heatmap generated in r studio  (RStudio)

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