|
| Status |
Public on Mar 30, 2015 |
| Title |
NOMO1.H3K9ac |
| Sample type |
SRA |
| |
|
| Source name |
human AML-derived cell line NOMO1, H3K9ac ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NOMO1
cell type: MLL-AF9 human leukemia cell line
chip antibody: anti-H3K9ac (Abcam; ab4441)
|
| Treatment protocol |
None
|
| Growth protocol |
The MOLM13, MonoMac6, and NOMO1 cells were cultured in 10% RPMI plus 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as previously described (Bernt et al. 2011 Cancer Cell). Briefly, cells samples were crosslinked by 1% formaldehyde for 10 minutes, and the reaction was stopped by addition of glycine to 125 mM final concentration. The fixed cells were lysed in SDS buffer, and the chromatin was fragmented by sonication. The sheared chromatin was incubated with the indicated antibodies, and recovered by binding to protein A/G agarose (Millipore).
Eluted DNA fragments were processed for the HeliScope according to the manufacturer's protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Helicos HeliScope |
| |
|
| Data processing |
Reads were filtered for quality and aligned to the human genome (hg18) using Helicos open source aligner IndexDP Genomic available at the open source HeliSphere.
To create density files, the reads were extended to 200 bp converted to tdf using igvtools (http://www.broadinstitute.org/igv/igvtools).
Genome_build: NCBI36 (hg18)
Supplementary_files_format_and_content: TDF files contain the read densities.
|
| |
|
| Submission date |
Oct 06, 2014 |
| Last update date |
Jul 24, 2015 |
| Contact name |
Richard Koche |
| E-mail(s) |
kocher@mskcc.org
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Street address |
417 E. 68th St.
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL14761 |
| Series (2) |
| GSE61022 |
DOT1L Inhibits SIRT1 and SUV39H1-Mediated H3K9 Modification to Maintain Gene Expression |
| GSE62100 |
DOT1L Inhibits SIRT1 and SUV39H1-Mediated H3K9 Modification to Maintain Gene Expression [ChIP-seq 2] |
|
| Relations |
| BioSample |
SAMN03097475 |
