README.md

---
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:
  # 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
  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

[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)

and [GSE236948](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236948)