GSM5800182: TG, JAK-FT (GEX); Mus musculus; RNA-Seq
4-8 mice were pooled per sample; all mice used in this experiment were females. Mice were euthanized and fresh thoracic dorsal root ganglia, nodose ganglia, and trigeminal ganglia were immediately processed to yield single nuclei suspensions. Trigeminal ganglia were further enriched for neuronal nuclei by labeling with rabbit polyclonal anti-NeuN antibody (ABN78, Sigma) followed by MACS purification. The flow through containing the neuron-depleted fraction (FT) was sequenced separately from the eluate containing the neuron-enriched fraction (N). Multiome 3v3.1 GEX and ATAC libraries were prepared as recommended by the 10x Genomics ChromiumNextGEM Multiome_ATAC_GEX_User_Guide_RevD (CG000338_ChromiumNextGEM_Multiome_ATAC_GEX_User Guide_RevD.pdf).  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle, 16 rxns PN-1000283, Chromium Next GEM Chip J Single Cell Kit, 48 rxns PN-1000234, Single Index Kit N Set A, 96 rxns PN-1000212 (ATAC), Dual Index Kit TT Set A, 96 rxns PN-1000215 (3v3.1 GEX), were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  GEX libraries were pooled and run over 0.05 of a NovaSeq6000 S4 flow cell using the XP workflow and running a 28x10x10x150 sequencing recipe in accordance with manufacturer's protocol.  Target coverage was 500M reads per sample.  ATAC libraries were pooled and run over 0.167 of a NovaSeq6000 S1 flow cell using the XP workflow and running a 51x8x16x51 sequencing recipe in accordance with manufacturer's protocol.  Target coverage was 250M reads per sample.