Journal: Cells

Article Title: Inflammatory Response of THP1 and U937 Cells: The RNAseq Approach

doi: 10.3390/cells13242062

Figure Lengend Snippet: PCA for differentially expressed genes in LPS-IFNG activated THP1 ( up ) and U937 ( down ) cells. Controls and LPS_IFNG are indicated as circles and squares, respectively. Colors represent connected pairs of one experiment. The plot shows the samples projected onto the two-dimensional space spanned by the covariance matrix’s first and second principal components. The expression levels used as input are raw data counts from the most influential 500 genes.

Article Snippet: The human monocytic cell lines THP1 and U937 were obtained from ATCC (TIB-202 and CRL-1593.2) and cultured in RPMI 1640 medium (Gibco Life Technologies, Carlsbad, CA, USA) supplemented with 10% FCS (Bio&Sell GmbH, Nuremberg, Germany) and 1% antibiotics in a humidified incubator at 37 °C with 5% CO 2 .

Techniques: Expressing

Journal: Cells

Article Title: Inflammatory Response of THP1 and U937 Cells: The RNAseq Approach

doi: 10.3390/cells13242062

Figure Lengend Snippet: Volcano plot analysis of differentially expressed genes in THP1 and U937 cells treated with LPS and IFNG. Volcano plot analysis identified upregulated (red) and downregulated (blue) genes in ( A ) THP1 and ( B ) U937 cells exposed to LPS and IFNG. The annotated dots are data points with the largest (Manhattan) distance from the origin and are above the thresholds indicated by the dashed line. The threshold was set at 2.0 −log10_padj significance level and 2.5-log2-fold change. While all 51 genes (43 up- and 8 down-regulated genes) are highlighted in the THP1 cells, only the top 100 genes out of 197 genes (94 up- and 103 down-regulated genes) are dyed in the U937 cells.

Article Snippet: The human monocytic cell lines THP1 and U937 were obtained from ATCC (TIB-202 and CRL-1593.2) and cultured in RPMI 1640 medium (Gibco Life Technologies, Carlsbad, CA, USA) supplemented with 10% FCS (Bio&Sell GmbH, Nuremberg, Germany) and 1% antibiotics in a humidified incubator at 37 °C with 5% CO 2 .

Techniques:

Journal: Cells

Article Title: Inflammatory Response of THP1 and U937 Cells: The RNAseq Approach

doi: 10.3390/cells13242062

Figure Lengend Snippet: Heat map analysis for differentially expressed genes in THP1 and U937 cells treated with LPS and IFNG. Red specifies high expression levels, while blue shows low levels, indicated by darker and lighter shades of red and blue. Genes with a 2.5-log2-fold change and a significance of 2.0 −log10 were included in this analysis. A relative color scheme uses the minimum and maximum values in each row to convert values to colors.

Article Snippet: The human monocytic cell lines THP1 and U937 were obtained from ATCC (TIB-202 and CRL-1593.2) and cultured in RPMI 1640 medium (Gibco Life Technologies, Carlsbad, CA, USA) supplemented with 10% FCS (Bio&Sell GmbH, Nuremberg, Germany) and 1% antibiotics in a humidified incubator at 37 °C with 5% CO 2 .

Techniques: Expressing

Journal: Cells

Article Title: Inflammatory Response of THP1 and U937 Cells: The RNAseq Approach

doi: 10.3390/cells13242062

Figure Lengend Snippet: Venn analysis of the genes expressed in THP1 and U937 cells exposed to LPS and IFNG. This analysis is restricted to the genes selected under 2.5-log2-fold change and a significance of 2.0 −log10. Red and blue frames represent up-and-down-regulated genes, respectively. Please note the 19 and 2 commonly up- and down-regulated genes.

Article Snippet: The human monocytic cell lines THP1 and U937 were obtained from ATCC (TIB-202 and CRL-1593.2) and cultured in RPMI 1640 medium (Gibco Life Technologies, Carlsbad, CA, USA) supplemented with 10% FCS (Bio&Sell GmbH, Nuremberg, Germany) and 1% antibiotics in a humidified incubator at 37 °C with 5% CO 2 .

Techniques:

Journal: Cells

Article Title: Inflammatory Response of THP1 and U937 Cells: The RNAseq Approach

doi: 10.3390/cells13242062

Figure Lengend Snippet: STRING analysis of up- and down-regulated genes in U937 cells exposed to LPS and IFNG. The protein–protein association network and functional enrichment analyses of the 197 genes with differential expression are shown. Red and blue frames represent the STRING analysis of 94 up- and 103 down-regulated genes, respectively.

Article Snippet: The human monocytic cell lines THP1 and U937 were obtained from ATCC (TIB-202 and CRL-1593.2) and cultured in RPMI 1640 medium (Gibco Life Technologies, Carlsbad, CA, USA) supplemented with 10% FCS (Bio&Sell GmbH, Nuremberg, Germany) and 1% antibiotics in a humidified incubator at 37 °C with 5% CO 2 .

Techniques: Functional Assay, Quantitative Proteomics

Journal: Cells

Article Title: Inflammatory Response of THP1 and U937 Cells: The RNAseq Approach

doi: 10.3390/cells13242062

Figure Lengend Snippet: G:Profiler analysis of differentially expressed genes in U937 with LPS and IFNG. Functional enrichment analysis, also known as over-representation analysis (ORA) or gene set enrichment analysis, was performed using the G:Profiler online tool. The red and blue frames represent the analysis of 94 up- and 103 down-regulated genes, respectively. Selected top significant pathways were highlighted and labeled numerically. Using the Benjamini–Hochberg method, the p value was adjusted (Padj) for multiple tests.

Article Snippet: The human monocytic cell lines THP1 and U937 were obtained from ATCC (TIB-202 and CRL-1593.2) and cultured in RPMI 1640 medium (Gibco Life Technologies, Carlsbad, CA, USA) supplemented with 10% FCS (Bio&Sell GmbH, Nuremberg, Germany) and 1% antibiotics in a humidified incubator at 37 °C with 5% CO 2 .

Techniques: Functional Assay, Labeling

Journal: Cells

Article Title: Inflammatory Response of THP1 and U937 Cells: The RNAseq Approach

doi: 10.3390/cells13242062

Figure Lengend Snippet: RT-PCR analysis of selected genes in ( A ) THP1 and ( B ) U937 cells exposed to LPS and IFNG. Cells were exposed to LPS and IFNG for 24h before RT-PCR analysis was performed. Statistical analysis was based on data from four independent experiments using ratio-paired t-test with untreated cells serving as controls.

Article Snippet: The human monocytic cell lines THP1 and U937 were obtained from ATCC (TIB-202 and CRL-1593.2) and cultured in RPMI 1640 medium (Gibco Life Technologies, Carlsbad, CA, USA) supplemented with 10% FCS (Bio&Sell GmbH, Nuremberg, Germany) and 1% antibiotics in a humidified incubator at 37 °C with 5% CO 2 .

Techniques: Reverse Transcription Polymerase Chain Reaction