[Credits]

Life Science Database Archive
ChIP-Atlas

Experiment list

Data detail

info Data name Experiment list
info DOI 
info Version List 
info Description of data contents 

A list of metadata of the reanalysed ChIP-Seq data archived in Sequence Read Archive (SRA), grouped by SRA Experiment ID, providing the information of reference genome data, antigen, or cell type. See details here: https://github.com/inutano/chip-atlas/wiki#downloads_doc

info Data file 
File name:
chip_atlas_experiment_list.zip
File URL:
https://dbarchive.biosciencedbc.jp/data/chip-atlas/LATEST/chip_atlas_experiment_list.zip
File size:
29 MB
info Simple search URL 
info Data acquisition method 

We have processed data downloaded from SRA by using a standard ChIP-Seq data analysis pipeline, then we curated metadata of archived data manually.

info Data analysis method 

See details of data processing here: https://github.com/inutano/chip-atlas/wiki

info Number of data entries 

439,593 entries

Data itemDescription
Experimental ID Experimental ID (SRX, ERX, DRX)
Genome assembly Genome assembly
Antigen class Antigen class
Antigen Antigen
Cell type class Cell type class
Cell type Cell type
Cell type description Cell type description
Processing logs Processing logs (# of reads, % mapped, % duplicates, # of peaks [q < 1E-05])
Title Title submitted by authors
Meta data Meta data submitted by authors
BigWig Link to a BigWig-formatted coverage score binary file.
Peak-call (BED) (q < 1E-05) Link to a BED4-formatted peak-call data file with the q-value threshold 1E-05.
Peak-call (BED) (q < 1E-10) Link to a BED4-formatted peak-call data file with the q-value threshold 1E-10.
Peak-call (BED) (q < 1E-20) Link to a BED4-formatted peak-call data file with the q-value threshold 1E-20.
Peak-call (BigBed) (q < 1E-05) Link to a BigBed-formatted peak-call data file binarized from the corresponding BED4 file (q < 1E-05).
Peak-call (BigBed) (q < 1E-10) Link to a BigBed-formatted peak-call data file binarized from the corresponding BED4 file (q < 1E-10).
Peak-call (BigBed) (q < 1E-20) Link to a BigBed-formatted peak-call data file binarized from the corresponding BED4 file (q < 1E-20).