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ddPCR > ddPCR Instruments and Software > Flashcards

ddPCR Instruments and Software Flashcards

1
Q

How long does it take to read a 96-well plate

A

~3 hours

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2
Q

What is the password to the laptop that comes with the QX200 reader?

A

QuantaLife

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3
Q

What types of supermixes can be selected on QuantaSoft?

A 
ddPCR Supermix for probes
ddPCR Supermix for probes (no dUTP)
Droplet PCR Supermix
QX200 ddPCR EvaGreen Supermix
One-Step RT-ddPCR kit for probes (replaced with Advanced kit)
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4
Q

What types of supermixes can be selected on QX ONE Software?

A

ddPCR Supermix for probes
ddPCR Supermix for probes (no dUTP)
ddPCR Multiplex Supermix
ddPCR Supermix for Residual DNA Quantification
One-Step RT-ddPCR advanced kit for probes

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5
Q

What is the file extension for QuantaSoft?

A

.qlp (.qlps for regulatory edition)

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6
Q

What is the file extension for QuantaSoft AP, QX Manager and QX ONE Software?

A

.ddpcr (.ddpcrs for regulatory edition)

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7
Q

When would you want dUTP in your supermix?

A

In FFPE samples, deamination of cytosine to uracil causes artificial C:G > T:A SNVs. Uracil DNA glycosylase (UDG) pretreatment lowers the frequency of C:G > T:A SNVs in highly fragmented DNA.

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8
Q

Which Bio-Rad thermal cyclers are compatible with ddPCR amplification?

A

C1000 Touch Deep Well

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9
Q

What are the Channels in QX200

A

FAM and HEX (or VIC)

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10
Q

What are the key applications of ddPCR

A

Absolute quantification (e.g. viral and microbial counts), CNV, rare mutation detection, gene expression, microRNA expression, NGS prep, single cell analysis, genome editing detection

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11
Q

Equation for CPD

A

CPD = -ln(1-p)

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12
Q

What is the percentage of positive/negative droplets for (a) 1 CPD, and (b) 4 CPD

A

(a) ~63% positive, (b) ~1.8% negatives

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13
Q

What detection chemistries are compatible with QX100 and QX200?

A

QX100 - probes only (EvaGreen will damage!)

QX200 - probes or EvaGreen

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14
Q

How long does it take to create droplets for one cartridge using the QX200 DG (manual DG)?

A

~2.5 min

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15
Q

What sounds are heard when using the QX200 DG (manual DG)?

A
  1. Pump moves
  2. Pressure on wells to make droplets
  3. Draw excess oil back from the droplet column
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16
Q

What ramp rate is recommended for ddPCR amplification?

A

2.5 °C/sec

17
Q

In QuantaSoft, how can you tell whether data is for a single well or merged wells?

A

Single wells are open data points; merged wells are closed data points.

18
Q

What functionalities does QuantaSoft AP have over QuantaSoft?

A
  1. Amplitude multiplexing
  2. Probe mixing multiplexing
  3. Drop off assay analysis for genome editing
  4. Advanced droplet classification

ddPCR (3 decks)

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