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Extensive oscillatory gene expression during C. elegans larval development [Ribosome footprinting]

ABSTRACT: We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE52905 | GEO | 2014/03/01

SECONDARY ACCESSION(S): PRJNA230441

REPOSITORIES: GEO

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Extensive oscillatory gene expression during C. elegans larval development [Ribosome footprinting]

Project description:We report the presence of extensive, transcriptionally controlled oscillations in the C. elegans, developmental transcriptome. Furthermore, using ribosome profiling, we show that these oscillating transcripts are actively translated. Ribosome-profiling analysis of a timecourse that was collected over C. elegans development

2014-03-01 | E-GEOD-52905 | biostudies-arrayexpress

Extensive oscillatory gene expression during C. elegans larval development [RNA-seq for polyA enriched mRNAs]

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Extensive oscillatory gene expression during C. elegans larval development

Project description:This SuperSeries is composed of the SubSeries listed below.

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Extensive oscillatory gene expression during C. elegans larval development

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

Project description:Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptideM-bM-^@M-^Pencoding genes in vertebrates, providing an entry point to define their function in vivo. Ribosome profiling experiments at five timepoints across zebrafish development in WT embryos

2014-04-04 | E-GEOD-53693 | biostudies-arrayexpress

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

Project description:Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged the periodicity of ribosome movement on the mRNA to define actively translated ORFs by ribosome footprinting. This approach identifies several hundred translated small ORFs in zebrafish and human. Computational prediction of small ORFs from codon conservation patterns corroborates and extends these findings and identifies conserved sequences in zebrafish and human, suggesting functional peptide products (micropeptides). These results identify micropeptide‐encoding genes in vertebrates, providing an entry point to define their function in vivo.

2014-04-04 | GSE53693 | GEO

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2022-12-31 | GSE169641 | GEO

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