GEO series

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

GSE15353 Homo sapiens Genome binding/occupancy profiling by high throughput sequencing 13 samples Submitted 2009/03/23 Platform GPL9052

Summary

We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIP-seq to map STAT1 targets in interferon stimulated and unstimulated human HeLa S3 cells, and compared the method's performance to ChIP-PCR and to ChIP-chip for four chromosomes. By ChIP-seq, using 15.1 and 12.9 million uniquely mapped sequence reads, and an estimated false discovery rate of less than 0.001, we identified 41,582 and 11,004 putative STAT1-binding regions in stimulated and unstimulated cells, respectively. Of the 34 loci known to contain STAT1 interferon-responsive binding sites, ChIP-seq found 24 (71%). ChIP-seq targets were enriched in sequences similar to known STAT1 binding motifs. Comparisons with two ChIP-PCR data sets suggested that ChIP-seq sensitivity was between 70% and 92% and specificity was at least 95%.

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Direct links to NCBI, no account and no request form: the whole study as GSE15353_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 13 samples. Raw sequencing reads are also available from ENA.

Whole study · RAW.tar ↓ Series matrix ↓ All supplementary files ↗ Raw reads on ENA ↗

Also filed as BioProject PRJNA115767 and SRA study SRP000661. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 17558387) ↗

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