The Advanced Bioinformatics Core will analyze and integrate data from multiple sources, e.g., affinity purification followed by mass spectrometry (AP-MS), chromatin immunoprecipitation followed by DNA sequencing (ChlP-Seq), gene expression by RNA-Seq and other methods to identify biologically relevant cellular pathways and processes in cardiac differentiation. It will make use of novel programs such as MiST for AP-MS data and other algorithms developed by the Gladstone Bioinformatics Core to accurately analyze ChlP-Seq and RNA-Seq data. This core will leverage the expertise in the existing Gladstone Bioinformatics Core but focus on protein-protein interaction data and its integration with other gene regulatory datasets to establish combinatorial interactions that control gene expression during cardiac differentiation.

Public Health Relevance

The networks we uncover in this study will inform our understanding of the molecular instrucfions that enable the embryo to make a heart, providing the underlying knowledge necessary to identify targets for therapeufic approaches to heart failure or severe heart damage.

Agency
National Institute of Health (NIH)
Institute
National Heart, Lung, and Blood Institute (NHLBI)
Type
Research Program Projects (P01)
Project #
5P01HL089707-07
Application #
8710320
Study Section
Heart, Lung, and Blood Program Project Review Committee (HLBP)
Project Start
Project End
Budget Start
2014-08-01
Budget End
2015-07-31
Support Year
7
Fiscal Year
2014
Total Cost
Indirect Cost
Name
J. David Gladstone Institutes
Department
Type
DUNS #
City
San Francisco
State
CA
Country
United States
Zip Code
94158
Celona, Barbara; Dollen, John von; Vatsavayai, Sarat C et al. (2017) Suppression of C9orf72 RNA repeat-induced neurotoxicity by the ALS-associated RNA-binding protein Zfp106. Elife 6:
Lobingier, Braden T; Hüttenhain, Ruth; Eichel, Kelsie et al. (2017) An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. Cell 169:350-360.e12
Overman, Jeroen; Fontaine, Frank; Moustaqil, Mehdi et al. (2017) Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice. Elife 6:
Judge, Luke M; Perez-Bermejo, Juan A; Truong, Annie et al. (2017) A BAG3 chaperone complex maintains cardiomyocyte function during proteotoxic stress. JCI Insight 2:
Du, Dan; Roguev, Assen; Gordon, David E et al. (2017) Genetic interaction mapping in mammalian cells using CRISPR interference. Nat Methods 14:577-580
Liu, S John; Horlbeck, Max A; Cho, Seung Woo et al. (2017) CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells. Science 355:
Anderson, Courtney M; Hu, Jianxin; Thomas, Reuben et al. (2017) Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites. Development 144:1235-1241
Barnes, Ralston M; Harris, Ian S; Jaehnig, Eric J et al. (2016) MEF2C regulates outflow tract alignment and transcriptional control of Tdgf1. Development 143:774-9
Huebsch, Nathaniel; Loskill, Peter; Deveshwar, Nikhil et al. (2016) Miniaturized iPS-Cell-Derived Cardiac Muscles for Physiologically Relevant Drug Response Analyses. Sci Rep 6:24726
Hota, Swetansu K; Bruneau, Benoit G (2016) ATP-dependent chromatin remodeling during mammalian development. Development 143:2882-97

Showing the most recent 10 out of 67 publications