The Molecular Phenotyping core provides instrumentation, training, and services for in vitro cell phenotyping. Specifically, we provide facilities and training for automated nucleic acids purification, microarray analysis, quantitative PCR, and automated immunofluorescence cell marker analysis and screening. In addition to maintaining facilities essential for the many NIH-funded investigators working at MMCRI, planned developments such as resources for analysis of next generation sequencing data and laboratory automation for high density microplate formats will ensure that the core keeps in step with investigators'needs. An efficient workflow for the analysis of gene expression from RNA preparation through transcriptome analysis, and validation of candidate genes has been established. The core facility provides equipment, training, and supplies for all steps in the process with the exception of microarray processing, which is provided by Vermont Genetics Network in a regional collaborative agreement. Both manual and automated epifluorescence microscopy is also provided by the facility. Currently we provide live cell time-lapse microscopy, and microscopy based screening in 6- to 96-well formats, and additional applications such as cell cycle analysis are in development. The core provides image analysis workstations running Metamorph and Image J, and training in specific applications of these software packages. Quantitative image analysis of tissue immunostaining is being provided in collaboration with the Histopathology Core (Lindner). Future developments of our transcriptome analysis capabilities will be in the following areas: i) Transition from 96- to 384-well format. Essential equipment including 384 well real-time PCR instrument and liquid handling station is available in the facility, and users are currently piloting the new platform, ii) Providing an analysis platform for Next Generation Sequencing data. In the cellular analysis area we will be focusing on increasing the number of analyses we can provide users of our automated microscopy platform. Furthermore, we will be transitioning to a 384 well format for microscopy-based screening applications. Longer term core development will be based on feedback from the user base, and input from the internal and external advisory committees of the COBRE.
State of the art resources for transcriptome analysis and cellular marker analysis are essential to nationally competitive biomedical research infrastructure. The Molecular Phenotyping core has developed these resources at MMCRI, and continues to add new resources in these areas on the basis of the needs of MMCRI investigators.
|Ufkin, Melanie L; Peterson, Sarah; Yang, Xuehui et al. (2014) miR-125a regulates cell cycle, proliferation, and apoptosis by targeting the ErbB pathway in acute myeloid leukemia. Leuk Res 38:402-10|
|Guay, Justin A; Wojchowski, Don M; Fang, Jing et al. (2014) Death associated protein kinase 2 is expressed in cortical interstitial cells of the mouse kidney. BMC Res Notes 7:345|
|Favreau, Amanda J; Vary, Calvin P H; Brooks, Peter C et al. (2014) Cryptic collagen IV promotes cell migration and adhesion in myeloid leukemia. Cancer Med 3:265-72|
|Han, Xiang Hua; Jin, Yong-Ri; Tan, Leonard et al. (2014) Regulation of the follistatin gene by RSPO-LGR4 signaling via activation of the WNT/*-catenin pathway in skeletal myogenesis. Mol Cell Biol 34:752-64|
|Peterson, Sarah M; Thompson, Jeffrey A; Ufkin, Melanie L et al. (2014) Common features of microRNA target prediction tools. Front Genet 5:23|
|Verma, Rakesh; Su, Su; McCrann, Donald J et al. (2014) RHEX, a novel regulator of human erythroid progenitor cell expansion and erythroblast development. J Exp Med 211:1715-22|
|Fetting, Jennifer L; Guay, Justin A; Karolak, Michele J et al. (2014) FOXD1 promotes nephron progenitor differentiation by repressing decorin in the embryonic kidney. Development 141:17-27|
|Guntur, Anyonya R; Le, Phuong T; Farber, Charles R et al. (2014) Bioenergetics during calvarial osteoblast differentiation reflect strain differences in bone mass. Endocrinology 155:1589-95|
|Li, Lei; Byrne, Susan M; Rainville, Nicole et al. (2014) Brief report: serpin Spi2A as a novel modulator of hematopoietic progenitor cell formation. Stem Cells 32:2550-6|