deseq2 v1.38.3  (RStudio)

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

Journal: bioRxiv

Article Title: Regionalization of gene expression and cell types in the silk gland of the pantry moth Plodia interpunctella

doi: 10.1101/2025.07.11.664249

Figure Lengend Snippet: A. Heatmap of the top 229 DEGs between MSG and PSG (adjusted p < 0.01, |log 2 FoldChange| > 3, DESeq2 normalized counts > 300). Gene expression profiles across tissues are shown with a Z-score transformation and sorted by hierarchical clustering (SalG: salivary glands ; Heads: larval heads). B. Scatter plot highlighting expression level difference of individual genes between the PSG and MSG (x-axis, log2FC), and their relative transcript abundance within their tissue of enrichment (y-axis, log 2 TPM). Coloring highlights genes with DESeq2 adjusted p < 0.05 and log 2 TPM > 0.01. Non-significant, lowly-expressed genes (log 2 TPM < -2) are not shown. Asterisks: the genes prospero ( pros ), rtoA , and DNAH2 are respectively adjacent to DEGs FibH, MG4 , and SerP150 , which may drive their enrichment in the corresponding tissues. C. Transcript representation within the PSG and MSG tissues (TPM as %). Ribosomal protein genes were pooled. D. Amino-acid composition of three major secreted proteins detected in the MSG, each showing extensive serine-rich stretches and repeats characteristic of sericin proteins. Accession numbers: XP_053622673 (Pi_Ser3b), XP_053622719 (Pi_MG4), XP_053613126 (Pi_SerP150).

Article Snippet: The count data generated by FeatureCounts was used to perform differential expression analysis using DESeq2 in RStudio .

Techniques: Gene Expression, Transformation Assay, Expressing