Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 69
Release date: Mar 25 2017
Last update date: Nov 30 2018
Access: Public
Chemicals: Ethanol
Dataset link Alignment of the Transcriptome with Individual Variation in Animals Selectively Bred for High Drinking-In-the-Dark (HDID).

Experimental Protocol


S27 HDID-1 selected line began with a “within family” selection design but was switched to mass selection at S5. All animals were on reversed light-dark cycle. Animals underwent the standard 4-day DID trial with three 2 hour exposures to a single bottle of 20% ethanol and a final day of 4 hour exposure. The DID trial always began 3 hours into the dark phase. BECs were obtained at the end of the 4th hour. A subgroup (N=20) of the animals were retested 3 weeks later. The remaining animals, 18 males and 17 females were sacrificed 3 weeks later and used for gene expression analyses. All animals were sacrificed between 10 AM and 2 PM. Mice were euthanized, brains removed and immediately frozen on dry ice. Frozen brains were slightly thawed and dissected by hand under RNAse-free conditions. Using the optic chiasm as the rostral marker, a 2 mm coronal slice of brain tissue was isolated. Beginning at the medial ventral aspect of the striatum and recognizing that the striatum has a partial cone shape, the dissection moved dorsal 1 mm, followed by a cut to the lateral boundary of the striatum, with a final cut following the lateral-ventral boundary. The isolated tissue was immediately placed into 1 ml of Trizol (Invitrogen, Carlsbad, CA).Among animals at risk for excessive ethanol consumption such as the HDID selected lines, there is considerable individual variation in the amount of ethanol consumed and the associated blood ethanol concentrations (BECs). For the HDID lines, this variation occurs even though the residual genetic variation associated with the DID phenotype has been largely exhausted and thus is most likely associated with epigenetic factors. Here we focus on the question of whether the genes associated with individual variation in HDID-1 mice are different from those associated with selection (risk) (Iancu et al. 2013). Thirty-three HDID-1 mice were phenotyped for their BECs at the end of a standard DID trial, were sacrificed 3 weeks later and RNA-Seq was used to analyze the striatal transcriptome. The data obtained illustrated that there is considerable overlap of the risk and variation gene sets; both focus on the fine tuning of NMDA mediated synaptic plasticity.

Repositories


GEO

GSE97032

ENA

SRP102454

BioProject

PRJNA380430

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Contact


Ovidiu Iancu