OriginLab corp origin software
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software medcalc version 9.30 (MedCalc Software Ltd)

MedCalc Software Ltd software medcalc version 9.30
Software Medcalc Version 9.30, supplied by MedCalc Software Ltd, 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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setd4cre (Shanghai Model Organisms Center)

Shanghai Model Organisms Center setd4cre

Figure 1. Characterization of Setd4-expressing intestinal cells (A) smFISH for Setd4 and Lgr5 expression in crypt (as indicated with dotted lines). Scale bar, 30 mm. (B) CD45EpCAM+CD44+ cells were sorted for sequencing using a 10X Genomics platform (n = 6 mice, age of 8 weeks). (C) Left, unsupervised clustering of scRNA-seq data from isolated crypt cells (n = 6,653 single-cell transcriptomes as classiﬁed in Figure S1D). Right, expression of Setd4 gene. (D) Cell proportions of the indicated genes that distinguish CBCs or RSCs in crypt cells. (E) Cellular composition of Setd4+ cells. (F) Left, violin plot of Mki67 expression. Middle, expression of proliferation markers (black outline) is overlaid on the t-SNE graph. Gene-expression values are shown as median of log10(CPM). Right, analysis of co-expression of Setd4+ cells with these proliferation markers with proportions shown (n = 237 Setd4+ cells). (G) Illustration of lineage tracing strategy in <t>Setd4cre-ERT2/+;</t> Rosa26lsl-tdTomato mice. (H) Detection of tdTomato and Setd4 mRNA transcripts (white transition point outline) by smFISH. Scale bar, 30 mm. (I) Left, image showing examples of tdT+ cells produced at +4 positions relative to the crypt base, with dotted lines indicating crypt boundaries. Right, position of tdT+ cells at 1 dpt (n = 371 cells from ﬁve mice). Scale bar, 30 mm. (J) Schematic of a 3D confocal imaging strategy of crypt and villus. Representative z stack images of villus and crypt, with sections at different depth of z axis. Scale bar, 50 mm.

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2017 n a agxt human tagged orf (OriGene)

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Figure 1. Dysregulated glycine and oxalate metabolism in patients and mice with atherosclerosis (A) Schematic representation of glycine metabolic pathways. (B–E) Targeted metabolomics assessing the ratios of glycine to (B) serine, (C) threonine, (D) alanine, and (E) oxalate in serum from age- and sex- matched patients with or without sCAD (n = 24). (F) En face analysis of atherosclerotic lesions in male Apoe/ mice fed a standard diet (SD) or Western diet (WD) for 12 weeks (n = 5). (G–J) Targeted metabolomics assessing the ratios of glycine to (G) serine, (H) threonine, (I) alanine, and (J) oxalate in plasma from male Apoe/ mice fed a SD or WD for 12 weeks (n = 5). (K) Western blot analysis of <t>AGXT</t> protein abun- dance in livers from Apoe/ mice fed a SD or WD for 12 weeks (n = 5). Mann-Whitney U test for (B)-(E), (G), (H), and (K). Unpaired t test for (F), (I), and (J). Data are pre- sented as mean ± SEM. All points and p values are shown.

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Image Search Results

Journal: Cell reports

Article Title: Embryogenic stem cell-derived intestinal crypt fission directs de novo crypt genesis.

doi: 10.1016/j.celrep.2022.111796

Figure Lengend Snippet: Figure 1. Characterization of Setd4-expressing intestinal cells (A) smFISH for Setd4 and Lgr5 expression in crypt (as indicated with dotted lines). Scale bar, 30 mm. (B) CD45EpCAM+CD44+ cells were sorted for sequencing using a 10X Genomics platform (n = 6 mice, age of 8 weeks). (C) Left, unsupervised clustering of scRNA-seq data from isolated crypt cells (n = 6,653 single-cell transcriptomes as classiﬁed in Figure S1D). Right, expression of Setd4 gene. (D) Cell proportions of the indicated genes that distinguish CBCs or RSCs in crypt cells. (E) Cellular composition of Setd4+ cells. (F) Left, violin plot of Mki67 expression. Middle, expression of proliferation markers (black outline) is overlaid on the t-SNE graph. Gene-expression values are shown as median of log10(CPM). Right, analysis of co-expression of Setd4+ cells with these proliferation markers with proportions shown (n = 237 Setd4+ cells). (G) Illustration of lineage tracing strategy in Setd4cre-ERT2/+; Rosa26lsl-tdTomato mice. (H) Detection of tdTomato and Setd4 mRNA transcripts (white transition point outline) by smFISH. Scale bar, 30 mm. (I) Left, image showing examples of tdT+ cells produced at +4 positions relative to the crypt base, with dotted lines indicating crypt boundaries. Right, position of tdT+ cells at 1 dpt (n = 371 cells from ﬁve mice). Scale bar, 30 mm. (J) Schematic of a 3D confocal imaging strategy of crypt and villus. Representative z stack images of villus and crypt, with sections at different depth of z axis. Scale bar, 50 mm.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Glycerol Sangon Biotech Cat# A600232-0500 ProLongTM glass antifade mountant Thermo Fisher Cat# P36980 Isoflurane RWD Cat# R510-22 Critical commercial assays Click-iT EdU Alexa Fluor 647 Imaging Kit Thermo Fisher Cat# C10640 Advanced Cell Diagnostics RNAscope 2.0 HD Detection Kit Advanced Cell Diagnostics Cat# 323100 Deposited data Raw RNA-seq data This manuscript SRA: PRJNA741073 Experimental models: Organisms/strains Mouse: C57BL/6J Shanghai Model Organisms Center N/A Mouse: Rosa26lsl-tdTomato Jackson Laboratory JAX No. 007905 Mouse: Rosa26mT/mG Jackson Laboratory JAX No. 007676 Mouse: Setd4cre/+ Shanghai Model Organisms Center This manuscript Mouse: Setd4cre-ERT2/+ Shanghai Model Organisms Center This manuscript Oligonucleotides Primers for Setd4, see Table S1 This manuscript N/A Primers for mT/mG, see Table S1 This manuscript N/A Primers for Foxg1, see Table S1 This manuscript N/A Primers for Globin, see Table S1 This manuscript N/A Primers for tdTomato, see Table S1 This manuscript N/A Mm-Lgr5 probe Advanced Cell Diagnostics Cat# 312171-C2 Mm-Clu probe Advanced Cell Diagnostics Cat# 427891-C3 TdTomato probe Advanced Cell Diagnostics Cat# 317041-C2 Mm-Setd4 probe Advanced Cell Diagnostics Cat# 874641-C1 Bacterial dapB probe Advanced Cell Diagnostics Cat# 320871 Software and algorithms FlowJo (V10) Treestar https://www.flowjo.com/solutions/ flowjo/downloads CytExpert software (V2.3) Beckman https://www.beckman.com/flow-cytometry/ research-flow-cytometers/cytoflex/software CellRanger (V3.1.0) 10X Genomics https://support.10xgenomics.com/single- cell-gene-expression/software/pipelines/ latest/installation Seurat (V3.1.0) Satija Lab http://seurat.r-forge.r-project.org/ ZEN Blue (V2.6) Zeiss N/A Olympus FV31-SW software (V2.3) Olympus N/A Leica Application Suite X (V3.3.0.16799) Leica N/A GraphPad Prism (V8.0.1) GraphPad https://www.graphpad.com/scientificsoftware/ prism/ ImageJ (V1.52p).

Techniques: Expressing, Sequencing, Isolation, Gene Expression, Produced, Imaging

Figure 3. Setd4+ cells are resistant to irradiation and produce Sca-1+ cells for tissue repair (A) Experimental overview. Setd4cre-ERT2/+; Rosa26lsl-tdTomato mice (age of 8–12 weeks) were pulsed with a single TAM injection, followed by irradiation and tissue analyses (at least three mice for each time point). (B and C) Whole-mount imaging (B) and section imaging (C) of gut tube from non-irradiated (non-IR) or irradiated (IR) mice at 1 day post irradiation (1 dpi) showing the resistance of Setd4+ cells to X-ray. Boxed areas were magniﬁed on the right with dotted lines indicating the crypt boundaries. Scale bar, 100 mm. (D) Absolute numbers of tdT+ cells per ten crypts at 1 dpi was quantiﬁed (n = 3 mice each; two-tailed unpaired Student’s t test; data are mean ± SEM). (E) Left, detection of Olfm4 in sections of the small intestine from non-IR or IR mice at 1 dpi. Scale bar, 100 mm. Right, western blot analysis of Olfm4 in non-IR and IR groups (n = 4 mice analyzed for each; two-tailed unpaired Student’s t test; data are mean ± SEM). (F) Left, detection of tdTomato and EdU in sections from non-IR mice or IR mice with 1-h EdU incorporation at 3 dpi. Each crypt (circled with dotted lines) is magniﬁed to the right. Right, the percentage of tdTomato+EdU+ cells was quantiﬁed (n = 3 mice analyzed for each; two-tailed unpaired Student’s t test; data are mean ± SEM). Scale bar, 50 mm. (G) Detection of tdTomato and Sca-1 with dotted lines indicating crypt boundaries. Scale bar, 50 mm. (H) Flow cytometry of Sca-1 and tdTomato in crypt cells (gating strategy plots in Figure S3B; n = 3 mice at non-IR group and n = 7 mice at IR group analyzed; two- tailed unpaired Student’s t test; data are mean ± SEM).

Journal: Cell reports

Article Title: Embryogenic stem cell-derived intestinal crypt fission directs de novo crypt genesis.

doi: 10.1016/j.celrep.2022.111796

Figure Lengend Snippet: Figure 3. Setd4+ cells are resistant to irradiation and produce Sca-1+ cells for tissue repair (A) Experimental overview. Setd4cre-ERT2/+; Rosa26lsl-tdTomato mice (age of 8–12 weeks) were pulsed with a single TAM injection, followed by irradiation and tissue analyses (at least three mice for each time point). (B and C) Whole-mount imaging (B) and section imaging (C) of gut tube from non-irradiated (non-IR) or irradiated (IR) mice at 1 day post irradiation (1 dpi) showing the resistance of Setd4+ cells to X-ray. Boxed areas were magniﬁed on the right with dotted lines indicating the crypt boundaries. Scale bar, 100 mm. (D) Absolute numbers of tdT+ cells per ten crypts at 1 dpi was quantiﬁed (n = 3 mice each; two-tailed unpaired Student’s t test; data are mean ± SEM). (E) Left, detection of Olfm4 in sections of the small intestine from non-IR or IR mice at 1 dpi. Scale bar, 100 mm. Right, western blot analysis of Olfm4 in non-IR and IR groups (n = 4 mice analyzed for each; two-tailed unpaired Student’s t test; data are mean ± SEM). (F) Left, detection of tdTomato and EdU in sections from non-IR mice or IR mice with 1-h EdU incorporation at 3 dpi. Each crypt (circled with dotted lines) is magniﬁed to the right. Right, the percentage of tdTomato+EdU+ cells was quantiﬁed (n = 3 mice analyzed for each; two-tailed unpaired Student’s t test; data are mean ± SEM). Scale bar, 50 mm. (G) Detection of tdTomato and Sca-1 with dotted lines indicating crypt boundaries. Scale bar, 50 mm. (H) Flow cytometry of Sca-1 and tdTomato in crypt cells (gating strategy plots in Figure S3B; n = 3 mice at non-IR group and n = 7 mice at IR group analyzed; two- tailed unpaired Student’s t test; data are mean ± SEM).

Techniques: Irradiation, Injection, Imaging, Two Tailed Test, Western Blot, Flow Cytometry

Figure 7. Sedt4+ cells contribute to the construction of new crypts after birth (A) Experimental overview. (B) Representative images of tdT+ clones in whole mounts of crypt. The white transition points outlined are magniﬁed in the corresponding boxed areas (n = 4 mice each point). Scale bar, 100 mm. (C) A representative whole-mount image of the crypt ﬁssion. Sections show differing z axis depths. Yellow arrows indicate a base-to-top (from Z = 1 to Z = 55) change of crypt lumens within a crypt undergoing ﬁssion. Scale bar, 20 mm. (D) Representative images of tdT+ clones in section of intestinal crypts at P6 and P15. Dotted lines indicate crypt boundaries. Scale bar, 50 mm. (E) Top, experimental overview. Bottom, representative whole-mount images of tdT+ clones at P35 and P55. Boxed areas are magniﬁed to the right. Yellow arrows indicate the n R 2 tdT+ crypts adjacent to each other. Scale bar, 1 mm. (F) Gross morphology of the small intestine and colon at P55 (50 dpt) showing the distribution of tdT+ clones. Scale bar, 3 mm. (G) Representative images of continuous crypts organized by tdT+ cells. Scale bar, 50 mm. (H) The percentage of continuous tdT+ crypt clones in total crypt clones labeled by tdTomato from the proximal (pro) small intestine quantiﬁed at indicated chase times (n = 3 mice respectively, two-tailed unpaired Student’s t test; data are mean ± SEM). (I) Left, model summarizing two possible ﬂuxes of tdT+ cells based on crypt ﬁssion. Right, a representative image of ribbons with continuous tdT+ crypts. Scale bar, 50 mm. (J) Experimental overview. Setd4cre-ERT2/+; Rosa26lsl-tdTomato mice were pulsed with a single TAM injection at P25 as control and chased at P75 (50 dpt). The P5 TAM-induced group was chased at P55 (50 dpt). (K) Left, representative whole-mount images of tdT+ clones (crypt-villus). Boxed areas (left) are magniﬁed to the right. Far right, tdTomato-inﬁltrate crypts identiﬁed as in the left image and the percentage of continuous tdT+ crypt clones in total crypt clones labeled by tdTomato and quantiﬁed (n = 3 mice respectively analyzed, two-tailed unpaired Student’s t test; data are mean ± SEM). Scale bar, 1 mm. (L) The number of tdT+ crypts per 1-mm2 area of the proximal (Pro) or distal (Dis) small intestinal epithelium from P5 and P25 TAM-induced groups was quantiﬁed at 50 dpt (n = 90 images as K analyzed; n = 3 mice each; two-tailed Mann-Whitney test; box edges show 25th and 75th percentile, with the central point as the median and minimum and maximum values also shown). See also Figure S6.

Journal: Cell reports

Article Title: Embryogenic stem cell-derived intestinal crypt fission directs de novo crypt genesis.

doi: 10.1016/j.celrep.2022.111796

Figure Lengend Snippet: Figure 7. Sedt4+ cells contribute to the construction of new crypts after birth (A) Experimental overview. (B) Representative images of tdT+ clones in whole mounts of crypt. The white transition points outlined are magniﬁed in the corresponding boxed areas (n = 4 mice each point). Scale bar, 100 mm. (C) A representative whole-mount image of the crypt ﬁssion. Sections show differing z axis depths. Yellow arrows indicate a base-to-top (from Z = 1 to Z = 55) change of crypt lumens within a crypt undergoing ﬁssion. Scale bar, 20 mm. (D) Representative images of tdT+ clones in section of intestinal crypts at P6 and P15. Dotted lines indicate crypt boundaries. Scale bar, 50 mm. (E) Top, experimental overview. Bottom, representative whole-mount images of tdT+ clones at P35 and P55. Boxed areas are magniﬁed to the right. Yellow arrows indicate the n R 2 tdT+ crypts adjacent to each other. Scale bar, 1 mm. (F) Gross morphology of the small intestine and colon at P55 (50 dpt) showing the distribution of tdT+ clones. Scale bar, 3 mm. (G) Representative images of continuous crypts organized by tdT+ cells. Scale bar, 50 mm. (H) The percentage of continuous tdT+ crypt clones in total crypt clones labeled by tdTomato from the proximal (pro) small intestine quantiﬁed at indicated chase times (n = 3 mice respectively, two-tailed unpaired Student’s t test; data are mean ± SEM). (I) Left, model summarizing two possible ﬂuxes of tdT+ cells based on crypt ﬁssion. Right, a representative image of ribbons with continuous tdT+ crypts. Scale bar, 50 mm. (J) Experimental overview. Setd4cre-ERT2/+; Rosa26lsl-tdTomato mice were pulsed with a single TAM injection at P25 as control and chased at P75 (50 dpt). The P5 TAM-induced group was chased at P55 (50 dpt). (K) Left, representative whole-mount images of tdT+ clones (crypt-villus). Boxed areas (left) are magniﬁed to the right. Far right, tdTomato-inﬁltrate crypts identiﬁed as in the left image and the percentage of continuous tdT+ crypt clones in total crypt clones labeled by tdTomato and quantiﬁed (n = 3 mice respectively analyzed, two-tailed unpaired Student’s t test; data are mean ± SEM). Scale bar, 1 mm. (L) The number of tdT+ crypts per 1-mm2 area of the proximal (Pro) or distal (Dis) small intestinal epithelium from P5 and P25 TAM-induced groups was quantiﬁed at 50 dpt (n = 90 images as K analyzed; n = 3 mice each; two-tailed Mann-Whitney test; box edges show 25th and 75th percentile, with the central point as the median and minimum and maximum values also shown). See also Figure S6.

Techniques: Clone Assay, Labeling, Two Tailed Test, Injection, Control, MANN-WHITNEY

Journal: Cell reports

Article Title: Dysregulated oxalate metabolism is a driver and therapeutic target in atherosclerosis.

doi: 10.1016/j.celrep.2021.109420

Figure Lengend Snippet: Figure 1. Dysregulated glycine and oxalate metabolism in patients and mice with atherosclerosis (A) Schematic representation of glycine metabolic pathways. (B–E) Targeted metabolomics assessing the ratios of glycine to (B) serine, (C) threonine, (D) alanine, and (E) oxalate in serum from age- and sex- matched patients with or without sCAD (n = 24). (F) En face analysis of atherosclerotic lesions in male Apoe/ mice fed a standard diet (SD) or Western diet (WD) for 12 weeks (n = 5). (G–J) Targeted metabolomics assessing the ratios of glycine to (G) serine, (H) threonine, (I) alanine, and (J) oxalate in plasma from male Apoe/ mice fed a SD or WD for 12 weeks (n = 5). (K) Western blot analysis of AGXT protein abun- dance in livers from Apoe/ mice fed a SD or WD for 12 weeks (n = 5). Mann-Whitney U test for (B)-(E), (G), (H), and (K). Unpaired t test for (F), (I), and (J). Data are pre- sented as mean ± SEM. All points and p values are shown.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Primer sequences for Agxt genotyping:, forward: 50-ACACCTCCACTGTCCTG TCC-30 Integrated DNA Technologies N/A Primer sequences for Agxt genotyping:, reverse: 50-GGTCAGATCTGCCTGCTA CC-30 Integrated DNA Technologies N/A Primer for Sanger sequencing:, 50-GCAGAGCTAGCTGGGAAATG-30 Integrated DNA Technologies N/A Primer sequences for Apoe genotyping:, forward: 50-GCCTAGCCGAGGGAGAG CCG-30 Integrated DNA Technologies N/A Primer sequences for Apoe genotyping:, reverse 1: 50-TGTGACTTGGGAGCTC TGCAGC-30 Integrated DNA Technologies N/A Primer sequences for Apoe genotyping:, reverse 2: 50-GCCGCCCCGACTGC ATCT-30 Integrated DNA Technologies N/A Primer sequences for qPCR, see Table S2 Integrated DNA Technologies N/A Recombinant DNA pAdDeltaF6 Jiandie Lin’s lab, University of Michigan; Guo et al., 2017 N/A pAAV2/8 Jiandie Lin’s lab, University of Michigan; Guo et al., 2017 N/A pAAV-TBG-GFP Jiandie Lin’s lab, University of Michigan; Guo et al., 2017 N/A pAAV-TBG-MCS Jiandie Lin’s lab, University of Michigan; Guo et al., 2017 N/A AGXT Human Tagged ORF Clone Origene CAT# RG212899 Software and algorithms ImageJ National Institutes of Health RRID:SCR_003070 https://imagej.nih.gov/ ij/download.html GraphPad Prism GraphPad Software Version 8.0 RRID:SCR_002798 https:// www.graphpad.com/scientific-software/ prism/ R statistics Hosted by Vienna, University of Economics and Business http://www.R-project.org/ RStudio RStudio Team (2020). https://www.rstudio.com/ RRID:SCR_000432 IBM SPSS software IBM Corporation Version 23.0; RRID:SCR_019096 https:// www.ibm.com/analytics/ spss-statistics-software FastQC Babraham Bioinformatics Version 0.11.8 RRID:SCR_014583 https:// www.bioinformatics.babraham.ac.uk/ projects/fastqc/ Trimmomatic Bolger et al., 2014 Version 0.35 RRID:SCR_011848 http:// www.usadellab.org/cms/? page=trimmomatic HISAT2 Kim et al., 2015 Version 2.1.0.13; RRID:SCR_015530 http:// daehwankimlab.github.io/hisat2/ download/ HTSeq Anders et al., 2015 Version 0.6.0; RRID:SCR_005514 https:// htseq.readthedocs.io/en/master/install. html (Continued on next page) Cell Reports 36, 109420, July 27, 2021 e3 Article ll OPEN ACCESS

Techniques: Western Blot, Clinical Proteomics, MANN-WHITNEY

Figure 2. AGXT deﬁciency exacerbates atherosclerosis in male Apoe/ mice (A) Western blot analysis conﬁrming the loss of AGXT in livers from male Agxt//Apoe/ mice (n = 6). (B) Glycine/oxalate ratio in plasma from male Agxt//Apoe/ mice and their Agxt+/+/Apoe/

Journal: Cell reports

Article Title: Dysregulated oxalate metabolism is a driver and therapeutic target in atherosclerosis.

doi: 10.1016/j.celrep.2021.109420

Figure Lengend Snippet: Figure 2. AGXT deﬁciency exacerbates atherosclerosis in male Apoe/ mice (A) Western blot analysis conﬁrming the loss of AGXT in livers from male Agxt//Apoe/ mice (n = 6). (B) Glycine/oxalate ratio in plasma from male Agxt//Apoe/ mice and their Agxt+/+/Apoe/

Techniques: Western Blot, Clinical Proteomics

Figure 3. Oxalate homeostasis is main- tained and atherosclerosis is unaltered in fe- male Agxt//Apoe/ mice (A) Western blot analysis conﬁrming the loss of AGXT in livers from female Agxt//Apoe/ mice (n = 6). (B) GlGlycine/oxalate ratio in plasma from female Agxt//Apoe/ and Agxt+/+/Apoe/ mice (n = 10). (C–G) Female Agxt//Apoe/ and Agxt+/+/ Apoe/ mice were fed a WD for 12 weeks (n = 10): (C) plasma TC, (D) atherosclerosis in the aortic tree, (E) H&E staining, (F) ORO staining, and (G) Mac-2 immunohistochemistry of aortic sinus. Scale bars, 200 mm. Unpaired t test for (B), (D), (E), and (G). Mann- Whitney U test for (C) and (F). Data are presented as mean ± SEM. All points and p values are shown.

Journal: Cell reports

Article Title: Dysregulated oxalate metabolism is a driver and therapeutic target in atherosclerosis.

doi: 10.1016/j.celrep.2021.109420

Figure Lengend Snippet: Figure 3. Oxalate homeostasis is main- tained and atherosclerosis is unaltered in fe- male Agxt//Apoe/ mice (A) Western blot analysis conﬁrming the loss of AGXT in livers from female Agxt//Apoe/ mice (n = 6). (B) GlGlycine/oxalate ratio in plasma from female Agxt//Apoe/ and Agxt+/+/Apoe/ mice (n = 10). (C–G) Female Agxt//Apoe/ and Agxt+/+/ Apoe/ mice were fed a WD for 12 weeks (n = 10): (C) plasma TC, (D) atherosclerosis in the aortic tree, (E) H&E staining, (F) ORO staining, and (G) Mac-2 immunohistochemistry of aortic sinus. Scale bars, 200 mm. Unpaired t test for (B), (D), (E), and (G). Mann- Whitney U test for (C) and (F). Data are presented as mean ± SEM. All points and p values are shown.

Techniques: Western Blot, Clinical Proteomics, Staining, Immunohistochemistry, MANN-WHITNEY

Figure 4. Dysregulated oxalate metabolism induces a pro-inﬂammatory response and CCL5 release (A–C) RNA sequencing of livers collected from male Agxt//Apoe/ and Agxt+/+/Apoe/ mice fed a WD for 12 weeks (n = 5): (A) volcano plot of DEGs (padj < 0.05, log2 fold change > 1) in male Agxt//Apoe/ versus Agxt+/+/Apoe/ mice (blue indicates downregulated; red indicates upregulated). (B) Kyoto Encyclopedia of Genes and Genomes (KEGG)-based pathway analysis. The signiﬁcance of the enrichment was determined by a right-tailed Fisher’s exact test followed by a Benjamini-Hochberg multiple testing adjustment. (C) Heatmap-based representation of 50 DEGs linking inﬂammation, ﬁbrogenesis, and the metabolism of lipids and sterols/steroids with atherosclerosis.

Journal: Cell reports

Article Title: Dysregulated oxalate metabolism is a driver and therapeutic target in atherosclerosis.

doi: 10.1016/j.celrep.2021.109420

Figure Lengend Snippet: Figure 4. Dysregulated oxalate metabolism induces a pro-inﬂammatory response and CCL5 release (A–C) RNA sequencing of livers collected from male Agxt//Apoe/ and Agxt+/+/Apoe/ mice fed a WD for 12 weeks (n = 5): (A) volcano plot of DEGs (padj < 0.05, log2 fold change > 1) in male Agxt//Apoe/ versus Agxt+/+/Apoe/ mice (blue indicates downregulated; red indicates upregulated). (B) Kyoto Encyclopedia of Genes and Genomes (KEGG)-based pathway analysis. The signiﬁcance of the enrichment was determined by a right-tailed Fisher’s exact test followed by a Benjamini-Hochberg multiple testing adjustment. (C) Heatmap-based representation of 50 DEGs linking inﬂammation, ﬁbrogenesis, and the metabolism of lipids and sterols/steroids with atherosclerosis.

Techniques: RNA Sequencing

Figure 5. Oxalate overload induces mito- chondrial dysfunction and overproduction of superoxide, leading to CCL5 release in macrophages (A) qPCR analyses of genes regulating redox ho- meostasis in livers from male Agxt//Apoe/

Journal: Cell reports

Article Title: Dysregulated oxalate metabolism is a driver and therapeutic target in atherosclerosis.

doi: 10.1016/j.celrep.2021.109420

Figure Lengend Snippet: Figure 5. Oxalate overload induces mito- chondrial dysfunction and overproduction of superoxide, leading to CCL5 release in macrophages (A) qPCR analyses of genes regulating redox ho- meostasis in livers from male Agxt//Apoe/

Techniques:

Figure 6. AAV-mediated overexpression of AGXT reduces oxidative stress and inﬂammation AAV-AGXT or AAV-GFP was injected into male Apoe/ mice and the mice were fed a WD for 12 weeks (n = 8). (A) Western blot analysis conﬁrming the over- expression of AGXT in livers from mice treated with AAV-AGXT. (B) Plasma glycine/oxalate ratio. (C and D) qPCR analyses of genes regulating (C) redox homeostasis and (D) inﬂammatory re- sponses. Gene expression levels were normalized to 18S. (E and F) Plasma concentrations of (E) CCL2 and (F) CCL5. (G) DHE ﬂuorescence and Mac-2 immunoﬂuores- cence in the aortic sinuses. Scale bars, 50 mm. Unpaired t test for (B), (E), and (G), and Mann- Whitney U test for (F). Statistical differences in gene expression in (C) and (D) were tested using unpaired t test or Mann-Whitney U test, depending on normality tests. *P < 0.05, **P <0.01, ***P <0.001 versus mice injected with AAV-GFP. Data are presented as mean ± SEM. All points and p values are shown.

Journal: Cell reports

Article Title: Dysregulated oxalate metabolism is a driver and therapeutic target in atherosclerosis.

doi: 10.1016/j.celrep.2021.109420

Figure Lengend Snippet: Figure 6. AAV-mediated overexpression of AGXT reduces oxidative stress and inﬂammation AAV-AGXT or AAV-GFP was injected into male Apoe/ mice and the mice were fed a WD for 12 weeks (n = 8). (A) Western blot analysis conﬁrming the over- expression of AGXT in livers from mice treated with AAV-AGXT. (B) Plasma glycine/oxalate ratio. (C and D) qPCR analyses of genes regulating (C) redox homeostasis and (D) inﬂammatory re- sponses. Gene expression levels were normalized to 18S. (E and F) Plasma concentrations of (E) CCL2 and (F) CCL5. (G) DHE ﬂuorescence and Mac-2 immunoﬂuores- cence in the aortic sinuses. Scale bars, 50 mm. Unpaired t test for (B), (E), and (G), and Mann- Whitney U test for (F). Statistical differences in gene expression in (C) and (D) were tested using unpaired t test or Mann-Whitney U test, depending on normality tests. *P < 0.05, **P <0.01, ***P <0.001 versus mice injected with AAV-GFP. Data are presented as mean ± SEM. All points and p values are shown.

Techniques: Over Expression, Injection, Western Blot, Clinical Proteomics, Gene Expression, MANN-WHITNEY

Figure 7. AAV-mediated overexpression of AGXT reduces atherosclerosis independent of circulating cholesterol AAV-AGXT or AAV-GFP was injected into male Apoe/ mice and the mice were fed a WD for 12 weeks (n = 8). (A) Plasma TC. (B) Atherosclerosis in the aortic tree. (C–E) H&E staining (D), ORO staining (D), and Mac- 2 immunohistochemistry (E) of aortic sinus. Scale bars, 200 mm. (F) Proposed model of dysregulated oxalate metabolism as a driver and therapeutic target in atherosclerosis. Unpaired t test for (A)–(E). Data are presented as mean ± SEM. All points and p values are shown.

Journal: Cell reports

Article Title: Dysregulated oxalate metabolism is a driver and therapeutic target in atherosclerosis.

doi: 10.1016/j.celrep.2021.109420

Figure Lengend Snippet: Figure 7. AAV-mediated overexpression of AGXT reduces atherosclerosis independent of circulating cholesterol AAV-AGXT or AAV-GFP was injected into male Apoe/ mice and the mice were fed a WD for 12 weeks (n = 8). (A) Plasma TC. (B) Atherosclerosis in the aortic tree. (C–E) H&E staining (D), ORO staining (D), and Mac- 2 immunohistochemistry (E) of aortic sinus. Scale bars, 200 mm. (F) Proposed model of dysregulated oxalate metabolism as a driver and therapeutic target in atherosclerosis. Unpaired t test for (A)–(E). Data are presented as mean ± SEM. All points and p values are shown.

Techniques: Over Expression, Injection, Clinical Proteomics, Staining, Immunohistochemistry

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