metadata
license: mit
language:
- en
tags:
- biology
- genomics
- yeast
- transcription-factors
- gene-expression
- binding
- chec
- perturbation
- rnaseq
- nascent rnaseq
pretty_name: Mahendrawada 2025 ChEC-seq and Nascent RNA-seq data
size_categories:
- 100K<n<1M
experimental_conditions:
temperature_celsius: 30
growth_phase_at_harvest:
od600: 1
media:
name: synthetic_complete
nitrogen_source:
- compound: yeast_nitrogen_base
concentration_percent: 0.17
specifications:
- without_ammonium_sulfate
- without_amino_acids
- compound: ammonium_sulfate
concentration_percent: 0.5
- compound: amino_acid_dropout_mix
concentration_percent: 0.06
- compound: adenine_sulfate
concentration_percent: 0.004
- compound: uracil
concentration_percent: 0.0002
configs:
- config_name: genomic_features
description: >-
Comprehensive genomic features and regulatory characteristics for yeast
genes
dataset_type: genomic_features
data_files:
- split: train
path: features_mahendrawada_2025.parquet
dataset_info:
features:
- name: gene_id
dtype: string
description: >-
Systematic gene name (ORF identifier) from SGD
(https://yeastgenome.org/)
- name: SGD_id
dtype: string
description: Unique identifier for each gene from SGD (https://yeastgenome.org/)
- name: gene_name
dtype: string
description: Common name of each gene
- name: chr
dtype: string
description: Chromosome number corresponding to gene
- name: strand
dtype: string
description: Strandedness of the gene (+ or -)
- name: start
dtype: int64
description: Start position of the ORF
- name: end
dtype: int64
description: End position of the ORF
- name: TSS
dtype: int64
description: >-
Transcription start site based on Park et al., 2014
(doi:10.1093/nar/gkt1366)
- name: TATA_category
dtype: string
description: >-
TATA box classification from Donczew et al., 2020 using consensus
TATAWAW (doi:10.7554/eLife.50109)
- name: expression
dtype: float64
description: >-
Average signal normalized to gene length from Donczew et al., 2020
(doi:10.7554/eLife.50109)
- name: +1 nucleosome
dtype: float64
description: >-
Position of +1 nucleosome from Chereji et al., 2018
(doi:10.1186/S13059-018-1398-0)
- name: '-1 nucleosome'
dtype: float64
description: >-
Position of -1 nucleosome from Chereji et al., 2018
(doi:10.1186/S13059-018-1398-0)
- name: NDR Center
dtype: float64
description: >-
Center of nucleosome depleted region from Chereji et al., 2018
(doi:10.1186/S13059-018-1398-0)
- name: NDR Width
dtype: float64
description: >-
Width of nucleosome depletion region from Chereji et al., 2018
(doi:10.1186/S13059-018-1398-0)
- name: tail-dependence
dtype: string
description: >-
Tail classification based on Mediator tail dependence from Warfield
L, Donczew R et al., 2022 (doi:10.1016/j.molcel.2022.09.016)
- name: coactivator
dtype: string
description: >-
Coactivator classification based on TFIID and/or SAGA dependence
from Donczew et al., 2020 (doi:10.7554/eLife.50109)
- name: LCID_center
dtype: string
description: >-
Genes near boundaries of chromosomal interacting domains from
Swygert et al., 2020 (doi:10.1016/j.molcel.2018.11.020)
- name: Rossi_classes
dtype: string
description: >-
Promoter classes from Rossi et al., 2021
(doi:10.1038/s41586-021-03314-8)
- name: RP_category
dtype: string
description: >-
Ribosomal protein (RP) and ribosomal biogenesis (RiBi) gene
classification from Zencir et al., 2020 (doi:10.1093/NAR/GKAA852)
- name: binding_cluster
dtype: string
description: >-
Clusters from unsupervised K-means clustering using binary binding
data of 178 transcription factors
- name: list_of_TFS_bound
dtype: string
description: >-
List of transcription factors bound to gene promoter (-400 to +200
bp from TSS; Homer peak calling)
- name: number_of_bound_tfs
dtype: int64
description: Number of transcription factors bound to each promoter
- name: locus_tag
dtype: string
description: Systematic gene identifier from yeast_genome_resources dataset
- name: symbol
dtype: string
description: Standard gene symbol from yeast_genome_resources dataset
- config_name: mahendrawada_chec_seq
description: >-
ChEC-seq transcription factor binding data with peak scores (original
authors' processed data)
default: true
dataset_type: annotated_features
metadata_fields:
- regulator_locus_tag
- regulator_symbol
data_files:
- split: train
path: chec_mahendrawada_2025.parquet
dataset_info:
features:
- name: sample_id
dtype: integer
description: >-
unique identifier for a specific sample, which uniquely identifies
one of the 178 TFs. Across datasets in this repo, the a given
sample_id identifies the same regulator.
- name: regulator_locus_tag
dtype: string
description: Systematic gene name (ORF identifier) of the transcription factor
- name: regulator_symbol
dtype: string
description: Standard gene symbol of the transcription factor
- name: target_locus_tag
dtype: string
description: Systematic gene name (ORF identifier) of the target gene
- name: target_symbol
dtype: string
description: Standard gene symbol of the target gene
- name: peak_score
dtype: float64
description: >-
ChEC signal around peak center (sum of ChEC signal from -150 to +150
bp from peak summit) normalized to Drosophila spike-in control
- name: processing_method
dtype: string
description: Method used for peak calling and quantification (original authors)
- config_name: chec_genome_map_meta
description: >-
Sample-level metadata for ChEC-seq experiments including regulator
information, experimental conditions, and replicate structure
dataset_type: metadata
applies_to:
- chec_mahendrawada_m2025_af_replicates
- chec_genome_map
data_files:
- split: train
path: chec_genome_map_meta.parquet
dataset_info:
features:
- name: sra_accession
dtype: string
description: >-
SRA (Sequence Read Archive) accession identifier for this biological
replicate
role: sample_id
- name: mahendrawada_symbol
dtype: string
description: Transcription factor symbol as reported in Mahendrawada et al. 2025
- name: replicate
dtype: string
description: Biological replicate identifier. One of A,B,C. All have 3 replicates
- name: condition
dtype:
class_label:
names:
- standard
- SM
- WT
- WT_SM
- admut
- admut_SM
- cAD
- cAD_SM
- dbdmut
- dbdmut_SM
- nAD
- nAD_SM
- ncAD
- ncAD_SM
- '30'
- '37'
- galactose
- raffinose
description: Experimental condition for this sample
role: experimental_condition
- name: regulator_locus_tag
dtype: string
description: >-
Systematic gene name (ORF identifier) of the depleted transcription
factor
role: regulator_identifier
- name: regulator_symbol
dtype: string
description: Standard gene symbol of the depleted transcription factor
role: regulator_identifier
- name: sample_id
dtype: int
description: >-
Unique identifier combining regulator, condition, and replicates
(used in combined datasets)
- config_name: chec_genome_map
description: >-
ChEC-seq data reprocessed in the Brent Lab. See scripts/ for more details.
These are bed format, therefore intervals are 0-based, half open, eg
chrI:0-10 in a bed format would be chr:1-10 in IGV which is 1-indexed,
closed interval
dataset_type: genome_map
data_files:
- split: train
path: chec_genome_map/sra_accession=*/*.parquet
dataset_info:
partitioning:
enabled: true
partition_by:
- sra_accession
features:
- name: sra_accession
dtype: string
description: >-
SRA accession identifier used for partitioning (links to
chec_genome_map_meta)
role: sample_id
- name: chr
dtype: string
description: Chromosome identifier (e.g., chrI, chrII, chrXVI)
- name: start
dtype: int
description: Feature start position (0-based half open)
- name: end
dtype: int
description: Feature end position (0-based, half open)
- name: name
dtype: string
description: >-
This stores the character `.`, one of the accepted characters for NA
in bed6
- name: score
dtype: int
description: The depth of 5 prime read ends at this location
role: quantitative_measure
- name: strand
dtype: string
description: >-
Strand orientation of the mapped fragment from which the 5 prime end
originates (+ or -)
- config_name: chec_genome_map_control_meta
description: Sample-level metadata for ChEC free MNase experiments
dataset_type: metadata
applies_to:
- chec_genome_map_control
data_files:
- split: train
path: chec_genome_map_control_meta.parquet
dataset_info:
features:
- name: sra_accession
dtype: string
description: >-
SRA (Sequence Read Archive) accession identifier for this biological
replicate
- name: replicate
dtype: string
description: Biological replicate identifier. One of A,B,C. All have 3 replicates
- name: notes
dtype: string
description: Additional notes or experimental details for this sample
- config_name: chec_genome_map_control
description: >-
ChEC free MNase genome-wide signal tracks partitioned by SRA accession,
providing position-level chromatin accessibility data
dataset_type: genome_map
data_files:
- split: train
path: chec_genome_map_control/sra_accession=*/*.parquet
dataset_info:
partitioning:
enabled: true
partition_by:
- sra_accession
features:
- name: sra_accession
dtype: string
description: >-
SRA accession identifier used for partitioning (links to
chec_genome_map_control_meta)
role: sample_id
- name: chr
dtype: string
description: Chromosome identifier (e.g., chrI, chrII, chrXVI)
- name: start
dtype: int
description: Feature start position (0-based half open)
- name: end
dtype: int
description: Feature end position (0-based, half open)
- name: name
dtype: string
description: >-
This stores the character `.`, one of the accepted characters for NA
in bed6
- name: score
dtype: int
description: The depth of 5 prime read ends at this location
role: quantitative_measure
- name: strand
dtype: string
description: >-
Strand orientation of the mapped fragment from which the 5 prime end
originates (+ or -)
- config_name: chec_mahendrawada_m2025_af_replicates
description: >-
ChEC-seq annotated features at biological replicate level with binding
peaks and statistical significance metrics
dataset_type: annotated_features
data_files:
- split: train
path: chec_mahendrawada_m2025_af_replicates.parquet
dataset_info:
features:
- name: sra_accession
dtype: string
description: >-
SRA (Sequence Read Archive) accession identifier for this biological
replicate
role: sample_id
- name: target_locus_tag
dtype: string
description: Systematic gene identifier for the target gene
role: target_identifier
- name: target_symbol
dtype: string
description: Standard gene symbol for the target gene
role: target_identifier
- name: seqnames
dtype: string
description: Chromosome identifier (e.g., chrI, chrII)
- name: start
dtype: int64
description: Peak start position (0-based coordinate)
- name: end
dtype: int64
description: Peak end position (0-based, exclusive)
- name: width
dtype: int64
description: Width of the peak in base pairs
- name: strand
dtype: string
description: Strand orientation (+ or -)
- name: enrichment
dtype: float64
description: Enrichment score for the binding peak
role: quantitative_measure
- name: poisson_pval
dtype: float64
description: P-value from Poisson distribution test for peak significance
role: quantitative_measure
- name: log_poisson_pval
dtype: float64
description: Log-transformed Poisson p-value
role: quantitative_measure
- name: hypergeometric_pval
dtype: float64
description: P-value from hypergeometric distribution test for peak significance
role: quantitative_measure
- name: log_hypergeometric_pval
dtype: float64
description: Log-transformed hypergeometric p-value
role: quantitative_measure
- name: poisson_qval
dtype: float64
description: FDR-adjusted q-value from Poisson test (multiple testing correction)
role: quantitative_measure
- name: hypergeometric_qval
dtype: float64
description: >-
FDR-adjusted q-value from hypergeometric test (multiple testing
correction)
role: quantitative_measure
- config_name: chec_mahendrawada_m2025_af_combined_meta
description: >-
Sample-level metadata for combined ChEC-seq experiments with regulator
information and experimental conditions
dataset_type: metadata
applies_to:
- chec_mahendrawada_m2025_af_combined
data_files:
- split: train
path: chec_mahendrawada_m2025_af_combined_meta.parquet
dataset_info:
features:
- name: sample_id
dtype: string
description: Unique identifier combining regulator, condition, and replicates
- name: regulator_locus_tag
dtype: string
description: >-
Systematic gene name (ORF identifier) of the depleted transcription
factor
role: regulator_identifier
- name: regulator_symbol
dtype: string
description: Standard gene symbol of the depleted transcription factor
role: regulator_identifier
- name: mahendrawada_symbol
dtype: string
description: Transcription factor symbol as reported in Mahendrawada et al. 2025
- name: condition
dtype:
class_label:
names:
- standard
- SM
- WT
- WT_SM
- admut
- admut_SM
- cAD
- cAD_SM
- dbdmut
- dbdmut_SM
- nAD
- nAD_SM
- ncAD
- ncAD_SM
- '30'
- '37'
- galactose
- raffinose
description: Experimental condition for this sample
role: experimental_condition
- config_name: chec_mahendrawada_m2025_af_combined
description: >-
Brent Lab reprocessed data from Mahendrawada 2025. See scripts/ for more
details.
dataset_type: annotated_features
data_files:
- split: train
path: chec_mahendrawada_m2025_af_combined.parquet
dataset_info:
features:
- name: sample_id
dtype: string
description: >-
Unique identifier for a specific regulator/condition. These are made
up of the replicates marked as `combine == TRUE` in the replicate
level metadata
- name: target_locus_tag
dtype: string
description: Systematic gene identifier for the target gene
role: target_identifier
- name: target_symbol
dtype: string
description: Standard gene symbol for the target gene
role: target_identifier
- name: seqnames
dtype: string
description: Chromosome identifier (e.g., chrI, chrII)
- name: start
dtype: int64
description: Peak start position (1-based)
- name: end
dtype: int64
description: Peak end position (1-based, inclusive)
- name: width
dtype: int64
description: Width of the peak in base pairs
- name: strand
dtype: string
description: Strand orientation (+ or -)
- name: enrichment
dtype: float64
description: Enrichment of experiment vs background
role: quantitative_measure
- name: poisson_pval
dtype: float64
description: P-value from Poisson distribution test for peak significance
role: quantitative_measure
- name: log_poisson_pval
dtype: float64
description: Log-transformed Poisson p-value
role: quantitative_measure
- name: hypergeometric_pval
dtype: float64
description: P-value from hypergeometric distribution test for peak significance
role: quantitative_measure
- name: log_hypergeometric_pval
dtype: float64
description: Log-transformed hypergeometric p-value
role: quantitative_measure
- name: poisson_qval
dtype: float64
description: FDR-adjusted q-value from Poisson test (multiple testing correction)
role: quantitative_measure
- name: hypergeometric_qval
dtype: float64
description: >-
FDR-adjusted q-value from hypergeometric test (multiple testing
correction)
role: quantitative_measure
- config_name: rna_seq
description: >-
Nascent RNA-seq differential expression data following transcription
factor depletion using 4TU metabolic labeling
dataset_type: annotated_features
metadata_fields:
- regulator_locus_tag
- regulator_symbol
data_files:
- split: train
path: rnaseq_mahendrawada_2025.parquet
dataset_info:
features:
- name: sample_id
dtype: integer
description: >-
unique identifier for a specific sample, which uniquely identifies
one of the 178 TFs. Across datasets in this repo, the a given
sample_id identifies the same regulator.
- name: db_id
dtype: integer
description: >-
an old unique identifer, for use internally only. Deprecated and
will be removed eventually. Do not use in analysis.
- name: regulator_locus_tag
dtype: string
description: >-
Systematic gene name (ORF identifier) of the depleted transcription
factor
- name: regulator_symbol
dtype: string
description: Standard gene symbol of the depleted transcription factor
- name: target_locus_tag
dtype: string
description: >-
Systematic gene name (ORF identifier) of the differentially
expressed target gene
- name: target_symbol
dtype: string
description: Standard gene symbol of the differentially expressed target gene
- name: log2fc
dtype: float64
description: >-
Log2 fold change (IAA/DMSO) for significantly affected genes
(DESeq2, padj <0.1, FC >= 1.3)
- config_name: rnaseq_reprocessed
description: >-
Reprocessed nascent RNA-seq differential expression data using DESeq2
without thresholding, comparing IAA-induced TF degradation versus DMSO
control
dataset_type: annotated_features
metadata_fields:
- regulator_locus_tag
- regulator_symbol
- sample_id
- env_condition
- timepoint
data_files:
- split: train
path: rnaseq_reprocessed.parquet
dataset_info:
features:
- name: sample_id
dtype: string
description: >-
Composite identifier combining regulator, condition, timepoint, and
treatment information from the merged IAA and DMSO sample IDs
role: sample_id
- name: regulator_locus_tag
dtype: string
description: Systematic gene identifier for the depleted transcription factor
role: regulator_identifier
- name: regulator_symbol
dtype: string
description: Standard gene symbol for the depleted transcription factor
role: regulator_identifier
- name: env_condition
dtype:
class_label:
names:
- standard_30C
- SM
- galactose
- raffinose
- heat_shock_37C
description: Environmental growth condition for this experiment
role: experimental_condition
- name: timepoint
dtype: float64
description: >-
Time point in minutes (standard is 30 minutes post-treatment. very
few other timepoints)
role: experimental_condition
- name: target_locus_tag
dtype: string
description: >-
Systematic gene identifier for the differentially expressed target
gene
role: target_identifier
- name: target_symbol
dtype: string
description: Standard gene symbol for the differentially expressed target gene
role: target_identifier
- name: baseMean
dtype: float64
description: Mean of normalized counts across all samples (DESeq2 output)
role: quantitative_measure
- name: log2FoldChange
dtype: float64
description: >-
Log2 fold change IAA versus DMSO (DESeq2 output, no thresholding
applied)
role: quantitative_measure
- name: lfcSE
dtype: float64
description: Standard error of the log2 fold change estimate (DESeq2 output)
role: quantitative_measure
- name: stat
dtype: float64
description: Wald test statistic (DESeq2 output)
role: quantitative_measure
- name: pvalue
dtype: float64
description: Wald test p-value (DESeq2 output)
role: quantitative_measure
- name: padj
dtype: float64
description: Benjamini-Hochberg adjusted p-value (DESeq2 output)
role: quantitative_measure
- config_name: degron_counts_meta
description: >-
Sample-level metadata for auxin-inducible degron perturbation experiments
with HTSeq count statistics
dataset_type: metadata
applies_to:
- degron_counts
data_files:
- split: train
path: degron_counts_meta.parquet
dataset_info:
features:
- name: sra_accession
dtype: string
description: SRA run accession identifier for this sample
role: sample_identifier
- name: gsm_accession
dtype: string
description: GEO sample accession identifier (GSM ID)
- name: regulator_locus_tag
dtype: string
description: Systematic gene identifier for the transcription factor
role: regulator_identifier
- name: regulator_symbol
dtype: string
description: Standard gene symbol for the transcription factor
role: regulator_identifier
- name: degron_treatment
dtype:
class_label:
names:
- DMSO
- IAA
description: Degron treatment condition (DMSO control or IAA degradation)
role: experimental_condition
- name: degron_variant
dtype:
class_label:
names:
- mini_N_terminal_IAA7
- full_or_short_IAA7
description: Type of auxin-inducible degron tag used
- name: env_condition
dtype:
class_label:
names:
- standard_30C
- SM
- galactose
- raffinose
- heat_shock_37C
description: Environmental growth condition
role: experimental_condition
- name: timepoint
dtype: float64
description: Time point for time-series experiments (minutes)
- name: replicate
dtype: string
description: Biological replicate identifier (A, B, or C)
- name: no_feature
dtype: int64
description: HTSeq count of reads not assigned to any feature
- name: ambiguous
dtype: int64
description: HTSeq count of reads mapping ambiguously to multiple features
- name: too_low_aQual
dtype: int64
description: HTSeq count of reads filtered due to low alignment quality
- name: alignment_not_unique
dtype: int64
description: HTSeq count of reads with non-unique alignments
- name: sample_id
dtype: string
description: Unique sample identifier combining replicates by treatment
- config_name: degron_counts
description: >-
HTSeq gene-level read counts for auxin-inducible degron perturbation
experiments
dataset_type: annotated_features
data_files:
- split: train
path: degron_counts.parquet
dataset_info:
features:
- name: sra_accession
dtype: string
description: SRA run accession identifier linking to sample metadata
role: sample_id
- name: target_locus_tag
dtype: string
description: >-
Systematic gene identifier from BrentLab yeast genomic features
(compatible with BrentLab yeast collection)
role: target_identifier
- name: target_symbol
dtype: string
description: >-
Standard gene symbol from BrentLab yeast genomic features
(compatible with BrentLab yeast collection)
role: target_identifier
- name: orig_locus_tag
dtype: string
description: >-
Original systematic gene identifier from R64-1-1 genome annotation
as reported by Mahendrawada et al. 2025
- name: count
dtype: int64
description: HTSeq gene-level read count from R64-1-1 genome annotation
role: quantitative_measure
- config_name: mnase_fusion_rnaseq_counts_meta
description: >-
Sample-level metadata for MNase fusion strain RNA-seq experiments with
HTSeq count statistics
dataset_type: metadata
applies_to:
- mnase_fusion_rnaseq_counts
data_files:
- split: train
path: mnase_fusion_rnaseq_counts_meta.parquet
dataset_info:
features:
- name: sra_accession
dtype: string
description: SRA run accession identifier for this sample
role: sample_identifier
- name: gsm_accession
dtype: string
description: GEO sample accession identifier (GSM ID)
- name: regulator_locus_tag
dtype: string
description: Systematic gene identifier for the MNase-tagged transcription factor
role: regulator_identifier
- name: regulator_symbol
dtype: string
description: Standard gene symbol for the MNase-tagged transcription factor
role: regulator_identifier
- name: env_condition
dtype:
class_label:
names:
- standard_30C
- SM
- galactose
- raffinose
- heat_shock_37C
description: Environmental growth condition
role: experimental_condition
- name: replicate
dtype: string
description: Biological replicate identifier (A, B, or C)
- name: no_feature
dtype: int64
description: HTSeq count of reads not assigned to any feature
- name: ambiguous
dtype: int64
description: HTSeq count of reads mapping ambiguously to multiple features
- name: too_low_aQual
dtype: int64
description: HTSeq count of reads filtered due to low alignment quality
- name: alignment_not_unique
dtype: int64
description: HTSeq count of reads with non-unique alignments
- name: sample_id
dtype: string
description: Unique sample identifier combining replicates by treatment
- config_name: mnase_fusion_rnaseq_counts
description: HTSeq gene-level read counts for MNase fusion strain RNA-seq experiments
dataset_type: annotated_features
data_files:
- split: train
path: mnase_fusion_rnaseq_counts.parquet
dataset_info:
features:
- name: sra_accession
dtype: string
description: SRA run accession identifier linking to sample metadata
role: sample_id
- name: target_locus_tag
dtype: string
description: >-
Systematic gene identifier from BrentLab yeast genomic features
(compatible with BrentLab yeast collection)
role: target_identifier
- name: target_symbol
dtype: string
description: >-
Standard gene symbol from BrentLab yeast genomic features
(compatible with BrentLab yeast collection)
role: target_identifier
- name: orig_locus_tag
dtype: string
description: >-
Original systematic gene identifier from R64-1-1 genome annotation
as reported by Mahendrawada et al. 2025
- name: count
dtype: int64
description: HTSeq gene-level read count from R64-1-1 genome annotation
role: quantitative_measure
- config_name: wt_baseline_counts_meta
description: >-
Sample-level metadata for wild-type baseline RNA-seq experiments with
HTSeq count statistics
dataset_type: metadata
applies_to:
- wt_baseline_counts
data_files:
- split: train
path: wt_baseline_counts_meta.parquet
dataset_info:
features:
- name: sra_accession
dtype: string
description: SRA run accession identifier for this sample
role: sample_identifier
- name: gsm_accession
dtype: string
description: GEO sample accession identifier (GSM ID)
- name: env_condition
dtype:
class_label:
names:
- standard_30C
- SM
- galactose
- raffinose
- heat_shock_37C
description: Environmental growth condition
role: experimental_condition
- name: replicate
dtype: string
description: Biological replicate identifier (A, B, or C)
- name: no_feature
dtype: int64
description: HTSeq count of reads not assigned to any feature
- name: ambiguous
dtype: int64
description: HTSeq count of reads mapping ambiguously to multiple features
- name: too_low_aQual
dtype: int64
description: HTSeq count of reads filtered due to low alignment quality
- name: alignment_not_unique
dtype: int64
description: HTSeq count of reads with non-unique alignments
- name: sample_id
dtype: string
description: Unique sample identifier combining replicates by treatment
- config_name: wt_baseline_counts
description: HTSeq gene-level read counts for wild-type baseline RNA-seq experiments
dataset_type: annotated_features
data_files:
- split: train
path: wt_baseline_counts.parquet
dataset_info:
features:
- name: sra_accession
dtype: string
description: SRA run accession identifier linking to sample metadata
role: sample_id
- name: target_locus_tag
dtype: string
description: >-
Systematic gene identifier from BrentLab yeast genomic features
(compatible with BrentLab yeast collection)
role: target_identifier
- name: target_symbol
dtype: string
description: >-
Standard gene symbol from BrentLab yeast genomic features
(compatible with BrentLab yeast collection)
role: target_identifier
- name: orig_locus_tag
dtype: string
description: >-
Original systematic gene identifier from R64-1-1 genome annotation
as reported by Mahendrawada et al. 2025
- name: count
dtype: int64
description: HTSeq gene-level read count from R64-1-1 genome annotation
role: quantitative_measure
- config_name: wt_degron_control_counts_meta
description: >-
Sample-level metadata for wild-type degron control RNA-seq experiments
with HTSeq count statistics
dataset_type: metadata
applies_to:
- wt_degron_control_counts
data_files:
- split: train
path: wt_degron_control_counts_meta.parquet
dataset_info:
features:
- name: sra_accession
dtype: string
description: SRA run accession identifier for this sample
role: sample_identifier
- name: gsm_accession
dtype: string
description: GEO sample accession identifier (GSM ID)
- name: degron_treatment
dtype:
class_label:
names:
- DMSO
- IAA
description: Degron treatment condition (DMSO control or IAA degradation)
role: experimental_condition
- name: replicate
dtype: string
description: Biological replicate identifier (A, B, or C)
- name: no_feature
dtype: int64
description: HTSeq count of reads not assigned to any feature
- name: ambiguous
dtype: int64
description: HTSeq count of reads mapping ambiguously to multiple features
- name: too_low_aQual
dtype: int64
description: HTSeq count of reads filtered due to low alignment quality
- name: alignment_not_unique
dtype: int64
description: HTSeq count of reads with non-unique alignments
- name: sample_id
dtype: string
description: Unique sample identifier combining replicates by treatment
- config_name: wt_degron_control_counts
description: >-
HTSeq gene-level read counts for wild-type degron control RNA-seq
experiments
dataset_type: annotated_features
data_files:
- split: train
path: wt_degron_control_counts.parquet
dataset_info:
features:
- name: sra_accession
dtype: string
description: SRA run accession identifier linking to sample metadata
role: sample_id
- name: target_locus_tag
dtype: string
description: >-
Systematic gene identifier from BrentLab yeast genomic features
(compatible with BrentLab yeast collection)
role: target_identifier
- name: target_symbol
dtype: string
description: >-
Standard gene symbol from BrentLab yeast genomic features
(compatible with BrentLab yeast collection)
role: target_identifier
- name: orig_locus_tag
dtype: string
description: >-
Original systematic gene identifier from R64-1-1 genome annotation
as reported by Mahendrawada et al. 2025
- name: count
dtype: int64
description: HTSeq gene-level read count from R64-1-1 genome annotation
role: quantitative_measure
Mahendrawada 2025
This data is taken from the Supplement of
and GSE236948