|
| Status |
Public on Jun 18, 2020 |
| Title |
SK-MEL-28_RNAseq_Hypoxia_r3 |
| Sample type |
SRA |
| |
|
| Source name |
SK-MEL-28 Hypoxia
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
cell line: SK-MEL-28
cell type: Melanoma cell line
treatment: 0.5% O2 24h
growth protocol: cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) with 10% fetal bovine serum (FBS), 5ml of 100 U/ml Penicillin-Streptomycin (Pen Strep, Life Technologies) and 5ml of L-Glutamine 200mM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RiboMinus Eukaryote System (Life technologies)
Briefly, total RNA was extracted using TRIzol (Invitrogen), and remaining DNA contaminants in 17-20ug of RNA was removed using Turbo DNase (Ambion) according to the manufacturers instruction. RNA was repurified using RNeasy Mini Kit (Qiagen).
Strand specific library preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
FastQ files were mapped to the reference genome (human:build GRCh37/hg19; mouse:mm10) using tophat (version 2.0.10).
Counrs were called byHTSeq (version 0.5.3p3)
Genome_build: hg19; mm10
Supplementary_files_format_and_content: Raw read files contain raw read counts for each sample
|
| |
|
| Submission date |
Sep 16, 2019 |
| Last update date |
Jun 19, 2020 |
| Contact name |
Jieyi Xiong |
| Organization name |
VIB-KULeuven Center for Cancer Biology
|
| Street address |
Herestraat 49, box 912
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE85353 |
DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [RNA] |
| GSE85356 |
DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance |
|
| Relations |
| BioSample |
SAMN12766942 |
| SRA |
SRX6853626 |
