| --- |
| 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 |
| doi: https://doi.org/10.1038/s41586-025-08916-0 |
| citation: >- |
| Mahendrawada L, Warfield L, Donczew R et al. Low overlap of transcription factor DNA |
| binding and regulatory targets. Nature. 2025. |
| experimental_conditions: |
| |
| temperature_celsius: 30 |
| growth_phase_at_harvest: |
| |
| od600: 1.0 |
| media: |
| |
| name: synthetic_complete |
| carbon_source: |
| |
| - compound: D-glucose |
| nitrogen_source: |
| - compound: yeast_nitrogen_base |
| |
| concentration_percent: 0.17 |
| specifications: |
| - without_ammonium_sulfate |
| - without_amino_acids |
| - compound: ammonium_sulfate |
| |
| concentration_percent: 0.5 |
| - compound: amino_acid_dropout_mix |
| |
| concentration_percent: 0.06 |
| - compound: adenine_sulfate |
| |
| concentration_percent: 0.004 |
| - compound: uracil |
| |
| concentration_percent: 0.0002 |
|
|
| 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: |
| - bp500_peaks |
| - intergenic_peaks |
| - kang_peaks |
| - mindel_peaks |
| fields: |
| - name: n_replicates |
| dtype: int64 |
| description: The number of replicates for which at least 1 peak occurs in the promoter region |
| role: quantitative_measure |
| - name: n_peaks |
| dtype: int64 |
| description: Number of peaks called for this promoter across replicates |
| role: quantitative_measure |
| - name: nearest_score |
| dtype: float64 |
| description: Score of the peak nearest to the promoter center. -log10(q-value) from HOMER peak calling. |
| role: quantitative_measure |
| - name: median_score |
| dtype: float64 |
| description: Median score of all peaks called for this promoter across replicates. -log10(q-value) from HOMER peak calling. |
| role: quantitative_measure |
| - name: max_score |
| dtype: float64 |
| description: Maximum score of all peaks called for this promoter across replicates. -log10(q-value) from HOMER peak calling. |
| role: quantitative_measure |
|
|
| - 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 |
| - bp500_peaks |
| - intergenic_peaks |
| - kang_peaks |
| - mindel_peaks |
| - 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: |
| |
| |
| |
| |
| 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: |
| |
| 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: |
| |
| |
| 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: |
| |
| 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. See https://github.com/BrentLab/checseq_promoter_enrichment_slurm_pipeline/tree/main/promoter_enrichment for scripts for creating the genome map files from alignments. |
| 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: bp500_peaks |
| description: >- |
| Homer peak calls according to the authors published protocol and reproduced at |
| https://github.com/BrentLab/checseq_promoter_enrichment_slurm_pipeline. |
| The peaks were intersected with the promoters defined as 500bp upstream of the start codon. |
| If there was a peak in a given promoter in at least 2 replicates, then it was retained. The |
| target is then scored by the nearest, median and max peak score (-log2(qvalue) from HOMER) |
| in the region. |
| dataset_type: annotated_features |
| data_files: |
| - split: train |
| path: bp500_peaks.parquet |
| 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 |
| dataset_info: |
| features: |
| - name: sample_id |
| dtype: int64 |
| description: Unique identifier for a sample. |
| role: sample_id |
|
|
| - config_name: intergenic_peaks |
| description: >- |
| Homer peak calls according to the authors published protocol and reproduced at |
| https://github.com/BrentLab/checseq_promoter_enrichment_slurm_pipeline. |
| The peaks were intersected with the promoters defined as the intergenic regions from SGD 5-1. |
| If there was a peak in a given promoter in at least 2 replicates, then it was retained. The |
| target is then scored by the nearest, median and max peak score (-log2(qvalue) from HOMER) |
| in the region. |
| dataset_type: annotated_features |
| data_files: |
| - split: train |
| path: intergenic_peaks.parquet |
| 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 |
| dataset_info: |
| features: |
| - name: sample_id |
| dtype: int64 |
| description: Unique identifier for a sample. |
| role: sample_id |
|
|
| - config_name: kang_peaks |
| description: >- |
| Homer peak calls according to the authors published protocol and reproduced at |
| https://github.com/BrentLab/checseq_promoter_enrichment_slurm_pipeline. |
| The peaks were intersected with the promoters defined as 700bp upsream of the promoter truncated by upstream features. |
| If there was a peak in a given promoter in at least 2 replicates, then it was retained. The |
| target is then scored by the nearest, median and max peak score (-log2(qvalue) from HOMER) |
| in the region. |
| dataset_type: annotated_features |
| data_files: |
| - split: train |
| path: kang_peaks.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. |
| role: sample_id |
|
|
| - config_name: mindel_peaks |
| description: >- |
| Homer peak calls according to the authors published protocol and reproduced at |
| https://github.com/BrentLab/checseq_promoter_enrichment_slurm_pipeline. |
| The peaks were intersected with the promoters defined |
| by Mindel et al. See huggingface/BrentLab/yeast_genome_resources. |
| If there was a peak in a given promoter in at least 2 replicates, then it was retained. The |
| target is then scored by the nearest, median and max peak score (-log2(qvalue) from HOMER) |
| in the region. |
| dataset_type: annotated_features |
| data_files: |
| - split: train |
| path: mindel_peaks.parquet |
| 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 |
| dataset_info: |
| features: |
| - name: sample_id |
| dtype: int64 |
| description: Unique identifier for a sample. |
| 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", "bp500_peaks", "intergenic_peaks", "kang_peaks", "mindel_peaks"] |
| 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: |
| |
| |
| 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: |
| |
| 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 |
| |
| 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 |
| |
| 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") |
| ``` |
|
|
