|
| Status |
Public on Jul 22, 2023 |
| Title |
Hep3B, DNMT1-WT, 25mM Glucose, Thiamet-G, Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver
cell line: Hep3B
cell type: Human epithelial liver
genotype: DNMT1-WT
treatment: 25mM Glucose + Thiamet-G
|
| Treatment protocol |
Cells were induced by treatment of 96 hours post confluent cells with or without 25mM Thiamet-G (Cayman Chemical).
|
| Growth protocol |
DMEM or DMEM high glucose, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using DNA mini kit with G-tip (Qiagen). 2 ug of genomic DNA was used for the construction of sequencing libraries.
DNA library for nanopore sequencing were constructed using Genomic DNA Ligation Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
PromethION |
| |
|
| Data processing |
Converting the signal data, indexing, and methylation call were performed using nanopolish version 0.11.1.
Indexing, Data aligned by minimap2 version 2.17.
Aligned reads were sorted using samtools version 1.10 in the hg19 genome.
UCSC genome browser tracks were established using bedGraphToBigWig.
Methylation percentage was averaged across CpG islands.
Assembly: Reads were aligned to hg19 genomes
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
Apr 25, 2022 |
| Last update date |
Jul 22, 2023 |
| Contact name |
Heon Shin |
| E-mail(s) |
hshin@coh.org
|
| Organization name |
City of Hope
|
| Street address |
1500 E Duarte Rd, Gonda, 2132B
|
| City |
Duarte |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL26167 |
| Series (1) |
| GSE201470 |
Inhibition of DNMT1 methyltransferase activity via glucose-regulated O-GlcNAcylation alters the epigenome |
|
| Relations |
| BioSample |
SAMN27765604 |
| SRA |
SRX14992341 |
