|
| 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 |
| E-mail(s) |
tbenoukraf@mun.ca
|
| Phone |
+1 (709) 864-6671
|
| Organization name |
Memorial University of Newfoundland
|
| Department |
Faculty of Medicine, Division of BioMedical Sciences
|
| 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 |
|
| Relations |
| BioSample |
SAMN09760121 |
| SRA |
SRX4501270 |
