title: Overlapping cell population expression profiling and regulatory inference in C. elegans.
abstract: BACKGROUND
  Understanding gene expression across the diverse metazoan cell types during development is critical to understanding their function and regulation. However, most cell types have not been assayed for expression genome-wide.
  
  
  RESULTS
  We applied a novel approach we term "Profiling of Overlapping Populations of cells (POP-Seq)" to assay differential expression across all embryonic cells in the nematode Caenorhabditis elegans. In this approach, we use RNA-seq to define the transcriptome of diverse partially overlapping FACS-sorted cell populations. This identified thousands of transcripts differentially expressed across embryonic cells. Hierarchical clustering analysis identified over 100 sets of coexpressed genes corresponding to distinct patterns of cell type specific expression. We identified thousands of candidate regulators of these clusters based on enrichment of transcription factor motifs and experimentally determined binding sites.
  
  
  CONCLUSIONS
  Our analysis provides new insight into embryonic gene regulation, and provides a resource for improving our knowledge of tissue-specific expression and its regulation throughout C. elegans development.
authors.affiliation: Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA. jburdick@mail.med.upenn.edu.
authors.forename: Joshua
authors.initials: J
authors.lastname: Burdick
authors.affiliation: Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA. twalton@fas.harvard.edu.
authors.forename: Travis
authors.initials: T
authors.lastname: Walton
authors.affiliation: Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA. eliciap@mail.med.upenn.edu.
authors.forename: Elicia
authors.initials: E
authors.lastname: Preston
authors.affiliation: Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA. azach@mail.med.upenn.edu.
authors.forename: Amanda
authors.initials: A
authors.lastname: Zacharias
authors.affiliation: Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA. arjunrajlab@gmail.com.
authors.forename: Arjun
authors.initials: A
authors.lastname: Raj
authors.affiliation: Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA. jmurr@mail.med.upenn.edu.|Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 437A Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA, 19104-6145, USA. jmurr@mail.med.upenn.edu.
authors.forename: John Isaac
authors.initials: JI
authors.lastname: Murray
mesh_terms: D000818:Animals; D001665:Binding Sites; D017173:Caenorhabditis elegans / Q000196:embryology / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000235:genetics*; D016000:Cluster Analysis; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018510:RNA, Helminth / Q000235:genetics; D017423:Sequence Analysis, RNA; D014157:Transcription Factors; D059467:Transcriptome
chemical_list: D029742:Caenorhabditis elegans Proteins; D018510:RNA, Helminth; D014157:Transcription Factors