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Status |
Public on Jun 04, 2024 |
Title |
A2 low BFI |
Sample type |
SRA |
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Source name |
sperm
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Organism |
Bos taurus |
Characteristics |
cell type: sperm cell gender: male
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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
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
HiSeq X Ten |
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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
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Submission date |
Aug 22, 2022 |
Last update date |
Jun 04, 2024 |
Contact name |
ying zhang |
E-mail(s) |
ying.zhang.2@ulaval.ca
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Organization name |
UNIVERSITY LAVAL
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Street address |
735 Ave.Neree tremblay
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City |
quebec |
ZIP/Postal code |
G1V4W5 |
Country |
Canada |
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Platform ID |
GPL24230 |
Series (1) |
GSE211794 |
Whole geneome methylation sequencing for bull fertility DNA mehylation biomarker |
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Relations |
BioSample |
SAMN30443512 |
Supplementary data files not provided |
Raw data are available in SRA |
Processed data are available on Series record |
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