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  • 99
    Thermo Fisher yeast bulk rna
    Yeast Bulk Rna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore bulk rna
    Bulk Rna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore bulk e coli trna
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    Bulk Rna, supplied by Roche, used in various techniques. Bioz Stars score: 89/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc bulk rna
    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    Bulk Rna, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 89/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    BGI Shenzhen rna bulks
    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    Rna Bulks, supplied by BGI Shenzhen, used in various techniques. Bioz Stars score: 86/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Agilent technologies bulk rna
    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    Bulk Rna, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 90/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Stratagene bulk rna sources
    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    Bulk Rna Sources, supplied by Stratagene, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    10X Genomics bulk rna seq data
    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    Bulk Rna Seq Data, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Biotechnology Information bulk rna seq datasets
    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    Bulk Rna Seq Datasets, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Data MATRIX bulk rna seq data
    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    Bulk Rna Seq Data, supplied by Data MATRIX, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc bulk rna seq data rna seq
    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    Bulk Rna Seq Data Rna Seq, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    Bulk Cortical Tissue Rna, supplied by NanoString Technologies Inc, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    N Reynei Gill Bulk Rna, supplied by SymBio, used in various techniques. Bioz Stars score: 85/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore bulk mrna
    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    Bulk Mrna, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore bulk rna alkylation k562 cells
    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    Bulk Rna Alkylation K562 Cells, supplied by Millipore, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Novogene bulk brain rnas
    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in <t>HeLa</t> S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk <t>RNA.</t> Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million
    Bulk Brain Rnas, supplied by Novogene, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Biotechnology Information bulk rna sequencing data
    Comparison of single-cell <t>RNA</t> sequencing, mass <t>cytometry,</t> and flow cytometry assessment of T lymphocyte frequencies in human bone marrow. ( A ) Mass cytometry for phenotyping of T cell populations visualized using viSNE analysis with expression of key markers shown. ( B ) Comparison of cell frequencies for each donor determined by mass cytometry (CyTOF) and flow cytometry. CM: central memory cells; EM: effector memory cells; TEMRA: terminally differentiated effector memory T cells; TE: effector T cells; DNT: double-negative T cells; DPT, double-positive T cells. ( C ) T cell frequencies for cell populations identified by mass cytometry, flow cytometry, and scRNA-Seq. Each dot represents a value from 1 sample. The thick line within each box represents median value. Box spans first to third quartile (IQR). Whiskers extend to the largest or smallest value no farther than 1.5 IQRs from the box. ( D ) Individual sample comparisons by scatter plot for each cell population. Each dot represents the cell subset frequency from 1 sample ( n = 8). All population comparisons are shown in the background in gray.
    Bulk Rna Sequencing Data, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    fluidigm bulk rna sequencing data
    Averaging gene expression estimates across all cells in single cell <t>RNA</t> sequencing shows good correspondence across platforms (A) Distribution of transcriptome coverage (# genes detected per cell) for <t>DropSeq</t> (left) and Fluidigm (right). (B) Correlation of averaged gene expression estimates between single molecule RNA FISH (smRNA FISH) and single cell RNA sequencing (scRNA-seq). (C) Correlation of average gene expression estimates between DropSeq and smRNA FISH at different levels of transcriptome coverage using four different population sizes (50, 250, 500, and 2000 cells). Error bars in (C) represent ± 1 standard deviation across bootstrap replicates. (D) Correlation of averaged gene expression estimates between sequencing platforms. Error bars in (B and D) represent two times the standard error of the mean (SEM).
    Bulk Rna Sequencing Data, supplied by fluidigm, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc stroma lcm bulk rna seq analysis illumina raw files
    Averaging gene expression estimates across all cells in single cell <t>RNA</t> sequencing shows good correspondence across platforms (A) Distribution of transcriptome coverage (# genes detected per cell) for <t>DropSeq</t> (left) and Fluidigm (right). (B) Correlation of averaged gene expression estimates between single molecule RNA FISH (smRNA FISH) and single cell RNA sequencing (scRNA-seq). (C) Correlation of average gene expression estimates between DropSeq and smRNA FISH at different levels of transcriptome coverage using four different population sizes (50, 250, 500, and 2000 cells). Error bars in (C) represent ± 1 standard deviation across bootstrap replicates. (D) Correlation of averaged gene expression estimates between sequencing platforms. Error bars in (B and D) represent two times the standard error of the mean (SEM).
    Stroma Lcm Bulk Rna Seq Analysis Illumina Raw Files, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 84/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc bulk rna sequencing libraries
    Averaging gene expression estimates across all cells in single cell <t>RNA</t> sequencing shows good correspondence across platforms (A) Distribution of transcriptome coverage (# genes detected per cell) for <t>DropSeq</t> (left) and Fluidigm (right). (B) Correlation of averaged gene expression estimates between single molecule RNA FISH (smRNA FISH) and single cell RNA sequencing (scRNA-seq). (C) Correlation of average gene expression estimates between DropSeq and smRNA FISH at different levels of transcriptome coverage using four different population sizes (50, 250, 500, and 2000 cells). Error bars in (C) represent ± 1 standard deviation across bootstrap replicates. (D) Correlation of averaged gene expression estimates between sequencing platforms. Error bars in (B and D) represent two times the standard error of the mean (SEM).
    Bulk Rna Sequencing Libraries, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 91/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in HeLa S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk RNA. Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million

    Journal: GigaScience

    Article Title: Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells

    doi: 10.1186/s13742-015-0091-4

    Figure Lengend Snippet: The landscape of the HPV-18/cellular fusion and diversity of HPV-host splicing and expression in HeLa S3 cells. a The overview of the HPV-18 cellular fusion based on HeLa cell transcriptome. Blue lines denote fusion events. b The read coverage of HPV-18 genome in single cells and the bulk RNA. Colored vertical lines denote nucleotides of SNPs detected in the transcriptome. Light green , A; red , T; orange , G; blue , C. c The read coverage of the host region on chromosome 8 in single cells and the bulk RNA. d The schematic diagram of the inferred HPV integration structure ( upper ) and splicing forms ( lower ). RPM stands for reads per million

    Article Snippet: All of the samples (40 single cells and five 10 pg total RNA replicates prepared by MIRALCS; and five single cells, three replicates 10 pg total RNA and one 5 ng bulk RNA from populations of HeLa S3 cells prepared by tube-based SMART-seq2 approach) were sequenced on Illumina HiSeq 2000 sequencing system.

    Techniques: Expressing

    Heterogeneity of gene expression in HeLa S3 single cells. a The mRNA molecular number in single cells and 10 pg RNA replicates. b The heat map of the FPKM values of extremely highly expressed genes (FPKM > 500 in bulk RNA) in single cells and 10 pg replicates. c Single-cell subpopulations identification based on cell cycle relative genes. The cells with underline are in G2/M phase. d Gene co-expression modules derived from 19 single cells based on RNA molecular number (modules are distinguished by colors). The detailed of each module stands for were shown on Additional file 4 : Table S7. The weighted gene correlation network was constructed using the WCGNA R package [ 38 ]

    Journal: GigaScience

    Article Title: Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells

    doi: 10.1186/s13742-015-0091-4

    Figure Lengend Snippet: Heterogeneity of gene expression in HeLa S3 single cells. a The mRNA molecular number in single cells and 10 pg RNA replicates. b The heat map of the FPKM values of extremely highly expressed genes (FPKM > 500 in bulk RNA) in single cells and 10 pg replicates. c Single-cell subpopulations identification based on cell cycle relative genes. The cells with underline are in G2/M phase. d Gene co-expression modules derived from 19 single cells based on RNA molecular number (modules are distinguished by colors). The detailed of each module stands for were shown on Additional file 4 : Table S7. The weighted gene correlation network was constructed using the WCGNA R package [ 38 ]

    Article Snippet: All of the samples (40 single cells and five 10 pg total RNA replicates prepared by MIRALCS; and five single cells, three replicates 10 pg total RNA and one 5 ng bulk RNA from populations of HeLa S3 cells prepared by tube-based SMART-seq2 approach) were sequenced on Illumina HiSeq 2000 sequencing system.

    Techniques: Expressing, Derivative Assay, Construct

    Comparison of single-cell RNA sequencing, mass cytometry, and flow cytometry assessment of T lymphocyte frequencies in human bone marrow. ( A ) Mass cytometry for phenotyping of T cell populations visualized using viSNE analysis with expression of key markers shown. ( B ) Comparison of cell frequencies for each donor determined by mass cytometry (CyTOF) and flow cytometry. CM: central memory cells; EM: effector memory cells; TEMRA: terminally differentiated effector memory T cells; TE: effector T cells; DNT: double-negative T cells; DPT, double-positive T cells. ( C ) T cell frequencies for cell populations identified by mass cytometry, flow cytometry, and scRNA-Seq. Each dot represents a value from 1 sample. The thick line within each box represents median value. Box spans first to third quartile (IQR). Whiskers extend to the largest or smallest value no farther than 1.5 IQRs from the box. ( D ) Individual sample comparisons by scatter plot for each cell population. Each dot represents the cell subset frequency from 1 sample ( n = 8). All population comparisons are shown in the background in gray.

    Journal: JCI Insight

    Article Title: Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry

    doi: 10.1172/jci.insight.124928

    Figure Lengend Snippet: Comparison of single-cell RNA sequencing, mass cytometry, and flow cytometry assessment of T lymphocyte frequencies in human bone marrow. ( A ) Mass cytometry for phenotyping of T cell populations visualized using viSNE analysis with expression of key markers shown. ( B ) Comparison of cell frequencies for each donor determined by mass cytometry (CyTOF) and flow cytometry. CM: central memory cells; EM: effector memory cells; TEMRA: terminally differentiated effector memory T cells; TE: effector T cells; DNT: double-negative T cells; DPT, double-positive T cells. ( C ) T cell frequencies for cell populations identified by mass cytometry, flow cytometry, and scRNA-Seq. Each dot represents a value from 1 sample. The thick line within each box represents median value. Box spans first to third quartile (IQR). Whiskers extend to the largest or smallest value no farther than 1.5 IQRs from the box. ( D ) Individual sample comparisons by scatter plot for each cell population. Each dot represents the cell subset frequency from 1 sample ( n = 8). All population comparisons are shown in the background in gray.

    Article Snippet: FCS files for flow cytometry and mass cytometry data sets have been deposited in FlowRepository (FR-FCM-ZYQ9, FR-FCM-ZYQB). scRNA-Seq and bulk RNA sequencing data sets have been deposited in the National Center for Biotechnology Information’s Gene Expression Omnibus (GSE120221, GSE120446).

    Techniques: RNA Sequencing Assay, Mass Cytometry, Flow Cytometry, Cytometry, Expressing

    Comparison of single-cell RNA sequencing and flow cytometry assessment of bone marrow cell type population frequencies from 22 samples (taken from 20 donors, including 2 biological replicates). ( A ) Frequencies for major cell populations in human bone marrow shown for single cell scRNA-Seq and flow cytometry. Each dot represents a value from 1 sample. The thick line within each box represents median value. Box spans first to third quartile (IQR). Whiskers extend to the largest or smallest value no farther than 1.5 IQRs from the box. ( B ) Individual sample comparisons by scatter plot for each cell population. Each dot represents the cell subset frequency from 1 sample. Population comparisons are shown in the background in gray. Population frequencies are reported as percentage of all CD45 + cells.

    Journal: JCI Insight

    Article Title: Human bone marrow assessment by single-cell RNA sequencing, mass cytometry, and flow cytometry

    doi: 10.1172/jci.insight.124928

    Figure Lengend Snippet: Comparison of single-cell RNA sequencing and flow cytometry assessment of bone marrow cell type population frequencies from 22 samples (taken from 20 donors, including 2 biological replicates). ( A ) Frequencies for major cell populations in human bone marrow shown for single cell scRNA-Seq and flow cytometry. Each dot represents a value from 1 sample. The thick line within each box represents median value. Box spans first to third quartile (IQR). Whiskers extend to the largest or smallest value no farther than 1.5 IQRs from the box. ( B ) Individual sample comparisons by scatter plot for each cell population. Each dot represents the cell subset frequency from 1 sample. Population comparisons are shown in the background in gray. Population frequencies are reported as percentage of all CD45 + cells.

    Article Snippet: FCS files for flow cytometry and mass cytometry data sets have been deposited in FlowRepository (FR-FCM-ZYQ9, FR-FCM-ZYQB). scRNA-Seq and bulk RNA sequencing data sets have been deposited in the National Center for Biotechnology Information’s Gene Expression Omnibus (GSE120221, GSE120446).

    Techniques: RNA Sequencing Assay, Flow Cytometry, Cytometry

    Averaging gene expression estimates across all cells in single cell RNA sequencing shows good correspondence across platforms (A) Distribution of transcriptome coverage (# genes detected per cell) for DropSeq (left) and Fluidigm (right). (B) Correlation of averaged gene expression estimates between single molecule RNA FISH (smRNA FISH) and single cell RNA sequencing (scRNA-seq). (C) Correlation of average gene expression estimates between DropSeq and smRNA FISH at different levels of transcriptome coverage using four different population sizes (50, 250, 500, and 2000 cells). Error bars in (C) represent ± 1 standard deviation across bootstrap replicates. (D) Correlation of averaged gene expression estimates between sequencing platforms. Error bars in (B and D) represent two times the standard error of the mean (SEM).

    Journal: Cell systems

    Article Title: Rare cell detection by single cell RNA sequencing as guided by single molecule RNA FISH

    doi: 10.1016/j.cels.2018.01.014

    Figure Lengend Snippet: Averaging gene expression estimates across all cells in single cell RNA sequencing shows good correspondence across platforms (A) Distribution of transcriptome coverage (# genes detected per cell) for DropSeq (left) and Fluidigm (right). (B) Correlation of averaged gene expression estimates between single molecule RNA FISH (smRNA FISH) and single cell RNA sequencing (scRNA-seq). (C) Correlation of average gene expression estimates between DropSeq and smRNA FISH at different levels of transcriptome coverage using four different population sizes (50, 250, 500, and 2000 cells). Error bars in (C) represent ± 1 standard deviation across bootstrap replicates. (D) Correlation of averaged gene expression estimates between sequencing platforms. Error bars in (B and D) represent two times the standard error of the mean (SEM).

    Article Snippet: To that end, we compared each single cell RNA sequencing dataset to bulk RNA sequencing data (DropSeq R = 0.94, Fluidigm R = 0.92) and compared Fluidigm and DropSeq to each other (R = 0.95)( ).

    Techniques: Expressing, RNA Sequencing Assay, Fluorescence In Situ Hybridization, Standard Deviation, Sequencing

    Estimates of gene expression heterogeneity in single cell RNA sequencing are highly dependent on transcriptome coverage (A) The Gini coefficient measures a gene’s expression distribution and captures rare cell population heterogeneity. (B) Population structure of SOX10 mRNA levels measured by DropSeq (pink), Fluidigm (blue), and single molecule RNA FISH (smRNA FISH, brown). (C) Gini coefficient for six genes measured by DropSeq (left y-axis) binned by levels of transcriptome coverage as well as Gini coefficients measured by smRNA FISH (right y-axis). (D) Pearson correlation between Gini coefficients measured through DropSeq and smRNA FISH across different levels of transcriptome coverage (# genes detected per cell). Error bars represent ± 1 standard deviation across bootstrap replicates. (E,F) Scatter Plot of the correspondence between Gini coefficients for 26 genes measured by both DropSeq and smRNA FISH. (G) Scatter Plot of the correspondence between Gini coefficients for 26 genes measured by Fluidigm and smRNA FISH. (H) Pearson correlation between Gini coefficient estimates measured by DropSeq and smRNA FISH using different population sizes (# of cells) and levels of transcriptome coverage. Error bars represent ± 1 standard deviation across bootstrap replicates. (I) Pearson correlation between Gini coefficient estimates measured by DropSeq and smRNA FISH after subsampling cells with high transcriptome coverage to different degrees of reads depth. Numbers inside the bars represent the number of reads subsampled. The x-axis represents the average number of genes detected across all cells at a given subsample depth. Error bars represent ± 1 standard deviation across bootstrap replicates.

    Journal: Cell systems

    Article Title: Rare cell detection by single cell RNA sequencing as guided by single molecule RNA FISH

    doi: 10.1016/j.cels.2018.01.014

    Figure Lengend Snippet: Estimates of gene expression heterogeneity in single cell RNA sequencing are highly dependent on transcriptome coverage (A) The Gini coefficient measures a gene’s expression distribution and captures rare cell population heterogeneity. (B) Population structure of SOX10 mRNA levels measured by DropSeq (pink), Fluidigm (blue), and single molecule RNA FISH (smRNA FISH, brown). (C) Gini coefficient for six genes measured by DropSeq (left y-axis) binned by levels of transcriptome coverage as well as Gini coefficients measured by smRNA FISH (right y-axis). (D) Pearson correlation between Gini coefficients measured through DropSeq and smRNA FISH across different levels of transcriptome coverage (# genes detected per cell). Error bars represent ± 1 standard deviation across bootstrap replicates. (E,F) Scatter Plot of the correspondence between Gini coefficients for 26 genes measured by both DropSeq and smRNA FISH. (G) Scatter Plot of the correspondence between Gini coefficients for 26 genes measured by Fluidigm and smRNA FISH. (H) Pearson correlation between Gini coefficient estimates measured by DropSeq and smRNA FISH using different population sizes (# of cells) and levels of transcriptome coverage. Error bars represent ± 1 standard deviation across bootstrap replicates. (I) Pearson correlation between Gini coefficient estimates measured by DropSeq and smRNA FISH after subsampling cells with high transcriptome coverage to different degrees of reads depth. Numbers inside the bars represent the number of reads subsampled. The x-axis represents the average number of genes detected across all cells at a given subsample depth. Error bars represent ± 1 standard deviation across bootstrap replicates.

    Article Snippet: To that end, we compared each single cell RNA sequencing dataset to bulk RNA sequencing data (DropSeq R = 0.94, Fluidigm R = 0.92) and compared Fluidigm and DropSeq to each other (R = 0.95)( ).

    Techniques: Expressing, RNA Sequencing Assay, Fluorescence In Situ Hybridization, Standard Deviation