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Status |
Public on Jun 18, 2020 |
Title |
mES Dnmt-WT_RNAseq_Hypoxia_r3 |
Sample type |
SRA |
|
|
Source name |
Dnmt-WT Hypoxia
|
Organism |
Mus musculus |
Characteristics |
tissue: inner cell mass cell line: mES Dnmt-WT cell type: Embryonic Stem cells treatment: 0.5% O2 24h growth protocol: cultured feeder-free in fibroblast-conditioned medium
|
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
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
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
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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 |
GPL13112 |
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 |
SAMN12766904 |
SRA |
SRX6853608 |