|
| Status |
Public on Jan 07, 2016 |
| Title |
MDA436_WCE_DMSO |
| Sample type |
SRA |
| |
|
| Source name |
MDA436
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA436
chip antibody: none
drug treatment: DMSO
duration: 12 hour
barcode (already removed): TGTACCTT
|
| Treatment protocol |
Cells were treated with 500 nM JQ1 or DMSO for the indicated time
|
| Growth protocol |
Cells were growed with SUM medium
|
| 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 NextSeq 500 |
| |
|
| Description |
ChIP-Seq whole cell extract input control from DMSO treated cells
|
| Data processing |
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences processed through MACS 1.4.2 and fragment pileup was outputted in .wig format
|
| |
|
| Submission date |
Aug 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
[email protected]
|
| Phone |
617-632-2106
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Polyak
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE63581 |
Response and resistance to BET bromodomain inhibitors in triple negative breast cancer [ChIP-Seq] |
| GSE63584 |
Response and resistance to BET bromodomain inhibitors in triple negative breast cancer |
|
| Relations |
| BioSample |
SAMN03952690 |
| SRA |
SRX1131554 |
