SAMPLE - ANALYSIS - RESULT

SAMPLE

KEY TO HIGH QUALITY BIOMARKER DATA ARE WELL TREATED SAMPLES

With Chipcytometry, you can analyze an virtually unlimited number of biomarkers on a single tissue- or cell suspension sample [Analysis].
The better the quality of the sample source (like blood or fresh frozen tissues) and the more gentle the sample preparation procedure, the better the biomarker data quality. Ideally, samples should be prepared on-site and then preserved and/or shipped in a way that protects all kinds of biomarkers from degradation during storage. 

At Zellkraftwerk, we have developed reagents, methods and hardware to provide our customers with a revolutionary new way for controlled, long-term biobanking of cells and tissue sections with unprecedented preservation of biomarkers – ZellSafe chips. Samples can be easily prepared and preserved on those chips even in remote locations and stored/shipped for centralized analysis in a controlled way without significant degradation of biomarkers.

SAMPLES ARE PRESERVED FOR A LONG TIME ON ZELLSAFE BIOREPOSITORIES

ZellSafe chips are small biorepositories with standardized connectors that can be handled by technicians/study nurses as well as by pipetting robots. Cell suspensions and tissue sections are prepared and deposited inside those biorepositories following standard operating procedures [SOP].

The samples are immobilzed on the chip surface and biomarker degradation is stopped for long term storage by adding fixatives. We offer a growing range of ZellSafe chips to meet your needs of different cell and tissue types:

ZellSafe.Basic

up to 250.000 cells

ZellSafe.XL

up to 1.000.000 cells

ZellSafe.Tissue

2 x 1 cm section / 6 biopsies

Coming soon: ZellSafe.XS

1 to 100 cells

Load cells / tissue on chip =
every cell gets a permanent individual address

Add fixation buffer & storage buffer =
stop degradation of biomarkers

Seal chip for biomarker preserving
longterm storage > 20 months

zellsafechips_biobanking

WATCH THE SIMPLE LOADING PROCEDURES OF ZELLSAFE BIOREPOSITORIES

WE CALL IT TrueBiobanking

When looking at the biomarker preservation data of our ZellSafe biorepositories, it turns out that cells and tissues stay intact and virtually no cell is lost during at least 24 month of storage, and only max 5% of biomarkers are lost during this period when compared to day 0. This is a world record – and therefore, we call it TrueBiobanking.

Loss of material or biomarkers after 2 years of storage

DNA at -80°C
20%
Cells frozen at -80°C
80%
Cells on ZellSafe Chips at 4°C
5%

Source: Zellkraftwerk, Christian Hennig

ANALYSIS

For analysis of cells and tissues inside the Zellsafe longterm biorepositories [Sample], we have developed an advanced form of iterative imaging cytometry called Chipcyometry.

  • advanced imaging: HDR imaging, 3D cell recognition, special designed filtersets for high-efficiency, protein-protecting fluorescence detection with unprecidented sensitivity
  • non-destructive analysis – sample is not consumed during analysis
  • recovery of detection channels: unlimited number of biomarkers per sample
  • mixed parallel and serial marker detection: no or very low setup time of panels compared to high-plex flow panels
analysis_sequential-multiplexing

ASSAY DEVELOPMENT

To get your samples analysed within a short time and with a maximum number of biomarkers, parallel analysis is theoretically the fastest way. However, the more biomarkers are analysed at the same time, the bigger the problems of antibody-antibody, antibody-dye and dye-dye (e.g., agglomerate formation or spillover) interactions within the cocktails gets. This might lead to a very long setup time of new cocktails or even to impossible-to -combine marker combinations. On the other hand, serial analysis of single markers (one-by-one) needs no setup time, but is much slower. As a compromise, we introduce mixed serial-parallel measurement:

Only max 5-plex assays are developed and validated. This should not take longer than 1 week. Each of these 5-plex assays can afterwards be combined with each other and stained in a serial approach (one-by-one). 

analysis_assaydevelopment

In this application note, we describe how to set up such multicolor cocktails:

DOWNLOAD PDF

As a consequence of sample storage capabilities (no ad-hoc analysis necessary) and assay development, the workflow in Chipcytometry differs from flow cytometry:

1. The chronological separation of sample acquisition and analysis time point allows valid, controlled sending of samples and centralized analysis even with world-wide sample acquisition.

2. In a screening phase, samples can be tested with a virtually unlimited number of markers using the serial single color approach with very low setup time.

3.+4. Throughput can be increased later by using serial analysis of 5plex assays and/or usage of switch-antibodies that do not require bleaching of remaining fluorescence [on request].

analysis_modes

RESULT

Generated data is worthless without knowledge about how the data was generated, what the data points mean and how data was transformed after initial acquisition. Reuse, sharing, and comparison of datasets is impossible without access to accompanying metadata. Therefore, Zellkraftwerk has integrated complete metadata recording for ALL processes from sample preparation through storage and analysis to data processing. Based on principles of the semantic web and ontologies, we developed a description language (EDL – experiment description language) that records every object and process involved in Chipcytometry. This is useful in a number of situations:

  1. Electronic lab book: All metadata (e.g. time points, durations, temperatures) are collected either automatically or via standardized user interfaces thus automatically building an electronic lab book.
  2. Seamless integration of all machines that understand and respond to EDL: All machines integrated in our Chipcytometry products understand and respond to EDL, thus new, more complex workflows can be realized just by software – applying the rules of 4th industrial revolution.
  3. Plug-and-play data processing with integrated, EDL-driven interface to R statistic computing language
  4. Easy forwarding of all necessary metadata to downstream data analysis pipelines (flow cytometry software like FlowJo®, pathology software like Definiens Tissue Studio®

ANALYZING A 37-PLEX DATA SET

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