Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1023727 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mice deficient in the LDL receptor (LDLR KO mice) fed with high fat diet (HFD) feeding have been widely used as a model to mimic human atherosclerosis. RNA-seq using aortic macrophages to investigate the effects of aortic macrophages on the plaque size progression. LDLR KO mice, 6-8 weeks old, were used, and fed with either an alternative HFD or a regular HFD. After aorta macrophages were isolated, RNeasy Mini Kit (Qiagen) was used to isolate mRNA. Single end (50bp), unstranded, SMART-Seq v4 plus nextera (SMART-Seq v4 Ultra Low Input RNA Kit (Takara) ). The RNA-seq libraries were prepared with SMART-Seq v4 Ultra Low Input RNA Kit (Takara).
2024-07-31 | E-MTAB-12759 | biostudies-arrayexpress
Project description:Embryos classified as euploid or aneuploid by PGT-A were re-biopsied and processed for RNA-Seq using a commercial kit (Takara Bio, USA, SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing) following the user manual. The resulting cDNAs were converted to libraries using a Nextera XT kit (Illumina, USA), with a modified protocol according to SMART-Seq v4 user manual. These libraries were pooled and sequenced using a NextSeq 550 instrument (Illumina, USA) with a MidOutput cartridge at 2x75 cycles. The sequencing reads in Fastq files were down-sampled to 6M total reads, aligned to the human genome assembly (hg38), and the number of transcripts per million (TPM) was determined using the CLC Genomics Workbench 12 (Qiagen, USA).
2022-09-07 | E-MTAB-12084 | biostudies-arrayexpress
Project description:We examined 36 biopsies taken from digital dermatitis lesions of Holstein cows. The target was the V3 -V4 variable region of 16S rRNA using Treponema specific primers. We identified 20 different taxa of Treponema using this approach.
2013-06-25 | GSE42426 | GEO
Project description:<p>The communities of marine bacteria that assemble around living microphytoplankton are predictably dominated by three taxonomic groups, each of which specializes in the use or transport of different components of the available metabolite pool: Rhodobacterales transport small and polar metabolites, Flavobacteriia use carbohydrate-rich polymers, and Gammaproteobacteria use compounds from both classes. The consistent ecological pattern involving these three taxa is widespread throughout the surface ocean, yet whether it reflects the outcome competition or niche partitioning of the phytoplankton-derived compounds is not clear. Addressing this question requires better knowledge than currently exists of the metabolites that link microbial autotrophs and heterotrophs in the surface ocean. Here we used two untargeted biological screening strategies that leverage bacterial proficiency for scavenging dilute substrates from chemically complex mixtures to characterize metabolite uptake by heterotrophic bacteria. In the first, expression patterns of transporters and diagnostic catabolic genes were analyzed in model marine bacteria grown individually in co-culture with the diatom Thalassiosira pseudonana. In the second, the ability of bacteria to draw down exometabolites from the culture medium was detected by novel approaches in mass spectrometry (MS) and nuclear magnetic resonance (NMR) analysis. These methods identified diverse chemical currencies mediating carbon transfer including low molecular weight metabolites (nucleosides, amino acids, organic acids, monomeric sugars, peptides, and sulfonates) and components of polysaccharides (chrysolaminarin, chitin oligomers, and alginate-like oligosaccharides). Bacterial utilization of bioreactive metabolites in the absence of competition indicated low resource overlap among strains and a dominance of resource partitioning over resource competition among the bacterial groups that process a major fraction of marine net primary production.</p><p><br></p><p><strong>NMR assay</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS1544' rel='noopener noreferrer' target='_blank'><strong>MTBLS1544</strong></a></p><p><strong>UPLC-MS assay</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1751' rel='noopener noreferrer' target='_blank'><strong>MTBLS1751</strong></a></p>
2020-09-15 | MTBLS1544 | MetaboLights
Project description:<p>The communities of marine bacteria that assemble around living microphytoplankton are predictably dominated by three taxonomic groups, each of which specializes in different components of the available metabolite pool: Rhodobacterales transport small and polar metabolites, Flavobacteriia use carbohydrate-rich polymers, and Gammaproteobacteria use compounds from both classes. The consistent ecological pattern involving these three taxa is widespread throughout the surface ocean, yet whether it reflects the outcome competition or niche partitioning of the phytoplankton-derived compounds is not clear. Addressing this question requires better knowledge than currently exists of the metabolites that link microbial autotrophs and heterotrophs in the surface ocean. Here we used two untargeted biological screening strategies that leverage bacterial proficiency for scavenging dilute substrates from chemically complex mixtures to characterize metabolite uptake by heterotrophic bacteria. In the first, expression patterns of transporters and diagnostic catabolic genes were analyzed in model marine bacteria grown individually in co-culture with the diatom Thalassiosira pseudonana. In the second, the ability of bacteria to draw down exometabolites from the culture medium was detected by novel approaches in mass spectrometry (MS) and nuclear magnetic resonance (NMR) analysis. These methods identified diverse chemical currencies mediating carbon transfer including low molecular weight metabolites (nucleosides, amino acids, organic acids, monomeric sugars, peptides, and sulfonates) and components of polysaccharides (chrysolaminarin, chitin oligomers, and alginate-like oligosaccharides). Bacterial utilization of bioreactive metabolites in the absence of competition indicated low resource overlap among strains and a dominance of resource partitioning over resource competition among the bacterial groups that process a major fraction of marine net primary production.</p><p><br></p><p><strong>UPLC-MS assay</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS1751' rel='noopener noreferrer' target='_blank'><strong>MTBLS1751</strong></a></p><p><strong>NMR assay</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS1544' rel='noopener noreferrer' target='_blank'><strong>MTBLS1544</strong></a></p>
2020-09-15 | MTBLS1751 | MetaboLights