Project description:An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. To determine whether different RNA isolation kits biased detection of certain exRNA cargo types, an integrative analysis was performed using pooled plasma and serum samples, where 10 different RNA isolation kits were applied.

2018-12-15 | GSE123865 | GEO

Quality evaluation of Methyl Binding Domain based kits for enrichment DNA-methylation sequencing

2013-01-23 | GSE42790 | GEO

Rapid DNA and RNA isolation from few or single cells using low-cost NAxtra magnetic nanoparticles

Project description:A low-cost nucleic acid (NA) isolation method for purification of total NA, DNA or RNA from two- or three-dimensional cell culture was recently developed at the Norwegian University of Science and Technology (NTNU) based on NAxtra magnetic nanoparticles. The method displayed similar yields to alternative isolation kits, as well as significant improvement in cost and speed. In molecular research, NA isolation from rare or single cells is of increasing interest. Here, we improved the sensitivity of the NAxtra-based NA isolation method to allow mid- to high-throughput purification from 10 000 cells down to single cells. Automated processing on KingFisher (Thermo Scientific) robot systems can be performed in 12-18 minutes for 96 samples. This method is considerably cheaper and faster than similar purification alternatives, while achieving comparable or superior detection by (RT)-qPCR. In addition, high-quality transcriptomics data can be obtained from RNA extracted from few or single cells.

2025-07-09 | GSE284534 | GEO

Homo sapiens whole blood infected with Candida spp. (here: Candida parapsilosis)

Project description:Homo sapiens fresh whole blood was infected with Candida parapsilosis. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Measurement of Homo sapiens gene expression.

2018-12-26 | GSE114177 | GEO

Homo sapiens whole blood infected with Candida spp. (here: Candida albicans)

Project description:Homo sapiens fresh whole blood was infected with Candida albicans SC5314. RNA-pool of both species extracted at 0min (control), 15, 30, 60, 120, 240 min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.

2018-12-26 | GSE114174 | GEO

Quality evaluation of Methyl Binding Domain based kits for enrichment DNA-methylation sequencing

Project description:Purpose: to compare different Methyl Binding Domain (MBD) based kits for DNA-methylation sequencing using Reduced Representation Bisulfite Sequencing (RRBS) data for validation, and to determine whether data quality can also be derived from inherent sequence data characteristics MBD-seq using 5 different kits (MethylCap, MethylCollector, MethylCollector Ultra, MethylMiner, MethylMagnet) was applied on 3 commonly used cell lines (DU145, HCT15, PC3), for which also RRBS data were generated.

2013-01-23 | E-GEOD-42790 | biostudies-arrayexpress

Gentle, Effective, and Timely Isolation of Extracellular Vesicles that is Amenable for Transcriptomics Using Next-Generation Aqueous Two-Phase System Technology

Project description:The isolation of extracellular vesicles (EVs) using currently available methods frequently compromises purity and yield to prioritize speed. Here, we present a next generation aqueous two-phase system (ATPS) for isolation of EVs regardless of scale and volume and is superior to conventional methods such as ultracentrifugation and commercial kits. This is made possible by the two aqueous phases, one rich in polyethylene glycol (PEG), and the other rich in dextran (DEX), whereby fully encapsulated lipid vesicles preferentially migrate to the DEX-rich phase to achieve a local energy minimum for the EVs. Isolated EVs as found in the DEX-rich phase are more amenable to biomarker analysis such as nanoscale flow cytometry when using various pre-conjugated antibodies specific for CD9, CD63, and CD81. TRIzol RNA isolation is further enabled by the addition of Dextranase, a critical component of this next generation ATPS method. This negates the use of specialized EV RNA extraction kits. The use of Dextranase also enables more accurate immunoreactivity of pre-conjugated antibodies for detection of EVs by nanoscale flow cytometry. Transcriptomics of isolated EVs with ATPS revealed strong overlap between micro RNA (miRNA), circular RNA (circRNA), and small nucleolar RNA (snoRNA) profiles of EVs isolated compared to UC and was superior to other kits. Overall, this ATPS method stands out as a rapid and highly effective approach to isolate EVs, ensuring optimal extraction and analysis of nucleic acids.

2025-03-26 | GSE269052 | GEO

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