other · Figshare · 2020

Data set preprocessing and relevant parameters.

Allison Jevitt (8729008), Deeptiman Chatterjee (8770931), Gengqiang Xie (167638), Xian-Feng Wang (335223), Taylor Otwell (8729014), Yi-Chun Huang (42150), Wu-Min Deng (42151)

Cited by 0Open access

Abstract

<p>(A) Schematic for the scRNA-Seq analysis pipeline. (B) Violin plots for nGene, nUMI, and percent.mito for preprocessed data set (14,825 cells) and the final data set (7,053 cells). (C) Feature counts were log-normalized and scaled. Pre- and post-normalization plots are shown for total nUMIs and sum of gene expression counts. (D) Elbow Plot to show the ranking of the PCs based on the percentage of variance explained by each; 100 PCs have been computed for the final data set, 29 were selected for clustering, and 75 were selected for visualizing on the final UMAP shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3000538#pbio.3000538.g001" target="_blank">Fig 1B</a>. Raw sequence files available from SRA repository (SRX7814226). Processed files using Cell Ranger, Seurat, and Monocle are available through GEO database (GSE146040). nGene, number of genes; nUMI, number of unique molecular identifiers; percent.mito, percentage of mitochondrial gene expression; PC, principal component; scRNA-Seq, single-cell RNA sequencing; UMAP, Uniform Manifold Approximation Projection.</p> <p>(TIF)</p>

Cite this paper

APA 7

(8729008), A. J., (8770931), D. C., (167638), G. X., (335223), X.-F. W., (8729014), T. O., (42150), Y.-C. H., & (42151), W.-M. D. (2020). Data set preprocessing and relevant parameters. Figshare. https://doi.org/10.1371/journal.pbio.3000538.s003

MLA 9

(8729008), Allison Jevitt, et al. “Data set preprocessing and relevant parameters.” Figshare, 2020, https://doi.org/10.1371/journal.pbio.3000538.s003.

Chicago

(8729008), Allison Jevitt, Deeptiman Chatterjee (8770931), Gengqiang Xie (167638), Xian-Feng Wang (335223), Taylor Otwell (8729014), Yi-Chun Huang (42150), and Wu-Min Deng (42151). 2020. “Data set preprocessing and relevant parameters.” Figshare. https://doi.org/10.1371/journal.pbio.3000538.s003.

Harvard

(8729008), A.J. et al. (2020) ‘Data set preprocessing and relevant parameters’, Figshare. Available at: https://doi.org/10.1371/journal.pbio.3000538.s003.

BibTeX

@misc{87290082020data,
  title = {{Data set preprocessing and relevant parameters.}},
  author = {(8729008), Allison Jevitt and (8770931), Deeptiman Chatterjee and (167638), Gengqiang Xie and (335223), Xian-Feng Wang and (8729014), Taylor Otwell and (42150), Yi-Chun Huang and (42151), Wu-Min Deng},
  journal = {Figshare},
  year = {2020},
  doi = {10.1371/journal.pbio.3000538.s003}
}

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