|
| Status |
Public on Jun 09, 2023 |
| Title |
Mouse # 65041 melanoma RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Bulk melanoma tissue
|
| Organism |
Mus musculus |
| Characteristics |
genotype: dKO
batch: 2
Sex: M
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Snap-frozen tumors were disrupted in QIAzol reagent (QIAGEN) by milling with zirconia beads (Fisher). After addition of chloroform (Sigma) and centrifugation, RNA was isolated from the aqueous phase using an RNEasy Mini kit (QIAGEN).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq of bulk melanoma tissue at 50 days post induction
|
| Data processing |
Raw reads were quasi-mapped to the Gencode M25 (GRCm38.p6) gene set using salmon v.1.2.1 (Patro et al., 2017).
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: fastq - raw Illumina reads; sf - table of gene expression counts and TPM generated by salmon
|
| |
|
| Submission date |
Apr 13, 2022 |
| Last update date |
Jun 09, 2023 |
| Contact name |
Dan Filipescu |
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Oncological Sciences
|
| Lab |
Emily Bernstein
|
| Street address |
1470 Madison Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE200725 |
MacroH2A restricts melanoma progression via inhibition of chemokine expression in cancer-associated fibroblasts [RNA-seq] |
| GSE200751 |
MacroH2A restricts melanoma progression via inhibition of chemokine expression in cancer-associated fibroblasts. |
|
| Relations |
| BioSample |
SAMN27562115 |
| SRA |
SRX14841418 |
