Under the leadership of Dr. Alan Michelson and the steering committee (Drs. Mark Knepper, Warren Leonard, Chris O'Donnell and Keji Zhao), the DIR DNA Sequencing and Genomics Core (DSGC) has provided a full spectrum of high-throughput genomics services, to facilitate basic and translational research at NHLBI and across the NIH. (1) Consultation and data acquisition: the DSGC has provided the state-of-the-art genomics services for DIR investigators in a cost effective and timely fashion. Diverse projects have been carried out including exon array, miRNA array, whole-genome sequencing, exome sequencing, transcriptome sequencing (RNA-seq and small RNA sequencing), ChIP-seq and PAR-CLIP (genome-wide interaction map and nucleosome occupancy), RIP-Seq, ChIA-PET, Mito-seq, RCA-seq, as well as several innovative NGS applications (e.g. TSS-seq, PA-seq) to interrogate genome/transcriptome diversity (2) In-depth data analysis: The DNA Sequencing and Genomics Core has explored and implemented a wide range of open source and commercially available software packages for primary and secondary NGS data analysis. In addition, project-specific data analysis is further achieved by in-house software and algorithm development. As the result, it provides a broad spectrum of tools for DIR investigators to convert the high-throughput data into biological meaningful findings for further examination. (3) Consultation and training: The DNA Sequencing Core has taken diverse venues to promote broad dissemination of NGS technology. Consultations are provided for experimental design and data analysis. The core also offers routine one-on-one training for library preparation and data analysis. (4) Research and development: Several R&D projects were carried out in collaboration with the DIR investigators. High priority was set for technologies that are beneficial to multiple users or expected to facilitate the broad applications of high-throughput sequencing platform. We have developed and optimized protocol for (a) RNA-seq with limited starting materials and/or strand specificity;(b) RCA-seq (rolling circle amplification and sequencing) to identify and characterize novel viral strain and/or variants;(C) genome-wide mapping of polyadenylation sites and alternative polyadenylation events;(d) single-cell transcriptome analysis with NuGen procedure and Fluidigm C1 platform. In addition, we have been developing computational pipelines and workflow for systematic identification of SNPs, alternative polyadenylation and other regulatory events in gene expression network.
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