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MetabolomicsAntiviral metabolite 3'-Deoxy-3',4'-didehydro-cytidine is detectable in serum and identifies acute viral infections including COVID-19

BACKGROUND: There is a critical need for rapid viral infection diagnostics to enable prompt case identification in pandemic settings and support targeted antimicrobial prescribing.

METHODS: Using untargeted high-resolution liquid chromatography coupled with...

2022-02-10 | MTBLS718 | MetaboLights
MetabolomicsStreamlining LC-MS/MS Data Analysis in R with Open-Source *xcms* and *RforMassSpectrometry*: An End-to-End Workflow

Despite untargeted LC-MS/MS data being a powerful approach for large-scale metabolomics analysis, a significant challenge in the field lies in the reproducible and efficient analysis of such data, in particular. The power of R-based analysis workflows lies in their high customizability and adapta...

2024-08-26 | MTBLS8735 | MetaboLights
TranscriptomicsGenome?wide analysis of pre?mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length: A-seq
Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we mapped transcriptome?wide both binding s...
ORGANISM(S): Homo sapiens 
2012-05-15 | E-GEOD-37037 | biostudies-arrayexpress
TranscriptomicsGenome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length: CLIP
Through alternative polyadenylation, human mRNAs acquire longer or shorter 3' untranslated regions, the latter typically associated with higher transcript stability and increased protein production. To understand the dynamics of polyadenylation site usage, we mapped transcriptome‐wide both binding s...
ORGANISM(S): Homo sapiens 
2012-05-15 | E-GEOD-37398 | biostudies-arrayexpress
TranscriptomicsAnalysis of Caenorhabditis elegans intestinal gene expression and alternative polyadenylation using fluorescence-activated nuclei sorting (FANS) and 3' end deep sequencing (3'end-seq)
Caenorhabditis elegans is a major eukaryotic experimental system employed to unravel a broad range of cellular and biological processes. Despite the many advantages of C. elegans, biochemical approaches to study tissue-specific gene expression in postembryonic stages are challenging. Here we report ...
ORGANISM(S): Caenorhabditis elegans 
2011-12-01 | E-GEOD-32165 | biostudies-arrayexpress
Transcriptomics3’READS+, a sensitive and accurate method for 3’ end sequencing of polyadenylated RNA
Sequencing of the 3’ end of poly(A)+ RNA identifies cleavage and polyadenylation sites (pAs) and measures transcript expression. We previously developed a method, 3’ region extraction and deep sequencing (3’READS), to address mispriming issues that often plague 3’ end sequencing. Here we rep...
ORGANISM(S): Homo sapiens 
2016-08-14 | E-GEOD-84170 | biostudies-arrayexpress
TranscriptomicsPARN mediates 3'-end trimming of Argonaute-cleaved precursor microRNAs
microRNAs (miRNAs) are typically generated as ~22-nucleotide double-stranded RNAs via processing of precursor hairpins by the RNase III enzyme Dicer, after which they are loaded into Argonaute (Ago) proteins to form RNA-induced silencing complex (RISC). However, the biogenesis of miR-451, an erythro...
ORGANISM(S): Danio rerio 
2013-11-13 | E-GEOD-51036 | biostudies-arrayexpress
TranscriptomicsA Comparison of HEEBO Microarray and 3'-end Sequencing for Expression Quantification (3SEQ) (Archival Tumor Samples)
Gene expression microarrays are the most widely used technique for genome-wide expression profiling. However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET). Consequently, microarrays cannot be effectively utilized to perform gene expression profiling on the vast ...
ORGANISM(S): Homo sapiens 
2010-03-25 | E-GEOD-18209 | biostudies-arrayexpress
TranscriptomicsThe systematic shortening of 3’ UTRs has limited influence on the relative change in protein abundance in proliferating cells
Alternative polyadenylation is an important cellular mechanism that enables generation of mRNA isoforms that differ in their 3' untranslated regions (3' UTRs) and consequently in their susceptibility to miRNA and RNA binding protein mediated regulation. A dramatic change in polyadenylation site usa...
ORGANISM(S): Homo sapiens 
2014-09-25 | E-GEOD-54950 | biostudies-arrayexpress
TranscriptomicsThe Nrd1-like protein Seb1 coordinates co-transcriptional 3’ end processing and polyadenylation site selection
Termination of RNAPII transcription is associated with RNA 3’ end formation. For coding genes, termination is initiated by the cleavage/polyadenylation machinery. In contrast, a majority of noncoding transcription events in S. cerevisiae do not rely on RNA cleavage for termination, but instead ter...
ORGANISM(S): Schizosaccharomyces pombe 
2016-07-22 | E-GEOD-82326 | biostudies-arrayexpress
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