|
| Status |
Public on Dec 15, 2021 |
| Title |
Piglet_overfed_vehicle_sample46 |
| Sample type |
SRA |
| |
|
| Source name |
Piglet_adipose tissue
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Visceral adipose tissue
age: 28 days
maternal diet treatment: overfed
piglet's intervention: vehicle
|
| Treatment protocol |
All piglets were sacrified at weaning (28 days) and visceral adipose tissue samples were collected and stored at -80ºC until processed.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
High quality genomic DNA (400ng) was isolated from adipose tissue samples with Gentra PureGene tissue kit (Qiagen) according to manufacturer's instructions. DNA was bisulfited with the EZ DNA Methylation-Gold Kit (Zymo Research), according to manufacturer's instructions. Bisulfite conversion rate was over 99%.
Libraries were were prepared for sequencing using standard Illumina protocols and Sequencing was performed on a HiSeq 3000 (Illumina).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Quality control of sequencing reads was performed using FastQC.
Adapter removal was carried out using Trim Galore! version 0.4.1.
Reads were then aligned to the reference genome using bismark v0.16.1, followed by methylation calling using the corresponding bismark functionality.
Differentially methylated cytosines in CpG sites were obtained after retrieval with Bioconductor Methylkit package v1.1.8. and filtering out Single Nucleotide Polymporphisms in CpG sites together with non-CpG cytosines.
Genome_build: susScr3
Supplementary_files_format_and_content: cov files with headers: <chromosome>,<position>,<strand>,<count methylated>, <count unmethylated>, <C-context>, <trinucleotide context>
|
| |
|
| Submission date |
Mar 24, 2021 |
| Last update date |
Dec 15, 2021 |
| Contact name |
Abel López-Bermejo |
| E-mail(s) |
alopezbermejo@idibgi.org
|
| Organization name |
IDIBGI
|
| Department |
Pediatrics
|
| Street address |
Dr. Castany s/n
|
| City |
Salt |
| State/province |
Girona |
| ZIP/Postal code |
17190 |
| Country |
Spain |
| |
|
| Platform ID |
GPL24486 |
| Series (1) |
| GSE169515 |
Methylome analysis by reduced representation bisulfite sequencing (RRBS) from adipose tissue samples of piglets from a swine model of maternal overfeeding and/or restriction |
|
| Relations |
| BioSample |
SAMN18473006 |
| SRA |
SRX10434819 |
