|
| Status |
Public on Oct 20, 2019 |
| Title |
U11 |
| Sample type |
SRA |
| |
|
| Source name |
prefrontal cortex
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
cognitive performance: nonperforming
age: aged
tissue: Prefrontal Cortex
|
| Treatment protocol |
Young (3 months) and aged (22 months) rats were trained and tested for attentional capacities in an operant task. Non-performing age-matched controls were given the same contextual experience as the performing animals but were never engaged in any cognitive activity. Brains were removed and medial prefrontal cortex was isolated for transcriptomic analysis.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNeasy Kit (Qiagen)
TruSeq stranded mRNA library. 1000ng total RNA from each sample was used to prepare the cDNA library
RNA-Seq (Illumina). Libraries were purified using AmPure beads, had a quality check on bioanalyzer (Agilent) and quantified with Qubit (Invitrogen). Sample libraries were subsequently pooled and loaded to the sequencer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Adaptor quality checked using Trimmomatic
Sequence data from FASTQ files were aligned to the Rnor 6.0 genome using Bowtie2 and TopHat2
HTSeq was used to generate gene-level count, using Rnor_6.0.87.gtf for annotation
Read counts derived from two lanes per sample were added together, and the Bioconductor package DESeq2 was used for count normalization and analysis.
Genome_build: Rnor 6.0
Supplementary_files_format_and_content: .txt file reports normalized counts for all samples
|
| |
|
| Submission date |
Oct 20, 2017 |
| Last update date |
Oct 20, 2019 |
| Contact name |
Vinay Parikh |
| E-mail(s) |
vinay.parikh@temple.edu
|
| Phone |
215-204-1572
|
| Organization name |
Temple University
|
| Department |
Psychology
|
| Street address |
1701 N. 13th Street, Weiss Hall
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19122 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE105453 |
Impact of cognitive performance and normal aging on transcriptomic changes in the prefrontal cortex of rats |
|
| Relations |
| BioSample |
SAMN07817570 |
| SRA |
SRX3306500 |
