Under the leadership of Dr. Alan Michelson and the steering committee (Drs. Mark Knepper, Warren Leonard and Keji Zhao), the DSC has become in shape within the last 5 months. Several areas we have been working on in order to meet the increasing demands of intramural investigators for high-throughput sequencing. (1) Equipment acquisition: The core has acquired the latest Illumina sequencing platform, HiSeq-2000. The instrument has been installed and extensively validated against the manufactures specifications. With a full-bloom run, it can generate up to 200 GB raw sequences (or two human genomes with 30x coverage) within one week. Other equipments have also been installed including Corvaris ultrasonicator, CryoPrep and ABI StepOnePlus Real-time PCR system, Agilent Bioanalyzer. Lastly, the core has acquired a Linux cluster, which is essential for data acquisition, analysis and storage. (2) SOP development: Another key function of the DSC is SOP development. Working closely with NHLBI 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;(b) mitochondria sequencing (C) genome-wide mapping transcriptional start sites and polyadenylation sites. In addition, we have been developing computational pipelines and workflow for systematic identification of SNPs, splicing variants and other regulatory events in gene expression network. (3) Consultation and data acquisition: While the DSC is still in early stage to reach its full capacity, we had offered consultations and sequencing services for intramural investigators with diverse research interests, including miRNA deep sequencing in LDL biology (Dr. Alan Remaley), expression profiling of iPS cell with RNA-seq (Drs. Manfred Boehm and Chengyu Liu), identification of mitochondria mutations (Dr. Hong Xu), genetic and epigenetic gene regulation in immune system (Drs. Keji Zhao and Warren Leonard). We also work closely with Drs. Alan Michelson, Bob Balaban, Adrian Wiestner, Mark Knepper, Robert Kotin, Nalini Ragharachari for their specific projects in basic and translational research. (4) Collaboration with Framingham Heart Study: the core was also involved in initiating a collaborative project with Dr. Chris O'Donnell at Framingham Heart Study. The initial goal is to obtain transcriptome profiles of a cohort of MI patient samples, which are selected with the guidance of existing GWAS data. The resulting gene expression profiles will be further integrated with other genome-wide data (e.g. exome sequencing, exon array, etc) to gain a better understanding of pathophysiology of myocardial infarction.

Project Start
Project End
Budget Start
Budget End
Support Year
1
Fiscal Year
2010
Total Cost
$594,273
Indirect Cost
Name
National Heart, Lung, and Blood Institute
Department
Type
DUNS #
City
State
Country
Zip Code
Zhao, Yuncheng; Ye, Shicheng; Liang, Dongli et al. (2018) In Vitro Modeling of Human Germ Cell Development Using Pluripotent Stem Cells. Stem Cell Reports 10:509-523
Agbor-Enoh, Sean; Tunc, Ilker; De Vlaminck, Iwijn et al. (2017) Applying rigor and reproducibility standards to assay donor-derived cell-free DNA as a non-invasive method for detection of acute rejection and graft injury after heart transplantation. J Heart Lung Transplant :
Wang, Junpeng; Tang, Chao; Wang, Qian et al. (2017) NRF1 coordinates with DNA methylation to regulate spermatogenesis. FASEB J 31:4959-4970
Ni, Ting; Yang, Wenjing; Han, Miao et al. (2016) Global intron retention mediated gene regulation during CD4+ T cell activation. Nucleic Acids Res 44:6817-29
Stoehr, Andrea; Yang, Yanqin; Patel, Sajni et al. (2016) Prolyl hydroxylation regulates protein degradation, synthesis, and splicing in human induced pluripotent stem cell-derived cardiomyocytes. Cardiovasc Res 110:346-58
Eicher, John D; Wakabayashi, Yoshiyuki; Vitseva, Olga et al. (2016) Characterization of the platelet transcriptome by RNA sequencing in patients with acute myocardial infarction. Platelets 27:230-9
Roychoudhuri, Rahul; Clever, David; Li, Peng et al. (2016) BACH2 regulates CD8(+) T cell differentiation by controlling access of AP-1 factors to enhancers. Nat Immunol 17:851-60
Lu, Falong; Liu, Yuting; Inoue, Azusa et al. (2016) Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell 165:1375-88
Joshi, Amit D; Andersson, Charlotte; Buch, Stephan et al. (2016) Four Susceptibility Loci for Gallstone Disease Identified in a Meta-analysis of Genome-Wide Association Studies. Gastroenterology 151:351-363.e28
Wan, Chi-Keung; He, Chang; Sun, Lin et al. (2016) Cutting Edge: IL-1 Receptor Signaling is Critical for the Development of Autoimmune Uveitis. J Immunol 196:543-6

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