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| Status |
Public on Apr 24, 2024 |
| Title |
zygotes 3C |
| Sample type |
SRA |
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| Source name |
embryos
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| Organism |
Bos taurus |
| Characteristics |
cell type: embryos
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Bovine oocytes and embryos from all study groups were digested with proteinase K (50 mg/mL) in M-Digestion buffer 10X (Zymo Research) for 20 minutes at 50 oC to remove the zona pellucida. Then, they were submitted to total DNA extraction using QuickDNA Microprep Kit (Zymo Research; D3020) following the manufacturer protocol.
Library construction was performed using the Enzymatic Methyl-Sequencing kit from New England Biolabs (E7120S), following the manufacturer protocol.
Enzymatic Methyl-Sequencing
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
zygotes
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| Data processing |
Sequencing adapters were removed using Trimmomatic and base calls with low quality score were removed. Reads with a minimal length of 50 nucleotides were kept for analysis.
Read conversion, alignment to the bovine mitochondrial genome (NC_006853.1) and methylation calls were obtained using Bismark.
Differentially methylated cytosines (DMC) between 2 consecutive stages were identify using the MethylKit R package
For each C-site, a logistic regression model is fitted to calculate p-values that are then adjusted to control for false discovery rate using the BH method implemented in R 4.2.1 p.adjust function (R Core Team 2022).
Assembly: bostau9
Supplementary files format and content: xlsx file containing the results of differential methylation between consecutive stages
Supplementary files format and content: .txt files contain number of methylated and unmethylated reads per C-site
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| Submission date |
Apr 24, 2023 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Marc-André Sirard |
| E-mail(s) |
Marc-Andre.Sirard@fsaa.ulaval.ca
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| Organization name |
Université Laval
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| Department |
Sciences Animales
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| Street address |
Offfice 2732, 2440 Hochelaga Blvd.
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| City |
Québec City |
| State/province |
Quebec |
| ZIP/Postal code |
G1V 0A6 |
| Country |
Canada |
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| Platform ID |
GPL26012 |
| Series (1) |
| GSE230476 |
Genome-wide methylation profile of mitochondrial DNA across bovine preimplantation development |
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| Relations |
| BioSample |
SAMN34361179 |
| SRA |
SRX20094503 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7224998_3C_S40_L004-dedup.CX_report.txt.gz |
3.5 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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