NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE150006 Query DataSets for GSE150006
Status Public on Apr 03, 2021
Title The connectome of neural crest enhancers reveals regulatory features of signaling systems
Organism Gallus gallus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary The neural crest is a migratory stem cell population that gives rise to a wide array of cell types. The formation and differentiation of neural crest cells are controlled by a complex transcriptional network, which endows these cells with unique features such as multipotency and stemness. During migration, signaling systems modulate subcircuits within this network to ensure that neural crest cells differentiate at the right time and place. The wingless (Wnt) signaling pathway, in particular, plays an important role in defining developmental potential of these cells but, surprisingly few direct Wnt-target genes have been identified in the neural crest transcriptional network. To address this, we generated a high-resolution contact map of active enhancers in the neural crest and identified the direct targets of Wnt signaling in the neural crest genome via CUT&RUN for its nuclear effectors LEF1 and CTNNB1 (bCat).
 
Overall design CUT&RUN data for Wnt signaling nuclear factors LEF1 and CTNNB1, and CTCF in chick neural crest cells at specification stage (HH9) CUT&RUN data for LEF1 in chick neural crest cells at specification stage (HH9) upon Wnt knockdown RNA-seq on neural crest cells upon Wnt knockdown. H2K27ac HiChIP for dissected neural folds and whole embryos at HH9
 
Contributor(s) Azambuja AP, Simoes-Costa M
Citation(s) 33852891
Submission date May 06, 2020
Last update date Jul 06, 2021
Contact name Marcos Simoes-Costa
E-mail(s) simoescosta@cornell.edu
Organization name Cornell University
Department Molecular Biology and Genetics
Lab Simoes-Costa Lab
Street address 526 Campus Rd
City Ithaca
State/province New York
ZIP/Postal code 14853
Country USA
 
Platforms (1)
GPL19787 Illumina NextSeq 500 (Gallus gallus)
Samples (25)
GSM4520613 bCAT_r1
GSM4520614 bCAT_r2
GSM4520615 LEF1_r1
Relations
BioProject PRJNA630814
SRA SRP260345

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
GSE150006_RAW.tar 2.0 Gb (http)(custom) TAR (of BEDPE, BW)
GSE150006_WntLOF_DE.csv.gz 546.9 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.