|
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 |