1352603996715_7fffb663120dd173020ed4b9bc223583

Applied Genomics Technology Center (AGTC)

Detroit, Michigan

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.

    Agilent RNA microarray
    Price on request

    Complete sample processing and Bioinformatics support for Agilent arrays

    Complete sample processing and Bioinformatics support for Agilent arrays

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    Agilent bioanalyzer
    Price on request

    The AGTC assesses RNA quality using the RNA 6000 Nano Assay for the Agilent 2100 Bioanalyzer.

    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... Show more »

    The AGTC assesses RNA quality using the RNA 6000 Nano Assay for the Agilent 2100 Bioanalyzer.

    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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    Bioinformatics
    Price on request

    Our services include analysis of the following types of data:
    - DNAseq
    - RNAseq
    - ChiP-seq
    - Illumina microarray
    - Affymetrix 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:
    - DNAseq
    - RNAseq
    - ChiP-seq
    - Illumina microarray
    - Affymetrix 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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    Chromatin immunoprecipitation (ChIP) data analysis
    Price on request
    Please contact Applied Genomics Technology Center (AGTC) for more information regarding this service.
    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) & the DropSense 96® (high-throughput), both UV/VIS spectrophotometry-based methods, and the Quantifiler™ Human DNA Quantification Kit, a 5' nuclease/TaqMan® probe-based method.

    The Applied Genomics Technology Center (AGTC) employs two methodologies for the determination of DNA quantity: The NanoDrop™ 1000 (low-throughput) & the DropSense 96® (high-throughput), both UV/VIS spectrophotometry-based methods, and the Quantifiler™ Human DNA Quantification Kit, a 5' nuclease/TaqMan® probe-based method.

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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 great... 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 state-of-the-art, automated, isolation systems: The EZ1® Advanced, a magnetic bead-based method, and the QIAcube, a sillica membrane-based method. Automated systems allow greater yield and uniformity as well as a decrease in turnaround time.

    For those samples requiring manual DNA isolation, the DNA Isolation Lab has the capabilities to run a vast array of manual DNA isolation protocols.

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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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    Illumina NGS
    Illumina next generation sequencing
    Price on request

    The Applied Genomics Technology Center is equipped with an Illumina Genome Analyzer II with Paired-end module for next generation sequencing, and an Illumina HiSeq 2500 Sequencer also for next generation sequencing. The HiSeq can be run in two modes: High Output mode which uses High Output flow cells containing eight lanes, and... Show more »

    The Applied Genomics Technology Center is equipped with an Illumina Genome Analyzer II with Paired-end module for next generation sequencing, and an Illumina HiSeq 2500 Sequencer also for next generation sequencing. The HiSeq can be run in two modes: High Output mode which uses High Output flow cells containing eight lanes, and Rapid mode which uses Rapid flow cells containing two lanes. A 50 cycle (bp) paired-end High Output run typically generates an average of 150 Gb of data in about 5 days.

    Current Services:
    - Genomic DNA resequencing and De novo sequencing
    - ChIP seq
    - Methylation analysis

    Capabilities:
    - 8 samples per flowcell
    - PhiX control DNA available
    - 18, 36, or 76 cycles in single read or paired end run
    - Multiplexing up to 12 samples in one lane (using Illumina indexing sequences)

    Our sequencing applications have typically included:
    - Whole-genome sequencing (DNA-Seq)
    - Targeted resequencing (Exome-Seq or custom-Seq)
    - Transcriptome sequencing (RNA-Seq or small RNA-Seq)
    - Epigenetics and gene regulation (ChIP-Seq or Whole-genome bisulfite sequencing)
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    Library Prep and Sample Submission Requirements

    The Core offers the investigator two options for library preps:

    Core-built libraries. The Core uses the Illumina TruSeq Sample Prep kit series for building libraries; however, you are able to request a specific supplier and kit if you wish. Samples may be submitted as:
    a. Tissue: Please refer to the DNA or RNA isolation services for submission requirements

    b. Nucleic acid (DNA or RNA): Please contact Alya'a Sammak for details regarding sample concentration and quantity requirements.

    The Core will perform a QC of the submitted samples. We do not assume responsibility for the data output if the investigator refuses the Core’s QC step. Alternatively, the investigator may provide their QC data for each sample (examples include spec readings, Agilent traces (BioAnalyzer or TapeStation), real time sample data and standard curve, etc.) The investigator will be contacted if a sample does not meet the minimum quality and quantity standards.

    User-built libraries. The investigator builds the libraries using kits that are compatible with the Illumina HiSeq 2500 platform. Please submit at least 20ul of 2nM of your pooled samples in 1.5 ml centrifuge tubes.
    To download the NGS sample submission form, click here.

    Multiplexing is available and varies depending on the kit and the investigator’s scientific question. Typically, the different library types are multiplexed as follows:

    TruSeq RNA libraries: multiplex six in one lane
    TruSeq DNA libraries: multiplex six in one lane
    TruSeq small RNA libraries: multiplex 48 in one lane
    TruSeq exome libraries: multiplex six in one lane
    TruSeq ChIP libraries: multiplex six in one lane
    Please discuss the desired depth of coverage with a bioinformatician or statistican. Please contact Adele Kruger, Ph.D. to inquire about the Core’s bioinformatics services.

    The core will contact the investigator to take back any unused sample at the end of the run.

    Sequencing Run

    The HiSeq 2500 can accommodate the following six run types:

    - single-read, non-indexed (sequencing in one direction, one sample per lane)
    - single-read, single-indexed (sequencing in one direction, pool of samples per lane, each with one index)
    - single-read, dual-indexed(sequencing in one direction, pool of samples per lane, each with two indices)
    - paired-end, non-indexed (sequencing in both directions, one sample per lane)
    - paired-end, single-indexed (sequencing in both directions, pool of samples per lane, each with one index)
    - paired-end, dual-indexed (sequencing in both directions, pool of samples per lane, each with two indices)

    We perform 50 and 100 cycles (base pairs) per read in the High Output mode. In addition to the 50 and 100 cycles per read, the Rapid mode also allows us to perform 150 cycles per read.

    Each flow cell must contain a DNA lane as a control. This can consist of DNA-Seq samples or exome-Seq samples. If neither is available, one lane can be chosen to have a 30% PhiX spike in to act as the control lane for the entire flow cell. This will be discussed with the investigator prior to the run. All lanes will have a 1% PhiX spike in as an internal control. Please note that we cannot guarantee the number of clusters per lane as clustering is based on random binding to the flow cell.

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    Illumina RNA microarray
    $220.00 USD
    per Sample

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

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

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    Methylation analysis
    Price on request

    The Applied Genomics Technology Center provides the following DNA methylation services:
    - Next-Generation Sequencing methylation analysis (click here for more information)
    - DNA methylation profiling using Illumina GoldenGate® Assay Technology - Illumina no longer offers this product
    - DNA methylation profiling... Show more »

    The Applied Genomics Technology Center provides the following DNA methylation services:
    - Next-Generation Sequencing methylation analysis (click here for more information)
    - DNA methylation profiling using Illumina GoldenGate® Assay Technology - Illumina no longer offers this product
    - DNA methylation profiling 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.

    DNA methylation profiling using Illumina Infinium® Assay Technology:
    - Submit 25ul of DNA at a concentration of 50ng/ul
    - The bisulfite conversion process requires 1ug of DNA in a specific volume, therefore the concentration listed above is necessary

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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, whole... 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.
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    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.
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    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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    NGS data analysis
    Next generation sequencing data analysis
    Price on request

    Demultiplexed data will be provided to the investigator in fastq format. The data will be transferred to the investigator’s server or onto an external hard drive provided by the investigator. The Core will attempt to maintain a copy of the data; however, this depends on storage availability on the Core’s servers.

    Demultiplexed data will be provided to the investigator in fastq format. The data will be transferred to the investigator’s server or onto an external hard drive provided by the investigator. The Core will attempt to maintain a copy of the data; however, this depends on storage availability on the Core’s servers.

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    RNA extraction
    $88.33 USD
    per Sample

    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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    SNP genotyping
    Single Nucleotide Polymorphism 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 GoldenGate® Assay Technology
    - SNP interrogation using Illumina Infinium® Assay Technology
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    Sample Requirements:
    -... Show more »

    The Applied Genomics Technology Center provides the following genotyping services:
    - SNP interrogation using TaqMan® 5’ Nuclease Chemistry
    - SNP interrogation using Illumina GoldenGate® Assay Technology
    - SNP interrogation using Illumina Infinium® Assay Technology
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    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 GoldenGate® Assay Technology:
    - Submit 10ul of DNA at a preferred concentration of 75 ng/ul, although a range of 50-150 ng/ul is acceptable.
    - For optimal clustering, an effort should be made to normalize all samples to the same approximate concentration
    - Samples are run in 96-well formats. For custom oligo pools (OPA), synthesis of oligos for a minimum of 480 samples is required.

    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
    $6.35 USD
    per Sample

    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... 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 seq
    Whole genome sequencing
    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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    aCGH microarray
    Agilent array comparative genomic hybridization microarray
    Price on request

    Complete sample processing and Bioinformatics support for Agilent aCGH

    Complete sample processing and Bioinformatics support for Agilent aCGH

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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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Lucas Bureau Waltzer gave a positive review for Illumina RNA microarray:

September 12, 2012
Very efficient and helpful!

Elizabeth Iorns gave a positive review for Microarray data analysis:

October 20, 2012
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.

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