|
| Status |
Public on Jun 09, 2023 |
| Title |
iDF dKO serum 0 min replicate 2 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
Cultured immortalized dermal fibroblasts
|
| Organism |
Mus musculus |
| Characteristics |
genotype: dKO
Sex: M
|
| Treatment protocol |
Cells were grown to confluence, then starved in 0.5% serum for 24h
|
| Growth protocol |
DMEM, 10% FBS, 1X Pen/Strep, 37ºC in 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cultured cells were lysed directly in their culture vessel in QIAzol. After addition of chloroform (Sigma) and centrifugation, RNA was isolated from the aqueous phase using an RNEasy Micro kit (QIAGEN).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq of cultured immortalized dermal fibroblasts prior to and after serum stimulation
|
| 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 |
SAMN27562093 |
| SRA |
SRX14841440 |
