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GEO Series: GSE148726

Title: Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endodermal gene regulatory network

Summary

We report the ChIP-seq analysis of Sox17 genome-wide binding and its loss-of-function transcriptomic analysis of both Sox17 and Ctnnb1 (beta-catenin) by RNA-seq.


Contributors: Kitt Paraiso, Kitt Paraiso, Aaron Zorn, Shreyasi Mukherjee

Experiment Type: ChIP-seq was performed to detect endogenous Sox17 binding (N&F stage 10.5) and RNA-seq was used to assess gene expression changes in Sox17 (N&F stages 9, 9.5, 10, 10.5, 11, 12) or Ctnnb1 (N&F stages 7, 8, 9, 9.5, 10, 10.5, 11, 12) in morpholino antisense oligo injected versus uninjected control embryos

Experiment Reagents: ctnnb1 MO2, sox17a MO5, sox17b.1/b.2 MO1.

Article: XB-ART-57340, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE - NF10.5 GSM4477762  GSM4477790  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5  
   WE + ctnnb1 MO - NF10.5 DEG GSM4477761  GSM4477789  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO2 ctnnb1 NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5  
WE - NF10 GSM4477760  GSM4477788  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10  
   WE + ctnnb1 MO - NF10 DEG GSM4477759  GSM4477787  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO2 ctnnb1 NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10  
WE - NF11 GSM4477764  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11  
   WE + ctnnb1 MO - NF11 DEG GSM4477763  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO2 ctnnb1 NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11  
WE - NF12 GSM4477766  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12  
   WE + ctnnb1 MO - NF12 DEG GSM4477765  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO2 ctnnb1 NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12  
WE - NF7 GSM4477752  GSM4477780  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 7  
   WE + ctnnb1 MO - NF7 DEG GSM4477751  GSM4477779  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO2 ctnnb1 NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 7  
WE - NF8 GSM4477754  GSM4477782  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
   WE + ctnnb1 MO - NF8 DEG GSM4477753  GSM4477781  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO2 ctnnb1 NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF9 GSM4477756  GSM4477784  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   WE + ctnnb1 MO - NF9 DEG GSM4477755  GSM4477783  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO2 ctnnb1 NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9.5 GSM4477758  GSM4477786  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   WE + ctnnb1 MO - NF9.5 DEG GSM4477757  GSM4477785  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO2 ctnnb1 NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF10 GSM4477744  GSM4477772  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10  
   WE + sox17a MO + sox17b.1/b.2 MO - NF10 DEG GSM4477743  GSM4477771  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection sox17b.1/b.2 MO1 sox17b.2 sox17b.1 NF stage 2- blastomere
morpholino injection sox17a MO5 sox17a NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10  
WE - NF10.5 GSM4477746  GSM4477774  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5  
   WE + sox17a MO + sox17b.1/b.2 MO - NF10.5 DEG GSM4477745  GSM4477773  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection sox17b.1/b.2 MO1 sox17b.2 sox17b.1 NF stage 2- blastomere
morpholino injection sox17a MO5 sox17a NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5  
WE - NF11 GSM4477748  GSM4477776  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11  
   WE + sox17a MO + sox17b.1/b.2 MO - NF11 DEG GSM4477747  GSM4477775  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection sox17b.1/b.2 MO1 sox17b.2 sox17b.1 NF stage 2- blastomere
morpholino injection sox17a MO5 sox17a NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 11  
WE - NF12 GSM4477750  GSM4477778  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12  
   WE + sox17a MO + sox17b.1/b.2 MO - NF12 DEG GSM4477749  GSM4477777  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection sox17b.1/b.2 MO1 sox17b.2 sox17b.1 NF stage 2- blastomere
morpholino injection sox17a MO5 sox17a NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12  
WE - NF9 GSM4477740  GSM4477768  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   WE + sox17a MO + sox17b.1 MO - NF9 DEG GSM4477739  GSM4477767  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection sox17b.1/b.2 MO1 sox17b.2 sox17b.1 NF stage 2- blastomere
morpholino injection sox17a MO5 sox17a NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9.5 GSM4477742  GSM4477770  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   WE + sox17a MO + sox17b.1/b.2 MO - NF9.5 DEG GSM4477741  GSM4477769  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection sox17b.1/b.2 MO1 sox17b.2 sox17b.1 NF stage 2- blastomere
morpholino injection sox17a MO5 sox17a NF stage 2- blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
pan-Sox17 WE - NF10.5 GSM4477737  GSM4477738  ChIP-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 Sox17a/b Ab2
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