|
| Status |
Public on Sep 27, 2024 |
| Title |
7163 |
| Sample type |
SRA |
| |
|
| Source name |
Blood
|
| Organism |
Bos taurus |
| Characteristics |
tissue: Blood
cell type: Blood
genotype: MRG
|
| Growth protocol |
The cows were raised in the same conditions on the farm
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
One mL of blood was sent to the Génome Québec sequencing platform for DNA extraction
DNA conversion step involves in three primary enzymes: TET2 and T4-BGT detect and transform 5mC and 5hmC into a product that cannot be deaminated by the APOBEC3A enzyme. Subsequently, APOBEC3A deaminates unmodified cytosines by converting them to uracils. As a result, unmethylated cytosines are transformed into uracils and then to thymines during PCR amplification, while methylated cytosines remain as cytosines
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads were filtered, trimmed, and deduplicated using fastp version 0.23.1 with default parameters
Read conversion, alignment to the Bos taurus reference genome (ARS-UCD1.2.104)
Methyl calling were performed using Bismark. This process was implemented in the DRAGEN Methylation Pipeline, which was run on an Illumina DRAGEN server using default parameters
Methylation calls from Bismark were filtered to retain CpG sites covered by at least six reads in a minimum of five samples per group.
The annotation was performed using the annotatePeak function in the default mode of the R ChIPseeker (version 1.32.1).
Assembly: ARS-UCD1.2
Supplementary files format and content: A tab-delimited text file includes information about differential methylated positions with q-values less than 0.01 and methylation differences greater than the absolute value of 25 and their annotations.
Supplementary files format and content: A tab-delimited text file includes information about differential methylated regionss with q-values less than 0.01 and methylation differences greater than the absolute value of 25 and their annotations. The regional analysis used a 500-bp sliding window with a 250-bp overlap and a minimum of five CpG per regions
Library strategy: Enzymatic methyl-seq (EM-seq)
|
| |
|
| Submission date |
Feb 20, 2024 |
| Last update date |
Sep 27, 2024 |
| Contact name |
Marc-André Sirard |
| E-mail(s) |
Marc-Andre.Sirard@fsaa.ulaval.ca
|
| Organization name |
Université Laval
|
| Department |
Sciences Animales
|
| Street address |
Offfice 2732, 2440 Hochelaga Blvd.
|
| City |
Québec City |
| State/province |
Quebec |
| ZIP/Postal code |
G1V 0A6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL26012 |
| Series (1) |
| GSE256195 |
Decoding epigenetic markers: implications of traits and genes through DNA methylation in resilience and susceptibility to mastitis in dairy cows |
|
| Relations |
| BioSample |
SAMN40000522 |
| SRA |
SRX23670153 |
