eBook: Optimizing Gene-Editing Workflows - 21

with different gene knockouts are mixed together in
pooled screens, complicated data deconvolution is
necessary to untangle the genotype-phenotype relationships.
Depending on the assay, analysis can be
relatively straightforward for arrayed screens. However,
for screens that use transfection (as opposed
to transduction), optimization is required to ensure
maximum editing efficiencies. This is especially true
when working with synthetic gRNAs.
Having the right equipment for the job
Pooled and arrayed screens differ in the equipment
required to conduct a screen. Whereas pooled screens
can be conducted with standard laboratory equipment,
arrayed screens often require automated plate
handling capabilities to facilitate high-throughput
transfection. In addition, a high-content system may
be necessary to analyze image-based phenotypes.
Up-front costs may be higher for
arrayed screens
One of the main benefits of pooled screens is that
they are relatively cost-effective to conduct. Thus, for
simple assays, these screens offer a feasible way to
interrogate the entire genome. Arrayed screens can
have a higher upfront cost, but because they can
provide so much information, they can ultimately
save money in the long run.
Thinking big picture: Leveraging a
combination of screening approaches
It is important to remember that pooled and arrayed
screens can both be useful in screening workflows.
Amanda Mah, Ph.D., is the creative communications
manager at Synthego.
Additional Resources
CRISPR Screening 101 eBook
For instance, if one aims to identify new drug targets,
a pooled format may be appropriate as a primary
screen to identify a broad set of target genes
in an easy-to-transfect cell model (e.g., immortalized
cell line). An arrayed format may then be used in a
secondary screen to validate the hits using a more
realistic model (e.g., primary cells). When designing
a target identification experiment, consider all the
tools at your disposal.
Pooled vs. arrayed screening formats:
Further reading
Choosing the right screening format can be confusing
at first, but understanding the costs and benefits
of each, and what data you can get from each can
help you pick the one most suitable to answer your
research question.
If you are looking for more details about the comparison
between pooled versus arrayed screens, or
other aspects of the screening process, visit Synthego's
interactive screening experience to examine
loss-of-function screening approaches, explore
our CRISPR-based workflow, and view 30+ valuable
screening resources.
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eBook: Optimizing Gene-Editing Workflows

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