Transcription profiling of rat dorsal root ganglia from L5 spinal nerve ligation model of neuropathic pain
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ABSTRACT: DRG samples were extracted at 28 and 50 days from L5 spinal nerve ligated rats and sham operated rats. Samples were pooled for each time point per group and hybridised to duplicate to RG_u34 genchips (A, B and C chips). Experiment Overall Design: Samples were pooled and therefore no biological replication was possible on the arrays
Project description:DRG samples were extracted at 28 and 50 days from L5 spinal nerve ligated rats and sham operated rats. Samples were pooled for each time point per group and hybridised to duplicate to RG_u34 genchips (A, B and C chips). Keywords: Disease state analysis
Project description:Expression profiling of L4 and L5 Dorsal Root Ganglion (DRG) in the spinal nerve ligation model of neuropathic pain. The goal of the study was to identify genes involved in neuropathic pain This series of samples comprises of contralateral and ipsilateral L4 and L5 DRG tissue collected 4 weeks after rats underwent a L5 spinal nerve ligation (SNL) or a sham operation with no L5 spinal nerve ligation. This defines 8 groups (i) contralateral L4 DRG from the sham cohort (n=5), (ii) ipsilateral L4 DRG from sham cohort (n=5), (iii) contralateral L4 DRG from SNL cohort (n=5), (iv) ipsilateral L4 DRG from the SNL chort (n=5), (v) contralateral L5 DRG from the sham cohort (n=5), (vi) ipsilateral L5 DRG from sham cohort (n=5), (vii) contralateral L5 DRG from SNL cohort (n=5), (viii) ipsilateral L5 DRG from the SNL cohort (n=5)
Project description:Inflammation plays a role in neuropathic pain conditions as well as in pain induced solely by an inflammatory stimulus. Robust mechanical hyperalgesia and allodynia can be induced by locally inflaming the L5 dorsal root ganglion (DRG) in rat. This model allows investigation of the contribution of inflammation per se to chronic pain conditions. Most previous microarray studies of DRG gene expression have investigated neuropathic pain models involving axon transection. To examine the role of inflammation, we used microarray methods to examine gene expression 3 days after local inflammation of the L5 DRG in rat. We observed significant regulation in a large number of genes (23% of observed transcripts), and examined 221 (3%) with a fold-change of 1.5-fold or more in more detail. Immune-related genes were the largest category in this group and included members of the complement system as well as several pro-inflammatory cytokines. However, these upregulated cytokines had no prior links to peripheral pain in the literature other than through microarray studies, though most had previously described roles in CNS (especially neuroinflammatory conditions) as well as in immune responses. The L5 dorsal root ganglion (DRG) was locally inflamed with zymosan/Incomplete Freund's Adjuvant. DRG were isolated 3 days later. Each sample was RNA extracted from a single DRG. 6 samples from rats with local DRG inflammation were compared with 6 samples from sham-operated rats.
Project description:Poly(A) enriched RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to RNA-seq analysis at different sequencing depths
Project description:RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to microarray analysis and expression was determined at the exon and gene level 6 biological replicates (3 case – SNT subjected L5-DRG tissue, 3 control – naïve L5-DRG tissue). Each sample was made from pooling 4 distinct animals. Sample preparation and hybridization were performed by UCL genomics, following Affymetrix instructions. The 6 replicates were also used for RNA-seq, see GSE53762.
Project description:RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to microarray analysis and expression was determined at the exon and gene level 6 biological replicates (3 case – SNT subjected L5-DRG tissue, 3 control – naïve L5-DRG tissue). Each sample was made from pooling 4 distinct animals. Sample preparation and hybridization were performed by UCL genomics, following Affymetrix instructions. The 6 replicates were also used for RNA-seq, see GSE53762.
Project description:RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to microarray analysis and expression was determined at the exon and gene level
Project description:RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to microarray analysis and expression was determined at the exon and gene level
Project description:Poly(A) enriched RNA derived from the L5 DRG 7 days following L5-SNT and from naïve L5-DRG tissue was subjected to RNA-seq analysis at different sequencing depths 6 biological replicates (3 case – SNT subjected L5-DRG tissue, 3 control – naïve L5-DRG tissue). Each biological replicate was divided B46into 3 technical replicates; each of the technical replicates for a given sample was sequenced to a depth of 17M, 25M or 50M reads. Reads were single stranded and 34bps in length. Multiplexing was used in order to generate the read depths of different sizes. The gene expression values and fold changes in expression between naive and SNT samples were compared to those generated by a microarray experiment carried out on further technical replicates of the same samples, details in the manuscript (submitted - under revision).
Project description:Expression profiling of L4 and L5 Dorsal Root Ganglion (DRG) in the spinal nerve ligation model of neuropathic pain. The goal of the study was to identify genes involved in neuropathic pain