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GenomicsLarge-scale methylation domains mark a functional subset of neuronally expressed genes
DNA methylation is essential for embryonic and neuronal differentiation, but the function of most genomic DNA methylation marks are poorly understood. Generally the human genome is highly methylated (>70%) except for CpG islands and gene promoters. However, it was recently shown that the IMR90 human...
ORGANISM(S): Homo sapiens 
2011-06-23 | E-GEOD-25930 | biostudies-arrayexpress
MetabolomicsEvaluation of ambient mass spectrometry tools for assessing inherent postharvest pepper quality

Horticulturists are interested in evaluating how cultivar, environment, or production system inputs can affect postharvest quality. Ambient mass spectrometry approaches enable analysis of minimally processed samples under ambient conditions and offer an attractive high-throughput alternative for ...

2022-03-04 | MTBLS2587 | MetaboLights
MetabolomicsInhibition of glycolysis and mitochondrial respiration promotes radiosensitisation of neuroblastoma and glioma cells

BACKGROUND: Neuroblastoma accounts for 7% of paediatric malignancies but is responsible for 15% of all childhood cancer deaths. Despite rigorous treatment involving chemotherapy, surgery, radiotherapy and immunotherapy, the 5-year overall survival rate of high-risk disease remai...

2022-11-30 | MTBLS858 | MetaboLights
TranscriptomicsGene expression analysis of Ox40-cre/ROSA-YFP CD4+ T cell subsets
An Ox40-cre allele was used for lineage marking of CD4 T cells. Naive T cells that had previously expressed OX40 demonstrated a partially activated phenotype that was distinct from that of the majority of naive T cells. These results are consistent with a minor subpopulation of naive T cells being...
ORGANISM(S): Mus musculus 
2010-04-03 | E-GEOD-13502 | biostudies-arrayexpress
GenomicsPartitioning the C. elegans genome by nucleosome modification, occupancy, and positioning
We have characterized two post-translational histone modifications in C. elegans on a genomic scale. Micrococcal nuclease digestion and immunoprecipitation were used to obtain distinct populations of single nucleosome cores, which were analyzed using massively parallel DNA sequencing to obtain pos...
ORGANISM(S): Caenorhabditis elegans 
2009-08-31 | E-GEOD-17284 | biostudies-arrayexpress
MetabolomicsGeographic variation of mutagenic exposures in kidney cancer genomes

International differences in the incidence of many cancer types indicate the existence of carcinogen exposures that have not been identified by conventional epidemiology yet potentially make a substantial contribution to cancer burden1. This pertains to clear cell renal cell carcinoma (ccRCC), fo...

2024-03-26 | MTBLS9394 | MetaboLights
TranscriptomicsTranscriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution
We used deep RNA sequencing to obtain high coverage RNA-Seq data of five C. crescentus cell cycle stages, each with three biological replicates. We found that 1,586 genes (over a third of the genome) display significant differential expression between stages. This gene list, which contains many gene...
ORGANISM(S): Caulobacter vibrioides 
2013-05-15 | E-GEOD-46915 | biostudies-arrayexpress
MetabolomicsMetabolic phenotyping of urine from a dementia research cohort
To better understand the molecular mechanisms underpinning physiological variation in human populations, metabolic phenotyping approaches are increasingly being applied to studies involving hundreds and thousands of biofluid samples. Hyphenated ultra-performance liquid chromatography-mass spectromet...
2022-03-01 | MTBLS719 | MetaboLights
MetabolomicsThe genetic origin of evolidine, the first cyclopeptide discovered in plants, and related orbitides

Cyclic peptides are reported to have antibacterial, antifungal and other bioactivities. Orbitides are a class of cyclic peptide that are small, head-to-tail cyclized, composed of proteinogenic amino acids, and lack disulfide bonds; they are also known in several genera of the plant family Rutacea...

2020-10-14 | MTBLS1963 | MetaboLights
MetabolomicsIdentification of pre-diagnostic lipid sets associated with liver cancer risk using untargeted lipidomics and chemical set analysis – a nested case-control study within the ATBC cohort

In pre-disposed individuals, a reprogramming of the hepatic lipid metabolism may support liver cancer initiation. We conducted a high-resolution mass spectrometry based untargeted lipidomics analysis of pre-diagnostic serum samples from a nested case-control study (219 liver cancer cases and 219 ...

2023-09-18 | MTBLS7776 | MetaboLights
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