snRNAseq of mouse dorsal root ganglia (DRG) to identify which cell types express a virally induced transgene

Single nuclei dataset of mouse dorsal root ganglion cells (DRG) to identify which cell types express a virally induced transgene. Mice where either i.t. injected with the virus or kept uninjected as controls. 

Protocol for nuclei extraction: Yang L. et al. 2021, Bio-protocol, DOI: 10.21769/BioProtoc.4102 

Cell type annotation done with help from: Renthal et al. 2020, doi: 10.1016/j.neuron.2020.07.026 

Experimental setup:

2 mice where injected with the AAV expressing the transgene or kept naive as controls. After 3 weeks all DRGs from the mice were dissected and flash frozen on dry ice. For each condition two mice were pooled. The DRG tissue was stored at -80C until nuclei extraction and 10X genomics sequencing.

The experiment was done as part of the revisions for https://www.biorxiv.org/content/10.1101/2023.03.03.530962v2. 

Data structure:

Here we have uploaded the CellRanger output before and after filtering together with the conos objects (con_neurons.qs and con_other.qs) for analysis in R. In the conos objects the dataset is split into neuronal and non_neuronal cells. The cluster annotations are found in the excel sheets named con_neurons_cluster annotation and con_other_cluster_annotation. 

In the dataset the transgene is named GCN4