Dataset Information


Genomic discovery of potent chromatin insulators for human gene therapy

ABSTRACT: This data includes regulatory factor profiling using ChIP-seq. Cells were grown according to the approved ENCODE cell culture protocols. Cells were crosslinked with 1% formaldehyde, and the reaction was quenched by the addition of glycine. Fixed cells were rinsed with PBS, lysed in nuclei lysis buffer, and the chromatin was sheared to 200-500 bp fragments using Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibodies at 4 degrees C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross linking in immunoprecipitated DNA was reversed and treated with RNase-A. Following proteinase K treatment, the DNA fragments were purified by phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. 20-50 ng of ChIP DNA was end-repaired, adenine ligated to Illumina adapters was added, and then a Solexa library was made for sequencing. ChIP-seq affinity is directly reflected in raw tag density (Raw Signal), which is shown in the track as density of tags mapping within a 150 bp sliding window (at a 20 bp step across the genome). ChIP-seq affinity zones (HotSpots) were identified using the HotSpot algorithm described in Sabo et al. (2004). 1.0% false discovery rate thresholds (FDR 0.01) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36mers. ChIP-seq affinity (Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm.

ORGANISM(S): Homo sapiens  

SUBMITTER: George Stamatoyannopoulos   John A Stamatoyannopoulos  Matthew T Maurano  Hao Wang  Mingdong Liu 

PROVIDER: E-GEOD-50611 | ArrayExpress | 2014-10-07



Similar Datasets

2011-06-29 | E-GEOD-30263 | ArrayExpress
2012-06-07 | E-GEOD-35583 | ArrayExpress
2012-10-03 | E-GEOD-37074 | ArrayExpress
2011-06-03 | E-GEOD-29692 | ArrayExpress
2015-09-02 | E-GEOD-61613 | ArrayExpress
2011-04-27 | E-GEOD-28867 | ArrayExpress
2012-09-19 | E-GEOD-40869 | ArrayExpress
2010-12-29 | E-GEOD-26328 | ArrayExpress
2013-03-20 | E-GEOD-36546 | ArrayExpress
2015-11-19 | E-GEOD-69243 | ArrayExpress