 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 04, 2024 |
| Title |
A1 low BFI |
| Sample type |
SRA |
| |
|
| Source name |
sperm
|
| Organism |
Bos taurus |
| Characteristics |
cell type: sperm cell
gender: male
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted with the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA).
EM-seq (Enzymatic methylation seq) workflow was adopted to perform the whole genome methylation sequencing, which reduced the DNA fragmentation and damage compared to the traditional bisulfite sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Adapter-removal and quality trimming of the libraries were performed with TRIMMOMATIC. BISMARK was then used to align the bisulfite-converted libraries to a synthetic converted bovine genome (ARS-UCD1.2, bosTau9)
The MethylKit package was also used for cytosine methylation analysis and searching of hypermethylated and hypomethylated regions with an adjusted p value.
Assembly: ARS-UCD1.2 and Btau_5.0.1
Supplementary files format and content: tab-delimited text files include corrected p value for DMR identification
Library strategy: EM-seq
|
| |
|
| Submission date |
Aug 22, 2022 |
| Last update date |
Jun 04, 2024 |
| Contact name |
ying zhang |
| E-mail(s) |
ying.zhang.2@ulaval.ca
|
| Organization name |
UNIVERSITY LAVAL
|
| Street address |
735 Ave.Neree tremblay
|
| City |
quebec |
| ZIP/Postal code |
G1V4W5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24230 |
| Series (1) |
| GSE211794 |
Whole geneome methylation sequencing for bull fertility DNA mehylation biomarker |
|
| Relations |
| BioSample |
SAMN30443513 |
| Supplementary data files not provided |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
