Transcriptomics,Genomics

Dataset Information

102

Hippocampal subfield transcriptomic profiles: Regional vulnerability to age and cognitive impairment


ABSTRACT: The current study employed next-generation RNA sequencing to examine gene expression related to brain aging and cognitive decline. Young and aged rats were trained on a spatial episodic memory task. Hippocampal regions CA1, CA3 and the dentate gyrus (DG) were isolated. Poly-A mRNA was examined using two different platforms, Illumina and Ion Proton. The Illumina platform was used to generate lists of genes that were differentially expressed across regions, ages, and in association with cognitive function. The gene lists were then retested using the Ion Proton platform. 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. Finally, for the memory task used, impaired performance of aged animals was linked to the regulation of Ca2+ and synaptic function in region CA1. Overall design: The study contains a total of 10 young (5-6 months) and 24 aged (17-22 months) Fischer 344 male rats which were used to investigate expression patterns associated with aging and behavior. Prior to gene analysis, the animals were characterized on an episodic memory task across two academic institutions to test the reliability of the task (University of Florida: 5 young rats and 13 aged rats; University of Arizona: 5 young rats and 11 aged rats). Following total RNA isolation for the CA1, CA3 and DG regions, next-generation sequencing (NGS) libraries were prepared for two platforms, Illumina and Ion Proton. For both platforms, poly-A selection of mRNA was performed followed by library preparation protocols for each NGS system. In addition, whole transcriptome sequencing in Illumina was also performed using the ribominus method to investigate differential expression of additional RNA species across the hippocampus. This Series includes only the samples examined using the Ion Proton platform.

INSTRUMENT(S): Ion Torrent Proton (Rattus norvegicus)

SUBMITTER: Thomas C Foster  

PROVIDER: GSE97608 | GEO | 2017-12-08

SECONDARY ACCESSION(S): PRJNA382422

REPOSITORIES: GEO

altmetric image

Publications

Hippocampal Transcriptomic Profiles: Subfield Vulnerability to Age and Cognitive Impairment.

Ianov Lara L   De Both Matt M   Chawla Monica K MK   Rani Asha A   Kennedy Andrew J AJ   Piras Ignazio I   Day Jeremy J JJ   Siniard Ashley A   Kumar Ashok A   Sweatt J David JD   Barnes Carol A CA   Huentelman Matthew J MJ   Foster Thomas C TC  

Frontiers in aging neuroscience 20171208


The current study employed next-generation RNA sequencing to examine gene expression differences related to brain aging, cognitive decline, and hippocampal subfields. Young and aged rats were trained on a spatial episodic memory task. Hippocampal regions CA1, CA3, and the dentate gyrus were isolated. Poly-A mRNA was examined using two different sequencing platforms, Illumina, and Ion Proton. The Illumina platform was used to generate seed lists of genes that were statistically differentially exp  ...[more]

Similar Datasets

| GSE101798 | GEO
| GSE97612 | GEO
2009-11-01 | GSE14723 | GEO
2007-11-06 | E-GEOD-3531 | ArrayExpress
2006-06-30 | GSE3531 | GEO
2009-11-01 | GSE14725 | GEO
2009-11-01 | GSE14724 | GEO
2016-05-17 | E-GEOD-75772 | ArrayExpress
| PRJNA93585 | ENA
2010-04-15 | GSE11697 | GEO