java treeview version 1.1.6r4  (SourceForge net)

Journal: Scientific Reports

Article Title: Congenital sideroblastic anemia model due to ALAS2 mutation is susceptible to ferroptosis

doi: 10.1038/s41598-022-12940-9

Figure Lengend Snippet: Genes associated with oxidative stress protection are differentially expressed during erythroid differentiation. Enrichment analysis of HUDEP-2 clones using Metascape . After 6 day differentiation with SFC, 1265, 1750, and 1386 genes were upregulated (> 2-fold) for HUDEP WT , HUDEP R170L , and HUDEP R170H , respectively, compared with the undifferentiated HUDEP WT . These genes were analyzed, and enriched gene clusters were displayed as a heatmap that shows hypergeometric P -values of each annotated term. The heatmap is visualized using Java TreeView version 1.1.6r4 (jtreeview.sourceforge.net). EIF2AK1, eukaryotic translation initiation factor 2-alpha kinase 1; HRI, heme-regulated inhibitor.

Article Snippet: The heatmap is visualized using Java TreeView version 1.1.6r4 (jtreeview.sourceforge.net).

Techniques: Clone Assay

Journal: Scientific Reports

Article Title: Congenital sideroblastic anemia model due to ALAS2 mutation is susceptible to ferroptosis

doi: 10.1038/s41598-022-12940-9

Figure Lengend Snippet: XLSA clones show transcriptional alterations of the genes associated with glutathione synthesis. ( a ) Expression profiles of the genes registered to hsa04216 (ferroptosis pathway) of Kyoto Encyclopedia of Genes and Genomes in HUDEP WT , HUDEP R170L , and HUDEP R170H after 6 day differentiation with sodium ferrous citrate (SFC). The genes are arranged from the bottom in the order of the fold change of differentiated HUDEP WT to undifferentiated HUDEP WT . The heatmap is visualized using Java TreeView version 1.1.6r4 (jtreeview.sourceforge.net). ( b ) Western blotting for BACH1, GCLC, GCLM, and α-tubulin in HUDEP-2 clones after differentiation with SFC. Representative images of three independent experiments are presented. The cropped gel images are delineated, and the uncropped images can be found in Supplementary Fig. . ( c , e ) Chromatin immunoprecipitation with sequencing (ChIP-seq) analysis of the binding of BACH1 and MAFK for the gene region in K562 for HMOX1 , GCLM , and GCLC ( c ); and FTH1 , FTL , and SLC40A1 ( e ). We used ChIP-seq data from GEO (Gene Expression Omnibus) data set: BACH1 in K562, GSM935576; MAFK in K562, GSM935311; NFE2 in K562, GSM935414; and NFE2 in human erythroblasts, GSM1427076. E-blast, erythroblast. ( d , f ) Quantitative reverse transcriptase-polymerase chain reaction analysis for HMOX1 , GCLM , and GCLC ( d ); and FTH1 , FTL , and SLC40A1 ( f ) in HUDEP-2 clones after differentiation with SFC. The data were normalized relative to the GAPDH expression levels. ( g ) Intracellular glutathione concentration of HUDEP-2 clones after differentiation with SFC (n = 3). In ( d ), ( f ), and ( g ), the graphs were plotted using GraphPad Prism 9 (GraphPad Software, San Diego, CA, www.graphpad.com ). The error bars represent the standard error of the mean. Each P value was calculated using Tukey’s test after a one-way analysis of variance. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: The heatmap is visualized using Java TreeView version 1.1.6r4 (jtreeview.sourceforge.net).

Techniques: Clone Assay, Expressing, Western Blot, Chromatin Immunoprecipitation, Sequencing, ChIP-sequencing, Binding Assay, Gene Expression, Reverse Transcription, Polymerase Chain Reaction, Concentration Assay, Software