Journal: Scientific Reports

Article Title: Evolution from adherent to suspension: systems biology of HEK293 cell line development

doi: 10.1038/s41598-020-76137-8

Figure Lengend Snippet: Comparisons of genomic and transcriptomic profiles of HEK293 cells showed taxonomic divergence between parental HEK293 and progeny cell lines. ( a ) A schematic overview of the lineage relationship of the six HEK293 cell lines used in this study. Blue dots represent adherent cells whereas grey dots represent suspension cell lines. ( b ) Genomic comparison between HEK293 cell lines based on Spearman correlation coefficients of read counts. Darker blue color indicates higher correlation. ( c ) Sample-to-sample comparison between transcriptomes illustrated by a heatmap and hierarchical clustering of taxonomical divergence between samples. Darker blue color indicates shorter Euclidean distance between samples and more similarity. ( d ) PCA plot showing the separation in expression pattern between samples. ( e ) RNA expression levels (in DESeq2 median of ratios) and standard deviations (n = 3) of stably integrated viral genes (EBNA-1, Large T, E1A and E1B) in HEK293 cell lineages determined by RNA sequencing.

Article Snippet: Figure 6 Gene expression validation of the 38 previously identified differentially expressed genes in 63 human cell lines, identified nine significantly differentially expressed genes between suspension and adherent cell lines. ( a ) PCA transcriptomic data of 63 human cell-lines from the Human Protein Atlas shows a clear separation of suspension and adherent cell lines from different tissues. ( b ) Range of normalized counts in HPA cell lines for each of the previously identified 38 genes, differentially expressed between all adherent and suspension HEK293 cell lines.

Techniques: Suspension, Comparison, Expressing, RNA Expression, Stable Transfection, RNA Sequencing

Journal: Scientific Reports

Article Title: Evolution from adherent to suspension: systems biology of HEK293 cell line development

doi: 10.1038/s41598-020-76137-8

Figure Lengend Snippet: Gene expression validation of the 38 previously identified differentially expressed genes in 63 human cell lines, identified nine significantly differentially expressed genes between suspension and adherent cell lines. ( a ) PCA transcriptomic data of 63 human cell-lines from the Human Protein Atlas shows a clear separation of suspension and adherent cell lines from different tissues. ( b ) Range of normalized counts in HPA cell lines for each of the previously identified 38 genes, differentially expressed between all adherent and suspension HEK293 cell lines. The black line in each box shows median of normalized counts for the gene. ( c ) Genes that are differentially expressed between adherent and suspension cells using a Mann–Whitney U-test, with p-values < 0.01, are highlighted in purple, where length of bars shows logarithmic fold change of median between two groups and the color of bars denotes degree of significance of p-value. Non-significant genes have gray bars.

Article Snippet: Figure 6 Gene expression validation of the 38 previously identified differentially expressed genes in 63 human cell lines, identified nine significantly differentially expressed genes between suspension and adherent cell lines. ( a ) PCA transcriptomic data of 63 human cell-lines from the Human Protein Atlas shows a clear separation of suspension and adherent cell lines from different tissues. ( b ) Range of normalized counts in HPA cell lines for each of the previously identified 38 genes, differentially expressed between all adherent and suspension HEK293 cell lines.

Techniques: Gene Expression, Biomarker Discovery, Suspension, MANN-WHITNEY

Journal: Cell Death Discovery

Article Title: ZFHX3 acts as a tumor suppressor in prostate cancer by targeting FTO-mediated m 6 A demethylation

doi: 10.1038/s41420-024-02060-w

Figure Lengend Snippet: a The genes involved in m 6 A modification are shown in the table as candidate targets of ZFHX3 and were analyzed by Chip-Enrich using the ZFHX3 Chip-Seq results. b ZFHX3 correlated with WTAP , FTO , and ALKBH5 when using a cluster of PCa patients containing mRNA expression of these genes. c The m 6 A level was detected by immunofluorescence in RWPE1 cells after knocking down ZFHX3, and the arrows indicated m 6 A translocating from the nucleus to the cytoplasm. n = 3. d The expression of ZFHX3, FTO, and ALKBH5 in human prostate epithelial cell lines, was determined by western blot. The efficiency of ZFHX3 knockdown was detected by western blot, and the global m 6 A levels were reduced by ZFHX3 knockdown and detected by RNA dot blot in RWPE1 ( e ) and LNCaP ( f ). n = 3. MB (methylene blue) represents the loading control of the RNA samples. *** P < 0.001.

Article Snippet: Human immortalized prostate epithelial cell line RWPE1 and other human PCa cell lines were purchased from KeyGEN Biotech (Jiangsu, China).

Techniques: Modification, ChIP-sequencing, Expressing, Immunofluorescence, Western Blot, Knockdown, Dot Blot, Control