metadata
license: mit
language:
- en
tags:
- transcription-factor
- binding
- chec-seq
- genomics
- biology
pretty_name: Barkai ChEC-seq Compendium
size_categories:
- 100M<n<1B
configs:
- config_name: genomic_coverage
description: Genomic coverage data with pileup counts at specific positions
dataset_type: genome_map
default: true
data_files:
- split: train
path: genome_map/*/*/part-0.parquet
dataset_info:
features:
- name: seqnames
dtype: string
description: Chromosome or sequence name (e.g., chrI, chrII, etc.)
- name: start
dtype: int32
description: Start position of the genomic interval (1-based coordinates)
- name: end
dtype: int32
description: End position of the genomic interval (1-based coordinates)
- name: pileup
dtype: int32
description: Number of tags (5' of read) at this genomic position
partition_info:
- name: Series
dtype: string
description: GEO series of the dataset
- name: Accession
dtype: string
description: GEO accession of the specific sample
- config_name: GSE178430_metadata
description: Metadata for GSE178430
dataset_type: metadata
data_files:
- split: train
path: GSE178430_metadata.parquet
dataset_info:
features:
- name: accession
dtype: string
description: Sample accession identifier
- name: regulator_locus_tag
dtype: string
description: >-
Systematic gene name (ORF identifier) of the tagged transcription
factor
- name: regulator_symbol
dtype: string
description: Standard gene symbol of the tagged transcription factor
- name: strainid
dtype: string
description: Strain identifier used in the experiment
- name: instrument
dtype: string
description: Sequencing instrument used for data generation
- name: genotype
dtype: string
description: Full genotype description of the experimental strain
- name: dbd_donor_symbol
dtype: string
description: >-
Gene symbol of the DNA-binding domain donor (for chimeric
constructs)
- name: ortholog_donor
dtype: string
description: Ortholog donor information for cross-species constructs
- name: paralog_deletion_symbol
dtype: string
description: Gene symbol of deleted paralog in the strain background
- name: paralog_resistance_cassette
dtype: string
description: Antibiotic resistance cassette used for paralog deletion
- config_name: GSE209631_metadata
description: ChEC-seq experiment metadata for transcription factor variant studies
dataset_type: metadata
data_files:
- split: train
path: GSE209631_metadata.parquet
dataset_info:
features:
- name: accession
dtype: string
description: Sample accession identifier
- name: regulator_locus_tag
dtype: string
description: >-
Systematic gene name (ORF identifier) of the tagged transcription
factor
- name: regulator_symbol
dtype: string
description: Standard gene symbol of the tagged transcription factor
- name: variant_type
dtype: string
description: Type of transcription factor variant tested in the experiment
- config_name: GSE222268_metadata
description: General experiment metadata for genomic studies
dataset_type: metadata
data_files:
- split: train
path: GSE222268_metadata.parquet
dataset_info:
features:
- name: title
dtype: string
description: Experiment title or sample description
- name: accession
dtype: string
description: GEO sample accession identifier
- name: extract_protocol_ch1
dtype: string
description: Protocol used for sample extraction and preparation
- name: description
dtype: string
description: Detailed description of the experimental sample or condition
- name: instrument_model
dtype: string
description: Model of sequencing instrument used for data generation
Barkai Compendium
This collects the ChEC-seq data from the following GEO series:
The metadata for each is parsed out from the SraRunTable, or in the case of GSE222268, the NCBI series matrix file (the genotype isn't in the SraRunTable)
The Barkai lab refers to this set as their binding compendium.
The genotypes for GSE222268 are not clear enough to me currently to parse well.
Dataset Details
genome_map stores the pileup of 5' end tags. See the Series and associated cited paper for details, but it is a
standard processing pipeline to count 5' ends.
The <series_accession>_metadata.parquet files store metadata. You may use the field accession to extract the corresponding
data.
See scripts/ for more parsing details.
Data Structure
genome_map/
This is a parquet dataset which is partitioned by Series and Accession
| Field | Description |
|---|---|
seqnames |
Chromosome or sequence name (e.g., chrI, chrII, etc.) |
start |
Start position of the genomic interval (1-based coordinates) |
end |
End position of the genomic interval (1-based coordinates) |
pileup |
Number of reads or signal intensity at this genomic position |
GSE178430 Metadata
| Field | Description |
|---|---|
accession |
Sample accession identifier |
regulator_locus_tag |
Systematic gene name (ORF identifier) of the tagged transcription factor |
regulator_symbol |
Standard gene symbol of the tagged transcription factor |
strainid |
Strain identifier used in the experiment |
instrument |
Sequencing instrument used for data generation |
genotype |
Full genotype description of the experimental strain |
dbd_donor_symbol |
Gene symbol of the DNA-binding domain donor (for chimeric constructs) |
ortholog_donor |
Ortholog donor information for cross-species constructs |
paralog_deletion_symbol |
Gene symbol of deleted paralog in the strain background |
paralog_resistance_cassette |
Antibiotic resistance cassette used for paralog deletion |
GSE209631 Metadata
| Field | Description |
|---|---|
accession |
Sample accession identifier |
regulator_locus_tag |
Systematic gene name (ORF identifier) of the tagged transcription factor |
regulator_symbol |
Standard gene symbol of the tagged transcription factor |
variant_type |
Type of transcription factor variant tested in the experiment |
GSE222268 Metadata
| Field | Description |
|---|---|
title |
Experiment title or sample description |
accession |
GEO sample accession identifier |
extract_protocol_ch1 |
Protocol used for sample extraction and preparation |
description |
Detailed description of the experimental sample or condition |
instrument_model |
Model of sequencing instrument used for data generation |
Usage
The entire repository is large. It may be preferrable to only retrieve specific files or partitions. You can use the metadata files to choose which files to pull.
from huggingface_hub import snapshot_download
import duckdb
import os
# Download only the partitioned dataset directory
repo_path = snapshot_download(
repo_id="BrentLab/barkai_compendium",
repo_type="dataset",
allow_patterns="_metadata.parquet"
)
dataset_path = os.path.join(repo_path, "GSE178430_metadata.parquet")
con = duckdb.connect()
meta_res = conn.execute("SELECT * FROM read_parquet(?) LIMIT 10", [dataset_path]).df()
print(meta_res)
We might choose to take a look at the file with accession GSM5417602
# Download only the partitioned dataset directory
repo_path = snapshot_download(
repo_id="BrentLab/barkai_compendium",
repo_type="dataset",
allow_patterns="genome_map/series=GSE179430/accession=GSM5417602/*parquet" # Only the parquet data
)
# The rest works the same
dataset_path = os.path.join(repo_path, "genome_map")
result = conn.execute("SELECT * FROM read_parquet(?) LIMIT 10",
[f"{dataset_path}/**/*.parquet"]).df()
print(result)
Dataset Author and Contact: Chase Mateusiak @cmatKhan