2.4. Bioinformatic analyses

Next, three lists of poly(A) RNAs were created that were differentially regulated in two of our comparisons. This revealed genes that were 1) dysregulated after injury and then normalized with NT3 treatment, 2) dysregulated after injury and not normalised with NT3 treatment, 3) not dysregulated after injury, but dysregulated with NT3 treatment (Supplementary Tables 6-8).

To identify genes that might be regulated in TrkC+ neurons by NT3 in our experiment, we next took advantage of a publicly available microarray dataset ({"type":"entrez-geo","attrs":{"text":"GSE38074","term_id":"38074"}}GSE38074) containing information about expression of mRNAs (but lacking information about small RNAs) in fluorescence-activated cell sorted TrkC⁺ neurons from the postnatal day 0 DRG either of mice with increased muscular NT-3 (mlcNT3 versus wildtype control; n = 2/group) or of mice lacking NT-3 (on a Bax knockout background to prevent cell death during development; NT3KO BaxKO versus BaxKO; n = 2/group) [2]. We sought genes whose levels correlated positively with NT3 levels in these two comparisons and in bPYX+NT3 versus bPYX+GFP.