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| Status |
Public on Jul 01, 2016 |
| Title |
nrFSL3 |
| Sample type |
SRA |
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| Source name |
ventral dentate gyrus
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
Sex: male
line: Flinders Sensitive Line (FSL)
lac phenotype: non-responder
treatment: LAC
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| Treatment protocol |
Tap water (vehicle), or L-acetyl-carnitine (LAC, Sigma, Stockholm, SE), dissolved in tap water, at a concentration of 0.3% (w/v), was available ad libitum in standard rat sipping bottles. The treatment was available for a total of 7 days, with fresh water and LAC prepared after 3 days. LAC intake (30 ml) did not differ from water intake (31 ml) per day. This corresponded to a daily LAC consumption of approximately 210 mg/kg body weight (p.o.).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Ventral dentate gyrus tissues were dissected and weighed before homogenization and about 130 mg of tissue was lysed. Total RNA was extracted using Qiazol reagent and RNeasy mini Kit (Qiagen, US), according to the manufacturer’s instructions. RNA quality was checked using the 2100 Bioanalyzer (Agilent Technologies, US) and quantified spectrophotometrically. The acceptance criteria for RNA quality were a 260/280 ratio ≥ 1.80 and ≤ 2.20.
After checking RNA for quality, Total RNA was extracted according to the manufacturer’s instructions (TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
FastQC v0.11.3
Trimmomatic v0.33 SE -phred33 ILLUMINACLIP:TruSeq3.fa:2:30:10 TRAILING:3 MINLEN:36
Tophat v2.0.9 --library-type fr-firststrand --GTF rattus_norvegicus_genes_UCSC_igenome.gtf --min-coverage-intron 50 --max-coverage-intron 20000
merge bam files
htseq-count v0.6.1 -s 'reverse'
EdgeR v3.12.0
Genome_build: RGSC 5.0/rn5
Supplementary_files_format_and_content: Tab delimited files with raw counts for each sample
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| Submission date |
Jun 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Carla Nasca |
| E-mail(s) |
cnasca@rockefeller.edu
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| Organization name |
The Rockefeller University
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| Lab |
Neuroendocrinology
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| Street address |
1230 York Avenue
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE83336 |
Epigenetics and energetics in ventral hippocampus mediate rapid antidepressant action: implications for treatment-resistance |
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| Relations |
| BioSample |
SAMN05244654 |
| SRA |
SRX1844193 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2199658_nrFSL3_rawCounts.txt.gz |
69.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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