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---
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:
- [GSE179430](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179430)
- [GSE209631](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE209631)
- [GSE222268](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=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](https://barkailab.wixsite.com/barkai) 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](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179430) 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](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=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](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=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.
```python
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`
```python
# 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](https://github.com/cmatkhan/) |