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GEO Series: GSE43652

Title: A Genome-Wide Survey of Maternal and Embryonic Transcripts during Xenopus tropicalis Development

Summary

To analyze the dynamics and diversity of coding and non-coding transcripts during development, both polyadenylated mRNA and ribosomal RNA-depleted total RNA were harvested across six developmental stages and subjected to high throughput sequencing. The maternally loaded transcriptome is highly diverse and consists of both polyadenylated and deadenylated transcripts. Many maternal genes show peak expression in the oocyte and include genes which are known to be the key regulators of events like oocyte maturation and fertilization. Of all the transcripts that increase in abundance between an early blastula and larval stages, about 30% of the embryonic genes are induced by fourfold or more by the late blastula stage and another 35% by late gastrulation. Using a gene model validation and discovery pipeline, we identified novel transcripts, the majority of which show hallmarks of being long non-coding RNAs both in terms of their coding potential and gene structure.


Contributors: Gert Jan Veenstra, Sarita Paranjpe, Ulrike Jacobi, Simon van Heeringen, Gert Veenstra

Experiment Type: Profiles of polyadenylated mRNA (6 stages) and ribosomal RNA-depleted total RNA (3 stages) through early Xenopus tropicalis development

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE - NF12 GSM1067626  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12  
WE - NF16 GSM1067627  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16  
WE - NF29/30 GSM1067628  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30  
WE - NF6 GSM1067624  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6 (32-cell)  
WE - NF6 rd GSM1067630  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6 (32-cell)  
WE - NF9 GSM1067625  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - NF9 rd GSM1067631  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
oocyte - unfertilized egg GSM1067623  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
oocyte unfertilized egg stage  
oocyte - unfertilized egg rd GSM1067629  RNA-Seq
Background: Xtr.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
oocyte unfertilized egg stage  
Select All 
Xtr   
Xla 

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