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Blog

Functional Genomic Screening

May 21st 2025

2 min read

Arrayed or pooled library? Make the right first move in your CRISPR screen.

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CRISPR screening enables researchers to investigate the biological activity of tens, hundreds, or even thousands of genes. This method assists in identifying genes that may be essential for various biological pathways, discovering potential drug targets, evaluating probes' functions, stratifying patients, and supporting numerous other important biological applications.

To fully leverage the potential of the screening assay, an initial and crucial step is to select a screening format that aligns with the specific biological questions you are exploring. Here are six common questions our screening services team asks to help guide our customers in choosing the appropriate library format:

What is the biological question you want to answer?
Can the phenotype be selected or separated from the background in the cell population?
Is your facility equipped with lab automation to perform high-throughput screening?
Is the handling of lentiviral particles allowed?
How much storage and cell culture space do you have in the facility?
What do you know about the transfectability and growth characteristics of cells?

Based on these factors, one format may be more appropriate than the other. To clarify, we have outlined various applications, benefits, and considerations for each format.

	Pooled screening: lentiviral	Arrayed screening: synthetic
Applications	Suitable for phenotypes that can be shifted in response to selective pressure, such as cell viability/proliferation assays or FACS analysis Identification of drug resistance genes Suitable for difficult-to-transfect cells	Simpler genotype-phenotype correlation Allows for complex screening assays, such as morphological phenotypes by microscopy Suitable for high-content screening assays
Advantages	Relatively consistent set-up regardless of library size Requires minimal automation or specialized equipment Requires less experimental manipulation Custom-made libraries are available Suitable for longer time points	Potential hits easily identifiable, one gene per well Can perform very complex readouts Multi-parametric readouts possible Custom-made libraries are available Applicable for 3D and co-culture studies Cells do not have to be actively dividing and growing
Special requirements	Ability to select/separate cells with particular phenotype(s) from the population Ability to start with a very large cell population and maintain large flasks throughout the screen Cells typically must be actively dividing and growing throughout the screen NGS and extensive bioinformatics required to deconvolute hits Viral handling required	Cells must be amenable to transfection or electroporation Requires automated liquid handling equipment Higher reagent costs due to consumables such as plates, media, tips required by automation Potential plate-to-plate or well-to-well variability May require sufficient freezer space Shorter assay time points

Expertise throughout your screening processes

Our preclinical team partners with you to design optimal screening strategies.

Arrayed or pooled - no matter which format you choose - we have predefined and custom libraries for CRISPR gene knockout and CRISPR gene modulation applications1-7. The guide RNAs used in our libraries are either validated in the literature, like in our CRISPR mod libraries8 or designed by a functionally validated proprietary algorithm that provides efficient knockout with unparalleled specificity.

Unlock therapeutic targets and biomarkers, from identification to patient stratification with our functional genomic screening services. Alternatively. you can explore our Dharmacon reagents for additional research tools.

Learn more