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Cell3™ Target

Cell3™ Target

Ordering & purchasing

Can I buy a combination of fragmentation and non-fragmentation kits?

What is included in the Cell3 Target: Capture enrichment reagents kit ?

What is included in the Cell3 Target: Library Preparation kit (a) ?

What is included in the Cell3 Target: Library Preparation kit (b) ?

What is included in the Cell3 Target: Probe set kit ?

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Analysing Cell3™ Target sequencing data

Do I set up my sequencer differently for applications with or without UMIs?

When do I use UMIs?

What are UMIs and why do I need them?

Included in my design files are BED files named target_merged.bed and covered.bed. Which file is relevant for coverage analysis and which for variant calling?

Cell3™ Target Library preparation

What are the input DNA requirements for Cell3 Target?

What is the complete workflow/time frame for Cell3 Target ?

How many libraries can I pool together in one hybridisation reaction for the Cancer 50 Panel or the exome kit?

What volume of probe set is included in the enrichment and capture kit for the Cancer 50 Panel?

I would like to run PCR free method of library prep. How is this done and what are the important points?

I am preparing to do whole genome-seq library prep on FFPE DNA with low DIN values but high concentration. How much starting material would you advise I use for the library preps?

The protocol states using M-270 Streptavidin beads. Can other types of beads, such as DynaOne beads be used instead?

The Cell3 Target protocol suggests using 16 cycles for targets <0.04Mb. My targeted region is very small <0.01Mb. Should I still only conduct 16 cycles of post capture PCR?

How should the beads look after drying? Are they always "fine" after 5 minutes? Or should I wait until they have cracks?

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Cell3™ Target Library preparation: methods, equipment and reagents

Is there a maximum time for the Hybridization reaction (Chapter 2)?

The maximum temperature for the lids of our cyclers is 99˚C. Is it possible to reduce temperature of the denaturation steps in step 1D (library amplification) to 95˚C with a lid heated to 99˚C?

I don't have a cycler where I can adjust the volume. Is this important?

I am using Cell3™ Xtract for cfDNA extraction from plasma or serum.

Can I combine Cell3 Target enrichment probes with libraries prepared from library prep kits from other manufacturers?

I extracted and stored my cfDNA at -20˚C prior to starting the library prep. What should I be aware of before I start?

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Cell3™ Target Library preparation: quality controls (QC) and troubleshooting

My TapeStation trace shows a peak at ~160bp representing adapter-dimers, what should I do?

The enzymatic shearing doesn’t look like it worked properly as the fragments are much longer than expected.

What QC steps do you recommend following extraction of DNA and prior to library preparation?

I performed a QC step, using a TapeStation High Sensitivity D1000 screen tape, on my extracted plasma cell free DNA (cfDNA) prior to starting my library prep.

Sequencing Cell3™ Target libraries

How does the use of UMIs impact input DNA quantities?

What are the input DNA requirements for FFPE samples ?

Can I sequence libraries prepared from cfDNA together with libraries prepared from FFPE DNA?

How many samples can I load on a NextSeq or NovaSeq to achieve 2X coverage for a whole human genome?

Can I sequence a mix of Cell3™ Target prepared libraries when some have been Enzymatically sheared and others Covaris sheared?

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