Quantification and quality assurance of isolated nuclei

This article is based on a poster originally authored by DeNovix.

Quality control checks are essential while isolating nuclei for single-cell sequencing procedures. The CellDrop Automated Cell Counter provides a simple and dependable way to quantify nuclei, measure extraction efficiency, and visualize debris in a sample.

1. Tissue preparation

Prepare fresh, frozen, or fixed tissue

Quantification and quality assurance of isolated nuclei

Image Credit: DeNovix Inc.

2. Extraction

Use an extraction buffer to isolate nuclei from tissue.

Quantification and quality assurance of isolated nuclei

Image Credit: DeNovix Inc.
10X Genomics™ and Miltenyi Biotec™ are registered trademarks.

3. Sample preparation

  1. Adjust AO/PI to room temperature.
  2. Add the AO/PI fluorescent label to the nuclei suspension at a 1:1 ratio and mix thoroughly.
  3. Thoroughly mix the sample immediately before loading. No incubation time is needed.

Note: Trypan Blue can be utilized, but the combined use of AO/PI and fluorescence eliminates subjectivity and provides higher accuracy

Quantification and quality assurance of isolated nuclei

Image Credit: DeNovix Inc.

4. Counting protocol

Quantification and quality assurance of isolated nuclei

Image Credit: DeNovix Inc.

The CellDrop Automated Cell Counter features an Nuclei AO/PI application with options for protocol customization. The 50 µm chamber height preserves sample, requiring as little as 2.5 µL of sample in addition to AO/PI. Protocols can be set, saved, and easily selected to streamline nuclei quantification.

5. Imaging and nuclei counting

Quantification and quality assurance of isolated nuclei

Image Credit: DeNovix Inc.

AO/PI fluorescence

Acridine Orange (AO) is a cell membrane-permeable fluorophore that binds to nucleic acids, staining the nuclei of all cells in a sample.

Propidium Iodide (PI) is a nucleic acid-binding dye that cannot penetrate intact cells, but it is suitable for staining isolated nuclei.

6. Analysis

Quantification and quality assurance of isolated nuclei

Image Credit: DeNovix Inc.

7. Downstream applications

After verifying sample quality, customers can proceed to downstream applications such as:

  • RNA-seq
  • ATAC-seq
  • Flow Cytometry

Quantification and quality assurance of isolated nuclei

Image Credit: DeNovix Inc.

The CellDrop Automated Cell Counter specializes in rapid, accurate analysis of cells and isolated nuclei samples, even those containing debris.

Count nuclei without slides! The CellDrop, which won the Sustainable Laboratory Product of the Year award from SelectScience®, eliminates the need for disposable plastic slides with its unique DirectPipette technology. Load, measure, and wipe the permanent sample surface clean.

Download this infographic from DeNovix Inc. to explore recommended strategies for optimizing nuclei counts before downstream sequencing applications.

Download the full poster to learn more

About DeNovix, Inc.

WELCOME TO DENOVIX

Award-Winning products for Life Science

Our multi-award winning products include the Reviewers’ Choice Life Science Product of the Year and Platinum Seal awarded- DS-11 Series Spectrophotometer / Fluorometer and CellDrop Automated Cell Counter. CellDrop is the first instrument of its kind to Count Cells Without Slides. These powerful instruments integrate patented DeNovix technology with easy-to-use software designed by life scientists for life scientists.

Researchers tell us they love the industry leading performance, smart-phone-like operation, and the flexible connectivity of the instruments. When support is needed, the DeNovix team is here to help. DeNovix received the prestigious Life Sciences Customer Service of the Year based on independent reviews posted by scientists worldwide!

CellDrop: Sustainable laboratory product of the year

The CellDrop Automated Cell Counter has been awarded Sustainable Laboratory Product of the Year in the SelectScience® Scientists’ Choice Awards®!

CellDrop’s patented DirectPipette technology distinguishes it as the only cell counter to eliminate the need for cell counting slides. This innovation saves millions of single-use plastic slides from use and disposal each year.


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Last updated: Sep 13, 2024 at 11:46 AM

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