18 Works

Additional file 11 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 11: Figure S4. Dynamic interactions between the EC and MC. A. Relative proportions of epithelial cell clusters and TME cell clusters in the KUL3 cohort. Samples were clustered according to the distribution pattern of epithelial cells with the corresponding TME cell cluster distribution shown in the right panel. B–E. Bar plot showing the number of incoming events and outgoing events for epithelial cells communicating with TME cells in normal tissues of the SMC...

Additional file 1 of Early-life antibiotic exposure increases the risk of childhood overweight and obesity in relation to dysbiosis of gut microbiota: a birth cohort study

Ping Li, Xuelian Chang, Xiaoyu Chen, Chuan Wang, Yu Shang, Dongyi Zheng & Kemin Qi
Supplementary Material 1

Additional file 14 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 14: Figure S7. Characterization of stromal cells in the KUL3 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 trajectory inferred by Monocle2. Dots represent stromal cells colored by identified cell cluster. D. Heat map plot of the top ranked regulons. E. Dot plot of the correlation between...

Additional file 15 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
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 8 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
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 1 of Early-life antibiotic exposure increases the risk of childhood overweight and obesity in relation to dysbiosis of gut microbiota: a birth cohort study

Ping Li, Xuelian Chang, Xiaoyu Chen, Chuan Wang, Yu Shang, Dongyi Zheng & Kemin Qi
Supplementary Material 1

Additional file 9 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
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 10 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 10: Figure S3. Epithelial heterogeneity validation in KUL3 cohort. A. Volcano plot of the differentially expressed genes between colorectal cancer cells at the core (up) or border (down) and adjacent normal epithelial cells. Genes with FDR values less than 0.05 and absolute log2FC values greater than 1 are colored blue (upregulated in adjacent normal epithelial cells) or red (upregulated in cancer and border tissues). GO enrichment plot is shown on each side with...

Additional file 10 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 10: Figure S3. Epithelial heterogeneity validation in KUL3 cohort. A. Volcano plot of the differentially expressed genes between colorectal cancer cells at the core (up) or border (down) and adjacent normal epithelial cells. Genes with FDR values less than 0.05 and absolute log2FC values greater than 1 are colored blue (upregulated in adjacent normal epithelial cells) or red (upregulated in cancer and border tissues). GO enrichment plot is shown on each side with...

Additional file 12 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
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 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
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 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
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 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
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 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
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 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
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 11 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 11: Figure S4. Dynamic interactions between the EC and MC. A. Relative proportions of epithelial cell clusters and TME cell clusters in the KUL3 cohort. Samples were clustered according to the distribution pattern of epithelial cells with the corresponding TME cell cluster distribution shown in the right panel. B–E. Bar plot showing the number of incoming events and outgoing events for epithelial cells communicating with TME cells in normal tissues of the SMC...

Additional file 14 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
Additional file 14: Figure S7. Characterization of stromal cells in the KUL3 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 trajectory inferred by Monocle2. Dots represent stromal cells colored by identified cell cluster. D. Heat map plot of the top ranked regulons. E. Dot plot of the correlation between...

Additional file 13 of Decoding the colorectal cancer ecosystem emphasizes the cooperative role of cancer cells, TAMs and CAFsin tumor progression

Rongfang Shen, Ping Li, Botao Zhang, Lin Feng & Shujun Cheng
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....

Registration Year

  • 2022
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Resource Types

  • Image
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Affiliations

  • The First Affiliated Hospital of Jinzhou Medical University
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  • Capital Medical University
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  • Xi'an Jiaotong University
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  • Guangdong Provincial Hospital of Traditional Chinese Medicine
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  • Zhongda Hospital Southeast University
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  • Ministry of Education of the People's Republic of China
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  • Nanjing University
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  • China Pharmaceutical University
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  • Beijing Institute of Technology
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  • Shanghai Jiao Tong University
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