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GEO Series: GSE72657

Title: Tissue- and stage-specific cellular context regulates Wnt target gene expression subsequent to β-catenin recruitment

Summary

The aim of our study is to identify direct target genes of Wnt/β-catenin signaling operating in gastrula-stage X. tropicalis embryos. We characterized the genomic loci bound by the Wnt signaling downstream component β-catenin in intact X. tropicalis gastrulae using ChIP-seq. We also determined the normal mRNA expression profile in control (uninjected and control-MO-injected) embryos and altered mRNA expression profiles in two experimental samples: embryos where endogenous wnt8a function was knocked down with wnt8a MO, and where we experimentally re-instated Wnt8a expression with a DNA construct (pCSKA-wnt8a) in the same wnt8a knock down.


Contributors: Stefan Hoppler, Yukio Nakamura, Eduardo Alves

Experiment Type: For ChIP-seq, one ChIP DNA and one input control DNA samples pooled from three independent ChIP experiments using early gastrula embryos were sequenced. For RNA-seq, Twelve total RNA samples (triplicates of each experimental samples: uninjected, CoMO-injected, wnt8aMO-injected, wnt8aMO and pCSKA-wnt8a-coinjected) from early gastrula embryos were sequenced.

Experiment Reagents: hbg1 cMO1, wnt8a MO5, wnt8a.L.

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
input WE - NF10.25 GSM1867401  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.25  
   beta Catenin WE - NF10.25 GSM1867400  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.25 Ctnnb1 Ab2
WE - NF10.25 GSM1867402  GSM1867406  GSM1867410  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.25  
   WE + hbg1 MO - NF10.25 DEG GSM1867403  GSM1867407  GSM1867411  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection hbg1 cMO1 hbg1 NF stage 3 (4-cell) ventral marginal zone
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.25  
   WE + wnt8a MO + wnt8a - NF10.25 DEG GSM1867405  GSM1867409  GSM1867413  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection wnt8a MO5 wnt8a NF stage 3 (4-cell) ventral marginal zone
mRNA injection wnt8a.L wnt8a.L NF stage 3 (4-cell) ventral marginal zone
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.25  
   WE + wnt8a MO - NF10.25 DEG GSM1867404  GSM1867408  GSM1867412  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection wnt8a MO5 wnt8a NF stage 3 (4-cell) ventral marginal zone
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.25  
Select All DEG      Select All 
Xtr   
Xla 

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