heat map generated with cluster 3.0 and java treeview software  (SourceForge net)

Journal: Cell Death Discovery

Article Title: CAMK2D: a novel molecular target for BAP1 -deficient malignant mesothelioma

doi: 10.1038/s41420-023-01552-5

Figure Lengend Snippet: a Generation of BAP1 ‐KO cell lines using the CRISPR/Cas9 system using a single guide RNA sequence against exon 4 of the BAP1 gene locus. b Establishment of BAP1 -KO cell clones using human mesothelial cell lines, MeT‐5A and HOMC-D4. BAP1 protein expression was determined by Western blot analysis using GAPDH as the internal control. c Gene expression analysis represented by heatmap of upregulated (seven genes; fold change, >3) and downregulated (40 genes, fold change, <0.1) genes in BAP1 ‐KO cells (#1 and #2) compared with parental (P) and BAP1 -WT (Ctrl) cells. The heatmap was constructed based on the normalized values of all samples using TreeView (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ). The corresponding upregulated or downregulated genes in the heatmap are shown on the right side. d RT-PCR analysis for mRNA expression levels of upregulated or downregulated genes in the MeT-5A and HOMC-D4 cells. Representative agarose gels for the RT-PCR products from the parental cells (P), BAP1 -WT cells (Ctrl), and BAP1 -KO cell lines (#1 and #2) are shown.

Article Snippet: The heatmap was constructed based on the normalized values of all samples using TreeView (Cluster 3.0) http://jtreeview ( http://jtreeview.sourceforge.net ).

Techniques: CRISPR, Sequencing, Clone Assay, Expressing, Western Blot, Control, Gene Expression, Construct, Reverse Transcription Polymerase Chain Reaction