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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.

NovaSeq 6000

MiSeq

Illumina-Compatible Library Preparation

10x Genomics Chromium Single Cell Libraries

Oxford Nanopore Library Preparation

Oxford Nanopore Flow Cells

High Molecular Weight Genomic DNA Extraction

Sanger Sequencing

Genotyping/Fragment Analysis

QuantStudio 7 Flex qPCR

SmartChip RT-qPCR

NanoString

TapeStation and Bioanalyzer Analysis

Qubit Fluorometric Quantitation

Covaris Sonicator


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.

Download a PDF of this table.

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

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
Price per Sample

8 or fewer samples submitted
in individual tubes
$7 $8

9-16 samples submitted in 8-strip
PCR tubes or 96-well plate

$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
(sizing range 35 - 1,000 bp)

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
(sizing range 100 - 5,000 bp).

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
(sizing range 200 - 60,000 bp)

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
(sizing range 50 - 7,000 bp)

For analysis of prepared libraries, dsDNA PCR
products,or fragmented DNA.

$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
total RNA.

Quantitation range: 20 - 1000 ng.

$1.40
Qubit RNA HS (High Sensitivity) Assay

Fluorometric quantitation of
total RNA.

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