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| Status |
Public on Dec 18, 2020 |
| Title |
Sample11_Con_HPC_11 |
| Sample type |
SRA |
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| Source name |
hippocampus
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| Organism |
Cavia porcellus |
| Characteristics |
maternal treatment: Saline
subject id: 11
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from the hippocampus and whole blood of each animal was extracted using AllPrep Mini Kit (Qiagen: Cat#80204) and QIAamp DNA Mini Kit (Qiagen: Cat#51304) respectively.
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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| Description |
GP_HPC_counts_fdr.txt
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| Data processing |
Adaptor sequences were trimmed using Trim Galore.
Additional filtering was performed to remove reads that did not contain an MspI site signature at the 5’ end 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 sorted by Samtools (version 1.7).
We then used MethPipe (version 3.4.2) to identify significant differentially methylated CpG sites (DMCs) 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).
Genome_build: Broad/cavPor3
Supplementary_files_format_and_content: Tab-delimited text files with at least 10X reads (formatted as "chr", "loc", "strand", "fdr", )
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| Submission date |
Dec 17, 2020 |
| Last update date |
Dec 20, 2020 |
| Contact name |
Stephen Matthews |
| Organization name |
University of Toronto
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| Street address |
1 King's College Circle
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5S1A8 |
| Country |
Canada |
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| Platform ID |
GPL29163 |
| Series (1) |
| GSE163447 |
DNA methylome signatures of prenatal exposure to synthetic glucocorticoids in hippocampus and peripheral whole blood of female guinea pigs in early life |
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| Relations |
| BioSample |
SAMN17106078 |
| SRA |
SRX9698846 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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