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GEO Series: GSE73870

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

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 Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 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 GSM1904671  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 10  
WE - NF12 GSM1904672  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 12  
WE - NF14 GSM1904673  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 14  
WE - NF16 GSM1904674  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 16  
WE - NF18 GSM1904675  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 18  
WE - NF2 GSM1904664  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 2 (2-cell)  
WE - NF20 GSM1904676  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 20  
WE - NF23 GSM1904677  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 23  
WE - NF26 GSM1904678  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 26  
WE - NF29/30 GSM1904679  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 29 and 30  
WE - NF33/34 GSM1904680  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 33 and 34  
WE - NF6 GSM1904665  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6 (32-cell)  
WE - NF6.5 GSM1904666  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 6.5  
WE - NF7 GSM1904667  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 7  
WE - NF8 GSM1904668  GSM1904669  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 8  
WE - NF9 GSM1904670  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo NF stage 9  
WE - mature egg GSM1904663  RNA-Seq
Background: Xla.Outbred
Conditions:
Tissue Assay Stages ChIP Antibody
embryo mature egg stage  
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