Composition of raw plant-based food items
Ontology highlight
ABSTRACT:
ORGANISM(S): Malus Domestica/musa Acuminata/solanum Lycopersicum/lactuca Sativa/fragaria X Ananassa/daucus Carota/prunus Persica/allium Cepa/spinacia Oleracea/capsicum Annuum/zea Mays/allium Sativum/ocimum Basilicum/solanum Tuberosum/glycine Max/phaseolus Vulgaris/olea Europaea/cicer Arietinum/beta Vulgaris/pyrus Communis
TISSUE(S): Plant
PROVIDER: ST002492 | MetabolomicsWorkbench |
REPOSITORIES: MetabolomicsWorkbench
Dataset's files
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| mwtab | Other |
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Project description: Not available
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2013-09-01 | E-MTAB-1815 | biostudies-arrayexpress
Project description:Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is a widely used approach to study DNA methylation genome-wide. Here, we present a novel MeDIP-Seq protocol compatible with the Ion Torrent semiconductor-based sequencing platform that is scalable and accurately identifies sites of differential DNA methylation. Additionally, we demonstrate that the high-throughput data derived from MeDIP-Seq on the Ion Torrent platform provides adequate coverage of CpG cytosines, the methylation states of which we validated at single-base resolution on the Infinium HumanMethylation450K Beadchip array. We applied this integrative approach to further investigate the role of DNA methylation in alternative splicing and to profile 5-mC and 5-hmC variants of DNA methylation in normal human brain tissue that we observed localize over distinct genomic regions. These applications of MeDIP-Seq on the Ion Torrent platform have broad utility and add to the current methodologies for profiling genome-wide DNA methylation states in normal and disease conditions. MeDIP-Seq on Ion Torrent Platform in HCT116 and Human Brain
2015-06-10 | E-GEOD-61968 | biostudies-arrayexpress
Project description:Cancer-associated fibroblasts (CAFs) have been recognized as important contributors to cancer development and progression. However, opposing evidence has been published whether CAFs, in addition to epigenetic, also undergo somatic genetic alterations and whether these changes contribute to carcinogenesis and tumour progression. We combined multiparameter DNA flow cytometry, flow-sorting and 6K SNP-arrays to study DNA aneuploidy, % S-phase, loss of heterozygosity (LOH) and copy number alterations (CNAs) to study somatic genetic alterations in cervical cancer-associated stromal cell fractions (n = 58) from formalin-fixed, paraffin-embedded (FFPE) samples. Tissue sections were examined for the presence of CAFs. Microsatellite analysis was used to study LOH. By flow cytometry we found no proof for DNA aneuploidy in the vimentin-positive stromal cell fractions of any samples (CV G0G1 population 3.7% +/- 1.2; S-phase 1.4% +/- 1.8). The genotype concordance between the stromal cells and the paired normal endometrium samples was > 99.9%. No evidence for CNAs or LOH was found in the stromal cell fractions. In contrast, high frequencies of DNA content abnormalities (43/57), a significant higher S-phase (14.6% +/- 8.5)(p = 0.0001) and substantial numbers of CNAs and LOH were identified in the keratin-positive epithelial cell fractions (CV G0G1 population 4.1% +/- 1.0). Smooth muscle actin and vimentin immunohistochemistry verified the presence of CAFs in all cases tested. LOH hot-spots on chromosomes 3p, 4p and 6p were confirmed by microsatellite analysis but the stromal cell fractions showed retention of heterozygosity only. From our study we conclude that stromal cell fractions from cervical carcinomas are DNA diploid, have a genotype undistinguishable from patient-matched normal tissue and are genetically stable. Stromal genetic changes do not seem to play a role during cervical carcinogenesis and progression. In addition, the stromal cell fraction of cervical carcinomas can be used as reference allowing large retrospective studies of archival FFPE tissues for which no normal reference tissue is available. Paired experiment, Endometrial (non-tumor) cells vs stromal cells from cervical tumors. Biological replicates: 58 patients. From 5 tumors also the tumor fraction was profiled.
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2012-08-29 | E-GEOD-31828 | biostudies-arrayexpress
Project description:The purpose of this research was to investigate the characteristics of different plant-based sources rich in protein, chickpea flour (CPF), hazelnut oil cake (HOC), soy protein isolate (SPI) and concentrate (SPC), and pea protein isolate (PPI) for their subsequent use in the manufacture of meat analogs. The protein sources were analyzed for dry matter, ash, protein, fat, starch, dietary fiber, water holding capacity, granulosity, color parameters (L*, a*, b*, C*, YI), antioxidant activity before and after gastrointestinal in vitro digestion, and amino acid and mineral compositions. The highest dry matter content was determined in hazelnut oil cake and pea protein isolate. For the protein content, maximum values were obtained for the protein isolate and concentrate samples, from 52.80% to 80.50%, followed by hazelnut oil cake and chickpea flour. The water-holding capacity of all plant sources was directly influenced by the values of protein content, dietary fiber, and granulosity. The results obtained after gastrointestinal digestion also showed quite significant antioxidant activity, which is due to the process of hydrolysis and denaturation of plant-based protein sources in the gastrointestinal tract. Major amino acids identified in the analyzed samples were glutamic acid, leucine, arginine, phenylalanine, serine, valine, alanine, and tyrosine from minerals P, Na, Mg, and Ca. Principal component analysis (PCA) was used to illustrate the relationship between physicochemical characteristics, amino acid composition, mineral composition, and antioxidant activity determined in the plant-based materials.
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