heatmap function of r studio  (RStudio)

Journal: Nature Communications

Article Title: Fn -OMV potentiates ZBP1-mediated PANoptosis triggered by oncolytic HSV-1 to fuel antitumor immunity

doi: 10.1038/s41467-024-48032-7

Figure Lengend Snippet: Heatmap showing the expression of signature genes related to inflammasomes and certain key innate sensor-related genes in five types of tumor cells infected with oHSV (MOI = 1, 24 h) ( a ) and Venn diagram showed the increased gene intersections of five types of tumor cells infected with oHSV. Specifically, the two genes in the center indicate that two genes, Zbp1 and Nlrp6 , are commonly upregulated in all five cell lines infected with oHSV ( b ). c Five types of tumor cells were infected with oHSV (MOI = 1, 24 h), and cellular protein was analyzed by western blotting to detect the expression level of ZBP1 and NLRP6. Western blotting was done thrice independently with similar results. d oHSV-treated or untreated 4T1 tumor tissue lysates were analyzed of the expression of ZBP1 and NLRP6 by western blotting. Western blotting was done thrice independently with similar results. e Effect of ZBP1 and NLRP6 expression on relative cell viability in the 4T1 cells treated with oHSV (MOI = 1, 24 h). n.s. not significant. f The effect of ZBP1 and NLRP6 expression on the injury of 4T1 cells after oHSV (MOI = 1, 24 h) treatment was detected by LDH release assay. n.s. not significant. g The expression of Z-NA and ZBP1 in tumor cells after oHSV (MOI = 1, 24 h) treatment was evaluated using a Confocal Laser Scanning Microscope. Scale bars = 10 μm. h , i Western blotting analysis assessing ZBP1 expression in the cytoplasm and nucleus of 4T1 cells with or without oHSV treatment (MOI = 1, 24 h). Western blotting was done thrice independently with similar results. j , k Western blotting analysis assessing ZBP1 expression in the cytoplasm and nucleus of 4MOSC1 cells with or without oHSV treatment (MOI = 1, 24 h). Western blotting was done thrice independently with similar results. n = 3 independent experiments for a , e , f . Statistical significance was determined using two-tailed Student’s t test in e , f , i , k . Data represent the mean ± s.e.m. Scale bar, 10 μm. Source data are provided in the Source Data file.

Article Snippet: To effectively illustrate the qRT-PCR results, we utilized the heatmap function in R Studio software to plot the normalized gene expression data.

Techniques: Expressing, Infection, Western Blot, Lactate Dehydrogenase Assay, Laser-Scanning Microscopy, Two Tailed Test

Journal: Nature Communications

Article Title: Fn -OMV potentiates ZBP1-mediated PANoptosis triggered by oncolytic HSV-1 to fuel antitumor immunity

doi: 10.1038/s41467-024-48032-7

Figure Lengend Snippet: a Heatmap showing the expression of signature genes related to ISG mRNA in oHSV-treated (MOI = 1, 24 h) 4T1 (left) and 4MOSC1 (right) cells. b Heatmap indicated the expression of signature genes related to ISG mRNA with high editing indices in oHSV-treated (MOI = 1, 24 h) 4T1 (left) and 4MOSC1 (right) cells. c Heatmap demonstrated the influence of the expression of ISG mRNA with high editing indices on oHSV-treated (MOI = 1, 24 h) 4T1 cells after IFNAR-1 blockade. d 4T1 cells were infected with oHSV (MOI = 1, 24 h) and IFNAR-1 blockade, the cellular protein was analyzed by western blotting to detect the expression level of ZBP1. Western blotting was done thrice independently with similar results. e The expression of Z-NA and ZBP1 in 4T1 tumor cells after oHSV (MOI = 1, 24 h) alone and oHSV combined with DNase I (25 UmL −1 ) treatment was evaluated using a Confocal Laser Scanning Microscope. Scale bars = 10 μm. Data were repeated thrice independently with similar results. f The expression of Z-RNA in tumor cells after oHSV (MOI = 1, 24 h) treatment and IFNAR-1 blockade was evaluated using a Confocal Laser Scanning Microscope. Scale bars = 10 μm. Data were repeated thrice independently with similar results. g Model diagram illustrating the upregulation of ZBP1 by oHSV through the induction of Z-RNA accumulation. The release of LDH (left) and ATP (right) from 4T1 ( h ) tumor cells after oHSV (MOI = 1, 24 h) treatment and IFNAR-1 blockade. n = 3 independent experiments for ( a – c , h ). Statistical significance was determined using two-tailed Student’s t test in ( h ). Data represent the mean ± s.e.m. Scale bar, 10 μm. Source data are provided in the Source Data file.

Article Snippet: To effectively illustrate the qRT-PCR results, we utilized the heatmap function in R Studio software to plot the normalized gene expression data.

Techniques: Expressing, Infection, Western Blot, Laser-Scanning Microscopy, Two Tailed Test

Journal: Nature Communications

Article Title: Fn -OMV potentiates ZBP1-mediated PANoptosis triggered by oncolytic HSV-1 to fuel antitumor immunity

doi: 10.1038/s41467-024-48032-7

Figure Lengend Snippet: Evaluation of cell apoptosis by flow cytometry at 24 h in different treatment groups. Representative flow cytometric plots ( a ) and relative cell viability ( b ) of different treatment groups are shown in the 4T1 (left) and 4MOSC1 (right) cells. The release of LDH ( c ) and ATP ( d ) from 4T1 cells after oHSV (MOI = 1) treatment and Fn -OMV (1 μg ml – 1 ) alone or in combination. e Immunofluorescence detection of HMGB1 expressed on 4T1 (left) and 4MOSC1 (right) cells was observed using a Confocal Laser Scanning Microscope. Scale bars, 20 μm. f 4T1 cell culture supernatants were assayed for TNF-α by ELISA after oHSV (MOI = 1) treatment and Fn -OMV (1 μg ml – 1 ) alone or in combination. g Heatmap showing the expression of signature genes related to mRNA expression of M1 macrophage markers (upper) and M2 macrophage markers (below) in oHSV treatment and Fn -OMV alone or in combination. h Schematic illustration shows the effect of oHSV and Fn -OMV on the polarization regulation ability of macrophages. Heatmap ( i ) and bar graphs ( j ) showing relative mRNA levels of inflammatory-associated genes in M2 macrophages following treatment with oHSV and Fn -OMV alone or in combination. n = 3 independent experiments for b – d , f , g , i , j . Statistical significance was calculated via one-way ANOVA with Tukey’s multiple comparisons test. n.s. not significant. Data represent the mean ± s.e.m. Source data are provided as a Source Data file.

Article Snippet: To effectively illustrate the qRT-PCR results, we utilized the heatmap function in R Studio software to plot the normalized gene expression data.

Techniques: Flow Cytometry, Immunofluorescence, Laser-Scanning Microscopy, Cell Culture, Enzyme-linked Immunosorbent Assay, Expressing

Journal: Nature Communications

Article Title: Fn -OMV potentiates ZBP1-mediated PANoptosis triggered by oncolytic HSV-1 to fuel antitumor immunity

doi: 10.1038/s41467-024-48032-7

Figure Lengend Snippet: a Schematic representation of 4T1 (upper) and 4MOSC1 (below) tumor inoculation and treatment with oHSV and Fn -OMV. S.C. = Subcutaneous. b Average 4T1 (left) and 4MOSC1 (right) tumor growth curve depicted as mean ± s.e.m. for each treatment group ( n = 5 mice). Statistical significance was evaluated using two-way ANOVA. c Heatmap shows a 17-gene expression profile associated with inflammation produced in mice of different treatment groups. d Immunological profile of TDLNs. This includes the frequency of the lymph nodes CD80 + CD86 + population in CD11c + cells in 4T1 (left) and 4MOSC1 (right) tumors. e CD8 + T cell populations in the tumors were measured using flow cytometry, and quantitative analyses were performed in 4T1 (left) and 4MOSC1 (right) tumors. f Heatmap shows the expression signature of four selected genes, all highly associated with CD8 + T cell activation, across different treatment groups. g Representative images of immunohistochemical analysis of CD8 and Granzyme B (GZMB) expression in different treatment groups of 4T1 tumors (left) and 4MOSC1 tumors (right), Scale bars, 50 μm. The images of immunostaining ( g ) were representative of those generated from five mice in each group. h CD86 + macrophages and CD206 + macrophages in the tumors were measured using flow cytometry, and quantitative analyses were performed. i CD25 + and FOXP3 + Treg cell populations in the TDLNs were measured using flow cytometry, and quantitative analyses were performed. j Representative images of immunohistochemical analysis of FOXP3 expression in different treatment groups of 4T1 tumors (upper) and 4MOSC1 tumors (below), Scale bars, 50 μm. The images of immunostaining ( j ) were representative of those generated from five mice in each group. k A schematic diagram illustrating the transformation of “cold” tumors into “hot” tumors by the combined treatment of oHSV and Fn -OMV. All data are shown as the mean ± s.e.m. n = 3-5 independent experiments for ( c – f , h , i ). Statistical significance was calculated via one-way ANOVA with Tukey’s multiple comparisons test in ( d , e , h , i ). n.s. not significant. Source data are provided as a Source Data file.

Article Snippet: To effectively illustrate the qRT-PCR results, we utilized the heatmap function in R Studio software to plot the normalized gene expression data.

Techniques: Gene Expression, Produced, Flow Cytometry, Expressing, Activation Assay, Immunohistochemical staining, Immunostaining, Generated, Transformation Assay

Journal: Scientific Reports

Article Title: Epithelial membrane protein 2 (EMP2) regulates hypoxia-induced angiogenesis in the adult retinal pigment epithelial cell lines

doi: 10.1038/s41598-022-22696-x

Figure Lengend Snippet: RNA sequencing of ARPE-19 cells for RPE and retinal markers. Wild type (WT), EMP2 overexpressing (OE), and EMP2 knock down (KD) ARPE-19 cells were queried for differential expression of classical RPE markers and retinal markers. A control cell line, MCF12A (immortalized breast cancer cell line) was analyzed in parallel, and results are presented as a heatmap generated in R studio using pheatmap, version 1.0.12 ( https://CRAN.R-project.org/package=pheatmap .) High expression of RPE markers and low expression of retinal markers was observed in ARPE-19 cells, regardless of EMP2 expression. Both MCF12A and ARPE-19 cells showed low expression of most retinal markers (gray indicating zero transcripts identified). All samples were performed in triplicate.

Article Snippet: A control cell line, MCF12A (immortalized breast cancer cell line) was analyzed in parallel, and results are presented as a heatmap generated in R studio using pheatmap, version 1.0.12 ( https://CRAN.R-project.org/package=pheatmap .)

Techniques: RNA Sequencing, Knockdown, Quantitative Proteomics, Control, Generated, Expressing

Journal: Scientific Reports

Article Title: Epithelial membrane protein 2 (EMP2) regulates hypoxia-induced angiogenesis in the adult retinal pigment epithelial cell lines

doi: 10.1038/s41598-022-22696-x

Figure Lengend Snippet: EMP2 regulates gene sets related to blood vessel morphogenesis. ( A ) Intersection of genes involved in neoangiogenesis and its related pathways depicted using a chord diagram. The chord diagram was generated in "GOplot", version 1.0.2 ( https://CRAN.R-project.org/package=GOplot ). ( B ) Heatmap of EMP2, HIF1α, and VEGFA expression in ARPE-19 cells with modified EMP2 levels. Successful EMP2 transcript alteration was confirmed for wild type (WT), EMP2 overexpressing (OE), and EMP2 knock down (KD) ARPE-19 cells. HIF1α and VEGFA expression correlates with EMP2 expression, with increased transcript levels in OE and decreased transcript levels in KD. The housekeeping genes MT-RNR1 (16S rRNA) and VCP were used as controls for normalization. All samples were performed in triplicate. ( C ) HIF1α expression is induced in ARPE-19 WT under hypoxic conditions. Analysis of HIF1α and EMP2 protein expression in WT ARPE-19 cells under normoxic conditions and following 2–4 h of hypoxic stress (0.5% O 2 ). Bands were visualized using autoradiography. Bar diagrams depict mean values and standard error of the mean. Statistical significance was established using a Student’s t -test (unpaired, two-tailed). **, p = 0.0076. Original, uncropped blots are presented in Supplementary Fig. .

Article Snippet: A control cell line, MCF12A (immortalized breast cancer cell line) was analyzed in parallel, and results are presented as a heatmap generated in R studio using pheatmap, version 1.0.12 ( https://CRAN.R-project.org/package=pheatmap .)

Techniques: Generated, Expressing, Modification, Knockdown, Autoradiography, Two Tailed Test