Description

The Zymo-Seq UDI Primer Sets contain pre-mixed Unique Dual Index (UDI) primers that can be used to barcode any library containing TruSeq® adapters. Indexes in the Zymo-Seq UDI Primer Set (Indexes 1-12) are dispensed in 1.5 mL tubes (Cat. No. D3008), and the Zymo-Seq UDI Primer Plate (Indexes 1-96), Zymo-Seq UDI Primer Plate (Indexes 1-96, 10-bp) and Zymo-Seq UDI Primer Plate (Indexes 97-192, 10-bp) are dispensed in single-use foil-sealed 96-well plates (Cat. No. D3096, D3097, and D3098 respectively).

Indexed libraries are compatible with any Illumina® sequencer. These indexes are compatible with the Zymo-Seq RiboFree Total RNA Library Kit and Zymo-Seq SwitchFree 3′ mRNA Library Kit. For greater multiplexing capability, consider the Zymo-Seq UDI Primer Plate (Indexes 1-96, 10-bp) and the Zymo-Seq UDI Primer Plate (Indexes 97-192, 10-bp) (Cat. No. D3097 and D3098 respectively). These plates can be used together to multiplex up to 192 libraries.

Resources

Documents

Protocol: D3008/D3096 | D3097/D3098

SDS (MSDS): D3008 | D3096 | D3097 | D3098

Barcode Sequences Table:  D3008/D3096  | D3097/D3098 

FAQ

Q1: Are these individual primers or pre-mixed primer sets?

Each tube contains a pre-mixed forward and reverse primer set that contain a unique i5 and i7 index, respectively. The concentration of each UDI primer pre-mix is 5 µM total (2.5 µM each primer).

Q2: What are the sequences of the indexes?

For the index sequences of the D3008 tubes and the D3096 plate, please refer to the "D3096" barcode sheet. For the 10-bp indexes of the D3097 or D3098 plate please refer to the "D3097/D3098" barcode sheet.

Q3: What library kits are compatible with these UDI primers?

In addition to library kits such as the Zymo-Seq RiboFree Total RNA Library Kit and Zymo-Seq SwitchFree 3′ mRNA Library Kit, the primers are compatible with libraries that use the Illumina TruSeq® adapter structure. They are not compatible with libraries that use the Illumina Nextera® adapter structure.

Q4: Can I multiplex libraries prepared with the D3097 or D3098 plates with the D3008 or D3096?

Libraries indexed with the D3097 and D3098 primers are generally multiplexable with libraries prepared with the similar D3008 and D3096 primers. However, certain D3008/D3096 indexes have a Hamming distance ≤ 2 with either the i5 or i7 indexes of the D3097/D3098 primers. To avoid any barcode mismatch when multiplexing D3097/D3098 with D3008/D3096, please observe the following:

Q5: How do I use the 10-bp D3097 or D3098 primers in a Zymo-Seq library preparation protocol?

The D3097 and D3098 primers are prepared at the same concentration of the D3008 and D3096 described in the Zymo-Seq library preparation protocols. Therefore, please use the D3097 and D3098 primers in the same way as described in the relevant protocol.

Q6: Do any other Zymo Research primers use the same index sequences as D3097/D3098?

Yes, D3097 and D3098 share the same index sequences as the primers found in the Quick-16S Plus NGS Library Prep Kit (V4), specifically catalog numbers D6430-PS1 and D6430-PS2 (which are also included in D6432). If intending to sequence these 16S libraries together with libraries indexed with D3097 or D3098, please ensure that different index sequences are used. Please note that while the index sequences are the same, the D3097/D3098 primers are not interchangeable with the primers from the aforementioned Quick-16S kit.

Illumina®, TruSeq®, and Nextera® are registered trademarks of Illumina, Inc.