|
| Status |
Public on Aug 17, 2022 |
| Title |
MPNST-38 |
| Sample type |
SRA |
| |
|
| Source name |
MPNST tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: MPNST tumor
genotype: PRC2 loss of function
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were isolated from tumor tissues using Trizol (Thermo Fisher #15596026).
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq by poly (A) capture
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The sequence data were processed and mapped to the human reference genome (hg20) using STAR v2.3 (Dobin et al., 2013)
Gene expression was quantified to transcripts-per-million (TPM) using the STAR (Trapnell et al., 2010) and Log 2 transformed.
Assembly: hg20
Supplementary files format and content: tab-delimited text file includes raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jun 21, 2022 |
| Last update date |
Aug 17, 2022 |
| Contact name |
Ping Chi |
| E-mail(s) |
chip@mskcc.org
|
| Phone |
(646) 888-4166
|
| Organization name |
MEMORIAL SLOAN KETTERING CANCER CTR
|
| Street address |
1275 YORK AVENUE
|
| City |
NEW YORK |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE206527 |
Transcriptome analysis between PRC2-loss and PRC2-wt in human malignant peripheral nerve sheath tumor (MPNST) |
|
| Relations |
| BioSample |
SAMN29220716 |
| SRA |
SRX15806037 |
