DNA Sequencing & Other Services

EnGGen equipment and testing materials

Schedule Instrument Use

EnGGen users are expected to be trained on the correct use of any instrumentation they plan to use and to schedule their use in advance. Instrument use is first-come, first-served. Users may schedule instruments via the LabAgenda website. Users must be invited to the EnGGen facilities calendar via LabAgenda. For more information on the equipment available in EnGGen, see our Information and Resources page.

Professional Services

In addition to providing users with state-of-the-art genetic analyzers and supporting equipment and facilities, the EnGGen research staff is available to conduct genetic analyses of various sample types.

Description of EnGGen services.

Fee-for-Services at EnGGen:

Item

Description

Pipet tips

Sterile, racked pipet tips are available in 10uL, 200uL and 1250uL sizes that fit popular pipettors. Barrier tips, robotic tips, and Ovation pipettor tips are also available.

Plastics and seals

PCR plates (96 or 384 well) are available as well as foil or Microseal B seals for storage. We also have black fluorescence plates for use in a plate reader and Qiagen collection tube racks for sample processing.

PCR 2X mastermix

Several Thermo Scientific PCR mastermixes are provided in 1250uL aliquots. Polymerase options include Maxima Taq, Phire HotStart II and Phusion HotStart II. All are provided with or without green tracking dye included, and all utilize hot start enzymes.

PCR service

We perform the PCR for you.

PCR cleanup

Cleanup to eliminate primers and available nucleotide triphosphates in a PCR reaction. Required prior to cycle sequencing, or in between certain steps.

BigDye aliquot

50uL aliquots of BigDye v3.1 are available so you only purchase as much as you need to perform your own cycle sequencing reactions.

Cleanup solution

PEG-based cleanup solution for your nucleic acid samples.

PicoGreen aliquot

1mL aliquots of pre-diluted PicoGreen are available for fluorometric quantification of your samples.

Extraction reagents

Aliquots of solutions required for several DNA extraction methods are available. Methods include sorbitol (good for plants), high molecular weight (tissue-versitile method), and proteinase K (good for tissues). Supplied volumes will enable about 24 samples to be processed.

Sequencing prep

Cycle sequencing using Applied Biosystems BigDye v3.1 and subsequent cleanup for 3130 or 3730 injection. Requires cleaned PCR product as reaction template. Pricing is available for low- (48 samples, priced per sample) and high-throughput needs (priced per 96 well plate).

Fragment analysis prep

We mix formamide and size standard, add your fluorescently labeled PCR product, and denature your sample for capillary analysis.

Agarose gel analysis

We run a gel of your samples. Required between certain steps.

3130 run

A single injection on our 4 capillary array 3130 sequencer (sequencing or fragment analysis). Good for working out new protocols or when working with only a few samples.

3730 run

A single injection on our 96 capillary array 3730xl sequencer (sequencing or fragment analysis). Good for projects where many samples must be assayed.

Nextera XT prep

The gold standard for Illumina sequencing of small genomes, Nextera XT kits take just 1 ng of input DNA and produce randomly fragmented libraries for sequencing on Illumina instruments. You provide the DNA, we do the prep.

Agilent Bioanalyzer chip

Use of a single chip and necessary reagents. Useful for assessing the quality of fragmented DNA for MiSeq sequencing preps and for assessing the quality of RNA extracts prior to cDNA synthesis.

qPCR Q/C

This is used to quantify the clusterable fraction of a prep meant for sequencing on the Illumina MiSeq. Each sample is run in triplicate and must be run simultaneously with a set of standards of known quantity.

PippinPrep size selection service

The PippinPrep can select size ranges with high reproducibility from Illumina library preps.  This is especially useful for genomic assemblies or for RADseq libraries.

Illumina MiSeq run

The MiSeq can be run in various configurations. Most of the time it is used for sequencing both ends (paired-end sequencing) of short sequences. A 2x150 run (300 cycle) will read 150 bases from each end of every sequence. Since the 2x150 kit contains "v2" chemistry, you can reasonably expect sequence from 10-15 million clusters. v3 chemistry modes (150 and 600 cycle) will yield 15-25 million sequence clusters.

Amplicon prep

Prep samples for metagenetic analysis of complex environmental samples. We have primers for 16S (515F/806R or 515Fmod/926R), fungal-specific ITS2 (5.8S_Fun/ITS4_Fun), large subunit rRNA (LR0R/LR3), and AMF-specific small subunit rRNA (WANDA/AML2). Details for these primers can be found here. Custom designs can be requested. Users can prep a small number of samples and wait for a run to fill up or can choose to purchase a full sequencing run in order to receive data more quickly. We currently have 384 separate indexes for amplicon preps. Submitted samples must be PCR quality.

RADseq prep

Samples are prepped for RADseq using enzymes EcoRI/MseI. We can use alternative enzymes, though some additional cost may be incurred. Samples submitted for RADseq need to be high quality and purity. We typically require at least 25ng per sample, but have achieved success with as little as 1ng input.

Data analysis

We perform post-laboratory analysis of your data. A consultation is required prior to any data analysis service.

Price schedule

Pricing schedule as of April 1, 2017 (external pricing reflects a 49% overhead charge) 


Fee-for-Services: 

Standard plastics (tips, plates and seals)
Service/ItemUnitInternalExternal
10uL tipsrack$2.86$4.26
300uL tipsrack$3.08$4.58
1250uL tipsrack$3.34$4.98
10uL filter tipsrack$6.69$9.97
200uL filter tipsrack$6.69$9.97
1000ul filter tipsrack$8.30$12.37
96 well plate (half-skirt)plate$2.64$3.93
96 well plate (full-skirt)plate$3.15$4.70
384 well plateplate$4.02$5.99
Foil sealseal$0.75$1.12
Microseal Bseal$2.57$3.83

Specialty plastics (extraction, fluorescence, robotic applications)
Service/ItemUnitInternalExternal
2mL screw-top tubes (50 count)bag$7.35$10.95
2.3mm steel beads (10g)     bag$2.14$3.19
Qiagen collection tubes (rack)rack of 96$17.87$26.62
Qiagen collection tube caps (12 strips)12 8-strips$3.97$5.92
250uL Ovation tipsrack$7.73$11.51
250uL Ovation filter tipsrack$11.47$17.09
1250uL Ovation tipsrack$8.88$13.23
20uL robotipsrack$6.86$10.22
200uL robotipsrack$6.86$10.22
96 well black fluorescence platerack$6.86$10.22
384 well black fluorescence platerack$5.80$8.64

DNA extraction reagents
Service/ItemUnitInternalExternal
Sorbitol extraction buffer (40mL)40mL$11.27$16.79
Sorbitol lysis buffer (10mL)10mL$11.07$16.49
HMW lysis buffer (15mL)15mL$11.16$16.63
5M KOAc (5mL)5mL$11.12$16.57
Proteinase K buffer (15mL)15mL$10.90$16.25
Proteinase K (500uL)500uL$31.89$47.52
Chloroform/isoamyl-OH (30mL)30mL$26.81$39.95

PCR reagents
Service/ItemUnitInternalExternal
Maxima Taq polymerase mastermix1250uL$33.88$50.48
Phire HS II polymerase mastermix1250uL$39.84$59.36
Phusion HS II polymerase mastermix1250uL$73.65$109.74
Large agarose gel (B2)gel$3.60$5.36
Small agarose gel (B1A)gel$2.98$6.84

Sequencing and fragment analysis reagents
Service/ItemUnitInternalExternal
BigDye v3.1 (50uL)50uL$100.55$149.82
BigDye v3.1 sequencing buffer (200uL)200uL$13.74$20.47
Genescan 500 LIZ standard (20uL)20uL$35.23$52.50
Genescan 1200 LIZ standard (20uL)20uL$42.01$62.59
HiDi formamide (1mL)1mL$4.59$6.84

Other reagents
Service/ItemUnitInternalExternal
18% PEG solution (10mL)10mL$44.94$66.96
25% PEG solution (10mL)10mL$44.94$66.96
Picogreen (1mL)1mL$7.39$11.02
PippinPrep 2% agarose cassettecassette$62.04$92.44
Indexed primer setplate$91.89$136.91

Sanger sequencing instruments
Service/ItemUnitInternalExternal
3730 runinjection (96 capillary)$80.97$120.64
3130 runinjection (4 capillary)$8.36$12.45

Illumina sequencing (MiSeq)
Service/ItemUnitInternalExternal
50 cycles (v2)run$1,108.93$1,1652.30
300 cycles (v2)run$1,519.73$2,264.39
500 cycles (v2)run$1,785.99$2,661.13
500 cycles nano mode (v2)run$677.79$1,009.90
150 cycles (v3)run$1,314.55$1,958.68
600 cycles (v3)run$2,354.61$3,508.37
50 cycles, user-supplied reagentsrun$86.50$128.89
300 cycles, user-supplied reagentsrun$209.84$312.66
500 cycles, user-supplied reagentsrun$316.50$471.59
500 cycles nano, user-supplied reagentsrun$236.50$352.39
150 cycles, user-supplied reagentsrun$189.84$282.86
600 cycles, user-supplied reagentsrun$423.17$630.52

Laboratory services
Service/ItemUnitInternalExternal
DNA extraction (sorbitol)sample$12.28$18.30
DNA extraction (high MW)sample$12.22$18.20
DNA extraction (proteinase K)sample$13.32$19.84
PCRreaction$1.73$2.58
Agarose gelgel$17.13$25.52
Sample quantification (picogreen)sample$4.01$5.98
Sample quantification (picogreen)plate$68.52$102.10
Sample normalizationplate$65.06$96.93
PEG cleanupplate$117.09$174.46
Low-throughput sequencing prep
(<48 samples)
sample$6.51$9.70
High-throughput sequencing prep
(>48 samples)
plate$176.28$262.65
Fragment analysis prepsample$5.54$8.25
AFLP prepsample$31.98$47.66
RADseq prepsample$23.93$35.66
DIP prepsample$22.25$33.15
Nextera XT prepsample$76.89$114.57
Amplicon prepsample$22.55$33.61
PippinPrepcassette$86.85$129.41
Bioanalyzer DNA1000chip$66.24$98.69
Bioanalyzer High Sensitivitychip$97.85$145.80
Bioanalyzer RNA pico6000chip$64.96$96.79
Library QClibrary$110.29$164.33

Bioinformatics and consulting services
Service/ItemUnitInternalExternal
Technician timehour$49.84$74.26
Compute timeCPU hour$0.63$0.94

Retrieve your data (on-campus or VPN connection required)

Instructions for retrieval

Use a credit card to pay for EnGGen services