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own umap clustering  (Azenta)

 
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    Structured Review

    Azenta own umap clustering
    (A) Results for <t>targeting</t> <t>HDAC</t> classes I, II, and IV (B) Results for targeting HDAC class III. <t>UMAP</t> embedding performed after univariate data imputation and scaling. Samples color-coded by HDAC class. N1 and N2 are negative controls treated by scramble siRNA on Plate 1 and Plate 2 respectively. U1 and U2 are untreated controls on Plate 1 and Plate 2 respectively. Dotted lines mark samples that clustered relatively tight and far away from the control groups. For U1 group, n=4; for all other treatment groups, n=3. Bi-clustering heatmaps display log2 transformed expression values, sorted by their adjusted p-value for top 30 differentially expressed genes between the HDAC9 knockdown group and corresponding negative control ( C ) and between the SIRT3 knockdown group and corresponding negative control ( D ). Volcano plots display global transcriptional change across HDAC9 knockdown group and negative control ( E ) and across SIRT3 knockdown group and negative control ( F ). Each dot represents one gene. Genes with adjusted p-value < 0.05 and log2 fold change > 1 are colored red and are considered up-regulated. Genes with adjusted p-value < 0.05 and log2 fold change < −1 are colored green and are considered downregulated in the knockdown group compared to the control.
    Own Umap Clustering, supplied by Azenta, 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/own umap clustering/product/Azenta
    Average 86 stars, based on 1 article reviews
    own umap clustering - by Bioz Stars, 2026-05
    86/100 stars

    Images

    1) Product Images from "Comparative transcriptomics analysis of histone deacetylases, transcription factors, and ion channel genes in human iPSC-cardiomyocytes vs. the adult human heart"

    Article Title: Comparative transcriptomics analysis of histone deacetylases, transcription factors, and ion channel genes in human iPSC-cardiomyocytes vs. the adult human heart

    Journal: bioRxiv

    doi: 10.64898/2026.01.16.700033

    (A) Results for targeting HDAC classes I, II, and IV (B) Results for targeting HDAC class III. UMAP embedding performed after univariate data imputation and scaling. Samples color-coded by HDAC class. N1 and N2 are negative controls treated by scramble siRNA on Plate 1 and Plate 2 respectively. U1 and U2 are untreated controls on Plate 1 and Plate 2 respectively. Dotted lines mark samples that clustered relatively tight and far away from the control groups. For U1 group, n=4; for all other treatment groups, n=3. Bi-clustering heatmaps display log2 transformed expression values, sorted by their adjusted p-value for top 30 differentially expressed genes between the HDAC9 knockdown group and corresponding negative control ( C ) and between the SIRT3 knockdown group and corresponding negative control ( D ). Volcano plots display global transcriptional change across HDAC9 knockdown group and negative control ( E ) and across SIRT3 knockdown group and negative control ( F ). Each dot represents one gene. Genes with adjusted p-value < 0.05 and log2 fold change > 1 are colored red and are considered up-regulated. Genes with adjusted p-value < 0.05 and log2 fold change < −1 are colored green and are considered downregulated in the knockdown group compared to the control.
    Figure Legend Snippet: (A) Results for targeting HDAC classes I, II, and IV (B) Results for targeting HDAC class III. UMAP embedding performed after univariate data imputation and scaling. Samples color-coded by HDAC class. N1 and N2 are negative controls treated by scramble siRNA on Plate 1 and Plate 2 respectively. U1 and U2 are untreated controls on Plate 1 and Plate 2 respectively. Dotted lines mark samples that clustered relatively tight and far away from the control groups. For U1 group, n=4; for all other treatment groups, n=3. Bi-clustering heatmaps display log2 transformed expression values, sorted by their adjusted p-value for top 30 differentially expressed genes between the HDAC9 knockdown group and corresponding negative control ( C ) and between the SIRT3 knockdown group and corresponding negative control ( D ). Volcano plots display global transcriptional change across HDAC9 knockdown group and negative control ( E ) and across SIRT3 knockdown group and negative control ( F ). Each dot represents one gene. Genes with adjusted p-value < 0.05 and log2 fold change > 1 are colored red and are considered up-regulated. Genes with adjusted p-value < 0.05 and log2 fold change < −1 are colored green and are considered downregulated in the knockdown group compared to the control.

    Techniques Used: Control, Transformation Assay, Expressing, Knockdown, Negative Control



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    own umap clustering  (Azenta)
    86
    Azenta own umap clustering
    (A) Results for <t>targeting</t> <t>HDAC</t> classes I, II, and IV (B) Results for targeting HDAC class III. <t>UMAP</t> embedding performed after univariate data imputation and scaling. Samples color-coded by HDAC class. N1 and N2 are negative controls treated by scramble siRNA on Plate 1 and Plate 2 respectively. U1 and U2 are untreated controls on Plate 1 and Plate 2 respectively. Dotted lines mark samples that clustered relatively tight and far away from the control groups. For U1 group, n=4; for all other treatment groups, n=3. Bi-clustering heatmaps display log2 transformed expression values, sorted by their adjusted p-value for top 30 differentially expressed genes between the HDAC9 knockdown group and corresponding negative control ( C ) and between the SIRT3 knockdown group and corresponding negative control ( D ). Volcano plots display global transcriptional change across HDAC9 knockdown group and negative control ( E ) and across SIRT3 knockdown group and negative control ( F ). Each dot represents one gene. Genes with adjusted p-value < 0.05 and log2 fold change > 1 are colored red and are considered up-regulated. Genes with adjusted p-value < 0.05 and log2 fold change < −1 are colored green and are considered downregulated in the knockdown group compared to the control.
    Own Umap Clustering, supplied by Azenta, 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/own umap clustering/product/Azenta
    Average 86 stars, based on 1 article reviews
    own umap clustering - by Bioz Stars, 2026-05
    86/100 stars
    		  Buy from Supplier

    Image Search Results


    (A) Results for targeting HDAC classes I, II, and IV (B) Results for targeting HDAC class III. UMAP embedding performed after univariate data imputation and scaling. Samples color-coded by HDAC class. N1 and N2 are negative controls treated by scramble siRNA on Plate 1 and Plate 2 respectively. U1 and U2 are untreated controls on Plate 1 and Plate 2 respectively. Dotted lines mark samples that clustered relatively tight and far away from the control groups. For U1 group, n=4; for all other treatment groups, n=3. Bi-clustering heatmaps display log2 transformed expression values, sorted by their adjusted p-value for top 30 differentially expressed genes between the HDAC9 knockdown group and corresponding negative control ( C ) and between the SIRT3 knockdown group and corresponding negative control ( D ). Volcano plots display global transcriptional change across HDAC9 knockdown group and negative control ( E ) and across SIRT3 knockdown group and negative control ( F ). Each dot represents one gene. Genes with adjusted p-value < 0.05 and log2 fold change > 1 are colored red and are considered up-regulated. Genes with adjusted p-value < 0.05 and log2 fold change < −1 are colored green and are considered downregulated in the knockdown group compared to the control.

    Journal: bioRxiv

    Article Title: Comparative transcriptomics analysis of histone deacetylases, transcription factors, and ion channel genes in human iPSC-cardiomyocytes vs. the adult human heart

    doi: 10.64898/2026.01.16.700033

    Figure Lengend Snippet: (A) Results for targeting HDAC classes I, II, and IV (B) Results for targeting HDAC class III. UMAP embedding performed after univariate data imputation and scaling. Samples color-coded by HDAC class. N1 and N2 are negative controls treated by scramble siRNA on Plate 1 and Plate 2 respectively. U1 and U2 are untreated controls on Plate 1 and Plate 2 respectively. Dotted lines mark samples that clustered relatively tight and far away from the control groups. For U1 group, n=4; for all other treatment groups, n=3. Bi-clustering heatmaps display log2 transformed expression values, sorted by their adjusted p-value for top 30 differentially expressed genes between the HDAC9 knockdown group and corresponding negative control ( C ) and between the SIRT3 knockdown group and corresponding negative control ( D ). Volcano plots display global transcriptional change across HDAC9 knockdown group and negative control ( E ) and across SIRT3 knockdown group and negative control ( F ). Each dot represents one gene. Genes with adjusted p-value < 0.05 and log2 fold change > 1 are colored red and are considered up-regulated. Genes with adjusted p-value < 0.05 and log2 fold change < −1 are colored green and are considered downregulated in the knockdown group compared to the control.

    Article Snippet: Whole-transcriptome analysis of the HDAC/SIRT knockdowns in hiPSC-CM samples included our own UMAP clustering and differentially expressed gene (DEG) analysis performed by and provided by GENEWIZ/Azenta (South Plainfield, NJ).

    Techniques: Control, Transformation Assay, Expressing, Knockdown, Negative Control