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Series GSE121324 Query DataSets for GSE121324
Status Public on Oct 09, 2019
Title Reconstruction of the global neural crest gene regulatory network in vivo [Capture-C]
Organism Gallus gallus
Experiment type Other
Summary Precise control of developmental processes is encoded in the genome in the form of gene regulatory networks (GRNs). Such multi-factorial systems are difficult to decode in vertebrates owing to their complex gene hierarchies and transient dynamic molecular interactions. Here we present a genome-wide in vivo reconstruction of the GRN underlying development of neural crest (NC), an emblematic embryonic multipotent cell population. By coupling NC-specific epigenomic and single-cell transcriptome profiling with genome/epigenome engineering in vivo, we identify multiple regulatory layers governing NC ontogeny, including NC-specific enhancers and super-enhancers, novel trans-factors and cis-signatures. Assembling the NC regulome has allowed the comprehensive reverse engineering of the NC-GRN at unprecedented resolution. Furthermore, identification and dissection of divergent upstream combinatorial regulatory codes has afforded new insights into opposing gene circuits t hat define canonical and neural NC fates. Our integrated approach, allowing dissection of cell-type-specific regulatory circuits in vivo, has broad implications for GRN discovery and investigation.
 
Overall design Capture-C was performed in key neural crest regulators to determine their topologically associated domains and promoter-enhancer communications in vivo.
 
Contributor(s) Williams RM, Candido-Ferreira I, Repapi E, Gavriouchkina D, Senanayake U, Telenius J, Ling I, Taylor S, Hughes J, Sauka-Spengler T
Citation(s) 31639368
Submission date Oct 16, 2018
Last update date Jan 27, 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)
GPL19064 Illumina MiSeq (Gallus gallus)
Samples (6)
GSM3431471 dorsal_neural_tubes_5-6ss rep1 Capture-C
GSM3431472 dorsal_neural_tubes_5-6ss rep2 Capture-C
GSM3431473 dorsal_neural_tubes_5-6ss rep3 Capture-C
This SubSeries is part of SuperSeries:
GSE121527 Reconstruction of the global neural crest gene regulatory network in vivo
Relations
BioProject PRJNA497063
SRA SRP165867

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE121324_RAW.tar 14.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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