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| Status |
Public on Dec 08, 2017 |
| Title |
Next-Generation sequencing of the hippocampus transcriptome in aged and cognitive impaired rats |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The current study employed next generation RNA sequencing using two different platforms (Illumina and Ion Proton) to examine gene expression differences related to brain aging, cognitive decline, and hippocampus subregions (CA1, CA3, DG). Young and aged rats were trained on a spatial episodic memory task. The results describe regional differences in gene expression and point to regional differences in vulnerability to aging. Aging was associated with increased expression of immune response related genes, particularly in the dentate gyrus. For the memory task, impaired performance of aged animals was linked to the regulation of Ca2+ and synaptic function in region CA1. Finally, we provided a transcriptomic characterization of the three subregions regardless of age or cognitive status, highlighting and confirming a correspondence between cytoarchitectural boundaries and molecular profiling.
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| Overall design |
Male Fisher 344 rats of two ages, young (5-6 months, total n = 10; n = 5 AZ, n = 5 FL) and aged (17-22 months, total n = 24; n = 11 AZ, n = 13 FL) were obtained from National Institute on Aging's colonies (Taconic, FL; Charles River, AZ). Animals were maintained on a 12:12 hour light/dark schedule, and provided ad libitum access to food and water prior to the set shifting task. The Morris Water Maze test was conducted, and behavioural data were acquired with either Noldus EthoVision computer tracking software (Noldus Information Technology, (Leesburg, VA) in FL or AnyMaze (Wood Dale, IL) in AZ) and included path-length and time in the goal and opposite quadrants. Two weeks following water maze testing, rats were anesthetized with isoflurane (Piramal Healthcare), decapitated and the brain was rapidly removed. The hippocampus was isolated, a 1-2 mm slice was removed from the dorsal hippocampus, and the CA1, CA3 and dentate gyrus (DG) regions were dissected [1, 8]. The collected tissue was immediately frozen in liquid nitrogen and stored in -80ºC until processed.
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| Web link |
https://doi.org/10.3389/fnagi.2017.00383
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| Contributor(s) |
Ianov L, De Both M, Chawla MK, Rani A, Kennedy AJ, Piras IS, Day JJ, Siniard A, Kumar A, Sweatt JD, Foster TC, Barnes CA, Huentelman MJ |
| Citation(s) |
29276487 |
| Submission date |
Jul 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Matthew Huentelman |
| Organization name |
TGen
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| Department |
Neurogenomics
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| Lab |
Huentelman
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| Street address |
445 N 5th St
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| City |
Phoenix |
| State/province |
AZ |
| ZIP/Postal code |
85004 |
| Country |
USA |
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| Platforms (1) |
| GPL18694 |
Illumina HiSeq 2500 (Rattus norvegicus) |
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| Samples (102)
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| Relations |
| BioProject |
PRJNA395547 |
| SRA |
SRP113452 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE101798_AZ_WT_normalizedCounts.csv.gz |
13.5 Mb |
(ftp)(http) |
CSV |
| GSE101798_AZ_mRNA_normalizedCounts.csv.gz |
13.7 Mb |
(ftp)(http) |
CSV |
| GSE101798_UF_mRNA_normalizedCounts.csv.gz |
14.5 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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