GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE43194 Query DataSets for GSE43194
Status Public on Apr 16, 2013
Title Spatial Transcriptional Profile of the Chick and Mouse Endocardial Cushions Identify Novel Regulators of Endocardial EMT in vitro
Organisms Gallus gallus; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Objective: We developed an unbiased strategy to identify genes important in endocardial epithelial-to-mesenchymal transformation (EMT) using a spatial transcriptional profile.
Methods and Results: Endocardial cells overlaying the cushions of the atrioventricular canal (AVC) and outflow tract (OFT) undergo an EMT to yield VICs. RNA sequencing (RNA-seq) analysis of gene expression between AVC, OFT, and ventricles (VEN) isolated from chick and mouse embryos at comparable stages of development (chick HH18; mouse E11.0) was performed. EMT occurs in the AVC and OFT cushions, but not VEN at this time. 210 genes in the chick (n=1) and 105 genes in the mouse (n=2) were enriched 2-fold in the cushions. Gene regulatory networks (GRN) generated from cushion-enriched gene lists confirmed TGFβ as a nodal point and identified NF-κB as a potential node. To reveal previously unrecognized regulators of EMT four candidate genes, Hapln1, Id1, Foxp2, and Meis2, and a candidate pathway, NF-κB, were selected. In vivo spatial expression of each gene was confirmed by in situ hybridization and a functional role for each in endocardial EMT was determined by siRNA knockdown in a collagen gel assay.
Conclusions: Our spatial-transcriptional profiling strategy yielded gene lists which reflected the known biology of the system. Further analysis accurately identified and validated previously unrecognized novel candidate genes and the NF-κB pathway as regulators of endocardial cell EMT in vitro.
Overall design 3 separate regions of the developing heart tube were dissected and processed for RNA sequencing analysis in both HH18 chick and E11.0 ICR mouse (done in duplicate)
Contributor(s) DeLaughter DM, Christodoulou DC, Robinson JY, Seidman CE, Baldwin H, Seidman JG, Barnett JV
Citation(s) 23557753
Submission date Dec 28, 2012
Last update date May 15, 2019
Contact name Daniel DeLaughter
Organization name Vanderbilt University Medical School
Department Cell and Developmental Biology
Lab Scott Baldwin Laboratory
Street address Preston Research Building Room 460
City Nashville
State/province TN
ZIP/Postal code 37203
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL16133 Illumina HiSeq 2000 (Gallus gallus)
Samples (9)
GSM1058118 E11.0 AVC rep1
GSM1058119 E11.0 OFT rep1
GSM1058120 E11.0 VEN rep1
BioProject PRJNA184872
SRA SRP017709

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
GSE43194_E11_ICR_abundance_rep1.txt.gz 1.3 Mb (ftp)(http) TXT
GSE43194_E11_ICR_abundance_rep2.txt.gz 1.4 Mb (ftp)(http) TXT
GSE43194_HH18chick_abundance.txt.gz 886.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap