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: 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 6: Figure S6. HDAC2 inhibition promoted the expression of Serpine1. A SDS-PAGE identification of the proteins pulled-down by DNA fragment of Serpine1 promoter. The gel was stained with Coomassie blue. The indicated differential bands were excised with a scalpel and identified by LC-MS. B Total ion chromatogram of proteins. C–E Serpine1 expression analysed using RT-qPCR and western blot in trichostatin A (TSA)-treated MLE-12 cells. Data show mean ± SEM; Data was analysed using...

Additional file 6: Figure S6. HDAC2 inhibition promoted the expression of Serpine1. A SDS-PAGE identification of the proteins pulled-down by DNA fragment of Serpine1 promoter. The gel was stained with Coomassie blue. The indicated differential bands were excised with a scalpel and identified by LC-MS. B Total ion chromatogram of proteins. C–E Serpine1 expression analysed using RT-qPCR and western blot in trichostatin A (TSA)-treated MLE-12 cells. Data show mean ± SEM; Data was analysed using...

Additional file 15: Figure S6. circPVT1 promotes the migration and invasion of NPC cells by regulating cell adhesion andcytoskeleton remodeling. The 231 differentially expressed proteins regulated by c-Myc from LC-MS/MS data using the Ingenuity Pathway Analysis (IPA) software.

Supplementary Material 7

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 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....

Additional file 9: Figure S2. Functional heterogeneity of CRC epithelial cells in the SMC cohort. A. UMAP feature plot of the top 10 upregulated genes in the SMC cohort. B. Correlation heat map of 123 programs identified by cNMF. The Pearson correlation coefficient is indicated by the color. C. Heatmap of the relative mean signature score of cancer cell functional signatures across C1-C7. The signature score was calculated using the “AUCell” package. D. Heatmap of...

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.

BETA PRIME: Phase I study of AdAPT-001 as monotherapy and combined with a checkpoint inhibitor in superficially accessible, treatment-refractory solid tumors Infographic

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 1.

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

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: 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...

Supplemental material, sj-tif-3-onc-10.1177_11795549221134735 for First-Line Osimertinib in Patients With EGFR-Mutated Non-Small Cell Lung Cancer: Effectiveness, Resistance Mechanisms, and Prognosis of Different Subsequent Treatments by Naifu Nie, Jianghua Li, Jian Zhang, Jie Dai, Zhulin Liu, Zhenyu Ding, Yubo Wang, Mengxiao Zhu, Chen Hu, Rui Han, Huan Tang, Li Li and Yong He in Clinical Medicine Insights: Oncology