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| Status |
Public on Jun 01, 2021 |
| Title |
high BHB [2258] |
| Sample type |
SRA |
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| Source name |
high BHB_blood
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| Organism |
Bos taurus |
| Characteristics |
cell type: high BHB
cell type: blood cell
birthdate: 27-Feb-18
gender: female
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted with the DNeasy Blood & Tissue Kit (Qiagen, Valencia, CA, USA).
Genomic DNA from calf blood underwent bisulfite conversion and the libraries were constructed with the Pico Methyl-SeqTMLibrary Prep Kit (Catalog Nos.D5455).
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
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| Description |
2258
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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 Bioconductor package BSseq was then used to perform methylation smoothing and identification of differentially methylated cytosines and differentially methylated regions.
The MethylKit package was also used for cytosine methylation analysis and searching of hypermethylated and hypomethylated regions with an adjusted p value.
Genome_build: bosTau9
Supplementary_files_format_and_content: tab-delimited text files include corrected p value for DMR identification
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| Submission date |
May 31, 2021 |
| Last update date |
Jun 01, 2021 |
| 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) |
| GSE175855 |
Comparing the whole genome methylation landscape of dairy calf blood cells revealed potential intergenerational inheritance of the maternal metabolic status |
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| Relations |
| BioSample |
SAMN19471406 |
| SRA |
SRX11033776 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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