Pooled Genetic Screens: Library Design, Selection and Reading a Hit List · seed 1 · A4, ink-friendly. The answer key prints on its own page for grown-ups.
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One pool, thousands of guides

Science · Genetics & Evolution · ages 23-24
Name ______________________   Date ____________
  1. A 20,000-guide library needs average coverage of 500 guide-bearing cells per guide at the stated stage. How many guide-bearing cells are required? Type the number.

    Answer: ______________

  2. Which plan describes a pooled single-guide CRISPR knockout screen?

    • Mix guide-bearing cells and compare guide counts before and after selection.
    • Keep each guide in a separate culture and call each culture the full pooled library.
    • Apply selection before adding guides and infer guide effects without an initial sample.
  3. You want genes whose knockout reduces growth or survival in this cell line. Which screen readout fits?

    • Positive selection: seek guides enriched among drug-resistant survivors.
    • Endpoint-only counting: call every rare guide essential without an initial sample.
    • Negative selection: seek guides depleted relative to their initial counts.
  4. In each of two independent repeat cultures, Gene X's four guides have fold enrichments 8, 1, 1, 1; Gene Y's have 3, 3, 3, 3. Non-targeting controls stay near 1. Which preliminary interpretation fits?

    • Declare Gene X causal because its largest guide effect exceeds every Gene Y effect.
    • Prioritize Gene Y for follow-up because its guides agree across both repeats.
    • Reject both genes because targeting guides must always match non-targeting controls.
  5. A drug kills susceptible control cells. You want perturbations that let cells survive this drug. Which selection design fits?

    • Negative selection: prioritize guides depleted as their cells become less likely to survive.
    • Positive selection: prioritize guides enriched among surviving cells.
    • No comparison: call every surviving guide causal without baseline counts or controls.
  6. What is the main use of non-targeting guides, designed without a genomic target, in this screen?

    • Provide a reference for background variation in guide counts.
    • Prove that every targeting guide cuts only its intended genomic site.
    • Reproduce all DNA-cutting effects caused by guides targeting genes.
  7. In a growth-depletion screen, confirmed active guides against genes required in this cell line remain near baseline. What is the best next step?

    • Declare all genes dispensable because these controls stayed near baseline.
    • Accept the hit list unchanged because these controls never need to deplete.
    • Troubleshoot conditions and readout before interpreting the hit list.
  8. An 8,000-guide library needs average coverage of 500 guide-bearing cells per guide after a loss step. Exactly 80% of starting guide-bearing cells remain, with guide proportions unchanged. How many guide-bearing cells must you start with?

    Answer: ______________

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Answer key

For grown-ups. Fold this page away before handing over the rest.

One pool, thousands of guides W1-mt_0n-a7GfLOL-s1

  1. 10000000 · Required guide-bearing cells = 20,000 × 500 = 10,000,000. This counts the represented population at the stated stage.
  2. Mix guide-bearing cells and compare guide counts before and after selection. · A pooled screen mixes guide-bearing cells and compares adjusted guide-tag counts across selection. Tags track assigned guides, not confirmed edits.
  3. Negative selection: seek guides depleted relative to their initial counts. · Growth-reducing knockouts can become less represented. Negative selection detects guide depletion relative to the initial sample.
  4. Prioritize Gene Y for follow-up because its guides agree across both repeats. · Gene Y shows consistent enrichment across guides and repeats relative to controls. Gene X's isolated effect needs investigation. Neither pattern proves causation.
  5. Positive selection: prioritize guides enriched among surviving cells. · Resistance-promoting perturbations can become enriched among survivors. This is positive selection, interpreted against initial counts and controls.
  6. Provide a reference for background variation in guide counts. · Non-targeting guide counts provide a background reference. They do not prove guide specificity or reproduce every effect of a DNA cut.
  7. Troubleshoot conditions and readout before interpreting the hit list. · The expected depletion controls did not respond. Investigate timing, conditions and readout before trusting hits. This does not establish that all genes are dispensable.
  8. 5000000 · The retained population needs 8,000 × 500 = 4,000,000 cells. Divide by the retained fraction: 4,000,000 / 0.8 = 5,000,000 starting cells.
Worksheet · LightMySky