Single Cells from FFPE samples for Flow Cytometry and NGS

Next Generation Single-Cell Sequencing (NGS) is becoming a valuable standard method in life science research and personalized medicine.

Formalin-fixed paraffin-embedded (FFPE) tissue samples are a relevant source of material for this because of its wide availability and broad spectrum of sample types.

However, making high quality single cells from FFPE samples accessible for NGS is a challenge. Reflecting the tumor or tissue heterogeneity to uncover different genetic and phenotypic characteristics is a real bottleneck.



The principle of single-cell sequencing

Tang et al. Cell Biosci. (2019) 9:53

Sample Input

FFPE 50 µm sections*

Sample Preparation

Antigen Retrieval

Enzymatic Pretreatment

Minimized 20 min enzyme treatment

TissueGrinder-Benchtop with Software and single-use Consumables


Fast but gentle mechanical dissociation
with the TissueGrinder

Single Cell Suspension after Centrifugation

Cell Staining

Antibody labeling

Pipetting single cells suspension

Cell Sorting

Isolation of pure tumor and stromal
cell populations

Cell Lysis

Access to pure tumor and stromal cell DNA

NGS and Data Analysis

Library preparation
Detection of tumor specific genetic characteristics on cell populations

We established a protocol* for generating relevant material of single cells from FFPE samples in reasonable time to support subsequent analysis.
After removing excess parafin, the tissue is cut into 4 sub-samples with 100-200mg and transferred into an Eppendorf Cap.
The samples are then incubated in a water bath at 65°C for 25 min using HistoChoice as a xylene substitute.
By incubating in a decreasing ethanol series for 2 x 15 min, the sample is rehydrated.
With repeated washing in ARS and DPBS, the masked epitopes in the tissue are unmasked and lost immunoreactivity is partially restored within 60 min.
With a minimal enzymatic pre-treatment, the subsequent mechanical dissociation with our TissueGrinder makes the cells from the tissue accessible to immunofluorescent staining, flow sorting and subsequent molecular analyses by e.g. next generation sequencing.
The enzymatic incubation time can be reduced from 50 to 20 minutes, resulting in faster workflow and much higher quality of the cells obtained.

* TissueGrinder optimised FFPE protocol is based on the following study:

The 40x microscopy image show examples of how the single cells from FFPE samples generated with our protocol are suitable for immunofluorescent staining.




Single Cells from FFPE samples

The single cells obtained with the TissueGrinder process are in a much better condition than those produced with a conventional enzymatic automation.

On the left, an example of single cells generated from FFPE samples with the TissueGrinder compared to a standard enzymatic dissociation on the right.

Above, an example of single cells generated from FFPE samples with the TissueGrinder compared to a standard enzymatic dissociation below.

TissueGrinder consumable unit with integrated filtration in standard labware
Benchtop-Device with single-use tissue dissociation consumable
Single cell suspension after centrifugation

Sounds too good to be true?

Then contact us to arrange a test run with your own samples!