Agilent rna 600 nano chip kit

After the last CSDS session, mice were singly housed for 1 week and killed by cervical dislocation between 8 a.m. and 11 a.m. Their medial prefrontal cortices (5 mm of either side of the midline between bregma 1.94—1.40) and ventral hippocampi (from bregma −3.40 to −3.88) were dissected on a chilled Petri dish and flash frozen in liquid N2. RNA was extracted with TriReagent (Cat# 15596026, Invitrogen™) followed by RNA quality control (2,100 Bioanalyzer, Agilent Technologies) using Agilent RNA 600 Nano Chip kit (Agilent Technologies).

Total RNA was extracted with TriReagent (Molecular Research Center Inc.) and RNA quality was assessed with a 2100 Bioanalyzer (Agilent Technologies) using Agilent RNA 600 Nano Chip kit (Agilent Technologies). rRNA was depleted with Ribo-Zero Gold rRNA Removal kit (Illumina Inc; mPFC and vHPC) or custom Insert Dependent Adaptor Cleavage (InDA-C) primers (BNST). RNA was fragmented using the S2 ultrasonicator (Covaris Inc.) and sequencing libraries were prepared with Nextera (Illumina; vHPC), ScriptSeq v2 (Epicentre; mPFC), or Ovation Universal RNA-Seq System (NuGEN; BNST) RNA-seq library preparation kits. Libraries were size-selected with Pippin Prep (Sage Science) and sequencing was conducted on HighSeq 2000 (vHPC, paired-end 91 bp, Illumina) or NextSeq 500 platforms (mPFC and BNST, single-end 96 bp; Illumina).
The RNA-seq reads were trimmed for adapters with Cutadapt v1.8.3 (vHPC) and FastX toolkit (mPFC, BNST) and PCR duplicates were removed with PRINSEQ v0.20.4. Reads were aligned using STARv 2.5.0c (Dobin et al., 2013 (link)) with default settings to mouse genome GRCm38, and annotated to gene exons with HTSeq v0.6.1 (Anders et al., 2015 (link)) using GTF release 86 (update 2016-10).