Mar 05, 2024
Protocol for long read sequencing of dorsal root ganglia from human organ donors
- Asta Arendt-Tranholm1,
- Juliet M Mwirigi1,
- Theodore Price1
- 1University of Texas at Dallas
- PRECISION Human Pain Network
Protocol Citation: Asta Arendt-Tranholm, Juliet M Mwirigi, Theodore Price 2024. Protocol for long read sequencing of dorsal root ganglia from human organ donors. protocols.io https://dx.doi.org/10.17504/protocols.io.n92ldmxenl5b/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: January 29, 2024
Last Modified: March 05, 2024
Protocol Integer ID: 94335
Keywords: long read sequencing, human DRG
Funders Acknowledgements:
NIH
Grant ID: U19NS130608
Abstract
In this protocol, we describe how to extract RNA from dorsal root ganglia sourced from human organ donors, and subsequently perform long read sequencing with PacBio IsoSeq.
Materials
RNaseZap RNase Decontamination Solution - Invitrogen, Catalog #:AM9780
RNeasy Plus Universal Mini Kit - Qiagen, Catalog #:73404
Precellys Tissue Homogenizing Mixed Beads Kit - Cayman Chemical Company, Catalog #10409
PacBio Iso-Seq Express SMRTbell Library Template Preparation Kit 2.0: PacBio, Catalog #: 100-938-900
Before start
Required PPE: All work must be done wearing appropriate PPE including lab coat and gloves. Any work with TRIzol/QIAzol should be carried out inside of a fume hood. Clean pipettes and lab bench area with 70% ethanol, followed by RNase decontamination solution, such as RNaseZap, prior to carrying out RNA extraction.
Harvesting and storing human dorsal root ganglia
Harvesting and storing human dorsal root ganglia
Lumbar dorsal root ganglia (DRGs) are recovered from human organ donors with no known history of chronic pain, through a collaboration with the Southwest Transplant Alliance. DRGs are recovered within 4 hours of cross-clamp and immediately frozen in powdered dry ice.
Human DRG (hDRGs) are stored in a -80C freezer until use.
RNA extraction
RNA extraction
<50mg hDRG tissue is isolated and submerged in 1ml QIAzol from RNeasy Plus Universal Mini kit. The sample is homogenized using Precellys Tissue Homogenizing Mixed Beads Kit and 1min shake in the Bertin Technologies Minilys, until no visible pieces appear. Pipette lysate into new tube.
The sample is kept on ice between each step.
RNA extraction is performed with reagents from the RNeasy Plus Universal Mini kit from Qiagen including RNeasy mini spin-columns:
100ul gDNA eliminator is added, followed by rigorous shaking for 15 seconds
180ul chloroform is added, followed by rigorous shaking for 15 seconds
2-3minute incubation at room temperature
Centrifuge samples at 12,000g for 15 minutes at 4C using a Bio-Rad Model 16K Microcentrifuge
Transfer lysate to new tube and add 500ul 70% EtOH
Add 700ul sample at a time to RNeasy mini spin-column placed in 2ml collection tube
15 second centrifuge at full-speed (16,000g) until all lysate has been passed through spin-column and flow-through is discarded
Add 700ul Buffer RWT to spin-column
Centrifuge for 15 seconds at full-speed and discard flow-through from collection tube
Add 500ul RPE to spin-column
Centrifuge for 15 seconds at full-speed and discard flow-through from collection tube
Repeat step 4.10-4.11 two times but centrifuge for 2 minutes
Place spin-column in new collection tube and centrifuge for 1 minute at full-speed
Place spin-column in new Eppendorf for RNA storage (1.5ml tube with cap) for final storage
Add 20-30ul RNAse free water
Centrifuge for 1 minute at full-speed
Repeat step 4.15-4.16 with the same elution water
Measure RNA quantity/quality with Qubit 3.0 Fluorometer and confirm with Agilent 5200 Fragment analyzer system
RNA is stored in -80C freezer until shipment to core facility at UC Davis. Samples are shipped on dry ice
Library preparation and long read RNA sequencing
Library preparation and long read RNA sequencing
The library is created using the PacBio Iso-Seq Express SMRTbell Library Template Preparation Kit 2.0
Circular consensus sequencing (CCS) is carried out using the Sequel II equipment for 3plex on 1 SMRT Cell 8M
Processing of long read RNA sequencing data
Processing of long read RNA sequencing data
Raw sequencing data is processed through the PacBio recommended Iso-Seq pipeline which
carries out the following steps:
Use lima to remove cDNA primers
Use isoseq refine to polyA tail and artificial concatemers
Use isoseq cluster2 to carry out de novo isoform-level clustering scalable to large number of reads
Use pbmm2 to align reads to the reference genome (GRCh38)
Use isoseq collapse to collapse redundant transcripts based on exonic structures
A GFF file is obtained which contains information for each sequence identified in the pooled samples as well as csv abundance files with information for each transcript in each sample