--- 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- Mahendrawada L, Warfield L, Donczew R et al. Low overlap of transcription factor DNA binding and regulatory targets. Nature. 2025. 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 carbon_source: # Carbon source is not specified in the paper; D-glucose is standard for SC media. - compound: D-glucose 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 features: - applies_to: - chec_genome_map_meta - chec_mahendrawada_m2025_af_combined_meta - mahendrawada_chec_seq - rna_seq - rnaseq_reprocessed - degron_counts_meta - mnase_fusion_rnaseq_counts_meta fields: - 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 - applies_to: - chec_mahendrawada_m2025_af_replicates - chec_mahendrawada_m2025_af_combined - chec_mahendrawada_m2025_af_replicates_mindel - chec_mahendrawada_m2025_af_combined_mindel - mahendrawada_chec_seq - rna_seq - rnaseq_reprocessed - degron_counts - mnase_fusion_rnaseq_counts - wt_baseline_counts - wt_degron_control_counts fields: - 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 - applies_to: - chec_mahendrawada_m2025_af_replicates_mindel - chec_mahendrawada_m2025_af_combined_mindel fields: - name: mindel_name dtype: string description: >- Name of the target from the original authors of this promoter set role: target_identifier - name: promoter_sequence dtype: string description: >- sequence of the promoter region for this target - name: in_mahendrawada_features dtype: boolean description: >- Whether this target is included in the mahendrawada_features dataset, which is filtered for protein coding, non dubious ORFs - name: promoter_exact_aligns dtype: int64 description: >- Description pending. This is from original authors of the promoters. Need to check it - applies_to: - chec_genome_map_meta - chec_mahendrawada_m2025_af_combined_meta fields: - 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. The standard condition is synthetic complete media at 30°C. Stress and induction conditions are used for specific TF depletion experiments (Gcn4, Hsf1, Msn2, Gal4). Gcn4 mutant derivative conditions (admut, cAD, dbdmut, nAD, ncAD) are used only in ChEC-seq binding experiments, not degron depletion. role: experimental_condition definitions: standard: description: >- Standard growth condition used for the majority of ChEC-seq experiments. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: # Methods: synthetic complete (SC) media per litre: 1.7g YNB (without # ammonium sulfate or amino acids), 5g ammonium sulfate, 40ug/ml # adenine sulfate, 0.6g amino acid dropout mix, supplemented with # 2ug/ml uracil and 0.01% other amino acids name: synthetic_complete supplements: - compound: yeast_nitrogen_base_without_ammonium_sulfate_without_amino_acids concentration_g_per_L: 1.7 - compound: ammonium_sulfate concentration_g_per_L: 5 - compound: adenine_sulfate concentration_ug_per_mL: 40 - compound: amino_acid_dropout_mix concentration_g_per_L: 0.6 - compound: uracil concentration_ug_per_mL: 2 SM: description: >- Amino acid starvation stress induced by sulfometuron methyl (SM), used for Gcn4 ChEC-seq and degron depletion experiments. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: # Methods: SC (-Ile-Val) media name: synthetic_complete_minus_ile_val chemical_treatment: compound: sulfometuron_methyl concentration_ug_per_mL: 0.5 duration_minutes: 60 WT: description: >- Wild-type Gcn4 strain grown under standard conditions without SM stress, used as baseline in Gcn4 activation domain mutant ChEC-seq experiments. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete supplements: - compound: yeast_nitrogen_base_without_ammonium_sulfate_without_amino_acids concentration_g_per_L: 1.7 - compound: ammonium_sulfate concentration_g_per_L: 5 - compound: adenine_sulfate concentration_ug_per_mL: 40 - compound: amino_acid_dropout_mix concentration_g_per_L: 0.6 - compound: uracil concentration_ug_per_mL: 2 WT_SM: description: >- Wild-type Gcn4 strain grown under SM stress conditions, used as induced baseline in Gcn4 activation domain mutant ChEC-seq experiments. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete_minus_ile_val chemical_treatment: compound: sulfometuron_methyl concentration_ug_per_mL: 0.5 duration_minutes: 60 admut: description: >- Gcn4 double activation domain deletion mutant (delta2-134, N-terminal and central ADs deleted) under standard conditions without SM stress. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete supplements: - compound: yeast_nitrogen_base_without_ammonium_sulfate_without_amino_acids concentration_g_per_L: 1.7 - compound: ammonium_sulfate concentration_g_per_L: 5 - compound: adenine_sulfate concentration_ug_per_mL: 40 - compound: amino_acid_dropout_mix concentration_g_per_L: 0.6 - compound: uracil concentration_ug_per_mL: 2 gcn4_mutation: "deltaAD (delta2-134): deletion of both N-terminal and central activation domains" admut_SM: description: >- Gcn4 double activation domain deletion mutant (delta2-134) under SM stress conditions. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete_minus_ile_val chemical_treatment: compound: sulfometuron_methyl concentration_ug_per_mL: 0.5 duration_minutes: 60 gcn4_mutation: "deltaAD (delta2-134): deletion of both N-terminal and central activation domains" cAD: description: >- Gcn4 central activation domain missense mutant (W120A, L123A, F124A) under standard conditions without SM stress. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete supplements: - compound: yeast_nitrogen_base_without_ammonium_sulfate_without_amino_acids concentration_g_per_L: 1.7 - compound: ammonium_sulfate concentration_g_per_L: 5 - compound: adenine_sulfate concentration_ug_per_mL: 40 - compound: amino_acid_dropout_mix concentration_g_per_L: 0.6 - compound: uracil concentration_ug_per_mL: 2 gcn4_mutation: "cAD: W120A, L123A, F124A (central activation domain inactivated)" cAD_SM: description: >- Gcn4 central activation domain missense mutant (W120A, L123A, F124A) under SM stress conditions. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete_minus_ile_val chemical_treatment: compound: sulfometuron_methyl concentration_ug_per_mL: 0.5 duration_minutes: 60 gcn4_mutation: "cAD: W120A, L123A, F124A (central activation domain inactivated)" dbdmut: description: >- Gcn4 DNA-binding domain triple mutant (N235A, R243A, S242A) under standard conditions without SM stress. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete supplements: - compound: yeast_nitrogen_base_without_ammonium_sulfate_without_amino_acids concentration_g_per_L: 1.7 - compound: ammonium_sulfate concentration_g_per_L: 5 - compound: adenine_sulfate concentration_ug_per_mL: 40 - compound: amino_acid_dropout_mix concentration_g_per_L: 0.6 - compound: uracil concentration_ug_per_mL: 2 gcn4_mutation: "DBD: N235A, R243A, S242A (DNA-binding domain inactivated)" dbdmut_SM: description: >- Gcn4 DNA-binding domain triple mutant (N235A, R243A, S242A) under SM stress conditions. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete_minus_ile_val chemical_treatment: compound: sulfometuron_methyl concentration_ug_per_mL: 0.5 duration_minutes: 60 gcn4_mutation: "DBD: N235A, R243A, S242A (DNA-binding domain inactivated)" nAD: description: >- Gcn4 N-terminal activation domain missense mutant (F67A, F69A, F97A, F98A) under standard conditions without SM stress. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete supplements: - compound: yeast_nitrogen_base_without_ammonium_sulfate_without_amino_acids concentration_g_per_L: 1.7 - compound: ammonium_sulfate concentration_g_per_L: 5 - compound: adenine_sulfate concentration_ug_per_mL: 40 - compound: amino_acid_dropout_mix concentration_g_per_L: 0.6 - compound: uracil concentration_ug_per_mL: 2 gcn4_mutation: "nAD: F67A, F69A, F97A, F98A (N-terminal activation domain inactivated)" nAD_SM: description: >- Gcn4 N-terminal activation domain missense mutant (F67A, F69A, F97A, F98A) under SM stress conditions. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete_minus_ile_val chemical_treatment: compound: sulfometuron_methyl concentration_ug_per_mL: 0.5 duration_minutes: 60 gcn4_mutation: "nAD: F67A, F69A, F97A, F98A (N-terminal activation domain inactivated)" ncAD: description: >- Gcn4 combined N-terminal and central activation domain missense mutant (F67A, F69A, F97A, F98A, W120A, L123A, F124A) under standard conditions without SM stress. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete supplements: - compound: yeast_nitrogen_base_without_ammonium_sulfate_without_amino_acids concentration_g_per_L: 1.7 - compound: ammonium_sulfate concentration_g_per_L: 5 - compound: adenine_sulfate concentration_ug_per_mL: 40 - compound: amino_acid_dropout_mix concentration_g_per_L: 0.6 - compound: uracil concentration_ug_per_mL: 2 gcn4_mutation: "ncAD: F67A, F69A, F97A, F98A, W120A, L123A, F124A (both ADs inactivated by missense)" ncAD_SM: description: >- Gcn4 combined N-terminal and central activation domain missense mutant (F67A, F69A, F97A, F98A, W120A, L123A, F124A) under SM stress conditions. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete_minus_ile_val chemical_treatment: compound: sulfometuron_methyl concentration_ug_per_mL: 0.5 duration_minutes: 60 gcn4_mutation: "ncAD: F67A, F69A, F97A, F98A, W120A, L123A, F124A (both ADs inactivated by missense)" "30": description: >- No-heat-shock control condition for Hsf1 and Msn2 experiments; incubated for 10 min at 30°C. temperature_celsius: 30 incubation_duration_minutes: 10 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete supplements: - compound: yeast_nitrogen_base_without_ammonium_sulfate_without_amino_acids concentration_g_per_L: 1.7 - compound: ammonium_sulfate concentration_g_per_L: 5 - compound: adenine_sulfate concentration_ug_per_mL: 40 - compound: amino_acid_dropout_mix concentration_g_per_L: 0.6 - compound: uracil concentration_ug_per_mL: 2 "37": description: >- Heat shock condition for Hsf1 and Msn2 experiments. Equal volume of 44°C media added to 30°C culture, then incubated at 37°C for 10 min. initial_temperature_celsius: 30 mixing_temperature_celsius: 44 final_temperature_celsius: 37 incubation_duration_minutes: 10 growth_phase_at_harvest: od600: 1.0 media: name: synthetic_complete supplements: - compound: yeast_nitrogen_base_without_ammonium_sulfate_without_amino_acids concentration_g_per_L: 1.7 - compound: ammonium_sulfate concentration_g_per_L: 5 - compound: adenine_sulfate concentration_ug_per_mL: 40 - compound: amino_acid_dropout_mix concentration_g_per_L: 0.6 - compound: uracil concentration_ug_per_mL: 2 galactose: description: >- Galactose induction condition for Gal4 experiments. Cells grown in YEP-Raffinose then induced with 2% galactose for 2 hours prior to RNA labelling. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: # Methods: YEP-Raffinose (1% yeast extract, 2% peptone, 2% raffinose) # induced with 2% galactose for 2h name: yeast_extract_peptone_raffinose_plus_galactose carbon_source: - compound: D-raffinose concentration_percent: 2 - compound: D-galactose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 galactose_induction_duration_hours: 2 raffinose: description: >- Uninduced raffinose condition for Gal4 experiments. Cells grown in YEP-Raffinose without galactose addition. temperature_celsius: 30 growth_phase_at_harvest: od600: 1.0 media: # Methods: YEP-Raffinose (1% yeast extract, 2% peptone, 2% raffinose) name: yeast_extract_peptone_raffinose carbon_source: - compound: D-raffinose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 - applies_to: - chec_mahendrawada_m2025_af_replicates_intergenic - chec_mahendrawada_m2025_af_combined_intergenic fields: - name: ir_name dtype: string description: >- Unique identifier of the intergenic region. See yeast_genome_resources/intergenic_regions_metadata_5_1.csv for details on the region (location, etc). Note that these intergenic regions are defined as the region between the end of one ORF and the start of the next, and are named according to the locus tags of the flanking ORFs (e.g., YAL001C-YAL002W). A intergenic region is assigned to a promoter only when the 5' end is continuous with the region. - applies_to: - chec_mahendrawada_m2025_af_replicates - chec_mahendrawada_m2025_af_combined - chec_mahendrawada_m2025_af_replicates_mindel - chec_mahendrawada_m2025_af_combined_mindel - chec_mahendrawada_m2025_af_replicates_start_codon_500bp - chec_mahendrawada_m2025_af_combined_start_codon_500bp - chec_mahendrawada_m2025_af_replicates_intergenic - chec_mahendrawada_m2025_af_combined_intergenic fields: - name: seqnames dtype: string description: Chromosome identifier (e.g., chrI, chrII) - name: start dtype: int64 description: Promoter start position (1-based) - name: end dtype: int64 description: Promoter end position (1-based, inclusive) - name: width dtype: int64 description: Width of the peak in base pairs - name: strand dtype: string description: Strand orientation of the promoter (+ or -) - name: enrichment dtype: float64 description: Enrichment score for the promoter (tagged TF sample vs free MNase control) role: quantitative_measure - name: poisson_pval dtype: float64 description: P-value from Poisson distribution test for the enrichment role: quantitative_measure - name: log_poisson_pval dtype: float64 description: Log-transformed Poisson p-value (using the log argument of the poisson function) role: quantitative_measure - name: hypergeometric_pval dtype: float64 description: P-value from hypergeometric distribution test for the enrichment role: quantitative_measure - name: log_hypergeometric_pval dtype: float64 description: Log-transformed hypergeometric p-value (using the log argument of the phyper function) 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 - applies_to: - degron_counts_meta - mnase_fusion_rnaseq_counts_meta - wt_degron_control_counts_meta - wt_baseline_counts_meta fields: - name: no_feature dtype: float64 description: HTSeq count of reads not assigned to any feature - name: ambiguous dtype: float64 description: HTSeq count of reads mapping ambiguously to multiple features - name: too_low_aQual dtype: float64 description: HTSeq count of reads filtered due to low alignment quality - name: alignment_not_unique dtype: float64 description: HTSeq count of reads with non-unique alignments 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: float64 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). Note that this is the only the standard condition data for the 178 transcription factors in that condition in the 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: >- NOTE: this needs to be checked -- I think it should be deprecated/removed and replaced with the sample_id in the chec_genome_map_meta. This dataset was not used for awhile as the rest of the repo developed. - 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 - 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_mahendrawada_m2025_af_replicates_mindel", "chec_mahendrawada_m2025_af_replicates_start_codon_500bp", "chec_mahendrawada_m2025_af_replicates_intergenic", "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. Use this as the primary sample identifier for an individual replicate. Note that there is also a `sample_id` column which identifies unique sets of (regulator, condition). role: sample_id - name: sample_id dtype: int64 description: >- A unique identifier for a regulator/condition (replicate set). This is the same sample_id that is used for the *_combined_* samples and can be used to related sra_accessions to replicate sets in that data. role: secondary_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 - 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: float64 description: Feature start position (0-based half open) - name: end dtype: float64 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: float64 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: float64 description: Feature start position (0-based half open) - name: end dtype: float64 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: float64 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: >- Promoter significance scores using the Yiming Kang promoters, calculated using the mahendrawada_annotated_features.R. This is a reprocessing of the original authors' data which counts all tags over a specific promoter region in the TF tagged sample and calculates an enrichment relative to the free MNase control. dataset_type: annotated_features genome_resources: region_sets: Kang: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/yiming_promoters.bed join_column: target_locus_tag 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 - config_name: chec_mahendrawada_m2025_af_replicates_mindel description: >- Promoter significance scores using the Mindel promoters, calculated using the mahendrawada_annotated_features.R. This is a reprocessing of the original authors' data which counts all tags over a specific promoter region in the TF tagged sample and calculates an enrichment relative to the free MNase control. dataset_type: annotated_features genome_resources: region_sets: Mindel: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/mindel_promoters.csv.gz join_column: target_locus_tag data_files: - split: train path: chec_mahendrawada_m2025_af_replicates_mindel.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA (Sequence Read Archive) accession identifier for this biological replicate role: sample_id - config_name: chec_mahendrawada_m2025_af_replicates_start_codon_500bp description: >- Promoter significance scores using promoters defined as 500bp upstream of the start codon. See scripts/mahendrawada_annotated_features.R. This is a reprocessing of the original authors' data which counts all tags over a specific promoter region in the TF tagged sample and calculates an enrichment relative to the free MNase control. dataset_type: annotated_features genome_resources: region_sets: start_codon_500bp: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/start_codon_500bp_upstream_promoters.bed join_column: target_locus_tag data_files: - split: train path: chec_mahendrawada_m2025_af_replicates_start_codon_500bp.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA (Sequence Read Archive) accession identifier for this biological replicate role: sample_id - config_name: chec_mahendrawada_m2025_af_replicates_intergenic description: >- Promoter significance scores using intergenic regions that are continuous with the 5' end of a target feature. See scripts/mahendrawada_annotated_features.R. This is a reprocessing of the original authors' data which counts all tags over a specific promoter region in the TF tagged sample and calculates an enrichment relative to the free MNase control. dataset_type: annotated_features genome_resources: region_sets: intergenic: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/intergenic_regions_metadata_5_1.csv join_column: ir_name data_files: - split: train path: chec_mahendrawada_m2025_af_replicates_intergenic.parquet dataset_info: features: - name: sra_accession dtype: string description: SRA (Sequence Read Archive) accession identifier for this biological replicate role: sample_id - 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","chec_mahendrawada_m2025_af_combined_mindel", "chec_mahendrawada_m2025_af_combined_start_codon_500bp", "chec_mahendrawada_m2025_af_combined_intergenic"] data_files: - split: train path: chec_mahendrawada_m2025_af_combined_meta.parquet dataset_info: features: - name: sample_id dtype: int64 description: Unique identifier combining regulator, condition, and replicates - name: mahendrawada_symbol dtype: string description: Transcription factor symbol as reported in Mahendrawada et al. 2025 - 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 genome_resources: region_sets: Kang: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/yiming_promoters.bed join_column: target_locus_tag dataset_info: features: - name: sample_id dtype: int64 description: >- Unique identifier for a sample. Each sample is the combination of replicates for a given regulator and condition prior to having promoter enrichment and significance calculated. - config_name: chec_mahendrawada_m2025_af_combined_mindel description: >- Brent Lab reprocessed data from Mahendrawada 2025. See scripts/ for more details. dataset_type: annotated_features genome_resources: region_sets: Mindel: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/mindel_promoters.csv.gz join_column: target_locus_tag data_files: - split: train path: chec_mahendrawada_m2025_af_combined_mindel.parquet dataset_info: features: - name: sample_id dtype: int64 description: >- Unique identifier for a sample. Each sample is the combination of replicates for a given regulator and condition prior to having promoter enrichment and significance calculated. - config_name: chec_mahendrawada_m2025_af_combined_start_codon_500bp description: >- Annotated feature dataset with binding score and statistics performed on combined replicates for a single sample per regulator/condition, using promoters defined as 500bp upstream of the start codon. See scripts/mahendrawada_annotated_features.R. dataset_type: annotated_features genome_resources: region_sets: start_codon_500bp: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/start_codon_500bp_upstream_promoters.bed join_column: target_locus_tag data_files: - split: train path: chec_mahendrawada_m2025_af_combined_start_codon_500bp.parquet dataset_info: features: - name: sample_id dtype: int64 description: >- Unique identifier for a sample. Each sample is the combination of replicates for a given regulator and condition prior to having promoter enrichment and significance calculated. - config_name: chec_mahendrawada_m2025_af_combined_intergenic description: >- Annotated feature dataset with binding score and statistics performed on combined replicates for a single sample per regulator/condition, using intergenic regions that are continuous with the 5' end of a target feature. See scripts/mahendrawada_annoted_features.R. dataset_type: annotated_features genome_resources: region_sets: intergenic: path: https://huggingface.co/datasets/BrentLab/yeast_genome_resources/blob/main/intergenic_regions_metadata_5_1.csv join_column: ir_name data_files: - split: train path: chec_mahendrawada_m2025_af_combined_intergenic.parquet dataset_info: features: - name: sample_id dtype: int64 description: >- Unique identifier for a sample. Each sample is the combination of replicates for a given regulator and condition prior to having promoter enrichment and significance calculated. - 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: float64 description: >- an old unique identifer, for use internally only. Deprecated and will be removed eventually. Do not use in analysis. - 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: env_condition dtype: class_label: names: ["standard_30C", "SM", "galactose", "raffinose", "heat_shock_37C"] description: Environmental growth condition for this experiment role: experimental_condition definitions: standard_30C: description: Standard synthetic complete medium at 30°C; the baseline growth condition. temperature_celsius: 30 media: name: synthetic_complete SM: description: >- Amino acid starvation induced by sulfometuron methyl (SM) in synthetic complete medium lacking Ile/Val. temperature_celsius: 30 media: name: synthetic_complete_minus_ile_val chemical_treatment: compound: sulfometuron_methyl concentration_ug_per_mL: 0.5 duration_minutes: 60 galactose: description: >- Galactose induction condition for Gal4 experiments; cells grown in YEP-Raffinose then induced with 2% galactose for 2 hours. temperature_celsius: 30 media: # Methods: YEP-Raffinose (1% yeast extract, 2% peptone, 2% raffinose) # induced with 2% galactose for 2h name: yeast_extract_peptone_raffinose_plus_galactose carbon_source: - compound: D-raffinose concentration_percent: 2 - compound: D-galactose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 galactose_induction_duration_hours: 2 raffinose: description: >- Uninduced raffinose condition for Gal4 experiments; cells grown in YEP-Raffinose without galactose addition. temperature_celsius: 30 media: # Methods: YEP-Raffinose (1% yeast extract, 2% peptone, 2% raffinose) name: yeast_extract_peptone_raffinose carbon_source: - compound: D-raffinose concentration_percent: 2 nitrogen_source: - compound: yeast_extract concentration_percent: 1 - compound: peptone concentration_percent: 2 heat_shock_37C: description: >- Heat shock to 37°C for 10 minutes, used for Hsf1 and Msn2 experiments; equal volume of 44°C medium added to 30°C culture. initial_temperature_celsius: 30 mixing_temperature_celsius: 44 final_temperature_celsius: 37 incubation_duration_minutes: 10 - name: timepoint dtype: int64 description: Time point in minutes (standard is 30 minutes post-treatment. very few other timepoints) role: experimental_condition - 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 - name: responsive dtype: bool description: >- TRUE/FALSE labeling based on authors recommended threshold on responsiveness where TRUE means that padj < 0.1 & abs(log2FoldChange) >= log2(1.3) - 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: sample_id dtype: float64 description: Unique sample identifier combining replicates by treatment - 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 definitions: DMSO: description: DMSO vehicle control; the auxin-inducible degron tag is inactive and the transcription factor is present. IAA: description: Indole-3-acetic acid (auxin) treatment to induce degradation of the IAA7-tagged transcription factor. chemical_treatment: compound: indole-3-acetic_acid # Methods: 500 μM IAA for 30 min concentration_uM: 500 duration_minutes: 30 - 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 definitions: standard_30C: description: Standard synthetic complete medium at 30°C; the baseline growth condition. temperature_celsius: 30 media: name: synthetic_complete SM: description: >- Amino acid starvation induced by sulfometuron methyl (SM) in synthetic complete medium lacking Ile/Val. temperature_celsius: 30 media: name: synthetic_complete_minus_ile_val chemical_treatment: compound: sulfometuron_methyl concentration_ug_per_mL: 0.5 duration_minutes: 60 galactose: description: >- Galactose induction condition for Gal4 experiments; cells grown in YEP-Raffinose then induced with 2% galactose for 2 hours. temperature_celsius: 30 media: name: yeast_extract_peptone carbon_source: - compound: D-raffinose concentration_percent: 2 - compound: D-galactose concentration_percent: 2 galactose_induction_duration_hours: 2 raffinose: description: >- Uninduced raffinose condition for Gal4 experiments; cells grown in YEP-Raffinose without galactose addition. temperature_celsius: 30 media: name: yeast_extract_peptone carbon_source: - compound: D-raffinose concentration_percent: 2 heat_shock_37C: description: >- Heat shock to 37°C for 10 minutes, used for Hsf1 and Msn2 experiments; equal volume of 44°C medium added to 30°C culture. initial_temperature_celsius: 30 final_temperature_celsius: 37 incubation_duration_minutes: 10 - name: timepoint dtype: float64 description: Time point for time-series experiments (minutes) - name: replicate dtype: string description: Biological replicate identifier (A, B, or C) - 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: 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: float64 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: env_condition dtype: class_label: names: ["standard_30C", "SM", "galactose", "raffinose", "heat_shock_37C"] description: Environmental growth condition role: experimental_condition definitions: standard_30C: description: Standard synthetic complete medium at 30°C; the baseline growth condition. temperature_celsius: 30 media: name: synthetic_complete SM: description: >- Amino acid starvation induced by sulfometuron methyl (SM) in synthetic complete medium lacking Ile/Val. temperature_celsius: 30 media: name: synthetic_complete_minus_ile_val chemical_treatment: compound: sulfometuron_methyl concentration_ug_per_mL: 0.5 duration_minutes: 60 galactose: description: >- Galactose induction condition for Gal4 experiments; cells grown in YEP-Raffinose then induced with 2% galactose for 2 hours. temperature_celsius: 30 media: name: yeast_extract_peptone carbon_source: - compound: D-raffinose concentration_percent: 2 - compound: D-galactose concentration_percent: 2 galactose_induction_duration_hours: 2 raffinose: description: >- Uninduced raffinose condition for Gal4 experiments; cells grown in YEP-Raffinose without galactose addition. temperature_celsius: 30 media: name: yeast_extract_peptone carbon_source: - compound: D-raffinose concentration_percent: 2 heat_shock_37C: description: >- Heat shock to 37°C for 10 minutes, used for Hsf1 and Msn2 experiments; equal volume of 44°C medium added to 30°C culture. initial_temperature_celsius: 30 final_temperature_celsius: 37 incubation_duration_minutes: 10 - name: replicate dtype: string description: Biological replicate identifier (A, B, or C) - name: sample_id dtype: float64 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: 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: float64 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: sample_id dtype: float64 description: Unique sample identifier combining replicates by treatment - 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 definitions: standard_30C: description: Standard synthetic complete medium at 30°C; the baseline growth condition. temperature_celsius: 30 media: name: synthetic_complete SM: description: >- Amino acid starvation induced by sulfometuron methyl (SM) in synthetic complete medium lacking Ile/Val. temperature_celsius: 30 media: name: synthetic_complete_minus_ile_val chemical_treatment: compound: sulfometuron_methyl concentration_ug_per_mL: 0.5 duration_minutes: 60 galactose: description: >- Galactose induction condition for Gal4 experiments; cells grown in YEP-Raffinose then induced with 2% galactose for 2 hours. temperature_celsius: 30 media: name: yeast_extract_peptone carbon_source: - compound: D-raffinose concentration_percent: 2 - compound: D-galactose concentration_percent: 2 galactose_induction_duration_hours: 2 raffinose: description: >- Uninduced raffinose condition for Gal4 experiments; cells grown in YEP-Raffinose without galactose addition. temperature_celsius: 30 media: name: yeast_extract_peptone carbon_source: - compound: D-raffinose concentration_percent: 2 heat_shock_37C: description: >- Heat shock to 37°C for 10 minutes, used for Hsf1 and Msn2 experiments; equal volume of 44°C medium added to 30°C culture. initial_temperature_celsius: 30 final_temperature_celsius: 37 incubation_duration_minutes: 10 - name: replicate dtype: string description: Biological replicate identifier (A, B, or C) - 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: 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: float64 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: sample_id dtype: float64 description: Unique sample identifier combining replicates by treatment - 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 definitions: DMSO: description: DMSO vehicle control; the auxin-inducible degron tag is inactive and the transcription factor is present. IAA: description: Indole-3-acetic acid (auxin) treatment to induce degradation of the IAA7-tagged transcription factor. chemical_treatment: compound: indole-3-acetic_acid # Methods: 500 μM IAA for 30 min concentration_uM: 500 duration_minutes: 30 - name: replicate dtype: string description: Biological replicate identifier (A, B, or C) - 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: 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: float64 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) ## Accessing Data The examples below require [labretriever](https://github.com/cmatKhan/labretriever#installation) (`pip install labretriever`) and/or the [HuggingFace Hub client](https://huggingface.co/docs/huggingface_hub/installation) (`pip install huggingface_hub`). ### Accessing Data with labretriever This repository is part of a collection configured as a unified database using [labretriever.VirtualDB](https://cmatkhan.github.io/labretriever/virtual_db_configuration/). Download the [collection config](https://github.com/BrentLab/tfbpshiny/blob/main/tfbpshiny/brentlab_yeast_collection.yaml) and use it to query the data directly in Python, or with an AI assistant using the [labretriever plugin](https://cmatkhan.github.io/labretriever/mcp_server/#quick-install-claude-code-plugin). ```python from labretriever.virtual_db import VirtualDB from labretriever.datacard import DataCard # Citation and metadata card = DataCard("BrentLab/mahendrawada_2025") info = card.info() print(info["doi"]) print(info["citation"]) # path to the downloaded brentlab_yeast_collection.yaml vdb = VirtualDB("/path/to/brentlab_yeast_collection.yaml") print(vdb.get_dataset_description("chec_m2025")) print(vdb.get_dataset_description("degron")) vdb.query("SELECT * FROM chec_m2025 LIMIT 5") ``` ### Direct parquet access The repository contains more data than what is exposed through the collection configuration. Use `DataCard.info()` to inspect available files, then download and query with DuckDB. Most files in this repository are single parquet files and can be read directly. The example below downloads the ChEC-seq annotated features; the degron RNA-seq dataset is available as `rnaseq_reprocessed.parquet`. ```python from huggingface_hub import snapshot_download import duckdb repo_path = snapshot_download( repo_id="BrentLab/mahendrawada_2025", repo_type="dataset", allow_patterns="chec_mahendrawada_m2025_af_combined.parquet", ) conn = duckdb.connect() # returns a pandas DataFrame with the first 5 rows conn.execute( "SELECT * FROM read_parquet(?) LIMIT 5", [f"{repo_path}/chec_mahendrawada_m2025_af_combined.parquet"], ).df() ``` ### Accessing using R Clone the repository and read parquet files directly with [arrow](https://arrow.apache.org/docs/r/): ```r # install.packages("arrow") arrow::read_parquet("chec_mahendrawada_m2025_af_combined.parquet") ```