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Sample GSM3317488 Query DataSets for GSM3317488
Status Public on Aug 10, 2018
Title HCT116_WT_WGBS
Sample type SRA
Source name HCT116 cell lines
Organism Homo sapiens
Characteristics tissue: colon
cell line: HCT116
Treatment protocol No treatment
Growth protocol HCT116 cells were grown in RPMI 1640 medium with 10% FBS.
Extracted molecule genomic DNA
Extraction protocol The DNA was extracted using Qiagen DNeasy Blood & Tissue Kits.
After samples DNA testing, negative control DNAs were added into the initial DNA pool, and then fragmented into a 200-300bp range using Covaris S220. Next, terminal repairing, A-ligation, methylation sequencing adapters ligation were performed to DNA fragments. Then, DNA fragments undergone a bisulfite treatment using the EZ DNA Methylation Gold Kit from Zymo Research. Library concentration was firstly quantified by Qubit 2.0, and then is diluted to 1 ng/ul before an insert size verification using the Agilent Bioanalyzer 2100 and followed by Q-PCR. Finally, the library was paired-end sequenced using the Illumina HiSeq 4000.
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 4000
Data processing Raw datasets underwent read quality check by FastQC, as well as quality and adapter trimming using Trim Galore.
Short reads in high quality were aligned to hg38 with Bismark using Bowtie2 and the default parameters
Methylation states in CpG context were extracted by Bismark methylation extractor module
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph of CpG beta scores (methylation scores)
Submission date Aug 02, 2018
Last update date Aug 10, 2018
Contact name Touati Benoukraf
Phone +1 (709) 864-6671
Organization name Memorial University of Newfoundland
Department Faculty of Medicine, Discipline of Genetics
Street address Craig L. Dobbin Genetics Research Centre,
City St. John's
State/province NL
ZIP/Postal code A1B 3V6
Country Canada
Platform ID GPL20301
Series (1)
GSE118030 MethMotif: An integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles
BioSample SAMN09760121
SRA SRX4501270

Supplementary file Size Download File type/resource
GSM3317488_HCT116_WGBS_CpG.bedGraph.gz 319.5 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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