NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6502522 Query DataSets for GSM6502522
Status Public on Jun 04, 2024
Title A2 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 SAMN30443512

Supplementary data files not provided
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap