|
| Status |
Public on Jun 01, 2020 |
| Title |
1534-ADC-6: 7860_wt_D300-2 |
| Sample type |
SRA |
| |
|
| Source name |
786-0 RCC cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 786-0
treatment: 300nM Decitabine
replicate: rep 2
|
| Treatment protocol |
Cells were treated daily with DMSO of Decitabine (100nM or 300nM) for three days. Fresh media added on day 4 and cells were harvested on day 5.
|
| Growth protocol |
Cells cultured
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the miRNeasy Kit (Qiagen)
Illumina libraries prepared using poly-A enrichment.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing reads were aligned against the human GENCODE genome (V28), Version Hg19 (January 2017 freeze, GRCh37, Ensembl 87) using the Spliced Transcripts Alignment to a Reference (STAR) software
Reads were preprocessed and index using SAMtools
Mapped reads were annotated and quantified using featureCounts
Normalization and differential expression was performed using DESeq2
Expression matrix produced using variance stabilized transformation function
Genome_build: human GENCODE genome (V28), Version Hg19 (January 2017 freeze, GRCh37, Ensembl 87)
Supplementary_files_format_and_content: tab-delimited text files include Raw Counts values for each Sample
|
| |
|
| Submission date |
Dec 19, 2019 |
| Last update date |
Jun 02, 2020 |
| Contact name |
Aguirre A de Cubas |
| E-mail(s) |
a.decubas@vumc.org
|
| Organization name |
Vanderbilt University Medical Center
|
| Department |
Hematology and Oncology
|
| Lab |
Rathmell Lab
|
| Street address |
2220 Pierce Ave
|
| City |
NASHVILLE |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE142381 |
DNA Demethylation promotes ERV expression and activation of immune signaling in renal cell cancer cells |
|
| Relations |
| BioSample |
SAMN13636161 |
| SRA |
SRX7416333 |
