Journal: Journal of Biomolecular Techniques : JBT

Article Title: Benchmarking Single-Cell mRNA–Sequencing Technologies Uncovers Differences in Sensitivity and Reproducibility in Cell Types With Low RNA Content

doi: 10.7171/3fc1f5fe.dbeabb2a

Figure Lengend Snippet: Testing overview for SSsc and SSlp kits. For all testing schema, sample preparation was followed by library preparation, Illumina sequencing, and analysis using Cogent AP software. (A) Workflow for testing cultured cells (GM12878 and CHO cells) isolated by Fluorescence-activated cell sorting (FACS). This workflow was used for a performance comparison between SSsc and SS2 and for verifying compatibility with miniaturized volumes on the MANTIS (Formulatrix) and mosquito (SPT Labtech) (Figs. 2 and 5). (B) Workflow for performance comparison between SSsc and SS3. CD3+ T cells were isolated from human PBMCs by FACS, and the appropriate user manual or protocol was followed for RNA isolation (Fig. 3). (C) Workflow for performance comparison between SSsc PLUS (SSsc + SSlp) and Nextera XT using isolated RNA (control mouse brain RNA; Fig. 4).

Article Snippet: Outliers are plotted as empty circles. ( C ) Gene counts for transcripts per million (TPM) > 0.1 with SSsc PLUS compared with Nextera XT [ n = 6; medians = 14,643 (SSlp) and 14,494 (Nextera XT)]. ( D ) Representative x - y plots of 2 example libraries from the same cDNA prepared with SSsc PLUS or Nextera XT in duplicate and the same cDNA library compared between Nextera XT and PLUS.

Techniques: Sample Prep, Illumina Sequencing, Software, Cell Culture, Isolation, Fluorescence, FACS, Comparison, Control

Journal: Journal of Biomolecular Techniques : JBT

Article Title: Benchmarking Single-Cell mRNA–Sequencing Technologies Uncovers Differences in Sensitivity and Reproducibility in Cell Types With Low RNA Content

doi: 10.7171/3fc1f5fe.dbeabb2a

Figure Lengend Snippet: Comparing library preparation of Nextera XT and SSsc PLUS. A) Higher library yields for SSsc PLUS (n = 6 for each; median = 10.5 and 55.4 nM, respectively). The boxes denote the interquartile range (IQR) (i.e., the 25th and 75th quartiles); the whiskers are 1.5´ IQR from the median value and represent the extremes of the data. Outliers are plotted as empty circles. (B) Comparable distribution of reads for major genomic categories (i.e., mitochondria, rRNA, intergenic, intronic, and exonic; n = 6). The boxes denote the IQR (i.e., the 25th and 75th quartiles); the whiskers are 1.5´ IQR from the median value and represent the extremes of the data. Outliers are plotted as empty circles. (C) Gene counts for transcripts per million (TPM) > 0.1 with SSsc PLUS compared with Nextera XT [n = 6; medians = 14,643 (SSlp) and 14,494 (Nextera XT)]. (D) Representative x-y plots of 2 example libraries from the same cDNA prepared with SSsc PLUS or Nextera XT in duplicate and the same cDNA library compared between Nextera XT and PLUS. R2 values are shown in the graph; Nextera XT R2 = 0.9961, PLUS R2 = 0.9978, and Nextera XT versus PLUS R2 = 0.9579.

Article Snippet: Outliers are plotted as empty circles. ( C ) Gene counts for transcripts per million (TPM) > 0.1 with SSsc PLUS compared with Nextera XT [ n = 6; medians = 14,643 (SSlp) and 14,494 (Nextera XT)]. ( D ) Representative x - y plots of 2 example libraries from the same cDNA prepared with SSsc PLUS or Nextera XT in duplicate and the same cDNA library compared between Nextera XT and PLUS.

Techniques: cDNA Library Assay

Journal: Journal of Biomolecular Techniques : JBT

Article Title: Benchmarking Single-Cell mRNA–Sequencing Technologies Uncovers Differences in Sensitivity and Reproducibility in Cell Types With Low RNA Content

doi: 10.7171/3fc1f5fe.dbeabb2a

Figure Lengend Snippet: Testing overview for SSsc and SSlp kits. For all testing schema, sample preparation was followed by library preparation, Illumina sequencing, and analysis using Cogent AP software. (A) Workflow for testing cultured cells (GM12878 and CHO cells) isolated by Fluorescence-activated cell sorting (FACS). This workflow was used for a performance comparison between SSsc and SS2 and for verifying compatibility with miniaturized volumes on the MANTIS (Formulatrix) and mosquito (SPT Labtech) (Figs. 2 and 5). (B) Workflow for performance comparison between SSsc and SS3. CD3+ T cells were isolated from human PBMCs by FACS, and the appropriate user manual or protocol was followed for RNA isolation (Fig. 3). (C) Workflow for performance comparison between SSsc PLUS (SSsc + SSlp) and Nextera XT using isolated RNA (control mouse brain RNA; Fig. 4).

Article Snippet: To compare reproducibility of library preparation between different samples using SSlp or Nextera XT, triplicate cDNA were first generated using SSsc from 10 pg of mouse brain RNA ( C ).

Techniques: Sample Prep, Illumina Sequencing, Software, Cell Culture, Isolation, Fluorescence, FACS, Comparison, Control

Journal: Journal of Biomolecular Techniques : JBT

Article Title: Benchmarking Single-Cell mRNA–Sequencing Technologies Uncovers Differences in Sensitivity and Reproducibility in Cell Types With Low RNA Content

doi: 10.7171/3fc1f5fe.dbeabb2a

Figure Lengend Snippet: Comparing library preparation of Nextera XT and SSsc PLUS. A) Higher library yields for SSsc PLUS (n = 6 for each; median = 10.5 and 55.4 nM, respectively). The boxes denote the interquartile range (IQR) (i.e., the 25th and 75th quartiles); the whiskers are 1.5´ IQR from the median value and represent the extremes of the data. Outliers are plotted as empty circles. (B) Comparable distribution of reads for major genomic categories (i.e., mitochondria, rRNA, intergenic, intronic, and exonic; n = 6). The boxes denote the IQR (i.e., the 25th and 75th quartiles); the whiskers are 1.5´ IQR from the median value and represent the extremes of the data. Outliers are plotted as empty circles. (C) Gene counts for transcripts per million (TPM) > 0.1 with SSsc PLUS compared with Nextera XT [n = 6; medians = 14,643 (SSlp) and 14,494 (Nextera XT)]. (D) Representative x-y plots of 2 example libraries from the same cDNA prepared with SSsc PLUS or Nextera XT in duplicate and the same cDNA library compared between Nextera XT and PLUS. R2 values are shown in the graph; Nextera XT R2 = 0.9961, PLUS R2 = 0.9978, and Nextera XT versus PLUS R2 = 0.9579.

Article Snippet: To compare reproducibility of library preparation between different samples using SSlp or Nextera XT, triplicate cDNA were first generated using SSsc from 10 pg of mouse brain RNA ( C ).

Techniques: cDNA Library Assay

Journal: Nucleus

Article Title: Chromatin accessibility: methods, mechanisms, and biological insights

doi: 10.1080/19491034.2022.2143106

Figure Lengend Snippet: DNA sequencing-based methods for mapping nucleosomes and/or chromatin accessibility.

Article Snippet: SMAC-Seq , Similar to Fiber-seq and SAMOSA, except that cells were treated with M.CviPI, M.EcoGII, and M.SssI. Long-read libraries were sequenced with Nanopore [ ]. , Shipony et al. 2020.

Techniques: Sequencing, Genome Wide, Produced, Sonication, Titration, Bisulfite Sequencing, Methylation, Enzyme-linked Immunosorbent Assay, Footprinting, In Vitro, Fluorescence, Microscopy, Modification, Binding Assay, High Throughput Screening Assay, Mass Spectrometry, Purification, Pulse Chase, In Vivo, ChIP-sequencing