Pricing
Pricing is identical for MSU researchers and for off-campus researchers. However, payments from non-MSU accounts (i.e. off-campus researchers) will be subject to a 2% University Administrative Fee. MSU also requires the addition of a 26% Facilities and Administrative Cost charge to services provided to for-profit companies.
Illumina-Compatible Library Preparation
10x Genomics Chromium Single Cell Libraries
Oxford Nanopore Library Preparation
High Molecular Weight Genomic DNA Extraction
TapeStation and Bioanalyzer Analysis
Qubit Fluorometric Quantitation
Illumina Sequencing
NovaSeq 6000
The NovaSeq 6000 is Illumina's most advanced sequencing instrument. It makes use of a patterned flow cell like the NextSeq and two-dye chemistry to reduce sequencing costs and run times and to increase sequence yields. Four different sizes of flow cells can be used with the NovaSeq. These flow cells have two or four lanes. Sequence yields range from approximately 362 million reads and 36 Gbp for a single end 100 bp run on one lane of the SP flow cell to 2.25 billion reads and 675 Gbp for a paired end 150 bp run on one lane of the S4 flow cell.
Shared S4 lanes
The S4 flow cells generate sequence for as little as $8.66 per Gbp. While most researchers will not have projects that can make use of a complete S4 lane, we will pool samples from different researchers for sequencing on a shared S4 lane. Because of the necessity for accurately tracking barcode usage in a shared lane, only libraries that are prepared by the Genomics Core will be eligible for the shared S4 lane option. Initially, only Illumina TruSeq Nano DNA libraries and New Illumina stranded mRNA libraries will be eligible for shared lane pooling.
All shared S4 lanes will be sequenced as paired end 150 bp runs. Researchers can indicate the sequencing format in which their data should be returned, such as single end 100 bp.
Researchers should note that because of the large capacity of the S4 flow cell there may extended wait times before a sufficient number of samples are ready for sequencing on the S4 flow cell. If quick data return is important, purchasing a single lane on a smaller flow cell may be more expedient.
Sequencing for Gene Expression Analysis
Researchers will notice that the single end 50 bp sequencing format that is popular for gene expression analysis is not available on the NovaSeq 6000. The single end 100 bp format is recommended for gene expression analysis. Alternatively, RNA-seq libraries made by the Genomics Core may be run on a shared S4 lane. The paired end 150 bp sequencing format on the shared S4 lane has the benefit of allowing more accurate read mapping to gene families or to paralogous genes in polyploid genomes. If a researcher has a very large number gene expression samples, the S4 flow cell has a single end 35 bp option that has sufficient reagents to stretch to a single end 50 bp run, but to make use of this option, the entire S4 flow cell must be purchased.
| Flow Cell Type | Sequence Format1 | Average # Reads (Millions) | Average Gbp | # of Lanes | Price |
|---|---|---|---|---|---|
| Shared Lane on S4 Flow Cell2 | 2 x 150bp paired end | 200 | 60 | $641 for 1/10th of a lane (200 M read pairs) | |
| SP | 1 x 100bp single end | 362 | 36 | 1 lane | $1,656 |
| SP | 1 x 100bp single end | 724 | 72 |
2 lanes (flow cell) |
$3,312 |
| SP | 2 x 100bp paired end | 724 | 144 |
2 lanes (flow cell) |
$4,214 |
| SP | 2 x 150bp paired end | 362 | 108 | 1 lane | $2,424 |
| SP | 2 x 150bp paired end | 724 | 216 |
2 lanes (flow cell) |
$4,848 |
| SP | 2 x 250bp paired end | 724 | 362 |
2 lanes (flow cell) |
$6,810 |
| S1 | 1 x 100bp single end | 725 | 73 | 1 lane | $2,717 |
| S1 | 1 x 100bp single end | 1,450 | 146 |
2 lanes (flow cell) |
$5,434 |
| S1 | 2 x 100bp paired end | 1,450 | 292 |
2 lanes (flow cell) |
$7,240 |
| S1 | 2 x 150bp paired end | 1,450 | 436 |
2 lanes (flow cell) |
$8,408 |
| S2 | 1 x 100bp single end | 3,700 | 370 |
2 lanes (flow cell) |
$9,302 |
| S2 | 2 x 100bp paired end | 3,700 | 740 |
2 lanes (flow cell) |
$12,098 |
| S2 | 2 x 150bp paired end | 3,700 | 1,110 |
2 lanes (flow cell) |
$13,664 |
| S4 | 1 x 35bp single end | 9,000 | 158 |
4 lanes (flow cell) |
$14,112 |
| S4 | 2 x 100bp paired end | 9,000 | 1,800 |
4 lanes (flow cell) |
$19,588 |
| S4 | 2 x 150bp paired end | 2,250 | 675 | 1 lane | $5,846 |
| S4 | 2 x 150bp paired end | 9,000 | 2,700 |
4 lanes (flow cell) |
$23,384 |
1 Other sequencing formats available, but custom formats may require the purchase of a complete flow cell.
2 Samples must be TruSeq Nano DNA libraries or Illumina Stranded mRNA libraries that are prepared by the Genomics Core. User-prepared libraries require their own sequencing lane.
MiSeq
| Kit Type/Size | Sequence Format | Per Lane | Approximate Output (Gbp) |
Reads (Millions)3 |
|---|---|---|---|---|
| v2 Standard 50 cycle | 1 x 50bp single end | $1,064 | 0.6-0.75 | 12-15 |
| v2 Standard 300 cycle | 2 x 150bp paired end | $1,398 | 3.6-4.5 | 12-15 |
| v2 Standard 500 cycle | 2 x 250bp paired end | $1,519 | 6.0-7.5 | 12-15 |
| v2 Micro 300 cycle | 2 x 150bp paired end | $696 | 1.2 | 4 |
| v2 Nano 300 cycle | 2 x 150bp paired end | $524 | 0.3 | 1 |
| v2 Nano 500 cycle | 2 x 250bp paired end | $647 | 0.5 | 1 |
| v3 150 cycle | 2 x 75bp paired or 1 x 150bp single end |
$1,196 | 3.3-3.8 | 22-25 |
| v3 600 cycle | 2 x 300bp paired end | $2,043 | 13-15 |
22-25 |
3 When sequencing low diversity libraries, e.g. amplicon libraries for metagenomics, output will be reduced by ~30%.
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 (gtsf@msu.edu) for more information.
| Library Kit Name | Use | Price Per Library |
|---|---|---|
| Illumina TruSeq Nano DNA | Shotgun DNA Library Preparation. | $83 |
| TakaraBio SMARTer ThruPLEX DNA‑Seq | Low Input DNA Library Preparation or ChIP-seq Library Preparation. | $83 |
| Illumina Stranded mRNA Library | Library preparation of poly-adenylated mRNA. | $74 |
| Illumina TruSeq Stranded mRNA Library | For legacy projects only. Library preparation of poly-adenylated mRNA. | $114 |
| Qiagen QIAseq FastSelect rRNA depletion with TruSeq Stranded Total RNA Library | Library preparation of ribosomal RNA depleted total RNA. Qiagen FastSelect kit must be purchased by researcher and provided to the Genomics Core. |
$122 |
| Illumina TruSeq Small RNA Library | Library preparation of microRNA from 22 - 30 nt. Libraries can also be made from small RNAs > 30 nt, contact the Genomics Core to discuss project. | $247 |
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. UMIs are included in the library prep so that PCR duplicates can be identified and eliminated before read analysis. Contact the Genomics Core (gtsf@msu.edu) if you do not want the UMIs to be included in your library prep.
| Library Kit Name | Price Per Library (up to 47 samples) | Price Per Library (48-71 samples) | Price Per Library (≥72 samples) |
|---|---|---|---|
| Lexogen QuantSeq 3'mRNA‑Seq Library Prep Kit FWD with Unique Molecular Indentifiers (UMIs) | $67 | $60 | $58 |
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.
| Library Kit Name | Price Per Library |
|---|---|
|
Swift BioSciences Accel‑NGS Methyl‑Seq DNA Library |
$189 |
Amplicon Library Services
| Service | Use | Price per Library |
|---|---|---|
| 16S V4 Amplicon Library |
Amplicon library preparation of the 16S V4 region. |
$8 |
| 16S V3V4 Amplicon Library | Amplicon library preparation of the 16S V3V4 region. | $8 |
| Amplicon barcoding4 | Barcoding of user-prepared primary PCR products such as ITS or other regions of interest. | $8 |
| QC of amplicon library pool | QC includes Qubit dsDNA, Agilent 4200 TapeStation D1000 HS, and Kapa qPCR assays. | $38 |
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
| Service | Use | Price |
|---|---|---|
| Invitrogen Collibri Library Quantification of Genomics Core prepared library pool | qPCR quantification of a pool of libraries that have been prepared by the Genomics Core. | $27/pool |
| QC of submitter prepared library or pool | QC of submitter-prepared library or pool of submitter-prepared libraries. QC includes Qubit dsDNA, Agilent 4200 TapeStation D1000 HS, and Invitrogen Collibri Library Quantification (qPCR) assays. | $38/library or pool |
Blue Pippin Size Selection
| Service | Use | Price |
|---|---|---|
|
Size Selection of 1 to 4 libraries using the Blue Pippin (size range is 100-600 bp). Libraries must be processed at the same time. |
Please contact Genomics Core (gtsf@msu.edu) to discuss availability. | $110 |
10x Genomics Chromium Single Cell Libraries
The success of a single cell sequencing project depends on starting with high-quality cell or nuclei preparations. Because sample standards are very high, researchers must have a consultation with the Genomics Core before we will be able to schedule the delivery of cell or nuclei preparations. Please contact the Genomics Core at gtsf@msu.edu for more information. If you have a project with more than 50 samples, contact us to discuss pricing.
| Library Kit Name | Price Per Library for 1 sample |
Price Per Library for 2 to 4 samples |
Price Per Library for 5 to 8 samples |
|---|---|---|---|
| Chromium Next GEM Single Cell 3′ Kit v3.1 |
$2,362 | $2,026 | $1,835 |
Oxford Nanopore Library Preparation
Nanopore library preparations that are offered by the Genomics Core are listed below. Descriptions of these library kits can be found on the Nanopore Sequencing Technology page. One library preparation is required for each sequencing flow cell, and flow cell prices are listed below. Sequencing yields with current Nanopore library kits and the current flow cells is highly dependent on sample quality. The Nanopore Sequencing Technology page has some guidance on yields. Also see the Nanopore Sample Requirements page for information about submission requirements. Please contact the Genomics Core (gtsf@msu.edu) if you have questions.
| Library Kit Name | Nanopore Kit ID | Sequencing Target | Price Per Library5 |
|---|---|---|---|
| 1D Ligation Sequencing Kit | LSK109/LSK110 | Genomic DNA | $429 |
| 1D Ligation Sequencing Kit with barcoding | LSK109 + NBD104 | Genomic DNA or Amplicons | $429 + $15/barcode (up to 24 samples) |
| Rapid Barcoding Kit (up to 12 samples) |
RBK004 | Multiplexed Genomic DNA (small genomes) | $304 |
| Direct RNA Sequencing Kit | RNA002 | Full Length RNA | $328 |
| cDNA-PCR Sequencing Kit (no barcoding) | PCS109 | Full Length cDNA | $471 |
| cDNA-PCR Sequencing Kit with barcoding (up to 12 samples) | PCS109, PBK004 | Multiplexing Full Length cDNA for a single flow cell | $390 + $107/barcode |
| Direct cDNA Sequencing Kit | DCS109 | Full Length cDNA | $423 |
5 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-MIN106D flow cells are well suited for fungal or other small genomes. The FLO-MIN111 flow cell generate slightly 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 in the table above. Flow cells are not available for sale directly to researchers. Please contact the Genomics Core if you have questions.
| Flow Cell Name | Version | Instrument | Price |
|---|---|---|---|
| FLO‑MIN106D | R9.4.1 | GridION | $854 |
| FLO‑MIN111 | R10.3 | GridION | $854 |
| FLO-PRO002 | R9.4.1 | PromethION | $1,675 |
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. A minimum 1g tissue is required. 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.
| Sample Type | Price Per Extraction 1 sample submitted |
Price Per Extraction 2 or more samples submitted |
|---|---|---|
| Plant, Fungal, or Oomycete | $164 | $127 |
Sanger Sequencing
The Genomics Core offers a quick turnaround time on Sanger sequencing using an Applied Biosystems 3730xl DNA Analyzer. See our Sanger Sequencing Sample Requirements webpage for more information about submission requirements.
| Description | Standard Reaction Price per Sample |
1st Tier Reaction6 |
|---|---|---|
| 8 or fewer samples submitted in individual tubes |
$7 | $8 |
|
9-16 samples submitted in 8-strip |
$5 | $6 |
| 17 or more samples submitted in 96-well plate(s) |
$3.50 | $4.50 |
6 DMSO added to reaction, appropriate for high GC DNA or plasmids > 10 kbp.
Genotyping/Fragment Analysis
| Service | Description | Price Per Sample |
|---|---|---|
| Fragment Analysis | AFLP DNA fingerprinting or Short Tandem Repeat (STR) | $1.50 |
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. Researchers submit completely assembled reactions in 96- or 384-well plates. For 96-well plate(s) submissions, the price includes transfer from 96-well plate(s) to 384-well plate and processing on QuantStudio 7 Flex.
| Service | Submission | Price Per Run |
|---|---|---|
| Absolute Quantitation | 1 x 96 well plate | $50 |
| 2 x 96 well plate | $60 | |
| 3 x 96 well plate | $71 | |
| 4 x 96 well plate | $82 | |
| 1 x 384 well plate | $32 | |
| Dissociation Curve | Cost in addition to Absolute Quantitation above | $8.50 |
qPCR Supplies Available for Purchase
| Item | Price Per Item |
|---|---|
| 384 well optical plate | $5 |
| Optical sealing film | $2.50 |
Other Expression Analysis Services
The Genomics 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.
SmartChip RT-qPCR
| Description | Price per Run |
|---|---|
| Flexible, very high-throughput RT-qPCR with 5,184 qPCR reactions. Researcher supplies prepared 384-well plates. | $424 |
NanoString nCounter
| Description | Price7 |
|---|---|
| mRNA assays with Gene Expression Panels, Custom CodeSets or Elements TagSets |
$423/12 sample cassette |
| miRNA assays with NanoString miRNA Panels | $477/12 sample cassette |
| Multiplexed mRNA assays with nCounter PlexSets | $524/96 samples in 12 well cassette |
7 Price 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
| Instrument | Assay | Price |
|---|---|---|
| TapeStation |
High Sensitivity RNA ScreenTape Assay. For analysis of total RNA. |
$9/sample |
| TapeStation |
High Sensitivity D1000 ScreenTape Assay For analysis of prepared libraries, dsDNA PCR products, or fragmented DNA from 35 to 1,000 bp. |
$9/sample |
| TapeStation |
High Sensitivity D5000 ScreenTape Assay For analysis of prepared libraries, dsDNA PCR products, or fragmented DNA from 100 to 5,000 bp. Examples of samples that will be run with this assay are cDNA and ATAC-Seq libraries. |
$13/sample |
| TapeStation |
Genomic DNA ScreenTape Assay For analysis of high molecular weight genomic DNA. |
$13/sample |
Bioanalyzer Analysis Services
Eleven samples can be analyzed per chip on the Bioanalyzer.
| Instrument | Assay | Price |
|---|---|---|
| Bioanalyzer |
RNA 6000 Pico Assay. For analysis of total RNA. |
$137/chip |
| Bioanalyzer |
High Sensitivity DNA Assay For analysis of prepared libraries, dsDNA PCR |
$147/chip |
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. See the Common Use Equipment Room webpage to make a reservation.
| Qubit Kit Name | Description | Price per sample or standard |
|---|---|---|
| Qubit dsDNA BR (Broad Range) Assay |
Fluorometric quantitation of double-stranded DNA. Quantitation range: 2 - 1000 ng. |
$1.40 |
| Qubit dsDNA HS (High Sensitivity) Assay |
Fluorometric quantitation of double-stranded DNA. Quantitation range: 0.2 - 100 ng. |
$1.40 |
| Qubit RNA BR (Broad Range) Assay |
Fluorometric quantitation of Quantitation range: 20 - 1000 ng. |
$1.40 |
| Qubit RNA HS (High Sensitivity) Assay |
Fluorometric quantitation of Quantitation range: 5 - 100 ng. |
$1.40 |
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 520045) and large tubes (1 ml tube, p/n 520135) for purchase. Please contact the Genomics Core (gtsf@msu.edu) to schedule a training session. See the Common Use Equipment Room webpage to make a reservation.
| Description | Price |
|---|---|
| Sample Shearing | $1.50/sample |
| Small Tube (130 µl tube, p/n 520045) | $6.50/tube |
| Large Tube (1 ml tube, p/n 520135) | $7/tube |