Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

86 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

TDP 43 Knockdown

ABSTRACT: RNA_BINDING, identify global RNA binding sites for TDP43 protein

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-527 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

TDP-43 iCLIP in mESC and hESC

Project description:Genome-wide analysis of rna-TDP43 interactions at single nucleotide resolution in mouse and human embryonic stem cells

2019-03-31 | E-MTAB-5100 | biostudies-arrayexpress

CLIP-Seq of human brain and neuroblastoma sample to characterisethe RNA targets and position-dependent splicing regulation by TDP-43

Project description:iCLIP (UV-crosslinking and immunoprecipitation followed by sequencing ) analysis of TDP-43 RNA binding sites

2011-07-21 | E-MTAB-530 | biostudies-arrayexpress

3'end RNA sequencing of TDP-43 depleted and mutant TDP-43-rescued Hek-293 FlpIn lines

Project description:This project studies TDP43, which is an RNA binding protein implicated in Motor Neuron Disease. As an RNA-binding protein, TDP43 is known to influences poly-adenylation site choice. For this project, we have inserted a single copy of the GFP-tagged TDP43 gene into the FLPIn Locus of HEk293 cells. We use these Hek293 FLipIn lines to instigate the effect of different deletion and mutation constructs of TDP-43 in their ability to rescue the depletion (siRNA) of the endogenous TDP-43 protein. We are comparing siRNA mediated KD in triplicates for each of the 7 cell lines to the Dox-induced rescues in triplicates. We are using a customised Lexogen Quantseq 3’ end sequencing method that allows us to multiplex cDNAs straight after the reverse transcription. The samples were pooled into barcoded sub-groups, each group will have the Lexogen barcode (i7 indices) in addition.

2021-07-21 | E-MTAB-9410 | biostudies-arrayexpress

Stage-specific control of oligodendrocyte survival and morphogenesis by TDP-43

Project description:We performed bulk RNA-seq on FACS-isolated oligodendrocytes from P30 Mobp-TDP43 and Mog-TDP43 mouse lines to determine the effect of TDP-43 loss at different stages of oligodendrocyte development.

2022-01-03 | GSE188903 | GEO

TDP-43 iCLIP of SHSY5Y cells

Project description:TDP-43 is an important RNA binding protein. To better understand its binding targets in human neurons, we performed TDP-43 iCLIP on SHSY5Y cells.

2022-02-02 | E-MTAB-11243 | biostudies-arrayexpress

TDP-43 aggregation mirrors TDP-43 knockdown, affecting the expression levels of a common set of proteins.

Project description: Not available

| S-EPMC5036055 | biostudies-literature

TDP-43 expression impairs sleep in Drosophila and is rescued by Ataxin-2 knockdown

Project description:Exploring the intricate link between sleep and brain degeneration holds great promise for the development of effective therapeutics. Here we provide novel insights into the role of TDP-43 and Atx2 in regulating sleep and neurodegeneration using Drosophila. We demonstrate that expression of TDP-43 severely disrupts sleep, resulting in reduced sleep duration of the affected animals. Sleep disruption by TDP-43 is completely rescued by Atx2 knockdown. To unravel the underlying mechanism of TDP43 sleep disruption and Atx2-mediated rescue, we conducted brain RNA sequencing analysis from flies expressing TDP-43 with or without Atx2 knockdown. Among RNAseq changes, we observed upregulation of genes associated with small molecule metabolism with TDP-43 expression, followed by their subsequent downregulation upon Atx2 knockdown. Utilizing these Atx2-regulated genes, we conducted an RNAi screen to identify additional sleep modifiers that interact with TDP-43.

2023-11-17 | GSE234468 | GEO

U6 snRNA expression prevents toxicity in TDP-43-knockdown cells.

Project description: Not available

| S-EPMC5681290 | biostudies-literature

iCLIP of TDP-43

Project description: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 complexes were isolated by immuno-precipitation and cDNAs were generated to allow preparation of Illumina compatible DNA libraries as described in Huppertz et al. (2014).

2017-05-01 | E-MTAB-4733 | biostudies-arrayexpress

Knockdown of transactive response DNA-binding protein (TDP-43) downregulates histone deacetylase 6.

Project description: Not available

| S-EPMC2808372 | biostudies-literature