Return to search results Title: A Molecular Atlas of the Developing Ectoderm Defines Neural, Neural Crest, Placode and Non-Neural Progenitor Identity in Vertebrates.

Summary

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 Non-Negative 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.

Contributors: Anne-Helene Monsoro-Burq, Jean-Louis Plouhinec, Sofía Medina-Ruiz, Caroline Borday, Elsa Bernard, Jean-Philippe Vert, Michael Eisen, Richard Harland, Anne Monsoro-Burq

Experiment Type: Xenopus laevis ectodermal sample were dissected at embryonic stages 12.5, 14, and 17 and mRNA profiles were generated by deep sequencing using an Illumina HiSeq 2000

Article: XB-ART-54144, PubMed

Source: NCBI GEO, Xenbase Download

Sample	View		GSMs	Assay Type
WE - NF14 GSM2758863  GSM2758864  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 14      anterior neural fold, preplacodal ectoderm - NF14 DEG GSM2758846  GSM2758852  GSM2758854  GSM2758859  GSM2758862  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody anterior neural fold NF stage 14   preplacodal ectoderm NF stage 14      anterior non-neural ectoderm - NF14 DEG GSM2758843  GSM2758858  GSM2758861  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody non-neural ectoderm NF stage 14      chordal neural plate - NF14 DEG GSM2758840  GSM2758848  GSM2758855  GSM2758860  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody chordal neural plate NF stage 14      chordal neural plate border - NF14 DEG GSM2758810  GSM2758842  GSM2758853  GSM2758857  GSM2758867  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody chordal neural plate border NF stage 14      neural plate - NF14 DEG GSM2758815  GSM2758816  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody neural plate NF stage 14      neural plate border - NF14 DEG GSM2758813  GSM2758814  GSM2758883  GSM2758887  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody neural plate border NF stage 14      posterior non-neural ectoderm - NF14 DEG GSM2758844  GSM2758850  GSM2758851  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody non-neural ectoderm NF stage 14      pre-chordal neural plate - NF14 DEG GSM2758839  GSM2758845  GSM2758847  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody pre-chordal neural plate NF stage 14      pre-chordal neural plate border - NF14 DEG GSM2758809  GSM2758841  GSM2758849  GSM2758856  GSM2758865  GSM2758866  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody pre-chordal neural plate border NF stage 14   WE - NF12.5 GSM2758870  GSM2758877  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 12.5      chordal neural plate - NF12.5 DEG GSM2758817  GSM2758824  GSM2758832  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody chordal neural plate NF stage 12.5      chordal neural plate border - NF12.5 DEG GSM2758818  GSM2758825  GSM2758833  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody chordal neural plate border NF stage 12.5      lateral neural plate border - NF12.5 DEG GSM2758819  GSM2758826  GSM2758834  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody neural plate border NF stage 12.5      non-neural ectoderm - NF12.5 DEG GSM2758820  GSM2758827  GSM2758835  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody non-neural ectoderm NF stage 12.5      pre-chordal neural plate - NF12.5 DEG GSM2758821  GSM2758828  GSM2758836  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody pre-chordal neural plate NF stage 12.5      pre-chordal neural plate border - NF12.5 DEG GSM2758822  GSM2758829  GSM2758831  GSM2758837  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody pre-chordal neural plate border NF stage 12.5      pre-chordal neural plate border, preplacodal ectoderm - NF12.5 DEG GSM2758823  GSM2758830  GSM2758838  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody pre-chordal neural plate border NF stage 12.5   preplacodal ectoderm NF stage 12.5   WE - NF16-17 GSM2758873  GSM2758880  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 16 to NF stage 17      neural crest - NF17 DEG GSM2758811  GSM2758812  GSM2758882  GSM2758884  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody neural crest NF stage 17      preplacodal ectoderm - NF17 DEG GSM2758885  GSM2758886  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody preplacodal ectoderm NF stage 17   WE - NF11.5 GSM2758868  GSM2758875  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 11.5   WE - NF12 GSM2758869  GSM2758876  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 12   WE - NF13 GSM2758871  GSM2758878  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 13   WE - NF14-15 GSM2758872  GSM2758879  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 14 to NF stage 15   WE - NF18-19 GSM2758874  GSM2758881  RNA-Seq Xla   [-] [+] Background: Xla.Outbred Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 18 to NF stage 19

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