|
| Status |
Public on Jul 12, 2023 |
| Title |
RNA-Seq Dentate Gyrus cells, Attacker Group, Rep 5 |
| Sample type |
SRA |
| |
|
| Source name |
Dentate Gyrus
|
| Organism |
Microtus ochrogaster |
| Characteristics |
tissue: Dentate Gyrus
Sex: Male
genotype: WT
behavioral group: Attacker
|
| 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 |
total RNA |
| Extraction protocol |
RNA was isolated using the Qiagen AllPrep DNA/RNA Micro Kit (Qiagen, #80284) according to the manufacturer's protocol. 150ng of RNA was used as input for subsequent library preparation.
Ribo-depleted RNA was prepared from extracted total RNA using NEBNext rRNA Depletion Kit (New England Biolabs, #E6310L). RNA-seq libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, #E7765S)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| 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)
Trimmed sequences were aligned to the prairie vole genome MicOch1.0 using STAR (sjdb_overhang = maxReadLength - 1)
Read count extraction was performed by featureCounts, counting gene-level features.
Normalized values were calculated in R using programs included in the EdgeR library.
Assembly: MicOch1.0
Supplementary files format and content: tab-delimited text file, which includes raw RNAseq read counts for each annotated gene.
|
| |
|
| 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) |
| GSE214797 |
Transcription and DNA methylation signatures of paternal care in hippocampal dentate gyrus of prairie voles (RNA-Seq) |
| GSE214799 |
Transcription and DNA methylation signatures of paternal care in hippocampal dentate gyrus of prairie voles |
|
| Relations |
| BioSample |
SAMN31152719 |
| SRA |
SRX17796589 |
