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oklahoma medical research foundation

7 ARTICLES PUBLISHED IN JoVE

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JoVE Journal

Infinium Assay for Large-scale SNP Genotyping Applications
Adam J. Adler 1, Graham B. Wiley 1, Patrick M. Gaffney 1
1Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation

A protocol is described that uses Illumina's Infinium assays to perform large-scale genotyping. These assays can reliably genotype millions of SNPs across hundreds of individual DNA samples in three days. Once generated, these genotypes can be used to check for associations with a variety of different diseases or phenotypes.

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Biology

Targeted DNA Methylation Analysis by Next-generation Sequencing
Dustin R. Masser 1, David R. Stanford 1, Willard M. Freeman 1,2
1Department of Physiology, University of Oklahoma College of Medicine, 2Department of Geriatric Medicine, University of Oklahoma College of Medicine

Bisulfite amplicon sequencing (BSAS) is a method for quantifying cytosine methylation in targeted genomic regions of interest. This method uses bisulfite conversion paired with PCR amplification of target regions prior to next-generation sequencing to produce absolute quantitation of DNA methylation at a base-specific level.

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Genetics

Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System
Joseph C. Siefert 1,2, Emily A. Clowdus 1,2, Duane Goins 1, Amnon Koren 3, Christopher L. Sansam 1,2
1Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, 2Department of Cell Biology, University of Oklahoma Health Sciences Center, 3Department of Molecular Biology and Genetics, Cornell University

Zebrafish were recently used as an in vivo model system to study DNA replication timing during development. Here is detailed the protocols for using zebrafish embryos to profile replication timing. This protocol can be easily adapted to study replication timing in mutants, individual cell types, disease models, and other species.

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Immunology and Infection

A Method for the Measurement of Salivary Gland Function in Mice
Harini Bagavant 1, Marta Trzeciak 1, Joanna Papinska 1, Indranil Biswas 1, Micah L Dunkleberger 1, Anna Sosnowska 1, Umesh S Deshmukh 1
1Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation

Salivary gland hypofunction is a frequent consequence of autoimmune disease and radiation therapy. Reproducible evaluation of salivary gland function in mouse models of these diseases is a technical challenge. Here, a simple method for accurate and reproducible measurement of saliva production in mice is described.

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Medicine

Early Pathological and Magnetic Resonance Detection of Cerebral Injury Using a Rat Model of Neonatal Hypoxic Ischemic Encephalopathy
Michael G. Melek 1, Rheal Towner 2,3, Johannes Kung 1, Debra Saunders 4, Michelle Zales 3,4, Faizah Bhatti 1,3
1Department of Pediatrics, University of Oklahoma Health Sciences Center, 2Department of Chemistry, University of Prince Edward Island, 3Center for Neuroscience, University of Oklahoma Health Sciences Center, 4Oklahoma Medical Research Foundation

The present protocol describes a rodent model of newborn hypoxic-ischemic injury for identifying early changes in cerebral tissue by gross morphology and magnetic resonance imaging. This has benefits over existing models, which can be used to study late injury but do not allow the evaluation of reproducible early changes.

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Biology

Cell-Specific Paired Interrogation of the Mouse Ovarian Epigenome and Transcriptome
Sarah R. Ocañas *1,2,3, José V. V. Isola *1,3, Tatiana D. Saccon 1, Kevin D. Pham 2, Ana J. Chucair-Elliott 2, Augusto Schneider 4, Willard M. Freeman 2,3, Michael B. Stout 1,3
1Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, 2Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, 3Oklahoma City Veterans Affairs Medical Center, 4Nutrition College, Federal University of Pelotas

In this protocol, the translating ribosome affinity purification (TRAP) method and the isolation of nuclei tagged in specific cell types (INTACT) method were optimized for the paired interrogation of the cell-specific ovarian transcriptome and epigenome using the NuTRAP mouse model crossed to a Cyp17a1-Cre mouse line.

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Immunology and Infection

Real-Time Measurement of the Mitochondrial Bioenergetic Profile of Neutrophils
Sunitha Pulikkot 1, Meng Zhao 2,3, Zhichao Fan 1
1Department of Immunology, School of Medicine, UConn Health, 2Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, 3Department of Microbiology and Immunology, University of Oklahoma Health Science Center

We describe stepwise protocols measuring the mitochondrial respiration of mouse and human neutrophils and HL60 cells using the metabolic extracellular flux analyzer.

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