|
| Status |
Public on Mar 30, 2015 |
| Title |
shSirt1-EPZ4777.H3K79me2 |
| Sample type |
SRA |
| |
|
| Source name |
Murine MLL-AF9 leukemic cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MLL-AF9 transformed leukemic cells
treatment: shSirt1 RNA interference
agent: EPZ4777
time: 6d
chip antibody: anti-H3K79me2 (Abcam; ab3594; Lot: GR46675-1)
|
| Treatment protocol |
Cells were incubated with EPZ4777 (3uM) or DMSO in standard culture medium for 6 days.
|
| Growth protocol |
Murine MLL-AF9 leukemic cells were cultured in IMDM plus 15% FBS supplemented with 20 ng/ml murine SCF, 10 ng/ml murine IL-3 and 10 ng/ml murine IL-6. Lineage(-)Sca1(+)cKit(+) i.e. LSK cells were sorted from fresh isolated wild-type C57BL/6 mouse bone marrow.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were crosslinked by 1% formaldehyde for 10 minutes, and the reaction was stopped by addition of glycine to 125 mM final concentration as previously described (Bernt et al. 2011 Cancer Cell).
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 used directly for qPCR or subjected to high-throughput sequencing using Illumina HiSeq 2000 platform.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned using Bowtie2 version 2.1.0 with the default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using UCSC BedTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing the read densities
|
| |
|
| Submission date |
Sep 02, 2014 |
| Last update date |
May 15, 2019 |
| 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 |
GPL13112 |
| Series (2) |
| GSE61021 |
DOT1L Inhibits SIRT1 and SUV39H1-Mediated H3K9 Modification to Maintain Gene Expression (ChIPseq) |
| GSE61022 |
DOT1L Inhibits SIRT1 and SUV39H1-Mediated H3K9 Modification to Maintain Gene Expression |
|
| Relations |
| BioSample |
SAMN03015746 |
| SRA |
SRX692077 |
