Platform:
LifeTechnologies OpenArray Panels
Category:
Gene Expression Analysis
Primary Contact:

Christopher Krebs, Manager, UM DNA Sequencing Core

ckrebs@umich.edu

734-763-8891

 

Typical Cost:

Panels: $147.00 to $187.20 per sample.

RNA Processing: $125 to $144 per sample.

Typical Output:

Report containing statistical assessment of comparative groups is provided along with the raw Ct data in format compatible with Microsoft Excel.

How to request:

Sample Submission: go to http://seqcore.brcf.med.umich.edu then choose “Microarray Gene Expression Analysis”

Sample requirements:

A minimum of 250 ng total RNA for Standard Processing

A minimum of 10 ng total RNA for High Sensitivity Processing

Typical Turnaround:

3 to 4 weeks, however, timing is dependent on availability of arrays, which are purchased as needed.

Critical information:

RNA quality and concentration are confirmed for an additional fee (see QC FAQ) before beginning any Microarray project. Please consult with the Manager before submitting samples that are known or suspected to be of low concentration or highly degraded (i.e., from FFPE sources

More information:

For a list of arrays available, product descriptions and additional technical information, go to the ThermoFisher Scientific website or the Life Technologies PunchOut via M-Marketsite:

For more information about RNA quality checks, go to: FAQ for QC

For other options for gene expression analysis (e.g., RNA-seq) go to: FAQ for Next Generation Sequencing (NGS).

Platform:
Qiagen RT2 Profiler Array Plates
Category:
Gene Expression Analysis
Primary Contact:

Christopher Krebs, Manager, UM DNA Sequencing Core

ckrebs@umich.edu

734-763-8891

Typical Cost:

Panels: $283.50 per plate (1 plate can analyze up to 4 samples).

RNA Processing: $58.50 per sample.

Typical Output:

Report containing statistical assessment of comparative groups is provided along with the raw Ct data in format compatible with Microsoft Excel.

How to request:

Sample Submission: go to http://seqcore.brcf.med.umich.edu/ then choose “Microarray Gene Expression Analysis”

Sample requirements:

A minimum of 100 ng total RNA for Standard Processing

 

A minimum of 25 ng total RNA for High Sensitivity Processing

 

Typical Turnaround:

3 to 4 weeks, however, timing is dependent on availability of arrays, which are purchased as needed.

Critical information:

RNA quality and concentration are confirmed for an additional fee (see QC FAQ) before beginning any Microarray project. Please consult with the Manager before submitting samples that are known or suspected to be of low concentration or highly degraded (i.e., from FFPE sources).

More information:

For a list of arrays available, product descriptions and additional technical information, go to the Qiagen website: https://www.qiagen.com/us/shop/pcr/primer-sets/rt2-profiler-pcr-arrays/

 

For more information about RNA quality checks, go to: FAQ for QC

 

For other options for gene expression analysis (e.g., RNA-seq) go to: FAQ for Next Generation Sequencing (NGS).

Platform:
Illumina iScan
Category:
GeneExpression
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 theCore Technician hours to complete the project and Illumina BeadChip Kit costs. Core Tech Hours can vary based on the purity of the samples and whether they need additional purification using the Agencourt RNACleanXP bead protocol.

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 Whole Genome GeneExpression BeadChip kit (Illumina, Inc) plus shipping costs.

Typical Output:

For human, >47,000 probes are analyzed to generate a GeneExpression Profile. Illumina offers two GeneExpression Analysis products for mice: 1). >25,000 RefSeq probes analyzed and 2). > 45,000 probes designed from RefSeq, the MEEBO set and the RIKEN FANTOM2 database. For generating Gene Expression Profiles, the iScan is set to record data that can be used with the Illumna GenomeStudio data analysis software package as well as other software such as Bioconductor, GeneSpring, and ArrayExpress.

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:

Quantity: We request 100ng/ul (25ul). If you do not have this concentration, please contact Susan Dagenais (sdagenai@umich.edu)

Quality: NanoDrop – the manufacturer of the Illumina TotalPrep RNA Amplification kit recommends that the 260/280 and 260/230 ratios should be >2.0 for best results in generating labled cRNA. A 260/280 ratio <1.8 indicates protein in the prep and a 260/230 ratio <1.5 suggest there is an excess of salts, which may affect amplification.

It is important that the total RNA is free of genomic DNA contamination.

BioAnalyzer – Request that RNAs have a RIN value >8.0 as RNA degradation can lead to incorrect conclusions of the expression data. RNA samples isolated using TRIzol® should be further cleaned by the Qiagen RNA cleanup procedure or the Agencourt RNAClean XP procedure.

RNA QC for quantity and quality is required BEFORE Illumina Whole Genome Gene Expression kit will be ordered.

Typical Turnaround:

Typical turnaround time is 2-4 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. Computer Workstations are available for clients to perform their own analysis using the Illumina GenomeStudio DNA Analysis Software packages.
  3. The Client must perform their own data analysis or consult with a Bio-informatics specialist.
More information:
Platform:
Fragment Analysis
Category:
Genotyping - Microsatellite
Primary Contact:

Suzanne Genik genik@umich.edu 734-764-8067

Typical Cost:
  Core Made CE Plate Running CE Plate
Internal $23.00 $29.90
External $38.00 $49.40
Typical Output:

Raw data .fsa files are generated from the 96 well CE plate.

GeneMarker software from SoftGenetics is available for clients to check out to analyze fragment analysis data.

How to request:

Sample Submission: go to https://client-seqcore.brcf.med.umich.edu then choose ‘Submit Fragment Analysis Samples or CE plates’

Sample requirements:

CE Loading plates submitted by clients must contain a size standard in 12ul/well of Hi- Di Formamide plus 1 ul of sample diluted in water.Clients may choose the number of wells to fill with samples.All wells must have 12ul of a liquid in them (Hi-Di Formamide or water with no sample).

Typical Turnaround:

Between 1 to 3 days, depending on how much business Sanger sequencing is processing.

Critical information:

Contact the core to consult the compatibility of the fluorescentdyes used with your samples and calibration dyes for our 3730XL Genetic  Analyzer Instrument .A proper dilution of PCR products in CE Loading plates isnecessary to prevent over loading of array capillaries with highfluorescent signal intensities and could contaminate the next plate run.It is important to Label your CE loading plates with the identification plate number assigned by our database on submission.

More information:

Clients must have an account set up with the DNA Sequencing Core prior to submission of samples. The clients can use any of our drop off locations listed on our web page: http://seqcore.brcf.med.umich.edu/.

Ce Plates received from outside the University of Michigan can be shipped to: University of Michigan, DNA Sequencing Core, NCRC Bld 14, Room 122, 2800 Plymouth Road, Ann Arbor, MI 48109-2800. Plates must be shipped on gel ice packs.

CE loading plates prepared and submitted by clients are required to use ABI Optical plates or Optical ABI compatible 96 well plates with a barcode.

Acceptable bar coded plates are:

  • 96 Well Optical Reaction Plates with Barcode code 128 from Life Technologies-AppliedBiosystems Part Number 4306737
  • 96 Well Semi-Skirted plate w/Raised rim, Barcoded from BioExpress Part Number T-3107-1BCCS
  • Hi-Di Formamide from Life Technologies-AppliedBiosystems Part Number 4311320C.
Platform:
Fragment Analysis
Category:
Genotyping with Identifiler Plus Kit
Primary Contact:

Suzanne Genik genik@umich.edu 734-764-8067

Typical Cost:

The cost for each Identifiler Plus sample is $34.00. This includes PCR reactions performed by the core, samples run on the 3730XL DNA Genetic Analyzer and analysis of data with GeneMapper software. The cost for processing of Identifiler Plus samples submitted from outside the University is $44.20 per sample.

Typical Output:

Raw data .fsa files are generated for each sample. GeneMappersoftware is used to analyze the data and .pdf documents aregenerated  of the analyzed data. HID GeneMarker softwarefrom SoftGenetics is available for clients to check out andanalyze data themselves.

How to request:

Sample Submission: go to https://client-seqcore.brcf.med.umich.edu then choose ‘Submit Fragment Analysis Samples or CE plates‘.

Sample requirements:

Submit 20ul of DNA sample at a concentration of 0.1 ng/ul in Ultra pure RNase, DNase free water or EB Buffer.

Typical Turnaround:

Between 1 to 3 days. The Identifiler Plus samples take a couple of days to process.

Critical information:

Submit samples in 1.5 ml microcentrifudge tubes. It is important to Label each tubes with the identification number assigned by our database on submission of your samples.

More information:

The HID GeneMarker software is available to check out at room 2568 MSRB II.

Clients must have an account set up with the DNA Sequencing Core prior to submission of samples.

The clients can use any of our drop off locations listed on our web page: http://seqcore.brcf.med.umich.edu/.

Identifiler Plus samples received from outside the University of Michigan can be shipped to: University of Michigan, DNA Sequencing Core, NCRC Bld 14, Room 122, 2800 Plymouth Road, Ann Arbor, MI 48109-2800.

Platform:
MassARRAY® (Sequenom, dba Agena Bioscience)
Category:
Genotyping
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 $1220
Half Chip 192 $820
Quadrant 96 $630
Pinset 24 $420

 

Typical Output:

Excel files containing allele calls—separate file for each assay, delivered via email.

How to request:

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

Sample requirements:

For each SNP-plex reaction, we need 5-10uL of 50-100ng/uL genomic DNA if quantitated on nanodrop, 25-50ng/uL if quantitated with picogreen on fluorimeter.

Typical Turnaround:

Depends on number of samples and number of targets 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:

  • Assay design—2 to 4 hours, depending on number of targets
  • Sample processing—4 to 6 hours, depending on number of samples/SNPs
  • Reaction spotting—2 to 4 hours, depending on total number of chips
  • Data analysis—2 to 4 hours per chip
More information:

All custom primer orders are billed to a short code provided by the client: e.g., the interrogation of 40 variants requires 3 primers per target = 120 primers @ ~$5 per primer = ~$600. This order would yield enough primer to investigate at least 1,000 samples.

Platform:
Affymetrix Microarray
Category:
Gene Expression Analysis
Primary Contact:

Christopher Krebs, Manager, UM DNA Sequencing Core

ckrebs@umich.edu

734-763-8891

Typical Cost: Typical Output:

Over 40,000 RefSeq transcripts and over 10,000 lncRNAs are compared in a single gene expression experiment.

Over 30,000 mature miRNAs are compared with the latest miRNA arrays.

Data quality and group comparisons are assessed statistically and provided in a brief report. Raw data is exported as .CEL files and in an Excel spreadsheet. Help is available for submitting the data to external repositories (e.g., Gene Expression Omnibus (GEO) at NCBI).

How to request:

Login through https://client-seqcore.brcf.med.umich.edu and then choose “Sample QC” to submit samples.

Sample requirements:

A minimum of 250 ng total RNA for Standard Processing

A minimum of 10 ng total RNA for High Sensitivity Processing

Typical Turnaround:

3 to 4 weeks, however, timing is dependent on availability of arrays, which are purchased as needed.

Critical information:

RNA quality and concentration are confirmed for an additional fee before beginning any Microarray project. Please consult with the Manager before submitting samples that are known or suspected to be of low concentration or highly degraded (i.e., from FFPE sources).

More information:

For a list of arrays available, product descriptions and additional technical information, go to the Affymetrix website at: http://www.affymetrix.com

For more information about RNA quality checks, go to: FAQ for QC

For other options for gene expression analysis (e.g., RNA-seq) go to: FAQ for Next Generation Sequencing (NGS).

Platform:
Illumina iScan
Category:
Genotyping
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 theCore Technician hours to complete the project and Illumina BeadChip Kit costs. Core Tech Hours can vary based on the amount of normalization that must be done to the samples prior to starting the assay.

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 Whole Genome Genotyping BeadChip kit (Illumina, Inc) plus shipping costs.

Typical Output:

Typical call rates are >99% for all standard Illumina GoldenGate, Infinium, and LCG Array products.

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:

DNA Concentration Request – dependent upon how the stock DNA concentration was determined.

  1. PicoGreen/Qubit – 50-55ng/ul (10-12ul)
  2. NanoDrop - 100ng/ul (20-25ul)
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. For Plate submissions, the Core will assign Core Sample ID numbers and a Core Plate ID numbers, which will be written on the side of the plate.
  2. The Core offers Qubit/PicoGreen and Normalization service for $2/sample (see link in More Information).
  3. If samples need to be normalized to 50-55ng/ul, they should be submitted in 1.5mL tubes with the BeadArray Core Sample ID written on top.
  4. If samples are normalized to 50-55ng/ul (PicoGreen/Qubit), the samples can be submitted in either in 1.5mL tubes or in plates with samples arranged in columns (A1, B1, C1, etc).
  5. Unused DNA will be returned after project is completed.
  6. Computer Workstations are available for clients to perform their own analysis using the Illumina GenomeStudio DNA Analysis Software packages.
  7. For the Illumina BeadArray platform, the Client must perform their own data analysis or consult with a Bio-informatics specialist.
More information: