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dna microarray core facilities  (SUNY Upstate Medical University)

 
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    SUNY Upstate Medical University dna microarray core facilities
    Dna Microarray Core Facilities, supplied by SUNY Upstate Medical University, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/cdna+microarray+facility/microarray+core+facility/us08663914-132-5-11
    Average 90 stars, based on 1 article reviews
    dna microarray core facilities - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    other:

    Article Title: Oligodendroglial cells express and secrete reelin.
    Article Snippet: The authors gratefully acknowledge Ms. Karen Gentile and the SUNY Upstate Medical University Microarray Core Facility for processing all the RNA samples, and Dr. Frank Middleton for his assistance with the microarray data analysis.

    Article Title: Loss of Ezh2 cooperates with Jak2V617F in the development of myelofibrosis in a mouse model of myeloproliferative neoplasm
    Article Snippet: The authors thank Alexandar Tarakhovsky (Rockefeller University) for providing the Ezh2 floxed mouse and Frank Middleton (SUNY Upstate Medical University) for expert help with microarray and ChIP sequencing data analysis.

    Article Title: Intrinsic response of thoracic propriospinal neurons to axotomy.
    Article Snippet: We gratefully acknowledge Ms. Karen Gentile and the SUNY Upstate Medical University Microarray Core Facility, for processing all the samples.

    Microarray:

    Article Title: Targeting the alternative sigma factor RpoN to combat virulence in Pseudomonas aeruginosa
    Article Snippet: RNA samples were analyzed for quality with a Bioanalyzer (Agilent) and for DNA contamination by PCR. .. Microarray studies were carried out at the Microarray Core Facility at SUNY Upstate Medical University (Syracuse, NY). .. Microarray experiments were performed as indicated in the Affymetrix GeneChip® Expression Analysis Technical Manual (Pub.

    Article Title: Differential Gene Expression to Investigate the Effects of Low-level Electrochemical Currents on Bacillus subtilis
    Article Snippet: .. We thank Prof. Frank Middleton and Ms. Karen Gentle at SUNY Upstate Medical University for helping with DNA microarray hybridization. ..

    Article Title: Genomic investigation of ?-Synuclein multiplication and parkinsonism
    Article Snippet: .. 2008 Jun; 63(6): 10.1002/ana.21380. doi: 10.1002/ana.21380 PMCID: PMC3850281 NIHMSID: NIHMS110782 Owen A. Ross , PhD, 1, * Adam T. Braithwaite , BSc, 1 Lisa M. Skipper , PhD, 1 Jennifer Kachergus , BSc, 1 Mary M. Hulihan , MS, 1 Frank A. Middleton , PhD, 2 Kenya Nishioka , MD, 3 Julia Fuchs , MD, 4 Thomas Gasser , MD, 4 Demetrius M. Maraganore , MD, 5 Charles H. Adler , MD, 6 Lydie Larvor , PhD, 7 Marie-Christine Chartier-Harlin , MD, 7 Christer Nilsson , MD, 8 J. William Langston , MD, 9 Katrina Gwinn , MD, 10 Nobutaka Hattori , MD, 3 and Matthew J. Farrer , PhD 1 1 Neurogenetics, Department of Neuroscience, College of Medicine, Mayo Clinic, Jacksonville, Florida, USA 2 Center for Neuropsychiatric Genetics, Microarray Core Facility, SUNY Upstate Medical University, Syracuse, NY, USA 3 Department of Neurology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo 113-8421, Japan 4 Hertie-Institute for Clinical Brain Research, Department of Neurodegenerative Diseases, Center for Neurology, University of Tübingen, Germany 5 Department of Neurology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA 6 Department of Neurology, Mayo Clinic College of Medicine, Scottsdale, Arizona, USA 7 EA2683 MENRT, Diagnostic and Physiopathology of Parkinson’s disease, IRCL, Place deVerdun, 59045 Lille Cedex 8 Department of Clinical Medicine, Division of Geriatric Psychiatry, Lund University, Lund, Sweden 9 The Parkinson’s Institute and Clinical Center, Sunnyvale, CA, USA 10 Neurogenetics, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA * Corresponding author: Matthew J. Farrer PhD, Morris K. Udall Parkinson's Disease Research Center of Excellence, Mayo Clinic, Department of Neuroscience, 4500 San Pablo Road South, Jacksonville, Florida 32224, Tel: (904)-953-0158; Fax: (904)-953-7370, Email: ude.oyam@wehttam.rerraf Author information ► Copyright and License information ► Copyright notice and Disclaimer The publisher's final edited version of this article is available at Ann Neurol See other articles in PMC that cite the published article. ..

    Article Title: System and method for controlling bacterial cells with weak electric currents
    Article Snippet: The quality and quantity of the total RNA samples were evaluated using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, Calif.) and the microarray hybridizations were performed using E. coli Genome 2.0 Arrays (Affymetrix, Inc., Santa Clara, Calif.). .. Both were performed using the DNA microarray core facilities at the SUNY Upstate Medical University (Syracuse, N.Y.). ..

    Gentle:

    Article Title: Differential Gene Expression to Investigate the Effects of Low-level Electrochemical Currents on Bacillus subtilis
    Article Snippet: .. We thank Prof. Frank Middleton and Ms. Karen Gentle at SUNY Upstate Medical University for helping with DNA microarray hybridization. ..

    Hybridization:

    Article Title: Differential Gene Expression to Investigate the Effects of Low-level Electrochemical Currents on Bacillus subtilis
    Article Snippet: .. We thank Prof. Frank Middleton and Ms. Karen Gentle at SUNY Upstate Medical University for helping with DNA microarray hybridization. ..

    Diagnostic Assay:

    Article Title: Genomic investigation of ?-Synuclein multiplication and parkinsonism
    Article Snippet: .. 2008 Jun; 63(6): 10.1002/ana.21380. doi: 10.1002/ana.21380 PMCID: PMC3850281 NIHMSID: NIHMS110782 Owen A. Ross , PhD, 1, * Adam T. Braithwaite , BSc, 1 Lisa M. Skipper , PhD, 1 Jennifer Kachergus , BSc, 1 Mary M. Hulihan , MS, 1 Frank A. Middleton , PhD, 2 Kenya Nishioka , MD, 3 Julia Fuchs , MD, 4 Thomas Gasser , MD, 4 Demetrius M. Maraganore , MD, 5 Charles H. Adler , MD, 6 Lydie Larvor , PhD, 7 Marie-Christine Chartier-Harlin , MD, 7 Christer Nilsson , MD, 8 J. William Langston , MD, 9 Katrina Gwinn , MD, 10 Nobutaka Hattori , MD, 3 and Matthew J. Farrer , PhD 1 1 Neurogenetics, Department of Neuroscience, College of Medicine, Mayo Clinic, Jacksonville, Florida, USA 2 Center for Neuropsychiatric Genetics, Microarray Core Facility, SUNY Upstate Medical University, Syracuse, NY, USA 3 Department of Neurology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo 113-8421, Japan 4 Hertie-Institute for Clinical Brain Research, Department of Neurodegenerative Diseases, Center for Neurology, University of Tübingen, Germany 5 Department of Neurology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA 6 Department of Neurology, Mayo Clinic College of Medicine, Scottsdale, Arizona, USA 7 EA2683 MENRT, Diagnostic and Physiopathology of Parkinson’s disease, IRCL, Place deVerdun, 59045 Lille Cedex 8 Department of Clinical Medicine, Division of Geriatric Psychiatry, Lund University, Lund, Sweden 9 The Parkinson’s Institute and Clinical Center, Sunnyvale, CA, USA 10 Neurogenetics, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA * Corresponding author: Matthew J. Farrer PhD, Morris K. Udall Parkinson's Disease Research Center of Excellence, Mayo Clinic, Department of Neuroscience, 4500 San Pablo Road South, Jacksonville, Florida 32224, Tel: (904)-953-0158; Fax: (904)-953-7370, Email: ude.oyam@wehttam.rerraf Author information ► Copyright and License information ► Copyright notice and Disclaimer The publisher's final edited version of this article is available at Ann Neurol See other articles in PMC that cite the published article. ..

    DNA Sequencing:

    Article Title: Biochemical Reconstitution and Phylogenetic Comparison of Human SET1 Family Core Complexes Involved in Histone Methylation
    Article Snippet: .. We are grateful to Vicky Lyle at the DNA Sequencing Core Facility at SUNY Upstate Medical University. ..



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    cdna microarray facility  (AECOM International Development)
    90
    AECOM International Development cdna microarray facility
    Complementary-template reverse-transcription (CT-RT) of single-stranded DNA primers reverse-transcribed from FFPE-RNA. ( a ) RNA extracted from FFPE tissue is reverse-transcribed, the mRNA/DNA duplex is filtered on an YM-50 column and the DNA is single-stranded with RNase-H and column purified. The 5′-NB-Oligo-dA (24) -cT7-3′ (complementary to the T7 promoter) is annealed to the <t>FFPE-cDNA</t> primers. ( b ) Total RNA from universal human reference (UHR, Stratagene) is amplified using the Sense-Amp cRNA amplification kit from Genisphere to provide RNA with the same orientation as messenger RNA . ( c ) Single-stranded DNA primers are hybridized to their sense-RNA template between 70 and 42°C for 90 min. The hybridized products are reverse-transcribed by a process described as CT-RT. The restored FFPE-cDNAs are doubled stranded and transcribed in vitro using T7 polymerase. (See Supplementary Data for technical description of points 1 through 6.)
    Cdna Microarray Facility, supplied by AECOM International Development, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/cdna+microarray+facility/cdna+microarrays/pmc01976468-129-11-19
    Average 90 stars, based on 1 article reviews
    cdna microarray facility - by Bioz Stars, 2026-09
    90/100 stars
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    Complementary-template reverse-transcription (CT-RT) of single-stranded DNA primers reverse-transcribed from FFPE-RNA. ( a ) RNA extracted from FFPE tissue is reverse-transcribed, the mRNA/DNA duplex is filtered on an YM-50 column and the DNA is single-stranded with RNase-H and column purified. The 5′-NB-Oligo-dA (24) -cT7-3′ (complementary to the T7 promoter) is annealed to the FFPE-cDNA primers. ( b ) Total RNA from universal human reference (UHR, Stratagene) is amplified using the Sense-Amp cRNA amplification kit from Genisphere to provide RNA with the same orientation as messenger RNA . ( c ) Single-stranded DNA primers are hybridized to their sense-RNA template between 70 and 42°C for 90 min. The hybridized products are reverse-transcribed by a process described as CT-RT. The restored FFPE-cDNAs are doubled stranded and transcribed in vitro using T7 polymerase. (See Supplementary Data for technical description of points 1 through 6.)

    Journal: Nucleic Acids Research

    Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

    doi: 10.1093/nar/gkm510

    Figure Lengend Snippet: Complementary-template reverse-transcription (CT-RT) of single-stranded DNA primers reverse-transcribed from FFPE-RNA. ( a ) RNA extracted from FFPE tissue is reverse-transcribed, the mRNA/DNA duplex is filtered on an YM-50 column and the DNA is single-stranded with RNase-H and column purified. The 5′-NB-Oligo-dA (24) -cT7-3′ (complementary to the T7 promoter) is annealed to the FFPE-cDNA primers. ( b ) Total RNA from universal human reference (UHR, Stratagene) is amplified using the Sense-Amp cRNA amplification kit from Genisphere to provide RNA with the same orientation as messenger RNA . ( c ) Single-stranded DNA primers are hybridized to their sense-RNA template between 70 and 42°C for 90 min. The hybridized products are reverse-transcribed by a process described as CT-RT. The restored FFPE-cDNAs are doubled stranded and transcribed in vitro using T7 polymerase. (See Supplementary Data for technical description of points 1 through 6.)

    Article Snippet: Arrays used for the studies were designed and printed at the cDNA Microarray Facility, Albert Einstein College of Medicine (AECOM), Bronx, NY.

    Techniques: Reverse Transcription, Purification, Amplification, In Vitro

    Experimental procedure utilized for the analysis of 10-year-old matched frozen and formalin-fixed paraffin embedded breast cancer samples. ( a ) Five micrograms of RNA extracted from the 10-year-old frozen portion of the sample, is reverse-transcribed and the cDNA is double stranded (dsDNA), in four individual reactions. The dsDNA of three reactions undergoes IVT-amplification (MessageAmpII, Ambion), which gives rise to complementary RNA (cRNA) for cDNA microarray analyses. The dsDNA of one reaction is used for PCR experiments. ( b ) Five micrograms of RNA extracted from the 10-year-old FFPE portion of the sample underwent the exact same process. ( c ) Single-stranded DNA (ssDNA) obtained by RT of 5 μg of FFPE-RNA is purified and hybridized to the sense-RNA template library. The restored ssDNA is double stranded and purified. Three of the CT-RT reactions undergo IVT-amplification, while the dsDNA of one reaction is used for PCR experiments.

    Journal: Nucleic Acids Research

    Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

    doi: 10.1093/nar/gkm510

    Figure Lengend Snippet: Experimental procedure utilized for the analysis of 10-year-old matched frozen and formalin-fixed paraffin embedded breast cancer samples. ( a ) Five micrograms of RNA extracted from the 10-year-old frozen portion of the sample, is reverse-transcribed and the cDNA is double stranded (dsDNA), in four individual reactions. The dsDNA of three reactions undergoes IVT-amplification (MessageAmpII, Ambion), which gives rise to complementary RNA (cRNA) for cDNA microarray analyses. The dsDNA of one reaction is used for PCR experiments. ( b ) Five micrograms of RNA extracted from the 10-year-old FFPE portion of the sample underwent the exact same process. ( c ) Single-stranded DNA (ssDNA) obtained by RT of 5 μg of FFPE-RNA is purified and hybridized to the sense-RNA template library. The restored ssDNA is double stranded and purified. Three of the CT-RT reactions undergo IVT-amplification, while the dsDNA of one reaction is used for PCR experiments.

    Article Snippet: Arrays used for the studies were designed and printed at the cDNA Microarray Facility, Albert Einstein College of Medicine (AECOM), Bronx, NY.

    Techniques: Formalin-fixed Paraffin-Embedded, Reverse Transcription, Amplification, Microarray, Purification

    Signal intensity and heat-map analysis of the correlation between the log 2 ratios measured by cDNA microarrays. ( a ) Signal intensity of one sample grid in the red channel (Cy5) across all microarrays. Top three panels display the grids obtained from three repeats using cRNA from 10-year-old frozen RNA (Frozen-Amp 1–3). Three mid-panels show the signal of three repeats using cRNA obtained by restoration and IVT-amplification of RNA from 10-year-old FFPE tissue (FFPE-Restored 1–3). Three bottom panels display the signal of three repeats using cRNA obtained by direct IVT-amplification of RNA from 10-year-old FFPE tissue. ( b ) Heat map displaying the log 2 of expression ratios ranging between 0.5 and 2 for 1044 genes detected in frozen tissue on a 28 032 features cDNA microarray and represented in the UHR library. From left to right are displayed the ratios obtained by IVT-amplification of RNA from 10-year-old frozen tissue (Frozen-Amp 1–3), restoration and IVT-amplification of RNA from 10-year-old FFPE tissue (FFPE-Restored 1–3) and direct IVT-amplification of RNA from 10-year-old FFPE tissue (FFPE-Amp 1–3). Each column represents an individual hybridization and each line a different feature. Red and blue represent up-regulated and down-regulated genes, respectively.

    Journal: Nucleic Acids Research

    Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

    doi: 10.1093/nar/gkm510

    Figure Lengend Snippet: Signal intensity and heat-map analysis of the correlation between the log 2 ratios measured by cDNA microarrays. ( a ) Signal intensity of one sample grid in the red channel (Cy5) across all microarrays. Top three panels display the grids obtained from three repeats using cRNA from 10-year-old frozen RNA (Frozen-Amp 1–3). Three mid-panels show the signal of three repeats using cRNA obtained by restoration and IVT-amplification of RNA from 10-year-old FFPE tissue (FFPE-Restored 1–3). Three bottom panels display the signal of three repeats using cRNA obtained by direct IVT-amplification of RNA from 10-year-old FFPE tissue. ( b ) Heat map displaying the log 2 of expression ratios ranging between 0.5 and 2 for 1044 genes detected in frozen tissue on a 28 032 features cDNA microarray and represented in the UHR library. From left to right are displayed the ratios obtained by IVT-amplification of RNA from 10-year-old frozen tissue (Frozen-Amp 1–3), restoration and IVT-amplification of RNA from 10-year-old FFPE tissue (FFPE-Restored 1–3) and direct IVT-amplification of RNA from 10-year-old FFPE tissue (FFPE-Amp 1–3). Each column represents an individual hybridization and each line a different feature. Red and blue represent up-regulated and down-regulated genes, respectively.

    Article Snippet: Arrays used for the studies were designed and printed at the cDNA Microarray Facility, Albert Einstein College of Medicine (AECOM), Bronx, NY.

    Techniques: Amplification, Expressing, Microarray, Hybridization