPSc-to-TEP	iPSc-to-TEP	LON71 iPSc	iPSc_to_TEP_differentitation_protocol	day 22	2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	iPSc_to_TEP_J22_rep1	Library name: J22_1	Illumina NovaSeq 6000	WT	tissue=iPSc-to-TEP; cell line=LON71 iPSc; cell type=iPSc-derived; genotype=WT; treatment=iPSc_to_TEP_differentitation_protocol; timepoint=day 22; batch=2
+TEC_1	Thymus		2	TEC_rep1	GSE304598	Homo sapiens	Thymus	Thymus	primary TEC			2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	TEC_rep1	Library name: TEC_1	Illumina NovaSeq 6000	WT	tissue=Thymus; cell type=primary TEC; genotype=WT; batch=2
+TEC_2	Thymus		2	TEC_rep2	GSE304598	Homo sapiens	Thymus	Thymus	primary TEC			2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	TEC_rep2	Library name: TEC_2	Illumina NovaSeq 6000	WT	tissue=Thymus; cell type=primary TEC; genotype=WT; batch=2
+TEC_3	Thymus		2	TEC_rep3	GSE304598	Homo sapiens	Thymus	Thymus	primary TEC			2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	TEC_rep3	Library name: TEC_3	Illumina NovaSeq 6000	WT	tissue=Thymus; cell type=primary TEC; genotype=WT; batch=2
+TEC_4	Thymus		2	TEC_rep4	GSE304598	Homo sapiens	Thymus	Thymus	primary TEC			2	GPL24676	RNA-Seq	GSE304598_series_matrix.txt.gz	TEC_rep4	Library name: TEC_4	Illumina NovaSeq 6000	WT	tissue=Thymus; cell type=primary TEC; genotype=WT; batch=2

GSE304598_c2/study_description.txt

@@ -0,0 +1,7 @@
+We differentiated the human iPSC line LON71 toward thymic epithelial progenitors (TEPs) with an iPSC-to-TEP protocol and harvested cells on days 0, 1, 2, 3, 7, 9, 10, 14, 15, 17 and 22 (1 to 6 samples per day, 29 in all). The harvest day is in the `time` column (the `timepoint` column repeats it); day 0 is the undifferentiated iPSC stage before induction, and the other days count from induction. Four primary pediatric thymic epithelial cell (TEC) samples were added for comparison; their `time` is empty. The `group` column only separates iPSCs (iPSc), differentiating cells (iPSc-to-TEP) and TECs (Thymus).
+
+Each LON71 sample is one harvest of cultures on one day, with its own RNA sample and library, and no technical replicates are recorded. All LON71 samples come from this one cell line, but no column identifies a differentiation or culture, and as far as we know no two samples come from the same culture.
+
+GEO gives every sample a batch number (`batch`, repeated in `src_batch`: 1, 2 or 3) without saying what it stands for. All samples of days 0, 3 and 10 have batch 2, so there is no batch variable among the samples of this question, and we have no other record of processing batches. We have no other variable we consider relevant either; the remaining columns are GEO annotations. The data are bulk 3′ RNA-seq (3′ DGE-seq), given as raw UMI counts per gene (RefSeq genes); two batch 3 samples, from days 14 and 17, have no counts for 3,827 genes.
+
+For this question the harvest days are the groups we compare, not a time trend, so there is no separate time variable. We want to find the genes that are differentially expressed at day 10 of the differentiation compared with day 0, the undifferentiated iPSCs, using the samples of days 0, 3 and 10 ("day 0", "day 3" and "day 10" in `time`: 3, 4 and 4 samples). The other days and the TEC samples are not part of this question.

GSE306518/metadata.tsv

@@ -0,0 +1,11 @@
+sample_id	group	original_sample_id	study_id	organism	tissue	specimen	disease	platform	assay	source_file	title_short	sample_description	instrument	characteristics
+SD34_S31	MC	SD34 white adipose tissue	GSE306518	Homo sapiens	Omental white adipose tissue	Omental white adipose tissue	MC	GPL11154	RNA-Seq	GSE306518_series_matrix.txt.gz	SD34 white adipose tissue	Library name: SD34_S31	Illumina HiSeq 2000	tissue=Omental white adipose tissue; disease state=MC; disease=Obese
+SD36_S33	MH	SD36 white adipose tissue	GSE306518	Homo sapiens	Omental white adipose tissue	Omental white adipose tissue	MH	GPL11154	RNA-Seq	GSE306518_series_matrix.txt.gz	SD36 white adipose tissue	Library name: SD36_S33	Illumina HiSeq 2000	tissue=Omental white adipose tissue; disease state=MH; disease=Obese
+SD38_S35	MC	SD38 white adipose tissue	GSE306518	Homo sapiens	Omental white adipose tissue	Omental white adipose tissue	MC	GPL11154	RNA-Seq	GSE306518_series_matrix.txt.gz	SD38 white adipose tissue	Library name: SD38_S35	Illumina HiSeq 2000	tissue=Omental white adipose tissue; disease state=MC; disease=Obese
+SD39_S36	MH	SD39 white adipose tissue	GSE306518	Homo sapiens	Omental white adipose tissue	Omental white adipose tissue	MH	GPL11154	RNA-Seq	GSE306518_series_matrix.txt.gz	SD39 white adipose tissue	Library name: SD39_S36	Illumina HiSeq 2000	tissue=Omental white adipose tissue; disease state=MH; disease=Obese
+SD44_S41	MC	SD44 white adipose tissue	GSE306518	Homo sapiens	Omental white adipose tissue	Omental white adipose tissue	MC	GPL11154	RNA-Seq	GSE306518_series_matrix.txt.gz	SD44 white adipose tissue	Library name: SD44_S41	Illumina HiSeq 2000	tissue=Omental white adipose tissue; disease state=MC; disease=Obese
+SD46_S43	MC	SD46 white adipose tissue	GSE306518	Homo sapiens	Omental white adipose tissue	Omental white adipose tissue	MC	GPL11154	RNA-Seq	GSE306518_series_matrix.txt.gz	SD46 white adipose tissue	Library name: SD46_S43	Illumina HiSeq 2000	tissue=Omental white adipose tissue; disease state=MC; disease=Obese
+SD49_S46	MH	SD49 white adipose tissue	GSE306518	Homo sapiens	Omental white adipose tissue	Omental white adipose tissue	MH	GPL11154	RNA-Seq	GSE306518_series_matrix.txt.gz	SD49 white adipose tissue	Library name: SD49_S46	Illumina HiSeq 2000	tissue=Omental white adipose tissue; disease state=MH; disease=Obese
+SD50_S47	MH	SD50 white adipose tissue	GSE306518	Homo sapiens	Omental white adipose tissue	Omental white adipose tissue	MH	GPL11154	RNA-Seq	GSE306518_series_matrix.txt.gz	SD50 white adipose tissue	Library name: SD50_S47	Illumina HiSeq 2000	tissue=Omental white adipose tissue; disease state=MH; disease=Obese
+SD52_S49	MH	SD52 white adipose tissue	GSE306518	Homo sapiens	Omental white adipose tissue	Omental white adipose tissue	MH	GPL11154	RNA-Seq	GSE306518_series_matrix.txt.gz	SD52 white adipose tissue	Library name: SD52_S49	Illumina HiSeq 2000	tissue=Omental white adipose tissue; disease state=MH; disease=Obese
+SD53_S50	MC	SD53 white adipose tissue	GSE306518	Homo sapiens	Omental white adipose tissue	Omental white adipose tissue	MC	GPL11154	RNA-Seq	GSE306518_series_matrix.txt.gz	SD53 white adipose tissue	Library name: SD53_S50	Illumina HiSeq 2000	tissue=Omental white adipose tissue; disease state=MC; disease=Obese

GSE306518/study_description.txt

@@ -0,0 +1,7 @@
+We collected omental white adipose tissue during bariatric surgery (vertical sleeve gastrectomy) from 10 adolescents with obesity, one tissue sample per person. Based on clinical parameters of metabolic disease, each individual was classified as having obesity with metabolic disease or metabolically healthy obesity; those with metabolic disease had, for example, higher HbA1c. This is a cross-sectional comparison: each sample was taken once, at surgery, without any experimental intervention, so there is no time variable.
+
+The metabolic status is in the `group` column: MC means obesity with metabolic disease (5 individuals) and MH means metabolically healthy obesity (5 individuals); the `disease` column repeats the same labels. Each sample comes from a different person (the SD numbers in `sample_id` are all different), so the samples are independent. Each library was sequenced once; there are no technical replicates.
+
+We have no record of processing or sequencing batches. Sex, age and BMI are not in the metadata, and there is no other variable we consider relevant; the remaining columns are GEO annotations. The data are bulk RNA-seq of the whole tissue, given as gene-level integer counts per Ensembl gene that were deposited as raw counts (Kallisto pseudo-alignment to the hg38 transcriptome, summarized to genes).
+
+Our question is which genes are differentially expressed in omental adipose tissue of individuals with metabolic disease (MC) compared with metabolically healthy individuals (MH).

GSE309123/metadata.tsv

@@ -0,0 +1,10 @@
+sample_id	group	original_sample_id	study_id	organism	tissue	specimen	cell_type	treatment	platform	assay	source_file	title_short	sample_description	instrument	genotype	characteristics	replicate
+DMSO_Day5_Rep1	DMSO	DMSO_Day5_Rep1	GSE309123	Homo sapiens	HNES1	HNES1	HNES1	DMSO	GPL34295	RNA-Seq	GSE309123_series_matrix.txt.gz	DMSO_Day5_Rep1	Library name: library1	Element AVITI	Wild-type	cell line=HNES1; cell type=Human pluripotent stem cell; genotype=Wild-type; treatment=DMSO	Rep1
+DMSO_Day5_Rep2	DMSO	DMSO_Day5_Rep2	GSE309123	Homo sapiens	HNES1	HNES1	HNES1	DMSO	GPL34295	RNA-Seq	GSE309123_series_matrix.txt.gz	DMSO_Day5_Rep2	Library name: library2	Element AVITI	Wild-type	cell line=HNES1; cell type=Human pluripotent stem cell; genotype=Wild-type; treatment=DMSO	Rep2
+DMSO_Day5_Rep3	DMSO	DMSO_Day5_Rep3	GSE309123	Homo sapiens	HNES1	HNES1	HNES1	DMSO	GPL34295	RNA-Seq	GSE309123_series_matrix.txt.gz	DMSO_Day5_Rep3	Library name: library3	Element AVITI	Wild-type	cell line=HNES1; cell type=Human pluripotent stem cell; genotype=Wild-type; treatment=DMSO	Rep3
+PROTAC_Day5_Rep2	PROTAC	PROTAC_Day5_Rep2	GSE309123	Homo sapiens	HNES1	HNES1	HNES1	PROTAC	GPL34295	RNA-Seq	GSE309123_series_matrix.txt.gz	PROTAC_Day5_Rep2	Library name: library4	Element AVITI	Wild-type	cell line=HNES1; cell type=Human pluripotent stem cell; genotype=Wild-type; treatment=PROTAC	Rep2
+PROTAC_Day5_Rep3	PROTAC	PROTAC_Day5_Rep3	GSE309123	Homo sapiens	HNES1	HNES1	HNES1	PROTAC	GPL34295	RNA-Seq	GSE309123_series_matrix.txt.gz	PROTAC_Day5_Rep3	Library name: library5	Element AVITI	Wild-type	cell line=HNES1; cell type=Human pluripotent stem cell; genotype=Wild-type; treatment=PROTAC	Rep3
+PROTAC_Day_5_Rep_1	PROTAC	PROTAC_Day_5_Rep_1	GSE309123	Homo sapiens	HNES1	HNES1	HNES1	PROTAC	GPL34295	RNA-Seq	GSE309123_series_matrix.txt.gz	PROTAC_Day_5_Rep_1	Library name: library6	Element AVITI	Wild-type	cell line=HNES1; cell type=Human pluripotent stem cell; genotype=Wild-type; treatment=PROTAC	Rep1
+UNC_Day5_Rep1	UNC	UNC_Day5_Rep1	GSE309123	Homo sapiens	HNES1	HNES1	HNES1	UNC	GPL34295	RNA-Seq	GSE309123_series_matrix.txt.gz	UNC_Day5_Rep1	Library name: library7	Element AVITI	Wild-type	cell line=HNES1; cell type=Human pluripotent stem cell; genotype=Wild-type; treatment=UNC	Rep1
+UNC_Day5_Rep2	UNC	UNC_Day5_Rep2	GSE309123	Homo sapiens	HNES1	HNES1	HNES1	UNC	GPL34295	RNA-Seq	GSE309123_series_matrix.txt.gz	UNC_Day5_Rep2	Library name: library8	Element AVITI	Wild-type	cell line=HNES1; cell type=Human pluripotent stem cell; genotype=Wild-type; treatment=UNC	Rep2
+UNC_Day5_Rep3	UNC	UNC_Day5_Rep3	GSE309123	Homo sapiens	HNES1	HNES1	HNES1	UNC	GPL34295	RNA-Seq	GSE309123_series_matrix.txt.gz	UNC_Day5_Rep3	Library name: library9	Element AVITI	Wild-type	cell line=HNES1; cell type=Human pluripotent stem cell; genotype=Wild-type; treatment=UNC	Rep3

GSE309123/study_description.txt

@@ -0,0 +1,7 @@
+We transitioned naive human pluripotent stem cells of the line HNES1 toward a primed-like state under one of three treatments: the EED PROTAC degrader UNC6852 (2.5 µM), the EZH1/2 catalytic inhibitor UNC1999 (1 µM), or DMSO vehicle. The drugs were added 24 hours before the transition started (day 0) and renewed daily, and all cultures were harvested on day 5 of the transition, so all samples share one time point and there is no time variable. The treatment is in the `group` column: PROTAC for UNC6852, UNC for UNC1999 and DMSO for the vehicle; the `treatment` column repeats the same labels.
+
+Each sample is one HNES1 culture under one treatment. All nine come from the same cell line, so there are no donors, and no two samples come from the same culture. The whole experiment was performed independently three times, and each experiment included one DMSO, one PROTAC and one UNC culture. The `replicate` column (Rep1, Rep2, Rep3, taken from the end of the sample names) records which experiment a culture belongs to, so the three experiments are three experimental batches. Each library was sequenced once; there are no technical replicates.
+
+Apart from the experiments, we have no record of processing or sequencing batches, and no other variable we consider relevant; the remaining columns are GEO annotations. The data are bulk RNA-seq, given as raw directional read counts per gene from SeqMonk (Ensembl v113 annotation).
+
+Our question is which genes are differentially expressed in PROTAC-treated cultures compared with DMSO-treated cultures on day 5. We would like to use all nine samples, including the UNC1999 cultures from the same experiments.

GSE309279/metadata.tsv

@@ -0,0 +1,26 @@
+sample_id	group	batch	original_sample_id	study_id	organism	tissue	specimen	cell_type	treatment	src_batch	platform	assay	source_file	title_short	sample_description	instrument	strain	characteristics	day
+Day.2.control.rep.1	hydrated control	day 16	Arthrobacter sp. AZCC_0090, day 2 control, replicate 1	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	hydrated control	day 16	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day2_control_rep1	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=hydrated control; batch=day 16	2
+Day.2.control.rep.2	hydrated control	day 16	Arthrobacter sp. AZCC_0090, day 2 control, replicate 2	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	hydrated control	day 16	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day2_control_rep2	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=hydrated control; batch=day 16	2
+Day.2.control.rep.7	hydrated control	day 16	Arthrobacter sp. AZCC_0090, day 2 control, replicate 7	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	hydrated control	day 16	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day2_control_rep7	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=hydrated control; batch=day 16	2
+Day.2.treatment.rep.3	desiccated-rehydrated	day 2	Arthrobacter sp. AZCC_0090, day 2 treatment, replicate 3	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 2	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day2_treatment_rep3	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 2	2
+Day.2.treatment.rep.4	desiccated-rehydrated	day 2	Arthrobacter sp. AZCC_0090, day 2 treatment, replicate 4	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 2	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day2_treatment_rep4	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 2	2
+Day.2.treatment.rep.5	desiccated-rehydrated	day 2	Arthrobacter sp. AZCC_0090, day 2 treatment, replicate 5	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 2	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day2_treatment_rep5	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 2	2
+Day.8.control.rep.1	hydrated control	day 2	Arthrobacter sp. AZCC_0090, day 8 control, replicate 1	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	hydrated control	day 2	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day8_control_rep1	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=hydrated control; batch=day 2	8
+Day.8.control.rep.3	hydrated control	day 2	Arthrobacter sp. AZCC_0090, day 8 control, replicate 3	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	hydrated control	day 2	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day8_control_rep3	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=hydrated control; batch=day 2	8
+Day.8.control.rep.5	hydrated control	day 2	Arthrobacter sp. AZCC_0090, day 8 control, replicate 5	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	hydrated control	day 2	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day8_control_rep5	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=hydrated control; batch=day 2	8
+Day.8.treatment.rep.2	desiccated-rehydrated	day 8	Arthrobacter sp. AZCC_0090, day 8 treatment, replicate 2	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 8	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day8_treatment_rep2	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 8	8
+Day.8.treatment.rep.3	desiccated-rehydrated	day 8	Arthrobacter sp. AZCC_0090, day 8 treatment, replicate 3	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 8	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day8_treatment_rep3	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 8	8
+Day.8.treatment.rep.4	desiccated-rehydrated	day 8	Arthrobacter sp. AZCC_0090, day 8 treatment, replicate 4	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 8	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day8_treatment_rep4	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 8	8
+Day.8.treatment.rep.5	desiccated-rehydrated	day 8	Arthrobacter sp. AZCC_0090, day 8 treatment, replicate 5	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 8	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day8_treatment_rep5	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 8	8
+Day.14.control.rep.2	hydrated control	day 8	Arthrobacter sp. AZCC_0090, day 14 control, replicate 2	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	hydrated control	day 8	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day14_control_rep2	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=hydrated control; batch=day 8	14
+Day.14.control.rep.3	hydrated control	day 8	Arthrobacter sp. AZCC_0090, day 14 control, replicate 3	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	hydrated control	day 8	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day14_control_rep3	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=hydrated control; batch=day 8	14
+Day.14.control.rep.5	hydrated control	day 8	Arthrobacter sp. AZCC_0090, day 14 control, replicate 5	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	hydrated control	day 8	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day14_control_rep5	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=hydrated control; batch=day 8	14
+Day.14.treatment.rep.1	desiccated-rehydrated	day 14	Arthrobacter sp. AZCC_0090, day 14 treatment, replicate 1	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 14	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day14_treatment_rep1	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 14	14
+Day.14.treatment.rep.2	desiccated-rehydrated	day 14	Arthrobacter sp. AZCC_0090, day 14 treatment, replicate 2	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 14	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day14_treatment_rep2	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 14	14
+Day.14.treatment.rep.5	desiccated-rehydrated	day 14	Arthrobacter sp. AZCC_0090, day 14 treatment, replicate 5	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 14	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day14_treatment_rep5	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 14	14
+Day.16.control.rep.2	hydrated control	day 14	Arthrobacter sp. AZCC_0090, day 16 control, replicate 2	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	hydrated control	day 14	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day16_control_rep2	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=hydrated control; batch=day 14	16
+Day.16.control.rep.3	hydrated control	day 14	Arthrobacter sp. AZCC_0090, day 16 control, replicate 3	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	hydrated control	day 14	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day16_control_rep3	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=hydrated control; batch=day 14	16
+Day.16.control.rep.5	hydrated control	day 14	Arthrobacter sp. AZCC_0090, day 16 control, replicate 5	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	hydrated control	day 14	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day16_control_rep5	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=hydrated control; batch=day 14	16
+Day.16.treatment.rep.1	desiccated-rehydrated	day 16	Arthrobacter sp. AZCC_0090, day 16 treatment, replicate 1	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 16	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day16_treatment_rep1	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 16	16
+Day.16.treatment.rep.2	desiccated-rehydrated	day 16	Arthrobacter sp. AZCC_0090, day 16 treatment, replicate 2	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 16	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day16_treatment_rep2	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 16	16
+Day.16.treatment.rep.4	desiccated-rehydrated	day 16	Arthrobacter sp. AZCC_0090, day 16 treatment, replicate 4	GSE309279	Arthrobacter sp. AZCC_0090	batch cultured cells	batch cultured cells	batch cultured cells	desiccated-rehydrated	day 16	GPL36285	RNA-Seq	GSE309279_series_matrix.txt.gz	Arthrobacter sp. AZCC_0090	Library name: day16_treatment_rep4	NextSeq 2000	AZCC_0090	strain=AZCC_0090; cell type=batch cultured cells; treatment=desiccated-rehydrated; batch=day 16	16