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ProteomicsRecommendations for Automating Hydrogen/Deuterium Exchange Mass Spectrometry Measurements using Data-Independent Acquisition Methods
Two test HX-DIA datasets, Phosphorylase B kinetics and nanobody binding, that can be used to explore the features of DIA-HX and the AutoHX software.
ORGANISM(S): Homo sapiens (Human) 
2025-01-22 | PXD060028 | Pride
Autohx Data-independent acquistion Hx-ms2 Hydrogen deuterium exchange Hx-dia 
ProteomicsAutomating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology
We developed an HX-MS2 strategy that supports the acquisition of CID-generated fragment ions alongside their peptide precursors. The approach enables true auto-validation of HX data by mining the rich set of deuterated fragments, using the extra dimension of data to simultaneously confirm the peptid...
ORGANISM(S): Homo sapiens (Human) Oryctolagus cuniculus (Rabbit) 
2023-09-08 | PXD045012 | Pride
Dia Lc-ms Swath-ms Dna-pk Hx-ms 
ProteomicsThe HisRS-like domain of GCN2 is a pseudoenzyme that can bind uncharged tRNA - HX-MS Data
GCN2 is a stress response kinase that phosphorylates the translation initiation factor eIF2to inhibit general protein synthesis when activated by uncharged tRNA and stalled ribosomes. The presence of a HisRS-like domain in GCN2, normally associated with the ability to bind and aminoacylate tRNAs, le...
ORGANISM(S): Homo sapiens (Human) 
2024-02-01 | PXD049090 | Pride
Hdx-ms 
UnknownAutomating data analysis for hydrogen/deuterium exchange mass spectrometry using data-independent acquisition methodology.
Not available
S-EPMC10928179 | biostudies-literature
GenomicsChIP-seq analysis of Foxa2 binding sites in midbrain dopaminergic progenitors
Embryonic stem (ES) cells were differentiated in culture to midbrain dopaminergic (mDA) progenitors and subjected to ChIP-seq analysis to resolve genome-wide binding sites of forkhead box protein A2 (Foxa2). Foxa2 was found to directly regulate multiple lineage pathways to specify midbrain dopaminer...
ORGANISM(S): Mus musculus 
2012-07-01 | E-MTAB-1137 | biostudies-arrayexpress
TranscriptomicsGenome wide gene-expression analysis of facultative reproductive diapause in the two-spotted spider mite Tetranychus urticae
Investigating essential physiological processes in diapausing mites by analyzing genome wide gene expression changes using custom-built microarray. We investigated the molecular biology of facultative reproductive diapause in the chelicerate Tetranychus urticae (Acari: Tetranychidae) by analyzing ge...
ORGANISM(S): Tetranychus urticae 
2013-11-29 | E-GEOD-48858 | biostudies-arrayexpress
TranscriptomicsATAC-seq on ESCs undergoing directed differentiation towards defined neural fates
We have used ATAC-seq to track cell state changes that occur during the differentiation of mouse embryonic stem cells to defined neural progenitor fates. We have performed ATAC-seq every 24 hours in cells en route to 3 distinct neural progenitors fates, anterior, hindbrain and spinal cord. This has ...
ORGANISM(S): Mus musculus 
2018-08-27 | E-MTAB-6337 | biostudies-arrayexpress
TranscriptomicsHigh-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridiz
We attempted to identify candidate genes that are expressed more highly in the ICM than in TE cells. Mouse ES cells are cultured from the ICM, whereas mouse TS cells are cultured from the TE. Although these cells have been cultured in vitro, they represent the in vitro equivalents of the ICM and TE....
ORGANISM(S): Mus musculus 
2010-06-09 | E-GEOD-3214 | biostudies-arrayexpress
TranscriptomicsSingle cell transcriptional profiling of mouse molar and incisor tooth assembloids
Throughout the various stages of tooth development, reciprocal epithelial-mesenchymal interactions are the driving force, for instance crucially involved in the differentiation of mature enamel-forming ameloblasts and dentin-producing odontoblasts. Here we established mouse tooth ‘assembloids’, comp...
ORGANISM(S): Mus musculus 
2023-04-19 | E-MTAB-12544 | biostudies-arrayexpress
TranscriptomicsTimecourse expression data from sciatic nerve distal stump of C57BL/6 and C57BL/6 OlaHsd-Wlds mice.
Wallerian degeneration (WD) involves the fragmentation of axonal segments disconnected from their cell bodies, segmentation of the myelin sheath, and removal of debris by Schwann cells and immune cells. The removal and downregulation of myelin-associated inhibitors of axonal regeneration and synthes...
ORGANISM(S): Mus musculus 
2011-06-01 | E-GEOD-22291 | biostudies-arrayexpress
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