Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA localization is a key determinant of neurite-enriched proteome - RNAseq

ABSTRACT: RNA localization and local translation are important biological processes that underlie establishment of body axis, cell migration and synaptic plasticity. However, it is unclear to which extent mRNA localization contributes toward local proteome and how much of protein localization is achieved via protein transport or local translation of uniformly distributed mRNAs. To address this question, we performed genome-wide analysis of the local proteome, transcriptome, and translation rates in neurites and cell bodies of neurons differentiated from mouse embryonic stem cells.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Altuna Akalin

PROVIDER: E-MTAB-4978 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

RNA localization is a key determinant of neurite-enriched proteome - Riboseq

Project description:RNA localization and local translation are important biological processes that underlie establishment of body axis, cell migration and synaptic plasticity. However, it is unclear to which extent mRNA localization contributes toward local proteome and how much of protein localization is achieved via protein transport or local translation of uniformly distributed mRNAs. To address this question, we performed genome-wide analysis of the local proteome, transcriptome, and translation rates in neurites and cell bodies of neurons differentiated from mouse embryonic stem cells.

2017-07-23 | E-MTAB-4979 | biostudies-arrayexpress

3' mRNA-seq of neurites and soma isolated from mESC-derived neurons

Project description:3' mRNA-seq was performed with QuantSeq 3' mRNA-Seq kit (Lexogen 015) according to the manufacturer’s recommendations. 3' mRNA-seq was done in biological triplicates (soma) or duplicates (neurites), using 260 ng of total RNA from neurites or soma of mESC-derived neurons per sample. Libraries were pooled and sequenced on Illumina NextSeq 500 system with a single-end 150-cycle run.

2019-01-12 | E-MTAB-7251 | biostudies-arrayexpress

mRNA-Seq of neuronal compartments in shRNA-mediated knockdown of Larp1 in mouse primary cortical neurons

Project description:To study the effect of Larp1 on the abundance and subcellular localization of 5'TOP containing mRNAs, Larp1 was depleted from mouse primary cortical neurons using shRNAs. RNA from subcellular compartments (neurite and soma cytoplasm) was isolated and sequenced in parallel with scrambled control shRNA expressing samples.

2023-07-12 | E-MTAB-12886 | biostudies-arrayexpress

mRNA-Seq of neuronal compartments with perturbed mRNA degradation machinery (overexpression of dnCaf1) in mouse primary cortical neurons

Project description:To study the correlation between mRNA stability and subcellular mRNA localisation we globally interferred with mRNA degradation in primary cortical neurons by overexpressing a catalytic mutant of deadenylase CAF1 that functions as a dominant negative form. Neurons were separated into subcellular compartments (neurite, soma-cytoplasm and nucleus) and sequenced in parallel with respective compartments from GFP- expressing control neuons.

2023-07-12 | E-MTAB-12887 | biostudies-arrayexpress

QuaNCAT analysis comparing proteins synthesized in neurites and soma in ASCL1-iNeurons

Project description:Local translation in ASCL1-iNeurons was probed using QuaNCAT

2018-10-17 | PXD005059 | Pride

Depletion of m6A methylation by conditional Mettl3 knockout in Ascl1-induced neurons

Project description:We have perturbed RNA methylation machinery and investigated the change in subcellular localization of mRNA in Ascl1-induced neurons (iNeurons). Mutant iNeuron line harbouring tagged endogenous Mettl3 was generated which allowed for the selective and targeted depletion of Mettl3 protein with the addition of dTAG. Cells were treated with dTAG for 40 hours then separated into compartments (neurites and soma) and then sequenced in parallel with samples which received no dTAG treatment.

2023-07-12 | E-MTAB-9643 | biostudies-arrayexpress

RNA-seq of neuronal compartments with perturbed mRNA degradation machinery

Project description:We have perturbed mRNA degradation machinery and investigated the change in subcellular localization of mRNA in Ascl1-induced neurons (iNeurons). Mutant iNeuron line harbouring a ponasteroneA-inducible heterozygous dominant-negative Caf1 (dnCaf1) was generated, separated into neuronal compartments (soma and neurites) and sequenced in parallel with compartments from the Wild Type iNeurons (WT). Differential localization of mRNA between soma and neurites in the WT was then compared to the localization in dnCaf1 in order to identify the changes in localization.

2023-12-31 | E-MTAB-9398 | biostudies-arrayexpress

SlamSeq of subcellular compartments in mouse primary cortical neurons

Project description:We performed SlamSeq (thiol(SH)-linked alkylation for metabolic sequencing) to estimate mRNA half-lives in subcellular compartments (neurites, soma-cytoplasm and nucleus) of primary cortical neurons.

2023-07-12 | E-MTAB-12888 | biostudies-arrayexpress

Global proteome of neurite and soma isolated from primary cortical neurons

Project description:Proteome comparison of neurite and soma total protein extracts isolated from mouse cortical neurons.

2022-11-15 | PXD028300 | Pride

Localization of functionally distinct CDC42 isoforms in neurons requires alternative 3'UTR usage

Project description:The proper subcellular localization of RNAs and local translational regulation is crucial in highly compartmentalized cells, such as neurons. RNA localization is mediated by specific cis-regulatory elements usually found in mRNA 3'UTRs. Therefore, processes that generate alternative 3'UTRs – alternative splicing and polyadenylation – have the potential to diversify mRNA localization patterns in neurons. Here, we performed mapping of alternative 3'UTRs in neurites and soma isolated from mESC-derived neurons. Our analysis identified 593 genes with differentially localized 3'UTR isoforms. In particular, we have shown that two isoforms of Cdc42 gene with distinct functions in neuronal polarity are differentially localized between neurites and soma of mESC-derived and mouse primary cortical neurons, at both mRNA and protein level. Using reporter assays and 3'UTR swapping experiments, we have identified the role of alternative 3’UTRs and mRNA transport in differential localization of alternative CDC42 protein isoforms. Moreover, we used SILAC to identify isoform-specific Cdc42 3'UTR-bound proteome with potential role in Cdc42 localization and translation. Our analysis points to usage of alternative 3'UTR isoforms as a novel mechanism to provide for differential localization of functionally diverse alternative protein isoforms.

2018-12-07 | PXD011518 | Pride

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