Under the leadership of Dr. Alan Michelson and the steering committee (Drs. Mark Knepper, Warren Leonard and Keji Zhao), the DIR DNA Sequencing and Genomics Core (DSGC) has provided a full spectrum of high-throughput genomics services, including both NextGen Sequencing and microarray platforms, to facilitate basic and translational research at NHLBI. (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 3'IVT expression assay, 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, reverse barcode sequencing (viral integration and ribozyme evolution), 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 large variety 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) mitochondria sequencing with Fluidigm platform and/or rolling circle amplification;(C) genome-wide mapping transcriptional start sites and polyadenylation sites;(d) improved ChIP-seq with limited input DNA quantity;(e) single-cell transcriptome analysis with NuGen procedure;(f) working with ABRF/FDA sequencing control consortium on the evaluation of different sequencing platforms and methods for library construction using MAQC and ERCC standards and degraded/FFPE samples. 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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