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TranscriptomicsRNAi profiling of mouse embryonic stem cells using short hairpin RNAs against Nanog, Oct4, Sox2, Esrrb, Tbx3, Tcl1, Mm.343880 and Dppa4
We present an integrated approach to identify genetic mechanisms that control self-renewal in mouse embryonic stem (ES) cells. Short hairpin RNA (shRNA) techniques are employed to down regulate a set of gene-products whose expression patterns suggest self-renewal regulatory functions. We focus on ...
ORGANISM(S): Mus musculus 
2008-06-13 | E-GEOD-4679 | biostudies-arrayexpress
TranscriptomicsTranscription profiling by array of honey bee queens Apis mellifera L. to investigate the differential effects of insemination volume and substance on reproductive changes
Mating causes dramatic changes in female insects at the behavioral, physiological, and molecular levels. The factors driving these changes (e.g., seminal proteins, seminal volume) and the molecular pathways by which these factors are operating have been characterized only in a handful of insect spe...
ORGANISM(S): Apis mellifera 
2013-05-21 | E-MEXP-3681 | biostudies-arrayexpress
ProteomicsA chemoproteomics approach to profile phospholipase D-derived phosphatidyl alcohol interactions
Alcohol consumption leads to formation of phosphatidylethanol (PEth) via the transphosphatidylation activity of phospholipase D (PLD) enzymes. Though this non-natural phospholipid routinely serves as a biomarker of chronic alcoholism, its pathophysiological roles remain unknown. We use a minimalist ...
ORGANISM(S): Homo sapiens (Human) 
2024-01-04 | PXD029749 | Pride
Cuaac Basigin Phosphatidyl ethanol Phosphatidic acid Diazirene Photoaffinity label Click chemistry Phospholipase d Phosphatidyl alcohol 
TranscriptomicsMurine skin gene expression analysis of skin-specific Scd1-deficient and control mice
To help elucidate the metabolic changes in the skin that contribute to the obesity resistance and skin pathology in mice lacking Scd1, we performed microarray analysis of skin gene expression in male skin Scd1 knockout (SKO) and Scd1 flox/flox control (Lox) mice fed a standard rodent diet. We identi...
ORGANISM(S): Mus musculus 
2011-05-09 | E-GEOD-24243 | biostudies-arrayexpress
TranscriptomicsGenome-wide analysis of mouse intestinal adenoma identifies early steps in the formation of cancer-specific DNA methylation patterns
Aberrant CpG methylation is a universal trait of cancer cell genomes and can result in epigenetic modulation of gene activity; however, at which stages tumour-specific epigenetic patterns arise is unknown. Here, we analyse the methylome of APCM in mouse intestinal adenoma as a model of intestinal ca...
ORGANISM(S): Mus musculus 
2013-04-03 | E-GEOD-38983 | biostudies-arrayexpress
TranscriptomicsNucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein
Human CMV (hCMV) establishes lifelong infections in most of us, causing developmental defects in human embryos and life-threatening disease in immunocompromised individuals. During productive infection, the viral >230,000-bp dsDNA genome is expressed widely and in a temporal cascade. The hCMV genome...
ORGANISM(S): Human Herpesvirus 5 
2013-07-17 | E-GEOD-48875 | biostudies-arrayexpress
ProteomicsFlorigen activation complex forms via multifaceted assembly in Arabidopsis
'Florigen', encoded by FT genes, is synthesized in leaves and transported to the shoot apical meristem (SAM) to induce flower development. At the SAM, 14-3-3 proteins are proposed to act as receptors for FT and to mediate the indirect interaction between FT and the bZIP transcription factor FD to fo...
ORGANISM(S): Arabidopsis thaliana (Mouse-ear cress) 
2025-09-02 | PXD067955 | Pride
Florigen activation complex Ip-ms 14-3-3 Phosphorylation Flowering Ft Fd 
GenomicsDe novo assembly of 150 Danish genomes reveals rich structural complexity
Most known genetic variation in human genomes has been called from comparison of short reads to the reference genome, an approach biased against finding complex variation. We sequenced 150 individuals from 50 parent-offspring trios with multiple insert-size libraries to very high coverage. We show t...
EGAS00001002108 | EGA
ProteomicsGrafting systems for plant cadmium research: insights for basic plant physiology and applied mitigation
Cadmium (Cd) is a highly toxic and carcinogenic pollutant that poses a threat to human and animal health by affecting several major organ systems. Urbanization and human activities have led to significant increases in Cd concentration in the environment, including in agroecosystems. To protect again...
ORGANISM(S): Solanum lycopersicum 
2023-06-26 | PXD041184 | Pride
Abiotic stress  cadmium mitigation  environmental research  heavy metals  plant grafting  stress tolerance 
Genomicsena-DATASET-DTU-19-07-2017-19:09:46:884-206 - samples
The MHC vcf call set was generated using a modified AsmVar and BayesTyper pipeline. In contrast to the original pipeline, where variant calling is performed using alignment of collapsed assemblies to a reference genome, the MHC call set was produced using alignment of phased MHC haplotypes. Two iter...
EGAD00001003455 | EGA
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