Update README.md

README.md

@@ -1,20 +1,182 @@
 ---
 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
+  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
+  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
+  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
+  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
-- GSE209631
-- GSE222268
+- [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
 
-### Data Structure
+`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.
+
+## Data Structure
+
+### [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                        |
+
+
+**Dataset Author and Contact**: Chase Mateusiak [@cmatKhan](https://github.com/cmatkhan/)