|
| Status |
Public on Dec 07, 2016 |
| Title |
xeno_OS-1_23 |
| Sample type |
SRA |
| |
|
| Source name |
xenograft (athymic nude mice strain strain NCr nu/nu) of canine osteosarcoma cells OS-1
|
| Organisms |
Canis lupus familiaris; Mus musculus |
| Characteristics |
host mouse strain: athymic nude mice strain strain NCr nu/nu
cell line: OS-1
tissue: xenograft canine osteosarcoma cells OS-1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from primary intratibial tumors and from cell lines using Qiagen miRNeasy Mini Kit.
Sequencing libaries were prepared using Illumina TruSeq Library Preparation Kits
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
xenograft tumor OS-1 replicate
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to a HISAT2 index for mapping which was built from a multi-sequence fasta file containing both the canine (canFam3) and murine (mm10) genomes with the HISAT2 aligner (2.0.2-beta) using default parameters.
Rsubread featureCounts (1.4.6) was used to estimate transcript abundance using default parameters.
Genome_build: mm10 and canFam3
Supplementary_files_format_and_content: tab-delimited text file include count values for each sample and includes data for both dog and mouse genes.
|
| |
|
| Submission date |
Nov 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Milcah Scott |
| E-mail(s) |
scot0340@umn.edu
|
| Organization name |
University of Minnesota
|
| Department |
Department of Microbiology and Immunology
|
| Lab |
WMBB 2-260
|
| Street address |
2101 6th Street Se
|
| City |
Minneapolis |
| State/province |
MN |
| ZIP/Postal code |
55455 |
| Country |
USA |
| |
|
| Platform ID |
GPL22673 |
| Series (1) |
| GSE89835 |
Heterotypic mouse models of canine osteosarcoma recapitulate tumor heterogeneity and biological behavior |
|
| Relations |
| BioSample |
SAMN06015675 |
| SRA |
SRX2346883 |
