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| Status |
Public on Jun 18, 2020 |
| Title |
mES Tet-TKO_WGBS 2 |
| Sample type |
SRA |
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| Source name |
Embryonic Stem Cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: inner cell mass
treatment: none
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| Growth protocol |
cultured feeder-free in fibroblast-conditioned medium
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
cultured cells were washed on ice with ice-cold phosphate-buffer saline (PBS), detached using cell scrapers and collected by centrifugation (400 ×G, 4°C). Nucleic acids were subsequently extracted using the Wizard Genomic DNA Purification (Promega, Leiden, The Netherlands) kit according to instructions, dissolved in 80 µL PBS with RNAse A (200 units, NEB, Ipswich, MA, USA), incubated for 10 minutes at 37°C. After proteinase K addition (200 units) and incubation for 30 minutes at 56°C, DNA was purified using the QIAQuick blood and tissue kit, eluted in 100 µL of a 10 mM Tris, 1mM EDTA solution (pH 8) and stored at -80°C until further processing.
DNA libraries were prepared using methylated adapters and the NEBNext DNA library prep master mix set following manufacturer recommendations. Libraries were bisulfite-converted using the Imprint DNA modification kit (Sigma) as recommended, and PCR amplified for 12 cycles using barcoded primers (NEB) and the KAPA HiFi HS Uracil+ ready mix (Sopachem, Eke, Belgium) according to manufacturers instructions.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Tet-TKO
TKO.methylation.inHIPPeaks.WGBS.txt
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| Data processing |
FastQ files were mapped to the mouse genome (build mm10) using bismark (version 0.10.1).
Read counts at HIF peak areas were quantified in each sample using SeqMonk, and background-normalized to enable enrichment assessment.
Genome_build: mm10
Supplementary_files_format_and_content: file contains read numbers overlaping with HIF peaks in TET TKO mouse
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| Submission date |
Aug 09, 2016 |
| Last update date |
Jun 18, 2020 |
| Contact name |
Jieyi Xiong |
| Organization name |
VIB-KULeuven Center for Cancer Biology
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| Street address |
Herestraat 49, box 912
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| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE85355 |
DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [WGBS] |
| GSE85356 |
DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance |
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| Relations |
| BioSample |
SAMN05540304 |
| SRA |
SRX2009299 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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