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GEO Series: GSE145619

Title: Combinatorial action of transcription factors in open chromatin contributes to early cellular heterogeneity and organizer mesendoderm specification

Summary

We applied chromatin accessibility and single cell transcriptome analyses to explore the emergence of heterogeneity and underlying gene-regulatory mechanisms during early gastrulation in Xenopus. TF activity was inferred by integrating chromatin accessibility and single cell transcriptomics. Our results show that combinatorial activity of zygotically expressed transcription factors acts on maternally-regulated accessible chromatin to induce organizer gene expression.


Contributors: Ann Bright, Ann Bright, Siebe van Genesen, Qingqing Li, Alexia Grasso, Gert Veenstra

Experiment Type: ATAC-seq on Xenopus embryos (stage 9, 10.5, 12 and 16) and gastrula stage embryo explants (Animal cap and Dorsal marginal zone). RNA-seq on animal caps overexpressed with Foxb1, Foxb1 + Eomes, Eomes, Irx3, Irx3 + Otx2 and Lhx8 mRNA. ScRNA-seq on Animal cap and Dorsal marginal zone explants

Experiment Reagents: eomes, foxb1, irx3,

Phenotypes:
Xtr Wt + eomes + animal cap explant + animal cap NF10.5 (RNA-Seq (RNA))

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE - NF10.5 GSM4322285  GSM4322286  ATAC-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 to NF stage 10.5  
   animal cap - NF10.5 GSM4322291  GSM4322292  ATAC-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5 to NF stage 10.5  
   dorsal marginal zone - NF10.5 GSM4322293  GSM4322294  ATAC-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
dorsal marginal zone NF stage 10.5 to NF stage 10.5  
animal cap explant - NF10.5 GSM4322295  GSM4322296  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5 to NF stage 10.5  
   animal cap explant - eomes - NF10.5 DEG GSM4322301  GSM4322302  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection eomes eomes NF stage 1 animal pole
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5 to NF stage 10.5  
   animal cap explant - foxb1 + eomes - NF10.5 DEG GSM4322299  GSM4322300  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection foxb1 foxb1 NF stage 1 animal pole
mRNA injection eomes eomes NF stage 1 animal pole
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5 to NF stage 10.5  
   animal cap explant - foxb1 - NF10.5 DEG GSM4322297  GSM4322298  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection foxb1 foxb1 NF stage 1 animal pole
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5 to NF stage 10.5  
   animal cap explant - irx3 + otx2 - NF10.5 DEG GSM4322305  GSM4322306  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection irx3 irx3 NF stage 1 animal pole
mRNA injection otx2 otx2 NF stage 1 animal pole
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5 to NF stage 10.5  
   animal cap explant - irx3 - NF10.5 DEG GSM4322303  GSM4322304  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection irx3 irx3 NF stage 1 animal pole
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5 to NF stage 10.5  
   animal cap explant - lhx8 - NF10.5 DEG GSM4322309  GSM4322310  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection lhx8 lhx8 NF stage 1 animal pole
explant   NF stage 8 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5 to NF stage 10.5  
   animal cap explant - otx2 - NF10.5 DEG GSM4322307  GSM4322308  RNA-Seq
Background: Xtr.Outbred
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection otx2 otx2 NF stage 1 animal pole
explant   NF stage 1 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5 to NF stage 10.5  
WE - NF12 GSM4322287  GSM4322288  ATAC-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12 to NF stage 12  
WE - NF16 GSM4322289  GSM4322290  ATAC-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16 to NF stage 16  
WE - NF9 GSM4322283  GSM4322284  ATAC-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 to NF stage 9  
Select All DEG      Select All 
Xtr   
Xla 

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