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MetabolomicsMolecular investigation of Tuscan sweet cherries sampled over three years: gene expression analysis coupled to metabolomics and proteomics

Sweet cherry (Prunus avium L.) is a stone fruit widely consumed and appreciated for its organoleptic properties, as well as its nutraceutical potential. We here investigated the characteristics of six non-commercial Tuscan varieties of sweet cherry maintained at the Regional Germplasm Ba...

2021-10-29 | MTBLS1803 | MetaboLights
GenomicsPING 2.0: An R/Bioconductor package for nucleosome positioning using next-generation sequencing data
MNase-Seq and ChIP-Seq have evolved as popular techniques to study chromatin and histone modification. Although many tools have been developed to identify enriched regions, software tools for nucleosome positioning are still limited. We introduce a flexible and powerful open-source R package, PING 2...
ORGANISM(S): Saccharomyces cerevisiae 
2013-07-11 | E-GEOD-47073 | biostudies-arrayexpress
ProteomicsMulti-level microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles
The anaerobic digestion microbiomes has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a holistic evaluation of the microbial community through fingerprinting or by targeted monit...
ORGANISM(S): human gut metagenome anaerobic digester metagenome 
2021-05-26 | PXD024788 | Pride
16s rrna gene amplicon sequencing Anaerobic digestion Metabolomics Flow cytometry Microbial fingerprinting Metaproteomics 
ProteomicsProfiling tissue-specific modulation of gene expression in response to insulin signalling in Drosophila
We investigated tissue-specific regulation of gene expression in a long lived Drosophila IIS mutant (dilp2-3,5) compared to its control (wDah). As in the majority of Drosophila laboratory strains, the endosymbiont Wolbachia was present; in the absence of Wolbachia, life extension through dilp2-3,5 i...
ORGANISM(S): Drosophila melanogaster (Fruit fly) 
2021-04-21 | PXD011589 | Pride
Drosophila tissue-specific insulin longevity lifespan aging shotgun 
GenomicsGenentech Colon Cancer Screen
Identifying and understanding changes in cancer genomes is essential for the development of targeted therapeutics. Here we analyse systematically more than 70 pairs of primary human colon tumours by applying next-generation sequencing to characterize their exomes, transcriptomes and copy-number alte...
EGAS00001000288 | EGA
MetabolomicsLC-MS metabolic profiling of mouse plasma and cell culture medium in relation to ABCC6 expression
Pseudoxanthoma elasticum (PXE) is an autosomal recessive disease characterized by progressive ectopic mineralization of the skin, eyes and arteries, for which no effective treatment exists. PXE is caused by inactivating mutations in the gene encoding ABCC6 (MRP6), an ATP-dependent efflux transporter...
2013-11-14 | MTBLS61 | MetaboLights
ProteomicsA novel translocon for biogenesis of multi-pass membrane proteins
A novel 370 kDa translocon comprising Sec61 and five accessory factors acting co-translationally with ribosomes to fold and insert multi-pass membrane proteins was identified, purified and analyzed structurally by single particle cryo-EM and cross-linking mass spectrometry. The purified ribosome-tr...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2019-07-08 | MSV000084065 | MassIVE
TranscriptomicsMLL Fusion Proteins Preferentially Regulate a Small Set of Wild Type MLL Target Genes in the Leukemic Genome
MLL encodes a histone methyltransferase that is critical in maintaining gene expression during embryonic development and hematopoiesis. 11q23 translocations encode chimeric MLL fusions that act as potent drivers of acute leukemia. However, it remains unclear what portion of the leukemic genome is un...
ORGANISM(S): Mus musculus 
2011-04-28 | E-GEOD-24794 | biostudies-arrayexpress
MetabolomicsAspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis

Gene rv3722c of Mycobacterium tuberculosis is essential for in vitro growth, and encodes a putative pyridoxal phosphate-binding protein of unknown function. Here we use metabolomic, genetic and structural approaches to show that Rv3722c is the primary aspartate aminotransferase of M. tuberculosis...

2020-05-01 | MTBLS1559 | MetaboLights
UnknownEscherichia coli cold-shock gene profiles in response to over-expression/deletion of CsdA, RNase R and PNPase and relevance to low-temperature RNA metabolism.
Not available
S-EPMC3456996 | biostudies-literature
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