Ontology highlight
ABSTRACT:
PROVIDER: PRJNA666749 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Performance Comparisons between Clustering Models for Reconstructing NGS Results from Technical Replicates
| PRJEB60499 | ENA
Project description:Reproducibility assessment is essential in extracting reliable scientific insights from high-throughput experiments. Inconsistency between technical replicates poses a challenge, particularly evident in NGS technologies based on immunoprecipitations, where the need for reproducibility in peak identification is a well-acknowledged limitation. While the Irreproducibility Discovery Rate (IDR) method has been instrumental in assessing reproducibility, its standard implementation is constrained to handling only two replicates. In the current era of steadly growing sample sizes, facilitated by multiplexing and reduced sequencing costs, highly performing methods that handle any number of replicates are desirable.
2024-01-03 | GSE248884 | GEO
Project description:Circulating tumor DNA (ctDNA) as a biomarker of disease activity in classic Hodgkin lymphoma (cHL) patients are still not well-defined. By profiling primary tumors and ctDNA, we identified common variants between primary tumors and longitudinal plasma samples in most of the cases, confirming high PBatial and temporal heterogeneity. Though ctDNA analyses mirrored HRS cell genetics overall, the prevalence of variants shows that none of them can be used as a single biomarker. Conversely, the estimation of hGE/mL, based in total ctDNA quantification, reflects disease activity and is almost perfectly correlated with standard parameters such as PET/CT that are associated with refractoriness.
2023-12-18 | GSE244989 | GEO
Project description:High-throughput single-cell RNA sequencing (scRNA-seq) workflows produce libraries that demand extensive sequencing. However, standard next-generation sequencing (NGS) methods remain expensive, contributing to the high running costs of single-cell experiments and often negatively affecting the sample numbers and statistical strength of such projects. In recent years, a plethora of new sequencing technologies have become available to researchers through several manufacturers, often providing lower-cost alternatives to standard NGS. In this study, we compared data generated from scRNA-seq libraries sequenced with both standard Illumina sequencing by synthesis (Illumina SBS) and MGI’s DNA nanoball sequencing (DNBSEQ). Our findings reveal similar overall performance using both technologies. DNBSEQ exhibited mildly superior sequence quality compared to Illumina SBS, as evidenced by higher Phred scores, lower read duplication rates, and a greater number of genes mapping to the reference genome. Yet, these improvements did not translate into meaningful differences in single-cell analysis parameters of our experiments, including detection of additional genes within cells, gene expression saturation levels, and numbers of identified cells, with both technologies demonstrating equally robust performance in these aspects. The data produced by both sequencing platforms also produced comparable analytical outcomes for single-cell analysis. No significant difference in the annotation of cells into different cell types was observed and the same top genes were differentially expressed between populations and experimental conditions. Overall, our data demonstrate that alternative technologies can be applied to sequence scRNA-seq libraries, generating virtually undiscernible results compared to standard methods, and providing cost-effective alternatives.
2025-09-01 | GSE277740 | GEO
Project description:Plasma proteomics has regained attention in recent years through advancements in mass spectrometry instrumentation and sample preparation, as well as new high-throughput affinity-based technologies. Here, we evaluate the analytical performance of the new Olink Reveal platform, a proximity extension assay based technology quantifying 1,034 proteins across biological pathways. Using spiked-in recombinant Interleukin-10 (IL-10) and vascular endothelial growth factor D (VEGF-D) in the NIST SRM 1950 plasma standard, we assessed the linearity, sensitivity, precision and accuracy of the Olink assay. The results demonstrated strong linear relationships (R² 0.922–0.953) for both IL-10 and VEGF-D across spiked-in concentrations, confirming the robust technical performance of Olink Reveal and underscoring its suitability for relative quantitation in large-scale studies. The resulting data contains no sensitive or personally identifiable information, and is available in public repositories, and therefore suitable for use in benchmarking and software development.
2025-06-03 | PAD000009 | Pride
Project description:The use of data-independent acquisition methods such as SWATH for mass spectrometry based proteomics is usually performed using peptide MS/MS reference ion assay libraries which enable identification and quantitation of peptide peak areas. Reference assay libraries can be generated locally through information dependent acquisition, or obtained from shared data repositories for commonly studied organisms. However, there have been no studies performed to systematically evaluate how locally-generated or repository-based assay libraries affect SWATH performance for proteomic studies. To undertake this analysis we developed a software workflow, SwathXtend, which generates extended peptide assay libraries using a local seed library and delivers statistical analysis of SWATH-based sample comparisons. We designed test samples using peptides from a yeast extract spiked into peptides from human K562 cell lysates at different ratios to simulate common protein abundance change comparisons. SWATH-MS data with 2, 5 and 10% of yeast peptides spiked into the human cell lysate were assessed using several local and repository-based assay libraries of different complexities and proteome compositions. We evaluated detection specificity and accuracy to detect differentially abundant proteins and reporting thresholds for statistical analyses. We demonstrate that extended assay libraries integrated with local seed libraries achieve better performance than local limited assay libraries alone from the aspects of the number of peptides and proteins identified and the specificity to detect differentially abundant proteins; the performance of extended assay libraries heavily depend on the similarity of the seed and add-on libraries; statistical analysis with multiple testing correction can improve the statistical rigor needed when using large, extended assay libraries.
2016-05-12 | PXD002836 | Pride
Project description:We evaluated the performance of ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) on formalin-fixed paraffin-embedded (FFPE) spleen samples from C57BL/6J mice. Nuclei were isolated from FFPE mouse spleen tissue, and ATAC-seq was performed at both the bulk and single-cell levels, with and without reverse crosslinking. The resulting datasets were compared to ATAC-seq and scATAC-seq profiles obtained from fresh spleen samples. Our analysis revealed a markedly reduced library complexity in FFPE-derived samples compared to fresh tissue, across both bulk and single-cell experiments. These findings highlight the technical limitations of applying standard ATAC-seq protocols to FFPE samples. Based on our results, we conclude that conventional ATAC-seq approaches are not well-suited for chromatin accessibility profiling in FFPE-preserved tissues.
2025-10-14 | GSE299388 | GEO
Project description:<p>The Nex-StoCT and ACMG recommend that validation of an NGS-based diagnostic test include performance test characteristics for assay accuracy, analytical sensitivity and specificity, reproducibility and repeatability. To measure these parameters for the GEDi capture and sequencing test, 4 samples (three randomly selected patient samples and the NA12878 HapMap sample) were prepared and sequenced in triplicate on each of three separate days. We also performed WES and SNP array genotyping analyses of these 4 samples using Agilent V4+UTR whole exome enrichment kit and Illumina Omni 2.5 SNP arrays, respectively.</p>
| phs000798 | dbGaP