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TranscriptomicsIdentification of Neuronal RNA Targets of TDP-43-Containing Ribonucleoprotein Complexes
We identify the RNA targets of TAR DNA-binding protein 43 (TDP-43) from cortical neurons by RNA immunoprecipitation followed by deep sequencing (RIP-seq). We identify 4352 highly enriched RNA targets of TDP-43. We determined that the canonical TDP-43 binding site (TG)n was 55.1-fold enriched in our ...
ORGANISM(S): Rattus norvegicus 
2010-11-04 | E-GEOD-25032 | biostudies-arrayexpress
TranscriptomicsTDP-43 Neurotoxicity in late D. melanogaster pupae
The aim of this study is to understand the mechanisms of TDP-43 neurotoxicity. Here, we perform a RNA-Seq analysis in TDP-43 gain-of-fucntion (GOF) , TDP-43 loss-of-function and wild-type late pupae heads (73-90 hours APF) and perform TDP-43 GOF vs wild type and TDP-43 LOF vs wild-type differential...
ORGANISM(S): Drosophila melanogaster 
2013-01-22 | E-GEOD-42844 | biostudies-arrayexpress
TranscriptomicsDisrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (RNA-seq)
Cross-linking and immunoprecipitation coupled with high-throughput sequencing was used to identify binding sites within 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein which when mutated causes Amyotrophic Lateral Sclerosis (ALS). Use of massively parallel sequencing and spli...
ORGANISM(S): Mus musculus 
2011-03-03 | E-GEOD-27218 | biostudies-arrayexpress
TranscriptomicsDisrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (CLIP)
Cross-linking and immunoprecipitation coupled with high-throughput sequencing was used to identify binding sites within 6,304 genes as the brain RNA targets for TDP-43, an RNA binding protein which when mutated causes Amyotrophic Lateral Sclerosis (ALS). Use of massively parallel sequencing and spli...
ORGANISM(S): Mus musculus 
2011-03-03 | E-GEOD-27201 | biostudies-arrayexpress
ProteomicsMass spectrometric analysis of accumulated TDP-43 in amyotrophic lateral sclerosis brains
TDP-43 is the major disease-associated protein involved in the pathogenesis and progression of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitin-positive inclusions linked to TDP-43 pathology (FTLD-TDP). Abnormal phosphorylation, truncation and cytoplasmic mis...
ORGANISM(S): Homo Sapiens (human) 
2020-03-01 | PXD012920 | JPOST Repository
ProteomicsInteractome of Flag-TDP-43, Flag-SUMO2-TDP-43 and Flag-4xSUMO2-TDP-43
Identifications of proteins interacting with TDP-43 or linear fusions of mono- or tetra-SUMO2 with TDP-43.
ORGANISM(S): Homo sapiens (Human) 
2025-09-08 | PXD050322 | Pride
Tdp-43 sumo 
TranscriptomicsLoss of nuclear TDP-43 in ALS causes altered expression of splicing machinery and widespread dysregulation of RNA splicing in motor neurons [NSC34]
Aims: Loss of nuclear TDP-43 characterises sporadic and most familial forms of amyotrophic lateral sclerosis (ALS). TDP-43 (encoded by TARDBP) has multiple roles in RNA processing. We aimed to determine whether 1) RNA splicing dysregulation is present in lower motor neurons in ALS and in a motor neu...
ORGANISM(S): Mus musculus 
2014-06-01 | E-GEOD-56503 | biostudies-arrayexpress
TranscriptomicsAltered Distributions of SMN-containing GEMs and Mitochondria in Motor Neurons of TDP-43 transgenic Mice
TDP-43, a DNA/RNA binding protein involved in RNA transcription and splicing has been associated with the pathophysiology of neurodegenerative diseases, including ALS. However, the function of TDP-43 in motor neurons remains undefined. Here, we employ both gain- and loss-of-function approaches to de...
ORGANISM(S): Mus musculus 
2010-07-30 | E-GEOD-22351 | biostudies-arrayexpress
ProteomicsIdentification of TDP-43 - TAU interactions by XL-MS
Identification of TDP-43 - TAU interactions by XL-MS (DSS). The interactions were identified in for equimolar amount of TDP-43 - TAU and, as control, TDP-43 and MBP. After 30 minutes from the induction of phase separation, samples were either analyzed (bulk condition) or subjected to centrifugation ...
ORGANISM(S): Homo sapiens (Human) 
2025-08-25 | PXD063858 | Pride
Xl-ms Tau Tdp-43 
TranscriptomicsiCLIP of TDP-43
A stable HEK293 FlpIn T-Rex cells expressing TDP-43 with an N-terminal eGFP-tag was generated that allowed inducible physiological expression of the protein (Ling et al. 2010). Duplicate iCLIP experiments were performed using an antibody targeting eGFP (Abcam ab290). Crosslinked RNA-protein complexe...
ORGANISM(S): Homo sapiens 
2017-05-01 | E-MTAB-4733 | biostudies-arrayexpress
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