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Sample GSM1150793 Query DataSets for GSM1150793
Status Public on May 30, 2013
Title HIV-1Tg_PFC_Nicotine rep8
Sample type SRA
 
Source name HIV-1Tg_PFC_Nicotine
Organism Rattus norvegicus
Characteristics strain: HIV-1Tg
tissue: Prefrontal cortex (PFC)
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 SRX287195
BioSample SAMN02182795

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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