|
| Status |
Public on Dec 31, 2019 |
| Title |
U37125_RNA |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain background: Mixed (predominately SvJ/129)
genotype/variation: Myf6(ICNm/WT) Trp53(F2-10/F2-10) ROSA26(LUSAP/Any)
tumor type: rhabodmyosarcoma, embryonal
sample type: primary tumor tissue; frozen tumor
|
| Growth protocol |
the mouse cell line C2C12 was grown in DMEM + 10% FBS + 1% P/S, while all other samples had no growth conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from preserved clinical tissue stored as cryopreserved tissue or FFPE tissue (except C2-C12, isolated from snap frozen cells folllowing harvesting from plateware). RNA isolation was performed at Beijing Genomics Institute
library construction was performed at Beijing Genomics Institute
Paired-End RNA sequencing of GEMM (mouse samples)
Single-End RNA sequencing (canine samples)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
raw reads aligned to CanFam3.1 canine reference genome or GRCHM38 mouse reference genome using STAR
aligned transcripts were quantified using RSEM
Genome_build: GEMM and the mouse cell line were aligned to GRCHM38 mouse genome
Genome_build: Canine samples were aligned to CanFam3.1 canine genome
Supplementary_files_format_and_content: result files are in tabular format. These files have quantified TPM data with addional information.
|
| |
|
| Submission date |
Dec 30, 2019 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Charles Keller |
| E-mail(s) |
charles@cc-tdi.org
|
| Organization name |
Children's Cancer Therapy Development Institute
|
| Street address |
12655 SW Beaverdam Rd. West
|
| City |
Beaverton |
| State/province |
OR |
| ZIP/Postal code |
97005 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE142775 |
Sequencing of canine and genetically-engineered mouse models for endotype identification of embryonal rhabdomyosarcoma |
|
| Relations |
| BioSample |
SAMN13702065 |
| SRA |
SRX7480826 |
