|
| Status |
Public on Dec 30, 2014 |
| Title |
hcc364_dmso |
| Sample type |
SRA |
| |
|
| Source name |
HCC364 cells, infected with empty vector & treated with DMSO
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung adenocarcinoma
cell line: HCC364
treatment: infected with empty vector & treated with DMSO
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from each of the indicated cell lines was extracted by RNeasy kit (Qiagen). In total, 2 ug of total RNA was used for deep sequencing library preparation using Illumina Truseq sample prep kits (Illumina) according to the manufacturer's protocols. Sequencing libraries with different indices were pooled and sequenced in paired end format to a length of 100bp using the HiSeq2500 platform at Center for Advanced Technology at UCSF.
Illumina Truseq sample prep kits
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned against NCBI build 37 (hg19) of the human genome using the NCBI Ensembl transcript annotation (version 75) with RSEM, which also yielded gene-level expression quantification.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm
|
| |
|
| Submission date |
Dec 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Saurabh Asthana |
| E-mail(s) |
saurabh.asthana@ucsf.edu
|
| Organization name |
UCSF
|
| Department |
Helen Diller Family Comprehensive Cancer Center
|
| Lab |
Olshen
|
| Street address |
1450 Third Street, Room HD276
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE64550 |
shRNA knockdown of YAP1 in HCC364 cells, various drug conditions |
|
| Relations |
| BioSample |
SAMN03273589 |
| SRA |
SRX825194 |
