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GEO Series: GSE56586

Title: Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs

Summary

Recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells. In contrast, single cell proteomics analyses have been restricted to targeted analyses, for example using flow cytometry with GFP fusions or mass cytometry. Here, we performed global absolute protein quantification of single Xenopus laevis eggs using mass spectrometry-based proteomics. We quantified over 5800 proteins, thus representing the largest single cell proteome that has been characterized to date. Absolute protein amounts in single eggs are highly comparable, thus indicating a tight regulation of global protein abundance. Comparison between the single-cell proteome and transcriptome reveal poor expression correlation. Finally, we identified 439 proteins that significantly change in abundance during early embryogenesis. Many of these proteins do not show regulation at the transcript level. Altogether, our data reveal that the transcriptome is a poor indicator of the proteome and that protein levels are tightly controlled in Xenopus leavis eggs.


Contributors: Gert Jan Veenstra, Arne Smits, Rik Lindeboom, Matteo Perino, Simon van Heeringen, GertJan Veenstra, Michiel Vermeulen

Experiment Type: RNA-seq in Xenopus laevis of 5 replicates of both single eggs and single embryos.

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE - NF1 rd GSM1364749  GSM1364750  GSM1364751  GSM1364752  GSM1364753  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
zygote NF stage 1  
WE - NF10.5 rd GSM1430926  GSM1430927  GSM1430928  GSM1430929  GSM1430930  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5  
WE - NF10.5 rd technical rep GSM1430931  GSM1430932  GSM1430933  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10.5  
Select All 
Xtr   
Xla 

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