Platform:
Qiagen/Autogen
Category:
Genomic DNA Isolation
Primary Contact:

Christopher Krebs, Manager, UM DNA Sequencing Core

ckrebs@umich.edu

734-763-8891

 

Typical Cost:

Fresh Whole Blood: $22.00 per sample

Frozen Blood: $30.00 per sample

Cell Lysate:: $12.00 per sample

Frozen Cell Lysate: $18.00 per sample

Saliva: $17.00 per sample

Typical Output:

160 – 500 ug DNA from 10 ml whole blood

5 – 10 ug DNA from 106 cells

1 – 10 ug DNA from 400 ul saliva + stabilizing solution (e.g., Norgen Biotek)

How to request:

Sample Submission: go to http://seqcore.brcf.med.umich.edu/ then choose “Genomic DNA Isolation”

Sample requirements:

Unfrozen whole blood or cell lysates must be delivered on ice.

Frozen blood, cells or lysates must be delivered on dry ice.

Saliva collection tubes from Norgen or Oragene contain stabilizers, compatible with our isolation methods that allow long-term storage and delivery at room temp.

Typical Turnaround:

48 to 72 hrs. for batches of 100 or less.

Throughput (throughput fluctuates when sample sizes > 200):

blood – 48 samples per week

saliva – 192 samples per week

Critical information:

For large projects with cumulative sample collection strategies, please consult with the Manager to coordinate workflow.

More information:

For more information on the products used for this service, go to the following websites:

http://www.autogen.com

http://www.qiagen.com

http://www.norgenbiotek.com

http://www.dnagenotek.com

Platform:
qPCR Instrument Rental
Category:
qPCR Instrument Rental
Primary Contact:

Christopher Krebs, Manager, UM DNA Sequencing Core

ckrebs@umich.edu

734-763-8891

Typical Cost:

All instruments are $16.00 per run

Typical Output:

Your results will be emailed to you shortly after your run is completed. The data (Ct-values) will be in the form of a text (.txt) file that can be opened in Microsoft Excel as well as in an instrument-specific format (.sds or .eds) that will require the instrument’s software to open.

How to request:

Reserve a time through the following link: https://client-seqcore.brcf.med.umich.edu/

Bring your plate to the appropriate drop-off location at or before your scheduled appointment. No submission required.

Sample requirements:

The plates must be compatible with the instrument of choice and be in ready-to-run condition when you drop them off.

Please make every effort to drop off your plates BEFORE your scheduled appointment time. Runs with Dissociation (aka. Melt) Curves and cycling conditions that deviate from the default settings ((95-degrees C, 15 sec, 60-degrees C, 1 min) x 40) can result in run times that extend beyond 2 hrs. If at all possible, please use the 11am or 4pm time slots for runs of this nature.

Typical Turnaround:

< 24 hrs

Critical information:

Recommended plates for each instrument.

ABI 7900HT:

MicroAmp Optical 384-well Reaction Plate (cat# 4343370)

MicroAmp Optical 96-well Reaction Plate (cat# 4316813)

 

ABI StepOne Plus

MicroAmp Fast Optical 96-Well Reaction Plate, 0.1 mL (cat# 4346907)

More information:

Users Principle Investigators (PIs) must be registered with the DNA Sequencing Core and have an account (shortcode) that is both active AND listed as an account associated with the PI.

Platform:
Qubit 2.0 Fluorometer
Category:
DNA and RNA QC
Primary Contact:

Christopher Krebs, Manager, UM DNA Sequencing Core

ckrebs@umich.edu

734-763-8891

Typical Cost:

All Qubit options (see Critical information) are $1.30 per sample

Typical Output:

You will get back the sample's concentration in a Microsoft Excel spreadsheet.

How to request:

Bring your samples to 2568 MSRB II or the DNA Sequencing Core in Building 14, NCRC where you will be asked to fill in contact and billing (shortcode) information on an electronic submission form.

Sample requirements:

We request a minimum of 5ul of each sample for analysis. The samples for “QC only” should be in a separate tube from the portion of sample intended for other services within the core. This assists us in minimizing freeze thaw cycles.

Typical Turnaround:

24 to 48 hrs

Critical information:

Assay Ranges:

Qubit RNA Assay: 0.25 - 100 ng/ul

Qubit High Sensitivity dsDNA Assay: 0.01 - 100 ng/ul

Qubit Broad Range dsDNA Assay: 0.1 – 1000 ng/ul

Qubit ssDNA Assay: 0.05 – 200 ng/ul

More information:

The Qubit® 2.0 Fluorometer utilizes specifically designed fluorometric technology using Molecular Probes® dyes. These fluorescent dyes emit signals

ONLY when bound to specific target molecules, even in the presence of free nucleotides or degraded nucleic acids. Qubit® fluorometric quantitation

provides the most specific and sensitive DNA and RNA quantitation available, even at low concentrations

 

Link to additional information about the Qubit: http://www.thermofisher.com/content/dam/LifeTech/migration/en/filelibrar...

Platform:
NanoDrop Spectrophotomer
Category:
DNA and RNA QC
Primary Contact:

Christopher Krebs, Manager, UM DNA Sequencing Core

ckrebs@umich.edu

734-763-8891

Typical Cost:

NanoDrop Measurement: $1.30 per sample

 

Typical Output:

You will get back an Excel spreadsheet report that contains the sample concentration and photometric values across several wavelengths, including O.D. 260/280 and O.D. 260/230 ratios to assess purity.

How to request:

Bring your samples to 2568 MSRB II or the DNA Sequencing Core in Building 14, NCRC where you will be asked to fill in contact and billing (shortcode) information on an electronic submission form.

Sample requirements:

We request a minimum of 5ul of each sample for analysis by NanoDrop. The samples for “QC only” should be in a separate tube from the portion of sample intended for other services within the core. This assists us in minimizing freeze thaw cycles.

Typical Turnaround:

24 to 48 hrs

Critical information:

Sensitivity:

5 - 3700 ng/ ul dsDNA

5 - 3000 ng/ ul RNA

5 - 2400 ng/ ul ssDNA

More information:

O.D.260/280: a ratio of ~1.8 is accepted as “pure” DNA and a ratio of ~2.0 is accepted as “pure” RNA. Phenol or protein contamination will appreciably lower this ratio.

O.D.260/230: a ratio above the O.D.260/280 ratio is accepted as “pure” nucleic acid. Typical values vary from 1.8 to 2.2. Appreciably lower values may indicate the presence of co-purified contaminants.

Link to additional information about NanoDrop: http://www.nanodrop.com/Productnd2000overview.aspx

Platform:
Agilent Bioanalyzer and TapeStation
Category:
DNA and RNA QC
Primary Contact:

Christopher Krebs, Manager, UM DNA Sequencing Core

ckrebs@umich.edu

734-763-8891

Typical Cost:

RNA 6000 Nano Chip (1 - 12 samples per chip): $36.00 per chip

RNA 6000 Pico Chip (1 - 11 samples per chip): $38.00 per chip

RNA small RNA Chip (1 – 11 samples per chip): $38.00 per chip

DNA 1000 Chip (1 - 12 samples per chip): $37.00 per chip

DNA 12K Chip (1 - 12 samples per chip): $37.00 per chip

DNA High Sensitivity Chip (1 - 11 samples per chip): $58.00 per chip

Typical Output:

You will get back a PDF report that contains the samples electropherogram and pseudo-gel images, as well as a concentration and, for RNA, a RIN value.

How to request:

Bring your samples to 2568 MSRB II or the DNA Sequencing Core in Building 14, NCRC where you will be asked to fill in contact and billing (shortcode) information on an electronic submission form.

Sample requirements:

We request a minimum of 5ul of each sample for analysis by Bioanalyzer. The samples for “QC only” should be in a separate tube from the portion of sample intended for other services within the core. This assists us in minimizing freeze thaw cycles.

Typical Turnaround:

24 to 48 hrs

Critical information:

Bioanalyzer

RNA 6000 Nano Kit: 5-500 ng/ul, RNA Size range: 25-6000 nt

RNA 6000 Pico Kit: 50-5000 pg/ul RNA Size range: 25-6000 nt

RNA small RNA Kit: 1-100 ng/ul RNA Size range: 6-150 nt

DNA 1000 Kit: 0.1-50 ng/ul DNA Size range: 25-1000 bp

DNA 12K Kit: 0.5-50 ng/ul DNA Size range: 100-12000 bp

DNA High Sensitivity Kit: 5-500 pg/ul DNA Size range: 50-7000 bp

TapeStation

RNA ScreenTape: 25-500 ng/ul, RNA Size range: 100-6000 nt

High Sensitivity RNA ScreenTape: 1-25 ng/ul RNA Size range: 100-6000 nt

DNA 1K ScreenTape: 0.1-50 ng/ul DNA Size range: 35-1000 bp

High Sensitivity DNA ScreenTape: 10-1000 pg/ul DNA Size range: 35-1000 bp

Genomic DNA ScreenTape: 5-300 ng/ul DNA Size range: 200-60,000 bp

More information:

The RIN, or RNA Integrity Number, is a method for determining RNA quality. RIN is calculated algorithmically by including the 28s/18s ratio, the region before the peaks, signal areas, and intensities. These calculations enable use of the whole graph to make RNA quality assessments. We make an initial assessment of total RNA QC based on 260/280 and 260/230 ratios. However, we place the highest reliance for QC on the Bioanalyzer integrity assessment. Each sample is assigned a RIN score: 10 corresponds to a pure, un-degraded total RNA sample while a RIN of 1 corresponds to a completely degraded sample. The core recommends only using samples with RIN's greater than 7.

Link to additional information for interpreting Agilent 2100 Bioanalyzer data: http://www.urmc.rochester.edu/fgc/documents/Bioanalyzer_Interpretations_forcustomers.pdf

Platform:
MassARRAY® (Sequenom, dba Agena Bioscience)
Category:
Methylation Analysis
Primary Contact:

Ellen Pedersen - Research Specialist: Sequenom and PyroMark Services University of Michigan DNA Sequencing Core - NCRC Building 14 Room 134 734-615-5646

Typical Cost:
Service rxns Cost
Full Chip 384 $1690
Half Chip 192 $1055
Quadrant 96 $748
Pinset 24 $450

 

Typical Output:

EpiReport Excel files containing tabulated methylation percentages and run metrics, and EpiGram jpeg files containing graphical representations of methylation levels.

How to request:

Contact Dr. Lyons for initial consultation; if he deems project appropriate for Sequenom, contact Ellen Pedersen.

Sample requirements:

Clients submit bisulfite converted and amplified products; these should be gel quantitated, according to the guidelines provided in the conversion and amplification kits recommended by Sequenom/Agena.

Typical Turnaround:

Depends on number of samples and number of amplicons to be assayed.

Critical information:

The fixed costs described above do not include labor, which is charged at the current approved rate and estimated as follows:

  • Sample processing—2 to 3 hours, depending on # of samples/amplicons
  • Reaction spotting—2 to 4 hours, depending on total number of chips
Platform:
Illumina iScan
Category:
Epigenetics
Primary Contact:

Susan Dagenais, Ph.D.
UM DNA Sequencing Core
e-mail: sdagenai@umich.edu
Phone: 734-615-8743
Fax: 734-763-8889

Typical Cost:

The DNA Sequencing Core will provide a Quote for Core Processing fees, which is based on the Estimation of the Core Technician hours to complete the project and Illumina BeadChip Kit costs.

Internal Costs:

The cost per project is based on an hourly rate of $86/hour and the number of Technician Hours to complete the project.

External Costs:

External projects are charged a 29% surcharge for Core Processing fees. We request the Client purchase kits directly from Illumina and ship them to the DNA Sequencing Core as we would need to charge a 29% surcharge for the cost of the kits. Please contact Susan Dagenais (sdagenai@umich.edu) for shipping information.

Core Services Billing:

Core service fees can only be bill after the work is completed. We cannot pre-bill for core services for clients wanting to spend expiring grant funds.

Illumina Kit Reagent Billing:

The Client will be billed for the cost of the entire Infinium Methylation450 BeadChip kit (Illumina, Inc) plus shipping costs.

Typical Output:

Methylation profiling of >450,000 loci. For generating Methylation Profiles, the iScan is set to record data that can be used with the Illumna GenomeStudio data analysis software as well as other software such packages such as Bioconductor.

How to request:

Sample Submission – Contact Susan Dagenais (sdagenai@umich.edu) and request a Project Quote. Please indicate the number of samples to be assayed and which Illumina BeadChip kit you would like used for the assay. We will e-mail you a Quote for the Illumina Kit costs and estimated Core Processing fees. Once we a signed Quote, we will place an order with Ilumina, assign a Core Project Number, and you will be sent a BeadArray submission form for sample submission.

Sample requirements:

The client will submit bi-sulfite converted DNA (8-10ul at 50ng/ul). Bi-sulfite converted DNA should be created using the Zymo EZ_DNA_Methylation kit (ZymoResearch) using Illumina incubation conditions (Appendix 6). For FFPE samples, we perform the Illumina FFPE Restoration protocol on bi-sulfite converted DNA submitted by the client.

Typical Turnaround:

Typical turnaround time is 1-3 weeks.

Critical information:
  1. The Core will assign Core Sample ID numbers, which you will write on top of 1.5mL tubes containing your samples.
  2. Illumina recommends using the Zymo EZ_DNA_Methylation kit (see link).  In Appendix 6 of the manual, there are conditions to be used for the Illumina platform.  If you start with 500ng of genomic DNA, then elute with 10ul to give 50ng/ul.   If you start with 1000ng of genomic DNA then elute with 20ul.
  3. Illumina recommends using the PicoGreen or Qubit assay to determine the starting concentration of your DNA.
  4. It is recommend that you have all of the DNA collected and concentrations verified before placing an order with Illumina for the kit.
  5. Computer Workstations are available for clients to perform their own analysis using the Illumina GenomeStudio DNA Analysis Software packages.
  6. The Client must perform their own data analysis or consult with a Bio-informatics specialist.
More information: