|
| Status |
Public on Jul 16, 2019 |
| Title |
64-AC |
| Sample type |
SRA |
| |
|
| Source name |
cortex
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: cortex
treatment: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen)
Stranded mRNA-seq was done by Vanderbilt Sequencing core facility using the TruSeq Stranded mRNA-Seq library prep kit to make sequencing libraries, which are typically sequenced on Illumina instruments with 100 bp paired end reads length.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Stranded mRNA (polyAselected)
CTX_counts.txt
1136-TS-5
|
| Data processing |
Quality control on raw reads was performed with FastQC (version 0.10.1) and adaptor trimming and removal of trimmed reads shorter than 20 bp was performed with Trimmomatic (Bolger et al., 2014).
Trimmed reads were mapped to the Rattus norvegicus rn5 genome.
Samtools (version 0.1.19 –96b5f2294a) were used to sort SAM files and de-duplicate reads.
Bowtie2 was used to align reads (Langmead and Salzberg, 2012).
The subread featureCounts function was used to obtain counts. EdgeR was used for normalization and calculation of fold changes (Robinson et al., 2010).
Genome_build: rn5
Supplementary_files_format_and_content: excel, counts
|
| |
|
| Submission date |
Jul 15, 2019 |
| Last update date |
Jul 16, 2019 |
| Contact name |
Teresa Hinkle Sanders |
| E-mail(s) |
teresa.hinkle.sanders@gmail.com
|
| Organization name |
University of Colorado, Boulder
|
| Street address |
1510 Quail Court
|
| City |
Golden |
| State/province |
CO |
| ZIP/Postal code |
80403 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE134309 |
RNA-Seq data from cortex and hippocampus (post novel object recognition test) of rats in a vagus nerve stimulation study |
|
| Relations |
| BioSample |
SAMN12277429 |
| SRA |
SRX6448044 |
