|
| Status |
Public on Jul 01, 2024 |
| Title |
7860_ko_D300-2 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney
cell line: 786-0
cell type: Clear cell renal cell carinoma
genotype: SETD2 KO
treatment: 300nM Decitabine
|
| 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
Assembly: 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 |
Jan 25, 2023 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Aguirre de Cubas |
| E-mail(s) |
decubas@musc.edu
|
| Organization name |
Medical University of South Carolina
|
| Department |
Microbiology and Immunology
|
| Street address |
86 Jonathan Lucas St
|
| City |
Charleston |
| State/province |
SC |
| ZIP/Postal code |
29425 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE223688 |
SETD2 loss sensitizes kidney cancer cells to DNA hypomethylating agents |
|
| Relations |
| BioSample |
SAMN32908471 |
| SRA |
SRX19165358 |
