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GEO Series: GSE56169

Title: E2a is necessary for Smad2/3 dependent transcription and the direct repression of lefty

Summary

We characterized the binding of Smad2/3 using ChIP-SEQ in both control gastrula-stage X. tropicalis embryos and embryos depleted of the transcription factor E2a (E2a-MO). We also characterized gene expression in control and E2a-depleted embryos by RNA-Seq. For ChIP-Seq, three biological replicates of E2a-MO were performed, and two biological replicates of Control embryos were performed. For RNA-Seq, two biological replicates of E2a-MO were performed, and two biological replicates of Control embryos were performed, and the mean expression levels of each gene were compared.


Contributors: Andrea Wills, Andrea Wills, Julie Baker

Experiment Type: For ChIP-Seq, three biological replicates were performed for E2a-depleted X. tropicalis embryos, and two biological replicates were performed for control gastrula-stage embryos. For RNA-Seq, two biological replicates were performed for both E2a-depleted embryos and control embryos, and the mean expression levels were compared for each gene.

Experiment Reagents: tcf3 MO1.

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples:
Sample View GSMs Assay Type
WE - NF10.5 GSM1357039  GSM1357040  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF10.5  
   WE + tcf3 MO - NF10.5 DEG GSM1357041  GSM1357042  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection tcf3 MO1 tcf3 NF2 blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF10.5  
input WE - NF10.5 GSM1357037  GSM1357038  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF10.5  
   Smad2/3 WE + tcf3 MO - NF10.5 GSM1357034  GSM1357035  GSM1357036  ChIP-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection tcf3 MO1 tcf3 NF2 blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF10.5 Smad2 Ab9
   Smad2/3 WE - NF10.5 GSM1357032  GSM1357033  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF10.5 Smad2 Ab9
Select All 
Xtr   
Xla 

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