ArticleGenome research2014
General approach for in vivo recovery of cell type-specific effector gene sets.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 33 citations in OpenAlex.
- A stage and anatomy ontology for embryogenesis in indirect-developing echinoderms.Development (Cambridge, England) · 2026Article
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- Live imaging of echinoderm embryos to illuminate evo-devo.Frontiers in cell and developmental biology · 2022Article
- Embryonic Temperature Programs Phenotype in Reptiles.Frontiers in physiology · 2020Review
- The evolution of a new cell type was associated with competition for a signaling ligand.PLoS biology · 2019Article
- Developmental effector gene regulation: Multiplexed strategies for functional analysis.Developmental biology · 2019Article
- Culture of and experiments with sea urchin embryo primary mesenchyme cells.Methods in cell biology · 2019Review
- Techniques for analyzing gene expression using BAC-based reporter constructs.Methods in cell biology · 2019Review
- Genome-wide analysis of chromatin accessibility using ATAC-seq.Methods in cell biology · 2019Review
- From genome to anatomy: The architecture and evolution of the skeletogenic gene regulatory network of sea urchins and other echinoderms.Genesis (New York, N.Y. : 2000) · 2018Review
- Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms.Briefings in functional genomics · 2018Review
- Global analysis of primary mesenchyme cell cis-regulatory modules by chromatin accessibility profiling.BMC genomics · 2018Article
- Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution.Genome biology · 2018Article
- Article
- Article
- Genome-wide assessment of differential effector gene use in embryogenesis.Development (Cambridge, England) · 2015Article
- Axud1 Integrates Wnt Signaling and Transcriptional Inputs to Drive Neural Crest Formation.Developmental cell · 2015Article
- Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.