Restructure repository with new dataset organization

.gitignore

@@ -0,0 +1 @@
+chec_genome_map_bed/

README.md

@@ -17,6 +17,35 @@ pretty_name: "Mahendrawada 2025 ChEC-seq and Nascent RNA-seq data"
 size_categories:
 - 100K<n<1M
 
+experimental_conditions:
+  # Mahendrawada et al 2025: "30 °C culture"
+  temperature_celsius: 30
+  growth_phase_at_harvest:
+    # Mahendrawada et al 2025: "A600 of ~1.0"
+    od600: 1.0
+  media:
+    # Mahendrawada et al 2025: "synthetic complete (SC) media"
+    name: synthetic_complete
+    nitrogen_source:
+      - compound: yeast_nitrogen_base
+        # Mahendrawada et al 2025: 1.7 g/L (without ammonium sulfate or amino acids (BD Difco))
+        concentration_percent: 0.17
+        specifications:
+          - without_ammonium_sulfate
+          - without_amino_acids
+      - compound: ammonium_sulfate
+        # Mahendrawada et al 2025: 5 g/L
+        concentration_percent: 0.5
+      - compound: amino_acid_dropout_mix
+        # Mahendrawada et al 2025: 0.6 g/L
+        concentration_percent: 0.06
+      - compound: adenine_sulfate
+        # Mahendrawada et al 2025: 40 μg/ml = 0.04 g/L
+        concentration_percent: 0.004
+      - compound: uracil
+        # Mahendrawada et al 2025: 2 μg/ml = 0.002 g/L
+        concentration_percent: 0.0002
+
 configs:
 - config_name: genomic_features
   description: Comprehensive genomic features and regulatory characteristics for yeast genes
@@ -135,113 +164,302 @@ configs:
       dtype: string
       description: Method used for peak calling and quantification (original authors)
 
-- config_name: reprocessed_chec_seq
-  description: ChEC-seq transcription factor binding data reprocessed with updated peak calling methodology
-  dataset_type: annotated_features
+- config_name: chec_genomemap_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_reprocessed_mahendrawada_2025.parquet
+    path: sample_meta.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: 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 transcription factor
+      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 transcription factor
+      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
+  applies_to: ["sample_meta"]
+  data_files:
+  - split: train
+    path: chec_genomemap/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_genomemap_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_freemnase_meta
+  description: Sample-level metadata for ChEC free MNase experiments
+  dataset_type: metadata
+  applies_to: ["chec_freemnase"]
+  data_files:
+  - split: train
+    path: chec_freemnase_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_freemnase
+  description: ChEC free MNase genome-wide signal tracks partitioned by SRA accession, providing position-level chromatin accessibility data
+  dataset_type: genome_map
+  applies_to: ["chec_freemnase_meta"]
+  data_files:
+  - split: train
+    path: chec_freemnase/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_freemnase_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 name (ORF identifier) of the target gene
+      description: Systematic gene identifier for the target gene
+      role: target_identifier
     - name: target_symbol
       dtype: string
-      description: Standard gene symbol of the target gene
+      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: ratio of experimental insertions to background insertions
+      description: Enrichment score for the binding peak
+      role: quantitative_measure
     - name: poisson_pval
       dtype: float64
-      description: enrichment poisson pvalue
+      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: reprocessed_diffcontrol_5prime
-  description: Comparing two different sets of control replicates, m2025 from the Mahendrawada 2025 paper, and h2021 from a previous paper from the Hahn lab
-  dataset_type: annotated_features
-  metadata_fields:
-    - control_source
-    - condition
-    - regulator_locus_tag
-  experimental_conditions:
-    # Mahendrawada et al 2025: "30 °C culture"
-    temperature_celsius: 30
-    cultivation_method: unspecified
-    growth_phase_at_harvest:
-      # Mahendrawada et al 2025: "A600 of ~1.0"
-      od600: 1.0
-    media:
-      # Mahendrawada et al 2025: "synthetic complete (SC) media"
-      name: synthetic_complete
-      carbon_source: unspecified
-      nitrogen_source:
-        - compound: yeast_nitrogen_base
-          # Mahendrawada et al 2025: 1.7 g/L (without ammonium sulfate or amino acids (BD Difco))
-          concentration_percent: 0.17
-          specifications:
-            - without_ammonium_sulfate
-            - without_amino_acids
-        - compound: ammonium_sulfate
-          # Mahendrawada et al 2025: 5 g/L
-          concentration_percent: 0.5
-        - compound: amino_acid_dropout_mix
-          # Mahendrawada et al 2025: 0.6 g/L
-          concentration_percent: 0.06
-        - compound: adenine_sulfate
-          # Mahendrawada et al 2025: 40 μg/ml = 0.04 g/L
-          concentration_percent: 0.004
-        - compound: uracil
-          # Mahendrawada et al 2025: 2 μg/ml = 0.002 g/L
-          concentration_percent: 0.0002
+- config_name: combined_sample_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: reprocess_diffcontrol_5prime.parquet
+    path: combined_sample_meta.parquet
   dataset_info:
     features:
-    - name: control_source
-      dtype: string
-      description: Source identifier for the control dataset (m2025 or h2021)
-    - name: condition
+    - name: sample_id
       dtype: string
-      description: Experimental condition. 'standard' is YPD.
+      description: Unique identifier combining regulator, condition, and replicates
     - name: regulator_locus_tag
       dtype: string
-      description: Systematic gene name (ORF identifier) of the transcription factor
+      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 name (ORF identifier) of the target gene
-    - name: chr
+      description: Systematic gene identifier for the target gene
+      role: target_identifier
+    - name: target_symbol
       dtype: string
-      description: Chromosome name of the promoter/target region
+      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: Start coordinate of the promoter region
+      description: Peak start position (1-based)
     - name: end
       dtype: int64
-      description: End coordinate of the promoter region
+      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 -) of the promoter/target
-    - name: input_vs_target_log2_fold_change
+      description: Strand orientation (+ or -) 
+    - name: enrichment
       dtype: float64
-      description: Log2 fold change of TF-tagged sample vs control (from DESeq2)
-    - name: input_vs_target_p_value
+      description: Enrichment of experiment vs background
+      role: quantitative_measure
+    - name: poisson_pval
       dtype: float64
-      description: P-value for differential enrichment (from DESeq2)
-    - name: input_vs_target_adj_p_value
+      description: P-value from Poisson distribution test for peak significance
+      role: quantitative_measure
+    - name: log_poisson_pval
       dtype: float64
-      description: Adjusted p-value (FDR-corrected) for differential enrichment (from DESeq2)
+      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
@@ -279,138 +497,320 @@ configs:
     - name: log2fc
       dtype: float64
       description: Log2 fold change (IAA/DMSO) for significantly affected genes (DESeq2, padj <0.1, FC >= 1.3)
----
-# Mahendrawada 2025
-
-This data is taken from the Supplement of
-
-[Mahendrawada, L., Warfield, L., Donczew, R. et al. Low overlap of transcription factor DNA binding and regulatory targets. Nature 642, 796–804 (2025). https://doi.org/10.1038/s41586-025-08916-0](https://doi.org/10.1038/s41586-025-08916-0)
-
-Please note that all column descriptions, except for those containing "locus_tag" and "symbol", are copy/pasted directly from the supplement or
-methods section of this paper.
-
-## Dataset Details
-
-This repo provides three datasets:
-
-- **genomic_features**: These are the genomic features provided in Supplemental Table 2
-- **chec_seq**: binding location data provided in Supplemental Table 3. the `peak_score` is defined to be the ChEC signal around peak center'
-  (sum of ChEC signal from -150 to +150 bp from peak summit) normalized to Drosophila spike-in control. How these scores are assigned to features
-  isn't well described in either the supplement or Methods section, but it is reasonable to believe that it is done with HOMER.
-- **rna_seq**: Nascent RNA-seq differential expression data following transcription factor depletion using 4TU metabolic labeling filtered for
-  significantly affected genes (DESeq2, padj <0.1, FC >= 1.3)
-
-## Data Structure
-
-This dataset provides the following three parquet files
-
-### ChEC-seq
-
-| Field                 | Description                                                                                                                                |
-|-----------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
-| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the transcription factor                                                                         |
-| `regulator_symbol`    | Standard gene symbol of the transcription factor                                                                                           |
-| `target_locus_tag`    | Systematic gene name (ORF identifier) of the target gene                                                                                  |
-| `target_symbol`       | Standard gene symbol of the target gene                                                                                                    |
-| `peak_score`          | ChEC signal around peak center (sum of ChEC signal from -150 to +150 bp from peak summit) normalized to Drosophila spike-in control     |
-
-### RNA-seq
 
-| Field                 | Description                                                                                                                                |
-|-----------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
-| `regulator_locus_tag` | Systematic gene name (ORF identifier) of the depleted transcription factor                                                                |
-| `regulator_symbol`    | Standard gene symbol of the depleted transcription factor                                                                                 |
-| `target_locus_tag`    | Systematic gene name (ORF identifier) of the differentially expressed target gene                                                         |
-| `target_symbol`       | Standard gene symbol of the differentially expressed target gene                                                                           |
-| `log2fc`              | Log2 fold change (IAA/DMSO) for significantly affected genes (DESeq2, padj <0.1, FC >= 1.3)                                             |
-
-### Features
-
-| Field                    | Description                                                                                                                                |
-|--------------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
-| `gene_id`                | Systematic gene name (ORF identifier) from SGD (https://yeastgenome.org/)                                                                |
-| `SGD_id`                 | Unique identifier for each gene from SGD (https://yeastgenome.org/)                                                                      |
-| `gene_name`              | Common name of each gene                                                                                                                   |
-| `chr`                    | Chromosome number corresponding to gene                                                                                                    |
-| `strand`                 | Strandedness of the gene (+ or -)                                                                                                         |
-| `start`                  | Start position of the ORF                                                                                                                  |
-| `end`                    | End position of the ORF                                                                                                                    |
-| `TSS`                    | Transcription start site based on Park et al., 2014 (doi:10.1093/nar/gkt1366)                                                           |
-| `TATA_category`          | TATA box classification from Donczew et al., 2020 using consensus TATAWAW (doi:10.7554/eLife.50109)                                     |
-| `expression`             | Average signal normalized to gene length from Donczew et al., 2020 (doi:10.7554/eLife.50109)                                           |
-| `+1 nucleosome`          | Position of +1 nucleosome from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)                                                     |
-| `-1 nucleosome`          | Position of -1 nucleosome from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)                                                     |
-| `NDR Center`             | Center of nucleosome depleted region from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)                                         |
-| `NDR Width`              | Width of nucleosome depletion region from Chereji et al., 2018 (doi:10.1186/S13059-018-1398-0)                                         |
-| `tail-dependence`        | Tail classification based on Mediator tail dependence from Warfield L, Donczew R et al., 2022 (doi:10.1016/j.molcel.2022.09.016)      |
-| `coactivator`            | Coactivator classification based on TFIID and/or SAGA dependence from Donczew et al., 2020 (doi:10.7554/eLife.50109)                   |
-| `LCID_center`            | Genes near boundaries of chromosomal interacting domains from Swygert et al., 2020 (doi:10.1016/j.molcel.2018.11.020)                  |
-| `Rossi_classes`          | Promoter classes from Rossi et al., 2021 (doi:10.1038/s41586-021-03314-8)                                                               |
-| `RP_category`            | Ribosomal protein (RP) and ribosomal biogenesis (RiBi) gene classification from Zencir et al., 2020 (doi:10.1093/NAR/GKAA852)          |
-| `binding_cluster`        | Clusters from unsupervised K-means clustering using binary binding data of 178 transcription factors                                     |
-| `list_of_TFS_bound`      | List of transcription factors bound to gene promoter (-400 to +200 bp from TSS; Homer peak calling)                                     |
-| `number_of_bound_tfs`    | Number of transcription factors bound to each promoter                                                                                     |
-| `locus_tag`              | Systematic gene identifier from yeast_genome_resources dataset                                                                             |
-| `symbol`                 | Standard gene symbol from yeast_genome_resources dataset                                                                                   |
-
-## Usage
-
-There are three parquet files in this repo. This is a way of getting that information programmatically
-
-```python
-from huggingface_hub import ModelCard
-from pprint import pprint
-
-card = ModelCard.load("BrentLab/hughes_2006", repo_type="dataset")
-
-# cast to dict
-card_dict = card.data.to_dict()
-
-# Get partition information
-dataset_paths_dict = {d.get("config_name"): d.get("data_files")[0].get("path") for d in card_dict.get("configs")}
-
-pprint(dataset_paths_dict)
-```
+- 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
 
-With the result
+- 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
 
-```raw
-{'chec_seq': 'chec_mahendrawada_2025.parquet',
- 'genomic_features': 'features_mahendrawada_2025.parquet',
- 'rna_seq': 'rnaseq_mahendrawada_2025.parquet'}
-```
+- 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
 
-I recommend using `huggingface_hub.snapshot_download` to pull the repository. After that, use your favorite
-method of interacting with `parquet` files (eg duckDB, but you could use dplyr in R or pandas, too).
+- 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
 
-```python
-from huggingface_hub import snapshot_download
-import duckdb
-import os
+- 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
 
-repo_id = "BrentLab/mahendrawada_2025"
+- 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
 
-# Download entire repo to local directory
-repo_path = snapshot_download(
-    repo_id=repo_id,
-    repo_type="dataset"
-)
+- 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
 
-print(f"Repository downloaded to: {repo_path}")
+- config_name: wt_degron_control_counts
+  description: HTSeq gene-level read counts for wild-type degron control RNA-seq experiments
+  dataset_type: annotated_features
+  applies_to: ["wt_degron_control_counts_meta"]
+  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
 
-# Construct path to the checseq parquet file
-parquet_path = os.path.join(repo_path, "chec_mahendrawada_2025.parquet")
-print(f"Parquet file at: {parquet_path}")
+This data is taken from the Supplement of
 
-# Connect to DuckDB and query the parquet file
-conn = duckdb.connect()
+[Mahendrawada, L., Warfield, L., Donczew, R. et al. Low overlap of transcription factor DNA binding and regulatory targets. Nature 642, 796–804 (2025). https://doi.org/10.1038/s41586-025-08916-0](https://doi.org/10.1038/s41586-025-08916-0)
 
-query = """
-SELECT * 
-FROM read_parquet(?)
-WHERE regulator_symbol = 'CST6'
-"""
+Please note that all column descriptions, except for those containing "locus_tag" and "symbol", are copy/pasted directly from the supplement or
+methods section of this paper.
 
-result = conn.execute(query, [parquet_path]).fetchall()
-print(f"Found {len(result)} rows for CST6")
-```

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