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GEO Series: GSE92382

Title: Regulatory remodeling in the allo-tetraploid frog Xenopus laevis

Summary

Genome duplication has played a pivotal role in the evolution of many eukaryotic lineages, including the vertebrates.The most recent vertebrate genome duplication is that in Xenopus laevis, which resulted from the hybridization of two closely related species about 17 million years ago. Here we generated epigenetic profiles and determined gene expression in X.laevis embryos to study the consequences of this duplication at the level of the genome, the epigenome and gene expression.


Contributors: Simon van Heeringen, Sarita Paranjpe, Georgios Georgiou, Ila van Kruijsbergen, Romain Gibeaux, Rebecca Heald, Simon van Heeringen, Gert Veenstra

Experiment Type: Genomic DNA of Xenopus tropicalis and Xenopus laevis; RNA-seq (two replicates) in stage 10.5 Xenopus laevis embryos; ChIP-seq for H3K4me3 and p300 (each two replicates) in Xenopus laevis (LELS), Xenopus tropicalis (TETS) and Xenopus tropicals x laevis (hybrid; LETS) embryos.

Article: XB-ART-54195, PubMed

Source: NCBI GEO, Xenbase Download

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
input WE - NF9 GSM2428823  GSM2428824  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   H3K4me3 WE - NF9 GSM2428817  GSM2428818  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 Tri-Methyl H3f3a Ab19
ep300 WE - NF10.5 GSM2428829  GSM2428830  ChIP-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 Ep300 Ab1
input WE - NF9 GSM2428821  GSM2428822  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
   H3K4me3 WE - NF9 GSM2428815  GSM2428816  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9 Tri-Methyl H3f3a Ab19
ep300 WE - NF10.5 GSM2428827  GSM2428828  ChIP-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5 Ep300 Ab1
WE - NF10.5 GSM2428813  GSM2428814  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5  
Select All DEG      Select All 
Xtr   
Xla 

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