raw rna seq data  (Databank Inc)

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

Journal: bioRxiv

Article Title: Elevated temperature drives the biosynthesis of novel acylated glucosinolates in Arabidopsis thaliana seeds

doi: 10.64898/2026.06.03.729804

Figure Lengend Snippet: a) Log 2 ([elevated temperature/control] average total accumulation) of metabolic categories (n≥3) at six different seed developmental stages. b) Untargeted metabolomic data statistical analysis. c) Differentially accumulated metabolic features during seed development. d) Number of major metabolic categories (Flavonoids, Cinnamic acids and derivatives, and Glucosinolates) induced by elevated temperature at each seed developmental stage. e) Transcriptomic data statistical analysis. f) Differentially expressed genes during seed development. g) Percentages of genes coding for enzymes putatively involved in specialized metabolite modifications (Acyltransferases, Glycosyltransferases, Hydroxylases and Methyltransferases) induced, and repressed, at each seed developmental stage by elevated temperature.

Article Snippet: Untargeted metabolomic raw data (.mzXML) for both negative and positive ESI modes, and metadata have been deposited at the MassiVE data repository portal with the following identifiers: The transcriptomic RNA-Seq raw data (FASTQ) have been deposited at the National Center for Biotechnology Information (NCBI) Transcriptome Shotgun Assembly Sequence Database (TSA) with BioProject identification PRJNA1344327.

Techniques: Control, Metabolomic

Journal: bioRxiv

Article Title: ATML1-GIR1-TPL/TPR transcriptional repression module controls glucosinolates and giant cells in Arabidopsis thaliana sepals

doi: 10.64898/2026.06.03.724713

Figure Lengend Snippet: (A) Sepals from stage 12 buds were taken for RNA-seq analysis of wild type (WT), gir1 and atml1 . GIR1 and ATML1 mRNA levels are decreased in each corresponding mutant background. FPKM, fragments per kilobase per million mapped reads. Asterisk indicates significant difference to WT (unpaired t -test with Welch’s correction, p < 0.05) (B) Binary comparison of differentially expressed genes (DEGs) in sepals for WT, gir1 mutant, and atml1 mutant genotypes. Blue bars correspond to downregulated genes and red bars represent upregulated genes. (C) Volcano plot illustrates the greater number of upregulated genes in gir1 in comparison to atml1 . Red dots represent upregulated genes and blue dots represent down-regulated genes. Genes with unchanged expression are indicated by grey dots. (D) Heatmap shows overview of DEGs between atml1 , gir1 , and WT sepals. Averaged relative expression between n=3 biological replicates is graded from low (blue) to high (red) (P < 0.05). A dendrogram depicting clustering of gene expression patterns is shown on the left of the heatmap. Individual replicates are shown for each genotype in Fig. S6. (E) Dot plot visualization of gene ontology (GO) enrichment analysis of upregulated genes of gir1 vs. atml1 . The y-axis shows GO terms while the x-axis shows the proportion of total genes identified in the gene set which are also associated with the GO term. Dot color reflects the statistical significance (-log10 (padj-value)) whereas the dot size corresponds to the number of genes in each GO term. (F) List of upregulated genes in gir1 sepals associated with the GO term GSL biosynthesis. Expression fold difference between gir1 and WT is provided for each gene. (G) Sepal RNA-seq data for MYB29 and MYB28 , two redundant regulators of GSL biosynthesis. MYB29 expression levels are >10-fold higher in gir1 as compared to WT, while MYB29 transcripts were not detected in atml1 . (H) Sepal RNA-seq data for other GSL biosynthesis genes upregulated in gir1 mutants, including aliphatic ( MAM1 , MAM3 , GSTU20 , IPMI SSU3 ) and indolic ( CYP79B2 , CYP79B3 ) GSL biosynthesis genes, as well as a genes involved in sulfur metabolism ( AKN2 ) and GSL catabolism ( ESP ), respectively. In (G) and (H) , significant differences between genotypes are marked by letters (one-way ANOVA, Tukey’s test, p < 0.05). RNA-seq data for additional genes is shown in Figs. S7-S8 and Table S2 .

Article Snippet: The RNA-seq raw data is available at the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) under accession GSE332896.

Techniques: RNA Sequencing, Mutagenesis, Comparison, Expressing, Gene Expression