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MetabolomicsDirect on-swab metabolic profiling of vaginal microbiome:host interactions during pregnancy and preterm birth

The pregnancy vaginal microbiome contributes to risk of preterm birth, the primary cause of death in children under 5 years of age. Here we describe direct on-swab metabolic profiling by Desorption Electrospray Ionization Mass Spectrometry (DESI-MS) for sample preparation-free characterisation of...

2021-09-23 | MTBLS717 | MetaboLights
MetabolomicsRapid Evaporative Ionisation Mass Spectrometry (REIMS) Provides Accurate Direct from Culture Species Identification within the Genus Candida
Members of the genus Candida, such as C. albicans and C. parapsilosis, are important human pathogens. Other members of this genus, previously believed to carry minimal disease risk, are increasingly recognised as important human pathogens, particularly because of variations in susceptibilities to wi...
2017-11-01 | MTBLS383 | MetaboLights
ProteomicsGeneralizable direct protein sequencing with InstaNexus
Critical protein therapeutics, such as antibodies and nanobodies, are often not encoded in reference genomes, limiting their accurate characterization via standard proteomics. Current methods rely on indirect inference, fragmented outputs, and labor-intensive workflows, which hinder functional insig...
ORGANISM(S): Bos taurus (Bovine) Homo sapiens (Human) 
2026-02-23 | PXD066160 | Pride
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
GenomicsSequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk
Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here we present sequential ChIP-bisulfite-sequencing (ChIP- BS-seq) as an approach to quantitatively ...
ORGANISM(S): Homo sapiens 
2012-03-27 | E-GEOD-28254 | biostudies-arrayexpress
TranscriptomicsTranscriptome of Aspergillus oryzae following ER stress
The Aspergillus oryzae, an important filamentous fungus used in food fermentation and enzyme industry, has been revealed to own prominent features in its genomic compositions by genome sequencing and various other tools. However, the functional complexity of the A. oryzae transcriptome has not yet b...
ORGANISM(S): Aspergillus oryzae 
2010-02-02 | E-GEOD-18851 | biostudies-arrayexpress
TranscriptomicsmiRNA high-throughput sequencing of follicular thyroid tumors
We report data obtaibed from high-throughput sequencing of small RNAs in 20 samples of follicular thyroid tumors. We analyzed a total of 4.7±1.5million reads per sample with 3 different pipelines. The main goal was to evaluate the usefulness of next generation sequencing in small RNA profiling and t...
ORGANISM(S): Homo sapiens 
2014-03-07 | E-GEOD-39112 | biostudies-arrayexpress
ProteomicsMS-based sequencing of the anti-FLAG-M2 antibody
We demonstrate a method for direct de novo sequencing of monoclonal IgG from the purified antibody products. The method uses a panel of multiple complementary proteases to generate suitable peptides for de novo sequencing by LC-MS/MS in a bottom-up fashion. Furthermore, we apply a dual fragmentation...
ORGANISM(S): Homo sapiens (Human) Mus musculus (Mouse) 
2021-01-11 | PXD023419 | Pride
Antibody Stepped hcd Ethcd De novo sequencing 
TranscriptomicsOverlapping and distinct functions of CstF64 and CstF64τ in mammalian mRNA 3’ processing
Our study of CstF64 and CstF64τ revealed both functional overlap and specificity of these two important mRNA 3’ processing factors and provided new insights into the regulatory mechanisms of mRNA 3’ processing. CstF64tau iCLIP-seq in HeLa cells; direct RNA sequencing (DRS) of control HeLa cells, Cs...
ORGANISM(S): Homo sapiens 
2013-09-30 | E-GEOD-51156 | biostudies-arrayexpress
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