Additional Reagents and Apparatus for Sample Preparation:

  • For General RNA Preparation *

    Name Recommended Manufacturer Catalog # Purpose
    AllPrep RNA/DNA Micro Kit QIAGEN 80284 RNA isolation from cells or tissues
    RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE Thermo Fisher AM1995 RNA isolation from FFPE tissues
    RNA 6000 Pico Kit Agilent 5067-1511 RNA quality control calculation
    High Sensitivity RNA Analysis Kit Advanced Analytical (AATI) DNF-472-1000 RNA quality control calculation
  • For DirectCell DriverMap Analysis *

    Name Recommended Manufacturer Catalog # Purpose
    TurboCapture 96 or 384 mRNA Kit QIAGEN 72251/72271 Direct use with cell lysate
    Buffer TCL, 2× (8.5 ml) QIAGEN 1031586 Cell lysis

Additional Reagents and Apparatus for cDNA Synthesis and Amplification:

Name Recommended Manufacturer Catalog # Purpose
Agencourt® AMPure® XP (Magnetic Beads) Beckman-Coulter A63881 PCR product purification
Dynabeads® MPC®-S (Magnetic Particle Concentrator) for 1.5 ml Test Tubes Thermo Fisher A13346 PCR product purification
Semi-skirted 96-well PCR plates Eppendorf 951020303 RT-PCR amplification
Clear Adhesive Film for 96-well plates Bio-Rad MSB1001 PCR plate seal
High Sensitivity DNA Kit Agilent 5067-4626 PCR product QC/quantification
High Sensitivity NGS Fragment Analysis Kit (1 bp – 6000 bp) Advanced Analytical (AATI) 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 (75 cycles) or HiSeq®/MiSeq® equivalent Illumina FC-404-2005 (NextSeq) Next-Gen Sequencing

Required Instrumentation:

The protocols were optimized using the specific 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 Applied Biosystems
Instrument or Gel System to
Analyze DNA Fragmentation
2100 Bioanalyzer® Agilent
Fragment Analyzer™ Advanced Analytical (AATI)
Standard gel imaging system many suppliers
DNA Quantification Qubit 3.0 Fluorometer Thermo Fisher
Next-Generation Sequencer NextSeq, HiSeq, or MiSeq Illumina

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

Last modified: Nov 09, 2018

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