|
| Status |
Public on Feb 15, 2024 |
| Title |
Run 1 UOK262 Mutant RNA-seq--Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
UOK262
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: UOK262
cell type: Renal Cell Carcinoma
genotype: Mutant
treatment: normoxia
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using Trizol Reagent according to the manufacture’s protocol. Following phase separation, the aqueous phase was applied to a Qiagen RNeasy Mini Kit column and RNA was purified according to kit instructions.
RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit v2 and sequenced on NextSeq 500 using paired-end sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read quality was checked with FastQC. Reads of the samples were trimmed for adapters using Cutadapt (v2.5) and aligned against a costume genome of repetitive sequences before alignment with the hg38 reference genome (gencode v35) using STAR v2.7.6a. PCR duplicates were marked and removed with Picard’s MarkDuplicates (v 2.25.0). Sample counts were obtained with HTSeq’s count (v 0.9.1) and differential gene expression was analyzed with DeSeq2.
Assembly: hg38
Supplementary files format and content: count matrix
|
| |
|
| Submission date |
Mar 29, 2023 |
| Last update date |
Feb 15, 2024 |
| Contact name |
Pedro J Batista |
| E-mail(s) |
pedro.batista@nih.gov
|
| Phone |
3014356294
|
| Organization name |
National Institutes of Health
|
| Department |
National Cancer Institute
|
| Lab |
Cell Biology
|
| Street address |
37 Convent Street Bldg 37
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE228525 |
Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma [RNA-Seq] |
| GSE228565 |
Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma |
|
| Relations |
| BioSample |
SAMN33986899 |
| SRA |
SRX19820018 |
