| title | author | date | output |
|---|---|---|---|
datasetsummary |
amb |
22/08/2021 |
html_document |
DRG subpopulation RNAseq
Spared nerve injury (SNI) was performed on transgenic animals, each labelling one of five sensory neuron subtypes of interest (general nociceptors (Scn10a), peptidergic (PEP, Calca) and non-peptidergic (NP, Mrgprd) nociceptors, C-LTMRs (Th), and AB-RA + Ad-LTMRs (Ntrk2)). Paired ipsilateral and contralateral lumbar DRG samples were then collected 3 days (3D) and 4 weeks (4W) after surgery. In each condition, both male and female samples were collected to enable sex analyses. Together, 160 samples were collected, with 154 passing QC.
Spared nerve injury (SNI) is one of many neuropathic injury models used. Here, it was selected as a localized model of neuropathic pain with an internal control (contralateral, uninjured tissue). SNI is a behaviourally relevant animal model, with sensory dysfunction similar to that in neuropathic pain patients.
Reads were mapped to the GRCm38 genome using STAR alignment and Samtools was used to sort, index, and merge BAM files. Quality control (QC) was performed with both FastQC and Samtools prior to gene counting with HTSeq. Count corrections for effective library sizes were performed in R using DESeq2, and normalized gene counts were fitted to a negative binomial distribution. Count transformations were performed using VST.
Hypothesis testing was performed on filtered using the Wald test and a weighted FDR correction (independent hypothesis weighting, IHW). Count data was first filtered to genes with an average of 5 reads in at least 10% of the samples.Full methodology can be seen in the published reports.