Dataset features

Specifications


Application: ChIP-seq analysis
Number of samples: 9
Release date: Mar 4 2011
Last update date: Feb 2 2015
Access: Public
Taxon: Drosophila melanogaster, Mus musculus
Dataset link modENCODE_Lieb and White Lab: unltra-deep sequencing data of genomic DNA, chromatin input, and ChIP of Su(Hw) and H3K36me3 from S2 cells on Illumina Genome Analyzer.

Experimental Protocol


S2 cells from the modENCODE batch were amplified before transferring to the plates. 15 plates were put in culture until the cells reached the appropriate concentration. Cells were harvested from 2 plates to extract the genomic DNA. The remaining 13 plates were then treated with formaldehyde at the same time and the chromatin were extracted. 3 plates were used to produce an Input sample corresponding to the chromatin DNA of the treated cells. Each plate corresponding to an eppendorff tube of chromatin, ChIP experiments were performed on 5 tubes for H3K36me3 and on 5 tubes for Su(Hw). ChIP and DNA extraction were performed independently on each tube. After the purification of the DNA, the tubes corresponding to the same sample (Su(Hw), H3K36me3, Input and gDNA) were pooled together. After mixing, each sample was aliquoted again into 5 tubes. 1 aliquot of each was used for ChIP-chip on Affymetrix tiling arrays for quality control, 1 aliquot was used for single-end sequencing at the University of Chicago HGAC, 1 aliquot was used for single-end sequencing at UNC, 1 aliquot was used for paired-end sequencing at UNC and the remaining aliquot was kept as a back-up of the original samples. For each sample, >100M single-end tags were produced (~5 runs), along with the tags from 1 lane of paired-end sequencing experiment. Besides several experimental factors, the performance of multiple peak callers were evaluated at different sequencing depths.

Repositories


GEO

GSE27679

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Contact


Yiwen Chen

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