Extraction of high quality total RNA from liquid nitrogen stocks
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE30819 | GEO | 2012/12/25
SECONDARY ACCESSION(S): PRJNA144201
REPOSITORIES: GEO
Similar Datasets
Project description:Microarray expression arrays on THP-1 acute myeloid leukemia cell line samples, contrasting expression profiles of freshly harvested cell pellets, cells replated into fresh media for 24 hours and cells directly pelleted from liquid nitrogen stocks. Nine samples were analysed, composed of 3 biological replicates for each state (fresh, replated, frozen)
2012-12-25 | E-GEOD-30819 | biostudies-arrayexpress
Project description:Fuel surrogates are mixtures that mimic the properties of real fuels with only a small number of components, simplifying the calculation and simulation of fuel-related processes. This work extends a previously published surrogate optimization algorithm toward the generation of fuel surrogates with a focus on liquid-liquid extraction characteristics. For this purpose, experimental liquid-liquid equilibrium data from batch extraction experiments are incorporated into the calculation procedure as an additional constraint. The use of the method is demonstrated by optimizing a surrogate for the catalytic reformate. Application of the surrogate to an extraction process and comparison with experimental data demonstrate that the resulting surrogate accurately depicts the properties of the real mixture with regard to liquid-liquid extraction performance. This demonstrates that the use of such surrogates is of particular interest for mixtures used as extracting agents for biofuels.
| S-EPMC10753540 | biostudies-literature
Project description:Liquid nitrogen frozen rumen fluid Raw sequence reads
| PRJNA739062 | ENA
Project description:In order to identify patterns of gene expression associated with biological effects in THP-1 cells induced by F3, we performed a transcriptomic analysis on the THP-1 control and F3-treated THP-1 cells by oligonucleotide microarray Experiment Overall Design: 10^7 cells/mL concentrations of THP-1 cells were seeded in 100 mm dish and incubated overnight. After that, cells were treated with F3 at a final concentration of 30 ug/mL. After incubated for 6 and 24 hours, the cell pellets were collected by centrifugation at 250g for 5 min, correspondingly. Controlled samples of un-induced cells were treated in the same way with the same amount of medium.
2009-05-16 | E-GEOD-16014 | biostudies-arrayexpress
Project description:Proteomics and metabolomics are essential in systems biology, and simultaneous proteo-metabolome liquid-liquid extraction (SPM-LLE) allows isolation of the metabolome and proteome from the same sample. Since the proteome is present as a pellet in SPM-LLE, it must be solubilized for quantitative proteomics. Solubilization and proteome extraction are critical factors in the information obtained at the proteome level. In this study, we investigated the performance of two surfactants (sodium deoxycholate (SDC), sodium dodecyl sulfate (SDS)) and urea in terms of proteome coverage and extraction efficiency of an interphase proteome pellet generated by methanol-chloroform based SPM-LLE. We also investigated how the performance differs when the proteome is extracted from the interphase pellet or by direct cell lysis. We quantified 12 lipids covering triglycerides and various phospholipid classes, and 25 polar metabolites covering central energy metabolism in chloroform and methanol extracts. Our study reveals that the proteome coverages between the two surfactants and urea for the SPM-LLE interphase pellet were similar, but the extraction efficiencies differed significantly. While SDS led to enrichment of basic proteins, which were mainly ribosomal and ribonuclear proteins, urea was the most efficient extraction agent for simultaneous proteo-metabolome analysis. The results of our study also show that the performance of surfactants for quantitative proteomics is better when the proteome is extracted through direct cell lysis rather than an interphase pellet. In contrast, the performance of urea for quantitative proteomics was significantly better when the proteome was extracted from an interphase pellet than by direct cell lysis. We demonstrated that urea is superior to surfactants for proteome extraction from SPM-LLE interphase pellets, with a particularly good performance for the extraction of proteins associated with metabolic pathways. Data are available via ProteomeXchange with identifier PXD027338.
| S-EPMC9990123 | biostudies-literature
Project description:Mangroves and salt marsh species are known to synthesize a wide spectrum of polysaccharides and polyphenols including flavonoids and other secondary metabolites which interfere with the extraction of pure genomic DNA. Although a plethora of plant DNA isolation protocols exist, extracting DNA from mangroves and salt marsh species is a challenging task. This study describes a rapid and reliable cetyl trimethylammonium bromide (CTAB) protocol suited specifically for extracting DNA from plants which are rich in polysaccharides and secondary metabolites, and the protocol also excludes the use of expensive liquid nitrogen and toxic phenols. Purity of extracted DNA was excellent as evident by A260/A280 ratio ranging from 1.78 to 1.84 and A260/A230 ratio was >2, which also suggested that the preparations were sufficiently free of proteins and polyphenolics/polysaccharide compounds. DNA concentration ranged from 8.8 to 9.9 μg μL(-1). The extracted DNA was amenable to RAPD, restriction digestion, and PCR amplification of plant barcode genes (matK and rbcl). The optimized method is suitable for both dry and fresh leaves. The success of this method in obtaining high-quality genomic DNA demonstrated the broad applicability of this method.
| S-EPMC4890884 | biostudies-literature
Project description:OVCAR3 and CCL218 cells were passaged in the presence or absence of hydroxychloroquine. Drug pulse chases were used, with 48h of drug exposure followed by replacement of fresh media. Cells were allowed to grow to near confluence and then another drug pulse-chase was performed. After 15 hydroxychloroquine pulse-chases, cells were allowed to proliferate for 7 days in drug-free media so that transient drug effects were no longer present. Cells were then pelleted and cell pellets were processed for concomitant bulk RNA-seq, whole-exome-sequencing, and single-cell RNA-seq. This project represents the bulk transcriptomic sequencing and analysis.
2024-03-18 | GSE245133 | GEO
Project description:Microfluidic platforms provide several advantages for liquid-liquid extraction (LLE) processes over conventional methods, for example with respect to lower consumption of solvents and enhanced extraction efficiencies due to the inherent shorter diffusional distances. Here, we report the development of polymer-based parallel-flow microfluidic platforms for LLE. To date, parallel-flow microfluidic platforms have predominantly been made out of silicon or glass due to their compatibility with most organic solvents used for LLE. Fabrication of silicon and glass-based LLE platforms typically requires extensive use of photolithography, plasma or laser-based etching, high temperature (anodic) bonding, and/or wet etching with KOH or HF solutions. In contrast, polymeric microfluidic platforms can be fabricated using less involved processes, typically photolithography in combination with replica molding, hot embossing, and/or bonding at much lower temperatures. Here we report the fabrication and testing of microfluidic LLE platforms comprised of thiolene or a perfluoropolyether-based material, SIFEL, where the choice of materials was mainly guided by the need for solvent compatibility and fabrication amenability. Suitable designs for polymer-based LLE platforms that maximize extraction efficiencies within the constraints of the fabrication methods and feasible operational conditions were obtained using analytical modeling. To optimize the performance of the polymer-based LLE platforms, we systematically studied the effect of surface functionalization and of microstructures on the stability of the liquid-liquid interface and on the ability to separate the phases. As demonstrative examples, we report (i) a thiolene-based platform to determine the lipophilicity of caffeine, and (ii) a SIFEL-based platform to extract radioactive copper from an acidic aqueous solution.
| S-EPMC4167834 | biostudies-literature
Project description:The less polar phase of liquid-liquid extraction systems has been studied extensively for improving metal separations; however, the role of the more polar phase has been overlooked for far too long. Herein, we investigate the extraction of metals from a variety of polar solvents and demonstrate that, the influence of polar solvents on metal extraction is so significant that extraction of many metals can be largely tuned, and the metal separations can be significantly enhanced by selecting suitable polar solvents. Furthermore, a mechanism on how the polar solvents affect metal extraction is proposed based on comprehensive characterizations. The method of using suitable polar solvents in liquid-liquid extraction paves a new and versatile way to enhance metal separations.
| S-EPMC6771523 | biostudies-literature
Project description:We report the investigation of dicopper(II) bistren cryptate, containing naphthyl spacers between the tren subunits, as a receptor for polycarboxylates in neutral aqueous solution. An indicator displacement assay for dicarboxylates was also developed by mixing the azacryptate with the fluorescent indicator 5-carboxyfluorescein in a 50:1 molar ratio. Fluorimetric studies showed a significant restoration of fluorophore emission upon addition of fumarate anions followed by succinate and isophthalate. The introduction of hexyl chains on the naphthalene groups created a novel hydrophobic cage; the corresponding dicopper complex was investigated as an extractant for dicarboxylates from neutral water into dichloromethane. The liquid-liquid extraction of succinate-as a model anion-was successfully achieved by exploiting the high affinity of this anionic guest for the azacryptate cavity. Extraction was monitored through the changes in the UV-visible spectrum of the dicopper complex in dichloromethane and by measuring the residual concentration of succinate in the aqueous phase by HPLC-UV. The successful extraction was also confirmed by 1H-NMR spectroscopy. Considering the relevance of polycarboxylates in biochemistry and in the environmental field, e.g., as waste products of industrial processes, our results open new perspectives for research in all contexts where recognition, sensing, or extraction of polycarboxylates is required.
| S-EPMC7581268 | biostudies-literature