Collibri™ PCR-free ES DNA Library Prep Kit for Illumina Systems, with UD indexes (Set A, 1-24), 24 preps - FAQs

View additional product information for Collibri™ PCR-free ES DNA Library Prep Kits for Illumina Systems - FAQs (A38603096, A38545024W, A43603024, A38603096W, A43604024, A43602024, A38602024, A38608196, A38545024)

11 product FAQs found

Can indexed adaptors or other modules be purchased separately for the Collibri DNA Library Prep kits?

Indexed adapters and other modules in the kit can be purchased separately. Please refer to thermofisher.com/collibriDNA and contact us for more details.

With the Collibri DNA Library Prep kits, what is the distribution of enzymatically sheared DNA in the library?

Fragment size ranges from 150 bp to 850 bp. For optimal results, we recommend and provide detailed instructions for 350 bp and 550 bp average size library construction.

With the Collibri DNA Library Prep kits, can I use indexed adaptors interchangeably between RNA-seq and DNA-seq applications?

No. They are specifically designed for a product and cannot be used interchangeably.

With the Collibri DNA Library Prep kits, why is my ligation master mix orange instead of red?

Dyes inside the master mix react with CO2 and change the color from red to orange. The mix is still usable when the color changes to orange. To prevent discoloration, avoid keeping it on dry ice.

Are Collibri DNA Library Prep kits compatible with FFPE samples?

Collibri PS DNA Library Prep Kit can be used for library construction from lower-quality DNA (such as FFPE samples). However, the yields of adaptor-ligated molecules are typically lower compared to the yields obtained with high-quality DNA.

Collibri ES DNA Library Prep Kit is not recommended for library construction from FFPE samples.

How do I assess the quality of the prepared Collibri DNA library?

Library size distribution and the absence of primer dimers and/or over-amplification products should be verified by an electrophoretic method (with Agilent 2100 Bioanalyzer instrument).

To achieve the highest-quality sequencing data, it is essential to create optimal cluster densities across the flow cell. The most accurate quantification methods to assess the quantity of adaptor-ligated molecules in the library are qPCR-based methods, and we recommend using the Collibri Library Quantification Kit. Quantification can be performed at different stages of the workflow, for example after the post-ligation cleanup or size-selection step (for PCR-free workflows), or after the post-amplification cleanup step (for amplified libraries).

What is the PCR-free limit for Collibri PS and ES DNA Library prep kits?

PCR-free libraries of ≥4 nM concentration using Collibri PS DNA Library Preparation Kit can be prepared from as little as 500 ng input DNA.

PCR-free libraries of ≥4 nM concentration using Collibri ES DNA Library Preparation Kit can be prepared from as little as 100 ng input DNA.

In the Collibri DNA Library Prep kits, what enzyme is used for library amplification?

Collibri kits contain Platinum SuperFi DNA Polymerase whose exceptionally strong proofreading activity helps ensure amplification of NGS libraries with supreme sequence accuracy, producing NGS error rates similar to PCR-free methods. The enzyme is a part of Collibri Library Amplification Master Mix, which is included in the kits with PCR option. Designed exclusively for NGS application, Collibri Library Amplification Master Mix is based on a proprietary reaction buffer that has been specially optimized for efficient and uniform amplification of NGS libraries regardless of GC content.

Note: Collibri DNA Library Prep kits are available with or without PCR library amplification.

Are Collibri DNA Library Prep reagents available in a customized, larger format?

Yes, customized formats can be accommodated by our custom services group. Please send an email to techsupport@thermofisher.com with your custom request and they will provide you with further details.

What do ES and PS abbreviations stand for in the Collibri DNA Library Prep kits?

ES - Enzymatically sheared. Collibri ES DNA Library Prep Kit includes reagents for enzymatic shearing and downstream DNA library preparation.
PS - Physically sheared. Collibri PS DNA Library Prep Kit is designed for library construction starting from physically sheared DNA.

Are adaptors included in the Collibri DNA Library Prep kits?

Yes, adaptors are included in the Collibri DNA Library Prep kits except in DNA Library Prep Core kits that contain only enzymatic and clean-up modules. The Collibri DNA Library Prep kits include ready-to-ligate adaptors with unique dual indexes (UDs), or combinatorial dual indexes (CDs) that allow pooling of up to 24 or 96 different samples with one kit before the sequencing run.

Each well in the combinatorial dual indexes (CDs) plate contains a single-use adaptor that consists of a unique combination of two 8 nucleotide identification barcodes. Combination of one D5 barcode with one D7 barcode in each ready-to-use adaptor allows pooling of up to 24 or 96 different samples before the sequencing run.

Each well in the unique dual indexes (UDs) plate contains a single-use adaptor that consists of two unique 8-nucleotide indexes of D5 and D7 when each index appears in the whole plate only once. The combinatorial approach is not used.

Use CDs and UDs to pool up to 192 preps for higher throughput. Other combinations are also possible, but do not pool together different sizes of kits containing the same type of indexed adaptors (CDs or UDs only) to avoid overlap of sequences.