Bulk RNA sequencing of human C2 dorsal root ganglia tissue from fusion surgeries

Study Purpose: In this study we used bulk RNAseq to characterize the transcriptome of cells in the C2 DRGs and characterize the differences in patients with chronic pain.

Data Collection: Illumina bulk RNAseq was performed on C2 DRG tissue collected patients with acute or chronic pain during atlanto-axial fusion/arthrodesis surgery.

Primary Conclusion: We identify transcriptomic changes in the C2 DRG recovered from patients undergoing fusion surgery for acute or chronic pain. Fourty genes were differentially expressed, 17 of which were upregulated in chronic pain.

Curator's Notes

Experimental Design: C2 dorsal root ganglia (DRGs) were collected during bilateral C2 DRG neurectomy procedures following C1 lateral mass screw and C2 pars screw placement for spinal fixation. DRGs were immediately placed in powdered dry ice to preserve RNA integrity and shipped for sequencing analysis. RNA was extracted from three 100μm sections using TRIzol lysis and chloroform extraction, followed by DNA depletion with Qiagen DNase I. RNA integrity was assessed using nanodrop and Qubit, with samples having RNA integrity numbers of 2.4-8.1 selected for paired-end mRNA sequencing on NextSeq2000. Bulk RNA sequencing data was processed using an automated workflow pipeline to assess transcriptomic differences associated with pain phenotype.

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: (DRGs) were collected from 13 donors (ages 49-88 years; 9 male, 4 female) with 17 samples total (5 with chronic pain and 8 with acute pain) during bilateral C2 DRG neurectomy procedures.

Primary vs derivative data: The primary data is organized by subject ID and subsequently by sample ID. Each folder contains CSV files with raw gene counts from the bulk RNA sequencing analysis pipeline. Raw sequencing data is not included. There is no derivative data folder.

Code Availability: The automated workflow pipeline for analyzing and processing Bulk-RNA seq data is available at https://github.com/utdal/Bulk-RNA-Seq-Nextflow-Pipeline