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GEO Series: GSE73904

Title: On the relationship of protein and mRNA dynamics in vertebrate embryonic development [RiboZero]

Summary

A biochemical explanation of development from the fertilized egg to the adult anatomy requires an understanding of the complement of proteins and RNAs expressed over time during embryogenesis. Here we present a comprehensive characterization of protein and mRNA dynamics across early development in Xenopus. Surprisingly, we find that most proteins change very little and duplicated genes are expressed similarly. While the correlation between mRNA levels and protein expression is poor, a mass action kinetics model parametrized by the protein synthesis and degradation rates regresses protein dynamics to RNA dynamics, corrected for initial protein concentration. This study provides a rich resource for developmental biologists, unveiling detailed data for absolute levels of ~10K proteins and ~28K transcripts via convenient web portal. It underscores the lasting impact of maternal dowry, finds surprisingly few cases where degradation alone drives a change in protein level, and highlights the importance of transcription in shaping the proteome.


Contributors: Esther Pearl, Leonid Peshkin, Martin Wuhr, Esther Pearl, Wilhelm Haas, Robert Freeman, John Gerhart, Allon Klein, Marko Horb, Steven Gygi, Marc Kirscher

Experiment Type: mRNA from 18 samples each at a different developmental stage. Libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification.

Article: Xenbase, PubMed

Source: NCBI GEO, Xenbase FTP

Samples: (DEG = Differentially Expressed Genes; GSM = GEO Sample Number)
Sample View GSMs Assay Type
WE - NF10 GSM1905645  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10  
WE - NF12 GSM1905646  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12  
WE - NF14 GSM1905647  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 14  
WE - NF16 GSM1905648  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16  
WE - NF18 GSM1905649  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 18  
WE - NF2 GSM1905638  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 2 (2-cell)  
WE - NF20 GSM1905650  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 20  
WE - NF23 GSM1905651  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 23  
WE - NF26 GSM1905652  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 26  
WE - NF29/30 GSM1905653  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30  
WE - NF33/34 GSM1905654  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 33 and 34  
WE - NF6 GSM1905639  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6 (32-cell)  
WE - NF6.5 GSM1905640  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6.5  
WE - NF7 GSM1905641  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 7  
WE - NF8 GSM1905642  GSM1905643  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF9 GSM1905644  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - mature egg GSM1905637  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo mature egg stage  
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