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TranscriptomicsRNAi knock down of known nonsense-mediated mRNA decay (NMD) factors in Drosophila cells
All eukaryotes studied to date have the capacity to detect and degrade mRNAs harboring premature translation termination codons (PTCs) in a process called nonsense-mediated mRNA decay (NMD) (reviewed in Wagner E & Lykke-Andersen J, 2002). This surveillance system allows the cell to prevent the expre...
ORGANISM(S): Drosophila melanogaster 
2005-11-01 | E-MEXP-202 | biostudies-arrayexpress
TranscriptomicsQuality control of transcription start site selection by Nonsense-Mediated-mRNA Decay
Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA quality-control pathway targeting transcripts such as messenger RNAs harboring premature stop-codons or short upstream open reading frame (uORFs). Our transcription start sites (TSSs) analysis of Saccharomyces cerevisiae cells deficie...
ORGANISM(S): Saccharomyces cerevisiae BY4741 
2015-04-24 | E-GEOD-64139 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of yeast to analyse mRNAs regulated by the nonsense-mediated and 5 to 3 mRNA Decay Pathways
Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA Decay Pathways in Yeast
ORGANISM(S): Saccharomyces cerevisiae 
2011-11-08 | E-MEXP-26 | biostudies-arrayexpress
TranscriptomicsTranscriptome profiling of Arabidopsis smg7 mutant in immune signaling blocked background
Goal of the study is the identification of transcriptome deregulation of smg7 pad4 mutants, which are deficient in nonsense-mediated mRNA decay and are blocked in immune signaling, which should avoid secondary responses from immune signaling Total RNA (ribosomal RNA depleted) illumina sequencing of ...
ORGANISM(S): Arabidopsis thaliana 
2014-09-10 | E-GEOD-55884 | biostudies-arrayexpress
ProteomicsNonsense-mediated decay in Plasmodium falciparum
We have HA-tagged two nonsense-mediated decay proteins, UPF1 and UPF2, in the malaria parasite Plasmodium falciparum. We then performed co-immunoprecipitation experiments to determine the protein-protein interactions of these nonsense-mediated decay components.
ORGANISM(S): Plasmodium falciparum (isolate 3D7) 
2021-04-16 | PXD023910 | Pride
Malaria Co-immunoprecipitation Mrna Nonsense-mediated decay Plasmodium falciparum 
TranscriptomicsTranscription profiling of mouse T-cell thymocytes and bone marrow-derived macrophages dervied from Upf2fl/fl;LysMCre and Upf2fl/fl;LckCre mice to test the importance of nonsense-mediated mRNA decay on global transcription
Knockdown experiments in transformed human cells, suggested that nonsense-mediated mRNA decay (NMD) components had extensive effects on the regulation of a significant fraction of the transcriptome In order to test the importance of NMD on global transcription we subjected BMDMs and T-cell thymocy...
ORGANISM(S): Mus musculus 
2008-11-06 | E-MEXP-1371 | biostudies-arrayexpress
ProteomicsNonsense-mediated mRNA decay relies on "two-factor authentication" by SMG5-SMG7
Eukaryotic gene expression is constantly regulated and controlled by the translation-coupled nonsense-mediated mRNA decay (NMD) pathway. Aberrant translation termination leads to NMD activation and robust clearance of NMD targets via two seemingly independent and redundant mRNA degradation branches....
ORGANISM(S): Homo sapiens (Human) 
2021-05-08 | PXD024747 | Pride
Smg6 Mrna degradation Gene expression Smg5-smg7 Nonsense-mediated mrna decay Upf1 
TranscriptomicsmRNA-Seq from control cells and two clones of Flp-In-T-REx-293 cells modified via CRISPR-Cas9 to knockout SMG7 in combination to knockdowns of control, SMG5, and SMG6
Mature mRNAs undergo quality control during translation that may lead to RNA degradation by triggering the nonsense mediated decay (NMD) pathway. Aberrant translation due to features such as the presence of a premature stop codon downstream on an exon-exon junction or an intron in the 3'UTR activate...
ORGANISM(S): Homo sapiens 
2021-05-07 | E-MTAB-9330 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of WT Flp-In T-REx 293 and UPF3B knockout cell lines with additional siRNA-mediated control or UPF3A knockdowns
UPF3A and UPF3B are paralogous genes in human cells that are involved in the nonsense-mediated decay (NMD) pathway. NMD is a cellular quality control mechanism that monitors mRNAs during translation. Aberrant translation due to features such as the presence of a premature stop codon downstream on an...
ORGANISM(S): Homo sapiens 
2022-04-25 | E-MTAB-10711 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of WT Flp-In T-REx 293, UPF3B knockout and UPF3A-UPF3B double knockout cell lines with additional siRNA-mediated control or UPF3B knockdowns
UPF3A and UPF3B are paralogous genes in human cells that are involved in the nonsense-mediated decay (NMD) pathway. NMD is a cellular quality control mechanism that monitors mRNAs during translation. Aberrant translation due to features such as the presence of a premature stop codon downstream on an...
ORGANISM(S): Homo sapiens 
2022-04-25 | E-MTAB-10716 | biostudies-arrayexpress
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