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| Status |
Public on Jun 01, 2024 |
| Title |
Sow1 |
| Sample type |
SRA |
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| Source name |
Peripheral blood
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| Organism |
Sus scrofa |
| Characteristics |
tissue: Peripheral blood
Stage: Adult
Sex: female
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| Treatment protocol |
None
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| Growth protocol |
The pigs for this study were obtained from the University of Missouri Swine Research Complex (Columbia, MO). The fetal tissues were dissected from sows bred via artificial insemination (AI). Dams were a mixture of Landrace and Large White breeds and bred to Choice Genetics (Choice USA 1415 28th Street Suite 400 West Des Moines, Iowa 50266) LR-M6 line. Gestation day 1 (GD1) was considered the day of AI. Dams were euthanized at GD45, GD60, and GD90 via electrical stunning and exsanguination at the University of Missouri abattoir, an USDA inspected commercial unit (Establishment #5077A).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The reproductive tract was removed from the dam at the abattoir. Individual fetuses, referred to as GD45, GD60, GD90 male or female (M or F) were removed from each uterine horn. No fetuses were taken from the tip of either horn or the body of the uterus. The skin and skull were cut downstream the mid-sagittal plane with a scalpel and removed near the ears. The whole brain was scooped out, weighed, measured at the longest point. Blood was collected from age-matched boars and sows. The animal was restrained using a snare and whole blood was collected with a syringe and needle from the jugular vein and put in ethylenediaminetetraacetic acid (EDTA) tubes to prevent from blood to clot. DNA from fetal brain was isolated from frozen homogenized tissue samples using AllPrep DNA/RNA Mini Kit (Qiagen, Cat No./ID: 80204) as per manufacturer’s instruction. DNA from blood was isolated using QIAamp DNA Blood Mini Kit (Qiagen, Cat No./ID: 51104) as per manufacturer’s instruction.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit as per manufacturer’s instruction.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
S1
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| Data processing |
Library strategy: Enzymatic methyl-seq
The raw sequences were assessed for quality with FastQC.
TrimGalore was the used to remove adapters and perform base quality trimming.
The reads obtained from the quality control steps were mapped to the reference genome of swine, Sscrofa11.1, using Bismark.
After alignment, the methylation sites were extracted by using the bismark_methylation_extractor algorithm implemented within Bismark to generate the coverage files for methylation sites.
The Bismark coverage files were then processed using edgeR
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: text file (gziped). These files contain information for methylation sites including the chromosome, start position, end position, methylation percentage, count methylated, and count unmethylated data.
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| Submission date |
Jun 27, 2021 |
| Last update date |
Jun 01, 2024 |
| Contact name |
SUSANTA BEHURA |
| E-mail(s) |
behuras@missouri.edu
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| Phone |
5738821722
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| Organization name |
University of Missouri
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| Street address |
920 East Campus Dr
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| City |
Columbia |
| State/province |
MO |
| ZIP/Postal code |
65211 |
| Country |
USA |
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| Platform ID |
GPL26351 |
| Series (1) |
| GSE178983 |
DNA methylation in developing fetal brain of pig |
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| Relations |
| BioSample |
SAMN19903157 |
| SRA |
SRX11237602 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5402719_S1_S8.bismark.cov.gz |
315.6 Mb |
(ftp)(http) |
COV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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