Supplementary Material 2

Supplementary Material 2

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...

Supplementary Material 1

Additional file 2: Fig. S2. The 5hmC/5mC Levels and Growth Curves in TET Gene Knockout hESCs, Related to Fig. 1. (A) Analysis of 5hmC and 5mC levels in each cell line by dot blot; (B) Analysis of 5hmC and 5mC levels in WT, TKO and TET2/3 DKO TET1 heterozygote cell lines by dot blot; (C) Growth curves for WT and TKO hESCs. Error bars indicate mean ± s.d. from three independent biological replicates.

Additional file 2: Fig. S2. The 5hmC/5mC Levels and Growth Curves in TET Gene Knockout hESCs, Related to Fig. 1. (A) Analysis of 5hmC and 5mC levels in each cell line by dot blot; (B) Analysis of 5hmC and 5mC levels in WT, TKO and TET2/3 DKO TET1 heterozygote cell lines by dot blot; (C) Growth curves for WT and TKO hESCs. Error bars indicate mean ± s.d. from three independent biological replicates.

Additional file 4: Fig. S4. RT-qPCR analysis for SOX17, BLIMP1, TFAP2C, NANOS3, POU5F1, SOX2 during hPGC differentiation in day 4 embryoids, Related to Fig. 1; n = 3 independent experiments. Data are presented as means ± s.d. Statistical analysis was performed by Student’s t-test (two-sided), compared to WT group, *p < 0.05, **p < 0.01, ***p < 0.001, Related to Fig. 1.

Additional file 5: Fig. S5. TET Gene Knockout Shows No Effect on iMeLCs Induction, Related to Fig. 1. (A) Bright filed of iMeLCs induction from WT and TKO hESCs (42 h); (B) RT-qPCR analysis for each gene during iMeLCs differentiation in 42 h; n = 3 independent experiments. Data are presented as means ± s.d; (C) Vectors for overexpression of DOX-inducible SOX17, and TMP-inducible NANOG transgenes in BLIMP1–mKate2 reporter hESCs.

Additional file 8. The other 4 abundant miRNAs mimics’ effects on mRNA expression of neurotoxic astrocyte markers. Quantitative analysis of mRNA expression of C3 and Lcn2 in astrocytes, neurotoxic astrocytes and neurotoxic astrocytes treated with 50 nM mimics of miR-21-5p(a), miR-22-3p(b), miR-24-3p(c), miR-26a-5p(d) by RT-QPCR. Data above are represented as mean ± SD. *, p < 0.05; **, p < 0.01; #, p>0.05. C3 complement c3, Lcn2 lipocalin-2.

Additional file 10. Detailed region where the representative images of Figure 5A selected from. LC, lesion cord.

Additional file 9. Detailed region where the representative images of Figure 2A selected from. LC, lesion cord.

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: 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 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 1: Fig. S1. Generation of TET Gene Knockout hESC Lines, Related to Fig. 1. (A) Design of the CRISPR targets for TET genes, using gRNAs (red arrows) that target the sequences corresponding to the beginning of the catalytic domain in TET1, TET2 and TET3; (B) The efficiency for the homozygous knockouts of the TET alleles. The knockouts (KO) were confirmed as bi-allelic frame-shift nonsense mutations. The others include wild-types or heterozygous mutants, or...

Additional file 1: Fig. S1. Generation of TET Gene Knockout hESC Lines, Related to Fig. 1. (A) Design of the CRISPR targets for TET genes, using gRNAs (red arrows) that target the sequences corresponding to the beginning of the catalytic domain in TET1, TET2 and TET3; (B) The efficiency for the homozygous knockouts of the TET alleles. The knockouts (KO) were confirmed as bi-allelic frame-shift nonsense mutations. The others include wild-types or heterozygous mutants, or...

Additional file 5: Fig. S5. TET Gene Knockout Shows No Effect on iMeLCs Induction, Related to Fig. 1. (A) Bright filed of iMeLCs induction from WT and TKO hESCs (42 h); (B) RT-qPCR analysis for each gene during iMeLCs differentiation in 42 h; n = 3 independent experiments. Data are presented as means ± s.d; (C) Vectors for overexpression of DOX-inducible SOX17, and TMP-inducible NANOG transgenes in BLIMP1–mKate2 reporter hESCs.

Additional file 6: Fig. S6. DNMT3B Deletion Partially Rescues Hypermethylation of NANOG and SOX17 Promoters in TKO hESCs, Related to Fig. 5. (A) RNA-seq analysis of DNMT1, DNMT3A and DNMT3B in WT hESCs, TKO hESCs, WT d4 PGCLCs and TKO day4 embryoids; n = 2 independent experiments. Data are presented as means ± s.d. Statistical analysis was performed by Student’s t-test (two-sided); (B) ChIP–qPCR for DNMT1 and DNMT3A at the SOX17 and NANOG promoters in...

Supplemental material, sj-png-2-taj-10.1177_20406223221143245 for Chest X-ray features facilitate screening for pulmonary hypertension caused by fibrosing mediastinitis by Mingfang Zhou, Bo Li, Yaling Chen, Aqian Wang, Yining Zhu, Yu Li, Hongling Su, Jingchun Fan, Yan Zhang and Yunshan Cao in Therapeutic Advances in Chronic Disease

Supplementary Material 1

Long non-coding RNAs (lncRNAs) are involved in developing hepatocellular carcinoma (HCC). The present study explored the role of lncRNA LINC01194, which is upregulated in HCC tissues and might be a vital regulator in HCC progression. Levels of LINC01194, microRNA (miR)-655-3p, and SMAD family member 5 (SMAD5) were assessed using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). The bioactivity of Huh-7 cells was assessed using cell counting kit-8 and transwell assays and flow cytometry. Western...

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: 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: 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 3: Fig. S3. hPGCLCs Differentiation is Sensitive to TET Gene Dosage, Related to Fig. 1. (A) Bright field and fluorescence images of day 4 embryoids with BLIMP1-mKste2 reporter in each cell line, Scale bar = 200 μm; (B) Representative FACS plots of TNAP/BLIMP1 positive cells at day 4 of hPGCLC differentiation for TET-knockout mutants; (C) Immunofluorescence of SOX17, TFAP2C, POU5F1, BLIMP1 and SOX2 at the day4 embryoids for TET-knockout mutants. Scale bar =...