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truXTRAC™ FFPE RNA and DNA

  • Active paraffin removal in an aqueous buffer
  • NGS-quality RNA and DNA from FFPE tissues
  • High extraction and purification yields
  • Simple, fast and scalable workflow
  • Seamless integration with NGS applications

cvtruChipWorkflow
With truXTRAC, Covaris has developed a solution utilizing its Adaptive Focused Acoustics (AFA) technology for the high efficiency extraction of nucleic acids from FFPE tissues. The highly simplified workflow ensures high yield extraction of nucleic acids and allows the seamless integration with NGS and other molecular applications.

Active paraffin removal in aqueous buffer

Paraffin is actively removed from the FFPE tissue sample by the finely controlled and reproducible acoustic energy provided by Covaris Focused-ultrasonicators. The entire process is performed in a single tube without transfer steps. DNA and RNA are typically ready for library preparation or other analytical methods in 3 hours.

  • Reproducible & operator independent process
  • Aqueous buffer, no organic solvent
  • Reduced hands on time
  • Complete paraffin removal for complete sample rehydration
Before after

NGS-grade RNA and DNA from FFPE tissues

Whole genome sequencing results from Covaris extracted FFPE DNA generates greater coverage depth across the genome, and coverage uniformity similar to that of DNA extracted from fresh frozen tissues. With other FFPE DNA extraction methods gene rich regions of the genome seem to lack consistent coverage depth indicating a bias in the library representation for regions of the chromatin with low abundance of genes. Coding and non-coding DNA regions are extracted with the same efficiency with Covaris truXTRAC, thereby effectively promoting an unbiased library preparation. A comparison of active and passive FFPE DNA extraction methods and effects on downstream analysis metrics (pdf).

FFPE_DNAseq
Sequencing track from Kit Q (red), Covaris (green) extracted FFPE kidney DNA, and fresh frozen (indigo) samples were loaded on the IGV viewer, and the coverage analyzed for chromosome 19. Coverage of >10x are indicated in dark colors, coverage of < 10X are indicated in light colors.

High extraction yields

Active paraffin removal results not only in efficient paraffin removal, but also promotes complete sample rehydration benefitting both tissue digestion by proteinase K as well as enhancing the dissociation of biomolecules for improved extraction of DNA or RNA.

FFPE_yield

Simple, fast and scalable workflow

Covaris Focused-ultrasonicators can process single samples or SBS format 96 microTUBE racks, and are easily integrated with automated liquid handling platforms.

  • 96 samples processed in a SBS format microTUBE FFPE rack
  • Rapid active paraffin removal of 96 FFPE samples with 2D barcoded 8 microTUBE strip
  • Fully automatable & scalable purification
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Seamless integration with NGS applications

Next Generation Sequencing applications require precisely controlled DNA fragmentation as part of the library preparation. Covaris AFA is the method of choice for DNA fragmentation in Genome Centers worldwide because the DNA fragment size is easily controlled and highly reproducible. As an option, the DNA shearing step can be integrated into the truXTRAC workflow, greatly simplifying the library preparation protocol from FFPE tissue samples.


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Covaris truXTRAC Kits

truXTRAC™ FFPE DNA Kit  (PN 520136): The kit contains reagents and consumables required for the high yield and high quality DNA extraction and purification from 25 FFPE tissue samples. Optimized to work with FFPE sections ≤ 25 μm and FFPE cores ≤ 1.25 mm diameter, containing ≤5 mg of tissue.

truXTRAC FFPE DNA microTUBE Kit for chemagen Technology (24) (PN 520176: The kit contains reagents and consumables required for the high yield and high quality DNA extraction from 24 FFPE tissue samples. Optimized to work with FFPE sections ≤ 25 μm and FFPE cores ≤ 1.25 mm diameter, containing ≤5 mg of tissue. This kit requires the use of a Perkin Elmer chemagen magnetic separation system for the purification of the extracted DNA. Please contact Covaris at ApplicationSupport@covarisinc.com.

truXTRAC™ FFPE RNA Kit (PN 520161) –  The kit contains reagents and consumables required for the high yield and high quality RNA extraction and purification from 25 FFPE tissue samples. Optimized to work with FFPE sections ≤ 25 μm containing ≤5 mg of tissue.

Note 1: truXTRAC FFPE kit requires use of an M, S, E or LE-Series Covaris Focused-ultrasonicator and associated rack or holder (see below).
Note 2: truXTRAC FFPE kit requires use of  Heat Block microTUBE Adapters to fit Covaris microTUBE into standard heating blocks.

Accessories

Heat Block microTUBE Adapters (quantity 10, PN 500406): Heat Block microTUBE Adapters are designed to fit a microTUBE into a heating block designed for 1.5 or 2 mL microcentrifuge tubes. It is required for Proteinase K incubation and to reverse formaldehyde crosslinks.

FFPE sectionPICK (quantity 25, PN 520149): sectionPICK is designed to collect FFPE tissue sections mounted on slides. Its shape is designed to collect the tissue scraped from the slide at the end of the tool. The sample is then easily transferred to a Covaris microTUBE. It is not designed for the collection of stained sections.

FFPE tissuePICK (quantity 25, PN 520163): The FFPE tissuePICK is designed to collect FFPE tissue from sections mounted on slides. The small cross section and unique surface properties of the FFPE tissuePICK allow for easy collection of small discrete areas as well as large tissue sections from single or multiple slides. It is not designed for the collection of stained sections.  It requires tissuePICK Forceps (PN 520164) for handling.

FFPE tissuePICK Forceps (quantity 5, PN 520164): Forceps for the tissuePICK.

FFPE sectionWARMER (quantity 1, PN 500403): sectionWARMER is designed to warm the FFPE section mounted on a slide, and such facilitate its collect with the FFPE sectionPICK.

Holders and Racks

For M-Series: M220 Holder XTU microTUBE (PN 500414) and M220 Holder XTU Insert microTUBE 130 μl (PN 500489)
For S-Series: Holder microTUBE Screw-Cap (PN 500339)
For E-Series: Rack 24 Place microTUBE Screw-Cap (PN 500308) and Intensifier (PN 500141)
For L-Series: Rack-XT 24 Place microTUBE Screw-Cap (PN 500388)

Focused-ultrasonicators

M220 Focused-ultrasonicator
S220 Focused-ultrasonicator

E220 Focused-ultrasonicator
LE220 Focused-ultrasonicator

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truXTRAC Kits

truXTRAC FFPE DNA Kit (pdf)

truXTRAC™ FFPE DNA microTUBE Kit for chemagen Technology (24) (pdf)

truXTRAC FFPE RNA Kit (pdf)

Protocol for simultaneous extraction and purification of DNA and RNA from FFPE Tissue Samples with truXTRAC (pdf)

Accessories

FFPE tissuePICK Product Insert (pdf)

FFPE tissuePICK Instruction Movie

FFPE sectionPICK Product Insert (pdf)

 

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Application Notes & Case Studies

Assessing FFPE DNA Quality: the “Illumina FFPE QC Kit” enables quantitation of improvements in FFPE DNA Extraction Technologies

A comparison of active and passive FFPE DNA extraction methods and effects on downstream analysis metrics

DNA Extraction from FFPE samples with Covaris Focused-ultrasonicators

Active paraffin removal from FFPE tissues with Adaptive Focused Acoustics

Poster

AGBT 2014  – Active Deparaffinization Drives Superior Yields, Quality and Sequencing Coverage from FFPE Tissue Samples

AGBT 2013 – Improved workflow for FFPE tissue Nucleic Acid extraction

Webinar

NGS-quality RNA and DNA from FFPE tissues with a novel method of active paraffin removal

Product Flyer

FFPE DNA Extraction Product Flyer

FFPE Kit MSDS Information

MSDS Information

Movie

A short sequence showing paraffin emulsification from a 7 μm FFPE section

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Selected publications

Improved FFPE DNA extraction for next generation sequencing using adaptive focused acoustics technology
Ling Lin, et al ; 2014.

Whole exome sequencing of muscle-invasive bladder cancer identifies recurrent mutations of UNC5C and prognostic importance of DNA repair gene mutations on survival
Kai Lee Yap, Kazuma Kiyotani, Kenji Tamura, et al ; 2014.

Somatic activating ARAF mutations in Langerhans cell histiocytosis
David S. Nelson, et al ; 2014.

SMRT® Sequencing of DNA and RNA Samples Extracted from Formalin-Fixed and Paraffin Embedded Tissues Using Adaptive Focused Acoustics by Covaris
Primo Baybayan, et al; 2015

 

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