Journal: Communications Biology

Article Title: A realistic FastQ-based framework FastQDesign for ScRNA-seq study design issues

doi: 10.1038/s42003-025-07938-8

Figure Lengend Snippet: a–c The UMAPs of the FastQ sample with 10% read depth of all cells, the UMI sample with 10% read depth of all cells, 10% cell and total read depth, were colored with the consistency of cell clustering match with the reference. d–f The pairwise minimal p-value 's of each gene among the clusters from the samples and the reference, x is \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$-\log 10(p\_val\_adj)$$\end{document} − log 10 ( p _ v a l _ a d j ) in the reference, y is the same value in the sample, only the significant DE genes in either reference or samples are shown. g–i The pairwise minimal p-value 's of each gene between the condition within the cluster from the samples and the reference, only the significant DE genes in either reference or samples are shown. j, k The impact of varying read depth, and cell numbers on ARI and Jaccard indexes, 10 simulations were conducted at each setting.

Article Snippet: The overall cost \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$g({N}^{{\prime} },{R}^{{\prime} })$$\end{document} g ( N ′ , R ′ ) for a 10X Genomics experiment is composed of library preparation cost( C p r e p ), and the sequencing cost( C s e q ) for a flow cell with the read capacity of a . Library preparation: Multiple samples can be prepared in the same library by using feature barcode technology (CellPlex kit).

Techniques:

Journal: Scientific Reports

Article Title: A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

doi: 10.1038/s41598-019-51997-x

Figure Lengend Snippet: Results of the experimentally determined composition of the MOCK Community (MC) at ( a ) family and ( b ) genus level with MinION and Illumina NGS techniques. The results are based on 16S rRNA amplicon sequencing. Experimentally determined 16S rRNA gene percentage abundance are compared against the actual composition of the MC as reported by the supplier (i.e. Zymo Research). Data points are an average of duplicate samples for Illumina and triplicate samples for MinION sequencing. Error bars indicate the standard deviation.

Article Snippet: At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results.

Techniques: Amplification, Sequencing, Standard Deviation

Journal: Scientific Reports

Article Title: A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

doi: 10.1038/s41598-019-51997-x

Figure Lengend Snippet: Molecular microbiology analysis of water samples from different water sources in the Kathmandu Valley. Numbers on the x-axis indicate the ID of the different sampling sites as described in Table . Data points for qPCR results are an average of technical triplicate samples and error bars indicate the standard deviation. Data points for Illumina NGS sequencing are an average of duplicate samples and error bars indicate the standard deviation. Library preparation for MinION NGS was unsuccessful for the sample from location 10 and thus data are not available (n.a), while the DNA extraction yield for the blank was too low for NGS, and for the sample from location 1, the yield was too low for all molecular microbiology methods.

Article Snippet: At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results.

Techniques: Sampling, Standard Deviation, Sequencing, DNA Extraction

Journal: Scientific Reports

Article Title: A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

doi: 10.1038/s41598-019-51997-x

Figure Lengend Snippet: Result of correlation analysis between different microbial water quality indicators determined with different methods: plate count, qPCR and NGS ( A : Illumina and B : MinION). The colour intensities of circles are proportional to the correlation coefficients (Spearman rank correlation, p < 0.05, n = 12), and the circled numbers represents statistically significant coefficients.

Article Snippet: At family and genera level, 16S rRNA amplicon sequencing results obtained with the low-cost, portable next generation sequencer MinION from Oxford Nanopore Technologies had significant Spearman rank correlations with Illumina MiSeq sequencing results.

Techniques: