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Series GSE125709 Query DataSets for GSE125709
Status Public on Nov 27, 2019
Title Early shaping of the chromatin landscape specifies vagal neural crest into distinct lineages [RNA-seq]
Organism Gallus gallus
Experiment type Expression profiling by high throughput sequencing
Summary Complex traits in enteropathies like Hirschsprung disease underscores a larger gene regulatory network (GRN) driving vagal neural crest (VNC) to form the enteric nervous system (ENS). To dissect the GRN and understand the function of non-coding regulatory regions, we used a novel highly conserved EdnrB E2 enhancer with a FoxD3 NC2 enhancer to generate a comprehensive map of VNC chromatin and transcriptional landscape during ENS development. Together with single-cell transcriptional profiles, we revealed three distinct lineages of VNC (glial, neuronal, and mesenchymal) that are each pre-specified by independent GRNs before delamination. We identified and functionally validated regulatory cores mediating the glial (Tfap2B and Sox10) and neuronal programmes (Sox3/Msx1) that in spatiotemporal combinations with other families of transcription factors, control the timing of enteric cell differentiation. Deconstructing the VNC-GRN identifies factors that pre-specifies cells to their presumptive fate and sheds light on how early GRN dysregulations influence the divergent neural phenotype in enteropathies.
 
Overall design Transcriptomic profilling of avian neural crest cells isolated from their in vivo context at HH12, HH18 and HH25
 
Contributor(s) Ling I, Sauka-Spengler T
Citation(s) 31792380, 33111104
Submission date Jan 27, 2019
Last update date Nov 02, 2020
Contact name Tatjana Sauka-Spengler
E-mail(s) tatjana.sauka-spengler@imm.ox.ac.uk
Organization name MRC Weatherall Institute of Molecular Medicine
Department University of Oxford
Lab Sauka-Spengler lab
Street address Radcliffe Department of Medicine
City Oxford
State/province Oxfordshire
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platforms (1)
GPL19787 Illumina NextSeq 500 (Gallus gallus)
Samples (16)
GSM3580747 H10E2_RNA_R1
GSM3580748 H10E2_RNA_R2
GSM3580749 H10neg_RNA_R1
This SubSeries is part of SuperSeries:
GSE125711 Early chromatin shaping predetermines multipotent vagal neural crest into neural, neuronal and mesenchymal lineages
Relations
BioProject PRJNA517322
SRA SRP182591

Download family Format
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE125709_RNA_featurecounts.txt.gz 2.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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