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General approach for in vivo recovery of cell type-specific effector gene sets

Barsi, Julius C. and Tu, Qiang and Davidson, Eric H. (2014) General approach for in vivo recovery of cell type-specific effector gene sets. Genome Research, 24 (5). pp. 860-868. ISSN 1088-9051. PMCID PMC4009615. https://resolver.caltech.edu/CaltechAUTHORS:20140530-105337152

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Abstract

Differentially expressed, cell type-specific effector gene sets hold the key to multiple important problems in biology, from theoretical aspects of developmental gene regulatory networks (GRNs) to various practical applications. Although individual cell types of interest have been recovered by various methods and analyzed, systematic recovery of multiple cell type-specific gene sets from whole developing organisms has remained problematic. Here we describe a general methodology using the sea urchin embryo, a material of choice because of the large-scale GRNs already solved for this model system. This method utilizes the regulatory states expressed by given cells of the embryo to define cell type and includes a fluorescence activated cell sorting (FACS) procedure that results in no perturbation of transcript representation. We have extensively validated the method by spatial and qualitative analyses of the transcriptome expressed in isolated embryonic skeletogenic cells and as a consequence, generated a prototypical cell type-specific transcriptome database.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1101/gr.167668.113 DOIArticle
http://genome.cshlp.org/content/24/5/860PublisherArticle
http://genome.cshlp.org/content/24/5/860/suppl/DC1PublisherSupplementary Information
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009615/PubMed CentralArticle
Additional Information:© 2014 Barsi et al. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. Received September 30, 2013; accepted March 4, 2014. Research was supported by NIH grant HD067454 to E.H.D. We thank Dina Malounda and Erika Vielmas for exceptional technical assistance in acquiring RNA in situ hybridization data sets; Diana Perez and Pat Koen for their effort to adapt the flow cytometer toward filtered seawater; Igor Antoshechkin for general guidance pertaining to Illumina sequencing; Michael Collins and Sagar Damle for critical reading of the manuscript; Jongmin Nam for practical discussions concerning the procedure described herein; Klara Stefflova for standardizing vector graphics across figures; and finally, above all, Rochelle Diamond for her expertise in all FACS-related matters. Author contributions: J.C.B. and E.H.D. designed the research; J.C.B. performed the research; J.C.B. and Q.T. analyzed the data; and J.C.B. and E.H.D. wrote the paper.
Funders:
Funding AgencyGrant Number
NIHHD067454
Issue or Number:5
PubMed Central ID:PMC4009615
Record Number:CaltechAUTHORS:20140530-105337152
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20140530-105337152
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:46002
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:30 May 2014 22:47
Last Modified:03 Oct 2019 06:39

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