Long read sequencing of human dorsal root ganglia

Asta Arendt-Tranholm, Ph.D.
Juliet M Mwirigi, Ph.D.
Theodore Price, Ph.D.

Long read sequencing was used to identify and characterize the isoforms expressed in the human dorsal root ganglion (hDRG). PacBio IsoSeq circular consensus sequencing was used on 3 hDRGs from 3 human organ donors.

Updated on April 6, 2024 (Version 2)

Corresponding Contributor:

Asta Arendt-Tranholm
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Dataset Overview

Study Purpose: This study was conducted to characterize RNA isoforms expressed in the human dorsal root ganglia (hDRG), with the goal of creating a resource to identify novel isoforms of functionally relevant genes associated with somatosensation and nociception.

Data Collection: PacBio long read sequencing was performed on 3 DRGs from 3 human organ donors. Isoforms were identified by mapping to the GRCh38 human reference genome. Sequence information and isoform abundance was obtained.

Primary Conclusion: Novel RNA isoforms of genes relevant in pain processing are identified in the hDRG including ASIC3, MRGPRX1 and HNRNPK.

Curator's Notes

Experimental Design: Lumbar dorsal root ganglia were obtained from three organ donors with no known history of chronic pain within 4 hours of cross-clamp and immediately frozen. RNA extraction was performed with the RNeasy Plus Universal Mini kit, followed by library preparation using the PacBio Iso-Seq Express kit. Samples were stored at -80°C and shipped on dry ice for analysis at the UC Davis core facility. Sequencing was carried out on the Sequel II instrument. Raw sequencing data were processed through the PacBio Iso-Seq pipeline. Isoforms were identified by mapping to the GRCh38 human reference genome, and sequence information along with isoform abundance was obtained.

Completeness: This dataset is part of a larger study titled "RNA isoform expression landscape of the human dorsal root ganglion (DRG) generated from long read sequencing."

Subjects & Samples: Samples from male (n=1) and female (n=2) human donors were used in this study.

Primary vs. derivative data: The Primary data folder is organized by subject and sample name and contains isoform expression quantification provided in a text file. Information for each sequence identified in the pooled samples was uploaded in a GFF format and is stored in the pool-1 folder. The derivative data folder contains summarized, fully analyzed data, including validated coding isoforms, 763 novel isoforms, top 100 expressed isoforms, and markers for both neuronal and non-neuronal isoforms.


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Publishing history

March 15, 2024
Originally Published
April 6, 2024 (Version 2)
Last Updated

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