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GEO Series: GSE93195

Title: Spemann organizer transcriptome induction by early β-Catenin, Wnt, Nodal and Siamois signals in Xenopus laevis

Summary

During Xenopus gastrulation, dorsal stabilization of β-Catenin at the earliest stage and subsequent target genes expression are critical for dorsal-ventral axis determination. However, many β-Catenin targets that mediate this process are still unkown. Here through RNA-seq analysis of β-Catenin knockdown embryos and self-regulating dorsal and ventral half embryos at early gastrula, we define an early β-Catenin gene signature that is downregulated by β-Catenin MO and enriched in dorsal gastrula tissues. This gene signature includes classic Spemann organizer genes, as well as other novel genes. Further analyses revealed that the early β-Catenin gene signature is positively correlated with LiCl treated, Wnt8 and Siamois mRNA-induced genes, consistent with their early role in dorsal-ventral axis formation. Our results also show that St 10.5 is the appropriate stage to uncover β-Catenin target genes that regulate dorsal-ventral patterning than St 9. Meanwhile, the multi-growth factor antagonist Cerberus inhibits part of the early β-Catenin gene signature and also controls the expression of a unique set of genes. Our findings provide new insight into the pivotal role of β-catenin in dorsal-ventral axis determination and can serve a fruitful resource for this field.


Contributors: Edward De Robertis, Yi Ding, Diego Ploper, Eric Sosa, Gabriele Colozza, Yuki Moriyama, Maria Benitez, Kelvin Zhang, Daria Merkurjev

Experiment Type: A genome-wide study of the effects of depleting the early dorsal b-Catenin signal which is responsible for the induction of the body axis.

Experiment Reagents: cer1.L, ctnnb1 MO1, Lithium chloride,

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples:
Sample View GSMs Assay Type
WE - NF10.5 GSM2446097  GSM2446102  GSM2446107  GSM2446117  GSM2446120  GSM2446123  RNA-Seq
Background: Xla.pigmentedNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF10.5  
   WE + LiCl - NF10.5 DEG GSM2446099  GSM2446109  RNA-Seq
Background: Xla.pigmentedNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical Lithium chloride   NF6 embryo
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF10.5  
   WE + cer1 - NF10.5 DEG GSM2446119  GSM2446122  GSM2446125  RNA-Seq
Background: Xla.pigmentedNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection cer1.L cer1.L NF3 blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF10.5  
   WE + ctnnb1 MO - NF10.5 DEG GSM2446098  GSM2446103  GSM2446108  RNA-Seq
Background: Xla.pigmentedNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO1 ctnnb1 NF2 blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF10.5  
   WE + sia1 - NF10.5 DEG GSM2446104  GSM2446110  RNA-Seq
Background: Xla.pigmentedNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection sia1.L sia1.L NF3 blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF10.5  
   WE + wnt8a - NF10.5 DEG GSM2446118  GSM2446121  GSM2446124  RNA-Seq
Background: Xla.pigmentedNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection wnt8a.L wnt8a.L NF3 blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF10.5  
   dorsal WE - dorsal explant - NF10.5 DEG GSM2446100  GSM2446105  GSM2446111  GSM2446113  GSM2446115  RNA-Seq
Background: Xla.pigmentedNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant     NF8 dorsal
Conditions:
Tissue Assay Stages ChIP Antibody
dorsal NF10.5  
embryo NF10.5  
   ventral WE - ventral explant - NF10.5 DEG GSM2446101  GSM2446106  GSM2446112  GSM2446114  GSM2446116  RNA-Seq
Background: Xla.pigmentedNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant     NF8 ventral
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF10.5  
ventral NF10.5  
WE - NF9 GSM2446126  GSM2446129  GSM2446132  GSM2446135  GSM2446139  RNA-Seq
Background: Xla.pigmentedNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF9  
   WE + LiCl - NF9 DEG GSM2446137  GSM2446141  RNA-Seq
Background: Xla.pigmentedNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
chemical Lithium chloride   NF6 embryo
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF9  
   WE + cer1 - NF9 DEG GSM2446128  GSM2446131  GSM2446134  RNA-Seq
Background: Xla.pigmentedNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection cer1.L cer1.L NF3 blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF9  
   WE + ctnnb1 MO - NF9 DEG GSM2446136  GSM2446140  RNA-Seq
Background: Xla.pigmentedNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection ctnnb1 MO1 ctnnb1 NF2 blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF9  
   WE + sia1 - NF9 DEG GSM2446138  GSM2446142  RNA-Seq
Background: Xla.pigmentedNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection sia1.L sia1.L NF3 blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF9  
   WE + wnt8a - NF9 DEG GSM2446127  GSM2446130  GSM2446133  RNA-Seq
Background: Xla.pigmentedNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection wnt8a.L wnt8a.L NF3 blastomere
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF9  
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