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| Status |
Public on Nov 06, 2024 |
| Title |
pnd14pfc, saline, rep2 |
| Sample type |
SRA |
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| Source name |
Prefrontal Cortex
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| Organism |
Cavia porcellus |
| Characteristics |
tissue: Prefrontal Cortex
cohort: pnd14
treatment: saline
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| Treatment protocol |
Pregnant guinea pigs were administered betamethasone or saline on gestational day 50/51.
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| 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.
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NextSeq 500 |
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| 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")
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| Submission date |
Oct 30, 2024 |
| Last update date |
Nov 06, 2024 |
| Contact name |
Stephen Matthews |
| Organization name |
University of Toronto
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| Street address |
1 King's College Circle, Rm 3302
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| City |
Toronto |
| ZIP/Postal code |
M5S1A8 |
| Country |
Canada |
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| Platform ID |
GPL29163 |
| Series (1) |
| GSE280726 |
Conserved DNA Methylation Signatures in the Prefrontal Cortex of Newborn and Juvenile Guinea Pigs Following Antenatal Betamethasone Exposure |
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| Relations |
| BioSample |
SAMN44513465 |
| SRA |
SRX26556990 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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