sw48  (ATCC)

Journal: International Journal of Molecular Sciences

Article Title: Transcriptomic Profiling Reveals Isoform-Specific Regulatory Roles of miR-196A and miR-196B in Colorectal Cancer Cells

doi: 10.3390/ijms27093959

Figure Lengend Snippet: Generation and functional validation of miR-196 knockout SW48 cells. ( A ) Sequence alignment of miR-196A and miR-196B showing a high degree of similarity between the two miRNA isoforms. ( B ) Quantitative RT-PCR analysis of miR-196 expression in parental SW48 cells and in miR-196A-KO or miR-196B-KO cells. Relative expression levels were normalized to an internal control RNA and presented as fold change compared with control cells. ( C ) Cell proliferation assay showing the relative growth rates of control, miR-196A-KO, and miR-196B-KO SW48 cells. Data represent the mean ± SD from independent experiments. Statistical significance is indicated (* p < 0.05, *** p < 0.001).

Article Snippet: The human colorectal cancer cell line SW48 (ATCC Cat. No. CCL-231) was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Functional Assay, Biomarker Discovery, Knock-Out, Sequencing, Quantitative RT-PCR, Expressing, Control, Proliferation Assay

Journal: International Journal of Molecular Sciences

Article Title: Transcriptomic Profiling Reveals Isoform-Specific Regulatory Roles of miR-196A and miR-196B in Colorectal Cancer Cells

doi: 10.3390/ijms27093959

Figure Lengend Snippet: Identification of differentially expressed genes following deletion of miR-196 isoforms in SW48 cells. ( A ) Volcano plot showing the distribution of differentially expressed genes (DEGs) in miR-196 knockout cells compared with control SW48 cells. Significantly up-regulated and down-regulated genes are highlighted based on predefined statistical thresholds. ( B ) Summary of DEGs identified in the transcriptomic analysis, showing the numbers of significantly up-regulated and down-regulated genes in miR-196 knockout cells relative to control cells. The vertical dashed lines indicate the fold-change thresholds, and the horizontal dashed line represents the statistical significance threshold (adjusted p -value cutoff). The grey shaded area indicates genes that are not significantly differentially expressed. ( C ) Venn diagram illustrating the overlap of DEGs between miR-196A-KO and miR-196B-KO cells. A subset of genes was commonly regulated by both miR-196 isoforms, while additional genes were uniquely altered in each knockout condition.

Article Snippet: The human colorectal cancer cell line SW48 (ATCC Cat. No. CCL-231) was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Knock-Out, Control

Journal: International Journal of Molecular Sciences

Article Title: Transcriptomic Profiling Reveals Isoform-Specific Regulatory Roles of miR-196A and miR-196B in Colorectal Cancer Cells

doi: 10.3390/ijms27093959

Figure Lengend Snippet: Functional enrichment analysis of differentially expressed genes following miR-196A or miR-196B deletion. ( A ) Functional categorization of differentially expressed genes (DEGs) identified in miR-196A-KO cells compared with control SW48 cells. The pie chart shows the percentage distribution of genes associated with major biological processes. The percentages may exceed 100% because individual genes can be associated with multiple functional categories and are therefore counted in more than one category. ( B ) Distribution of significantly up-regulated and down-regulated genes in each functional category in miR-196A-KO cells. ( C ) Expression profiles of representative genes altered in miR-196A-KO cells. Each point represents normalized RNA-seq expression values from independent samples. ( D ) Functional classification of DEGs identified in miR-196B-KO cells relative to control cells. The percentages may exceed 100% because individual genes can be associated with multiple functional categories and are therefore counted in more than one category. ( E ) Numbers of significantly up-regulated and down-regulated genes in each functional category in miR-196B-KO cells. ( F ) Expression patterns of representative genes affected by miR-196B deletion.

Article Snippet: The human colorectal cancer cell line SW48 (ATCC Cat. No. CCL-231) was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Functional Assay, Control, Expressing, RNA Sequencing

Journal: International Journal of Molecular Sciences

Article Title: Transcriptomic Profiling Reveals Isoform-Specific Regulatory Roles of miR-196A and miR-196B in Colorectal Cancer Cells

doi: 10.3390/ijms27093959

Figure Lengend Snippet: Hierarchical clustering and reproducibility assessment of RNA-seq data from miR-196 knockout SW48 cells. ( A – C ) Heatmap visualization of differentially expressed genes between miR-196 knockout cells and parental SW48 cells using fold-change thresholds of >1.5 ( A ), >2.0 ( B ), and >3.0 ( C ). Hierarchical clustering reveals distinct expression patterns associated with miR-196 deletion. ( D ) Pearson correlation heatmap showing strong correlations among biological replicates and experimental groups. Color intensity represents the Pearson correlation coefficient (r), ranging from −1 to 1, where values closer to 1 indicate stronger similarity between samples. The numerical values in each cell correspond to the correlation coefficients. ( E ) Pairwise scatter plot matrix demonstrating high concordance in gene expression profiles across samples. The red line represents the linear regression fit. Asterisks (***) indicate statistical significance ( p < 0.001).

Article Snippet: The human colorectal cancer cell line SW48 (ATCC Cat. No. CCL-231) was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: RNA Sequencing, Knock-Out, Expressing, Gene Expression

Journal: International Journal of Molecular Sciences

Article Title: Transcriptomic Profiling Reveals Isoform-Specific Regulatory Roles of miR-196A and miR-196B in Colorectal Cancer Cells

doi: 10.3390/ijms27093959

Figure Lengend Snippet: Functional enrichment analysis of genes altered following miR-196 deletion. Gene Ontology (GO) and KEGG pathway enrichment analyses were performed using differentially expressed genes identified from RNA-seq analysis of miR-196A-KO and miR-196B-KO SW48 cells. ( A ) Bubble plot showing significantly enriched GO terms and KEGG pathways in miR-196A-KO cells. Functional categories are grouped into biological process (BP), cellular component (CC), molecular function (MF), and KEGG pathways. Bubble size represents the number of genes associated with each term, and color intensity indicates the −log10( p -value). ( B ) Bubble plot showing enriched GO terms and KEGG pathways in miR-196B-KO cells using the same criteria. ( C ) Distribution of up-regulated and down-regulated genes contributing to each enriched functional category in miR-196A-KO cells. ( D ) Distribution of up-regulated and down-regulated genes contributing to each enriched functional category in miR-196B-KO cells.

Article Snippet: The human colorectal cancer cell line SW48 (ATCC Cat. No. CCL-231) was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Functional Assay, RNA Sequencing

Journal: International Journal of Molecular Sciences

Article Title: Transcriptomic Profiling Reveals Isoform-Specific Regulatory Roles of miR-196A and miR-196B in Colorectal Cancer Cells

doi: 10.3390/ijms27093959

Figure Lengend Snippet: Differential gene expression patterns in miR-196A-KO and miR-196B-KO SW48 cells. Radar charts display the top ten most highly upregulated and downregulated genes in each knockout condition. Left panels show average normalized expression values (log2); right panels show fold change relative to parental SW48 cells (SW48-vector). ( A ) Top ten upregulated genes in miR-196A-KO cells, including RIMS2 , ADGRL2 , and LAMA2 . ( B ) Top ten upregulated genes in miR-196B-KO cells, including PCCA , LAMA2 , and AKAP12 . ( C ) Top ten downregulated genes in miR-196A-KO cells, including KRT14 , KLK11 , and KRT16 . ( D ) Top ten downregulated genes in miR-196B-KO cells, including KRT16 , KRT14 , and KRT19 . ( E ) qPCR validation of selected miR-196-associated genes ( NT5E , PRRX1 , KITLG , CLDN4 , and FLG ) in parental SW48 and miR-196 isoform knockout cells, showing isoform-dependent differences in gene expression. Data are presented as mean ± SD ( n = 3).

Article Snippet: The human colorectal cancer cell line SW48 (ATCC Cat. No. CCL-231) was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA).

Techniques: Gene Expression, Knock-Out, Expressing, Plasmid Preparation, Biomarker Discovery