Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

42 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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. Ribosome-profiling analysis of a timecourse that was collected over C. elegans development

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Dimos Gaidatzis

PROVIDER: E-GEOD-52905 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (ribosome)

Project description:We present a basic characterization of the function of Y-box binding proteins in C. elegans. Besides playing an important role for fertility in the germline (all four CEY proteins), we found that the presence of CEY-1 and CEY-4 is essential for the assembly of larger polysomes in the soma. We therefore performed ribosome-profiling in combination with total RNA sequencing in wild type and cey-1,-4 double mutant animals to globally compare mRNA levels and their translation status. Ribosome-profiling analysis was peformed on wild type and cey-1,-4 mutant animals in duplicates. Four samples in total.

2015-01-08 | E-GEOD-62859 | biostudies-arrayexpress

Extensive oscillatory gene expression during C. elegans larval development

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

2014-03-01 | E-GEOD-52910 | biostudies-arrayexpress

Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes

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

2015-01-08 | E-GEOD-62861 | biostudies-arrayexpress

LEM-2 ChIP-seq to study chromatin anchoring

Project description:Chromatin Immunoprecipitation against the nuclear envelope protein LEM-2 to detect association to the nuclear periphery. LEM-2 ChIP was performed on early embryo fixed extracts for wild-type and two mutants that have altered position of a perinuclear chromatin reporter. LEM-2 ChIP on early embryo chromatin extracts of three different genotypes: wild-type, met-2 set-25_delta_delta and cec-4_delta, in two independent biological replicas

2015-12-11 | E-GEOD-74133 | biostudies-arrayexpress

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

Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (RNA-Seq)

Project description:We present a basic characterization of the function of Y-box binding proteins in C. elegans. Besides playing an important role for fertility in the germline (all four CEY proteins), we found that the presence of CEY-1 and CEY-4 is essential for the assembly of larger polysomes in the soma. We therefore performed ribosome-profiling in combination with total RNA sequencing in wild type and cey-1,-4 double mutant animals to globally compare mRNA levels and their translation status. Total RNA sequencing was peformed on RNA extacted from wild type and cey-1,-4 mutant animals in duplicates. Four samples in total.

2015-01-08 | E-GEOD-62858 | biostudies-arrayexpress

Defining soma-specific/enriched and germline-specific/enriched transcripts

Project description:To define what genes are predominantly or specifically expressed in either soma or germline in C. elegans adults, total RNA was extracted from germline-less glp-4 mutant animals or from dissected gonads, respectively. Total RNA sequencing was peformed in duplicates. Four samples in total.

2015-01-08 | E-GEOD-62857 | biostudies-arrayexpress

Functional characterization of C. elegans Y-box binding proteins reveals tissue-specific functions and a critical role in the formation of polysomes (RIP-Seq)

Project description:We present a basic characterization of the function of Y-box binding proteins (YBPs) in C. elegans. YBPs in other organisms are known RNA-binding proteins. Our global analysis of associated mRNAs supports a role of YBPs as general mRNA binders in C.elegans. FLAG IPs were performed on transgenic animals expressing FLAG-tagged versions of either CEY-1, CEY-2, or CEY-4. MYC IPs served as controls. All IPs were performed in duplicates. 12 samples in total.

2015-01-08 | E-GEOD-62856 | biostudies-arrayexpress

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

Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint

Project description:Exogenous double-stranded RNA (dsRNA) has been shown to exert homology-dependent effects at the level of both target mRNA stability and chromatin structure. Using C. elegans undergoing RNAi as an animal model, we have investigated the generality, scope, and longevity of chromatin-targeted dsRNA effects and their dependence on components of the RNAi machinery. Using high-resolution genome-wide chromatin profiling, we found that a diverse set of genes can be induced to acquire locus-specific enrichment of H3K9 trimethylation, with modification footprints extending several kilobases from the site of dsRNA homology and with locus specificity sufficient to distinguish the targeted locus from among all 20,000 genes in the C. elegans genome. Genetic analysis of the response indicated that factors responsible for secondary siRNA production during RNAi were required for effective targeting of chromatin. Temporal analysis revealed that H3K9 methylation, once triggered by dsRNA, can be maintained in the absence of dsRNA for at least two generations before being lost. These results implicate dsRNA-triggered chromatin modification in C. elegans as a programmable and locus-specific response defining a metastable state that can persist through generational boundaries. H3K9me3 nucleosome-IP sequencing and small RNA sequencing in C. elegans populations that underwent RNAi

2012-01-06 | E-GEOD-32631 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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