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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, TapeStation/Bioanalyzer analysis, or NanoString nCounter analysis must first request a LIMS account. See the LIMS Instructions for information on how to request an account, create a project and submit sample information.

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


TapeStation/Bioanalyzer submission

Sample submission forms to use when submitting DNA, RNA, dsDNA PCR products or Illumina libraries for Agilent TapeStation or Bioanalyzer 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.

The RTSF Genomics Core will include a negative, no template control (NTC) reaction on each plate of samples processed for amplicon sequencing.  Researchers will have the option to request that a positive control be included with 16S-V4 and 16S-V3V4 projects.  For more details, please see the Amplicon/Metagenomics guide.


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.

Use these forms for projects to be sequenced on the NovaSeq 6000.
Use these forms for projects to be sequenced on the MiSeq
The MSU Genomics Core no longer accepts submissions for sequencing on the HiSeq 4000

Illumina User prepared library submission

Sample submission forms to use when submitting already completed Illumina sequencing libraries. The Genomics Core requests you pool your libraries prior to submission.  See next section for files containing index IDs needed to completed these forms.

Use this form for projects to be sequenced on the NovaSeq 6000
Use this form for projects to be sequenced on the MiSeq
The MSU Genomics Core no longer accepts submissions for sequencing on the HiSeq 4000

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,  polyA RNA, or tissues/cells for library preparation and sequencing using the Oxford Nanopore GridION or PromethION.


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 reagents 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 Microsatellite. In addition to basic sample information you must also indicate what size standard should be used for your assay.