Journal: Frontiers in Plant Science

Article Title: Combined metabolomic and transcriptomic analysis reveals key components of OsCIPK17 overexpression improves drought tolerance in rice

doi: 10.3389/fpls.2022.1043757

Figure Lengend Snippet: PC biplot of the transcriptome and metabolome of rice seedlings under drought stress and identification of differentially expressed genes and metabolites. (A) PC biplot of transcriptome. (B) PC biplot of metabolome. (C) Volcano plot of differentially expressed genes between NIP and OsCIPK17 -OE9 under drought treatment. (D) Volcano plot of differentially expressed metabolites between NIP and OsCIPK17 -OE9 under drought treatment. (E) KEGG analysis of differentially expressed genes and metabolites between NIP and OsCIPK17 -OE9 under drought treatment. CK means control check, which means growth under normal conditions without drought treatment. D means under drought treatment. OE9 means OsCIPK17 overexpression line 9. NIP-D, NIP-CK, OE9-D, and OE9-CK mean combination of lines and treatment methods. The same meaning as the following figure.

Article Snippet: Suzhou PANOMIX Biomedical Tech Co., LTD sequenced the transcriptome of NIP and OE9 roots under normal (NIP-CK and OE9-CK) and drought (NIP-D and OE9-D) conditions.

Techniques: Control, Over Expression

Journal: Frontiers in Plant Science

Article Title: Combined metabolomic and transcriptomic analysis reveals key components of OsCIPK17 overexpression improves drought tolerance in rice

doi: 10.3389/fpls.2022.1043757

Figure Lengend Snippet: Metabolites and enzymes related to trehalose metabolism. (A) Contents of metabolites in the trehalose pathway. Black boxes indicate the substances detected by the metabolomic analysis, and red boxes indicate the substances not detected by the metabolomic analysis. (B) Expression of enzymes involved in trehalose pathway detected in the transcriptome. Data are presented as mean ± SD of six independent experiments, and significant differences between NIP-CK and OE9-CK/NIP-D or OE9-D and OE9-CK/NIP-D plants according to one-way ANOVA are indicated by asterisks. CK: NIP or OE9 materials without drought treatment. OE9: OsCIPK17 -OE9. D: drought treatment. Asterisks indicate significance (*p < 0.05, **p < 0.01, ***p < 0.001).

Article Snippet: Suzhou PANOMIX Biomedical Tech Co., LTD sequenced the transcriptome of NIP and OE9 roots under normal (NIP-CK and OE9-CK) and drought (NIP-D and OE9-D) conditions.

Techniques: Expressing

Journal: Advanced Science

Article Title: Highly Accurate Estimation of Cell Type Abundance in Bulk Tissues Based on Single‐Cell Reference and Domain Adaptive Matching

doi: 10.1002/advs.202306329

Figure Lengend Snippet: Overview of SCROAM. a) The deconvolution model that uses a reference requires two input datasets: bulk RNA‐seq count and a reference containing counts of scRNA‐seq reads. Additionally, the single‐cell transcriptome data must label the cell type to be quantified. b) SCROAM learns gene‐specific transformations of bulk data by utilizing the reference sequences observed in single‐cell data. This allows us to account for potential technical bias between sequencing technologies used in single‐cell and bulk RNA‐seq data. c) SCROAM begins with scRNA‐seq data and classifies the cells into different cell types, which were represented by different colors in the analysis. By calculating gene specificity in a given cell type, an expression matrix reflecting cell type specificity was constructed. d) SCROAM employs single‐cell reference data to estimate the cell type ratio in transformed bulk data.

Article Snippet: The raw sequencing reads from a cDNA library using the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline (v1.8) were processed.

Techniques: RNA Sequencing Assay, Sequencing, Expressing, Construct, Transformation Assay

Journal: The Journal of Experimental Medicine

Article Title: Intercrypt sentinel macrophages tune antibacterial NF-κB responses in gut epithelial cells via TNF

doi: 10.1084/jem.20210862

Figure Lengend Snippet: Receptor expression in IECs. (A–D) Confocal microscopy images of (A) the cecal patch, and (B) a mucosa-associated lymphoid follicle in fixed cecae of p65 GFP-FL mice i.v. injected with LPS at 1 h.p.inj. Boxes in overview images indicate insets. Arrowheads indicate p65 + nuclei. Arrows indicate p65 − nuclei. Scale bars: 50 µm (overview images) or 10 µm (insets). TLR4 staining in small intestine (C) and colon (D) of WT mice. Arrowheads indicate MHCII + cells. Arrows indicate IECs. Scale bars: 20 µm. Representative images of mice from two experiments. (E) Heat map depicting expression levels of Tlr2, Tlr4, Tlr6, Tlr11 , Tnfrsf1a (TNFR1), and Tnfrsf1b (TNFR2) in untreated or TNF-treated (5 ng/ml, 8 h) small intestinal epithelial organoids derived from SPF (SPF1, SPF2) or germ-free (GF) mice, m-IC c12 cells, and mouse embryonic fibroblasts (MEFs; reanalysis of a previously published transcriptome dataset, all detectable Tlrs depicted; ). (F) Cecal mucosa stained for TNFR1 at 1 h.p.inj. of LPS. Scale bars: 50 µm. Representative images of mice from three independent experiments ( n = 4–7).

Article Snippet: The transcriptome dataset described previously ( ) was partially reanalyzed with R Studio (version 3.6.0).

Techniques: Expressing, Confocal Microscopy, Injection, Staining, Derivative Assay

Journal: The Journal of Experimental Medicine

Article Title: Intercrypt sentinel macrophages tune antibacterial NF-κB responses in gut epithelial cells via TNF

doi: 10.1084/jem.20210862

Figure Lengend Snippet: TNF-mediated epithelial NF-κB activation occurs upon bacterial infection and induces an antibacterial response. (A) Representative two-photon microscopy images of cecal explants of streptomycin-pretreated p65 GFP-FL mice infected with S . Tm for 8–13.5 h ( n = 28). Categories for scoring of epithelial NF-κB activation status: “no activation” (green); “patchy activation” (blue); “full activation” (orange); “inflammation” (red; tissue distortion evident); “unspecified” (gray; was excluded from further analysis). Scale bars: 50 µm. (B) Distribution of the analyzed 28 samples of A among the four epithelial NF-κB activation categories (bottom). For simplification, the blue, orange, and red categories were summarized as “NF-κB signaling” (yellow, top). (C) Tnf transcript levels in the cecal mucosa of mice described in A and naive p65 GFP-FL mice, grouped according to the epithelial NF-κB activation status of the respective mice and depicted as 2 -ΔCT . Expression levels were normalized to Actb ( n = 33). (D) TNFa +/− or TNFa −/− > p65 GFP-FL x Tlr4 −/− BMCs were analyzed as described in A and B. (E) Log 2 ratios of selected genes in a transcriptome analysis of TNF-treated (8 h, 5 ng/ml) compared with untreated small intestinal epithelial organoids . FDR, false discovery rate. (F) C3 transcript levels in untreated and TNF-treated (5 ng/ml, 4 h) small intestinal organoids depicted as 2 -ΔCT . Expression levels were normalized to Actb . (G) Streptomycin-pretreated TNFa −/− mice and heterozygous littermates were orally infected with S . Tm for 36h. S . Tm in the cecal lumen (gated on O12 + cells, see ) were stained for surface C3 to assess coating of luminal bacteria by flow cytometry (C3 + population). MFI, median fluorescence intensity. Statistical analysis: Mann–Whitney U test (C, F, and G) or χ 2 test (D). *, P ≤ 0.05; **, P ≤ 0.01. Each circle represents one mouse (C and G) or one experiment (average; F). y axis in log 10 scale (C, F, and G). Combined data of three (G), four (F), five (A–C), or six (D) independent experiments.

Article Snippet: The transcriptome dataset described previously ( ) was partially reanalyzed with R Studio (version 3.6.0).

Techniques: Activation Assay, Infection, Microscopy, Expressing, Staining, Bacteria, Flow Cytometry, Fluorescence, MANN-WHITNEY