|
Status |
Public on Mar 09, 2018 |
Title |
IMR90 NT |
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: DMSO (NT: No Treatment)
|
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 |
SAMN03656625 |
SRA |
SRX1025880 |