|
| Status |
Public on Feb 22, 2013 |
| Title |
MM1.S_CDK9_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
Multiple myeloma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MM1.S
treated with: 0.05% DMSO for 6h
chip antibody: Cdk9
chip antibody vendor: Santa Cruz
chip antibody cat. #: SC-484
|
| Treatment protocol |
0.05% DMSO for 6h
|
| Growth protocol |
RPMI 1640 supplemented with 10% FCS and 1% GlutaMAX
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Chromatin IP against CDK9 in MM1.S multiple myeloma
barcode (already removed): GTGAAA
sample name: 08282012_C1260ACXX_5.GTGAAA
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
|
| |
|
| Submission date |
Feb 21, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard A Young |
| E-mail(s) |
young_computation@wi.mit.edu
|
| Phone |
617-258-5219
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Young Lab
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE42355 |
Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers [ChIP-seq] |
| GSE44931 |
Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers |
|
| Relations |
| SRA |
SRX244180 |
| BioSample |
SAMN01924281 |
