|
| 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 |
