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TranscriptomicsRNase G complementation of rne null mutation identifies functional interrelationships with RNase E
The Escherichia coli endoribonucleases RNase E (Rne) and RNase G (Rng) have sequence similarity and broadly similar sequence specificity. Whereas the absence of Rne normally is lethal, we show here that E. coli bacteria that lack the rne gene can be made viable by overexpression of Rng. Rng-compleme...
ORGANISM(S): Escherichia coli 
2005-08-13 | E-GEOD-3123 | biostudies-arrayexpress
ProteomicsE.coli total RNA RNase T1 and A digests LC-MS/MS
Four open-source software suites for the analysis of oligonucleotide data from tandem MS have been reported. These tools are all based on matching theoretical spectral libraries generated by silico digestion. While some software publications have included simple comparisons with previously published...
ORGANISM(S): Escherichia coli 
2026-03-09 | PXD075396 | Pride
E.coli rna Oligonucleotide Lc-ms/ms 
TranscriptomicsTranscription profiling of E. coli mutants lacking the rne gene and over expressing Rng
The Escherichia coli endoribonucleases RNase E (Rne) and RNase G (Rng) have sequence similarity and broadly similar sequence specificity. Whereas the absence of Rne normally is lethal, we show here that E. coli bacteria that lack the rne gene can be made viable by overexpression of Rng. Rng-compleme...
ORGANISM(S): Escherichia coli 
2005-07-11 | E-SMDB-1515 | biostudies-arrayexpress
ProteomicsNucleosides and Oligonucleotides analysis using LC-MS/MS in mouse liver
Here, we establish a sequence-resolved mouse liver small-RNA epitranscriptomic database by integrating nucleoside-level modification discovery with complementary RNase T1 and RNase A LC–MS/MS oligonucleotide mapping, enabling high-confidence modification-site annotation across tRNAs, 5S and 5.8S rRN...
ORGANISM(S): Mus musculus (Mouse) 
2026-08-31 | PXD082484 | Pride
Mouse Liver Oligonucleotide Nucleoside Lc-ms/ms 
UnknownRNase T1 mimicking artificial ribonuclease.
Not available
S-EPMC1874650 | biostudies-literature
ProteomicsComprehensive Evaluation of RNases, Nano-Flow HILIC Chromatography, and Mass Spectrometry for Shotgun RNomics of Native RNA
RNA modifications play crucial roles in regulating cellular processes, but comprehensive mapping of the human RNome still remains limited by technological challenges. Mass spectrometry is a valuable tool to analyse RNA modifications and complementing sequencing-based analysis. Current MS-based oligo...
ORGANISM(S): Escherichia coli 
2026-09-07 | PXD070755 | Pride
Rnase Rnome Oligonucleotide ms Hilic Nano-flow Lc-ms/ms 
UnknownNew Catalytic Residues and Catalytic Mechanism of the RNase T1 Family.
Not available
S-EPMC11487538 | biostudies-literature
ProteomicsHuman RNase 4 Improves mRNA Sequence Characterization by LC-MS/MS.
With the rapid growth of synthetic messenger RNA (mRNA)-based therapeutics and vaccines, the development of analytical tools for characterization of long, complex RNAs has become essential. Tandem liquid chromatography-mass spectrometry (LC-MS/MS) permits direct assessment of the mRNA primary sequen...
ORGANISM(S): synthetic RNA 
2022-07-26 | PXD033334 | Pride
Mrna  human rnase4 
ProteomicsIdentification of RSRC2 interactome through Immunoprecipitation (IP) coupled with LC-MS/MS-based protein analysis
We immunoprecipitate (IP) RSRC2 from HCT116 cells in the presence or absence of RNase A/T1 mix to identify RNA-mediated and RNA-independent RSRC2 protein-protein interaction networks. Four biological replicates were performed for each IP-MS in cells +/- RNase A/T1 Mix (EN0551, ThermoFisher) using Ig...
ORGANISM(S): Homo sapiens (Human) 
2026-03-12 | PXD059507 | Pride
Label-free quantification  interactome analysis  rsrc2  ip-ms 
TranscriptomicsGenome-wide assessments of transcriptional pauses and errors by nascent transcript sequencing combined with RNase footprinting (RNET-seq)
We developed native elongating transcript sequencing (NET-seq, Churchman and Weissman Nature 2011, PMID: 21248844) combined with RNase footprinting of nascent transcripts (RNET-seq) to visualize translocation dynamics and nascent transcript errors in paused RNA polymerases in E. coli. We employed R...
ORGANISM(S): Escherichia coli 
2015-04-29 | E-GEOD-62102 | biostudies-arrayexpress
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