|
| Status |
Public on May 18, 2023 |
| Title |
ww21_CFA_Saline |
| Sample type |
SRA |
| |
|
| Source name |
Brain / mPFC
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Brain / mPFC
pain: CFA
drug: Saline
|
| Treatment protocol |
CFA = injection of 0.1 mL in paw or saline as control; OXY = injection of 1 mg/g IP daily for 7 days or saline as control.
|
| Growth protocol |
Adult male Sprague-Dawley rats
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA from tissue punches (2mm punches obtained from the mPFC region) was isolated and purified using TRIzol (Ambion, Austin, TX) and the Qiagen total RNA kit with on-column DNase (Qiagen, Venlo, Netherlands). RNA concentrations were measured on a NanoDrop.
RNA libraries were constructed using the Illumina TruSeq Stranded Total RNA library prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ww21
S3
|
| Data processing |
alignment to Rn6 genome from UCSC using hisat2 (v2.1.0) followed by samtools to sort alignments
counting using htseq-count (v0.6.1) with 'intersection-strict'
indidivual count files were compiled into single csv using R/DESeq2
Assembly: Rn6
Supplementary files format and content: CSV files. Counts from HTSEQ-COUNT.
|
| |
|
| Submission date |
May 18, 2023 |
| Last update date |
May 18, 2023 |
| Contact name |
Fraser James Sim |
| E-mail(s) |
[email protected]
|
| Phone |
7168292151
|
| Organization name |
University at Buffalo
|
| Department |
Pharmacology
|
| Street address |
3435 Main Street
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14216 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE232804 |
EGR3 regulates opioid-related nociception and motivation in male rats |
|
| Relations |
| BioSample |
SAMN35158616 |
| SRA |
SRX20420853 |
