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LIMS Project Submission

The MSU Genomics Core uses the Illumina BaseSpace ClarityLIMS system to permit users to create sequencing projects, submit sample information and track progress. Each individual researcher submitting samples for Illumina sequencing, Oxford Nanopore sequencing, Bioanalyzer/TapeStation analysis, or NanoString nCounter analysis must first request a LIMS account. See the LIMS Instructions for information on how to request an account, create projects and submit sample information.

Visit our LIMS Login page to request an account or create a project.

TapeStation/Bioanalyzer submission

Due to reagent kit backorders on TapeStation reagents, all samples will be processed on the Bioanalyzer until further notice.  There may be a delay in data return as we try to conserve Bioanalyzer reagents by grouping samples for efficient processing.  When results are posted to Genomics Depot, a Genomics Core staff member will notify you by email.

Normal pricing for Bioanalyzer runs will be suspended, and the cost per sample will follow TapeStation analysis pricing.  Total RNA samples will be tested for $8 each. Fragmented DNA, dsDNA PCR products, and prepared libraries will be processed for $8.50 each.

Please note that plant total RNA samples may be analyzed with the non-plant eukaryotic setting which will affect the automatic calculation of the RIN score.  The Genomics Core will take this into account when assessing the quality of samples that are submitted for library preparation.

Please contact with any questions regarding TapeStation/Bioanalyzer analysis.

Sample submission forms to use when submitting DNA, RNA, dsDNA PCR products or Illumina libraries for Agilent Bioanalyzer or TapeStation analysis only (not for library preparation and/or sequencing). Choose the appropriate file depending on whether you are submitting samples in individual tubes or in 96 well plates. A maximum of 15 samples may be submitted in tubes; any number of samples may be submitted in plates.

Amplicon metagenomic project submission

Sample submission form to use when submitting microbial metagenomic DNA for 16S amplicon library preparation and Illumina sequencing, or primary PCR amplicons for addition of dual indexed Illumina library adapters. 

Illumina DNA-Seq and RNA-Seq project submission

Sample submission forms to use when submitting genomic DNA for WGS DNA-Seq libraries, ChIP DNA for ChIP-seq libraries, or total RNA for RNA-Seq or Small RNA-Seq library preparation and sequencing.

Illumina User prepared library submission

Sample submission forms to use when submitting already completed Illumina sequencing libraries. There are different forms to use if you are submitting individual libraries in tubes or 96 well plates or if you are submitting libraries which you have already pooled together. See next section for files containing index IDs needed to completed these forms.

Index ID lists for completion of user prepared library submission

These files include lists of Index IDs from a number of vendors which are to be used when completing any of the prepared library submission forms above. Files are available for either single index or dual index type libraries. Within each of these files are a number of worksheets (tabs along the bottom) for various vendors. Select the appropriate one for your library type. You must copy and paste the index IDs exactly as they appear in these files into the appropriate spaces on your submission form. If the indexes used for your libraries (e.g. custom libraries) do not appear in either of these files then you must contact the Genomics Core before completing and submitting your form.

Oxford Nanopore project submission

Sample submission form to use when submitting genomic DNA, amplicons, cDNA, total RNA, or polyA RNA for library preparation and sequencing using the Oxford Nanopore GridION system.

NanoString nCounter Expression Analysis project submission

Sample submission form to use when submitting total RNA or lysed cells for a NanoString nCounter Expression Analysis project. In addition to basic sample information you will also need information about the NanoString Gene Expression Panel (CodeSet) which will be used for your experiment. These reagents are typically shipped directly from NanoString to the RTSF Genomics Core. We require this information so that we can match your samples to the reagents sent by NanoString.

GeneScan Fragment Analysis project submission

Use one of these forms when you are submitting samples for one of the genotyping applications: AFLP, STR or Microsattelite. In addition to basic sample information you must also indicate what size standard should be used for your assay.