|
Status |
Public on Dec 07, 2016 |
Title |
cells_OS-1_A |
Sample type |
SRA |
|
|
Source name |
canine osteosarcoma cell line derivative OS-1
|
Organism |
Canis lupus familiaris |
Characteristics |
cell line: OS-1 tissue: osteosarcoma cell line
|
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 |
canine osteosarcoma cell line derivative OS-1
|
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 |
GPL20988 |
Series (1) |
GSE89835 |
Heterotypic mouse models of canine osteosarcoma recapitulate tumor heterogeneity and biological behavior |
|
Relations |
BioSample |
SAMN06015670 |
SRA |
SRX2346876 |