|
| Status |
Public on Nov 27, 2023 |
| Title |
Bisulfite-seq_cultured_ductal_methyl_1 |
| Sample type |
SRA |
| |
|
| Source name |
exocrine pancreas
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: exocrine pancreas
cell type: ductal
genotype: KPTS
condition: monolayer culture
|
| Treatment protocol |
"KPTS" genotype cells have enforced expression of oncogenic KRAS-G12V and CRISPR/Cas9 knockout of P16, P53, and SMAD4 .
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted with Zymo Quick-DNA miniprep kit.
Reduced-representation bisulfite converted DNA methylation libraries were contructed from genomic DNA with Illumina Truseq methyl capture kit, as per manufacturer instruction.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Genomic alignment and CpG calling was performed with Bismark 0.19.1.
Detected sites among all samples were collated, and only those withat least 10 read coverage (methylated + unmethylated) for all samples were retained for analysis.
Assembly: hg38
Supplementary files format and content: bismark.cov are tab delimited tables of all detected DNA methylation sites with beta value, methylated reads, and unmethylated reads for each site
Supplementary files format and content: DNA_methylation_beta_tab.txt.gz is a tab delimited table with beta value for all samples for all retained DNA methylation sites (2349323 sites)
|
| |
|
| Submission date |
Jan 18, 2023 |
| Last update date |
Nov 27, 2023 |
| Contact name |
Pei Wang |
| E-mail(s) |
wangp3@uthscsa.edu
|
| Organization name |
University of Texas Health San Antonio
|
| Department |
Cell Systems & Anatomy
|
| Street address |
7703 Floyd Curl Dr
|
| City |
San Antonio |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE222991 |
Functional Genomics of human pancreatic acinar and ductal cells |
| GSE223153 |
DNA methylation sequencing of human pancreatic acinar and ductal cells [Bisulfite-seq] |
|
| Relations |
| BioSample |
SAMN32782647 |
| SRA |
SRX19062490 |
