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PLoS Biol 2017 Oct 19;1510:e2004045. doi: 10.1371/journal.pbio.2004045.
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A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates.

Plouhinec JL , Medina-Ruiz S , Borday C , Bernard E , Vert JP , Eisen MB , Harland RM , Monsoro-Burq AH .

During vertebrate neurulation, the embryonic ectoderm is patterned into lineage progenitors for neural plate, neural crest, placodes and epidermis. Here, we use Xenopus laevis embryos to analyze the spatial and temporal transcriptome of distinct ectodermal domains in the course of neurulation, during the establishment of cell lineages. In order to define the transcriptome of small groups of cells from a single germ layer and to retain spatial information, dorsal and ventral ectoderm was subdivided along the anterior-posterior and medial-lateral axes by microdissections. Principal component analysis on the transcriptomes of these ectoderm fragments primarily identifies embryonic axes and temporal dynamics. This provides a genetic code to define positional information of any ectoderm sample along the anterior-posterior and dorsal-ventral axes directly from its transcriptome. In parallel, we use nonnegative matrix factorization to predict enhanced gene expression maps onto early and mid-neurula embryos, and specific signatures for each ectoderm area. The clustering of spatial and temporal datasets allowed detection of multiple biologically relevant groups (e.g., Wnt signaling, neural crest development, sensory placode specification, ciliogenesis, germ layer specification). We provide an interactive network interface, EctoMap, for exploring synexpression relationships among genes expressed in the neurula, and suggest several strategies to use this comprehensive dataset to address questions in developmental biology as well as stem cell or cancer research.

PubMed ID: 29049289
PMC ID: PMC5663519
Article link: PLoS Biol
Grant support: [+]

Species referenced: Xenopus laevis
Genes referenced: actn1 adamts1 agr2 alas1 aldh1l1 atad3a atp2b1 bbs5 bmp2 bmp4 bmp7.1 bmp7.2 btg1 c1h14orf119 ca14 cacng4 capn1 ccdc68 cdh1 cdon cdx2 cdx4 cep152 cers2 cib2 cimap1a cntrl crx dhrs3 disp1 dlx2 dmrta1 dusp5 dzip1l eef1a1 egr4 emx1l eno1 eomes epha2 ephb4 fezf2 fgfr1 foxb1 foxc2 foxd1 foxd3 foxi1 foxj1 frzb fth1.1 fzd8 gata4 gata5 gdf3 gmnc gne golph3 gria2 grpel2 gsc hes7.2 hesx1 hoxa3 hoxb1 hoxb3 hoxb6 hoxb8 hoxb9 hoxc10 hoxc4 hoxc5 hoxc6 hoxc8 hoxc9 hs6st1 hyal2 id2 katnb1 kremen2 krt12.4 larp6 lef1 lefty lhx1 lrrn1l man1a1 matn4 mgat4d mmp3 msgn1 msx2 myc myf5 myo9b myod1 mypop ngfr nkx3-1 nkx6-1 nkx6-2 not notch1 nradd nsmf nubp1 odc1 otx1 otx2 p2ry1 pax2 pax3 pdgfb pfkfb4 pfkp pitx1 pitx2 plk3 prickle1 prrt1 psmd6 ptch2 pzp rara rax rfx4 sall2 septin8 sh3pxd2a shb shh six3 six4 slc2a12 snai1 snai2 sox10 sox17a sox2 sox8 sox9 sp5 sp8 spry4 tcf7l1 tekt2 tfap2b thbs1 tmem63a tp63 vstm2b wnt3a wnt8a zc4h2 zic1 znf703

Disease Ontology terms: melanoma
GEO Series: GSE103240: Xenbase,  NCBI

Article Images: [+] show captions
References [+] :
Anders, HTSeq--a Python framework to work with high-throughput sequencing data. 2015, Pubmed