*When two or more libraries of the same type are submitted, a 10% discount will be applied to those library preparations.
 

Oxford Nanopore Flow Cells

The Genomics Core offers three different flow cells from Oxford Nanopore. The FLO-FLG001 flow cells are appropriate for small amplicon projects, very small genomes or test projects. The FLO-MIN106D flow cells are well suited for fungal or other small genomes. The FLO-MIN110 flow cell generate sslightly more accurate reads but with slightly less yield than the FLO-MIN106D. The FLO-PRO002 flow cells are the highest yielding flow cells from Oxford Nanopore, and they use the same pore chemistry as the FLO-MIN106D flow cells.

Researchers may submit their own libraries for sequencing in the Genomics Core, but it is necessary to contact the Genomics Core before submission in order to coordinate with us. One library preparation is required for each sequencing flow cell, and library preparation prices are listed above. Flow cells are not available for sale directly to researchers. Please contact the Genomics Core if you have questions.

*Please contact the Genomics Core (gtsf@msu.edu) to discuss availability of FLO-FLG001 flow cells.

High Molecular Weight Genomic DNA Extraction 

Nanopore genomic DNA sequencing requires highly purified high molecular weight DNA for successful library preparation and sequencing. Genomic DNA extractions are performed with Qiagen Genomic Tips with enzymatic digestions to help eliminate cell wall components. Typical yields are 10 to 30 µg. Contact us at gtsf@msu.edu for details about how to prepare tissue before sending samples to us for extraction and sequencing.

Illumina-Compatible Library Preparation 

Standard library preparation is performed using the following library preparation kits. Alternatives may be available for low-input or low-quality starting material. Please contact the Genomics Core for more information.

¹ Appropriate for high quality, eukaryotic RNA samples.

² These kits are species specific, please contact the Genomics Core for more information about availability.  
 

Lexogen QuantSeq Library Preparation

Quant-seq generates highly strand-specific libraries of reads from the 3' end of each mRNA in your samples. Only one read is created from each mRNA, and many fewer reads are required for gene expression analysis.

³UMIs are included in the library prep so that PCR duplicates can be identified and eliminated before read analysis.  Contact the Genomics Core if you do not want the UMIs to be included in your library prep.
 

Swift Methyl-Seq Library Preparation

Methyl‑Seq DNA Library Preparation. Whole Genome Bisulfite Sequencing (WGBS) and Reduced Representation Bisulfite Sequencing (RRBS) are possible. Contact the Genomics Core to discuss RRBS. Bisulfite conversion is performed using Zymo EZ DNA Methylation- Gold Kit.

Amplicon Library Services

⁴ For amplicon barcoding, a two-step PCR approach is used.  The user-prepared PCR uses target-specific primers with tags on the 5' ends that allow the addition of barcodes during the secondary PCR step.  Our sample requirements page describes the sequences that must be added to your target-specific primers in order to allow barcoding during the secondary PCR step.

Library QC Services

Illumina Sequencing

HiSeq 4000

HiSeq 4000 services are purchased on a per lane basis for single end 50 bp sequencing or paired end 150 bp sequencing.  Other sequencing formats are available (SE100, SE150, PE75), but require the researcher to purchase the entire flow cell (8 lanes).  Output per lane: Illumina's Specs: 264-312 million clusters passing filter (CPF); Genomics Core's frequent output: 320-400 million CPF.  For single end sequencing, each cluster will generate one forward read.  For paired end sequencing, each cluster will generate one forward read and one reverse read.

⁵ Other sequencing formats may be possible but would require the purchase of the entire flow cell (8 lanes). Please contact gtsf@msu.edu for more information.

NextSeq 500

Output per flow cell: Illumina specs: High output flow cells will generate up to 400 million clusters passing filter (CPF) and Mid output flow cells will generate up to 130 million CPF.  For single end sequencing, each cluster will generate one forward read.  For paired end sequencing, each cluster will generate one forward read and one reverse read.

MiSeq

⁶When sequencing low diversity libraries, e.g. amplicon libraries for metagenomics, output will be reduced by ~20%.

Sanger Sequencing

⁷Low throughput submission: DNA in 12µl, you may add a custom primer or Genomics Core will add standard primer.

⁸Submission of more than 8 samples in individual tubes will be charged the low throughput price.

⁹High throughput submission: DNA in 6µl, you may add a custom primer or Genomics Core will add standard primer.

¹⁰DMSO added to reaction, appropriate for high GC DNA or plasmids > 10 kbp.

¹¹Samples which are high molecular weight genomic DNA

¹²DMSO, betaine, and dGTPS added to reaction, appropriate for samples with hairpins or significant secondary structure.

Genotyping/Fragment Analysis

QuantStudio 7 Flex qPCR Services

The QuantStudio 7 Flex qPCR instrument is calibrated for the following dyes: FAM, SYBR, VIC, HEX, TAMRA, NED, ROX, ABY, JUN, and Mustang Purple.  Users submit completely assembled reactions in 96- or 384-well plates.

¹⁴Price includes transfer from 96-well plate(s) to 384-well plate and processing on QuantStudio 7 Flex.

qPCR Supplies Available for Purchase

Other Expression Analysis Services

The Genoimcs Core is only offering SmartChip and Nanostring services to on-campus researchers. On-campus researchers should contact the Genomics Core (gtsf@msu.edu) about the availability of the instruments.

¹⁵Price does not include reagents from NanoString. The listed prices are for sample processing only.

TapeStation & Bioanalyzer Analysis Services

The Genomics Core has an Agilent 4200 TapeStation and an Agilent 2100 Bioanalyzer.  Both instruments use automated electrophoresis to assess the quality and quantity of DNA and RNA.

All samples will be processed on the TapeStation, unless otherwise requested. The only exception is total RNA that will be used for small RNA or micro RNA library preparation; these samples will be analyzed on the Bioanalyzer because it is more sensitive to small RNA and micro RNA species. 

The 4200 TapeStation analysis is performed on a ScreenTape that has individually addressable lanes, where 1 sample is run per lane.  This allows for analysis of 1 or more samples at a time.  The TapeStation analysis is sold on a per sample basis.  

The 2100 Bioanalyzer analysis is performed on a chip containing 11 wells, which allows for analysis of 1 to 11 samples.  With the 2100 Bioanalyzer, reagents for 11 samples are used even if fewer than 11 samples are analyzed.  Therefore, the Bioanalyzer analysis is sold on a per chip basis (1 to 11 samples). 

Please see the TapeStation & Bioanalyzer Sample Requirements webpage for information regarding sample requirements and submission.

TapeStation Analysis Services

Bioanalyzer Analysis Services

Qubit Fluorometric Quantification

The Genomics Core has a Qubit 1.0 available for researchers to use for fluorometric quantitation of double-stranded DNA and total RNA.  The Qubit is a self-service instrument.  Users must receive training by Genomics Core staff prior to using this equipment.  Please contact the Genomics Core (gtsf@msu.edu) to schedule a training session.  See the Resource Calendar webpage to make a reservation.

Covaris Sonicator

The Genomics Core has a Covaris m220 focused-ultrasonicator available for researchers to use for fragmentation of DNA.  The Covaris is a self-service instrument.  The Genomics Core stocks small tubes (130 µl tube, p/n 520077) and large tubes (1 ml tube, p/n 520135) for purchase. Users must receive training by Genomics Core staff prior to using this equipment.  Please contact the Genomics Core (gtsf@msu.edu) to schedule a training session.  See the Resource Calendar webpage to make a reservation.