Ontology highlight
ABSTRACT:
PROVIDER: PRJEB33499 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3434000.fastq.gz | Fastqsanger.gz | |||
| ERR3434010.fastq.gz | Fastqsanger.gz | |||
| ERR3434020.fastq.gz | Fastqsanger.gz | |||
| ERR3434030.fastq.gz | Fastqsanger.gz | |||
| ERR3434040.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 106 |
Similar Datasets
Project description:Extracellular vesicles (EVs) have emerged as a promising source of disease biomarkers for non-invasive early-stage diagnoses, but a bottleneck in EV sample processing restricts their immense potential in clinical applications. Existing methods are limited by low EV yield and integrity, slow processing speeds, low sample capacity, and poor recovery efficiency. We aimed to address these issues with a high-throughput, automated workflow for EV isolation, EV lysis, protein extraction, and protein denaturation. The automation can process clinical urine samples in parallel, resulting in protein-covered beads ready for various analytical methods, including immunoassays, protein quantitation assays, and mass spectrometry. Compared to the standard manual lysis method for contamination levels, efficiency, and consistency of EV isolation, the automated protocol shows reproducible and robust proteomic quantitation with less than 10% median coefficient of variation. When we applied the method to clinical samples, we identified a total 3,793 unique proteins and 40,380 unique peptides, with 992 significantly upregulated proteins in kidney cancer patients versus healthy controls. These upregulated proteins were found to be involved in several important kidney cancer metabolic pathways also identified with a manual control. This hands-free workflow represents a practical EV extraction and profiling approach that can benefit both clinical and research applications, streamlining biomarker discovery, tumor monitoring, and early cancer diagnoses.
2023-10-20 | PXD045192 | JPOST Repository
Project description:We report a universal detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which consists of three mandatory steps, acidification, neutralization and digestion. SPEED is a universal method for peptide generation from various sources and is easily applicable even for lysis-resistant sample types. The protocol is highly reproducible, virtually loss-less and enables very rapid sample processing. SPEED is superior to detergent/chaotropic agent-based methods for quantitative proteomics and enhances proteome coverage for challenging samples.
2019-11-25 | PXD011189 | Pride
Project description:We compared 3 small RNA library prep kits (CleanTag, NEXTflex, QIAseq) and two RNA extraction methods (miRNeasy and MagnaZol) on plasma. We report that library preparation has a significant effect upon the miRNA profile detected, with QIAseq libraries exhibiting the least sequencing bias of the three library kits. RNA extraction methods also contribute, to a lesser extent, to the miRNA profile detected, with MagnaZol RNA extraction increasing the percentage of reads mapping to miRNAs and the number of individual miRNAs detected.
2019-05-21 | GSE118125 | GEO
Project description:Proteomic methods typically involve lengthy, multi-step sample preparation protocols (14-16 hrs), especially for the lysis and digestion of solid tissue samples or cells. We developed a streamlined proteomic sample preparation protocol termed Accelerated Barocycler Lysis and Extraction (ABLE), that substantially reduces the time and cost of tissue sample processing. ABLE is based on pressure cycling technology (PCT) for rapid tissue solubilisation and reliable, controlled proteolytic digestion. Here, the previously reported PCT protocol was optimised using 1-4 mg biopsy punches from rat kidney. The tissue denaturant urea was substituted with a combination of sodium deoxycholate (SDC) and N-propanol. ABLE produced comparable numbers of protein identifications in half the sample preparation time and with reduced cost, being ready for MS injection in 3 hrs (vs the conventional urea PCT method of 6 hrs). To validate the method, it was applied across a diverse range of rat tissues (kidney, lung, muscle, brain, testis), human HEK 293 cells and ovarian tumours by coupling PCT with SWATH-mass spectrometry (SWATH-MS). There were similar numbers of quantified proteins between ABLE-SWATH and PCT-SWATH methods, with greater than 70% overlap for all sample types, except muscle with 58% overlap. The ABLE tissue processing protocol offers a standardised, high-throughput, efficient and reproducible proteomic preparation method, accelerating sample throughput for any type of MS analysis. Coupled with SWATH-MS, ABLE has the potential to accelerate proteomics analysis towards a clinically relevant turn-around-time.
2019-01-21 | PXD010688 | Pride
Project description:Metaproteome analysis of a forest soil and a potting soil. Different protein extraction methods were compared to investigate protein extraction efficiency and compatibility with sample downstream processing.
2015-03-26 | PRD000542 | Pride
Project description:Measuring the global gene expression pattern in a single cell has been technically challenging, but is potentially very useful for understanding variation in biological processes between cells and for studying gene regulation during early embryo development with single cell resolution. To advance these applications, multiple systems for single-cell RNA extraction in addition to crude cell lysis followed by RNA profiling were examined and used for genomic data analysis. Our results indicate that some of these methods are suitable for analyzing even a portion of the total RNA from a single oocyte or embryo, with low variance among technical replicates across a wide dynamic range of expression. These methods will not only be helpful for genomic and epigenetic research to identify regulatory mechanisms of early development and molecular signatures of embryo classes, but can also provide great potential for clinical analysis of small biopsy samples or pre-implantation genetic disease screening. RNA from single mouse oocytes was purified using Qiagen Rneasy Mini or Arcturus PicoPure kits. Crude lysates of single oocytes were also prepared in NuGEN direct lysis buffer. Three replicate oocytes for each of the three sample preparation methods were used. Total RNA was amplified by NuGEN Ovation One-Direct ribo-SPIA, cDNA products were biotinylated, and labeled targets were hybridized to Affymetrix Mouse Gene 1.0ST Arrays.
2012-01-06 | E-GEOD-26486 | biostudies-arrayexpress
Project description:The quality of milk metabolome analyzed by nuclear magnetic resonance (NMR) is greatly influenced by the way samples are prepared. Although this analytical method is increasingly used to study milk metabolites, a thorough examination of available sample preparation protocols for milk has not been reported yet. We evaluated the performance of eight milk preparation methods namely (1) raw milk without any processing; (2) skimmed milk; (3) ultrafiltered milk; (4) skimming followed by ultrafiltration; (5) ultracentrifuged milk; (6) methanol; (7) dichloromethane; and (8) methanol/dichloromethane, in terms of spectra quality, repeatability, signal-to-noise ratio, extraction efficiency and yield criteria. A pooled sample of milk was used for all protocols. Skimming, ultracentrifugation and unprocessed milk protocols showed poor NMR spectra quality. Protocols involving multiple steps, namely methanol/dichloromethane extraction, and skimming followed by ultrafiltration produced inadequate results for signal-to-noise ratio parameter. Methanol and skimming associated to ultrafiltration provided good repeatability results compared to the other protocols. Chemical-based sample preparation protocols, particularly methanol, showed more efficient metabolite extraction compared to physical preparation methods. When considering all evaluation parameters, the methanol extraction protocol proved to be the best method. As a proof of utility, methanol protocol was then applied to milk samples from dairy cows fed a diet with or without a feed additive, showing a clear separation between the two groups of cows.
2019-06-13 | MTBLS623 | MetaboLights