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ProteomicsLyophilization prior to homogenisation and extraction increases membrane protein detection in Gram-negative bacterial proteomic analyses
Multi-drug resistant Gram-negative bacteria (GNB) are major contributors to the anti-microbial resistance (AMR) burden in humans and animals. AMR mechanisms are primarily mediated by proteoforms and, therefore, proteomic analyses of GNB offers a significant advantage in understanding the mechanisms ...
ORGANISM(S): Escherichia coli 
2026-03-08 | PXD075198 | Pride
Proteomics Antimicrobial resistance Membrane proteins Bacterial protein extraction 
GenomicsGenome-wide mapping of meiotic double-strand breaks by sequencing Spo11 oligos.
The nonrandom distribution of meiotic recombination shapes patterns of inheritance and genome evolution, but chromosomal features governing this distribution are poorly understood. Formation of the DNA double-strand breaks (DSBs) that initiate recombination results in accumulation of Spo11 protei...
ORGANISM(S): Saccharomyces cerevisiae 
2011-03-07 | E-GEOD-26449 | biostudies-arrayexpress
GenomicsWhole-genome nucleosome mapping in meiotic diploid S. cerevisiae
We determined nucleosome positions throughout the genome in diploid S. cerevisiae undergoing early stages of synchronous meiosis. This study sought to assess if systematic reorganization of nucleosomes occurs during meiotic prophase at or near sites of DNA double strand break formation. Six samples ...
ORGANISM(S): Saccharomyces cerevisiae 
2011-03-07 | E-GEOD-26452 | biostudies-arrayexpress
TranscriptomicsBernardo mesoderm differentiation
Transcriptional profiling of hESCs in chemically-defined culture media compared to hESCs differentiated for 36h in the additional presence of FGF, LY294002 and either BMP or ActivinA.
ORGANISM(S): Homo sapiens 
2011-08-24 | E-MTAB-464 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of human embryonic stem cells treated with BMP4 in chemically-defined medium, with and without inhibitors of Activin and FGF signalling to investigate the induction of extra-embryonic tissue differentiation by BMP signalling
Gene expression microarray analysis of hESCs treated with BMP4 in chemically-defined medium, with and without inhibitors of Activin and FGF signalling (which maintain pluripotency), to investigate the induction of extra-embryonic tissue (trophectoderm) differentiation by BMP signalling.
ORGANISM(S): Homo sapiens 
2009-07-31 | E-MEXP-1192 | biostudies-arrayexpress
TranscriptomicsTGF-beta stimulation in ovarian cancer cells
Genome-wide DNA methylation profiles of TGF-beta ovarian cancer cells were obtained using next generation Illumina Infinium 450k assay which includes over 450,000 GpG sites. DNA from 12 samples were hybridized to the Illumina's Infinium HumanMethylation 450 BeadChip
ORGANISM(S): Homo sapiens 
2015-04-07 | E-GEOD-56621 | biostudies-arrayexpress
MetabolomicsAntiviral metabolite 3'-Deoxy-3',4'-didehydro-cytidine is detectable in serum and identifies acute viral infections including COVID-19

BACKGROUND: There is a critical need for rapid viral infection diagnostics to enable prompt case identification in pandemic settings and support targeted antimicrobial prescribing.

METHODS: Using untargeted high-resolution liquid chromatography coupled with...

2022-02-10 | MTBLS718 | MetaboLights
TranscriptomicsCigarette Smoking Induces Small Airway Epithelial Epigenetic Changes with Corresponding Modulation of Gene Expression
The small airway epithelium (SAE), the first site of smoking-induced lung pathology, exhibits genome-wide changes in gene expression in response to cigarette smoking. Based on the increasing evidence that the epigenome can respond to external stimuli in a rapid manner, we assessed the SAE of smokers...
ORGANISM(S): Homo sapiens 
2013-08-05 | E-GEOD-43079 | biostudies-arrayexpress
GenomicsCistromic and epigenomic changes in Prdm16 knock-out brown adipose tissue
Prdm16 is a transcription factor that drives a complete program of brown adipocyte differentiation, but the mechanism by which Prdm16 activates gene transcription remains unknown. Utilizing ChIP-seq teqhnique, we found that Prdm16 binds to chromatin at/near many brown fat-selective genes in BAT. Int...
ORGANISM(S): Mus musculus 
2015-02-10 | E-GEOD-63965 | biostudies-arrayexpress
TranscriptomicsTranscription profiling of human embryonic stem cells and their differentiated progeny grown in chemically defined conditions
Comparison of H9 human embryonic stem cells, grown in chemically defined and animal-product free conditions, with their differentiated progeny - mesendodermal progenitors arisen as the result of changes made to chemically defined hESC growth conditions. Contributes to a larger work on the use of che...
ORGANISM(S): Homo sapiens 
2009-07-31 | E-MEXP-930 | biostudies-arrayexpress
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