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deseq2 workflow  (RStudio)

 
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    Structured Review

    RStudio deseq2 workflow
    Comparison of the transcriptomic effects of Foxo1 -KO and treatment with AS1842856 in murine BCR::ABL1 + B-ALL. (A) RNA-sequencing was performed in BCR::ABL1 + Cre-ERT2 Foxo1 fl/fl murine B-ALL cells treated with either 200 nM 4-OHT or an equivalent amount of vehicle EtOH or with 70 nM AS1842856 or equivalent amounts of DMSO vehicle. RNA was isolated after 24 and 48 hours. Analysis was performed using the <t>DESeq2</t> workflow in RStudio (version 2024.12.1). The unsupervised hierarchical clustering of all genes found in all samples is shown . (B) Hierarchical clustering of genes significantly ( P < .05; log 2 [FC] > 1.4) regulated was performed in both groups at 24 and 48 hours after respective treatment. (C) Volcano plot of differentially expressed genes. Significance threshold was set to adjusted P <.05 and log 2 (FC) >1.5. Significantly downregulated genes are shown in blue; significantly upregulated genes are shown in red. Canonical FOXO1 targets are highlighted and labeled in black. (D) Differentially expressed genes from days 1 and 2 of either Foxo1 -KO or AS1842856-treated samples were pooled and subjected to GSEA for “Hallmarks” gene sets using GSEA (version 4.3.3; ). (E) Differentially regulated genes in BCR::ABL1 + murine B-ALL after treatment with 70 nM AS1842856 or genetic Foxo1 -KO were subjected to Venn analysis. Exclusive and shared genes were cross-referenced to the ChEA 2022 database using Enrichr . ChEA, ChIP-X Enrichment Analysis; FC, fold change.
    Deseq2 Workflow, supplied by RStudio, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/deseq2 workflow/product/RStudio
    Average 90 stars, based on 1 article reviews
    deseq2 workflow - by Bioz Stars, 2026-05
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    Images

    1) Product Images from "Beyond FOXO1: AS1842856 inhibits GSK3 to enhance cytotoxic effects in B-ALL ∗ "

    Article Title: Beyond FOXO1: AS1842856 inhibits GSK3 to enhance cytotoxic effects in B-ALL ∗

    Journal: Blood Advances

    doi: 10.1182/bloodadvances.2024015560

    Comparison of the transcriptomic effects of Foxo1 -KO and treatment with AS1842856 in murine BCR::ABL1 + B-ALL. (A) RNA-sequencing was performed in BCR::ABL1 + Cre-ERT2 Foxo1 fl/fl murine B-ALL cells treated with either 200 nM 4-OHT or an equivalent amount of vehicle EtOH or with 70 nM AS1842856 or equivalent amounts of DMSO vehicle. RNA was isolated after 24 and 48 hours. Analysis was performed using the DESeq2 workflow in RStudio (version 2024.12.1). The unsupervised hierarchical clustering of all genes found in all samples is shown . (B) Hierarchical clustering of genes significantly ( P < .05; log 2 [FC] > 1.4) regulated was performed in both groups at 24 and 48 hours after respective treatment. (C) Volcano plot of differentially expressed genes. Significance threshold was set to adjusted P <.05 and log 2 (FC) >1.5. Significantly downregulated genes are shown in blue; significantly upregulated genes are shown in red. Canonical FOXO1 targets are highlighted and labeled in black. (D) Differentially expressed genes from days 1 and 2 of either Foxo1 -KO or AS1842856-treated samples were pooled and subjected to GSEA for “Hallmarks” gene sets using GSEA (version 4.3.3; ). (E) Differentially regulated genes in BCR::ABL1 + murine B-ALL after treatment with 70 nM AS1842856 or genetic Foxo1 -KO were subjected to Venn analysis. Exclusive and shared genes were cross-referenced to the ChEA 2022 database using Enrichr . ChEA, ChIP-X Enrichment Analysis; FC, fold change.
    Figure Legend Snippet: Comparison of the transcriptomic effects of Foxo1 -KO and treatment with AS1842856 in murine BCR::ABL1 + B-ALL. (A) RNA-sequencing was performed in BCR::ABL1 + Cre-ERT2 Foxo1 fl/fl murine B-ALL cells treated with either 200 nM 4-OHT or an equivalent amount of vehicle EtOH or with 70 nM AS1842856 or equivalent amounts of DMSO vehicle. RNA was isolated after 24 and 48 hours. Analysis was performed using the DESeq2 workflow in RStudio (version 2024.12.1). The unsupervised hierarchical clustering of all genes found in all samples is shown . (B) Hierarchical clustering of genes significantly ( P < .05; log 2 [FC] > 1.4) regulated was performed in both groups at 24 and 48 hours after respective treatment. (C) Volcano plot of differentially expressed genes. Significance threshold was set to adjusted P <.05 and log 2 (FC) >1.5. Significantly downregulated genes are shown in blue; significantly upregulated genes are shown in red. Canonical FOXO1 targets are highlighted and labeled in black. (D) Differentially expressed genes from days 1 and 2 of either Foxo1 -KO or AS1842856-treated samples were pooled and subjected to GSEA for “Hallmarks” gene sets using GSEA (version 4.3.3; ). (E) Differentially regulated genes in BCR::ABL1 + murine B-ALL after treatment with 70 nM AS1842856 or genetic Foxo1 -KO were subjected to Venn analysis. Exclusive and shared genes were cross-referenced to the ChEA 2022 database using Enrichr . ChEA, ChIP-X Enrichment Analysis; FC, fold change.

    Techniques Used: Comparison, RNA Sequencing, Isolation, Labeling



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    Comparison of the transcriptomic effects of Foxo1 -KO and treatment with AS1842856 in murine BCR::ABL1 + B-ALL. (A) RNA-sequencing was performed in BCR::ABL1 + Cre-ERT2 Foxo1 fl/fl murine B-ALL cells treated with either 200 nM 4-OHT or an equivalent amount of vehicle EtOH or with 70 nM AS1842856 or equivalent amounts of DMSO vehicle. RNA was isolated after 24 and 48 hours. Analysis was performed using the <t>DESeq2</t> workflow in RStudio (version 2024.12.1). The unsupervised hierarchical clustering of all genes found in all samples is shown . (B) Hierarchical clustering of genes significantly ( P < .05; log 2 [FC] > 1.4) regulated was performed in both groups at 24 and 48 hours after respective treatment. (C) Volcano plot of differentially expressed genes. Significance threshold was set to adjusted P <.05 and log 2 (FC) >1.5. Significantly downregulated genes are shown in blue; significantly upregulated genes are shown in red. Canonical FOXO1 targets are highlighted and labeled in black. (D) Differentially expressed genes from days 1 and 2 of either Foxo1 -KO or AS1842856-treated samples were pooled and subjected to GSEA for “Hallmarks” gene sets using GSEA (version 4.3.3; ). (E) Differentially regulated genes in BCR::ABL1 + murine B-ALL after treatment with 70 nM AS1842856 or genetic Foxo1 -KO were subjected to Venn analysis. Exclusive and shared genes were cross-referenced to the ChEA 2022 database using Enrichr . ChEA, ChIP-X Enrichment Analysis; FC, fold change.
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    bioconductor deseq2 workflow  (RStudio)
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    Comparison of the transcriptomic effects of Foxo1 -KO and treatment with AS1842856 in murine BCR::ABL1 + B-ALL. (A) RNA-sequencing was performed in BCR::ABL1 + Cre-ERT2 Foxo1 fl/fl murine B-ALL cells treated with either 200 nM 4-OHT or an equivalent amount of vehicle EtOH or with 70 nM AS1842856 or equivalent amounts of DMSO vehicle. RNA was isolated after 24 and 48 hours. Analysis was performed using the <t>DESeq2</t> workflow in RStudio (version 2024.12.1). The unsupervised hierarchical clustering of all genes found in all samples is shown . (B) Hierarchical clustering of genes significantly ( P < .05; log 2 [FC] > 1.4) regulated was performed in both groups at 24 and 48 hours after respective treatment. (C) Volcano plot of differentially expressed genes. Significance threshold was set to adjusted P <.05 and log 2 (FC) >1.5. Significantly downregulated genes are shown in blue; significantly upregulated genes are shown in red. Canonical FOXO1 targets are highlighted and labeled in black. (D) Differentially expressed genes from days 1 and 2 of either Foxo1 -KO or AS1842856-treated samples were pooled and subjected to GSEA for “Hallmarks” gene sets using GSEA (version 4.3.3; ). (E) Differentially regulated genes in BCR::ABL1 + murine B-ALL after treatment with 70 nM AS1842856 or genetic Foxo1 -KO were subjected to Venn analysis. Exclusive and shared genes were cross-referenced to the ChEA 2022 database using Enrichr . ChEA, ChIP-X Enrichment Analysis; FC, fold change.
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    Comparison of the transcriptomic effects of Foxo1 -KO and treatment with AS1842856 in murine BCR::ABL1 + B-ALL. (A) RNA-sequencing was performed in BCR::ABL1 + Cre-ERT2 Foxo1 fl/fl murine B-ALL cells treated with either 200 nM 4-OHT or an equivalent amount of vehicle EtOH or with 70 nM AS1842856 or equivalent amounts of DMSO vehicle. RNA was isolated after 24 and 48 hours. Analysis was performed using the <t>DESeq2</t> workflow in RStudio (version 2024.12.1). The unsupervised hierarchical clustering of all genes found in all samples is shown . (B) Hierarchical clustering of genes significantly ( P < .05; log 2 [FC] > 1.4) regulated was performed in both groups at 24 and 48 hours after respective treatment. (C) Volcano plot of differentially expressed genes. Significance threshold was set to adjusted P <.05 and log 2 (FC) >1.5. Significantly downregulated genes are shown in blue; significantly upregulated genes are shown in red. Canonical FOXO1 targets are highlighted and labeled in black. (D) Differentially expressed genes from days 1 and 2 of either Foxo1 -KO or AS1842856-treated samples were pooled and subjected to GSEA for “Hallmarks” gene sets using GSEA (version 4.3.3; ). (E) Differentially regulated genes in BCR::ABL1 + murine B-ALL after treatment with 70 nM AS1842856 or genetic Foxo1 -KO were subjected to Venn analysis. Exclusive and shared genes were cross-referenced to the ChEA 2022 database using Enrichr . ChEA, ChIP-X Enrichment Analysis; FC, fold change.
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    Image Search Results


    Comparison of the transcriptomic effects of Foxo1 -KO and treatment with AS1842856 in murine BCR::ABL1 + B-ALL. (A) RNA-sequencing was performed in BCR::ABL1 + Cre-ERT2 Foxo1 fl/fl murine B-ALL cells treated with either 200 nM 4-OHT or an equivalent amount of vehicle EtOH or with 70 nM AS1842856 or equivalent amounts of DMSO vehicle. RNA was isolated after 24 and 48 hours. Analysis was performed using the DESeq2 workflow in RStudio (version 2024.12.1). The unsupervised hierarchical clustering of all genes found in all samples is shown . (B) Hierarchical clustering of genes significantly ( P < .05; log 2 [FC] > 1.4) regulated was performed in both groups at 24 and 48 hours after respective treatment. (C) Volcano plot of differentially expressed genes. Significance threshold was set to adjusted P <.05 and log 2 (FC) >1.5. Significantly downregulated genes are shown in blue; significantly upregulated genes are shown in red. Canonical FOXO1 targets are highlighted and labeled in black. (D) Differentially expressed genes from days 1 and 2 of either Foxo1 -KO or AS1842856-treated samples were pooled and subjected to GSEA for “Hallmarks” gene sets using GSEA (version 4.3.3; ). (E) Differentially regulated genes in BCR::ABL1 + murine B-ALL after treatment with 70 nM AS1842856 or genetic Foxo1 -KO were subjected to Venn analysis. Exclusive and shared genes were cross-referenced to the ChEA 2022 database using Enrichr . ChEA, ChIP-X Enrichment Analysis; FC, fold change.

    Journal: Blood Advances

    Article Title: Beyond FOXO1: AS1842856 inhibits GSK3 to enhance cytotoxic effects in B-ALL ∗

    doi: 10.1182/bloodadvances.2024015560

    Figure Lengend Snippet: Comparison of the transcriptomic effects of Foxo1 -KO and treatment with AS1842856 in murine BCR::ABL1 + B-ALL. (A) RNA-sequencing was performed in BCR::ABL1 + Cre-ERT2 Foxo1 fl/fl murine B-ALL cells treated with either 200 nM 4-OHT or an equivalent amount of vehicle EtOH or with 70 nM AS1842856 or equivalent amounts of DMSO vehicle. RNA was isolated after 24 and 48 hours. Analysis was performed using the DESeq2 workflow in RStudio (version 2024.12.1). The unsupervised hierarchical clustering of all genes found in all samples is shown . (B) Hierarchical clustering of genes significantly ( P < .05; log 2 [FC] > 1.4) regulated was performed in both groups at 24 and 48 hours after respective treatment. (C) Volcano plot of differentially expressed genes. Significance threshold was set to adjusted P <.05 and log 2 (FC) >1.5. Significantly downregulated genes are shown in blue; significantly upregulated genes are shown in red. Canonical FOXO1 targets are highlighted and labeled in black. (D) Differentially expressed genes from days 1 and 2 of either Foxo1 -KO or AS1842856-treated samples were pooled and subjected to GSEA for “Hallmarks” gene sets using GSEA (version 4.3.3; ). (E) Differentially regulated genes in BCR::ABL1 + murine B-ALL after treatment with 70 nM AS1842856 or genetic Foxo1 -KO were subjected to Venn analysis. Exclusive and shared genes were cross-referenced to the ChEA 2022 database using Enrichr . ChEA, ChIP-X Enrichment Analysis; FC, fold change.

    Article Snippet: Analysis was performed using the DESeq2 workflow in RStudio (version 2024.12.1).

    Techniques: Comparison, RNA Sequencing, Isolation, Labeling