Genomics and Bioinformatics Core (Core 2) The overall objective of the Genomics and Bioinformatics Core is to provide PPG investigators access to state- of-the-art genomics and bioinformatics technologies via both performance and teaching-based approaches. The Genomics and Bioinformatics Core works with PPG investigators to help design, execute, and interpret experiments that maximize significance of the data obtained while consuming the minimal resources required. The Genomics and Bioinformatics Core is directed by Drs. Patrick Gallagher, PI, and Dr. Vincent Schulz, Scientific Director. The Core performs a variety of assays that leverage the power of ultrahigh throughput sequencing. RNA expression-based techniques include RNA-seq and single cell transcriptome profiling. Genome wide analysis of DNA methylation status is assessed via enhanced reduced representation bisulfite sequencing and of chromatin accessibility via ATAC sequencing. Histone architecture is assessed via ChIP-seq. Control of gene expression at the level of translation is assessed via ribosomal profiling. A critical aspect of these studies is application of strategies to perform analyses on small numbers of cells, allowing protocol development for study of unamplified, primary human erythroid cells. Comprehensive bioinformatic services provided include analyses of RNA expression, DNA methylation, chromatin accessibility, and histone architecture. The Core also provides analysis of protein expression via ribosome profiling and via analysis of proteomic data sets. The influence of genetic variation is characterized in transcriptome, epigenetic, and proteomic data sets. Various strategies are utilized to integrate all of these data types to gain a more complete understanding of erythropoiesis. For these studies, comprehensive quality control procedures are in place. An additional aim of the Bioinformatics Core is to provide training and education to PPG investigators and guidance in the use of these technologies, to provide specialized services, and to evaluate and optimize the application of expression, genomic, and proteomic analyses to solve challenging problems confronting hematology researchers. Finally, an ongoing function of the Core is to monitor and adopt, where indicated, the newest and most promising novel bioinformatics programs and algorithms, as well as updates to currently existing programs, for use by PPG investigators.

Public Health Relevance

Genomics and Bioinformatics Core (Core 2) The goal of the Genomics and Bioinformatics Core is to help researchers perform and analyze genomics-related data to better understand how genes inside blood cells work. This is a poorly understood, complex process with many parts. We will help PPG researchers use highly advanced technology that has only recently been developed. Understanding how genes work in different types of blood cells may help us reduce the problems faced by some patients with blood diseases leading to anemia.

Agency
National Institute of Health (NIH)
Institute
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Type
Research Program Projects (P01)
Project #
5P01DK032094-30
Application #
9565393
Study Section
Special Emphasis Panel (ZDK1)
Project Start
Project End
Budget Start
2018-08-01
Budget End
2019-07-31
Support Year
30
Fiscal Year
2018
Total Cost
Indirect Cost
Name
New York Blood Center
Department
Type
DUNS #
073271827
City
New York
State
NY
Country
United States
Zip Code
10065
Qu, Xiaoli; Zhang, Shijie; Wang, Shihui et al. (2018) TET2 deficiency leads to stem cell factor-dependent clonal expansion of dysfunctional erythroid progenitors. Blood 132:2406-2417
Huang, Yumin; Hale, John; Wang, Yaomei et al. (2018) SF3B1 deficiency impairs human erythropoiesis via activation of p53 pathway: implications for understanding of ineffective erythropoiesis in MDS. J Hematol Oncol 11:19
Ali, Abdullah Mahmood; Huang, Yumin; Pinheiro, Ronald Feitosa et al. (2018) Severely impaired terminal erythroid differentiation as an independent prognostic marker in myelodysplastic syndromes. Blood Adv 2:1393-1402
Yan, Hongxia; Hale, John; Jaffray, Julie et al. (2018) Developmental differences between neonatal and adult human erythropoiesis. Am J Hematol 93:494-503
Han, Xu; Zhang, Jieying; Peng, Yuanliang et al. (2017) Unexpected role for p19INK4d in posttranscriptional regulation of GATA1 and modulation of human terminal erythropoiesis. Blood 129:226-237
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Ivanovska, Irena L; Shin, Jae-Won; Swift, Joe et al. (2015) Stem cell mechanobiology: diverse lessons from bone marrow. Trends Cell Biol 25:523-32

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