|
| Status |
Public on Jan 07, 2016 |
| Title |
SUM159R_JQ1_CHEM_SEQ_R1 |
| Sample type |
SRA |
| |
|
| Source name |
SUM159R
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM159R
sonicated nuclear lysates incubated with: Biotin-JQ1
dna fragments precipitated using: Streptavidin
barcode (already removed): TAGCTT
|
| Treatment protocol |
Sonicated nuclear lysates were incubated with Biotin-JQ1 for 6 hour
|
| 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 precipitated using streptavidin conjugated beads. Purified precipitated 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 |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Chem-Seq for Biotin JQ1
|
| Data processing |
library strategy: Chem-Seq
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 |
Nov 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
|
| 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) |
| GSE63284 |
Response and resistance to BET bromodomain inhibitors in triple negative breast cancer [Chem-Seq] |
| GSE63584 |
Response and resistance to BET bromodomain inhibitors in triple negative breast cancer |
|
| Relations |
| BioSample |
SAMN03178261 |
| SRA |
SRX836253 |
