Showing papers by "Carrie A. Davis published in 2020"
University of Massachusetts Medical School1, Broad Institute2, Stanford University3, Cold Spring Harbor Laboratory4, University of Washington5, University of California, San Diego6, Massachusetts Institute of Technology7, Ludwig Institute for Cancer Research8, University of California, San Francisco9, Salk Institute for Biological Studies10, California Institute of Technology11, University of California, Irvine12, Pennsylvania State University13, Lawrence Berkeley National Laboratory14, University of Connecticut Health Center15, McGill University16, Université de Montréal17, University of Minnesota18, Florida State University19, Yale University20, University of Alabama in Huntsville21, University of Chicago22, University of California, Merced23, University of Colorado Boulder24, Icahn School of Medicine at Mount Sinai25, Pompeu Fabra University26, University of Southern California27, University of California, Berkeley28, Harvard University29, Tongji University30, Boston University31
TL;DR: The authors summarize the data produced by phase III of the Encyclopedia of DNA Elements (ENCODE) project, a resource for better understanding of the human and mouse genomes, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development.
Abstract: The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal (https://www.encodeproject.org), including phase II ENCODE1 and Roadmap Epigenomics2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis-regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.
999 citations
TL;DR: This cellular composition is found to be a characteristic signature of tissues and to reflect tissue morphological heterogeneity and histology, and it is found that departures from the normal cellular composition correlate with histological phenotypes associated with disease.
Abstract: We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural, and blood cells. These act as basic components of many tissues and organs. Based on gene expression, these cell types redefine the basic histological types by which tissues have been traditionally classified. We identified genes whose expression is specific to these cell types, and from these genes, we estimated the contribution of the major cell types to the composition of human tissues. We found this cellular composition to be a characteristic signature of tissues and to reflect tissue morphological heterogeneity and histology. We identified changes in cellular composition in different tissues associated with age and sex, and found that departures from the normal cellular composition correlate with histological phenotypes associated with disease.
24 citations
TL;DR: In this article, RNA sequencing data for a number of primary cells from different locations in the human body was used to identify genes whose expression is specific to these cell types, and from these genes, the contribution of the major cell types to the composition of human tissues was estimated.
Abstract: We have produced RNA sequencing data for a number of primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, which define five major cell types: epithelial, endothelial, mesenchymal, neural and blood cells. These act as basic components of many tissues and organs. Based on gene expression, these cell types redefine the basic histological types by which tissues have been traditionally classified. We identified genes whose expression is specific to these cell types, and from these genes, we estimated the contribution of the major cell types to the composition of human tissues. We found this cellular composition to be a characteristic signature of tissues, and to reflect tissue morphological heterogeneity and histology. We identified changes in cellular composition in different tissues associated with age and sex and found that departures from the normal cellular composition correlate with histological phenotypes associated to disease. One Sentence Summary A few broad transcriptional programs define the major cell types underlying the histology of human tissues and organs.
4 citations