Single-Cell RNA Sequencing: From Droplets to a Count Matrix · seed 1 · A4, ink-friendly. The answer key prints on its own page for grown-ups.

From droplets to a table of cells

Science · Genetics & Evolution · ages 22-23
Name ______________________   Date ____________

  1. Reads sharing one barcode and one molecular identifier collapse into what?

    • One hundred cells
    • One molecule count
    • One new gene

  2. What does the cell barcode on a read tell you?

    • Which droplet and cell the transcript came from
    • The age of the scientist
    • The gene's function in the body

  3. Molecular identifiers correct for capture loss of molecules never caught.

    Circle one:   True   False

  4. A cluster looks exactly like a mix of two known types and its barcodes show high molecule totals. What is the likely artefact?

    • Dropout
    • A doublet
    • Ambient RNA alone

  5. One molecule is amplified into 50 reads. How many molecule counts does it contribute after collapsing?

    • 50
    • 0
    • 1

  6. A gene shows zero in a cell although the cell type usually expresses it. What should you ask first?

    • What the scientist had for lunch
    • Whether dropout lost its molecules during capture
    • Nothing, zeros are always final

  7. Every droplet including empty ones carries liver gene reads, and cells of all types show a liver tint. What is happening?

    • Every cell truly became a liver cell
    • The barcodes all broke identically
    • Ambient RNA from burst liver cells leaking into all droplets

  8. A student announces a new intermediate cell type from mixed profiles without doublet filtering. What is the flaw?

    • Mixed profiles are the expected doublet artefact, so filtering must come first
    • New types are impossible in principle
    • Clustering always removes doublets by itself
LightMySky · lightmysky.comW1-mt_QCoqY7w_De-s1

Answer key

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

From droplets to a table of cells W1-mt_QCoqY7w_De-s1

  1. One molecule count · Shared tags mean PCR copies of a single original molecule.
  2. Which droplet and cell the transcript came from · The barcode maps each transcript back to its droplet of origin.
  3. False · Uncaught molecules leave no tag, so identifiers cannot rescue them.
  4. A doublet · Two cells in one droplet fake an intermediate with a heavy total.
  5. 1 · All copies share tags, so they collapse to one.
  6. Whether dropout lost its molecules during capture · Dropout makes true expression vanish, so zeros need an alibi.
  7. Ambient RNA from burst liver cells leaking into all droplets · Free floating RNA contaminates every droplet and blurs all profiles toward liver.
  8. Mixed profiles are the expected doublet artefact, so filtering must come first · Unfiltered doublets fake intermediates, so the claim runs ahead of its controls.
Worksheet · LightMySky