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DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces

A High-throughput Cell Microarray Platform for Correlative Analysis of Cell Differentiation and Traction Forces

Published on: March 1, 2017

Optimizing cell arrays for accurate functional genomics.

Sven Fengler¹, Philippe I H Bastiaens, Hernán E Grecco

¹Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany.

BMC Research Notes

|July 19, 2012

Summary

A new quality control protocol quantifies and minimizes contamination in cell arrays (CA). A washing step after cell seeding significantly reduces contamination in HeLa cells but is unnecessary for MCF7 cells, optimizing functional genomics screenings.

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Area of Science:

Cellular biology
Genomics
Biochemistry

Background:

Cellular responses involve complex biochemical networks requiring methods for rapid, high-throughput gene product perturbation.
Cell arrays (CA) facilitate microscopy-based experiments via reverse transfection but are prone to interspot contamination, hindering accurate quantification.
Existing methods focus on transfection rates, overlooking the critical issue of contamination in cell-based screening.

Purpose of the Study:

To develop and validate a quality control protocol for quantifying and minimizing interspot contamination in cell arrays.
To identify the primary sources of contamination in cell arrays and assess cell-type specific contamination levels.
To optimize cell seeding protocols for improved data accuracy in functional genomics screenings using cell arrays.

Main Methods:

Development of a quality control protocol for cell arrays.
Imaging of checkered cell arrays expressing distinct fluorescent proteins.
Image segmentation to quantify transfection efficiency and interspot contamination.
Comparative analysis of contamination levels with and without a post-seeding washing step for different cell lines (HeLa, MCF7).

Main Results:

A 3-fold reduction in contaminants was observed in HeLa cell arrays treated with a post-seeding wash step.
Nucleic acid uptake during cell seeding was identified as the primary source of contamination, not cell migration.
MCF7 cell arrays showed a 7-fold lower contamination rate without the washing step, indicating cell-specific contamination properties.

Conclusions:

The developed quality control protocol is essential for assessing contamination, a key factor causing false positives/negatives in microscopy-based functional genomics screenings.
A post-seeding washing step improves cell array quality for HeLa cells but is not required for MCF7 cells.
This methodology enables the determination of optimal seeding protocols for novel cell lines used in cell arrays.