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TranscriptomicsRibo-seq of HEK293T overexpressing WT and G240R GARS
Charcot-Marie-Tooth (CMT) disease can be caused by mutations in Aminoacyl-tRNA-Synthetases, including G240R mutation in Glycyl-tRNA-Synthetase (GARS). Ribo-seq generates snapshots of translating ribosomes on mRNA and therefore allows analysis of ribosome pausing mRNA. Here we performed Ribo-seq on l...
ORGANISM(S): Homo sapiens 
2021-09-14 | E-MTAB-10342 | biostudies-arrayexpress
TranscriptomicsSlamseq of whole mouse primary cortical neurons (mPCN) with perturbed mRNA degradation machinery
We perturbed mRNA degradation machinery in mouse primary cortical neurons (mPCN) and investigated the change in mRNA half-lives. We performed SLAMseq Metabolic RNA Labeling on Mutant mPCN line harbouring a ponasteroneA-inducible heterozygous dominant-negative Caf1 (dnCaf1) and on GFP-transfected mPC...
ORGANISM(S): Mus musculus 
2022-11-14 | E-MTAB-11575 | biostudies-arrayexpress
ProteomicsQuaNCAT analysis comparing proteins synthesized in neurites and soma in ASCL1-iNeurons
Local translation in ASCL1-iNeurons was probed using QuaNCAT
ORGANISM(S): Mus musculus (Mouse) 
2018-10-17 | PXD005059 | Pride
Azidohomoalanine Mouse Silac 
TranscriptomicsmRNA-seq of neuronal compartments with perturbed mRNA degradation machinery in mouse primary cortical neurons (mPCN)
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 compartment...
ORGANISM(S): Mus musculus 
2022-11-14 | E-MTAB-11572 | biostudies-arrayexpress
Transcriptomics3' mRNA-seq of neurites and soma isolated from mESC-derived neurons
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 po...
ORGANISM(S): Mus musculus 
2019-01-12 | E-MTAB-7251 | biostudies-arrayexpress
Transcriptomicsm6A-RIP-seq of Ascl1-induced neurons.
We performed m6A-RIPs in Ascl1-induced neurons (iNeurons) to investigate the neuronal m6A epitranscriptome. Immunoprecipitation was done twice using two different antibodies, acquired from Abcam and Synaptic Systems (SySy), allowing for a more robust detection of m6A modification marks. Additionally...
ORGANISM(S): Mus musculus 
2023-07-12 | E-MTAB-9542 | biostudies-arrayexpress
TranscriptomicsmRNA-Seq of neuronal compartments with perturbed mRNA degradation machinery (overexpression of dnCaf1) in mouse primary cortical neurons
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 com...
ORGANISM(S): Mus musculus 
2023-07-12 | E-MTAB-12887 | biostudies-arrayexpress
TranscriptomicsmRNA-Seq of neuronal compartments in shRNA-mediated knockdown of Larp1 in mouse primary cortical neurons
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 shRN...
ORGANISM(S): Mus musculus 
2023-07-12 | E-MTAB-12886 | biostudies-arrayexpress
TranscriptomicsSlamSeq of subcellular compartments in mouse primary cortical neurons
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.
ORGANISM(S): Mus musculus 
2023-07-12 | E-MTAB-12888 | biostudies-arrayexpress
TranscriptomicsSlamseq of subcellular compartments in neurons
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 investig...
ORGANISM(S): Mus musculus 
2023-07-12 | E-MTAB-9400 | biostudies-arrayexpress
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