|
| Status |
Public on Sep 13, 2022 |
| Title |
S1-07 |
| Sample type |
SRA |
| |
|
| Source name |
soft tissue sarcoma
|
| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: soft tissue sarcoma
histological diagnosis: perivascular wall tumor
molecular identity: perivascular wall tumor
tumor grade: 2
tumor size: 3.1 x 2.5 cm
age_(y): 12
reproductive status: FS
breed: Plott hound mix
tumor location: Thoracic wall
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Two 50 micron thickness sections were obtained from each FFPE tumor sample and processed for total RNA extraction using an Qiagen RNeasy FFPE kit. One microgram of total RNA was enriched for mRNA using Ribominus Eukaryotic V2.
Sequencing libraries were constructed using 200 nanograms of enriched mRNA and the Ion Total RNA-Seq Kit V2 without further fragmentation while all purification and size selection were performed using AMPureXP beads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
RNA extracted from a canine soft tissue sarcoma
|
| Data processing |
RNA seq reads were aligned to a recent canine reference genome (ROS-canfam-01) using STAR2 and counted using htseq-count.
Assembly: ROS-canfam-01
Supplementary files format and content: comma separated values (csv) file containing counts of aligned reads produced by htseq-count
|
| |
|
| Submission date |
Jul 20, 2022 |
| Last update date |
Sep 13, 2022 |
| Contact name |
Eric Aaron Shelden |
| E-mail(s) |
eshelden@wsu.edu
|
| Organization name |
Washington State University
|
| Department |
School of Molecular Biosciences
|
| Lab |
Shelden
|
| Street address |
1770 NE Stadium Way
|
| City |
PULLMAN |
| State/province |
WA |
| ZIP/Postal code |
99164-7520 |
| Country |
USA |
| |
|
| Platform ID |
GPL27923 |
| Series (1) |
| GSE208664 |
Comparative whole transcriptome analysis of gene expression in three canine soft tissue sarcoma types |
|
| Relations |
| BioSample |
SAMN29849674 |
| SRA |
SRX16360162 |
