(Core Leader: Bing Zhang) The Biotechnology and Bioinformatics Core provides service in RNA-Seq data generation, analysis, Interpretation, and sharing. These services are powered by cutting edge experimental and computational infrastructures at the HudsonAlpha Institute of Technology (where the RNA-Seq data generation and low-level data analysis will be performed) and the Vanderbilt University (where high-level RNA-Seq data analysis, data interpretation and sharing will be performed). The HudsonAlpha Institute has ten Illumina HiSeq sequencing instruments, and its capacity for next-gen sequencing on the Illumina systems is more than 3,200 lanes per year. It also has a centralized computational infrastructure that includes a 256- core cluster with 640TB of available space in fast disk storage in RAID5 format (over 1PB of total storage). The Vanderbilt computational infrastructure includes a high performance computing cluster that has about 3,000 processor cores and has a theoretical peak performance of 12 TeraFLOPS. The file system provides over 200TB of disk space, 144GB of disk cache, and can sustain 60Gb/s of disk bandwidth to the cluster. Both HudsonAlpha and Vanderbilt are members of the Internet2 advanced technology community, allowing extremely rapid transfer of the very large datasets that will be generated in the proposed projects between the institutions. Bioinformatics and Computational tools such as Perl, BioPeri, R, BioConductor, MySQL, BioMart, FASTX-Toolkit, SAMtools, the """"""""Tuxedo"""""""" software suite (Bowtie, TopHap and Cufflinks), Genome Analysis Toolkit (GATK), Integrated Genomics Viewer (IGV), WebGestalt, Cytoscape, etc. are readily available through the computational infrastructures. The Biotechnology and Bioinformatics Core is required In both research projects to enable in-depth analysis of the extracellular RNA inventory and the regulation of extracellular RNA export. Core personnel have worked and will continue to work closely with project leaders to ensure effective support and two-way communication.
| Zhang, Qin; Jeppesen, Dennis K; Higginbotham, James N et al. (2018) Mutant KRAS Exosomes Alter the Metabolic State of Recipient Colonic Epithelial Cells. Cell Mol Gastroenterol Hepatol 5:627-629.e6 |
| Hinger, Scott A; Cha, Diana J; Franklin, Jeffrey L et al. (2018) Diverse Long RNAs Are Differentially Sorted into Extracellular Vesicles Secreted by Colorectal Cancer Cells. Cell Rep 25:715-725.e4 |
| Sung, Bong Hwan; Weaver, Alissa M (2018) Directed migration: Cells navigate by extracellular vesicles. J Cell Biol 217:2613-2614 |
| Maas, Sybren L N; Breakefield, Xandra O; Weaver, Alissa M (2017) Extracellular Vesicles: Unique Intercellular Delivery Vehicles. Trends Cell Biol 27:172-188 |
| McKenzie, Andrew J; Hoshino, Daisuke; Hong, Nan Hyung et al. (2016) KRAS-MEK Signaling Controls Ago2 Sorting into Exosomes. Cell Rep 15:978-987 |
| Higginbotham, James N; Zhang, Qin; Jeppesen, Dennis K et al. (2016) Identification and characterization of EGF receptor in individual exosomes by fluorescence-activated vesicle sorting. J Extracell Vesicles 5:29254 |
| Dou, Yongchao; Cha, Diana J; Franklin, Jeffrey L et al. (2016) Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes. Sci Rep 6:37982 |
| Patton, James G; Franklin, Jeffrey L; Weaver, Alissa M et al. (2015) Biogenesis, delivery, and function of extracellular RNA. J Extracell Vesicles 4:27494 |
| Quesenberry, Peter J; Aliotta, Jason; Camussi, Giovanni et al. (2015) Potential functional applications of extracellular vesicles: a report by the NIH Common Fund Extracellular RNA Communication Consortium. J Extracell Vesicles 4:27575 |
| Cha, Diana J; Franklin, Jeffrey L; Dou, Yongchao et al. (2015) KRAS-dependent sorting of miRNA to exosomes. Elife 4:e07197 |
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