|
| Status |
Public on Mar 09, 2018 |
| Title |
IMR90 Etop_12 |
| Sample type |
SRA |
| |
|
| Source name |
Fetal lung fibroblasts IMR90
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
cell type: Human fetal lung fibroblasts
growth protocol: Cells were grown in DMEM supplemented with 10%FBS
treatment prototcol: 6μM Etoposide for 12 hours
|
| Treatment protocol |
Samples were treated with either vehicle (DMSO) or indicated doses of etoposide for indicated amout of time before extraction of RNA
|
| Growth protocol |
Cells were passaged in 10cm corningware dishes using media described in Samples section in a 37°C humidified incubator
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from sub-confluent 10cm dishes using Qiagen RNeasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
|
| |
|
| Submission date |
May 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Yidong Chen |
| E-mail(s) |
cheny8@uthscsa.edu
|
| Phone |
2105629163
|
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Population Health Sciences
|
| Street address |
8403 Floyd Curl Drive, MSC 7784
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE68836 |
BRCA1, R-loops and Recombination defects in Ewing's sarcoma (RNA-seq) |
| GSE68847 |
BRCA1, R-loops and Recombination defects in Ewing's sarcoma |
|
| Relations |
| BioSample |
SAMN03656627 |
| SRA |
SRX1025882 |
