|
| Status |
Public on Dec 01, 2020 |
| Title |
HeLa_LSH_KO_RRBS |
| Sample type |
SRA |
| |
|
| Source name |
HeLa
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
genotype/variation: LSH KO
|
| Treatment protocol |
No treatment.
|
| Growth protocol |
Human cervical cancer cell line (HeLa) was maintained in DMEM medium (Gibco) containing 10% fetal calf serum (Gemini), 100 U/mL penicillin and 100μg/mL streptomycin (Milipore). Human colon cancer cells (HCT116) was maintained in McCoy’s 5A medium (Gibco) containing 10% fetal calf serum (Gemini), 100 U/mL penicillin and 100μg/mL streptomycin (Milipore). The cultured cells were maintained at 37 °C in a humidified incubator with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
To prepare genomic DNA for RRBS analysis, cells were resuspended with cell lysis buffer (10mM Tris pH 7.5, 10 mM EDTA, 10 mM NaCl, 0.5% sarcosyl, 0.1 mg/mL RNase (CWBIO)) and incubated at 37°C overnight. Then, protease K was added to a final concentration of 0.2 mg/mL and incubated at 65°C for 24 hr. Genomic DNA was extracted by phenol/chloroform and ethanol precipitated. The DNA were dissolve in ddH2O.Total RNA for RNA-seq analysis was extracted from cells using RNAiso Plus Reagent (Takara) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
RRBS reads were mapped to human genome hg38 by bismark (v0.19.0) . Only unique mapped reads were kept and CpGs with >= 5 reads mapped were used for further analysis. Paired-end 2 replicates RNA-seq reads for HeLa wild type and LSH KO cells were mapped to hg38 by STAR (v2.4.0d) and then quantified by Cuffdiff (v2.2.1) . Differentially expressed genes (DEGs) were required p-value<=1e-2 and fold change >=2 as reported by Cuffdiff.
Supplementary_files_format_and_content: The RRBS processed data were the output of bismark tab-delimited text file for each sample. For RNA-seq data the cuffdiff output differential expressed genes with name of gene_exp.diff were used.
Genome_build: hg38
|
| |
|
| Submission date |
Sep 05, 2019 |
| Last update date |
Dec 02, 2020 |
| Contact name |
Yaqiang Cao |
| E-mail(s) |
caoyaqiang0410@gmail.com
|
| Organization name |
NHLBI
|
| Department |
System Biology Center
|
| Lab |
Laboratory of Epigenome Biology
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (1) |
| GSE136931 |
LSH facilitates DNA methylation primarily by promoting UHRF1 DNA accessibility and DNA methylation by DNMT1 |
|
| Relations |
| BioSample |
SAMN12699161 |
| SRA |
SRX6805948 |
