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| Status |
Public on Jan 11, 2023 |
| Title |
LSD1_HCT116_KO |
| Sample type |
SRA |
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| Source name |
HCT116
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: colorectal cancer cell line
genotype: LSD1 knockout
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| Growth protocol |
Human colorectal carcinoma HCT116 cell line was cultured in McCoy’s 5A medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin/streptomycin (Procell, Wuhan, China, CM-0096). Human colonic epithelial cell line NCM460 was cultured in DMEM medium (Gibco, NY, USA, C11965500BT) supplemented with 10% FBS (Lonsera, S712-012S) and 100 U/mL penicillin/streptomycin (Gibco, USA, 15140122).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted with a HiPure Tissue DNA Mini Kit (Magen, D3121-02).
The DNA samples were digested using methylation-insensitive restriction enzyme Mspl. All the cytosines were subjected to methylation-modified sequencing adaptors, DNA fragments with insert lengths within the range of 40-220 base pairs were cut from the gel and bisulfite treatment was carried out using an EZ DNA Methylation Gold Kit (Zymo Research). PCR amplification was then performed to obtain the final DNA library. After quality checks of the DNA library, the samples were sent for Illumina HiSeq 2500/4000 sequencing.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The quality controls of all reads were checked using FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/).
Filter sequencing adapters and low-quality reads using TrimGalore (v0.6.6).
Cleaned reads were aligned to the hg38 genome with Bismark (v0.19.0)
Assembly: GRCh38/hg38
Supplementary files format and content: Bismark coverage file
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| Submission date |
Jan 11, 2023 |
| Last update date |
Jan 12, 2023 |
| Contact name |
Cao Qiang |
| E-mail(s) |
csqasds@gmail.com
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| Organization name |
Sun Yat-sen University
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| Department |
School of Medicine
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| Street address |
No. 66 Gongchang Road, Guangming District, Shenzhen
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| City |
Shenzhen |
| ZIP/Postal code |
518000 |
| Country |
China |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE222611 |
Pan-cancer analysis revealed H3K4me1 at bivalent promoters premarks DNA hypermethylation during tumor development and identified the regulatory role of DNA methylation in relation to histone modifications [RRBS] |
| GSE222612 |
Pan-cancer analysis revealed H3K4me1 at bivalent promoters premarks DNA hypermethylation during tumor development and identified the regulatory role of DNA methylation in relation to histone modifications |
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| Relations |
| BioSample |
SAMN32675326 |
| SRA |
SRX19001682 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6927779_HCT116_LSD1KO_RRBS.pe.bismark.merged_CpG_evidence.cov.gz |
26.8 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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