|
| Status |
Public on Jan 07, 2016 |
| Title |
SUM149_DMSO_12H_R2 |
| Sample type |
SRA |
| |
|
| Source name |
SUM149
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SUM149
drug treatment: DMSO
duration: 12h
barcode (already removed): GTGAAA
|
| 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 |
total RNA was extracted using the standard QIAGEN RNeasy kit (74106). RNA concentrations were measured and quality controlled on a Bioanalyzer, RNA-Seq libraries were made using Illumina True-Seq RNA kits using the Sciclone NGSx workstation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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_SUM149_RNASEQ.genes.fpkm_table.txt
|
| |
|
| 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) |
| 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 |
SAMN03952537 |
| SRA |
SRX1130269 |
