density plots Search Results


density plots  (OriginLab corp)
90
OriginLab corp density plots
Density Plots, supplied by OriginLab corp, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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density plots - by Bioz Stars, 2026-07
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charts and density plots  (GraphPad Software Inc)
90
GraphPad Software Inc charts and density plots
Charts And Density Plots, supplied by GraphPad Software Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rna-seq read density and polr2a occupancy plots  (GraphPad Software Inc)
90
GraphPad Software Inc rna-seq read density and polr2a occupancy plots
H2AFZ non-CPR-TSSs display distinct patterns of <t>POLR2A</t> and RNA-seq reads density in primary and transformed cells. (A) and (B) POLR2A ChIP-seq read density at all CPR-TSSs (A) and all non-CPR-TSSs (B) are highly similar. (C) and (D) RNA-seq read density in the same regions as plotted in (A) and (B), respectively, also shows a similar pattern between CPR (C) and non-CPR-TSSs (D) as well as primary and transformed cells, especially in immediate flanks where −1 and +1 positioned nucleosomes are expected to be located. (E) and (F) POLR2A occupancy at CPR-TSSs (E) and non-CPR-TSSs (F) specifically for H2AFZ, a positioned nucleosome component, showed striking dissimilarity that stands out of the pooled analysis of all 8 histone modifications (A) and (B). The POLR2A showed enrichment at approximately 100 to 200 bp flanks of H2AFZ CPR-TSSs (E) which increased to approximately 300 to 500 bp flanks of H2AFZ non-CPR-TSSs (F). At the H2AFZ non-CPR-TSSs, the primary and transformed cells showed the strongest difference in POLR2A occupancy. (G) and (H) In the same regions as in (E) and (F), RNA-seq reads were plotted. At H2AFZ CPR-TSSs (G), the RNA-seq reads recapitulated the pattern of POLR2A occupancy (E) in both primary and transformed cells. However, as shown in (H), RNA-seq reads in the H2AFZ non-CPR-TSSs showed good correlation only for transformed cells, not primary cells. Values plotted on Y -axis are median and interquartile range (IQR) for 13 primary and 9 transformed cell lines for (A), (B), (E), and (F), and 9 primary and 18 transformed cell lines for (C), (D), (G), and (H). Correlation plots and Pearson coefficients for pairs of POLR2A and RNA-seq data plotted here are shown in Supplemental Figure S5 . CPR indicates ChIP-seq Peak Regions, TSSs, transcription start sites.
Rna Seq Read Density And Polr2a Occupancy Plots, supplied by GraphPad Software Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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rna-seq read density and polr2a occupancy plots - by Bioz Stars, 2026-07
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bivariate plot with nonparametric density contours  (SAS institute)
90
SAS institute bivariate plot with nonparametric density contours
H2AFZ non-CPR-TSSs display distinct patterns of <t>POLR2A</t> and RNA-seq reads density in primary and transformed cells. (A) and (B) POLR2A ChIP-seq read density at all CPR-TSSs (A) and all non-CPR-TSSs (B) are highly similar. (C) and (D) RNA-seq read density in the same regions as plotted in (A) and (B), respectively, also shows a similar pattern between CPR (C) and non-CPR-TSSs (D) as well as primary and transformed cells, especially in immediate flanks where −1 and +1 positioned nucleosomes are expected to be located. (E) and (F) POLR2A occupancy at CPR-TSSs (E) and non-CPR-TSSs (F) specifically for H2AFZ, a positioned nucleosome component, showed striking dissimilarity that stands out of the pooled analysis of all 8 histone modifications (A) and (B). The POLR2A showed enrichment at approximately 100 to 200 bp flanks of H2AFZ CPR-TSSs (E) which increased to approximately 300 to 500 bp flanks of H2AFZ non-CPR-TSSs (F). At the H2AFZ non-CPR-TSSs, the primary and transformed cells showed the strongest difference in POLR2A occupancy. (G) and (H) In the same regions as in (E) and (F), RNA-seq reads were plotted. At H2AFZ CPR-TSSs (G), the RNA-seq reads recapitulated the pattern of POLR2A occupancy (E) in both primary and transformed cells. However, as shown in (H), RNA-seq reads in the H2AFZ non-CPR-TSSs showed good correlation only for transformed cells, not primary cells. Values plotted on Y -axis are median and interquartile range (IQR) for 13 primary and 9 transformed cell lines for (A), (B), (E), and (F), and 9 primary and 18 transformed cell lines for (C), (D), (G), and (H). Correlation plots and Pearson coefficients for pairs of POLR2A and RNA-seq data plotted here are shown in Supplemental Figure S5 . CPR indicates ChIP-seq Peak Regions, TSSs, transcription start sites.
Bivariate Plot With Nonparametric Density Contours, supplied by SAS institute, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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bivariate plot with nonparametric density contours - by Bioz Stars, 2026-07
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density plots  (SAS institute)
90
SAS institute density plots
H2AFZ non-CPR-TSSs display distinct patterns of <t>POLR2A</t> and RNA-seq reads density in primary and transformed cells. (A) and (B) POLR2A ChIP-seq read density at all CPR-TSSs (A) and all non-CPR-TSSs (B) are highly similar. (C) and (D) RNA-seq read density in the same regions as plotted in (A) and (B), respectively, also shows a similar pattern between CPR (C) and non-CPR-TSSs (D) as well as primary and transformed cells, especially in immediate flanks where −1 and +1 positioned nucleosomes are expected to be located. (E) and (F) POLR2A occupancy at CPR-TSSs (E) and non-CPR-TSSs (F) specifically for H2AFZ, a positioned nucleosome component, showed striking dissimilarity that stands out of the pooled analysis of all 8 histone modifications (A) and (B). The POLR2A showed enrichment at approximately 100 to 200 bp flanks of H2AFZ CPR-TSSs (E) which increased to approximately 300 to 500 bp flanks of H2AFZ non-CPR-TSSs (F). At the H2AFZ non-CPR-TSSs, the primary and transformed cells showed the strongest difference in POLR2A occupancy. (G) and (H) In the same regions as in (E) and (F), RNA-seq reads were plotted. At H2AFZ CPR-TSSs (G), the RNA-seq reads recapitulated the pattern of POLR2A occupancy (E) in both primary and transformed cells. However, as shown in (H), RNA-seq reads in the H2AFZ non-CPR-TSSs showed good correlation only for transformed cells, not primary cells. Values plotted on Y -axis are median and interquartile range (IQR) for 13 primary and 9 transformed cell lines for (A), (B), (E), and (F), and 9 primary and 18 transformed cell lines for (C), (D), (G), and (H). Correlation plots and Pearson coefficients for pairs of POLR2A and RNA-seq data plotted here are shown in Supplemental Figure S5 . CPR indicates ChIP-seq Peak Regions, TSSs, transcription start sites.
Density Plots, supplied by SAS institute, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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composite probability density plots  (Midcontinent Livestock Supplements)
90
Midcontinent Livestock Supplements composite probability density plots
H2AFZ non-CPR-TSSs display distinct patterns of <t>POLR2A</t> and RNA-seq reads density in primary and transformed cells. (A) and (B) POLR2A ChIP-seq read density at all CPR-TSSs (A) and all non-CPR-TSSs (B) are highly similar. (C) and (D) RNA-seq read density in the same regions as plotted in (A) and (B), respectively, also shows a similar pattern between CPR (C) and non-CPR-TSSs (D) as well as primary and transformed cells, especially in immediate flanks where −1 and +1 positioned nucleosomes are expected to be located. (E) and (F) POLR2A occupancy at CPR-TSSs (E) and non-CPR-TSSs (F) specifically for H2AFZ, a positioned nucleosome component, showed striking dissimilarity that stands out of the pooled analysis of all 8 histone modifications (A) and (B). The POLR2A showed enrichment at approximately 100 to 200 bp flanks of H2AFZ CPR-TSSs (E) which increased to approximately 300 to 500 bp flanks of H2AFZ non-CPR-TSSs (F). At the H2AFZ non-CPR-TSSs, the primary and transformed cells showed the strongest difference in POLR2A occupancy. (G) and (H) In the same regions as in (E) and (F), RNA-seq reads were plotted. At H2AFZ CPR-TSSs (G), the RNA-seq reads recapitulated the pattern of POLR2A occupancy (E) in both primary and transformed cells. However, as shown in (H), RNA-seq reads in the H2AFZ non-CPR-TSSs showed good correlation only for transformed cells, not primary cells. Values plotted on Y -axis are median and interquartile range (IQR) for 13 primary and 9 transformed cell lines for (A), (B), (E), and (F), and 9 primary and 18 transformed cell lines for (C), (D), (G), and (H). Correlation plots and Pearson coefficients for pairs of POLR2A and RNA-seq data plotted here are shown in Supplemental Figure S5 . CPR indicates ChIP-seq Peak Regions, TSSs, transcription start sites.
Composite Probability Density Plots, supplied by Midcontinent Livestock Supplements, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1d kernel density plot node  (KNIME GmbH)
90
KNIME GmbH 1d kernel density plot node
H2AFZ non-CPR-TSSs display distinct patterns of <t>POLR2A</t> and RNA-seq reads density in primary and transformed cells. (A) and (B) POLR2A ChIP-seq read density at all CPR-TSSs (A) and all non-CPR-TSSs (B) are highly similar. (C) and (D) RNA-seq read density in the same regions as plotted in (A) and (B), respectively, also shows a similar pattern between CPR (C) and non-CPR-TSSs (D) as well as primary and transformed cells, especially in immediate flanks where −1 and +1 positioned nucleosomes are expected to be located. (E) and (F) POLR2A occupancy at CPR-TSSs (E) and non-CPR-TSSs (F) specifically for H2AFZ, a positioned nucleosome component, showed striking dissimilarity that stands out of the pooled analysis of all 8 histone modifications (A) and (B). The POLR2A showed enrichment at approximately 100 to 200 bp flanks of H2AFZ CPR-TSSs (E) which increased to approximately 300 to 500 bp flanks of H2AFZ non-CPR-TSSs (F). At the H2AFZ non-CPR-TSSs, the primary and transformed cells showed the strongest difference in POLR2A occupancy. (G) and (H) In the same regions as in (E) and (F), RNA-seq reads were plotted. At H2AFZ CPR-TSSs (G), the RNA-seq reads recapitulated the pattern of POLR2A occupancy (E) in both primary and transformed cells. However, as shown in (H), RNA-seq reads in the H2AFZ non-CPR-TSSs showed good correlation only for transformed cells, not primary cells. Values plotted on Y -axis are median and interquartile range (IQR) for 13 primary and 9 transformed cell lines for (A), (B), (E), and (F), and 9 primary and 18 transformed cell lines for (C), (D), (G), and (H). Correlation plots and Pearson coefficients for pairs of POLR2A and RNA-seq data plotted here are shown in Supplemental Figure S5 . CPR indicates ChIP-seq Peak Regions, TSSs, transcription start sites.
1d Kernel Density Plot Node, supplied by KNIME GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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density plots  (Gallus BioPharmaceuticals)
90
Gallus BioPharmaceuticals density plots
H2AFZ non-CPR-TSSs display distinct patterns of <t>POLR2A</t> and RNA-seq reads density in primary and transformed cells. (A) and (B) POLR2A ChIP-seq read density at all CPR-TSSs (A) and all non-CPR-TSSs (B) are highly similar. (C) and (D) RNA-seq read density in the same regions as plotted in (A) and (B), respectively, also shows a similar pattern between CPR (C) and non-CPR-TSSs (D) as well as primary and transformed cells, especially in immediate flanks where −1 and +1 positioned nucleosomes are expected to be located. (E) and (F) POLR2A occupancy at CPR-TSSs (E) and non-CPR-TSSs (F) specifically for H2AFZ, a positioned nucleosome component, showed striking dissimilarity that stands out of the pooled analysis of all 8 histone modifications (A) and (B). The POLR2A showed enrichment at approximately 100 to 200 bp flanks of H2AFZ CPR-TSSs (E) which increased to approximately 300 to 500 bp flanks of H2AFZ non-CPR-TSSs (F). At the H2AFZ non-CPR-TSSs, the primary and transformed cells showed the strongest difference in POLR2A occupancy. (G) and (H) In the same regions as in (E) and (F), RNA-seq reads were plotted. At H2AFZ CPR-TSSs (G), the RNA-seq reads recapitulated the pattern of POLR2A occupancy (E) in both primary and transformed cells. However, as shown in (H), RNA-seq reads in the H2AFZ non-CPR-TSSs showed good correlation only for transformed cells, not primary cells. Values plotted on Y -axis are median and interquartile range (IQR) for 13 primary and 9 transformed cell lines for (A), (B), (E), and (F), and 9 primary and 18 transformed cell lines for (C), (D), (G), and (H). Correlation plots and Pearson coefficients for pairs of POLR2A and RNA-seq data plotted here are shown in Supplemental Figure S5 . CPR indicates ChIP-seq Peak Regions, TSSs, transcription start sites.
Density Plots, supplied by Gallus BioPharmaceuticals, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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ct number to electron density conversion plot of the siemens c-arm cbct  (Siemens AG)
90
Siemens AG ct number to electron density conversion plot of the siemens c-arm cbct
H2AFZ non-CPR-TSSs display distinct patterns of <t>POLR2A</t> and RNA-seq reads density in primary and transformed cells. (A) and (B) POLR2A ChIP-seq read density at all CPR-TSSs (A) and all non-CPR-TSSs (B) are highly similar. (C) and (D) RNA-seq read density in the same regions as plotted in (A) and (B), respectively, also shows a similar pattern between CPR (C) and non-CPR-TSSs (D) as well as primary and transformed cells, especially in immediate flanks where −1 and +1 positioned nucleosomes are expected to be located. (E) and (F) POLR2A occupancy at CPR-TSSs (E) and non-CPR-TSSs (F) specifically for H2AFZ, a positioned nucleosome component, showed striking dissimilarity that stands out of the pooled analysis of all 8 histone modifications (A) and (B). The POLR2A showed enrichment at approximately 100 to 200 bp flanks of H2AFZ CPR-TSSs (E) which increased to approximately 300 to 500 bp flanks of H2AFZ non-CPR-TSSs (F). At the H2AFZ non-CPR-TSSs, the primary and transformed cells showed the strongest difference in POLR2A occupancy. (G) and (H) In the same regions as in (E) and (F), RNA-seq reads were plotted. At H2AFZ CPR-TSSs (G), the RNA-seq reads recapitulated the pattern of POLR2A occupancy (E) in both primary and transformed cells. However, as shown in (H), RNA-seq reads in the H2AFZ non-CPR-TSSs showed good correlation only for transformed cells, not primary cells. Values plotted on Y -axis are median and interquartile range (IQR) for 13 primary and 9 transformed cell lines for (A), (B), (E), and (F), and 9 primary and 18 transformed cell lines for (C), (D), (G), and (H). Correlation plots and Pearson coefficients for pairs of POLR2A and RNA-seq data plotted here are shown in Supplemental Figure S5 . CPR indicates ChIP-seq Peak Regions, TSSs, transcription start sites.
Ct Number To Electron Density Conversion Plot Of The Siemens C Arm Cbct, supplied by Siemens AG, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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ct number to electron density conversion plot of the siemens c-arm cbct - by Bioz Stars, 2026-07
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density plots jmp version 10  (SAS institute)
90
SAS institute density plots jmp version 10
H2AFZ non-CPR-TSSs display distinct patterns of <t>POLR2A</t> and RNA-seq reads density in primary and transformed cells. (A) and (B) POLR2A ChIP-seq read density at all CPR-TSSs (A) and all non-CPR-TSSs (B) are highly similar. (C) and (D) RNA-seq read density in the same regions as plotted in (A) and (B), respectively, also shows a similar pattern between CPR (C) and non-CPR-TSSs (D) as well as primary and transformed cells, especially in immediate flanks where −1 and +1 positioned nucleosomes are expected to be located. (E) and (F) POLR2A occupancy at CPR-TSSs (E) and non-CPR-TSSs (F) specifically for H2AFZ, a positioned nucleosome component, showed striking dissimilarity that stands out of the pooled analysis of all 8 histone modifications (A) and (B). The POLR2A showed enrichment at approximately 100 to 200 bp flanks of H2AFZ CPR-TSSs (E) which increased to approximately 300 to 500 bp flanks of H2AFZ non-CPR-TSSs (F). At the H2AFZ non-CPR-TSSs, the primary and transformed cells showed the strongest difference in POLR2A occupancy. (G) and (H) In the same regions as in (E) and (F), RNA-seq reads were plotted. At H2AFZ CPR-TSSs (G), the RNA-seq reads recapitulated the pattern of POLR2A occupancy (E) in both primary and transformed cells. However, as shown in (H), RNA-seq reads in the H2AFZ non-CPR-TSSs showed good correlation only for transformed cells, not primary cells. Values plotted on Y -axis are median and interquartile range (IQR) for 13 primary and 9 transformed cell lines for (A), (B), (E), and (F), and 9 primary and 18 transformed cell lines for (C), (D), (G), and (H). Correlation plots and Pearson coefficients for pairs of POLR2A and RNA-seq data plotted here are shown in Supplemental Figure S5 . CPR indicates ChIP-seq Peak Regions, TSSs, transcription start sites.
Density Plots Jmp Version 10, supplied by SAS institute, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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probability density plots  (Becton Dickinson)
90
Becton Dickinson probability density plots
H2AFZ non-CPR-TSSs display distinct patterns of <t>POLR2A</t> and RNA-seq reads density in primary and transformed cells. (A) and (B) POLR2A ChIP-seq read density at all CPR-TSSs (A) and all non-CPR-TSSs (B) are highly similar. (C) and (D) RNA-seq read density in the same regions as plotted in (A) and (B), respectively, also shows a similar pattern between CPR (C) and non-CPR-TSSs (D) as well as primary and transformed cells, especially in immediate flanks where −1 and +1 positioned nucleosomes are expected to be located. (E) and (F) POLR2A occupancy at CPR-TSSs (E) and non-CPR-TSSs (F) specifically for H2AFZ, a positioned nucleosome component, showed striking dissimilarity that stands out of the pooled analysis of all 8 histone modifications (A) and (B). The POLR2A showed enrichment at approximately 100 to 200 bp flanks of H2AFZ CPR-TSSs (E) which increased to approximately 300 to 500 bp flanks of H2AFZ non-CPR-TSSs (F). At the H2AFZ non-CPR-TSSs, the primary and transformed cells showed the strongest difference in POLR2A occupancy. (G) and (H) In the same regions as in (E) and (F), RNA-seq reads were plotted. At H2AFZ CPR-TSSs (G), the RNA-seq reads recapitulated the pattern of POLR2A occupancy (E) in both primary and transformed cells. However, as shown in (H), RNA-seq reads in the H2AFZ non-CPR-TSSs showed good correlation only for transformed cells, not primary cells. Values plotted on Y -axis are median and interquartile range (IQR) for 13 primary and 9 transformed cell lines for (A), (B), (E), and (F), and 9 primary and 18 transformed cell lines for (C), (D), (G), and (H). Correlation plots and Pearson coefficients for pairs of POLR2A and RNA-seq data plotted here are shown in Supplemental Figure S5 . CPR indicates ChIP-seq Peak Regions, TSSs, transcription start sites.
Probability Density Plots, supplied by Becton Dickinson, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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filtered lco data for pixel violin plots and density plots  (RStudio)
90
RStudio filtered lco data for pixel violin plots and density plots
H2AFZ non-CPR-TSSs display distinct patterns of <t>POLR2A</t> and RNA-seq reads density in primary and transformed cells. (A) and (B) POLR2A ChIP-seq read density at all CPR-TSSs (A) and all non-CPR-TSSs (B) are highly similar. (C) and (D) RNA-seq read density in the same regions as plotted in (A) and (B), respectively, also shows a similar pattern between CPR (C) and non-CPR-TSSs (D) as well as primary and transformed cells, especially in immediate flanks where −1 and +1 positioned nucleosomes are expected to be located. (E) and (F) POLR2A occupancy at CPR-TSSs (E) and non-CPR-TSSs (F) specifically for H2AFZ, a positioned nucleosome component, showed striking dissimilarity that stands out of the pooled analysis of all 8 histone modifications (A) and (B). The POLR2A showed enrichment at approximately 100 to 200 bp flanks of H2AFZ CPR-TSSs (E) which increased to approximately 300 to 500 bp flanks of H2AFZ non-CPR-TSSs (F). At the H2AFZ non-CPR-TSSs, the primary and transformed cells showed the strongest difference in POLR2A occupancy. (G) and (H) In the same regions as in (E) and (F), RNA-seq reads were plotted. At H2AFZ CPR-TSSs (G), the RNA-seq reads recapitulated the pattern of POLR2A occupancy (E) in both primary and transformed cells. However, as shown in (H), RNA-seq reads in the H2AFZ non-CPR-TSSs showed good correlation only for transformed cells, not primary cells. Values plotted on Y -axis are median and interquartile range (IQR) for 13 primary and 9 transformed cell lines for (A), (B), (E), and (F), and 9 primary and 18 transformed cell lines for (C), (D), (G), and (H). Correlation plots and Pearson coefficients for pairs of POLR2A and RNA-seq data plotted here are shown in Supplemental Figure S5 . CPR indicates ChIP-seq Peak Regions, TSSs, transcription start sites.
Filtered Lco Data For Pixel Violin Plots And Density Plots, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Image Search Results


H2AFZ non-CPR-TSSs display distinct patterns of POLR2A and RNA-seq reads density in primary and transformed cells. (A) and (B) POLR2A ChIP-seq read density at all CPR-TSSs (A) and all non-CPR-TSSs (B) are highly similar. (C) and (D) RNA-seq read density in the same regions as plotted in (A) and (B), respectively, also shows a similar pattern between CPR (C) and non-CPR-TSSs (D) as well as primary and transformed cells, especially in immediate flanks where −1 and +1 positioned nucleosomes are expected to be located. (E) and (F) POLR2A occupancy at CPR-TSSs (E) and non-CPR-TSSs (F) specifically for H2AFZ, a positioned nucleosome component, showed striking dissimilarity that stands out of the pooled analysis of all 8 histone modifications (A) and (B). The POLR2A showed enrichment at approximately 100 to 200 bp flanks of H2AFZ CPR-TSSs (E) which increased to approximately 300 to 500 bp flanks of H2AFZ non-CPR-TSSs (F). At the H2AFZ non-CPR-TSSs, the primary and transformed cells showed the strongest difference in POLR2A occupancy. (G) and (H) In the same regions as in (E) and (F), RNA-seq reads were plotted. At H2AFZ CPR-TSSs (G), the RNA-seq reads recapitulated the pattern of POLR2A occupancy (E) in both primary and transformed cells. However, as shown in (H), RNA-seq reads in the H2AFZ non-CPR-TSSs showed good correlation only for transformed cells, not primary cells. Values plotted on Y -axis are median and interquartile range (IQR) for 13 primary and 9 transformed cell lines for (A), (B), (E), and (F), and 9 primary and 18 transformed cell lines for (C), (D), (G), and (H). Correlation plots and Pearson coefficients for pairs of POLR2A and RNA-seq data plotted here are shown in Supplemental Figure S5 . CPR indicates ChIP-seq Peak Regions, TSSs, transcription start sites.

Journal: Cancer Informatics

Article Title: Distinct DNA Sequence Preference for Histone Occupancy in Primary and Transformed Cells

doi: 10.1177/1176935119843835

Figure Lengend Snippet: H2AFZ non-CPR-TSSs display distinct patterns of POLR2A and RNA-seq reads density in primary and transformed cells. (A) and (B) POLR2A ChIP-seq read density at all CPR-TSSs (A) and all non-CPR-TSSs (B) are highly similar. (C) and (D) RNA-seq read density in the same regions as plotted in (A) and (B), respectively, also shows a similar pattern between CPR (C) and non-CPR-TSSs (D) as well as primary and transformed cells, especially in immediate flanks where −1 and +1 positioned nucleosomes are expected to be located. (E) and (F) POLR2A occupancy at CPR-TSSs (E) and non-CPR-TSSs (F) specifically for H2AFZ, a positioned nucleosome component, showed striking dissimilarity that stands out of the pooled analysis of all 8 histone modifications (A) and (B). The POLR2A showed enrichment at approximately 100 to 200 bp flanks of H2AFZ CPR-TSSs (E) which increased to approximately 300 to 500 bp flanks of H2AFZ non-CPR-TSSs (F). At the H2AFZ non-CPR-TSSs, the primary and transformed cells showed the strongest difference in POLR2A occupancy. (G) and (H) In the same regions as in (E) and (F), RNA-seq reads were plotted. At H2AFZ CPR-TSSs (G), the RNA-seq reads recapitulated the pattern of POLR2A occupancy (E) in both primary and transformed cells. However, as shown in (H), RNA-seq reads in the H2AFZ non-CPR-TSSs showed good correlation only for transformed cells, not primary cells. Values plotted on Y -axis are median and interquartile range (IQR) for 13 primary and 9 transformed cell lines for (A), (B), (E), and (F), and 9 primary and 18 transformed cell lines for (C), (D), (G), and (H). Correlation plots and Pearson coefficients for pairs of POLR2A and RNA-seq data plotted here are shown in Supplemental Figure S5 . CPR indicates ChIP-seq Peak Regions, TSSs, transcription start sites.

Article Snippet: RNA-seq read density and POLR2A occupancy plots were generated by aggregate option in bwtool to calculate signal at base level and visualized in GraphPad Prism 7.

Techniques: RNA Sequencing, Transformation Assay, ChIP-sequencing