Depending on the type of samples and procedural options followed in the protocol, several of the following items will be required to run the assay.

For General DNA Preparation

Name Recommended Manufacturer Catalog # Purpose
DNeasy Blood & Tissue Kit QIAGEN 69506 DNA isolation from PBMC, T/B cells or tissues
Tempus Blood RNA tubes/Spin RNA isolation kit Thermo Fisher 4342792/4380204 DNA and RNA isolation from whole blood
PAXgene Blood DNA kit/tubes Qiagen 761133/761165 DNA isolation from whole blood
All Prep DNA/RNA FFPE kit Qiagen 80234 DNA and RNA isolation from FFPE tissues

Additional Reagents for cDNA Synthesis, Amplification and Amplified Libraries QC

Name Recommended Manufacturer Catalog # Purpose
Agencourt® AMPure® XP (Magnetic Beads) Beckman-Coulter A63881 RNA-RevGSP hybrid and PCR product purification
Dynabeads® MPC®-S (Magnetic Particle Concentrator) for 1.5 ml Test Tubes
Magnetic Stand-96 for 96-well PCR plates
Thermo Fisher A13346/AM10027 RNA-RevGSP hybrid and PCR product purification
96-well PCR plates Thermo-Fisher A43673 RT-PCR reactions
Clear Adhesive Film for 96-well plates Bio-Rad MSB1001 PCR plate seal
High Sensitivity DNA Kit for Bioanalyzer Agilent 5067-4626 PCR product QC/ quantification
High Sensitivity NGS Fragment Analysis Kit (1 bp – 6000 bp) for Fragment Analyzer Agilent DNF-474-1000 PCR product QC/ quantification
Qubit® dsDNA HS (High Sensitivity) Assay Kit Thermo Fisher Q32851 Quantify Indexed Libraries for NGS
NextSeq® 500/550 High Output Kit v2.5 (300 cycles) /NovaSeq Illumina 20024908
(NextSeq)
Next-Gen Sequencing

Recommended Instrumentation

This protocol is optimized for the instruments specified below. Some modifications and optimization to the protocol may be necessary if using different models or instruments from other manufacturers.

Description Model Manufacturer
Spectrophotometer (NanoDrop or equivalent) NanoDrop® ND-2000 Thermo Fisher
Thermal Cycler (Veriti 96-Well or equivalent) Veriti® 96-Well Thermo Fisher
Instrument or Gel System to
Analyze DNA Fragmentation
2100 Bioanalyzer® Agilent
Fragment Analyzer™ Agilent
Standard gel imaging system many suppliers
DNA Quantification Qubit 3.0 Fluorometer Thermo Fisher
Next-Generation Sequencer NextSeq, NovaSeq Illumina
Thermomixer R (for microsampling AIR profiling) Thermomixer R with heat block for 1.5-ml test tubes Eppendorf/Fisher Scientific

Other than the specific reagents and instruments listed above, the protocol assumes the user has access to standard materials (e.g., polypropylene tubes, pipette tips), equipment (tabletop centrifuges, pipettes), and common reagents (e.g., TE buffer, ethanol) and buffers used in a typical life science laboratory.

Last modified: 13 February 2023

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