Abstract

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.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Heart, Lung, and Blood Institute (NHLBI)
Type
Research Program Projects (P01)
Project #
2P01HL089707-06
Application #
8590749
Study Section
Heart, Lung, and Blood Initial Review Group (HLBP)
Project Start
Project End
Budget Start
2013-08-01
Budget End
2014-07-31
Support Year
6
Fiscal Year
2013
Total Cost
$145,634
Indirect Cost
$69,386

  Institution

Name
J. David Gladstone Institutes
Department
Type
DUNS #
099992430
City
San Francisco
State
CA
Country
United States
Zip Code
94158

  Publications

Libby, Ashley Rg; Joy, David A; So, Po-Lin et al. (2018) Spatiotemporal mosaic self-patterning of pluripotent stem cells using CRISPR interference. Elife 7:
Miyaoka, Yuichiro; Mayerl, Steven J; Chan, Amanda H et al. (2018) Detection and Quantification of HDR and NHEJ Induced by Genome Editing at Endogenous Gene Loci Using Droplet Digital PCR. Methods Mol Biol 1768:349-362
Sun, Xin; Hota, Swetansu K; Zhou, Yu-Qing et al. (2018) Cardiac-enriched BAF chromatin-remodeling complex subunit Baf60c regulates gene expression programs essential for heart development and function. Biol Open 7:
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
Thomas, Reuben; Thomas, Sean; Holloway, Alisha K et al. (2017) Features that define the best ChIP-seq peak calling algorithms. Brief Bioinform 18:441-450
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
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
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:

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