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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
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
BioProject PRJNA497063
SRA SRP165867

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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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