|
| Status |
Public on Jul 12, 2023 |
| Title |
RRBS Dentate Gyrus cells, Father Group, Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
Dentate Gyrus
|
| Organism |
Microtus ochrogaster |
| Characteristics |
tissue: Dentate Gyrus
Sex: Male
genotype: WT
behavioral group: Father
|
| Treatment protocol |
Adult Voles were exposed to conspecific pups and their behavioral response was recorded. Samples were separated based on this response for virgin animals or based on sex for pair-bonded individuals.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA and RNA were isolatted from the same tissue using the Qiagen AllPrep DNA/RNA Mircro Kit (Qiagen, #80284) according to the manufacturer's protocol.
100ng of genomic DNA was digested using MspI, and RRBS libraries were constructed using the Premium RRBS Kit (Diagenode, #C02030032)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls were performed using bcl2fastq for Novaseq output.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore (minimum quality 20, minimum length 20)
Sequences were aligned to the prairie vole genome using Bismark methylation alignment software.
Methylation calls were extracted using the built-in methylation extractor program provided in the Bismark suite.
Values were not normalized prior to import into DSS general for differential methylation analysis.
Assembly: MicOch1.0
Supplementary files format and content: files per sample are formatted for use in DSS-general for differential methylation analysis. Columns are as follows: Chromosome, Position, N = number of reads covering this position, X = number of reads with methylation call at this position.
|
| |
|
| Submission date |
Oct 04, 2022 |
| Last update date |
Jul 12, 2023 |
| Contact name |
Nicholas James Waddell |
| E-mail(s) |
[email protected]
|
| Organization name |
Florida State University
|
| Department |
Biological Sciences
|
| Lab |
Laboratory of Jian Feng
|
| Street address |
319 Stadium Dr
|
| City |
Tallahassee |
| State/province |
FL |
| ZIP/Postal code |
32306 |
| Country |
USA |
| |
|
| Platform ID |
GPL28499 |
| Series (2) |
| GSE214798 |
Transcription and DNA methylation signatures of paternal care in hippocampal dentate gyrus of prairie voles (RRBS) |
| GSE214799 |
Transcription and DNA methylation signatures of paternal care in hippocampal dentate gyrus of prairie voles |
|
| Relations |
| BioSample |
SAMN31152594 |
| SRA |
SRX17796472 |
