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SRX2851953: GSM2640298: AMC5_RNAseq; Rattus norvegicus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 25.1M spots, 1.3G bases, 762.1Mb downloads

Submitted by: NCBI (GEO)
Study: Integrative epigenomic analyses of early-life hypothalamic response to augmented maternal care [RNA-seq]
show Abstracthide Abstract
The quality of maternal care in early-life plays a crucial role in mammalian neurodevelopment. Augmented maternal care (AMC) is a well-established rodent model of enhanced neonatal care. Rats that have undergone AMC have improved stress resilience and cognition compared with rats that have experienced normal levels of maternal care or adverse neonatal stress. However, the epigenomic basis of long-lived responses to AMC has not been previously explored. Thus, we employed whole-genome bisulfite sequencing (WGBS), RNA-sequencing (RNA-seq), and a multiplex microRNA (miRNA) assay to assess DNA cytosine methylation, gene expression, and miRNA expression, respectively. The integrated results identify a suite of 20 prioritized candidates impacted by AMC. Overall, these results identified AMC-induced regulatory differences in genes related to neurotransmission, neurodevelopment, protein synthesis, and oxidative phosphorylation in addition to the expected stress response genes. Together, these unbiased results represent a key progression in understanding the complex mechanisms underlying the early-life mechanisms for AMC programming stress resiliency. Overall design: DNA methylation and RNA were assayed in augmented maternal care male rats as well as controls.
Sample: AMC5_RNAseq
SAMN07163653 • SRS2223815 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 2500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Extracted and purified using the Qiagen RNeasy kit Total RNA was isolated from AMC and control hypothalamus using the RNeasy Kit (Qiagen, Valencia, CA). Total RNA samples were then processed with a Gene Read ribosomal RNA depletion kit (Qiagen, Germantown PA) prior to Illumina Hi-Seq library preparation using a directional RNA-seq library kit (NEB, Ipswich, MA). Libraries were checked by Bioanalyzer analysis (Agilent, Santa Clara, CA) for quality, then 50 base pair, single end reads were acquired on a Hi-Seq 2500 (Illumina, San Diego, CA) at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkley.
Experiment attributes:
GEO Accession: GSM2640298
Links:
Runs: 1 run, 25.1M spots, 1.3G bases, 762.1Mb
Run# of Spots# of BasesSizePublished
SRR559764625,135,3821.3G762.1Mb2019-04-22

ID:
4091148

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