|
| Status |
Public on Oct 01, 2019 |
| Title |
Patient2 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor specimens of patients with high-grade serous ovarian cancer
|
| Organism |
Homo sapiens |
| Characteristics |
patient diagnosis: high-grade serous ovarian cancer
tissue: ovarian tumor
|
| Growth protocol |
Tissue samples were obtained intra-operatively from surgical tumor specimens of patients with high-grade serous ovarian cancer at the time of the planned cytoreductive surgery under a tissue repository protocol from 2009 to 2014.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from each ovarian cancer tissue sample using an RNeasy Plus Kit (Qiagen), with QIAshredder spin columns for homogenization and on-column DNaseI digestion (79254, Qiagen). The total RNA was analyzed for integrity using an Agilent 2100 Bioanalyzer. The RNA collected was then processed for whole-genome polyadenylated RNA sequencing (polyA+ RNA-seq). The total RNA samples were enriched for polyA+ RNA using Dynabead Oligo(dT)25 (Invitrogen) and strand-specific RNA-seq libraries were prepared from the polyA+ RNA as described previously. The RNA-seq libraries were sequenced using an Illumina HiSeq 2500 (single-end, 50 nt; SE50; one replicate).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The RNA-seq reads were aligned to the hg19 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and bigwig files were generated to for presentation as browser tracks using BedGraph and BigWig function of UCSC tool kit.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig
|
| |
|
| Submission date |
Aug 21, 2019 |
| Last update date |
Oct 02, 2019 |
| Contact name |
W. Lee Kraus |
| E-mail(s) |
lee.kraus@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-8511 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE136155 |
ADP-ribosylation Levels Correlate with Gene Expression Patterns and Clinical Outcomes in Ovarian Cancers |
|
| Relations |
| BioSample |
SAMN12617490 |
| SRA |
SRX6749702 |
