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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 F43 |
| 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 dataset was part of a larger RNA-Sequencing study examining gene expression in the bHR/bLR hippocampus, a region critical for emotional regulation. The original study compared repeated injections of either antidepressant medication (fluoxetine or desipramine) or vehicle (VEH=1:1 saline and water) solution in bHR and bLR rats (14 days of intraperitoneal injections - P78-P92, 1 per day) under either standard laboratory housing conditions or chronic variable stress. This upload includes only the data from the control subjects: generation F43 adult male bHR VEH rats and bLR VEH rats housed in standard conditions (n=5/group). Prior to sacrifice, at age P92, the rats underwent social interaction testing after 15 minutes of exposure to an anxiogenic environment (the elevated plus maze). The results from the social interaction testing are provided here along with the gene expression data.
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| Overall design |
Overall Design: This dataset was part of a larger RNA-Sequencing study examining gene expression in the bHR/bLR hippocampus. The original study compared repeated injections of either antidepressant medication (fluoxetine or desipramine) or vehicle (VEH=1:1 saline and water) solution in bHR and bLR rats (14 days of intraperitoneal injections - P78-P92, 1 per day) under either standard laboratory housing conditions or chronic variable stress. This upload only includes the data from the control subjects: generation F43 adult male bHR VEH rats and bLR VEH rats housed in standard conditions (n=5 rats/group). Behavioral Testing: At age P92, the rats underwent social interaction testing (protocol: Aydin et al. 2015, Behav Neurosci. 129: 679–682) after 15 minutes of exposure to an anxiogenic environment (the elevated plus maze, protocol: Isgor et al. 2004, Hippocampus. 14: 636–648). Sacrifice & RNA Extraction: One hour after undergoing testing on the elevated plus maze, the animals were sacrificed by rapid decapitation and the brains were flash frozen in isopentane cooled on dry ice. The whole hippocampus was dissected from each brain on a dry ice and wet ice mixture and immediately put in TRIzol™. RNA was extracted using the Zymo RNA isolation Kit and shipped to the University of Michigan DNA Sequencing Core (https://seqcore.brcf.med.umich.edu). RNA Sequencing: At the sequencing core, the RNA was re-assessed for quality using the TapeStation automated sample processing system (Agilent, Santa Clara, CA) and only samples with RNA integrity numbers (RINs) of >8 were included in the analysis. The cDNA library was constructed using 0.1-3ug of total RNA and the Illumina TruSeq Stranded mRNA Library Preparation kit (Catalog #s RS-122-2101, RS-122-2102) (Illumina, San Diego, CA). The final cDNA libraries were checked for quality once again by TapeStation (Agilent) as well as qPCR through the use of Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835, Kapa Biosystems,Wilmington MA). The samples were clustered on a cBot automated cluster generation system (Illumina) for clonal amplification. The samples were then hybridized to the slide (“flow cell”) of a HiSeq 2000 (Illumina) and underwent non-stranded short read (50-bp length) single-end sequencing in High Output mode using version 3 reagents. RNA-Seq Data Preprocessing: Following sequencing and demultiplexing, the RNA-Seq reads were aligned to the rat genome (Rnor_6.0) using the SubRead aligner (Liao et al. 2014, Bioinformatics. 30: 923–930) using default parameters with the exception of indel detection (maximum length of indel that can be detected=0). The featureCounts program (Liao et al. 2014, Bioinformatics. 30: 923–930) then generated the gene-level RNA-Seq count summaries for each sample based on ENSEMBL annotation (Ensembl v.85). This RNA-Seq count summary dataset was then filtered to exclude rows of data from genes that did not meet a minimum threshold of 5 samples with greater than or equal to 16 counts. Our current analysis used the log2 fragments per million gene-level summary output for each sample provided by the voom() function (R package limma; Ritchie et al. 2015, Nucleic Acids Res. 43: e47). Quality control included 1) visualization of the overall log (base2) transformed transcript expression across all subjects via boxplot, 2) examination of the overall reads (mean and standard deviation) per subject, 3) visualization of a subject/subject correlation matrix to identify particularly atypical samples (R<.95). No outlier samples were identified.
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| Contributor(s) |
Hagenauer MH, Aydin C, Meng F, Birt IA, Watson SJ, 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 12, 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 (10)
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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 |
PRJNA589093 |
| SRA |
SRP229627 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE140287_MBNI_RNASeq_F43.csv.gz |
919.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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