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Applied Genomics Technology Center (AGTC)

Detroit, Michigan, US

The Applied Genomics Technology Center (AGTC), a part of Wayne State University School of Medicine’s Department of Obstetrics and Gynecology, is an exceptional research support core facility located on campus. Housed on the ground floor of the C.S. Mott Center for Human Growth and Development, the AGTC is a state-of-the-art, fee-for-service genomics center that provides a wide range of genomic technologies to the medical research community. In addition to instrumentation, AGTC personnel are available to work with investigators to optimize experiments to meet their scientific goals.

Applied Genomics Technology Center (AGTC) has not listed any services.

Illumina Sequencing
Price on request

NGS on Illumina MiSeq

NGS on Illumina MiSeq

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Bioinformatics
Price on request

Our services include analysis of the following types of data:
- RNAseq
- Illumina microarray
- Infinium methylation

The type and level of analysis is project-dependent. Investigators are encouraged to discuss data requirements with our bioinformatician prior to analysis.

Our services include analysis of the following types of data:
- RNAseq
- Illumina microarray
- Infinium methylation

The type and level of analysis is project-dependent. Investigators are encouraged to discuss data requirements with our bioinformatician prior to analysis.

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DNA Quantification
Price on request

The Applied Genomics Technology Center (AGTC) employs two methodologies for the determination of DNA quantity: The NanoDrop™ 1000 (low-throughput) and the DropSense 96® (high-throughput) UV/VIS spectrophotometry-based platforms, or the Qubit® 2.0 Fluorometer for more sensitive applications.

The Applied Genomics Technology Center (AGTC) employs two methodologies for the determination of DNA quantity: The NanoDrop™ 1000 (low-throughput) and the DropSense 96® (high-throughput) UV/VIS spectrophotometry-based platforms, or the Qubit® 2.0 Fluorometer for more sensitive applications.

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Genomic DNA Extraction
Price on request

The Applied Genomics Technology Center (AGTC) has vast experience with genomic DNA isolation from a variety of sample sources including whole blood, blood clots, dried bloodspots, buffy coats, plasma, serum, urine, saliva, mouthwashes, buccal swabs, cultured cells, fresh/frozen tissues, and paraffin-embedded tissues. We offer a... Show more »

The Applied Genomics Technology Center (AGTC) has vast experience with genomic DNA isolation from a variety of sample sources including whole blood, blood clots, dried bloodspots, buffy coats, plasma, serum, urine, saliva, mouthwashes, buccal swabs, cultured cells, fresh/frozen tissues, and paraffin-embedded tissues. We offer a great variety of methodologies to our investigators which allows for successful genomic DNA isolation from even the most challenging of starting materials.

The DNA Isolation Lab is equipped with two automated, magnetic bead-based isolation systems: The Qiagen EZ1® Advanced and QIASymphony. Automated systems allow greater yield and uniformity as well as a decrease in turnaround time.

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Illumina DNA Microarray
Price on request

The Microarray facility offers complete sample processing services for select products for the Illumina BeadChip® platform.

The Microarray facility offers complete sample processing services for select products for the Illumina BeadChip® platform.

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Global Methylation Analysis
Price on request

The Applied Genomics Technology Center provides the following DNA methylation services:
- Next-Generation Sequencing methylation analysis
- DNA methylation profiling using Illumina Infinium® Assay Technology

Sample Requirements:

Submit 20 ul of DNA at a concentration of 50ng/ul

Note: The AGTC staff will work with... Show more »

The Applied Genomics Technology Center provides the following DNA methylation services:
- Next-Generation Sequencing methylation analysis
- DNA methylation profiling using Illumina Infinium® Assay Technology

Sample Requirements:

Submit 20 ul of DNA at a concentration of 50ng/ul

Note: The AGTC staff will work with investigators to optimize these assays for their specific sample types.

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Microarray Data Analysis
Price on request

The Microarray facility offers complete sample processing services for select products for the Illumina BeadChip® platform for single-color micorarray analysis and the Agilent Microarray platform for both one and two-color assays. Each platform offers a variety of gene expression analysis options including 3’, whole transcript,... Show more »

The Microarray facility offers complete sample processing services for select products for the Illumina BeadChip® platform for single-color micorarray analysis and the Agilent Microarray platform for both one and two-color assays. Each platform offers a variety of gene expression analysis options including 3’, whole transcript, whole genome, and focused array products. Please consult with the AGTC to determine the best platform/product for your specific experiment.


Sample Requirements:
- 1 ug of purified total RNA in 20 ul of nuclease-free water is required for most microarray applications. Please consult the Microarray Department regarding alternatives. Samples may be submitted in nuclease-free 0.5 ml or 1.5 ml microcentrifuge tubes, or in a properly sealed (PCR foil seals) 96-well PCR plate.
- RNA samples must be stored at -80°C and transported to the AGTC on dry ice.


Turn-around time: approximately 2 weeks from sample submission date

*Note: The microarray lab makes every effort to complete projects within 2 weeks of sample submission date. However, processing times will vary depending on current AGTC workload, project scope, array platform, and product availability.

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RNA Extraction
Price on request

Total RNA isolation services are available for cultured cells, blood, fresh frozen tissue, and formalin-fixed paraffin embedded (FFPE) tissue. Cells and tissue are disrupted and homogenized in QIAzol™ Lysis Reagent (Qiagen), nucleic acids retrieved by Chloroform extraction, and total RNA purified using the Qiagen EZ1® Advanced.... Show more »

Total RNA isolation services are available for cultured cells, blood, fresh frozen tissue, and formalin-fixed paraffin embedded (FFPE) tissue. Cells and tissue are disrupted and homogenized in QIAzol™ Lysis Reagent (Qiagen), nucleic acids retrieved by Chloroform extraction, and total RNA purified using the Qiagen EZ1® Advanced. Tissues that require more vigorous physical manipulation are homogenized using the Qiagen TissueLyser II®.

Total RNA isolation from blood is performed using the PAXgene™ Blood RNA System (PreAnalytiX). This method requires specific sample collection tubes available from PreAnalytiX and specific handling instructions.

FFPE samples are processed using the RecoverAll™ Total Nucleic Acid Isolation Kit (Ambion, AM1975)

NOTE:

For miRNA (micro RNAs), the AGTC currently employs a high-throughput, automated method which requires a minimum of 48 samples. Please inquire for specific details regarding miRNA sample requirements and options.

Sample Requirements -Total RNA

All samples submitted for RNA isolation should be prepared as described in the following flowchart . Cells and tissues must be submitted in an appropriately labeled, Eppendorf BioPur Safe-Lock 2.0 ml microcentrifuge tube (cat.# 022600044). If you do not have access to these tubes, the AGTC will supply them for you. Blood must be submitted in PAX Blood RNA collection tubes. FFPE sections (8 x 10µm) must be submitted in flip-top, nuclease-free, 1.5 ml microcentrifuge tubes.

All Cell/Tissue/Blood samples must be stored at -80°C and transported to the AGTC on dry ice. FFPE at room temperature.

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RNA quality control
Price on request

The AGTC assesses RNA quality using the RNA Assay for the Agilent 2200 TapeStation The assay generates an electrophoretogram of the total RNA fragments, a 28S/18S ratio, and an RNA Integrity Number (RIN) which are collectively used to determine the overall quality. This service is also available in conjunction with RNA isolation services and microarray sample processing.

The AGTC assesses RNA quality using the RNA Assay for the Agilent 2200 TapeStation The assay generates an electrophoretogram of the total RNA fragments, a 28S/18S ratio, and an RNA Integrity Number (RIN) which are collectively used to determine the overall quality. This service is also available in conjunction with RNA isolation services and microarray sample processing.

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Agilent 2200 TapeStation
Single Nucleotide Polymorphism (SNP) Genotyping
Price on request

The Applied Genomics Technology Center provides the following genotyping services:
- SNP interrogation using TaqMan® 5’ Nuclease Chemistry
- SNP interrogation using Illumina Infinium® Assay Technology


Sample Requirements:
- All the sample requirements listed below are guidelines established by the various vendors. ... Show more »

The Applied Genomics Technology Center provides the following genotyping services:
- SNP interrogation using TaqMan® 5’ Nuclease Chemistry
- SNP interrogation using Illumina Infinium® Assay Technology


Sample Requirements:
- All the sample requirements listed below are guidelines established by the various vendors. The AGTC staff will work with investigators to optimize these assays for their specific sample types.

SNP interrogation using TaqMan® 5’ Nuclease Chemistry:
- Submit DNA at a concentration of 5-20 ng/ul
- For optimal clustering, an effort should be made to normalize all samples to the same approximate concentration
- Volumes will vary based on project size

SNP interrogation using Illumina Infinium® Assay Technology:
- Submit 20ul of DNA at a concentration of 50 ng/ul.
- The sample concentration range for this assay must be kept very tight for optimal clustering and copy number analysis, therefore the concentration listed above is necessary.

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Sanger Sequencing
Price on request

The AGTC DNA Sequencing Lab provides fast, reliable and accurate DNA sequencing for a variety of sample types including plasmid DNA as well as PCR product. The Sequencing Lab is equipped with an Applied Biosystems ABI Prism 3730 DNA Analyzer, which is able to sequence as many as 96 samples per sequencing plate and over 570 samples... Show more »

The AGTC DNA Sequencing Lab provides fast, reliable and accurate DNA sequencing for a variety of sample types including plasmid DNA as well as PCR product. The Sequencing Lab is equipped with an Applied Biosystems ABI Prism 3730 DNA Analyzer, which is able to sequence as many as 96 samples per sequencing plate and over 570 samples per day. The DNA sequencing is accomplished using the ABI BigDye® Terminator v3.1 Cycle Sequencing Kit. With the BigDye® Terminator v3.1 chemistry, you get robust, highly flexible chemistries for a wide range of applications, including de novo sequencing and resequencing.

We offer the investigator two options for sequencing: you can perform your own sequencing reactions with the ABI BigDye® Terminator v3.1 Cycle Sequencing Kit or the reactions will be done by our staff using the ABI BigDye® Terminator v3.1 chemistry.

The researcher can submit his/her own custom-designed primers (see primer concentrations for details) or use our common primers ((T7, T3, SP6, M13 Forward & M13 Reverse) provided by the Sequencing Lab at no additional charge.

The price for DNA sequencing at the AGTC DNA Sequencing Lab is listed below:

  • Individual samples (one sample with one primer) with the
    researcher doing the BigDye Terminator reaction = $6.35 per sequence
  • Individual samples (one sample with one primer) with the
  • Sequencing Lab doing the BigDye Terminator reaction = $11.24 per sequence
    96-well plate of samples with the researcher doing the
  • BigDye Terminator reaction = $333.26 per plate
    96-well plate of samples with the Sequencing Lab doing the
  • BigDye Terminator reaction = $366.48 per plate

Please contact the Sequencing Lab for our high volume sequencing project pricing.

Extra charges added to sequencing price:
- Color printouts of the chromatogram = $1.00 per sequence
- Sequencing GC rich samples (reaction by the Sequencing Lab) = $3.09 per sequence

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Whole Genome Amplification
Price on request

The Applied Genomics Technology Center (AGTC) has a great deal of experience in Whole Genome Amplification (WGA) techniques which have become a valuable tool for the genomics research community. With the ability to vastly increase the quantity of genomic DNA, WGA gives investigators the opportunity to obtain valuable genetic... Show more »

The Applied Genomics Technology Center (AGTC) has a great deal of experience in Whole Genome Amplification (WGA) techniques which have become a valuable tool for the genomics research community. With the ability to vastly increase the quantity of genomic DNA, WGA gives investigators the opportunity to obtain valuable genetic information from even the most limited of sample types. Two of the most prominent methods available are Multiple Displacement Amplification (MDA), a strand displacement-based methodology, and OmniPlex™ Technology, a random fragmentation-based methodology. Both have a variety of commercial kits available for specific sample types and desired DNA yield.

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qPCR
Quantitative PCR
Price on request

The Applied Genomics Technology Center (AGTC) is equipped to perform Applied Biosystems TaqMan® Gene Expression Assays in both standard and micro fluid card 384-well formats.

We are not able to run 96-well formats at this time.

The Applied Genomics Technology Center (AGTC) is equipped to perform Applied Biosystems TaqMan® Gene Expression Assays in both standard and micro fluid card 384-well formats.

We are not able to run 96-well formats at this time.

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Genotyping Services
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DNA Sequencing
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DNA Extraction and Purification
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DNA Microarrays
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Epigenetic Analysis
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Biology
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Biostatistics & Bioinformatics
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Nucleic Acid Analysis
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Nucleic Acid Data Analysis
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Next Generation Sequencing
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PCR
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DNA
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RNA
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DNA Amplification
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Computational & Statistical Analysis
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Biochemistry & Molecular Biology
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Nucleic Acid Services
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October 21, 2012

Positive review received for Microarray Data Analysis:

"Working with Daniel and Adele was a great experience - this is the third time I have worked with them and they have consistently provided an excellent and timely service."

September 13, 2012

Positive review received for Illumina RNA microarray:

"Very efficient and helpful!"

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