|
| Status |
Public on Nov 15, 2010 |
| Title |
H3K9me3_K562_ChIP-seq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
chronic myeloid leukemia cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
harvest date: 2010-04-22
chip antibody: CST rabbit anti-H3K9me3
vendor: Cell Signaling Technology
catalog#: 9754S
lot#: 1
|
| Growth protocol |
All cells were grown according to ENCODE standards (http://genomewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP against H3K9me3
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the human genome assembly hg18 (March, 2006) or hg19 (February, 2009) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks were called with Sole-Search (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi)
|
| |
|
| Submission date |
Oct 12, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Philip Cayting |
| E-mail(s) |
pcayting@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Lab |
Snyder
|
| Street address |
1501 S California Ave
|
| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE24632 |
ZNF274 colocalizes with the histone methyltransferase SETDB1 at ZNF 3' ends. |
|
| Relations |
| SRA |
SRX028594 |
| BioSample |
SAMN00115777 |
