Journal: bioRxiv

Article Title: Comparative Transcriptomic and Metabolomic Analyses in Response to Cold in Tartary Buckwheat ( Fagopyrum tataricum )

doi: 10.1101/278432

Figure Lengend Snippet: (A) Heatmap analysis of the phenylpropanoid biosynthetic genes in tartary buckwheat plants in response to cold. The response of the phenylpropanoid biosynthetic genes was obtained from RNA-sequencing analysis. The log 2 fold change values for each time point were calculated. Scales indicate the color assigned to each log2 fold change. (B) QRT-PCR analysis of the phenylpropanoid biosynthetic genes in tartary buckwheat plants in response to cold. Six-day-old light-grown plants were treated at 4°C for varying periods of time (hour), and total RNA isolated was subjected to quantitative RT-PCR. Relative fold changes were plotted after normalization to histone H3. Mean values and SE from triplicate biological experiments are plotted. Asterisks indicate significant differences compared with the plant at 0 h using Student’s t test (*P < 0.05; **P < 0.01). PAL, phenylalanine ammonia-lyase; C4H, cinnamate 4-hydroxylase; 4CL, 4-coumarate-CoA ligase; OMT, O-methyltransferase; HCT, hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase; CHS, chalcone synthase; CHI, chalcone isomerase; CHIL, chalcone isomerase like; F3H, flavanone-3-hydroxylase; F3’H, flavonoid-3’-hydroxylase; FLS, flavonol synthase; DFR, dihydroflavonol reductase; ANS, anthocyanin synthase.

Article Snippet: Our Illumina RNA sequencing data for Fagopyrum tataricum have been deposited in the NCBI Short Read Archive database under accession number SRP132029.

Techniques: RNA Sequencing Assay, Quantitative RT-PCR, Isolation

Journal: iScience

Article Title: Mining RNAseq data reveals dynamic metaboloepigenetic profiles in human, mouse and bovine pre-implantation embryos

doi: 10.1016/j.isci.2022.103904

Figure Lengend Snippet: Oocyte and embryo developmental stage, method of collection and sequencing for DNA methylation

Article Snippet: Mouse , MII, 2, 4, 8C, MO, ICM and TE , In vivo , Single-cell multi-omics sequencing technology (single-cell COOL-seq) , Illumina HiSeq 2500 , ( ) .

Techniques: Sequencing, In Vivo, In Vitro, Methylation Sequencing, Biomarker Discovery

Journal: Nature Communications

Article Title: Medium from human iPSC-derived primitive macrophages promotes adult cardiomyocyte proliferation and cardiac regeneration

doi: 10.1038/s41467-025-58301-8

Figure Lengend Snippet: a Schematic diagram of the protocols to generate hiPMs from human iPSCs. Relevant growth factors and duration of differentiation steps are as indicated. Cartoon elements used in the schematic diagram were created using BioRender. b Flow cytometry analysis of cells double positive for KDR and CD235 during hemogenic epithelium (HE) specification at day 5 after the start of hiPM differentiation. c Flow cytometry analysis of cells positive for CD45 during myeloid progenitor generation at day 11 after the start of hiPM differentiation. d Flow cytometry analysis of hiPMs positive for CD11b and CD14 at day 32 after the start of hiPM differentiation. e Immunofluorescence images for CD11b and CD14 expression in hiPMs. iPSCs were used as a negative control. Cells were stained with CD11b (red) and CD14 (green); nuclei were counterstained with Hoechst (blue). Scale bar, 10 µm. The experiment was repeated three times independently with similar results. f Phagocytosis assessment of hiPMs with FITC-conjugated Dextran (green). Human iPSC-derived cardiac fibroblasts (hiCFs) were used as a negative control. Scale bar, 50 μm. g Flow cytometry analysis of CCR2 expression in hiPMs. THP-1Ms were used as a positive control. The experiment was repeated three times independently with similar results. h Principal component analysis of RNA sequencing data revealing in-group clusters with minimal overlap between hiPMs and THP-1Ms. n = 4 biological repeats per group. i Barplot of differentially expressed genes (hiPMs vs THP-1Ms) specific to primitive macrophages. Differentially expressed genes were identified with a cutoff of |Fold change | > 2 and adjusted p -value < 0.05. j Measurement of LYVE1 , FOLR2 , CD163 , and MAF mRNA levels in hiPMs and THP-1Ms via qPCR analysis. β-actin was used as a control. n = 3 biological repeats per group. k Representative immunofluorescence images for LYVE1 expression in hiPMs. THP-1Ms were used as a negative control. Cells were stained with LYVE1 (green); nuclei were counterstained with Hoechst (blue). Scale bar, 20 μm. Quantitative data are presented as the mean ± SEM. Groups were compared using a two-tailed unpaired Student’s t test ( j ) or ANOVA ( i ). Source data are provided as a Source Data file.

Article Snippet: All the RNA sequencing data have been deposited to the National Center for Biotechnology Information Sequence Read Archive (SRA) under accession number PRJNA1154450 and PRJNA1154419 .

Techniques: Flow Cytometry, Immunofluorescence, Expressing, Negative Control, Staining, Derivative Assay, Positive Control, RNA Sequencing, Control, Two Tailed Test

Journal: Nature Communications

Article Title: Medium from human iPSC-derived primitive macrophages promotes adult cardiomyocyte proliferation and cardiac regeneration

doi: 10.1038/s41467-025-58301-8

Figure Lengend Snippet: a Immunofluorescence staining of Ki67-positive human cardiomyocytes treated with FM, hiPM-cm, hiPM-cm components retained by or passing through 3-kDa filters. Human cardiomyocytes were labeled with cTnT (red) and Ki67 (green); nuclei were counterstained with Hoechst (blue). Scale bar, 10 μm. n = 3 biological repeats per group. b Experimental strategy for analyzing protein components from hiPMpre-cm or hiPM-cm collected in RPMI medium by LC/MS. Cartoon elements used in the schematic diagram were created using BioRender. c Venn diagram showing the overlap between upregulated proteins identified in hiPM-cm versus hiPMpre-cm by LC/MS and upregulated genes encoding secreted proteins in CCR2 - human cardiac tissue-resident macrophages versus CCR2 + human monocyte-derived macrophages in the heart. d Unsupervised clustering analysis of relative pro-proliferative potentials of pairwise protein combinations evaluated by the percentages of Ki67-positive human cardiomyocytes. e Immunofluorescence staining of Ki67-positive human cardiomyocytes treated with a five-protein combination including C1QB, NRP1, PLTP, FUCA1, and SERPING1 (5-P combo). Scale bar, 10 μm. n = 3 biological repeats per group. f Principal component analysis of RNA sequencing data from human cardiomyocytes treated with FM and hiPM-cm. n = 3 biological repeats per group. g Volcano plot illustrating DEGs between human cardiomyocytes treated with FM and hiPM-cm. h Representative KEGG terms of cell proliferation-related genes upregulated in cardiomyocytes incubated with hiPM-cm versus FM. i Immunoblotting analysis showing the phosphorylated and total protein levels of AKT, ERK, and STAT3 in human cardiomyocytes treated with FM and hiPM-cm. GAPDH was used as a loading control. n = 3 biological repeats per group for phosphorylated and total ERK; n = 6 biological repeats per group for the other proteins. j Quantification of Ki67-positive human cardiomyocytes treated with hiPM-cm and inhibitors for PI3K-AKT (A-674563), ERK (PD0325901), and JAK-STAT (Stattic) pathways in single or in combination. n = 3 biological repeats per group. Quantitative data are presented as the mean ± SEM. Groups were compared using a two-tailed unpaired Student’s t test ( i ) or one-way ANOVA followed by post hoc Tukey test ( a , e , and j ). Source data are provided as a Source Data file.

Article Snippet: All the RNA sequencing data have been deposited to the National Center for Biotechnology Information Sequence Read Archive (SRA) under accession number PRJNA1154450 and PRJNA1154419 .

Techniques: Immunofluorescence, Staining, Labeling, Liquid Chromatography with Mass Spectroscopy, Derivative Assay, RNA Sequencing, Incubation, Western Blot, Control, Two Tailed Test