|
| Status |
Public on Sep 04, 2023 |
| Title |
RCC4, IFNg + TNF treated, biol rep 2, DRS |
| Sample type |
SRA |
| |
|
| Source name |
RCC4
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RCC4
cell type: Renal cell carcinoma epithelial cell
treatment: IFNg + TNF
|
| Treatment protocol |
RCC4 cells were treated with pro-inflammatory cytokines IFN-γ (1000U/mL) and TNF (25 ng/mL) for 24 hours before harvested for RNA extraction. 3 flasks of T75s were used for each biological replicate
|
| Growth protocol |
RCC4 cells were maintained at 37C in a humidified atmosphere of 5% CO2 and grown in complete Dulbecco’s Modified Eagle’s Medium (DMEM). Complete DMEM media was prepared by using DMEM, supplemented with 10% foetal bovine serum (FCS), 1% 200 mM L-Glutamine and 1% penicillin/streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were first washed with ice-cold PBS (Gibco), followed by lysis with Qiazol (Qiagen). Total RNA was extracted using RNeasy RNA extraction kit (Qiagen) with an additional Dnase I digestion (QIAGEN) according to manufacturer's instruction. Poly(A)+ RNA molecules were enriched from total RNA with the Dynabeads mRNA purification kit (Thermo Fisher).
Sequencing libraries were generated using the SQK-RNA002 sequencing kit using 500ng of polyA enriched RNA following manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
| |
|
| Data processing |
RNAseq reads with a minimum MinKNOW read quality threshold of Q<7 were mapped to hg38 with minimap2 (version 2.24) using the recommended parameters for Oxford Nanopore Technologies direct RNA sequencing (-ax splice -uf -k14). Samtools (version 1.16) was used to filter out low mapping quality alignments (MAPQ < 10). Reads per gene were counted using featureCounts (version 2.0.0) with long-read counting mode (-L).
Assembly: hg38
Supplementary files format and content: Tab-delimited count matrix files containing raw read counts mapped to the reference genome
|
| |
|
| Submission date |
Aug 31, 2023 |
| Last update date |
Sep 04, 2023 |
| Contact name |
Joshua Lee |
| E-mail(s) |
josh.lee@york.ac.uk
|
| Organization name |
University of York
|
| Department |
Hull York Medical School
|
| Street address |
University Road
|
| City |
York |
| ZIP/Postal code |
YO10 5DD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL26167 |
| Series (1) |
| GSE242084 |
Long read transcriptome sequencing of ccRCC tumour cell line RCC4 |
|
| Relations |
| BioSample |
SAMN37217652 |
| SRA |
SRX21566074 |
