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MetabolomicsN6-methyladenosine modification is not a general trait of positive-sense RNA viral genomes

Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-seq, an antibody-dependent technique with...

2024-01-25 | MTBLS6978 | MetaboLights
TranscriptomicsTranscriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation
We mapped CstF64-RNA interactions at the transcriptome level and studied CstF64-mediated regulation of global mRNA alternative polyadenylation by using iCLIP-seq and direct RNA sequencing analyses. CstF64 iCLIP-seq in HeLa cells; direct RNA sequencing (DRS) of control HeLa cells, CstF64-RNAi cells ...
ORGANISM(S): Homo sapiens 
2012-10-01 | E-GEOD-40859 | biostudies-arrayexpress
TranscriptomicsComputational and Analytical Framework for Small RNA Profiling by High-Throughput Sequencing
This SuperSeries is composed of the following subset Series: GSE14694: Computational and Analytical Framework for Small RNA Profiling by High-Throughput Sequencing (reproducibility) GSE14695: Computational and Analytical Framework for Small RNA Profiling by High-Throughput Sequencing (standards) Ref...
ORGANISM(S): Arabidopsis thaliana 
2009-06-02 | E-GEOD-14696 | biostudies-arrayexpress
ProteomicsEnzymatic Site-specific Biotinylation Enables Analysis of RNA-protein Interactions and Enrichment of Cellular RNA
The importance of RNA in regulating cellular processes has generated tremendous interest in methods to reliably characterize RNAs and their interactions within cells. Existing methodologies rely on noncovalent interactions to facilitate RNA affinity purification, hindering the purification of less a...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2020-03-13 | MSV000085100 | MassIVE
GenomicsHigh resolution transcriptome-wide RNA cytosine methylome of Mouse Embryonic Fibroblasts
We report high resolution transcriptome-wide RNA cytosine methylome of Mouse Embryonic Fibroblasts (MEFs) revealed by an optimized new RNA bisulfite sequencing approach. Comparison of RNA methylation profile from wild-type and Dnmt2 -/- MEFs shows that only C38 in three tRNAs (tRNA-Asp, Gly and Val...
ORGANISM(S): Mus musculus 
2013-04-21 | E-GEOD-44359 | biostudies-arrayexpress
UnknownComprehensive identification of diverse ribosomal RNA modifications by targeted nanopore direct RNA sequencing and JACUSA2.
Not available
S-EPMC10464549 | biostudies-literature
TranscriptomicsPhosphate-independent small RNA sequencing of WT and mir-249 mutant C. elegans
MicroRNAs (miRNA), discovered in C. elegans, are short non-coding RNAs that bind and regulate the expression of target mRNAs in animals and plants. C. elegans miRNAs bind to partially complementary sequences in the 3' UTR of the target mRNA, which results in translational repression through mRNA des...
ORGANISM(S): Caenorhabditis elegans 
2013-08-08 | E-GEOD-41900 | biostudies-arrayexpress
TranscriptomicsIdentification of direct targets and modified bases of RNA cytosine methyltransferases
We report development of a mechanism-based technique, Aza-IP, that utilizes the stable covalent linkage formed in vivo between an RNA methyltransferase (m5C-RMT) and 5-azacytidine (5-aza-C) incorporated within the target RNA to enable specific target enrichment, coupled with high-throughput sequenci...
ORGANISM(S): Homo sapiens 
2013-04-21 | E-GEOD-38957 | biostudies-arrayexpress
TranscriptomicsComputational and Analytical Framework for Small RNA Profiling by High-Throughput Sequencing (reproducibility)
The purpose of this work was to describe a computational and analytical methodology for profiling small RNA by high-throughput sequencing. The datasets here were used to assess the reproducibility of small RNA datasets produced using Illumina sequencing-by-synthesis technology (SBS). We analyzed th...
ORGANISM(S): Arabidopsis thaliana 
2009-06-02 | E-GEOD-14694 | biostudies-arrayexpress
ProteomicsNovel splicing and open reading frames revealed by long-read direct RNA sequencing of adenovirus transcripts
Adenovirus is a common human pathogen that relies on host cell processes for transcription and processing of viral RNA and protein production. Although adenoviral promoters, splice junctions, and cleavage and polyadenylation sites have been characterized using low-throughput biochemical techniques o...
ORGANISM(S): Homo sapiens (Human) 
2022-08-30 | PXD034464 | Pride
Targeted ms Splicing Adenovirus 
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