BrentLab/barkai_compendium

Barkai Compendium

This collects the ChEC-seq data from the following GEO series:

• GSE179430
• GSE209631
• GSE222268

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

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

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

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