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GEO Series: GSE118024

Title: Endodermal maternal transcription factors establish super enhancers during zygotic genome activation

Summary

We examined the combinatorial function of the Xenopus tropicalis maternal transcription factors Foxh1, Vegt and Otx1. The study involved combinatorial ectopic expression of vegt and otx1 RNA in the putative ectoderm; and combinatorial knock-down of vegt and otx1 in the putative endoderm both followed by transcriptomic analysis (RNA-seq). We performed chromatin immunoprecipitation combined with high throughput sequencing (ChIP-seq) to assess the chromatin association of Vegt and Otx1 prior to zygotic gene activation. In addition, we performed ChIP-seq on H3K4me1 on endoderm tissue to identify active regulatory regions in an unbiased manner.


Contributors: Kitt Paraiso, Kitt Paraiso, Ken Cho

Experiment Type: Screen for animally and vegetally expressed transcription factors: In biological triplicates, the animal and vegetal blastomeres of 8-cell stage embryos were separated. Subsequently, RNA was harvested from both set of blastomeres and whole embryos at the same stage and prepared for RNA sequencing. Combinatorial ectopic expression experiment: In biological duplicates, titrating levels of vegt and otx1 RNA were combinatorially microinjected into 1-cell stage embryos. Animal caps (putative ectoderm) were microdissected at stage 9 (6 hpf) from uninjected and injected samples, and RNA was harvested at stage 10.5 (7 hpf) for RNA sequencing. Double morpholino experiment: In biological duplicates, Vegt and Otx1 morpholinos were injected in 1-cell stage embryos independently or together. Vegetal masses (putative endoderm) were microdissected at stage 9 (6 hpf) and RNA was harvested from uninjected and injected samples at stage 10.5 (7 hpf) for RNA sequencing. Vegt and Otx1 ChIP-seq analysis: Developmentally synchronized embryos were harvested at stage 8 (prior to zygotic gene activation) and fixed with formaldehyde in biological duplicates. Chromatin immunoprecipitation as performed using anti-Vegt or anti-Otx1 antibody and DNA was purified for sequencing. H3K4me1 ChIP-seq analysis: Developmentally synchronized embryos were harvested at stage 10.5 and fixed with formaldehyde in biological duplicates. The vegetal tissue was disssected from the fixed embryos, and ChIP-seq was performed using anti-H3K4me1 antibody. Previously published Foxh1 ChIP-seq from GSE85273 was re-analyzed along with this study. GSM2263590 and GSM2263598 used to generate: GSE118024_foxh1_IDR_optimal_peaks.bed.gz GSM2263598 used to generate: GSE118024_otx1_IDR_optimal_peaks.bed.gz, GSE118024_vegt_IDR_optimal_peaks.bed.gz

Experiment Reagents: otx1, otx1 MO2, vegt,

Article: XB-ART-55999, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE - NF4 GSM3317420  GSM3317421  GSM3317422  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 4 (8-cell)  
   animal blastomere - NF4 DEG GSM3317414  GSM3317415  GSM3317416  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
animal blastomere NF stage 4 (8-cell)  
   vegetal blastomere - NF4 DEG GSM3317417  GSM3317418  GSM3317419  RNA-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
vegetal blastomere NF stage 4 (8-cell)  
animal cap - animal cap explant - NF10.5 GSM3317423  GSM3317431  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5  
   animal cap - otx1 + vegt + animal cap explant - NF10.5 DEG GSM3317429  GSM3317437  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection otx1 otx1 NF stage 1 zygote
mRNA injection vegt vegt NF stage 1 zygote
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5  
   animal cap - vegt + animal cap explant - NF10.5 DEG GSM3317424  GSM3317432  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection vegt vegt NF stage 1 zygote
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5  
   animal cap - vegt + animal cap explant - NF10.5 DEG GSM3317425  GSM3317433  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection vegt vegt NF stage 1 zygote
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5  
   animal cap - vegt + animal cap explant - NF10.5 DEG GSM3317426  GSM3317434  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection vegt vegt NF stage 1 zygote
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5  
   animal cap - vegt + animal cap explant - NF10.5 DEG GSM3317427  GSM3317435  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection vegt vegt NF stage 1 zygote
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5  
   animal cap - vegt + otx1 + animal cap explant - NF10.5 DEG GSM3317428  GSM3317436  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection vegt vegt NF stage 1 zygote
mRNA injection otx1 otx1 NF stage 1 zygote
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5  
   animal cap - vegt + otx1 + animal cap explant - NF10.5 DEG GSM3317430  GSM3317438  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
mRNA injection vegt vegt NF stage 1 zygote
mRNA injection otx1 otx1 NF stage 1 zygote
explant   NF stage 9 animal cap
Conditions:
Tissue Assay Stages ChIP Antibody
animal cap NF stage 10.5  
vegetal yolk mass - vegetal yolk mass explant - NF10.5 GSM3317439  GSM3317443  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
explant   NF stage 9 vegetal yolk mass
Conditions:
Tissue Assay Stages ChIP Antibody
vegetal yolk mass NF stage 10.5  
   vegetal yolk mass - otx1 MO + vegetal yolk mass explant - NF10.5 DEG GSM3317441  GSM3317445  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection otx1 MO2 otx1 NF stage 1 zygote
explant   NF stage 9 vegetal yolk mass
Conditions:
Tissue Assay Stages ChIP Antibody
vegetal yolk mass NF stage 10.5  
   vegetal yolk mass - vegt MO + otx1 MO + vegetal yolk mass explant - NF10.5 DEG GSM3317442  GSM3317446  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection vegt MO10 vegt NF stage 1 zygote
morpholino injection otx1 MO2 otx1 NF stage 1 zygote
explant   NF stage 9 vegetal yolk mass
Conditions:
Tissue Assay Stages ChIP Antibody
vegetal yolk mass NF stage 10.5  
   vegetal yolk mass - vegt MO + vegetal yolk mass explant - NF10.5 DEG GSM3317440  GSM3317444  RNA-Seq
Background: Xtr.NigerianNasco
Manipulations:
Manipulation Type Reagent Target Gene Stage Treatment Area
morpholino injection vegt MO10 vegt NF stage 1 zygote
explant   NF stage 9 vegetal yolk mass
Conditions:
Tissue Assay Stages ChIP Antibody
vegetal yolk mass NF stage 10.5  
H3K4me1 vegetal yolk mass - NF10.5 GSM3638163  GSM3638164  ChIP-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
vegetal yolk mass NF stage 10.5 methyl-H3f3a Ab13
Otx1 WE - NF8 GSM3317449  GSM3317450  ChIP-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8 Otx1 Ab1
VegT WE - NF8 GSM3317447  GSM3317448  ChIP-Seq
Background: Xtr.NigerianNasco
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8 VegT Ab2
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