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 AVITI (Element Biosciences) sequencing, Illumina sequencing, Oxford Nanopore sequencing, TapeStation analysis, GeneScan/Fragment Analysis, or NanoString nCounter analysis must first request a LIMS account.
See the video below or 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 submission
Sample submission forms to use when submitting DNA, RNA, dsDNA PCR products or Illumina libraries for Agilent 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.
Qubit Flex submission
Sample submission forms to use when submitting dsDNA or RNA. Samples must be submitted in 96-well plates. A base fee is charged for any number of samples up to 72; additional charges apply for samples after the first 72 samples
Amplicon metagenomic project submission
Sample submission form to use when submitting microbial metagenomic DNA for 16S-V4 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 projects. For more details, please see the Amplicon/Metagenomics guide.
AVITI DNA-Seq and RNA-Seq project submission
Sample submission forms to use when submitting genomic or metagenomic 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 on the Element Biosciences AVITI. Libraries that are compatible with Illumina sequencers are also compatible with the AVITI. Projects with 48 or more samples must be submitted in 96-well PCR-type plate(s).
Use these forms for projects using the *NEW* Bundled Flat Rate Pricing (per sample pricing for library preparation and a specific output per sample, Gbp for DNA, million read pairs for RNA).- AVITI Bundled Flat Rate DNA/RNA sample submission in tubes
- AVITI Bundled Flat Rate DNA/RNA sample submission in 96 well plate(s)
AVITI user prepared library submission
Sample submission form to use when submitting prepared libraries for sequencing on the AVITI. Libraries that are compatible with Illumina sequencers are also compatible with the AVITI. The Genomics Core requires you to pool your libraries prior to submission. See the "Index ID lists" section below for files containing index IDs needed to completed this form.
Illumina DNA-Seq and RNA-Seq project submission
Sample submission forms to use when submitting genomic or metagenomic 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 on the Illumina NovaSeq 6000 or MiSeq. Projects with 48 or more samples must be submitted in 96-well PCR-type plate(s).
Use these forms for projects to be sequenced on the MiSeq. NovaSeq 6000 submissions are no longer being accepted. Contact us at gtsf@msu.edu with any questions.Illumina user prepared library submission
Sample submission forms to use when submitting prepared Illumina sequencing libraries. The Genomics Core requires 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 MiSeq The NovaSeq 6000 will be retired in December 2024. Contact us at gtsf@msu.edu to discuss your project and instrument availability.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.
- Single index IDs for use with user prepared library submissions
- Dual index IDs for use with user prepared library submissions
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.