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Sample GSM8604950 Query DataSets for GSM8604950
Status Public on Nov 06, 2024
Title pnd1 pfc, beta, rep5
Sample type SRA
 
Source name Prefrontal Cortex
Organism Cavia porcellus
Characteristics tissue: Prefrontal Cortex
cohort: pnd1
treatment: beta
Treatment protocol Pregnant guinea pigs were administered betamethasone or saline on gestational day 50/51.
Extracted molecule genomic DNA
Extraction protocol DNA from the prefrontal cortex of each animal was extracted using the AllPrep DNA/RNA/miRNA Universal Kit from Qiagen.
RRBS libraries were generated from 100ng of high-quality dsDNA using the RRBS Methyl_seq System 1-16 (Ovation: Part #0353) and EpiTect Fast DNA Bisulfite kit (Qiagen: Cat. #59824) following the manufacturer’s protocols.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
Instrument model Illumina NextSeq 500
 
Data processing Quality control of data was performed using Trim Galore to trim low-quality reads (Phred <30) and accessory sequences from adaptors. Reads that did not contain an MspI site signature at the 5’ end were removed using a script provided by NuGEN (https://github.com/nugentechnologies/NuMetRRBS/blob/master/ trimRRBSdiversityAdaptCustomers.py). The reads were then aligned using Bismark (version 0.16.0) and Bowtie2 (v2.3.4.3) and sorted by Samtools (v1.9). We then used MethPipe (version 3.4.2) to identify significant differentially methylated CpG sites (DMCs). DMCs were filtered for those with at least 10X reads with FDR < 0.05. CompEpitool was used to annotate the differentially methylated CpG sites to the guinea pig genome (cavPor3).
Assembly: cavPor3
Supplementary files format and content: Tab-delimited text files of DMCs with at least 10X reads (formatted as "chr", "loc", "fdr", "MethDiff")
 
Submission date Oct 30, 2024
Last update date Nov 06, 2024
Contact name Stephen Matthews
Organization name University of Toronto
Street address 1 King's College Circle, Rm 3302
City Toronto
ZIP/Postal code M5S1A8
Country Canada
 
Platform ID GPL29163
Series (1)
GSE280726 Conserved DNA Methylation Signatures in the Prefrontal Cortex of Newborn and Juvenile Guinea Pigs Following Antenatal Betamethasone Exposure
Relations
BioSample SAMN44513469
SRA SRX26556986

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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