|
| Status |
Public on Aug 24, 2021 |
| Title |
ASPcKO tumor 1 |
| Sample type |
SRA |
| |
|
| Source name |
tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Flow-cytometry sorted tumor cell
genotype: aP2-Cre; SmoM2/tdTom; Pten f/f
background: mixed
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were excised and enzymatically (collagenase B/dispase II) and mechanically digested for 1 hour at 37C and filtered into single cells for flow cytometry. TdTomato+/PECAM1- population was used for RNA extraction with Qiazol's miRNeasy Micro Elution Kit.
The KAPA Hyper Prep library kit was used according to manufacturer's specifications.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
1860293_MEH173_SPA-862
|
| Data processing |
Total stranded RNA sequencing data were processed by the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60), mapped to mouse genome assembly (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (vM22) .
Genome_build: GRCm38(mm10)
Supplementary_files_format_and_content: gene-level RSEM raw count, TPM, FPKM txt files
|
| |
|
| Submission date |
Feb 16, 2021 |
| Last update date |
Aug 24, 2021 |
| Contact name |
Hongjian Jin |
| E-mail(s) |
hongjian.jin@STJUDE.ORG
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Center for Applied Bioinformatics
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38015 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE166808 |
Quantitative assessment of transcriptomic differences between ASPcKO and ASPcKOP7cKO flow cytometry-sorted murine FN-RMSs by RNA sequencing |
| GSE166906 |
Synthetic essentiality between PTEN and core dependency factor PAX7 dictates rhabdomyosarcoma identity |
|
| Relations |
| BioSample |
SAMN17923021 |
| SRA |
SRX10107260 |
