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MetabolomicsData processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

Systems biology is the study of complex living organisms, and as such, analysis on a systems-wide scale involves the collection of information-dense data sets that are representative of an entire phenotype. To uncover dynamic biological mechanisms, bioinformatics tools have become essential to fa...

2017-11-23 | MTBLS572 | MetaboLights
MetabolomicsCell Atlas and Novel Signal Processing Strategy in Primate Insular Cortex

The anterior insular cortex (AIC) is a critical hub integrating exteroceptive and interoceptive information into high-order cognition, yet its neural basis remains incompletely understood. Here, by combining whole-cell-based single-cell transcriptomics with Patch-seq recordings, we resolved and c...

2026-02-28 | MTBLS13927 | MetaboLights
MetabolomicsHost: Microbiome co-metabolic processing of dietary polyphenols – An acute, single blinded, cross-over study with different doses of apple polyphenols in healthy subjects
Apples are one of the most commonly consumed fruits and their high polyphenol content is considered one of the most important determinants of their health-promoting activities. Here we studied the nutrikinetics of apple polyphenols by UHPLC-HRMS metabolite fingerprinting, comparing the bioavailabili...
2018-10-11 | MTBLS473 | MetaboLights
TranscriptomicsThe effects of the 5' pocket motif of Dicer on miRNA biogenesis
A hallmark of RNA silencing is a class of ~22 nt RNAs which are processed from dsRNA precursor by Dicer. Accurate processing by Dicer is critical for the functionality of microRNAs (miRNAs). According to the current model, Dicer measures the length by anchoring the 3' overhang of the dsRNA terminus....
ORGANISM(S): Mus musculus 
2011-07-12 | E-GEOD-27903 | biostudies-arrayexpress
ProteomicsAngel2 phosphatase activity is required for non-canonical mitochondrial RNA processing
Canonical RNA processing in mammalian mitochondria is defined by tRNAs acting as recognition sites for nucleases to release flanking transcripts. The relevant factors, their structures, and mechanism are well described, but not all mitochondrial transcripts are punctuated by tRNAs, and their mode of...
ORGANISM(S): Mus musculus (Mouse) Drosophila melanogaster (Fruit fly) 
2022-09-01 | PXD033394 | Pride
Angel2 Mitochondria Processing Mouse Rna Drosophila 
ProteomicsTEFM regulates both transcription elongation and RNA processing in mitochondria
Regulation of replication and expression of mitochondrial DNA (mtDNA) is essential for cellular energy conversion via oxidative phosphorylation. The mitochondrial transcription elongation factor (TEFM) has been proposed to regulate the switch between transcription termination for replication primer ...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2019-04-25 | PXD013398 | Pride
Mtdna replication Rna processing Transcription elongation 
ProteomicsCoordination of nuclear RNA processing by speckle-localized kinase TAOK2
Nuclear speckles are membraneless organelles that act as active splicing hubs especially at sites of high transcription; emerging views of this dynamic subnuclear structure place it as a hub of RNA processing from transcription to export. To manage a complex microcosm of RNA metabolism, nuclear spec...
ORGANISM(S): Homo sapiens (Human) 
2026-09-07 | PXD069089 | Pride
Phosphoproteome Speckle-localized kinase taok2 Nuclear rna processing 
TranscriptomicsSystematic Mapping of ADAR1 Binding Reveals its Regulatory Roles in Multiple RNA Processing Pathways [small RNA-seq]
ADARs are the primary factors underlying A-to-I editing in metazoans. We conducted the first global study of ADAR1-RNA interaction in human cells using CLIP-Seq. In contrast to the expected predominant binding of ADAR1 to Alu repeats, thousands of CLIP sites were located in non-Alu regions. This une...
ORGANISM(S): Homo sapiens 
2015-03-11 | E-GEOD-55362 | biostudies-arrayexpress
TranscriptomicsMechanism for full-length RNA processing over intragenic heterochromatin
Mechanism for full-length RNA processing over intragenic heterochromatin
ORGANISM(S): Arabidopsis thaliana 
2014-04-22 | E-MTAB-4475 | biostudies-arrayexpress
GenomicsCBX3 Regulates Efficient RNA Processing Genome Wide
HP1 alpha, beta, and gamma play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, some HP1 family members may also participate in transcriptional regulation of genes. Recently, HP1 gamma binding to the bodies of a subset of genes has been observed in ...
ORGANISM(S): Homo sapiens 
2012-05-24 | E-GEOD-28115 | biostudies-arrayexpress
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