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SRX10660093: GSM5260874: 00078A1942_LHB; Rattus norvegicus; RNA-Seq
7 ILLUMINA (Illumina HiSeq 4000) runs: 24.3M spots, 2.4G bases, 906.7Mb downloads

Submitted by: NCBI (GEO)
Study: Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Lateral habenula]
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Research into the genetic influences of impulsivity and reward motivated behavior relies heavily on outbred animal populations, including Heterogeneous Stock (HS) rats, for the genetic diversity necessary to identify genotype-trait associations. Many such associations have been detected, but it is not always clear which gene or other feature near the identified genomic location is functionally responsible for the association. Since these traits are in part mediated by gene expression, mapping the associations between genotype and gene expression in these animals will enable the discovery and deeper understanding of these trait associations. We therefore obtained genotypes and RNA-Seq gene expression for five brain regions from 88 HS rats and mapped expression quantitative trait loci (eQTLs) for each region. We identified cis-eQTLs in over 3,000 genes per brain region and validated their effect sizes using allele specific expression. This resource will enable new discoveries of the genetic influences of complex behavioral traits. Overall design: mRNA profiles from 4-5 brain regions from each of 88 naïve HS rats
Sample: 00078A1942_LHB
SAMN18836063 • SRS8755076 • All experiments • All runs
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Selection: cDNA
Layout: SINGLE
Construction protocol: 1) Brain region dissection: Brains were taken out of a minus 80 degree freezer and cryosectioned into 60um sections, which were mounted onto RNase-free glass slides. Slides were stored in minus 80 degree until dissection. During dissection, slides were placed on a minus 20 degree cold plate. One drop (approximately 50 ul) of RNAlater was placed on the brain region of interest. Each brain region then was dissected out under a dissecting video camera by using a pair of fine tipped forceps with the assistance of an 18 gauge needle with a bent tip. Bilateral tissue of the same brain region from each rat was immediately transferred into 350 ul Buffer RLT (containing beta-mercaptoethanol) and placed on dry ice. Tissue was stored in minus 80 degree before RNA extraction. 2) RNA extraction: Tissue was thawed on ice and homogenized by using a clean stainless steel bead using Qiagen TissueLyser (40Hz, 3 min). AllPrep DNA/RNA mini kit (Qiagen) was used to extract RNA. Samples were processed by using the QIAcube robot following standard protocols. The optional DNase digestion step was included for RNA samples. RNA libraries were prepared for sequencing using standard Illumina protocols.
Experiment attributes:
GEO Accession: GSM5260874
Runs: 7 runs, 24.3M spots, 2.4G bases, 906.7Mb
Run# of Spots# of BasesSizePublished


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