Return to search results Title: Uncovering the mesendoderm gene regulatory network through multi-omic data integration

Summary

We report the ChIP-seq analysis of multiple Xenopus transcription factors binding. Also, we report loss-of-function transcriptomic analysis of Tcf7l1 by RNA-seq at different developmental stages. These newly generated datasets are analyzed using self-organizing maps, along with previously published Xenopus genomic data.

Contributors: Kitt Paraiso, Kitt Paraiso

Experiment Type: ChIP-seq was performed using antibodies against Xenopus tropicalis transcription factors (Mix1, Sia1, Smad1, Sox7, Vegt and Ventx2) where embryos were processed at different stages of early development. RNA-seq datasets were generated from uninjected embryos and Tcf7l1 morpholino injected embryos. These multi-omic datasets, along with literature curated ChIP-seq, RNA-seq and ATAC-seq datasets, were analyzed using Self-Organizing Maps to elucidate the gene regulatory network principles of early mesendoderm development.

Experiment Reagents: tcf7l1 MO2.

Article: XB-ART-58965, PubMed

Source: NCBI GEO, Xenbase Download

Sample	View		GSMs	Assay Type
WE - NF9 GSM4910712  GSM4910713  RNA-Seq Xtr   [-] [+] Background: Xtr.NigerianNasco Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9      WE + tcf7l1 MO - NF9 DEG GSM4910706  GSM4910707  RNA-Seq Xtr   [-] [+] Background: Xtr.NigerianNasco Manipulations: Manipulation Type Reagent Target Gene Stage Treatment Area morpholino injection tcf7l1 MO2 tcf7l1 NF stage 1 zygote Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 9   WE - NF10 GSM4910714  GSM4910715  RNA-Seq Xtr   [-] [+] Background: Xtr.NigerianNasco Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10      WE + tcf7l1 MO - NF10 DEG GSM4910708  GSM4910709  RNA-Seq Xtr   [-] [+] Background: Xtr.NigerianNasco Manipulations: Manipulation Type Reagent Target Gene Stage Treatment Area morpholino injection tcf7l1 MO2 tcf7l1 NF stage 1 zygote Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10   WE - NF10.5 GSM4910716  GSM4910717  RNA-Seq Xtr   [-] [+] Background: Xtr.NigerianNasco Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10.5      WE + tcf7l1 MO - NF10.5 DEG GSM4910710  GSM4910711  RNA-Seq Xtr   [-] [+] Background: Xtr.NigerianNasco Manipulations: Manipulation Type Reagent Target Gene Stage Treatment Area morpholino injection tcf7l1 MO2 tcf7l1 NF stage 1 zygote Conditions: Tissue Assay Stages ChIP Antibody embryo NF stage 10.5

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