bulk rna seq data analysis  (Azenta)

Journal: bioRxiv

Article Title: Developmental rewiring of EHMT1 function during human cortical neurogenesis

doi: 10.64898/2026.10.09.757098

Figure Lengend Snippet: A , scRNA-seq UMAP of d35 CN colored by assigned cell type, excitatory (EXC) and inhibitory (INH) neuronal subtypes, glioblasts, and unassigned cells. The numbers of cells per cluster are shown in parentheses. B, Violin plots of Seurat-normalized expression levels for cell-identity marker genes. C, UMAPs of d35 CNs exposed to different treatments (DMSO = blue; dTAG = red). D, DEGs per cell type after ES→CN depletion, as identified with Seurat FindMarkers (padj < 0.05, |log2FoldChange| > 0.5). E, Degree of similarity of combined DEGs identified in the indicated neuronal cell types, as indicated by log2FoldChange pairwise Pearson correlation. F, Functional enrichment (gProfiler; padj < 0.05) for ranked DEGs in the indicated neuronal subtypes. G, Violin plots showing subtype-specific (left) and shared (right) DEGs between neuronal subtypes. Upregulated DEGs highlighted in red and downregulated DEGs highlighted in blue. H, Impact of EHMT1 depletion on the neuronal maturation score in neuronal subtypes (see Methods). Mann-Whitney test with Bonferroni correction. I, As H for neuronal function score (see Methods). J, Transcription factors with regulons significantly affected by EHMT1 depletion (Mann-Whitney test with Bonferroni correction), as determined by SCENIC (see Methods). (+)(-) indicate positive and negative correlations between the expression of a transcription factor and its regulon, respectively. Arrows indicate significant (padj<0.05) log2FC (dTAG/DMSO) of the TF in the cell type.

Article Snippet: We conducted bioinformatic analysis of bulk RNA-seq data for d35 CN single-cell RNA-seq validation using Plasmidsaurus’s workflow.

Techniques: Expressing, Marker, Functional Assay, MANN-WHITNEY

Journal: iScience

Article Title: DHODH regulates trophoblast fusion via IFITM-reduced plasma membrane fluidity: Implications for hypertensive disorders of pregnancy

doi: 10.1016/j.isci.2026.116163

Figure Lengend Snippet: Increased IFITM and decreased DHODH expression characterize the placenta in the context of HDPs (A) Volcano plot of transcriptomic changes identified by RNA-seq. Transcripts highlighted in red or blue were significantly altered ( q value < 0.05). (B) Differentially expressed genes were classified by functional enrichment analysis using the Reactome pathway database and Gene Ontology (GO) biological processes or cellular components. (C) Heatmap of mitochondria-related genes downregulated in the placenta in the context of HDPs. Genes with higher expression are shown in green, and those with lower expression are shown in red. Ctrl: premature delivery, n = 5; HDP, n = 5. (D) Expression of DHODH, OPA1, DNM1L, MFN1, TFAM, and IFITM1-3 in trophoblast BeWo cells treated with forskolin (FSK, 2.5 μM) and rotenone (Rote, 50 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗ p < 0.05, ∗∗ p < 0.01 vs. FSK alone (Tukey’s test). (E) Expression of IFITMs in BeWo cells treated with FSK (2.5 μM), orludodstat (Orlu, 1 nM), or brequinar (Bre, 25 nM) for 48 h. GAPDH was used as a reference gene. The data are presented as the mean ± SEM from three independent experiments. ∗∗ p < 0.01 vs. Ctrl; † p < 0.05, †† p < 0.01, ††† p < 0.001 vs. FSK alone (Tukey’s test).

Article Snippet: • Raw RNA-seq data derived from human placental samples and trophoblast cell lines have been deposited at the DNA DataBank of Japan (DDBJ) Sequence Read Archive as DDBJ: DRA021720 and DRA021721 and are publicly available as of the date of publication.

Techniques: Expressing, RNA Sequencing, Functional Assay

Journal: iScience

Article Title: DHODH regulates trophoblast fusion via IFITM-reduced plasma membrane fluidity: Implications for hypertensive disorders of pregnancy

doi: 10.1016/j.isci.2026.116163

Figure Lengend Snippet: DHODH regulates IFITM expression via IRF1 (A–H) BeWo cells or DHODH-KD BeWo cells were treated with FSK (2.5 μM), Orlu (1 nM), or Bre (25 nM) for 48 h. (A) Volcano plot showing transcriptomic changes identified by RNA-seq. Transcripts highlighted in red or blue were considered differentially expressed, as indicated by an expression change ≥2-fold ( p < 0.05). (B) Correlation analysis of RNA-seq data from Orlu-, Bre-treated, and DHODH-KD cells. (C) Differentially expressed genes were classified by functional enrichment analysis using the Wiki pathway database and GO biological processes or cellular components. (D) RNA-seq was used to evaluate the expression levels of genes associated with syncytialization. (E) RNA-seq was used to evaluate the expression levels of IRF family genes. (F) Immunoblotting for IRF1, total IRF3, and p -IRF3. GAPDH was used as a loading control. Representative data from three independent experiments are shown. The graph shows the total IRF3 and p -IRF3 levels normalized to GAPDH levels from three independent experiments. ∗∗ p < 0.01, ∗∗∗ p < 0.001 vs. Ctrl (Tukey’s test). Values represent the mean ± SEM. (G) ChIP assay showing IRF1 binding to upstream regulatory regions (up to 3 kbp) of the IFITM1, IFITM2, and IFITM3 loci in BeWo cells treated with FSK alone (2.5 μM) for 48 h. ∗ p < 0.05 vs. Ctrl; † p < 0.05, †† p < 0.01, ††† p < 0.001 vs. FSK alone (Tukey’s test). (H) Immunofluorescence staining of IRF1 (red). Nuclei were counterstained with DAPI (blue). Scale bars, 5 μm. The graph shows the number of staining cells from three independent experiments. Values represent the mean ± SEM. ∗∗∗ p < 0.001 vs. FSK.

Article Snippet: • Raw RNA-seq data derived from human placental samples and trophoblast cell lines have been deposited at the DNA DataBank of Japan (DDBJ) Sequence Read Archive as DDBJ: DRA021720 and DRA021721 and are publicly available as of the date of publication.

Techniques: Expressing, RNA Sequencing, Functional Assay, Western Blot, Control, Binding Assay, Immunofluorescence, Staining