Jan 30, 2026

Public workspacePurification negative controls (PNCs) prepared on the Bravo NGS Workstation V.1

DOI
https://dx.doi.org/10.17504/protocols.io.bp2l6z235gqe/v1
  • Anna Schmidt1,
  • Sarah Nagel1
  • 1Max Planck Institute for Evolutionary Anthropology
  • MPI EVA Ancient DNA Core Unit
Ancient DNA Core Unit
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DOI: https://dx.doi.org/10.17504/protocols.io.bp2l6z235gqe/v1
Document Citation: Anna Schmidt, Sarah Nagel 2026. Purification negative controls (PNCs) prepared on the Bravo NGS Workstation. protocols.io https://dx.doi.org/10.17504/protocols.io.bp2l6z235gqe/v1
License: This is an open access document 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
Created: August 26, 2025
Last Modified: January 30, 2026
Document Integer ID: 225500
Keywords: purification negative control, purification, pnc, bravo ngs workstation protocol for the preparation, part of the dna extraction workflow, dna extraction workflow, protocol for the preparation, negative control, ancient dna core unit of the mpi, bravo ngs workstation protocol, fluidx tube, ancient dna core unit, bravo ngs workstation, ancient dna core
Funders Acknowledgements:
Max Planck Society
Grant ID: -
Abstract
Protocol for the preparation of purification negative controls (PNCs) in FluidX tubes using the Bravo NGS Workstation. PNCs are used as part of the DNA extraction workflow of the Ancient DNA Core Unit of the MPI-EVA.
Troubleshooting
Note

PNCs consist of 150 µl extraction buffer stock solution in FluidX screw-cap tubes. This document describes the preparation of a complete tube rack containing 96 PNCs.
Materials

Reagent/consumableSupplierCatalogue numberDecontamination *
Reagents
Extraction buffer stock solution (w/o Proteinase K)† self-UV
Consumables
FluidX screw-cap tubes in FluidX 96-tube rackBrooks Life Sciences68-1003-11 -
Bravo 96LT 250 µL, Sterile, Filtered TipsAgilent19477-022 -
HTS deep well reservoirKisker97813 -
* Decontamination of buffers should be performed as detailed in the documents below.
† See document in the Appendix for preparation of extraction buffer stock solution.

Equipment

  • Bravo-B NGS workstation G5522A with 96-channel LT pipette head
  • FluidX rack barcode reader (e.g. Brooks Life Sciences, cat. no 20-4018)
  • Tube decapper (e.g. Aperio 8-Channel Semi- Automatic Screw Top tube rack decapper, Brooks Life Sciences, cat. no. 46-6502)

Protocol

1. Get a new FluidX 96-tube rack and use the FluidX barcode reader to read the bottom barcodes of all empty tubes in the rack and the rack ID in the front.

2. Switch on the Bravo system. Switch on light and ventilation ("Betrieb") inside the robot hood.

3. Log into the VWworks software using the administrator account (password "a"). Load the buffer transfer protocol under
"S:\Bravo_protocols\MPI-EVAN-homebrew\forms\Reagent_preparation\BufferTransfer_to_FluidX_Tubes.VWForm".

4. Select the proper settings in the form file:
  • Buffer volume (150 µl)

  • Plate type for buffer transfer (0.8 ml FluidX tubes)


5. Fill the reservoir with approx. 30 - 50 ml extraction buffer stock solution (UV decontaminated) and place it on the position in the Bravo deck as indicated by the form file.

6. Unpack 1 Bravo Tip box and place it on the position in the Bravo deck as indicated by the form file.

7. Open the FluidX screw-cab tubes in the sample rack with the decapper and keep the lids by placing them in a clean 96 lid holder. You can find this holder next to the decapper.

8. Place the uncapped FluidX 96-tube rack into the position of the Bravo Deck as indicated by the form file.

9. Start Run by clicking the "Run" button (150 µl of extraction buffer stock solution buffer are now added to each tube).

10. After run has finished, close the FluidX tubes using the decapper. Use the lids from the lid holder.

Note
[Documentation]

Label the FluidX 96-tube rack with tube content (Purification Negative Controls), date and initials.

Save the document containing the tube IDs under
"P:\AncientDNA\FluidXBarCodeReader\FluidX_Data\Stock_Buffer_FluidXTubes" and label rack file with rack ID, tube content, date and initials.

11. Store PNCs at -20 °C until used.

Appendix
Document
NAME
UV decontamination of reagents/buffers
CREATED BY
Elena Essel

Document
Extraction buffer stock solution (w/o Proteinase K)
NAME
Extraction buffer stock solution (w/o Proteinase K)
CREATED BY
Ancient DNA Core Unit