title: Illumina HiSeq 2000 paired end sequencing; LincRNAs involved in DCS-induced fear extinction: Shedding light on the transcriptomic dark matter
design: LincRNAs involved in DCS-induced fear extinction: Shedding light on the transcriptomic dark matter
library_name: Sample 26_p
library_construction_protocol: Fear conditioning consisted of an electric foot shock; fear extinction consisted of behavioural fear extinction co-administered with either DCS or saline (intra-hippocampal). The light/dark avoidance test was used to evaluate anxiety-related behaviour that persisted after fear extinction, to subsequently group animals into well-adapted and maladapted subgroups used in the analyses.  These sub-groups included: control animals that received intra-hippocampal saline (CS, modelling a human control group); (ii) fear-conditioned animals that received intra-hippocampal saline (FS) and were maladapted (FSM, thus modelling a PTSD-like group), fear-conditioned animals that received intra-hippocampal DCS (FD) and were well-adapted (FDW, modelling a patient group exhibiting effective fear extinction due to treatment). We focussed on two sets of sub-group comparisons, namely the FSM vs. CS (modelling the fear conditioning process by comparing a PTSD-like group to controls) and FDW vs. FSM (modelling the fear extinction process by comparing a group that exhibit effective treatment-induced fear extinction to a PTSD-like group).  DCS and saline were administered intrahippocampally via indwelling guide cannulas, 30 min prior to the initiation of each fear extinction protocol for 6 consecutive days (postnatal day [PND] 62–67). Cannulas were surgically implanted on PND 59. Rats were anaesthetised by intraperitoneal injection of ketamine hydrochloride (Anaket-V, Bayer Healthcare, South Africa) and medetomide hydrochloride (Domitor, Pfizer, South Africa) (0.1 ml/100 g). Anaesthetised rats were placed in a David Kopf stereotaxic instrument. After exposing the skull, holes were drilled the precise coordinates obtained from the rat brain atlas of Paxinos and Watson corresponding to the target area (left and right dorsal hippocampus). RNA was isolated from the LDH simultaneously with DNA, but in separate fractions, using the RNeasy Plus Mini Kit (Qiagen, Hilden Germany) in conjunction with the RNeasy MinElute Cleanup Kit (Qiagen, Hilden Germany). The quantity and quality of the extracted RNA were assessed using the RNA Nano 6000 kit (Agilent Technologies, California, USA) on the 2100 Bioanalyzer platform (Agilent Technologies, California, USA). An RNA sample with a RIN value higher than 7 was regarded as good quality. One microgram of RNA was used as starting material for the sample preparation with the TruSeq RNA Sample Preparation Kit v2 (Illumina, California, USA).
attributes.tag: Experimental Factor: environmental stress
attributes.value: control
attributes.tag: Experimental Factor: stimulus
attributes.value: saline
attributes.tag: Experimental Factor: phenotype
attributes.value: control