Fig. 3: proteoCHIP EVO 96 SCP sample preparation reflects expected proteome changes in THP-1 cells upon LPS treatment. | Nature Communications

Fig. 3: proteoCHIP EVO 96 SCP sample preparation reflects expected proteome changes in THP-1 cells upon LPS treatment.

From: Automated single-cell proteomics providing sufficient proteome depth to study complex biology beyond cell type classifications

Fig. 3

a Schematic overview of the proteoCHIP-based workflow, including LPS treatment of THP-1 cells, unsupervised cluster normalization and batch correction followed by differential expression analysis. b Protein group identifications and c PCA of single cells prepared with the proteoCHIP EVO 96 and acquired on the timsTOF Ultra at 40SPD (30 min effective gradient) upon 12 h of 200 ng/mL (n = 84) LPS or DMSO vehicle control (n = 77) treatment. The colored bars represent the median and the error bar the MAD of protein groups identified. Ellipse represents 95% confidence interval. d Volcano plot of moderated two-sided, two-sample t-test results (200 ng/mL LPS over DMSO vehicle control). Log10 fold change and −10log10 p-value are shown, significantly regulated proteins with an adjusted p-value ≤ 0.05 are indicated in blue (down, 15 proteins) and brown (up, 214 of proteins). e Normalized Enrichment Scores (NES) of significantly enriched Reactome pathways identified by Gene Set Enrichment Analysis (GSEA) on two-sided, two-sample t-test results. All shown pathways are statistically significant with adjusted p-value < 0.01. Source data are provided as a Source Data file. Panel a was created with BioRender.com, released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license.

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