|
| Status |
Public on Mar 23, 2011 |
| Title |
K562_H3K9me3_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cultured K562 cells
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K9me3
antibody manufacturer: Abcam
antibody catalog number: ab8898
cell line: K562
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Described in Mikkelsen et al., Nature 2007. Chromatin was fixed and sheared to 200-600 bp using Branson Sonifer. After IP and adapter ligation library fragments of ~250 bp were isolated. 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 II |
| |
|
| Data processing |
Bed files: Any reads longer than 36 bases were first truncated to 36 bases. Reads were then aligned to the hg18 assembly using MAQ with default parameters. The fourth column of the bed file contains the actual 36 base read sequence.
Note file update 4/20/15. Previously the hg19 version of the bed file was uploaded for the K562 H3K9me3 samples only.
|
| |
|
| Submission date |
Dec 27, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason Ernst |
| E-mail(s) |
jason.ernst@ucla.edu
|
| Organization name |
UCLA
|
| Department |
Biological Chemistry
|
| Street address |
615 Charles E Young Dr South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (2) |
| GSE26320 |
Mapping and analysis of chromatin state dynamics in nine human cell types (ChIP-Seq) |
| GSE26386 |
Systematic determination and analysis of chromatin state dynamics in nine human cell types |
|
| Relations |
| SRA |
SRX038638 |
| BioSample |
SAMN00191176 |
