Chip Databases?

Question

[Dejian]

Are there some databases specifically collecting data about ChIP, ChIP-chip, and ChIP-seq?

Answer 1

[Pierre Lindenbaum]

try NCBI GEO: http://www.ncbi.nlm.nih.gov/geo/

[User 59]

Balance, Pierre's answer is spot on for your posted question. Please can you amend your question so that it reflects what you actually want to know about? It's too vague at the moment.

[Dejian]

Thank you, Pierre. But I don't think GEO is a ChIP database although there may be ChIP-chip or ChIP-seq data. I am thinking that ChIP databases can be useful to investigate regulation of gene expression.

Answer 2

[Jeremy Leipzig]

Here are some ChIP-Seq datasets:

Datasets included with QuEST

• http://mendel.stanford.edu/SidowLab/downloads/quest/

USeq

• http://sourceforge.net/projects/useq/files/

CAMDA2009

• http://archive.gersteinlab.org/proj/PeakSeq/Sequence_Data/HeLa-S3/PolII/Sequence_Reads/
• http://archive.gersteinlab.org/proj/PeakSeq/Sequence_Data/Stimulated_HeLa-S3/STAT1/Sequence_Reads/

Broad sets

• ftp://ftp.broad.mit.edu/pub/papers/chipseq/

Answer 3

[Casey Bergman]

For Drosophila and C. elegans, the modENCODE project has scores of ChIP-chip and ChIP-seq datasets.

For Drosophila you can also take a look at data compiled in Flynet.

There are a few mammalian ChIP-chip/ChIP-seq datasets (ids OREGDS00006-OREGDS00014) included in the ORegAnno database . e.g. http://www.oreganno.org/oregano/datasetview.action?dsid=OREGDS00006

EDIT:

A new Chip DB for mammals is now out with data for 492 experiments: http://jilab.biostat.jhsph.edu/database/cgi-bin/hmChIP.pl

Ensembl has just announced the inclusion of 243 chip datasets in their regulatory build: http://www.ensembl.info/blog/2011/04/05/243-encode-chip-seq-experiments/

[Dejian]

Thanks for your update.

Answer 4

[Ian]

Such a thing would be great, but as far as i know there isn't a central database, apart from what you can find in GEO or ArrayExpress.

MPromDb has a lot of data sets http://gdvtk.wistar.upenn.edu/data.html. But they are mammalian.

You can also find a lot of data sets at the UCSC browser, there are an increasing number of ENCODE whole genome studies coming through. This does tend to be genome version specific though, for example there is a lot of data for human hg18, but a lot less for hg19.

Answer 5

[marcomendozabpn]

I would like to mention that we have setup a database hosting quality scores for ChIP-seq and enrichment related public datasets.

This database www.ngs-qc.org is currently hosting more than 21,000 public entries and we are working in having basically all GEO entries indexed. Several functionalities were also included and exciting things are in preparation so I advice you to keep an eye o it.