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Sample GSM1224675 Query DataSets for GSM1224675
Status Public on Oct 07, 2014
Title K562-DS11508
Sample type SRA
 
Source name K562 erythroleukemia cells
Organism Homo sapiens
Characteristics experiment: CTCF ChIP-seq
replicate: 4
Growth protocol Cells were grown according to the approved ENCODE cell culture protocols.
Extracted molecule genomic DNA
Extraction protocol 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.
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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Peak: 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. DNase data used unthresholded hotspots.
Genome_build: hg19
Supplementary_files_format_and_content: .bed: peak locations generated using the hotspot algorithm
 
Submission date Sep 05, 2013
Last update date May 15, 2019
Contact name Matthew T Maurano
E-mail(s) maurano@nyu.edu
Organization name NYU School of Medicine
Department Institute for Systems Genetics
Lab Maurano
Street address 435 East 30th Street
City New York
State/province NY
ZIP/Postal code 10016
Country USA
 
Platform ID GPL11154
Series (1)
GSE50611 Genomic discovery of potent chromatin insulators for human gene therapy
Relations
BioSample SAMN02347405
SRA SRX345888

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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