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Series GSE35583 Query DataSets for GSE35583
Status Public on Jun 07, 2012
Title Histone Modifications by ChIP-seq from ENCODE/University of Washington
Project ENCODE
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary This data was generated by ENCODE. If you have questions about the data, contact the submitting laboratory directly (Richard Sandstrom If you have questions about the Genome Browser track associated with this data, contact ENCODE (

This track was produced as part of the ENCODE Project. This track displays genome-wide maps of histone modifications in different cell lines ( using ChIP-seq high-throughput sequencing.

For data usage terms and conditions, please refer to and
Overall design Cells were grown according to the approved ENCODE cell culture protocols ( Cells were cross-linked 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 a Fisher Dismembrator (model 500). Sheared chromatin fragments were immunoprecipitated with specific polyclonal antibodies at 4 °C with gentle rotation. Antibody-chromatin complexes were washed and eluted. The cross-linking in the 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. A quantity of 20-50 ng of ChIP DNA was end-repaired, followed by the addition of adenine, ligation to Illumina adapters, and creation of a Solexa library for sequencing.
ChIP-seq affinity was directly measured through the 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). One percent false discovery rate thresholds (FDR 1.0%) were computed for each cell type by applying the HotSpot algorithm to an equivalent number of random uniquely mapping 36-mers. ChIP-Seq affinities (Peaks) were identified as signal peaks within FDR 1.0% hypersensitive zones using a peak-finding algorithm.
All tracks have a False Discovery Rate of 1% (FDR 1.0%).
Data were verified by sequencing biological replicates displaying a correlation coefficient > 0.9.
Web link
Contributor(s) Sandstrom R
Citation(s) 22955617
BioProject PRJNA63443
Submission date Feb 07, 2012
Last update date Feb 21, 2019
Contact name ENCODE DCC
Organization name ENCODE DCC
Street address 300 Pasteur Dr
City Stanford
State/province CA
ZIP/Postal code 94305-5120
Country USA
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (171)
GSM945159 UW_ChipSeq_HMEC_H3K4me3
GSM945160 UW_ChipSeq_HRE_H3K27me3
GSM945161 UW_ChipSeq_SKMC_Input
SRA SRP015928

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE35583_RAW.tar 30.2 Gb (http)(custom) TAR (of BIGWIG, BROADPEAK, NARROWPEAK)
Raw data are available in SRA
Processed data provided as supplementary file

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