Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Developmental Timecourses total-RNA sequencing [Ribosome repleted total RNA]

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: GSE52864 | GEO | 2014/03/01

SECONDARY ACCESSION(S): PRJNA230377

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Developmental Timecourses total-RNA sequencing [Ribosome repleted total RNA]

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. Examination of two timecourses that were collected over C. elegans development and analyzed by RNA-seq of "RiboMinus" libraries

2014-03-01 | E-GEOD-52864 | biostudies-arrayexpress

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

2014-03-01 | GSE52905 | GEO

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]

2014-03-01 | GSE52861 | GEO

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

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. Examination of three timecourses that were collected over C. elegans development and analyzed by RNA-seq of mRNA libraries

2014-03-01 | E-GEOD-52861 | biostudies-arrayexpress

Rhythmic transcription drives mRNA level oscillations during C. elegans development [ChIP-Seq]

Project description:Thousands of transcripts accumulate in an oscillatory manner during C. elegans larval development. Here, we confirmed these oscillations to result from rhythmic RNA polymerase II (RNAPII) binding to these oscillating genes by performing RNAPII ChIP-seq and total RNA-seq on the same samples (see related submission)

2022-12-31 | GSE169641 | GEO

C. briggsae and C. elegans developmental timecourses

Project description:This SuperSeries is composed of the following subset Series: GSE15233: C. briggsae developmental timecourse GSE15234: C. elegans developmental timecourse Refer to individual Series

2009-08-31 | E-GEOD-15551 | biostudies-arrayexpress

Ribosome Profiling over a Zebrafish Developmental Timecourse

Project description:To experimentally-validate the non-coding status of annotated lncRNAs, we performed ribosome profiling over a developmental timecourse that matched our previously-published (Pauli et al. 2012) developmental transcriptome. We find that many previously-annotated lncRNAs appear to be translated, but in a pattern more akin to 5' leaders of coding genes. Ribosome profiling over 8 stages in early zebrafish development: 2-4 cell, 256 cell, 1K cell, Dome, Shield, Bud, 28hpf and 5dpf

2013-05-23 | E-GEOD-46512 | biostudies-arrayexpress

Ribosome Profiling over a Zebrafish Developmental Timecourse

2013-05-23 | GSE46512 | GEO

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data