Magnoliopsida
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB14113 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Effect of degenerate oligonucleotide primed PCR primer designs
| PRJNA269286 | ENA
Project description:Application of MIG-seq fora plant species including crops.
| PRJDB12735 | ENA
Project description:For microarray experiments starting with nanogram amounts of RNA it is essential to implement reproducible and powerful RNA amplification techniques. Available methods were mainly tested for reproducibility, only a few studies concentrated on potential amplification bias. We evaluated three amplification protocols, which are less time-consuming than the commonly used T7-RNA polymerase based in vitro transcription protocols and therefore may be more suitable for clinical use: Template Switching (TS)-PCR (SMART-PCR Kit, BD), Ribo-SPIA (single primer isothermal amplification, Oviation, Nugen) and a random primer-based PCR. Additionally a more sensitive labeling method, Dendrimer-labeling (Genisphere), was evaluated. All methods were compared to unamplified RNA labelled at reverse transcription. Hybridizations were carried out on a targeted two-colour oligonucleotide microarray. From our results we conclude that RNA amplification with TS-PCR is highly reproducible and results in a reliable representation of the starting RNA population. We then assessed whether RNA amplification of clinical breast and thyroid cancer samples with TS-PCR showed robust performance when altered cycle numbers or partially degraded RNA were used. According to our experiments TS-PCR proved to be a very reliable method for global RNA amplification, even when starting from partially degraded RNA down to a RNA Integrity Number (RIN) of 4.3. Keywords: microarray expression profiling, RNA amplification techniques, RNA integrity
2007-08-24 | GSE5588 | GEO
Project description:Microbiome PCR primer model is a Named Entity Recognition (NER) model that identifies and annotates microbiome target gene primers in texts. This is the final model version used to annotate metagenomics publications in Europe PMC and enrich metagenomics studies in MGnify with primer metadata from literature. For more information, please refer to the following blogs: http://blog.europepmc.org/2020/11/europe-pmc-publications-metagenomics-annotations.html https://www.ebi.ac.uk/about/news/service-news/enriched-metadata-fields-mgnify-based-text-mining-associated-publications
2022-02-21 | MODEL2202170011 | BioModels
Project description:Salmonella typhimurium 14028s invA::cam Transposon library recovered from spleen 2 days after IP passage of 2.2 x 10^6 through BALB/c mouse, compared to the initial Transposon library grown in LB broth (kanamycin 50ug/ml), O/N at 37°C with aeration Keywords: Transposon tag analysis 6 biological replicates analysed after arbitrarily primed sampling (Klenow, DOPR degenerate primer) + specific PCR amplification (Taq DNA Pol) + T7 in vitro transcription (AmpliScribe T7) + RT labeling (Cy3) + hybridization, compared to identically processed standard library (Cy5)
2008-08-31 | E-GEOD-7059 | biostudies-arrayexpress
Project description:The disruption of cholesterol homeostasis leads to an increase in cholesterol levels which results in the development of cardiovascular disease. Mitogen Inducible Gene 6 (Mig-6) is an immediate early response gene that can be induced by various mitogens, stresses, and hormones. To identify the metabolic role of Mig-6 in the liver, we conditionally ablated Mig-6 in the liver using the Albumin-Cre mouse model (Albcre/+Mig-6f/f; Mig-6d/d). Mig-6d/d mice exhibit hepatomegaly and fatty liver. Serum levels of total, LDL, and HDL cholesterol and hepatic lipid were significantly increased in the Mig-6d/d mice. The daily excretion of fecal bile acids was significantly decreased in the Mig-6d/d mice. DNA microarray analysis of mRNA isolated from the livers of these mice showed alterations in genes that regulate lipid metabolism, bile acid, and cholesterol synthesis, while the expression of genes that regulate biliary excretion of bile acid and triglyceride synthesis showed no difference in the Mig-6d/d mice compared to Mig-6f/f controls. These results indicate that Mig-6 plays an important role in cholesterol homeostasis and bile acid synthesis. Mice with liver specific conditional ablation of Mig-6 develop hepatomegaly and increased intrahepatic lipid and provide a novel model system to investigate the genetic and molecular events involved in the regulation of cholesterol homeostasis and bile acid synthesis. Defining the molecular mechanisms by which Mig-6 regulates cholesterol homeostasis will provide new insights into the development of more effective ways for the treatment and prevention of cardiovascular disease.
2011-08-31 | GSE31752 | GEO
Project description:Salmonella typhimurium 14028s Transposon library recovered after three consecutive rounds of growth to late log phase in M9 minimal medium (arabinose 0.4%) at 37°C with aeration, compared to an expansion of the initial library selected on Luria agar plates + kanamycin (50ug/ml), O/N at 37°C Keywords: Transposon tag analysis 2 biological replicates analysed after arbitrarily primed sampling (Klenow, DOPR degenerate primer) + specific PCR amplification (Taq DNA Pol) + T7 in vitro transcription (AmpliScribe T7) + RT labeling (Cy3) + hybridization, compared to identically processed standard library (Cy5)
2010-06-20 | E-GEOD-7058 | biostudies-arrayexpress
Project description:The challenge of discovering a completely new human tumor virus of unknown phylogeny or sequence depends on detecting viral molecules and differentiating them from host-derived molecules in the virus-associated neoplasm. We developed differential peptide subtraction (DPS) using differential mass-spectrometry (dMS) followed by targeted analysis to facilitate this discovery. To trace the non-human dMS identified peptides back to its genetic origin by next generation sequencing (NGS) cDNA libraries were generated using degenerate oligos corresponding to the identified peptides. In a pilot study DPS identified both viral and human biomarkers. Based on the identified peptides that are differentially expressed in the virus positive tumor sample, degenerate oligos were designed. Degenerate oligos or LNA modified degenerate oligos or a modified oligo(dT) SMART primer were used to facilitate reverse transcription from viral or viral and host RNA. NGS analysis revealed seven times more MCV reads in degenerate oligo primed RNAseq samples compared to polyA-based sequencing reads.
2020-10-20 | GSE157610 | GEO