Protocol

This section describes the Illumina DNA Prep with Enrichment protocol.

• Review the planned complete sequencing workflow, from sample through analysis, to ensure compatibility of products and experiment parameters.
• Before proceeding, confirm kit contents and make sure that you have the required components, equipment, and consumables. This protocol uses the Urinary Pathogen ID/AMR Panel, library prep and enrichment reagents, and index adapters included in these kits.
• Follow the protocol in the order shown, using the specified volumes and incubation parameters.

If you plan to use different libraries plexities from what is advised in the subsequent protocol, record information about your samples before starting library prep.

• For low-plexity sequence pooling strategies (2-plex to 9-plex), refer to the Index Adapters Pooling Guide.
• For index adapter sequences and information about recording the sequences, refer to Illumina Adapter Sequences.

The UPIP protocol for the UPIP is optimized for 3-plex enrichment. Although other enrichment plexities are possible, some plexities require additional pre-enrichment library prep and enrichment probe panel reagents.

Obtaining suitable enrichment yields for nonstandard enrichment plexities might require additional optimization. Optimal results are not guaranteed.

• Enrichment plexity—The number of pre-enriched libraries (3) pooled together in one enrichment reaction for hybridization with the enrichment probe panels. For example, combining 12 pre-enriched libraries together creates a 12-plex enrichment pool.
• Enrichment reaction —The number of unique enrichment reaction preparations, regardless of the number of pre-enriched libraries pooled per reaction.

This kit enables the generation of 96 pre-enriched libraries which are pooled together in 32 individual 3-plex enrichment reactions.

The following diagram illustrates this workflow.

• Safe stopping points are marked between steps
• Time estimates are based on processing 12 samples at 3-plex enrichment.