|
| Status |
Public on May 29, 2024 |
| Title |
Control Gestation Day 175: Postnatal Day 0 PMBC DNA 2132 |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Bos taurus |
| Characteristics |
tissue: PBMC
cell type: White Blood Cells
treatment: control
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from WBCs processed from whole blood using Qiagen DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany).
DNA samples were digested with 30 units of MspI, fragments purified with DNA Clean & Concentrator-5 and ligated to adapters with replacement of cytosine with 50-methyl-cytosine according to Illumina’s guidelines. Fragments greater than 50 base pairs were recovered and bisulfite treated using the EZ DNA Methylation-Lightning Kit . Samples were subjected to PCR with Illumina indices. Size and concentrations of purified products were confirmed with the Agilent 2200 TapeStation prior to sequencing on an Illumina platform
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CpG sites hypermethylated
|
| Data processing |
Quality of reads were checked with fastqc 0.11.9, reads were trimmed with trimgalore 0.6.4_dev
Reads were mapped to the bosTau9 genome using bismark 0.22.3
Obtained bam files were analyzed with methylKit 1.24.0
Assembly: bosTau9
Supplementary files format and content: bedGraph files generated from bismark for each sample
Supplementary files format and content: comma-delimited files for differentially methylated cytosines and regions
|
| |
|
| Submission date |
Feb 13, 2024 |
| Last update date |
May 29, 2024 |
| Contact name |
Thomas Hansen |
| E-mail(s) |
thomas.hansen@colostate.edu
|
| Phone |
9704918081
|
| Organization name |
Colorado State University
|
| Department |
Biomedical Sciences
|
| Street address |
3107 Rampart Rd
|
| City |
Fort Collins |
| State/province |
CO |
| ZIP/Postal code |
80523 |
| Country |
USA |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE255721 |
Epigenetic modifications of white blood cell DNA caused by transient fetal infection with bovine viral diarrhea virus |
|
| Relations |
| BioSample |
SAMN39935626 |
| SRA |
SRX23615777 |
