On the relationship of protein and mRNA dynamics in vertebrate embryonic development
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PXD002349
PROVIDER: PRJNA298391 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2589790_1.fastq.gz | Fastqsanger.gz | |||
| SRR2589790_2.fastq.gz | Fastqsanger.gz | |||
| SRR2589800_1.fastq.gz | Fastqsanger.gz | |||
| SRR2589800_2.fastq.gz | Fastqsanger.gz | |||
| SRR2589791_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 72 |
Similar Datasets
Project description:How the fertilized egg develops the anatomy of an adult ultimately must be explained at the biochemical level. Deeply connected to the anatomy is the complement of proteins and RNAs expressed during embryogenesis. The relationship of mRNA and respective protein expression dynamics during development has never been systematically explored. Here we present a comprehensive characterization of protein and mRNA dynamics across early development in Xenopus, between unfertilized egg and early tadpole stage. Surprisingly, most proteins change very little; there is an inverse correlation between abundance and rate of change. While the correlation of mRNA and protein expression is poor, a simple mass action kinetics model connects protein to RNA. Parameterized by two fixed parameters the median protein synthesis and degradation rates, the model depends on RNA dynamics, and initial protein concentration. Associated mRNA datasets in GEO: GSE73905 and GSE73870.
2015-10-20 | PXD002349 | Pride
Project description: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. 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.
2015-11-06 | E-GEOD-73870 | biostudies-arrayexpress
Project description: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. 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.
2015-11-06 | E-GEOD-73904 | biostudies-arrayexpress
Project description: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.
2015-11-06 | GSE73904 | GEO
Project description: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.
2015-11-06 | GSE73870 | GEO
Project description:A biochemical explanation of development from the fertilized egg to the adult requires an understanding of the proteins and RNAs expressed over time during embryogenesis. We present a comprehensive characterization of protein and mRNA dynamics across early development in Xenopus. Surprisingly, we find that most protein levels change little and duplicated genes are expressed similarly. While the correlation between protein and mRNA levels is poor, a mass action kinetics model parameterized using protein synthesis and degradation rates regresses protein dynamics to RNA dynamics, corrected for initial protein concentration. This study provides detailed data for absolute levels of ?10,000 proteins and ?28,000 transcripts via a convenient web portal, a rich resource for developmental biologists. 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 dynamics of the embryonic proteome.
| S-EPMC4776761 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-11-06 | E-GEOD-73905 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2015-11-06 | GSE73905 | GEO
Project description:Cell type repertoires have expanded extensively in metazoan animals, with some clade-specific cells being paramount to their evolutionary success. A prime example are the skeletogenic cells of vertebrates that form the basis of their developing endoskeletons. Depending on anatomical location, these cells originate from three different embryonic precursor lineages – the neural crest, the somites, and the lateral plate mesoderm – yet they converge developmentally towards similar cellular phenotypes. Furthermore, these lineages have gained ‘skeletogenic competency’ at distinct timepoints during vertebrate evolution, thus questioning to what extent different parts of the vertebrate skeleton rely on truly homologous cell types. Here, we investigate how lineage-specific molecular properties of the three precursor pools are integrated at the gene regulatory level, to allow for phenotypic convergence towards a skeletogenic cell fate. Using single-cell transcriptomics and chromatin accessibility profiling along the precursor-to-skeletogenic cell continuum, we examine the gene regulatory dynamics associated with this cell fate convergence. We find that distinct transcription factor profiles are inherited from the three precursor states, and that lineage-specific enhancer elements integrate these different inputs at the cis-regulatory level, to execute a core skeletogenic program. We propose a lineage-specific gene regulatory logic for skeletogenic convergence from three embryonic precursor pools. Early skeletal cells in different body parts thus share only a partial ‘deep homology’. This regulatory uncoupling may render them amenable to individualized selection, to help to define distinct morphologies and biomaterial properties in the different parts of the vertebrate skeleton.
2024-11-27 | GSE281763 | GEO
Project description:Cell type repertoires have expanded extensively in metazoan animals, with some clade-specific cells being paramount to their evolutionary success. A prime example are the skeletogenic cells of vertebrates that form the basis of their developing endoskeletons. Depending on anatomical location, these cells originate from three different embryonic precursor lineages – the neural crest, the somites, and the lateral plate mesoderm – yet they converge developmentally towards similar cellular phenotypes. Furthermore, these lineages have gained ‘skeletogenic competency’ at distinct timepoints during vertebrate evolution, thus questioning to what extent different parts of the vertebrate skeleton rely on truly homologous cell types. Here, we investigate how lineage-specific molecular properties of the three precursor pools are integrated at the gene regulatory level, to allow for phenotypic convergence towards a skeletogenic cell fate. Using single-cell transcriptomics and chromatin accessibility profiling along the precursor-to-skeletogenic cell continuum, we examine the gene regulatory dynamics associated with this cell fate convergence. We find that distinct transcription factor profiles are inherited from the three precursor states, and that lineage-specific enhancer elements integrate these different inputs at the cis-regulatory level, to execute a core skeletogenic program. We propose a lineage-specific gene regulatory logic for skeletogenic convergence from three embryonic precursor pools. Early skeletal cells in different body parts thus share only a partial ‘deep homology’. This regulatory uncoupling may render them amenable to individualized selection, to help to define distinct morphologies and biomaterial properties in the different parts of the vertebrate skeleton.
2024-11-27 | GSE281769 | GEO