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sequencing cost  (10X Genomics)

 
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    10X Genomics sequencing cost
    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 <t>\documentclass[12pt]{minimal}</t> \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.
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    1) Product Images from "A realistic FastQ-based framework FastQDesign for ScRNA-seq study design issues"

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

    Journal: Communications Biology

    doi: 10.1038/s42003-025-07938-8

    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.
    Figure Legend 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.

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    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 <t>\documentclass[12pt]{minimal}</t> \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.
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    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 <t>\documentclass[12pt]{minimal}</t> \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.
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    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 <t>\documentclass[12pt]{minimal}</t> \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.
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    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 <t>\documentclass[12pt]{minimal}</t> \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.
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    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.

    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: