08/23/2022
When returning to the lab after an extended shutdown or inactivity, it is important to make sure all lab resources are up and running and ready to be used. Below are best practices to check library prep, sequencing and microarray reagents and instruments to ensure a successful reopening.
Laboratory and Reagent Checks
Wipe down all lab surfaces with 10% bleach to remove any accumulated dust or contaminants.
Proper storage and handling of reagents, kits, and user-supplied materials should be followed according to documented procedures.
Check connectivity to network drives or servers used for file storage (output run folders, manifest files, cluster files, DMAPs) or data processing (IDAT repository).
Sequencing Instrumentation Considerations
For instruments that were left on:
Note: While the iSeq 100 and NextSeq 1000/2000 do not have onboard fluidics, a power cycle is recommended for these instruments as well.
For instruments that were turned off:
Note: If an additional maintenance/manual/standby wash using laboratory-grade water was not performed prior to instrument shutdown, perform three maintenance/manual washes to rehydrate the fluidics system, then run System Checks to test the fluidics delivery. System Check details are found in the appropriate system guides.
Library Preparation Considerations
Starting a New Library Prep
When starting new library preparation, Illumina recommends reviewing the best practices for the specific library prep kit being used. This information is found on the appropriate product support page.
Proceeding to a Sequencing Run with Stored Libraries
For any Illumina library that has been stored for longer than the recommended time, as specified in the reference guide, Illumina recommends repeating quality control (QC) and quantification prior to sequencing. Re-QC is beneficial because libraries can degrade during prolonged storage, leading to loss of overall yield. Recommended QC methods for most Illumina libraries are summarized in the Library quantification and quality control quick reference guide support bulletin.
For libraries requiring bead-based normalization, Illumina recommends storing the library at the last safe stopping point, just prior to the bead-based normalization step, as specified in the protocol guide. Libraries stored as double stranded DNA (dsDNA, before bead-based normalization) are more stable than libraries stored as single stranded DNA (ssDNA, after bead-based normalization). If a library has been stored long term after bead-based normalization, Illumina recommends repeating the bead-based normalization of the original dsDNA library.
Infinium Assay Considerations
Te-Flow and Water Circulator:
Tecan/Illumina Automated Pipetting System (IAPS):
iScan