Hot phenol
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE3684 | GEO | 2005/12/01
SECONDARY ACCESSION(S): PRJNA93825
REPOSITORIES: GEO
Similar Datasets
Project description:Determine differences between RNA isolation methods. Total RNA was isolated from yeast cells in stationary-phase cultures using three different isolation methods. All experimental samples are over an common reference. There are two replicates for each sample.
2010-06-30 | E-GEOD-3684 | biostudies-arrayexpress
Project description:In this study we used transgenic mouse model to comapre two isolation techniques INTACT and FANS for the isolation of activated neuronal nuclei. Comparison is perfomed on multiple levels like isolation efficiency, membrane integrity, transcriptional and epigenetic state using RNA-seq and ATAC-seq
2021-01-28 | GSE165644 | GEO
Project description:We compared the gene expression analysis of 2 different glomerular isolation techniques (laser capture microdissection with 2 rounds of RNA amplification and unamplified glomerular RNA after iron perfusion with glomerular sieving) and obtained different results depending on the glomerular isolation technique that was used Keywords: time course
2007-09-11 | GSE8998 | GEO
Project description:Extracellular vesicles (EVs) have gained significant attention in the field of extracellular communication, holding promise as intercellular messengers and diagnostic biomarkers. However, the challenges in isolating and purifying EVs from complex biological samples have hindered their widespread utility. This study presents a novel EV isolation strategy leveraging bioinformatics, utilizing the pH-low insertion peptide (pHLIP) to capture and release EVs under controlled conditions. The pHLIP-magnetic bead approach was developed to achieve efficient EV isolation, addressing the persistent issue of EV isolation method comparability. EVs from human plasma were isolated and characterized using various techniques, offering insights into the proposed isolation method's efficacy. A data science-driven statistical metric integrating multiple characterizations was applied to enable direct comparisons between different isolation methods. Next generation sequencing was applied to examine how the observed RNA-population differences across isolated EVs may lead researchers to different conclusions. This research contributes to the advancement of reliable and rigorous EV isolation methods and their potential clinical applications.
2024-01-31 | GSE246925 | GEO
Project description:Isolation and identification of phenol degrading bacteria
| PRJEB31471 | ENA
Project description:RNA isolation and purification steps greatly influence the results of gene expression profiling. There are two commercially available products for whole blood RNA collection, PAXgene and Tempus blood collection tubes, and each comes with their own RNA purification method. We examined the impact of RNA isolation methods on gene expression profiles. We demonstrated that peripheral blood RNA isoaltion can critically impact differential expression results, particularly in the clinical setting where fold-change differences are typically small and there is inherent variability within biological corhorts Keywords: micorarray quality assurance
2008-10-30 | GSE12710 | GEO
Project description:RNA isolation and purification steps greatly influence the results of gene expression profiling. There are two commercially available products for whole blood RNA collection, PAXgene and Tempus blood collection tubes, and each comes with their own RNA purification method. We examined the impact of RNA isolation methods on gene expression profiles. We demonstrated that peripheral blood RNA isoaltion can critically impact differential expression results, particularly in the clinical setting where fold-change differences are typically small and there is inherent variability within biological corhorts Keywords: micorarray quality assurance, phytohemagglutinin (PHA)
2008-10-30 | GSE12709 | GEO
Project description:Advances over the past decade have allowed for increasingly fine-grained labeling and isolation of rare cell samples for transcriptomic analysis, providing new insights into cell function and gene regulation. These samples often contain very little RNA for sequencing, and so have required new techniques to capture and amplify transcripts of interest. However, as new tools are developed, they are often optimized for mammalian samples. Thus, it is unclear for invertebrate samples what the best practices are for library preparation, and how differences in library preparation approaches affect final results. Here we compared two commercially available techniques: a commonly used polyA selection approach, and a newly developed ribodepletion approach, for which we designed a unique C. elegans-specific probe set. We performed a detailed comparison on multiple RNA samples and developed novel analysis methods to compare the results. Our analysis identifies clear strengths and weaknesses for both of these approaches in building libraries from low abundance RNA samples in C. elegans. We find that the polyA approach is superior in both percent reads mapped and rRNA removal, while the ribodepletion approach provides better detection for long and noncoding RNAs along with increased certainty of calling expression for low abundance transcripts. These insights will help guide researchers in designing future experiments in transcriptomics and provide a model for comparative analysis of library-building techniques.
2021-01-30 | GSE165793 | GEO
Project description:Recent methodological advances allowed the identification of an increasing number of RNAbinding proteins (RBPs) and their RNA-binding sites. RNA interactome capture is, however, limited to proteins interacting with polyadenylated RNAs while RBPs associating with nonadenylate RNA classes cannot be purified. Moreover, the vast majority of species that lack poly-A tails in their mRNAs (including all archea and bacteria) are not amenable to RNA interactome capture studies. To overcome these limitations, we have developed a novel protocol, Phenol Toluol extraction (PTex), that does not rely on a specific RNA sequence or motif for isolation of cross-linked ribonucleoproteins (RNPs), but rather purifies them based entirely on their physicochemical properties. PTex captures RBPs that bind to poly-A RNA, but also proteins associating with non-adenylate RNA species (rRNA, tRNA) as short as 30nt. PTex can be used to simplify complex work ows such as PAR-CLIP and reliably recovers RBPs from tissues and bacteria thus significantly expanding the experimental toolbox to species that could previously not be assessed experimentally.
2019-03-12 | PXD009571 | Pride