metadata
license: mit
language:
- en
tags:
- biology
- genomics
- yeast
- transcription-factors
- gene-expression
- binding
- chec
- perturbation
- rnaseq
- nascent rnaseq
pretty_name: Mahendrawada 2025 ChEC-seq and Nascent RNA-seq data
size_categories:
- 100K<n<1M
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
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:
'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
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
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
standard:
description: >-
Standard growth condition used for the majority of ChEC-seq
experiments.
temperature_celsius: 30
growth_phase_at_harvest:
od600: 1
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
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
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
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
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
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
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
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
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
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
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
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
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
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)
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
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
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
and GSE236948
Accessing Data
The examples below require
labretriever
(pip install labretriever) and/or the
HuggingFace Hub client
(pip install huggingface_hub).
Accessing Data with labretriever
This repository is part of a collection configured as a unified database using labretriever.VirtualDB. Download the collection config and use it to query the data directly in Python, or with an AI assistant using the labretriever plugin.
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.
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:
# install.packages("arrow")
arrow::read_parquet("chec_mahendrawada_m2025_af_combined.parquet")