Wednesday, May 15, 2013

Fwd: CistromeFinder for ChIP-seq and DNase-seq data reuse

Fwd: please follow footer link

CistromeFinder for ChIP-seq and DNase-seq data reuse: "

Summary: Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing have greatly accelerated the understanding of transcriptional and epigenetic regulation, although data reuse for the community of experimental biologists has been challenging. We created a data portal CistromeFinder that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse. The database currently contains 6378 samples over 4391 datasets, 313 factors and 102 cell lines or cell populations. Each dataset has gone through a consistent analysis and quality control pipeline; therefore, users could evaluate the overall quality of each dataset before examining binding sites near their genes of interest. CistromeFinder is integrated with UCSC genome browser for visualization, Primer3Plus for ChIP-qPCR primer design and CistromeMap for submitting newly available datasets. It also allows users to leave comments to facilitate data evaluation and update.

Availability:http://cistrome.org/finder.

Contact:xsliu@jimmy.harvard.edu or henry_long@dfci.harvard.edu

"

(Via Bioinformatics - current issue.)