|
| Status |
Public on Feb 15, 2024 |
| Title |
Mutant Run 1 input replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
UOK262
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: UOK262
cell type: renal cell carcinoma
genotype: Mutant
treatment: input
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected using Trizol reagent according to the manufacturer’s protocol. Following separation of the aqueous and organic phases, the aqueous phase was removed and purified with a Qiagen RNA kit according to the manufacturer’s protocol.
mRNA was polyA selected through two rounds of selection with oligo dT magnetic beads. Following polyA selection, mRNA was fragmented using ZnCl2 before selection with m6A-specific antibody. 3' adaptors sequencing adaptors were added with RNA ligase and reactions were reverse-transcribed with SuperScript IV. cDNA was circularized with circLigase and libraries were PCR amplified to add Illumina sequencing primers. Libraries were sequenced on a NextSeq 550 instrument.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Following sequencing, read quality was assessed with FastQC. Barcode split, read collapse, and adaptor trimming was performed using scripts from the icSHAPE pipeline. Trimmed reads were first mapped to a costume geneme that includes rRNA and repeat genome sequences. Reads that did not map to the costume genome were then aligned to hg38 using STAR (v/2.7.6.a). Peak analysis was performed using MACS2. Peaks were required to appear in at least 2 replicates for further analysis. Peak intersection with the hg38 longest transcript isoforms was performed using bedtools (v/2.30.0). Peak changes were identified in DESeq2 or edgeR.
Assembly: hg38
Supplementary files format and content: count matrix
|
| |
|
| Submission date |
Mar 30, 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 |
GPL21697 |
| Series (2) |
| GSE228558 |
Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma [m6A-IP] |
| GSE228565 |
Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma |
|
| Relations |
| BioSample |
SAMN33986919 |
| SRA |
SRX19820033 |
