|
| Status |
Public on Jan 07, 2016 |
| Title |
SUM159_DMSO_24H_1 |
| Sample type |
SRA |
| |
|
| Source name |
SUM159
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM159
drug treatment: DMSO
duration: 24h
barcode (already removed): CTTGTA
|
| Treatment protocol |
Cells were treated with 500nM JQ1 or DMSO for the indicated time
|
| Growth protocol |
Cells were growed with SUM medium
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA-Seq libraries were generated on a Sciclone NGS instrument (Perkin Elmer) using Illumina TrueSeq reagents. Briefly, mRNA was enriched from 1 ug of total RNA, fragmented and reverse transcribed. Following 2nd strand synthesis, next generation sequencing libraries were obtained by end repair, A-tailing and adapter ligation reactions with reagents from the Illumina TrueSeq kit. Libraries were amplified and purified before sequencing on a HiSeq instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-Seq in DMSO or JQ1 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
For all samples, transcriptome mapping was performed using tophat2 with default settings against the hg19 UCSC genes.gtf build. Quantification was performed using the cufflinks software suite by running the cuffquant command on all samples followed by the cuffnorm command. For all tophat2 and cufflinks data processing steps, default parameters were used.
Supplementary_files_format_and_content: TNBC_RNASEQ.FPKM.txt
|
| |
|
| Submission date |
Nov 24, 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 |
GPL11154 |
| Series (2) |
| GSE63582 |
Response and resistance to BET bromodomain inhibitors in triple negative breast cancer [RNA-Seq] |
| GSE63584 |
Response and resistance to BET bromodomain inhibitors in triple negative breast cancer |
|
| Relations |
| BioSample |
SAMN03218124 |
| SRA |
SRX767014 |
