|
| Status |
Public on Sep 10, 2020 |
| Title |
2BC4: Animal 4 treated PFC |
| Sample type |
SRA |
| |
|
| Source name |
Prefrontal cortex tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: F344
Sex: male
age: 18-month old
treatment: COM
|
| Treatment protocol |
COM was performed by an experienced Doctor of Osteopathy. Three of six rats underwent seven days of COM treatement after being anesthesized with 1.5-3% isoflurane. Untreated rats were anesthsized as well.
|
| Growth protocol |
All rats were provided with normal food and water ad libitum and housed with 12-hour light-dark cycle. All methods were performed in accordance with the relevant guidelines and regulations. All animal experimental procedures and animal housing were approved by the Institutional Animal Care and Use Committee of Virginia Tech (protocol No. 15-099) and University of Virginia (protocol No.3539).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rats were euthanized by cervical dislocation after seven days. Using a rat brain matrix, a 1mm coronal section from the dorsal end of prefrontal cortex was sampled from the euthanized rats. RNA was extracted using the PureLink™ RNA Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The STAR v2.7.3a software package was used to map the fastq format sequencing data. STAR was run with runThreadN=8, outSAMtype=BAM SortedByCoordinate, quantMode=GeneCounts, outSAMstrandField=intronMotif, and outFilterIntronMotifs=RemoveNoncanonicalreads.
The Cufflinks software suite was used to assemble transcriptomes and quantify RNA expression level for each sample.
Genome_build: Rattus_norvegicus.Rnor_6.0
Supplementary_files_format_and_content: Tab delimited file containing gene id and FPKM values calculated by cufflinks.
|
| |
|
| Submission date |
Sep 09, 2020 |
| Last update date |
Sep 10, 2020 |
| Contact name |
Ramu Anandakrishnan |
| E-mail(s) |
ramu@vt.edu
|
| Phone |
703-403-0234
|
| Organization name |
Edward Via College of Osteopathic Medici
|
| Department |
Biomedical Sciences
|
| Lab |
Molecular Mechanism of Disease
|
| Street address |
2265 Kraft Dr
|
| City |
Blacksburg |
| State/province |
VA |
| ZIP/Postal code |
24060 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE157736 |
Cranial manipulation modulates cholinergic pathway gene expression in an animal model of age-related cognitive decline |
|
| Relations |
| BioSample |
SAMN16090090 |
| SRA |
SRX9101455 |
