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Series GSE121527 Query DataSets for GSE121527
Status Public on Oct 09, 2019
Title Reconstruction of the global neural crest gene regulatory network in vivo
Organism Gallus gallus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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 Refer to individual Series
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, 35088714
Submission date Oct 19, 2018
Last update date Feb 08, 2022
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 (4)
GPL16133 Illumina HiSeq 2000 (Gallus gallus)
GPL19005 Illumina HiSeq 2500 (Gallus gallus)
GPL19064 Illumina MiSeq (Gallus gallus)
Samples (213)
GSM3431421 neural crest-5-6ss_FoxD3 rep1 ATAC-seq
GSM3431422 neural crest-5-6ss_FoxD3 rep2 ATAC-seq
GSM3431423 neural crest-5-6ss_Pax7 ATAC-seq
This SuperSeries is composed of the following SubSeries:
GSE121318 Reconstruction of the global neural crest gene regulatory network in vivo [ATAC-seq]
GSE121324 Reconstruction of the global neural crest gene regulatory network in vivo [Capture-C]
GSE121329 Reconstruction of the global neural crest gene regulatory network in vivo [ChIP-seq]
BioProject PRJNA497572

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Supplementary file Size Download File type/resource
GSE121527_RAW.tar 91.7 Mb (http)(custom) TAR (of BED, MTX, TSV, TXT)
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