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MetabolomicsFIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling

This repository contains the LC-MS/MS raw data for the RNA quantifications obtained from in vivo DMS probed RNAs from E.coli and MDA-MB231 cell lines.

2026-04-26 | MTBLS14382 | MetaboLights
TranscriptomicsWild type E.coli SE15 vs. LuxS mutant E.coli SE15
Transcriptional profiling of E.coli SE15 comparing wild type E.coli SE15 with Autoindecur 2 synthesis gene LuxS mutnat E.coli SE15. E.coli SE15 is isolated from indwelling catheter of urinary tract infected patient. Examine change of quorum sensing related gene by deleting autoinducer 2 synthesis g...
ORGANISM(S): Escherichia coli SE15 
2013-08-02 | E-GEOD-49474 | biostudies-arrayexpress
GenomicsRNA-seq analysis for E.coli dnd and dam derivatives
RNA-seq analysis for E.coli dnd and dam derivatives
PRJNA560689 | ENA
TranscriptomicsE.coli response to Antimicrobial Arylamides
We treated logarithmically growing cultures of E.coli with a sub-lethal dose of an antimicrobial arylamide compound (PMX 10070) and Polymyxin B sulfate to measure transcriptional responses in an effort to understand mechanism of action Treated samples were assayed at time = 20min and time = 60min af...
ORGANISM(S): Escherichia coli 
2011-08-02 | E-GEOD-31140 | 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 
ProteomicsRBS-ID: Comprehensive identification of RNA-binding sites at single amino acid-resolution
We developed RBS-ID, which greatly simplifies the RNA moiety by chemical cleavage, reducing the complexity of MS/MS search space to accurately identify and localize RBS in peptides. RBS-ID comprehensively and robustly identifies RNA-binding sites at both proteome and single protein level.
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2020-06-02 | PXD016254 | Pride
Human Rbp. rbs Rna Lc-ms/ms 
GenomicsRNA-seq reveals important sRNAs in E.coli O157:H7
RNA-seq reveals important sRNAs in E.coli O157:H7
PRJNA550337 | ENA
TranscriptomicsTranscription profiling of stationary phase E.coli wild type and crl::cat mutant strains to identify Crl-regulated genes
We wished to identify Crl-regulated genes in stationary phase in E.coli, and whether those overlap with the previously identified regulon of RpoS. Therefore wildtype E.coli (MC4100) and its isogenic crl::cat mutant were grown at 30oC. Total RNA was extracted at on OD (578nm) of 4 (during entry into ...
ORGANISM(S): Escherichia coli 
2007-01-01 | E-MEXP-720 | biostudies-arrayexpress
UnknownCharacterization of the E.coli poly(A) polymerase: nucleotide specificity, RNA-binding affinities and RNA structure dependence.
Not available
S-EPMC102612 | biostudies-literature
TranscriptomicsTranscription profiling of pNCF (non-conjugative factor of F plasmid) carrying E.coli biofilm
Three E.coli affymetrix antisense arrays were used to examine the global gene expression of pNCF carrying E.coli biofilm. The pNCF is the derivative of only 65 kb non-conjugative factor of F plasmid. It was introduced to E.coli MG1655 strains before prepare the biofilm samples. The biofilms were cul...
ORGANISM(S): Escherichia coli 
2007-09-01 | E-MEXP-1145 | biostudies-arrayexpress
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