Triggering receptor expressed on myeloid cells 1 (TREM1) participates in the development of endometritis. This study aims at identifying the effects and interaction of TREM1 and upstream stimulatory factor 2 (USF2) in endometritis by using a model of lipopolysaccharide (LPS)-induced human endometrial epithelial cells (HEnEpCs). ELISA was performed to determine the levels of interleukin (IL)-6, IL-1β, and tumor necrosis factor (TNF-α) after LPS stimulation. TREM1 and USF2 expression was examined with RT-qPCR and Western blot....

The dysregulated circular RNAs (circRNAs) are linked to progression and chemoresistance in colorectal cancer (CRC). However, the role of circRNA protein tyrosine kinase 2 (circPTK2) in CRC progression and chemoresistance is uncertain. The circPTK2, microRNA (miR)-136-5p, m6A ‘reader’ protein YTH domain family protein 1 (YTHDF1), β-catenin and cyclin D1 abundances were examined via quantitative reverse transcription PCR or Western blotting. The progression was investigated by cell counting kit-8 (CCK-8), colony formation, transwell and xenograft analysis....

Additional file 1: Figure S1. The mRNA level of CBFA1 in qRT-PCR (a) and RNA-Seq (b). *P < 0.05.

Additional file 4: Figure S4. HE (scale bar = 50 μm) and Masson (scale bar = 50 μm) staining were performed to evaluate ectopic bone formation in nude mice (n=4).

Additional file 3: Figure S1. (A, D, G) The heat map of 10 prognostic DEOSG expressions in the train (A), testing (D), and entire sets (G), respectively. (B, E, H) The comparison of 10 prognostic DEOSG expressions between high- and low-risk groups in the training (B), testing (E), and entire sets (H), respectively. (C, F, I) The correlations among 10 prognostic DEOSG between high- and low-risk groups in the training (C), testing (F), and entire...

Additional file 12: Figure S5. Characterization of myeloid cells in the KUL3 cohort. A. UMAP plot of myeloid cells colored by cell cluster and sample origin. B. Heatmap of marker genes identified through Seurat. For each cell cluster, cells were down-sampled to 100. C. Heatmap plot of the top 5 ranked regulons in TAM1-TAM4 identified by pySCENIC. D. Dot plot of the correlation between the proportions of C4 cells in epithelial cells and macrophages (left),...

Additional file 12: Figure S5. Characterization of myeloid cells in the KUL3 cohort. A. UMAP plot of myeloid cells colored by cell cluster and sample origin. B. Heatmap of marker genes identified through Seurat. For each cell cluster, cells were down-sampled to 100. C. Heatmap plot of the top 5 ranked regulons in TAM1-TAM4 identified by pySCENIC. D. Dot plot of the correlation between the proportions of C4 cells in epithelial cells and macrophages (left),...

Additional file 1: Figure S1. The AR−/− mice genotyping and the expression level of AR in AR−/− mice. (A) AR null allele were identified by northern blot analysis. The expected bands of ∼119 bp is observed in the wild-type mice while not seen in AR−/− mice. (B) Western blot analyze the AR expression in the AR−/− mice. (C) Immunofluorescence analyze the AR expression in the spinal cord of AR−/− mice at 3 day following BPRA...

Additional file 5: Figure S2. Median-joining network of Pv230 among eight geographically diverse populations. Haplotypes composed of nucleotide polymorphism in ICP of Pv230 with a frequency > 1 were used to create a median-joining network. Each node represents one haplotype, node size indicates haplotype frequency, and node color corresponds to the country of origin. Line length is proportional to genetic distance.

Additional file 3 Supplementary Fig. 3. The combined features about the zinc fingers (ZnFs) for all the mouse KRAB-ZFPs, including the composition specificity and frequency of occurrence. The detailed description is the same as that in Fig. 1C. Each row represents a single KRAB-ZFP.

Additional file 7 Supplementary Fig. 7. ZnF fingerprints analyses for human KRAB-ZFPs on chr19. The combined features about the ZnF fingerprints for KRAB-ZFPs for all the human KRAB-ZFPs on chromosome 19. The detailed description is the same as that in Fig. 1C. Each row represents a single KRAB-ZFP.

Additional file 1.

Supplementary Material 6

Supplementary Material 7

Additional file 1: Plots of RNA read length and Average reads quality.

Additional file 2: Plots of number of expressed transcripts and reads number (sequencing depth).

Additional file 3: Sample correlations between replicates and treatments in 'C34’.

Additional file 5: Numbers of expressed genes in three rice varieties.

Additional file 6: GO analysis of expressed genes in rice.

Additional file 8: Expression patterns of genes within 200 Kb around the predicted IncRNA ONT.9939.2.

Additional file 1: Supplementary Figure 1. MMP-13 levels in the medium of IL-1β-induced C28/I2 cells detected by ELISA.

Additional file 4: Figure S1. Validation of ω-transaminase activity based on color reaction. 1: Control 2: Empty vector plasmid strain breaking solution 3: Breaking solution of strain expressing He-ωTA protein 4: Breaking solution of strain expressing Cv-ωTA protein 5: Purified He-ωTA protein solution 6: Purified Cv-ωTA protein solution.

Additional file 15: Figure S8. Workflow of this study. Single-cell transcriptomes and bulk RNA-seq data were integrated to fully analyze the complicated relationship between colorectal epithelium and surrounding environment. C4 cells were featured with high invasive potential and related with TAMs and CAFs, and further validated in vitro using IHC and mIHC.

Additional file 13: Figure S6. Characterization of stromal cells in the SMC cohort. A. UMAP plot of stromal cells colored by cell cluster and sample origin. B. Heat map of marker genes identified through Seurat. For each cell cluster, cells were down-sampled to 100. C. Differentiation trajectories inferred by Monocle2. Dots represent stromal cells and are colored by identified cell cluster. D. Heat map of the top 5 ranked regulons in S5 and S6. E....

Additional file 8: Figure S1. Cellular landscape of CRC in the KUL3 cohort. A. UMAP plot of 26,268 cells colored by cell cluster, CMS and sample origin. Each dot represents a cell and cellular cluster is annotated with text. B. Proportions of the identified cell clusters distributed across tumor, border and adjacent normal tissues with the relative cell type proportions and total cell numbers. Upper: all cell clusters; lower: immune and stromal cell clusters. C....