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UnknownMEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.
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S-EPMC4915700 | biostudies-literature
ProteomicsTotal proteomes of starved Pseudomonas aeruginosa
We have characterized the responses of the opportunistic pathogen Pseudomonas aeruginosa to prolonged starvation for carbon or nitrogen sources, and to transitions between these states. We find that most cells survive both types of starvation for more than a week and maintain low but robustly detect...
ORGANISM(S): Pseudomonas aeruginosa (strain UCBPP-PA14) Bacteria 
2026-03-04 | PXD069186 | Pride
Nitrogen starvation Pseudomonas aeruginosa Label-free quantification Carbon starvation 
ProteomicsBONCAT (nascent) proteomes of starved Pseudomonas aeruginosa
We have characterized the responses of the opportunistic pathogen Pseudomonas aeruginosa to prolonged starvation for carbon or nitrogen sources, and to transitions between these states. We find that most cells survive both types of starvation for more than a week and maintain low but robustly detect...
ORGANISM(S): Pseudomonas aeruginosa (strain UCBPP-PA14) Bacteria 
2026-03-04 | PXD069190 | Pride
Nitrogen starvation Microbial dormancy Boncat Label-free quantification Pseudomonas aeruginosa Carbon starvation 
TranscriptomicsTransient Pairing of Homologous Oct4 Alleles Accompanies the Onset of Embryonic Stem Cell Differentiation
The relationship between chromatin organization and transcriptional regulation is an area of intense investigation. We have characterized the spatial relationships between alleles of the Oct4, Sox2, and Nanog genes in single cells during the earliest stages of mouse embryonic stem cell (ESC) differe...
ORGANISM(S): Mus musculus 
2015-02-03 | E-GEOD-65510 | biostudies-arrayexpress
TranscriptomicsTransposon insertion sequencing (Tn-Seq) to identify fitness determinants during nitrogen starvation, carbon starvation, and transitions between them in Pseudomonas aeruginosa
We performed Tn-Seq to identify genetic fitness determinants for starvation survival in Pseudomonas aeruginosa. A pooled mutant library of approximately 180,000 randomly inserted transposon mutants was grown into stationary phase in rich medium (lysogeny broth) and an aliquot of this mutant pool was...
ORGANISM(S): Pseudomonas aeruginosa 
2026-03-04 | E-MTAB-15727 | biostudies-arrayexpress
TranscriptomicsHippocampal expression data from FTY720- and vehicle-treated SCID mice following fear consolidation testing
FTY720/Fingolimod, an FDA-approved drug for treatment of multiple sclerosis, has beneficial effects in the CNS that are not yet well understood, independent of its effects on immune cell trafficking. Here we show that FTY720 enters the nucleus where it is phosphorylated by sphingosine kinase 2 (SphK...
ORGANISM(S): Mus musculus 
2014-05-12 | E-GEOD-57015 | biostudies-arrayexpress
ProteomicsCLPB disaggregase dysfunction impacts the functional integrity of the proteolytic SPY complex
CLPB is a mitochondrial intermembrane space AAA+ domain–containing disaggregase. CLPB mutations are associated with 3-methylglutaconic aciduria and neutropenia; however, the molecular mechanism underscoring disease and the contribution of CLPB substrates to disease pathology remains unknown. Interac...
ORGANISM(S): Homo sapiens (Human) 
2024-01-18 | PXD042313 | Pride
Disaggregase Protein transport Mitochondria Protein quality control Mitochondrial disease 
TranscriptomicsExpression data from cyclically stretched engineered neonatal rat ventricuar myocyte (NRVM) tissues
Mechanical overload in the heart induces pathological remodeling that typcially leads to heart failure. We sought to build an in vitro model of heart failure by applying cyclic stretch to engineered isotropic (iso) and anisotropic (aniso) NRVM tissues. We used micoarrays to determine the effects of ...
ORGANISM(S): Rattus norvegicus 
2013-01-30 | E-GEOD-43846 | biostudies-arrayexpress
GenomicsIdentifying targets of DSX with DamID-seq
We have adapted the DamID protocol for use with high throughput sequencing. We have used DamID to identify the positions within the Drosophila genome where the transcription factor DSX is bound. We sequenced DpnI-digested genomic DNA from fly tissues containing UAS-Dam (control) or UAS-Dam-DsxF or ...
ORGANISM(S): Drosophila melanogaster 
2014-10-30 | E-GEOD-27269 | biostudies-arrayexpress
ProteomicsSignaling pathways altered at the mitotic spindle in clathrin depleted cells
We present a snapshot of the regulation of mitotic-spindle proteins and their phosphorylation status in the absence of clathrin during metaphase. A reference list of proteins and phosphosites identified from a mitotic spindle preparation was generated using a label-free and a parallel chemical dimet...
ORGANISM(S): Homo sapiens (Human) 
2016-05-17 | PXD001603 | Pride
Hela Chc knock-down Tio2 Dimethylation Scx High ph reverse phase Lc-ms/ms 
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