|
| Status |
Public on May 30, 2013 |
| Title |
HIV-1Tg_HIP_Saline rep7 |
| Sample type |
SRA |
| |
|
| Source name |
HIV-1Tg_HIP_Saline
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: HIV-1Tg
tissue: Hippocampus (HIP)
tissue type: Disease model
|
| Treatment protocol |
Either nicotine (0.25 mg/ml) or saline (1 ml/kg of body weight) was administered twice a day (7:00 AM and 4:00 PM) by subcutaneous injection with a 23-gauge/1-cc syringe for 17 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PFC, STR and HIP were removed, flash frozen on dry ice, and RNA was extracted using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rn4 whole genome using tophat and bowtie 1.04 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflink program.
Genome_build: Rn4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
|
| |
|
| Submission date |
May 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Shaolin Wang |
| Organization name |
University of Virginia
|
| Department |
Psychiatry
|
| Lab |
Nerogenetics
|
| Street address |
1670 Discovery Dr. Suite
|
| City |
Charlottesville |
| State/province |
MD |
| ZIP/Postal code |
22911 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (1) |
| GSE47474 |
Transcriptome Sequencing of Gene Expression in the brain of HIV transgenic transgenic rat |
|
| Relations |
| SRA |
SRX287254 |
| BioSample |
SAMN02182760 |
