rapid mace seq kit  (GenXPro Inc)

 
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    GenXPro Inc rapid mace seq kit
    a) Schematic drawing of the experimental setup. <t>MACE-seq</t> was performed on samples from brain-like ECs (in co-culture with PCs), with or without 48 <t>h</t> <t>cARLA</t> treatment. b) Principal component analysis (PCA) plot of control and cARLA samples. c) Venn-diagram showing the number of genes upregulated (log 2 FC ≥ 0.2 and FDR < 0.01), downregulated (log 2 FC ≥ -0.2 and FDR < 0.01) or not changed (|log 2 FC| < 0.2 and/or FDR ≥ 0.01) upon cARLA treatment. Log 2 FC: log 2 (fold change), FDR: false discovery rate. d) Mean-difference (MD) plot presenting the range and distribution of all transcripts (circles) regarding their mean expression and log 2 FC upon cARLA treatment. Key transcripts related to different aspects of BBB function are highlighted. e) Functional enrichment analysis of up- and downregulated gene sets upon cARLA treatment using g:Profiler. Gene Ontology Biological Process (GO:BP) terms are ranked based on their gene ratio (the fraction of differentially expressed genes in a given term) and are colored based on statistical significance (FDR). f) Representative staining of F-actin (grey), with or without cARLA treatment. Nuclei were stained with Hoechst (blue). Bar: 40 µm. g) Validation of the definitive endothelial nature of human stem cell-derived brain-like ECs. Normalized counts of key epithelial and endothelial transcripts from our dataset are plotted on a 3-segment y-axis covering multiple orders of magnitude. h) Scaled heatmap of 92 transcripts that are enriched in mouse brain ECs and are well expressed at the human BBB. Genes upregulated, downregulated or not changed upon cARLA treatment as well as genes not expressed (normalized counts ≤ 1) in this model are shown separately, in alphabetical order. Color coding represents row z-scores after Min-Max normalization, the darkest color corresponding to the highest expression in a given row.
    Rapid Mace Seq Kit, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    rapid mace seq kit - by Bioz Stars, 2023-03
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    1) Product Images from "A small molecule cocktail for robust induction of blood-brain barrier properties"

    Article Title: A small molecule cocktail for robust induction of blood-brain barrier properties

    Journal: bioRxiv

    doi: 10.1101/2023.02.09.527899

    a) Schematic drawing of the experimental setup. MACE-seq was performed on samples from brain-like ECs (in co-culture with PCs), with or without 48 h cARLA treatment. b) Principal component analysis (PCA) plot of control and cARLA samples. c) Venn-diagram showing the number of genes upregulated (log 2 FC ≥ 0.2 and FDR < 0.01), downregulated (log 2 FC ≥ -0.2 and FDR < 0.01) or not changed (|log 2 FC| < 0.2 and/or FDR ≥ 0.01) upon cARLA treatment. Log 2 FC: log 2 (fold change), FDR: false discovery rate. d) Mean-difference (MD) plot presenting the range and distribution of all transcripts (circles) regarding their mean expression and log 2 FC upon cARLA treatment. Key transcripts related to different aspects of BBB function are highlighted. e) Functional enrichment analysis of up- and downregulated gene sets upon cARLA treatment using g:Profiler. Gene Ontology Biological Process (GO:BP) terms are ranked based on their gene ratio (the fraction of differentially expressed genes in a given term) and are colored based on statistical significance (FDR). f) Representative staining of F-actin (grey), with or without cARLA treatment. Nuclei were stained with Hoechst (blue). Bar: 40 µm. g) Validation of the definitive endothelial nature of human stem cell-derived brain-like ECs. Normalized counts of key epithelial and endothelial transcripts from our dataset are plotted on a 3-segment y-axis covering multiple orders of magnitude. h) Scaled heatmap of 92 transcripts that are enriched in mouse brain ECs and are well expressed at the human BBB. Genes upregulated, downregulated or not changed upon cARLA treatment as well as genes not expressed (normalized counts ≤ 1) in this model are shown separately, in alphabetical order. Color coding represents row z-scores after Min-Max normalization, the darkest color corresponding to the highest expression in a given row.
    Figure Legend Snippet: a) Schematic drawing of the experimental setup. MACE-seq was performed on samples from brain-like ECs (in co-culture with PCs), with or without 48 h cARLA treatment. b) Principal component analysis (PCA) plot of control and cARLA samples. c) Venn-diagram showing the number of genes upregulated (log 2 FC ≥ 0.2 and FDR < 0.01), downregulated (log 2 FC ≥ -0.2 and FDR < 0.01) or not changed (|log 2 FC| < 0.2 and/or FDR ≥ 0.01) upon cARLA treatment. Log 2 FC: log 2 (fold change), FDR: false discovery rate. d) Mean-difference (MD) plot presenting the range and distribution of all transcripts (circles) regarding their mean expression and log 2 FC upon cARLA treatment. Key transcripts related to different aspects of BBB function are highlighted. e) Functional enrichment analysis of up- and downregulated gene sets upon cARLA treatment using g:Profiler. Gene Ontology Biological Process (GO:BP) terms are ranked based on their gene ratio (the fraction of differentially expressed genes in a given term) and are colored based on statistical significance (FDR). f) Representative staining of F-actin (grey), with or without cARLA treatment. Nuclei were stained with Hoechst (blue). Bar: 40 µm. g) Validation of the definitive endothelial nature of human stem cell-derived brain-like ECs. Normalized counts of key epithelial and endothelial transcripts from our dataset are plotted on a 3-segment y-axis covering multiple orders of magnitude. h) Scaled heatmap of 92 transcripts that are enriched in mouse brain ECs and are well expressed at the human BBB. Genes upregulated, downregulated or not changed upon cARLA treatment as well as genes not expressed (normalized counts ≤ 1) in this model are shown separately, in alphabetical order. Color coding represents row z-scores after Min-Max normalization, the darkest color corresponding to the highest expression in a given row.

    Techniques Used: Co-Culture Assay, Expressing, Functional Assay, Staining, Derivative Assay

    Gene expressional changes after 48 h cARLA treatment were determined using MACE-seq profiling and are presented in panels a-i) by category. Mean ± SD, n =4. Red and blue color indicates up- and downregulation, respectively, upon cARLA treatment.
    Figure Legend Snippet: Gene expressional changes after 48 h cARLA treatment were determined using MACE-seq profiling and are presented in panels a-i) by category. Mean ± SD, n =4. Red and blue color indicates up- and downregulation, respectively, upon cARLA treatment.

    Techniques Used:

    mace seq kit  (GenXPro Inc)

     
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    GenXPro Inc mace seq kit
    Mace Seq Kit, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    mace seq kit  (GenXPro Inc)

     
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    GenXPro Inc mace seq kit
    Mace Seq Kit, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mace seq kit/product/GenXPro Inc
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    GenXPro Inc mace seq kit
    Mace Seq Kit, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mace seq kit/product/GenXPro Inc
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    mace seq kit  (GenXPro Inc)

     
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    GenXPro Inc mace seq kit
    Mace Seq Kit, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/mace seq kit/product/GenXPro Inc
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    GenXPro Inc mace seq kit v2 0
    Mace Seq Kit V2 0, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GenXPro Inc mace seq kit
    Mace Seq Kit, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GenXPro Inc mace seq kit
    A . All four vector constructs are depicted. Shown is only the expressed part of the different Sleeping Beauty vectors that have been used. Importantly, all inducible direct fusions were cloned into vectors that express constitutively eGFP and the Puromycin resistance genes, while the reciprocal vectors express constitutively dTom together with the Blasticidin resistance gene. Since the construction of these vectors was done by separating the <t>two</t> <t>cDNA</t> fragments by a short intronic sequence, proper splicing was validated by RT-PCR and sanger sequencing of the resulting PCR product (depicted as “validated splice junction)”. The red box with the annotation “1” represents AF6 exon 1. Pink boxes at the beginning or end of the fusion genes indicate the presence of Flag-Tags in all constructs. B The construction of all 6 cell lines is shown. The encoded MLL protein domains and portions are displayed in different blue colors, while encoded Afadin/AF6 protein domains and portions are displayed in different red colors. Important MLL domains are: M/LBS: MEN1/LEDGF Binding Site; CXXC: CXXC domain; PHD/BD: PHD/BD domain; HBS: HAT Binding Site (CREBBP/MOF1); SET: SET domain). Similarly, important Afadin/AF6 domains are: RBD1/2: RAS/RAP Binding Domain 1 and 2; PDZ: PDF domain; ABD: Actin Binding domain. Besides these 6 cell lines, a control cell line with a Sleeping Beauty mock vector was established as well (pSBtet-GP). This control cell line expresses a luciferase gene instead of a fusion gene, and constitutively expresses GFP (G) together with a Puromycin resistance gene (P). Induction with 1 µg/ml Doxycyclin was carried out for 48 h in all seven cell lines before RNA or DNA was harvested to investigate changes in gene expression <t>(MACE)</t> or chromatin accessibility (ATAC-Seq). RT-PCR experiments were performed to validate the correct expression of all fusion transgenes next to their wildtype counterparts (endogenous genes MLL and AF6 ). It was important to demonstrate that all transgenes were not very highly overexpressed, rather were expressed in all cells at physiological levels. Below: Expression of the vector backbone fluorescent proteins (FP’s). Pictures were taken from all six cell lines by making photographs from the green and red channels or were merged to demonstrate the expression of the FP’s from the appropriate vector backbones. A picture of the GFP-positive mock-cell line is not displayed.
    Mace Seq Kit, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    1) Product Images from "The role of reciprocal fusions in MLL -r acute leukemia: studying the chromosomal translocation t(6;11)"

    Article Title: The role of reciprocal fusions in MLL -r acute leukemia: studying the chromosomal translocation t(6;11)

    Journal: Oncogene

    doi: 10.1038/s41388-021-01983-3

    A . All four vector constructs are depicted. Shown is only the expressed part of the different Sleeping Beauty vectors that have been used. Importantly, all inducible direct fusions were cloned into vectors that express constitutively eGFP and the Puromycin resistance genes, while the reciprocal vectors express constitutively dTom together with the Blasticidin resistance gene. Since the construction of these vectors was done by separating the two cDNA fragments by a short intronic sequence, proper splicing was validated by RT-PCR and sanger sequencing of the resulting PCR product (depicted as “validated splice junction)”. The red box with the annotation “1” represents AF6 exon 1. Pink boxes at the beginning or end of the fusion genes indicate the presence of Flag-Tags in all constructs. B The construction of all 6 cell lines is shown. The encoded MLL protein domains and portions are displayed in different blue colors, while encoded Afadin/AF6 protein domains and portions are displayed in different red colors. Important MLL domains are: M/LBS: MEN1/LEDGF Binding Site; CXXC: CXXC domain; PHD/BD: PHD/BD domain; HBS: HAT Binding Site (CREBBP/MOF1); SET: SET domain). Similarly, important Afadin/AF6 domains are: RBD1/2: RAS/RAP Binding Domain 1 and 2; PDZ: PDF domain; ABD: Actin Binding domain. Besides these 6 cell lines, a control cell line with a Sleeping Beauty mock vector was established as well (pSBtet-GP). This control cell line expresses a luciferase gene instead of a fusion gene, and constitutively expresses GFP (G) together with a Puromycin resistance gene (P). Induction with 1 µg/ml Doxycyclin was carried out for 48 h in all seven cell lines before RNA or DNA was harvested to investigate changes in gene expression (MACE) or chromatin accessibility (ATAC-Seq). RT-PCR experiments were performed to validate the correct expression of all fusion transgenes next to their wildtype counterparts (endogenous genes MLL and AF6 ). It was important to demonstrate that all transgenes were not very highly overexpressed, rather were expressed in all cells at physiological levels. Below: Expression of the vector backbone fluorescent proteins (FP’s). Pictures were taken from all six cell lines by making photographs from the green and red channels or were merged to demonstrate the expression of the FP’s from the appropriate vector backbones. A picture of the GFP-positive mock-cell line is not displayed.
    Figure Legend Snippet: A . All four vector constructs are depicted. Shown is only the expressed part of the different Sleeping Beauty vectors that have been used. Importantly, all inducible direct fusions were cloned into vectors that express constitutively eGFP and the Puromycin resistance genes, while the reciprocal vectors express constitutively dTom together with the Blasticidin resistance gene. Since the construction of these vectors was done by separating the two cDNA fragments by a short intronic sequence, proper splicing was validated by RT-PCR and sanger sequencing of the resulting PCR product (depicted as “validated splice junction)”. The red box with the annotation “1” represents AF6 exon 1. Pink boxes at the beginning or end of the fusion genes indicate the presence of Flag-Tags in all constructs. B The construction of all 6 cell lines is shown. The encoded MLL protein domains and portions are displayed in different blue colors, while encoded Afadin/AF6 protein domains and portions are displayed in different red colors. Important MLL domains are: M/LBS: MEN1/LEDGF Binding Site; CXXC: CXXC domain; PHD/BD: PHD/BD domain; HBS: HAT Binding Site (CREBBP/MOF1); SET: SET domain). Similarly, important Afadin/AF6 domains are: RBD1/2: RAS/RAP Binding Domain 1 and 2; PDZ: PDF domain; ABD: Actin Binding domain. Besides these 6 cell lines, a control cell line with a Sleeping Beauty mock vector was established as well (pSBtet-GP). This control cell line expresses a luciferase gene instead of a fusion gene, and constitutively expresses GFP (G) together with a Puromycin resistance gene (P). Induction with 1 µg/ml Doxycyclin was carried out for 48 h in all seven cell lines before RNA or DNA was harvested to investigate changes in gene expression (MACE) or chromatin accessibility (ATAC-Seq). RT-PCR experiments were performed to validate the correct expression of all fusion transgenes next to their wildtype counterparts (endogenous genes MLL and AF6 ). It was important to demonstrate that all transgenes were not very highly overexpressed, rather were expressed in all cells at physiological levels. Below: Expression of the vector backbone fluorescent proteins (FP’s). Pictures were taken from all six cell lines by making photographs from the green and red channels or were merged to demonstrate the expression of the FP’s from the appropriate vector backbones. A picture of the GFP-positive mock-cell line is not displayed.

    Techniques Used: Plasmid Preparation, Construct, Clone Assay, Sequencing, Reverse Transcription Polymerase Chain Reaction, Binding Assay, Luciferase, Expressing

    mace seq kit analysis  (GenXPro Inc)

     
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    Mace Seq Kit Analysis, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    GenXPro Inc rapid mace seq kit
    a) Schematic drawing of the experimental setup. <t>MACE-seq</t> was performed on samples from brain-like ECs (in co-culture with PCs), with or without 48 <t>h</t> <t>cARLA</t> treatment. b) Principal component analysis (PCA) plot of control and cARLA samples. c) Venn-diagram showing the number of genes upregulated (log 2 FC ≥ 0.2 and FDR < 0.01), downregulated (log 2 FC ≥ -0.2 and FDR < 0.01) or not changed (|log 2 FC| < 0.2 and/or FDR ≥ 0.01) upon cARLA treatment. Log 2 FC: log 2 (fold change), FDR: false discovery rate. d) Mean-difference (MD) plot presenting the range and distribution of all transcripts (circles) regarding their mean expression and log 2 FC upon cARLA treatment. Key transcripts related to different aspects of BBB function are highlighted. e) Functional enrichment analysis of up- and downregulated gene sets upon cARLA treatment using g:Profiler. Gene Ontology Biological Process (GO:BP) terms are ranked based on their gene ratio (the fraction of differentially expressed genes in a given term) and are colored based on statistical significance (FDR). f) Representative staining of F-actin (grey), with or without cARLA treatment. Nuclei were stained with Hoechst (blue). Bar: 40 µm. g) Validation of the definitive endothelial nature of human stem cell-derived brain-like ECs. Normalized counts of key epithelial and endothelial transcripts from our dataset are plotted on a 3-segment y-axis covering multiple orders of magnitude. h) Scaled heatmap of 92 transcripts that are enriched in mouse brain ECs and are well expressed at the human BBB. Genes upregulated, downregulated or not changed upon cARLA treatment as well as genes not expressed (normalized counts ≤ 1) in this model are shown separately, in alphabetical order. Color coding represents row z-scores after Min-Max normalization, the darkest color corresponding to the highest expression in a given row.
    Rapid Mace Seq Kit, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/rapid mace seq kit/product/GenXPro Inc
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    mace seq kit  (GenXPro Inc)
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    GenXPro Inc mace seq kit
    a) Schematic drawing of the experimental setup. <t>MACE-seq</t> was performed on samples from brain-like ECs (in co-culture with PCs), with or without 48 <t>h</t> <t>cARLA</t> treatment. b) Principal component analysis (PCA) plot of control and cARLA samples. c) Venn-diagram showing the number of genes upregulated (log 2 FC ≥ 0.2 and FDR < 0.01), downregulated (log 2 FC ≥ -0.2 and FDR < 0.01) or not changed (|log 2 FC| < 0.2 and/or FDR ≥ 0.01) upon cARLA treatment. Log 2 FC: log 2 (fold change), FDR: false discovery rate. d) Mean-difference (MD) plot presenting the range and distribution of all transcripts (circles) regarding their mean expression and log 2 FC upon cARLA treatment. Key transcripts related to different aspects of BBB function are highlighted. e) Functional enrichment analysis of up- and downregulated gene sets upon cARLA treatment using g:Profiler. Gene Ontology Biological Process (GO:BP) terms are ranked based on their gene ratio (the fraction of differentially expressed genes in a given term) and are colored based on statistical significance (FDR). f) Representative staining of F-actin (grey), with or without cARLA treatment. Nuclei were stained with Hoechst (blue). Bar: 40 µm. g) Validation of the definitive endothelial nature of human stem cell-derived brain-like ECs. Normalized counts of key epithelial and endothelial transcripts from our dataset are plotted on a 3-segment y-axis covering multiple orders of magnitude. h) Scaled heatmap of 92 transcripts that are enriched in mouse brain ECs and are well expressed at the human BBB. Genes upregulated, downregulated or not changed upon cARLA treatment as well as genes not expressed (normalized counts ≤ 1) in this model are shown separately, in alphabetical order. Color coding represents row z-scores after Min-Max normalization, the darkest color corresponding to the highest expression in a given row.
    Mace Seq Kit, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    mace seq kit v2 0  (GenXPro Inc)
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    GenXPro Inc mace seq kit v2 0
    a) Schematic drawing of the experimental setup. <t>MACE-seq</t> was performed on samples from brain-like ECs (in co-culture with PCs), with or without 48 <t>h</t> <t>cARLA</t> treatment. b) Principal component analysis (PCA) plot of control and cARLA samples. c) Venn-diagram showing the number of genes upregulated (log 2 FC ≥ 0.2 and FDR < 0.01), downregulated (log 2 FC ≥ -0.2 and FDR < 0.01) or not changed (|log 2 FC| < 0.2 and/or FDR ≥ 0.01) upon cARLA treatment. Log 2 FC: log 2 (fold change), FDR: false discovery rate. d) Mean-difference (MD) plot presenting the range and distribution of all transcripts (circles) regarding their mean expression and log 2 FC upon cARLA treatment. Key transcripts related to different aspects of BBB function are highlighted. e) Functional enrichment analysis of up- and downregulated gene sets upon cARLA treatment using g:Profiler. Gene Ontology Biological Process (GO:BP) terms are ranked based on their gene ratio (the fraction of differentially expressed genes in a given term) and are colored based on statistical significance (FDR). f) Representative staining of F-actin (grey), with or without cARLA treatment. Nuclei were stained with Hoechst (blue). Bar: 40 µm. g) Validation of the definitive endothelial nature of human stem cell-derived brain-like ECs. Normalized counts of key epithelial and endothelial transcripts from our dataset are plotted on a 3-segment y-axis covering multiple orders of magnitude. h) Scaled heatmap of 92 transcripts that are enriched in mouse brain ECs and are well expressed at the human BBB. Genes upregulated, downregulated or not changed upon cARLA treatment as well as genes not expressed (normalized counts ≤ 1) in this model are shown separately, in alphabetical order. Color coding represents row z-scores after Min-Max normalization, the darkest color corresponding to the highest expression in a given row.
    Mace Seq Kit V2 0, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    mace seq kit analysis  (GenXPro Inc)
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    a) Schematic drawing of the experimental setup. <t>MACE-seq</t> was performed on samples from brain-like ECs (in co-culture with PCs), with or without 48 <t>h</t> <t>cARLA</t> treatment. b) Principal component analysis (PCA) plot of control and cARLA samples. c) Venn-diagram showing the number of genes upregulated (log 2 FC ≥ 0.2 and FDR < 0.01), downregulated (log 2 FC ≥ -0.2 and FDR < 0.01) or not changed (|log 2 FC| < 0.2 and/or FDR ≥ 0.01) upon cARLA treatment. Log 2 FC: log 2 (fold change), FDR: false discovery rate. d) Mean-difference (MD) plot presenting the range and distribution of all transcripts (circles) regarding their mean expression and log 2 FC upon cARLA treatment. Key transcripts related to different aspects of BBB function are highlighted. e) Functional enrichment analysis of up- and downregulated gene sets upon cARLA treatment using g:Profiler. Gene Ontology Biological Process (GO:BP) terms are ranked based on their gene ratio (the fraction of differentially expressed genes in a given term) and are colored based on statistical significance (FDR). f) Representative staining of F-actin (grey), with or without cARLA treatment. Nuclei were stained with Hoechst (blue). Bar: 40 µm. g) Validation of the definitive endothelial nature of human stem cell-derived brain-like ECs. Normalized counts of key epithelial and endothelial transcripts from our dataset are plotted on a 3-segment y-axis covering multiple orders of magnitude. h) Scaled heatmap of 92 transcripts that are enriched in mouse brain ECs and are well expressed at the human BBB. Genes upregulated, downregulated or not changed upon cARLA treatment as well as genes not expressed (normalized counts ≤ 1) in this model are shown separately, in alphabetical order. Color coding represents row z-scores after Min-Max normalization, the darkest color corresponding to the highest expression in a given row.
    Mace Seq Kit Analysis, supplied by GenXPro Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    a) Schematic drawing of the experimental setup. MACE-seq was performed on samples from brain-like ECs (in co-culture with PCs), with or without 48 h cARLA treatment. b) Principal component analysis (PCA) plot of control and cARLA samples. c) Venn-diagram showing the number of genes upregulated (log 2 FC ≥ 0.2 and FDR < 0.01), downregulated (log 2 FC ≥ -0.2 and FDR < 0.01) or not changed (|log 2 FC| < 0.2 and/or FDR ≥ 0.01) upon cARLA treatment. Log 2 FC: log 2 (fold change), FDR: false discovery rate. d) Mean-difference (MD) plot presenting the range and distribution of all transcripts (circles) regarding their mean expression and log 2 FC upon cARLA treatment. Key transcripts related to different aspects of BBB function are highlighted. e) Functional enrichment analysis of up- and downregulated gene sets upon cARLA treatment using g:Profiler. Gene Ontology Biological Process (GO:BP) terms are ranked based on their gene ratio (the fraction of differentially expressed genes in a given term) and are colored based on statistical significance (FDR). f) Representative staining of F-actin (grey), with or without cARLA treatment. Nuclei were stained with Hoechst (blue). Bar: 40 µm. g) Validation of the definitive endothelial nature of human stem cell-derived brain-like ECs. Normalized counts of key epithelial and endothelial transcripts from our dataset are plotted on a 3-segment y-axis covering multiple orders of magnitude. h) Scaled heatmap of 92 transcripts that are enriched in mouse brain ECs and are well expressed at the human BBB. Genes upregulated, downregulated or not changed upon cARLA treatment as well as genes not expressed (normalized counts ≤ 1) in this model are shown separately, in alphabetical order. Color coding represents row z-scores after Min-Max normalization, the darkest color corresponding to the highest expression in a given row.

    Journal: bioRxiv

    Article Title: A small molecule cocktail for robust induction of blood-brain barrier properties

    doi: 10.1101/2023.02.09.527899

    Figure Lengend Snippet: a) Schematic drawing of the experimental setup. MACE-seq was performed on samples from brain-like ECs (in co-culture with PCs), with or without 48 h cARLA treatment. b) Principal component analysis (PCA) plot of control and cARLA samples. c) Venn-diagram showing the number of genes upregulated (log 2 FC ≥ 0.2 and FDR < 0.01), downregulated (log 2 FC ≥ -0.2 and FDR < 0.01) or not changed (|log 2 FC| < 0.2 and/or FDR ≥ 0.01) upon cARLA treatment. Log 2 FC: log 2 (fold change), FDR: false discovery rate. d) Mean-difference (MD) plot presenting the range and distribution of all transcripts (circles) regarding their mean expression and log 2 FC upon cARLA treatment. Key transcripts related to different aspects of BBB function are highlighted. e) Functional enrichment analysis of up- and downregulated gene sets upon cARLA treatment using g:Profiler. Gene Ontology Biological Process (GO:BP) terms are ranked based on their gene ratio (the fraction of differentially expressed genes in a given term) and are colored based on statistical significance (FDR). f) Representative staining of F-actin (grey), with or without cARLA treatment. Nuclei were stained with Hoechst (blue). Bar: 40 µm. g) Validation of the definitive endothelial nature of human stem cell-derived brain-like ECs. Normalized counts of key epithelial and endothelial transcripts from our dataset are plotted on a 3-segment y-axis covering multiple orders of magnitude. h) Scaled heatmap of 92 transcripts that are enriched in mouse brain ECs and are well expressed at the human BBB. Genes upregulated, downregulated or not changed upon cARLA treatment as well as genes not expressed (normalized counts ≤ 1) in this model are shown separately, in alphabetical order. Color coding represents row z-scores after Min-Max normalization, the darkest color corresponding to the highest expression in a given row.

    Article Snippet: A total of 8 libraries (4 control and 4 cARLA) were constructed using the Rapid MACE-Seq kit (GenXPro GmbH, Frankfurt, Germany) according to the manufacturer’s protocol.

    Techniques: Co-Culture Assay, Expressing, Functional Assay, Staining, Derivative Assay

    Gene expressional changes after 48 h cARLA treatment were determined using MACE-seq profiling and are presented in panels a-i) by category. Mean ± SD, n =4. Red and blue color indicates up- and downregulation, respectively, upon cARLA treatment.

    Journal: bioRxiv

    Article Title: A small molecule cocktail for robust induction of blood-brain barrier properties

    doi: 10.1101/2023.02.09.527899

    Figure Lengend Snippet: Gene expressional changes after 48 h cARLA treatment were determined using MACE-seq profiling and are presented in panels a-i) by category. Mean ± SD, n =4. Red and blue color indicates up- and downregulation, respectively, upon cARLA treatment.

    Article Snippet: A total of 8 libraries (4 control and 4 cARLA) were constructed using the Rapid MACE-Seq kit (GenXPro GmbH, Frankfurt, Germany) according to the manufacturer’s protocol.

    Techniques: