NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7124107 Query DataSets for GSM7124107
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap