To obtain high-resolution clusters within the DRG neuron subset in all species-specific data, we first removed all non-neuronal nuclei barcodes, and then nuclei that express any satellite glial specific transcripts (Plp1 < 1 & Mpz < 1 & Sparc < 1) were removed. The resulting digital gene-expression matrix (DGE) was carried forward for clustering.
We annotated different subsets of large diameter myelinated A-LTMRs using Nefh, Slc17a7, Pvalb, Spp1, Calb1, Ntrk3, Scn5a, Ntrk2, Necab2, Cntnap2, and Fam19a1. Non-peptidergic C-fiber nociceptors(NPs) subsets were annotated using Gfra1, Gfra2, Trpc3, Lpar3, Mrgpra3, Mrgprd, Sst, Il31ra, Nppb, Trpv1, Trpa1, Ret, Scn10a, Scn11a, P2rx3, and Plxnc1. C-fiber peptidergic nociceptors (PEPs) subsets were annotated using Tac1, Adcyap1, Gal, Kit, Calca, Ntrk1, Trpa1, Scn10a, and Scn11a. Cold thermoreceptor subsets were annotated using Trpm8, Tac1, Foxp2, Cdh8, Penk, and Piezo2. Finally, C-LTMRs were annotated using Th, Slc17a8, Fam19a4, P2ry1, Gfra2, Piezo2, and Zfp521/ZNF521.
To avoid having one species dominate the downstream analyses including integration and to account for potential differences in each species’ clustering resolution, we downsampled the number of nuclei to have similar numbers across species at each DRG subtype cluster (e.g., A-LTMRs, PEPs, NPs, C-LTMRs) using the ‘downsample’ argument in the ‘subset()’ function of SeuratV3. These downsampled DGEs were used for cross-species cell-type mapping analyses including MetaNeighbor and Integration.
We annotated different subsets of large diameter myelinated A-LTMRs using Nefh, Slc17a7, Pvalb, Spp1, Calb1, Ntrk3, Scn5a, Ntrk2, Necab2, Cntnap2, and Fam19a1. Non-peptidergic C-fiber nociceptors(NPs) subsets were annotated using Gfra1, Gfra2, Trpc3, Lpar3, Mrgpra3, Mrgprd, Sst, Il31ra, Nppb, Trpv1, Trpa1, Ret, Scn10a, Scn11a, P2rx3, and Plxnc1. C-fiber peptidergic nociceptors (PEPs) subsets were annotated using Tac1, Adcyap1, Gal, Kit, Calca, Ntrk1, Trpa1, Scn10a, and Scn11a. Cold thermoreceptor subsets were annotated using Trpm8, Tac1, Foxp2, Cdh8, Penk, and Piezo2. Finally, C-LTMRs were annotated using Th, Slc17a8, Fam19a4, P2ry1, Gfra2, Piezo2, and Zfp521/ZNF521.
To avoid having one species dominate the downstream analyses including integration and to account for potential differences in each species’ clustering resolution, we downsampled the number of nuclei to have similar numbers across species at each DRG subtype cluster (e.g., A-LTMRs, PEPs, NPs, C-LTMRs) using the ‘downsample’ argument in the ‘subset()’ function of SeuratV3. These downsampled DGEs were used for cross-species cell-type mapping analyses including MetaNeighbor and Integration.
Free full text: Click here
