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| Status |
Public on Aug 30, 2019 |
| Title |
WGBS_SKN_3 |
| Sample type |
SRA |
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| Source name |
SKN-3 cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: SKN-3
cell type: Patient-derived head and neck squamous cell carcinoma cell line
genotype: NSD1 mutant
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| Growth protocol |
SKN-3 cells were cultured in Dulbecco's modified Eagles' medium (DMEM, Invitrogen) with 10% fetal bovine serum (FBS, Sigma).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from flash frozen cell pelets of about 5 million cells using DNeasy Blood & Tissue Kit from QIAGEN Cat. #69509
NxSeq AmpFREE Low DNA Library Kit (Lucigen). Samples were then bisulfite converted using the EZ-DNA Methylation Gold Kit (Zymo Research). DNA was amplified by 9 cycles of PCR using the Kapa Hifi Uracil + DNA polymerase (KAPA Biosystems).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters. After alignment, we sorted the bam files using samtools, then igvtools was used to generate wig files (igvtools count -w 25 -e 200). Finally, bigWig files were obtained using wigToBigWig.
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters. The bigWig files were generated similarly as ChIP-seq.
Raw reads from whole-genome bisulfite sequencing were aligned using BWA (version 0.6.1). Low-quality sequence at the 3′ ends were trimmed. After alignment, we filtered duplicated or poorly mapping reads (>2% mismatches or aberrant insert size). Samtools (version 0.1.18) in mpileup mode was applied to call CpG methylation. We used igvtools to generate the tdf files.
Genome_build: hg19, mm10 and dm6 for human, mouse and drosophila data, respectively
Supplementary_files_format_and_content: bigWig, tdf
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| Submission date |
Aug 20, 2018 |
| Last update date |
Aug 30, 2019 |
| Contact name |
Jacek Majewski |
| E-mail(s) |
jacek.majewski@mcgill.ca
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| Organization name |
McGill University
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| Department |
Human Genetics
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| Street address |
740 Dr. Penfield
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
QC H3A 1A4 |
| Country |
Canada |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE118785 |
H3K36me2 recruits DNMT3A and shapes intergenic DNA methylation landscapes |
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| Relations |
| BioSample |
SAMN09864101 |
| SRA |
SRX4579186 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3347569_SKN3_WGBS.tdf |
283.0 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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