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Sample GSM7124031 Query DataSets for GSM7124031
Status Public on Feb 15, 2024
Title 8_NCB_S8_R1
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 (Thermo Fisher) according to the manufacture’s protocol. Following phase separation, the aqueous phase was applied to a RNeasy Mini Kit (Qiagen) and RNA was purified according to kit instructions. Libraries were prepared using the QIAseq microRNA Library Kit from Qiagen.
Libraries were prepared using the QIAseq microRNA Library Kit from Qiagen and sequnecing using Illumina NovaSeq SP.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina NovaSeq 6000
 
Description NCB
V_count_matrix_maturemap_mature_miRNA_normoxia_262.csv
Data processing Reads for each sample were trimmed for adapters and low-quality bases using cutadapt (v 3.4) and umitools (v1.1.1). Reads were mapped to hg38 using STAR (v.2.7.6a) and were counted by htseq-count (v 0.9.1). Differential analysis was performed using DEseq2.
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 GPL24676
Series (2)
GSE228557 Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma [miRNA-seq]
GSE228565 Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma
Relations
BioSample SAMN33986909
SRA SRX19820024

Supplementary file Size Download File type/resource
GSM7124031_NCB_hpMIR_ReadsPerGene.out.tab.gz 6.1 Kb (ftp)(http) TAB
GSM7124031_NCB_matureMIR_ReadsPerGene.out.tab.gz 8.4 Kb (ftp)(http) TAB
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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