Spatial transcriptomics of human C2 dorsal root ganglia tissue from fusion surgeries
Visium spatial RNA sequencing was performed on 16 dorsal root ganglia from 8 patients (left and right of same level) undergoing C1-C2 fusion surgery.
Dataset Overview
Study Purpose: In this study we used spatial transcriptomics to characterize the transcriptome of C2 hDRGs and characterize the differences in patients with chronic pain.
Data Collection: 10X Visium spatial transcriptomics was performed on C2 DRG tissue collected from patients with acute or chronic pain during atlanto-axial fusion/arthrodesis surgery.
Primary Conclusion: We present a spatial transcriptomic characterization of the cervical hDRG transcriptome and identify distinct expression patterns of METRN, FGFBP2, SLCO2A1
Curator's Notes
Experimental Design: C2 dorsal root ganglia were collected from patients undergoing atlanto-axial fusion/arthrodesis surgery and immediately flash frozen in the operating room before storage at -80°C. Tissues were shipped to UTD on dry ice for processing. Fresh frozen tissue samples were sectioned and processed using 10X Visium Spatial Gene Expression kits with poly-A tail based mRNA sequencing. Tissue sections underwent fixation, hematoxylin and eosin staining, and imaging before cDNA amplification and library construction. Raw sequencing files were processed with the 10X Genomics SpaceRanger pipeline to generate count matrices of gene expression per Visium barcode. Gene expression analysis was performed using R version 4.3.3 for downstream processing, with Loupe Browser used to select barcodes of interest.
Completeness: This dataset is a part of a larger study: "Transcriptome of the human C2 dorsal root ganglia in C1-2 arthrodesis surgery: insight for neck pain."
Subjects & Samples: Female (n=3), male (n=5) human patients (ages 57-86 years) undergoing arthrodesis surgery were used in this study.
Primary vs derivative data: Primary data is organized by subject folders containing left (DRGL) and right (DRGR) DRG sample folders. Each sample contains 10X Visium spatial transcriptomics outputs including filtered and raw feature-barcode matrices (HDF5 format), Loupe Browser files (.cloupe), and spatial folders with tissue images (high and low resolution PNG/JPG), fiducial alignment files, scale factors (JSON), tissue position coordinates, and spatial enrichment analysis (CSV). There is no derivative data folder.
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Is Supplemented by
P Hofstetter, C., Tran, N., & Payne, C. (2024). Human Tissue Procurement from Atlanto-Axial Fusion Surgery v1. https://doi.org/10.17504/protocols.io.eq2lywoervx9/v1
Shiers, S., Tavares-Ferreira, D., Sankaranarayanan, I., Mazhar, K., & Price, T. (2024). Spatial RNA sequencing of human ganglia v1. https://doi.org/10.17504/protocols.io.j8nlk8jb6l5r/v1
Curatolo, M., Payne, C., Chiu, A. P., Tran, N. T., Yap, N., Hofstetter, C. P., Lesnak, J. B., Arendt-Tranholm, A., Price, T. J., Jarvik, J. G., & Turner, J. A. (2025). Patient phenotyping for molecular profiling of neck and low back pain – Study protocol. Neurobiology of Pain, 18, 100186. https://doi.org/10.1016/j.ynpai.2025.100186
Described by
Arendt-Tranholm, A., Sankaranarayanan, I., Payne, C., Mancilla Moreno, M., Mazhar, K., Yap, N., Chiu, A. P., Barry, A., Patel, P. J., Inturi, N. N., Tavares-Ferreira, D., Amin, A., Karandikar, M., Jarvik, J. G., Turner, J. A., Hofstetter, C. P., Curatolo, M., & Price, T. J. (2025). Transcriptome of the human C2 dorsal root ganglia in C1-2 arthrodesis surgery: insight for neck pain. Brain. https://doi.org/10.1093/brain/awaf370
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