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| Status |
Public on Jun 02, 2020 |
| Title |
Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats: RNA-Seq Data from Generation F29 |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The strong pattern of comorbidity amongst psychiatric disorders is believed to be generated by a spectrum of latent liability, arising from a complex interplay of genetic risk and environmental factors, such as stress and childhood adversity. At one end of this spectrum are internalizing disorders, which are associated with neuroticism, anxiety, and depression. At the other end of the spectrum are externalizing disorders, which are associated with risk-taking and novelty-seeking, as seen in mania, substance abuse, and impulse-control disorders. We model the genetic contributions underlying both extremes of this spectrum by selectively breeding rats that react differently to a novel environment. “Bred high responder” (bHR) rats are highly exploratory with a disinhibited, novelty-seeking temperament, including hyperactivity, aggression, and drug-seeking. “Bred low responder” (bLR) rats are highly-inhibited, exhibiting reduced locomotor activity and anxious and depressive-like behavior. These behavioral propensities are robust and stable, beginning early in development similar to temperament in humans. This RNA-sequencing study examined gene expression in the hippocampus, a region critical for emotional regulation, in generation F29 male bHR rats and bLR rats from two ages: P14 and adulthood (n=2/group).
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| Overall design |
Overall Design: This RNA-sequencing study examined gene expression in the hippocampus in generation F29 male bHR rats and bLR rats from two ages: P14 and adulthood (n=2/group). Sacrifice & RNA Extraction: Rats were sacrificed through rapid decapitation, followed by immediate brain extraction. The whole hippocampus was rapidly dissected on ice, fast-frozen at –40°C, and stored at –80°C before processing. TRIzol reagent (Invitrogen, Calsbad, CA) was used to extract total RNA, followed by purification using RNeasy RNA purification columns (Qiagen, Valencia, CA). The quality and concentration of the RNA was determined using an Agilent bioanalyzer (Palo Alto, CA) and wavelength absorbance (260/280 nm ratio) by Nanodrop. RNA Sequencing: Purified RNA was shipped to the Genomic Services Laboratory at HudsonAlpha (https://gsl.hudsonalpha.org/index) for short-read (50 bp length) single-end sequencing. RNA Qubit was used to assess concentration (range: 720-1120 ng/uL). The dilutions were denatured through heat application at 70˚C for two minutes and then checked for quality with a RNA Nano bioanalysis chip. Indexed non-stranded cDNA libraries were then prepared using standard Illumina procedures and a TruSeq library preparation kit (Illumina) after which they were pooled for sequencing with four samples per pool. The pooled libraries were clustered on a HiSeq flowcell (Illumina) and sequenced using a first generation HiSeq 2000 sequencer. RNA-Seq Data Preprocessing: Reads were mapped to the rat reference genome (RGSC v3.4) using Tophat2 and Bowtie2 with default parameters and a standard sequence read output. Only reads that aligned with the genome once were maintained for later differential expression analysis. Transcript assembly was collected using Cufflinks and Cuffmerge (Trapnell et al. 2012; Nat Protoc. 7: 562–578), and bHR vs. bLR differential expression was assessed for each age group (P14 and adult) using CuffDiff (Trapnell et al. 2012; Nat Protoc. 7: 562–578).
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| Contributor(s) |
Hagenauer MH, Clinton SM, Meng F, Birt IA, Watson SJ Jr, Akil H |
| Citation(s) |
32762937 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| P01 DA021633 |
Antecedents & Consequences of Drug Abuse: Heritability, Stress & Neurplasticity |
REGENTS OF THE UNIVERSITY OF MICHIGAN - ANN ARBOR |
HUDA AKIL |
| P01 MH042251 |
DEVELOPMENTAL STUDIES--DIFFERENCES IN EMOTIONAL REACT |
REGENTS OF THE UNIVERSITY OF MICHIGAN - ANN ARBOR |
HUDA AKIL |
| R01 DA013386 |
Stress & Vulnerability to Drug Abuse: Neural Correlates |
REGENTS OF THE UNIVERSITY OF MICHIGAN - ANN ARBOR |
HUDA AKIL |
| P01 DA021633 |
COCAINE IMPACT ON NEURAL PLASTICITY MODULATION BY GENETIC VULNERABILITY & STRESS |
REGENTS OF THE UNIVERSITY OF MICHIGAN - ANN ARBOR |
STANLEY J WATSON |
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| Submission date |
Nov 18, 2019 |
| Last update date |
Sep 01, 2020 |
| Contact name |
Megan Hastings Hagenauer |
| E-mail(s) |
hagenaue@umich.edu
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| Organization name |
University of Michigan
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| Department |
MBNI
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| Lab |
Dr. Huda Akil & Dr. Stanley Watson
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| Street address |
205 Zina Pitcher Pl.
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platforms (1) |
| GPL14844 |
Illumina HiSeq 2000 (Rattus norvegicus) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE140599 |
Hippocampal Gene Expression in bred High Responder (bHR) vs. bred Low Responder (bLR) Rats |
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| Relations |
| BioProject |
PRJNA590233 |
| SRA |
SRP230439 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE140597_Adult_HRvsLR_CuffDiff_gene_exp.diff.rtf.gz |
1.3 Mb |
(ftp)(http) |
RTF |
| GSE140597_P14_HRvsLR_CuffDiff_gene_exp.diff.rtf.gz |
1.2 Mb |
(ftp)(http) |
RTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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