Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of TDP-43 and FUS mRNA targets and pathways in the cytoplasmic compartment of motorneuronal cells NSC34

ABSTRACT: We performed RNA immunoprecipitation (IP) and microarray (RIP-chip) analyses to identify and compare the biological mRNA targets of two RNA-binding protein (RBP), TDP-43 and FUS, associated to cytoplasmic ribonucleoprotein (RNP) complexes of motoneuronal NSC34 cells with the final aim to unravel their role in mRNA transport, stability, and translation in neuronal cells. To identify the transcripts contained and bound in the isolated RNP complexes, a chip analysis was performed using the recovered mRNAs from triplicate experimantal RIP samples (TDP-43-IP samples, the FUS-IP samples and the control IgG-IP sample).

ORGANISM(S): Mus musculus

SUBMITTER: Claudia Colombrita

PROVIDER: E-GEOD-33159 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Identification of TDP-43 and FUS mRNA targets and pathways in the cytoplasmic compartment of motoneuronal NSC-34 cells

Project description:We performed RNA immunoprecipitation (IP) and microarray (RIP-chip) analyses to identify and compare the biological mRNA targets of two RNA-binding proteins (RBP), TDP-43 and FUS, associated to cytoplasmic ribonucleoprotein (RNP) complexes of motoneuronal NSC-34 cells with the final aim to unravel their role in mRNA transport, stability, and translation in neuronal cells.

2011-10-22 | GSE33159 | GEO

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (CLIP-Seq)

Project description:FUS/TLS and TDP-43 are RNA/DNA-binding proteins integrally involved in amyotrophic lateral sclerosis (ALS) and frontal temporal dementia. FUS/TLS is shown to bind RNAs from >5,500 genes in mouse and human brain, primarily through a GUGGU binding motif. A characteristic sawtooth-like binding pattern is identified, supporting co-transcriptional deposition of FUS/TLS. Depletion of FUS/TLS from the adult nervous system is shown to alter levels or splicing of >970 mRNAs, most of which are distinct from the RNAs whose maturation is dependent on TDP-43. Nonetheless, only 55 RNAs are reduced upon depletion of either TDP-43 or FUS/TLS from mouse brain and human neurons differentiated from pluripotent stem cells, including mRNAs transcribed from genes with exceptionally long introns and that encode proteins essential for neuronal integrity. A subset of these is significantly lowered in FUS/TLSR521G and TDP-43G298S mutant fibroblasts and in TDP-43 aggregate-containing motor neurons in sporadic ALS, evidence pointing to a common loss-of-function pathway as one component underlying motor neuron death from misregulation of TDP-43 or FUS/TLS. CLIP of Fus/Tls in 8 week mouse brain and adult human brain

2012-09-30 | E-GEOD-40651 | biostudies-arrayexpress

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (RNA-Seq)

2012-09-30 | E-GEOD-40652 | biostudies-arrayexpress

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs

Project description:This SuperSeries is composed of the following subset Series: GSE40649: Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (microarray) GSE40651: Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (CLIP-Seq) GSE40652: Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (RNA-Seq) Refer to individual Series

2012-09-30 | E-GEOD-40653 | biostudies-arrayexpress

Identification of Neuronal RNA Targets of TDP-43-Containing Ribonucleoprotein Complexes

Project description: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 TDP-43 library. Moreover, our analysis shows there is often an adenine in the middle of the motif, (TG)nTA(TG)m. TDP-43 RNA targets are particularly enriched for Gene Ontology terms related to RNA metabolism, neuronal development, and synaptic function. Examination of TDP-43 RNA targets in rat cortical neurons by RIP-seq. Chantelle F. Sephton isolated the TDP-43:RNA complexes and generated the cDNA library for deep sequencing. Email: chantelle.sephton@utsouthwestern.edu Phone: 214-648-4119 Fax: 214-648-1801 ULR: http://www8.utsouthwestern.edu/utsw/cda/dept120915/files/151135.html Organization name: University of Texas Southwestern Medical Center at Dallas Department: Neuroscience Lab: Gang Yu lab Street: 6000 Harry Hines Blvd. City: Dallas State: Texas ZIP: 75390 Country: USA

2010-11-04 | E-GEOD-25032 | biostudies-arrayexpress

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (microarray)

2012-09-30 | E-GEOD-40649 | biostudies-arrayexpress

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (RNA-Seq)

2012-09-30 | GSE40652 | GEO

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (CLIP-Seq)

2012-09-30 | GSE40651 | GEO

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs (microarray)

2012-09-30 | GSE40649 | GEO

Changes to the TDP43 and FUS Interactomes Induced by DNA Damage

Project description:The RNA-binding proteins TDP-43 and FUS are tied as the third leading known genetic cause for amyotrophic lateral sclerosis (ALS) and TDP-43 proteopathies are found in nearly all ALS patients. Both the natural function and contribution to pathology for TDP-43 remains unclear. The intersection of functions between TDP-43 and FUS can focus attention for those natural functions mostly likely to be relevant to disease. Here we compare the role played by TDP-43 and FUS maintaining chromatin stability for dividing HEK293T cells. We also determine and compare the interactomes of TDP-43 and FUS, quantitating changes in those before and after DNA damage. Finally, selected interactions with known importance to DNA damage repair were validated by co-immunoprecipitation assays. This study uncovered TDP-43 and FUS binding to several factors important to DNA repair mechanisms that can be either replication dependent, independent, or both. These results support recently published findings about the role TDP-43 plays in DNA repair and provide new ways that TDP-43 can bind the machinery that guard DNA integrity in cells.

2019-10-22 | MSV000084486 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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