|
| Status |
Public on Jul 15, 2022 |
| Title |
BLA, ER, biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: brain
treatment: enrichment removed
|
| Treatment protocol |
Adult male Sprague-Dawley rats were subjected to standard housing, environmentally enriched, or enrichment removed conditions. Brains were collected and micropunches of the basolateral amygdala (BLA) were used for subseqent analysis. Proportional samples from 10 rats per group were pooled for sequencing, yielding one biological replicate for each condition.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using RNA Mini kits kits (Qiagen). ~300ng of total RNA (which contained equal representation from 10 animals' RNA samples) was used for the construction of sequencing libraries. Samples underwent polyA RNA isolation using the NEBNext Poly(A) mRNA Magnetic Isolation Module prior to library preparation.
RNA libraries for RNA-seq were prepared using the NEBNext Ultra Directional RNA Library prep kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were aligned using Hisat2 aligner in R 4.0
Counts were generated using Rsubread (R.3.8)
Counts were normalized using Deseq2
Assembly: RGSC7.2
Supplementary files format and content: excel files include matrix of normalized counts for each sample
|
| |
|
| Submission date |
Jul 12, 2022 |
| Last update date |
Jul 15, 2022 |
| Contact name |
Marissa Ann Smail |
| E-mail(s) |
smailma@mail.uc.edu
|
| Phone |
7242167360
|
| Organization name |
University of Cincinnati
|
| Department |
Pharmacology and Systems Physiology
|
| Lab |
Herman
|
| Street address |
4227 Allendorf Drive, Apt 1
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45209 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (2) |
|
| Relations |
| BioSample |
SAMN29660022 |
| SRA |
SRX16132253 |
