README.md

---
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/)