|
Status |
Public on Feb 15, 2024 |
Title |
ND5 WT Sample 1 |
Sample type |
SRA |
|
|
Source name |
UOK262
|
Organism |
Homo sapiens |
Characteristics |
cell line: UOK262 cell type: renal cell carcinoma genotype: WT
|
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 RNeasy Mini Kit column and RNA was purified according to kit instructions. The 28S and mt-ND5 transcripts were reverse transcribed using transcript-specific primers downstream of the m1A sites with TGIRT following the manufacturer’s protocol. Transcripts were amplified with barcoded oligos targeting either 28S or mt-ND5. Barcoded samples were pooled and sequencing on an Illuminia Micro Miseq
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina MiSeq |
|
|
Description |
nd5_pileup_wildtype.csv
|
Data processing |
Demultiplexed reads were aligned to the human genome (hg38) using STAR (v.2.7.6a). The presence of m1A was quantified using samtools-mpileup to create individual base-pair frequencies for every position within the mt-ND5 and 28S rRNA transcripts. Assembly: hg38 Supplementary files format and content: csv count file
|
|
|
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 |
GPL15520 |
Series (2) |
GSE228563 |
Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma [m1A_pileup] |
GSE228565 |
Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma |
|
Relations |
BioSample |
SAMN33988060 |
SRA |
SRX19821178 |