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Sample GSM5402713 Query DataSets for GSM5402713
Status Public on Jun 01, 2024
Title Fetus1
Sample type SRA
 
Source name Fetal brain
Organism Sus scrofa
Characteristics tissue: Fetal brain
Stage: Day45_fetus
Sex: female
Treatment protocol None
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).
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.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description F_d45_Fem
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.
 
Submission date Jun 27, 2021
Last update date Jun 01, 2024
Contact name SUSANTA BEHURA
E-mail(s) behuras@missouri.edu
Phone 5738821722
Organization name University of Missouri
Street address 920 East Campus Dr
City Columbia
State/province MO
ZIP/Postal code 65211
Country USA
 
Platform ID GPL26351
Series (1)
GSE178983 DNA methylation in developing fetal brain of pig
Relations
BioSample SAMN19903163
SRA SRX11237596

Supplementary file Size Download File type/resource
GSM5402713_F_d45_Fem_S9.bismark.cov.gz 304.7 Mb (ftp)(http) COV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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