Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

40 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Inga Loedige

PROVIDER: E-MTAB-12887 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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

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

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

Slamseq of subcellular compartments in neurons

Project description:We performed a SLAMseq Metabolic RNA Labeling on neuronal subcellular compartments, e.g. neurites and soma, derived from Ascl1-induced neurons (iNeurons). This experimental approach provides a snapshot of mRNA kinetics which allows to estimate the half-lives of mRNAs. These data was used to investigate the influence of mRNA degradation machinery in both neuronal compartments.

2023-07-12 | E-MTAB-9400 | 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

mRNA-seq of neuronal compartments with perturbed mRNA degradation machinery in mouse primary cortical neurons (mPCN)

Project description:We have perturbed mRNA degradation machinery and investigated the change in subcellular localization of mRNA in mouse primary cortical neurons (mPCNs). Mutant mPCN 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 GFP-transfected cells (GFP, negative control).

2022-11-14 | E-MTAB-11572 | biostudies-arrayexpress

mRNA-seq of neuronal compartments in shRNA-mediated + small-molecule knockdown of Mettl3 in mouse primary cortical neurons (mPCN)

Project description:To study the effect of m6A modifications on subcellular mRNA localization we depleted m6A writer Mettl3 with shRNA and small molecule from mouse primary cortical neurons (mPCN) and sequenced neuritic and somatic compartments in parallel with scrambled shRNA control.

2023-07-12 | E-MTAB-11570 | biostudies-arrayexpress

mRNA-seq of neuronal compartments in shRNA-mediated knockdown of Ythdf1, -2 and -3 in mouse primary cortical neurons (mPCN)

Project description:To study the effect of m6A modifications on subcellular mRNA localization we depleted m6A readers Ythdf1, -2 and -3 with shRNAs from mouse primary cortical neurons (mPCN) and sequenced neuritic and somatic compartments in parallel with scrambled shRNA control.

2023-07-12 | E-MTAB-11569 | 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

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