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TranscriptomicsAntiviral RNA interference in mammalian cells
Plants and invertebrates protect themselves from viruses through RNA interference (RNAi), yet it remains unknown whether this defense mechanism exists in mammals. Antiviral RNAi involves the processing of viral long double-stranded (ds) RNA molecules into small interfering RNAs (siRNAs) by the ribon...
ORGANISM(S): Mus musculus 
2013-10-10 | E-GEOD-43153 | biostudies-arrayexpress
ProteomicsA causal model of ion interference enables assessment and correction of ratio compression in multiplex proteomics
We thoroughly characterize isobaric labeling (TMT)-associated reporter ion interference at the MS2 level using a defined two-proteome experimental system with known ground truth. We discover remarkably poor agreement between the apparent precursor purity in the isolation window and the actual level ...
ORGANISM(S): Homo sapiens (Human) Saccharomyces cerevisiae Saccharomyces cerevisiae (Baker's yeast) 
2023-12-19 | PXD040449 | Pride
Ion interference Tmt Ratio compression Isobaric label 
TranscriptomicsCooler temperatures destabilize RNA interference and increase susceptibility of disease vector mosquitoes to viral infection
The impact of global climate change on the transmission dynamics of infectious diseases is the subject of extensive debate. The transmission of mosquito-borne viral diseases is particularly complex, with climatic variables directly affecting many parameters associated with the prevalence of disease ...
ORGANISM(S): Aedes albopictus 
2013-08-13 | E-GEOD-46204 | biostudies-arrayexpress
ProteomicsA Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments
Isobaric labeling is a powerful strategy for quantitative mass spectrometry-based proteomic investigations. A complication of such analyses has been the co-isolation of multiple analytes of similar mass-to-charge resulting in the distortion of relative protein abundance measurements across samples. ...
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) 
2019-08-23 | MSV000084230 | MassIVE
ProteomicsTKO6: A Peptide Standard to Assess Interference for Unit-Resolved Isobaric Labeling Platforms
Protein abundance profiling using isobaric labeling is a well-established quantitative mass spectrometry technique. However, ratio distortion resulting from co-isolated and co-fragmented ions - commonly referred to as interference - remains a caveat of this technique. Tribrid mass spectrometers, suc...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2019-03-07 | PXD011653 | Pride
Tko  interference  tmt  itraq  sps-ms3 
ProteomicsAssessing Interference in Isobaric Tag-based Sample Multiplexing using an 18-plex Interference Standard
Reporter ion interference remains a limitation of isobaric tag-based sample multiplexing. Advances in instrumentation and data acquisition modes, such as the recently developed real-time database search (RTS), can reduce interference. However, interference persists as does the need to benchmark upst...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-01-06 | PXD029458 | Pride
Faims Eclipse Ifi Sps-ms3 Rts Tmtpro18 
TranscriptomicsHigh throughput decoding of anti trypanosomal drug efficacy and resistance
We used all five current human African trypanosomiasis drugs for genome-scale RNA interference (RNAi) target sequencing (RIT-seq) screens in Trypanosoma brucei, revealing the transporters, organelles, enzymes and metabolic pathways that function to facilitate anti-trypanosomal drug action. RIT-seq p...
ORGANISM(S): Trypanosoma brucei 
2011-11-29 | E-ERAD-30 | biostudies-arrayexpress
TranscriptomicsGlobal effects of the CSR-1 RNA interference pathway on transcriptional landscape
Argonaute proteins and their small RNA co-factors short interfering RNAs (siRNAs) are known to inhibit gene expression at the transcriptional and post-transcriptional levels. In Caenorhabditis elegans, the Argonaute CSR-1 binds thousands of endogenous siRNAs (endo-siRNAs) antisense to germline trans...
ORGANISM(S): Caenorhabditis elegans 
2014-02-28 | E-GEOD-49946 | biostudies-arrayexpress
ProteomicsA Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments
Isobaric labeling is a powerful strategy for quantitative mass spectrometry-based proteomic investigations. A complication of such analyses has been the co-isolation of multiple analytes of similar mass-to-charge resulting in the distortion of relative protein abundance measurements across samples. ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2017-10-26 | PXD008009 | Pride
Ion interference Ms standard Tmt Muiltinotch Lumos Orbitrap fusion 
GenomicsHuman melanoma Cells (A2058): Control interference fragment transfected vs. PARP1 interference fragment transfected
Human melanoma Cells (A2058): Control interference fragment transfected vs. PARP1 interference fragment transfected
PRJNA756736 | ENA
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