Illumina HiSeq 2500 paired end sequencing; Transcriptome responses to dexamethasone of the hypothalamus of pigs with different genotypes at the GRAla610Val mutation
Transcriptome responses to dexamethasone of the hypothalamus of pigs with different genotypes at the GRAla610Val mutation
The experiment procedures took place at approximately the same time (10:00 to 12:00 AM). Three hours after the treatment  of dexamethasone,  the animals were anesthetized by an intravenous (i.v.) administration of a combination of ketamine (Ursotamin; Serum-Werk Bernburg, Bernburg, Germany) and azaperone (Stresnil; Janssen-Cilag, Neuss, Germany), and euthanized by an i.v. administration of T61 (Intervet, Unterschleißheim, Germany). Tissue samples were quickly dissected (<10min), frozen in liquid nitrogen, and stored at -80ºC. The experimental protocol (7221.3-1-024/16) has been approved by the Animal Care Committee of the Leibniz Institute for Farm Animal Biology and the State Mecklenburg-Western Pomerania (Landesamt für Landwirtschaft, Lebensmittelsicherheit und Fischerei). 11 or 22 are genotypes of the pigs at the NR3C1 c.1829C>T (rs335303636, SNP) which 11 stands for homozygous CC and 22 stands for TT (Reyer et a. 2016; PMID 27736993) Total RNA was isolated using TRI reagent (Sigma-Aldrich, Taufkirchen, Germany). DNA traces were removed by DNaseI-treatment (Baseline-Zero DNase; Biozym, Hessisch Oldendorf, Germany), and the RNA was cleaned-up using the RNA Clean&Concentrator-25 Kit (Zymo Research, Freiburg, Germany). RNA quantity was determined using a Qubit fluorometer (ThermoFisher Scientific, Germany), and integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).  2 µg of total RNA with RIN > 8 was used for library preparation using a TruSeq Stranded mRNA Kit with 11 cycles of PCR-amplification according to the manufacture's recommendation (Illumina).
Experimental Factor: genotype
homozygous SNP NR3C1 c.1829CC
Experimental Factor: compound
none