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TranscriptomicsGene expression signature of cerebellum hypoplasia in a mouse model of Down syndrome (Part II).
We designed a large scale gene expression study in cerebellar external granular layer in Ts1Cje mice at P0 in order to measure the effects of trisomy 21 on in a enriched cell population (dissected layer) that is affected in Down syndrome in order to correlate gene expression changes to the phenotype...
ORGANISM(S): Mus musculus 
2008-03-31 | E-GEOD-11472 | biostudies-arrayexpress
ProteomicsPredicting electrophoretic mobility of proteoforms for large-scale top-down proteomics
Large-scale top-down proteomics characterizes proteoforms in cells globally with high confidence and high throughput using reversed-phase liquid chromatography (RPLC)-tandem mass spectrometry (MS/MS) or capillary zone electrophoresis (CZE)-MS/MS. The false discovery rate (FDR) from the target-decoy ...
ORGANISM(S): Escherichia coli 
2020-02-17 | PXD017265 | Pride
Top-down proteomics Electrophoretic mobility Cze-ms Proteoform 
TranscriptomicsGene expression signature of cerebellum hypoplasia in a mouse model of Down syndrome (Part I).
We designed a large scale gene expression study in Ts1Cje mice between P0 and P10 in order to measure the effects of trisomy 21 on a large number of samples (56 in total) in a tissue that is affected in Down syndrome (the cerebellum) and to quantify the defect during development in order to correlat...
ORGANISM(S): Mus musculus 
2009-03-31 | E-GEOD-11448 | biostudies-arrayexpress
TranscriptomicsSkin healing and scale regeneration in fed and unfed sea bream, Sparus auratus
Fish scales are an important reservoir of calcium and phosphorus and together with the skin function as an integrated barrier against environmental changes and external aggressors. Histological studies have revealed that the skin and scales regenerate rapidly in fish when they are lost or damaged. I...
ORGANISM(S): Sparus aurata 
2012-01-24 | E-GEOD-30717 | biostudies-arrayexpress
TranscriptomicsRNA-Seq of rRNA depleted circulating endothelial progenitor cells (cEPCs) in trisomy 21 and euploid samples
Massive-scale RNA-seq on rRNA-depleted samples allowed us to survey in a specific cell type, affected in Down syndrome, the complete set of coding and non-coding RNA species - emerging as novel contributors to pathogenic mechanisms - to an unprecedented level of resolution and sensitivity. In partic...
ORGANISM(S): Homo sapiens 
2011-05-04 | E-GEOD-27443 | biostudies-arrayexpress
TranscriptomicsDown syndrome
Endothelial progenitor cells were isolated from euploid and Down syndrome (DS) affected individuals. Gene expression was analyzed on total RNA extracted before or after infection with a human pathogen Bartonella hensaele. For euploid uninfected and infected cells, 2 biological replicates were perfor...
ORGANISM(S): Homo sapiens 
2010-01-12 | E-MTAB-312 | biostudies-arrayexpress
ProteomicsCapillary zone electrophoresis-tandem mass spectrometry with activated ion electron transfer dissociation for large-scale top-down proteomics
Capillary zone electrophoresis (CZE)-tandem mass spectrometry (MS/MS) has been recognized as an efficient approach for top-down proteomics recently for its high-capacity separation and highly sensitive detection of proteoforms. However, the commonly used collision-based dissociation methods often ca...
ORGANISM(S): Escherichia coli 
2019-06-11 | PXD012247 | Pride
Top-down proteomics E. coli Cze-ms Ai-etd 
ProteomicsLC-MS of S. cerevisiae scale-down cultivations
Chemostat cultivation mode imposes selective pressure on cells, which may result slow adaptation in the physiological state over time. We applied a two-compartment scale-down chemostat system simulating glucose gradients to characterize the long-term (100’s of hours) response of S. cerevisiae to flu...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-06-09 | PXD015536 | Pride
Scale-down Glucose gradients Fermentation Proteome S. cerevisiae 
ProteomicsLarge-scale Top-down Proteomics of the Arabidopsis thaliana Leaf and Chloroplast Proteomes
We present a large-scale top-down proteomics study of plant leaf and chloroplast proteins, achieving the identification of over 4700 unique proteoforms. Using capillary zone electrophoresis coupled with tandem mass spectrometry analysis of offline size-exclusion chromatography fractions, we identify...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2023-01-05 | PXD034368 | Pride
Arabidopsis thaliana Post-translational modification Proteoform Transit peptide Singlet oxygen Chloroplast 
TranscriptomicsDomestication causes large-scale effects on gene expression in rainbow trout
This SuperSeries is composed of the following subset Series: GSE16889: Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the brain transcriptome GSE16897: Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the liver trans...
ORGANISM(S): Oncorhynchus mykiss 
2010-05-16 | E-GEOD-16903 | biostudies-arrayexpress
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