organism: Rattus norvegicus
description: Protocols: 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: ENA-FIRST-PUBLIC
attributes.value: 2020-03-01T04:03:13Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2020-01-09T17:26:35Z
attributes.tag: External Id
attributes.value: SAMEA6462950
attributes.tag: INSDC center name
attributes.value: UZH
attributes.tag: INSDC first public
attributes.value: 2020-03-01T04:03:13Z
attributes.tag: INSDC last update
attributes.value: 2020-01-09T17:26:35Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8647:Sample 27
attributes.tag: age
attributes.value: 67
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: common name
attributes.value: Norway rat
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: environmental stress
attributes.value: control
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: individual
attributes.value: s29
attributes.tag: organism part
attributes.value: brain
attributes.tag: phenotype
attributes.value: control
attributes.tag: sample name
attributes.value: E-MTAB-8647:Sample 27
attributes.tag: sampling site
attributes.value: left dorsal hippocampus
attributes.tag: scientific_name
attributes.value: Rattus norvegicus
attributes.tag: sex
attributes.value: male
attributes.tag: stimulus
attributes.value: saline
attributes.tag: strain
attributes.value: Sprague-Dawley