Fig. 2: Expanding QMAP-Seq to multiple cell lines.
From: Quantitative and multiplexed chemical-genetic phenotyping in mammalian cells with QMAP-Seq
a Experimental workflow for QMAP-Seq with five cell lines. b Pie chart showing breakdown of 180 compounds by stage of development. c Pie chart showing breakdown of 180 compounds by pathway. d Schematic of competition experiment to optimize the starting representation of the five co-cultured breast cancer cell lines. Original cell line pools were prepared by mixing equal numbers of one cell line expressing ZsGreen with each of the other four cell lines expressing dTomato. Flow cytometry analysis measured the percentage of GFP positive cells in each pool over time. e Heat maps displaying the percentage of GFP positive cells at various time points as measured using flow cytometry. Left: Original cell line pools that started with 20% of each cell line on Day 0. Right: Optimized cell line pools predicted to contain 20% of each cell line on Day 7. Source data and gating strategy are provided as a Source data file. f Representation of five breast cancer cell lines as measured by counting the number of sequencing reads for each cell line barcode across the 96 DMSO samples. g Representation of sgRNAs as measured by counting the number of sequencing reads for each sgRNA barcode relative to the total number of sequencing reads for that cell line across the 96 DMSO samples. h Standard deviation of the interpolated cell number for each cell line-sgRNA pair across the 96 DMSO samples. Dotted line indicates threshold for excluding cell line-sgRNA pairs with high variability. Source data are available in the Source data file.
