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GEO Series: GSE96655

Title: Innate Immune Response and Off-Target Mis-splicing Are Common Morpholino-Induced Side Effects in Xenopus

Summary

We report on the implications of genetic KO versus MO-mediated KD of the mesoderm-specifying Brachyury paralogues in the Western clawed frog Xenopus tropicalis. While both KO and KD embryos fail to activate the same core gene regulatory network, resulting in virtually identical morphological defects, embryos injected with control or target MOs also show a systemic GC content dependent immune response and many off-target splicing defects.


Contributors: George Gentsch, George Gentsch, James Smith

Experiment Type: Comparison of poly(A) transcriptome between Brachyury null mutants and morphants over two tailbud stages.

Experiment Reagents: tbxt MO2, tbxt MO3, tbxt.2 MO3,

Phenotypes:
Xtr.tbxt-/+,tbxt.2-/+ + NF26 (RNA-Seq)

Article: XB-ART-54637, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE - NF26 GSM2537311  GSM2537312  GSM2537313  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 26 to NF stage 26  
   WE + hbg1 cMO - NF26 DEG GSM2537314  GSM2537315  GSM2537316  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection   hbg1 NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 26 to NF stage 26  
   WE + tbxt+/+, tbxt.2+/+ - NF26 DEG GSM2537329  GSM2537330  GSM2537331  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 26 to NF stage 26  
   WE + tbxt-/+, tbxt.2-/+ - NF26 DEG GSM2537332  GSM2537333  GSM2537334  RNA-Seq
Background: Xtr.tbxt,tbxt.2emJcsm
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 26 to NF stage 26  
   WE + tbxt-/-, tbxt.2-/- - NF26 DEG GSM2537335  GSM2537336  GSM2537337  RNA-Seq
Background: Xtr.tbxt,tbxt.2emJcsm
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 26 to NF stage 26  
   WE +tbxt MO + tbxt.2 MO - NF26 DEG GSM2537317  GSM2537318  GSM2537319  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection tbxt MO2 tbxt NF stage 1 zygote
morpholino injection tbxt.2 MO4 tbxt.2 NF stage 1 zygote
morpholino injection tbxt.2 MO3 tbxt.2 NF stage 1 zygote
morpholino injection tbxt MO3 tbxt NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 26 to NF stage 26  
WE - NF34 GSM2537320  GSM2537321  GSM2537322  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 33 and 34 to NF stage 33 and 34  
   WE + hbg1 cMO - NF34 DEG GSM2537323  GSM2537324  GSM2537325  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection   hbg1 NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 33 and 34 to NF stage 33 and 34  
   WE + tbxt+/+, tbxt.2+/+ - NF34 DEG GSM2537338  GSM2537339  GSM2537340  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 33 and 34 to NF stage 33 and 34  
   WE + tbxt-/+, tbxt.2-/+ - NF34 DEG GSM2537341  GSM2537342  GSM2537343  RNA-Seq
Background: Xtr.tbxt,tbxt.2emJcsm
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 33 and 34 to NF stage 33 and 34  
   WE + tbxt-/-, tbxt.2-/- - NF34 DEG GSM2537344  GSM2537345  GSM2537346  RNA-Seq
Background: Xtr.tbxt,tbxt.2emJcsm
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 33 and 34 to NF stage 33 and 34  
   WE +tbxt MO + tbxt.2 MO - NF34 DEG GSM2537326  GSM2537327  GSM2537328  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection tbxt MO2 tbxt NF stage 1 zygote
morpholino injection tbxt.2 MO4 tbxt.2 NF stage 1 zygote
morpholino injection tbxt.2 MO3 tbxt.2 NF stage 1 zygote
morpholino injection tbxt MO3 tbxt NF stage 1 zygote
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 33 and 34 to NF stage 33 and 34  
Select All DEG      Select All 
Xtr   
Xla 

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