Spatial transcriptomics of human dorsal root ganglia from subjects with a history of diabetes

Study Purpose: This study was conducted to study the transcriptome of dorsal root ganglia tissue in subjects with a history of diabetes.

Data Collection: Visium spatial RNA sequencing was performed on 16 human dorsal root ganglia (DRG) tissue sections collected from 7 different DRGs, from 6 human subjects with a history of diabetes.

Primary Conclusion: Our findings solve a 100-year mystery of the nature of Nageotte nodules linking these pathological structures to pain and sensory loss in diabetic peripheral neuropathy (DPN).

Curator's Notes

Experimental Design: All human tissue procurement procedures were approved by the Institutional Review Boards at the University of Texas at Dallas. Human DRGs were procured from organ donors through a collaboration with the Southwest Transplant Alliance. RNA sequencing of human dorsal root ganglia (DRG) was performed using the 10X Genomics Visium platform. Fresh frozen DRG samples were stored at -80°C, embedded in OCT, and sectioned (10 µm) onto Visium Spatial Slides per Demonstrated Protocol CG000240. After imaging and coverslip removal, slides were processed for library construction and sequenced at the UTD Genome Center. Raw data were processed with the 10X SpaceRanger pipeline to generate gene expression count matrices. Barcodes of interest were selected in Loupe Browser, and downstream analysis was performed in R (version 4.3.3).

Completeness: This dataset is complete.

Subjects & Samples: Samples from male (n=5) and female (n=1) human donors were used in this study.

Primary vs derivative data: The Primary data folder is organized by subject and sample name and contains Cell Ranger pipeline output. Sequencing data were processed and mapped to the human (GRCh38) genome using the 10X Genomics Cellranger pipeline (for details on version, please refer to metadata_nageotteSamples_SPARC.docx). Each sample folder contains processed gene expression data (raw and filtered), visualization files compatible with Loupe Browser, and barcode annotations. The dataset does not contain raw sequencing data. There is no derivative data folder.

Important Notes: This dataset is associated with a publication preprint, "Nageotte nodules in human DRG reveal neurodegeneration in painful diabetic neuropathy," and contributed to the overall findings on Nageotte nodules and their involvement in pain and sensory loss in diabetic peripheral neuropathy (DPN). doi: https://doi.org/10.1101/2024.08.22.609215

Code Availability: The Code folder contains analysis scripts and pipelines used for processing, visualization, and downstream analysis of the spatial gene expression data.