Illumina Next Generation Sequencing

Illumina Library Preparation

Standard library preparation is performed with Illumina TruSeq kits. Alternatives are available for low-input or low-quality starting material. Please contact the Genomics Core for more information. 
Kit Type Use 1-16 Libraries 17-32 Libraries 33+ Libraries
TruSeq Nano DNA Shotgun DNA Library Preparation $109.00 $92.00 $86.00
TruSeq Stranded mRNA Sequencing of poly-adenylated mRNA 1 $140.00 $122.00 $115.00
TruSeq Stranded Total RNA Sequencing of RNA with RiboZero rRNA depletion2 $207.00 $188.00 $182.00
TruSeq Small RNA Sequencing of miRNA $176.00 $168.00 $165.00
1Appropriate for high quality, eukaryotic RNA samples
2May be used for bacterial RNA, low-quality (e.g. degraded) eukaryotic RNA, or when you wish to capture ncRNA along with mRNA

Other Library Services

Service Use Per Library
16S V4 or 16S V3V4 amplicon library 1 Amplicon library preparation of the 16S V4 or V3V4 region. $8 per sample
Amplicon barcoding 1 Barcoding of primary PCR product. $8 per sample
Nextera Mate Pair Sequencing libraries with large span distance between paired reads, user specified in range from 2-10kbps $550.00 First library from an input DNA sample; one size specified
    $50.00 For each additional size requested from input DNA (up to two additional)
QC of submitter prepared library Qubit dsDNA, Caliper LabChipGX and Kapa qPCR assays $20.00/library or pool
Size selection of completed library Sage Blue Pippin instrument is used to isolate library fragments in a narrow size range than produced by standard library preparation. Cost is in addition to standard library prep cost. $15.00/library or pool, sizes < 6kbp
    $21.50/Per library or pool, sizes ≥ 6kbp
1See our sample requirements page for more information.

HiSeq 4000

HiSeq 4000 services are purchased per lane. Each lane will output 350-370 million (paired) reads.
Kit Type/Size Sequence Format3 Per Lane Expected Output (Gbp)
50 cycle 1 x 50bp single end $911.00 17.5 - 18.5
300 cycle 2 x 150bp paired end $2,347.00 105 - 111
3Other sequencing formats may be possible but would require the purchase of the entire flow cell (8 lanes). Please contact Emily Crisovan for more information.


Kit Type/Size Sequence Format Per Lane Expected Output(GBp)4 Reads Output (M)
v2 Standard 50 cycle 1 x 50bp single end $909.00 0.6-0.75 12-15
v2 Standard 300 cycle 2 x 150bp paired end $1,200.00 3.6-4.5 12-15
v2 Standard 500 cycle 2 x 250bp paired end $1,315.00 6.0-7.5 12-15
v2 Micro 300 cycle 2 x 150bp paired end $610.00 1.2 4
v2 Nano 300 cycle 2 x 150bp paired end $465.00 0.3 1
v2 Nano 500 cycle 2 x 250bp paired end $581.00 0.5 1
v3 150 cycle 2 x 75bp paired OR 1 x 150bp single end $1,017.00 3.3-3.8 22-25
v3 600 cycle 2 x 300bp paired end $1,799.00 13-15


4When sequencing low diversity libraries, e.g. amplicon libraries for metagenomics, output will be reduced by ~20%.


Sanger Sequencing and Genotyping

Service Description Per Sample      
Cell ID Cell line authentication with Promega GenePrint $35.00      
Fragment Analysis AFLP DNA fingerprinting $1.50      
Short Tandem Repeat(STR)   $1.50      
    Standard Reaction 1st Tier5 Genomic6 GTP7
Low throughput (recommended for ≤8 samples)1,2 Submit in individual tubes $7.00 $8.00 $12.00 $13.00
High throughput (9-16 samples)3,4 Submit in 96 well plates (arrange by column) $5.00 $6.00 $12.00 $13.00
High throughput (≥17 samples) Submit in 96 well plates (arrange by column) $3.50 $4.50 $12.00 $13.00
1Low throughput submission: DNA in 12µl, you may add a custom primer or RTSF will add standard primers
2Submission of more than 8 samples in individual tubes will still be charged at the Low throughput price
3High throughput submission: DNA in 6µl, you may add a custom primer or RTSF will add standard primers
4Submission of 9-16 samples may be in 8-tube strips
5DMSO added to reaction, appropriate for high GC DNA or plasmids > 10kbp
6Samples which are high molecular weight genomic DNA
7DMSO, betaine, and dGTPS added to reaction, appropriate for samples with hairpins or significant secondary structure


QuantStudio 7 Flex qPCR Services

For custom services not listed, please contact Emily Crisovan.

qPCR Services

Users submit completely assembled reactions in 96 or 384 well plates.
Service Submission Per 7900 Run
Absolute Quantitation1 1 x 96 well plate $45.00
  2 x 96 well plate $60.00
  3 x 96 well plate $75.00
  4 x 96 well plate $90.00
  1 x 384 well plate $40.00
Dissociation Curve Cost in addition to Absolute Quantitation above $8.50
1Price includes transfer from 96 to 384 well plates and processing on QuantStudio 7 Flex.

qPCR Supplies Available for Purchase

Item Price
384 well optical plate $5.00 each
Optical sealing film $1.50 each


Other Expression Analysis Services

Service Description Price
SmartChip RT-qPCR (Takarabio/Wafergen) Flexible, very high-throughput RT-qPCR with 5,184 qPCR reactions $430.00 per basic run (user supplies prepared 384-well plates)
    $490.00 per basic run (Genomics Core assembles 384-well assay and sample plates)
NanoString nCounter Direct DNA/RNA counting with predefined panels mRNA $260.00/12 sample cassette
    miRNA $370.00/12 sample cassette
    PlexSet $345.00/96 samples in 12 well cassette
    CNV $435.00/12 sample cassette



Sample QC and Other

Service Description Price
Qubit1 Fluorometric DNA/RNA quantitation $0.60/sample
Agilent 2100 Bioanalyzer1 - DNA/RNA microcapilliary based sizing and quality assay DNA 1000 Chip - up to 12 samples/chip $35.00/chip
  DNA High Sensitivity Chip - up to 11 samples/chip $55.00/chip
  RNA Pico Chip - up to 11 samples/chip $35.00/chip
Covaris AFA DNA shearing1 Acoustic shearing of dsDNA $8.50/sample (includes cost of Covaris tube)
1These are self-service equipment. All users must be trained by Genomics Core staff prior to use. To schedule a training session, please contact


All payment methods, besides MSU accounts, will be subject to a 2% University Administrative Fee.