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| Status |
Public on Jun 18, 2020 |
| Title |
SK-MEL-28_SeqCapEpi_BSseq_r2 |
| Sample type |
SRA |
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| Source name |
Melanoma cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
treatment: none
growth protocol: cultured at 37°C in Roswell Park Memorial Institut 1640 Medium (RPMI) 10% FBS 1% Pen Strep and 1% L-Glutamine.
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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. Fragments were selected from these libraries using the SeqCap Epi CpGiant Enrichment Kit (Roche) following the manufacturers instructions, sequenced from both ends for 100 bases on a HiSeq 2000.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
SK-MEL-28
BT931.methylation.status.bedGraph
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| Data processing |
FastQ files were mapped to the human genome (build GRCh37/hg19) using bismark (version 0.10.1).
Methylation status were extract using bismark, replicated were pooled for the extraction.
Genome_build: hg19
Supplementary_files_format_and_content: Methylation status for all C's in the captured region.
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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 |
GPL11154 |
| Series (2) |
| GSE85354 |
DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [SeqCapEpi] |
| GSE85356 |
DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance |
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| Relations |
| BioSample |
SAMN05537947 |
| SRA |
SRX2009297 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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