Extended Data Fig. 1: Characterization of SK-N-SH cells and genome-wide CRISPR library fitness parameters.
From: TMEFF1 is a neuron-specific restriction factor for herpes simplex virus
a-b, SK-N-SH, SH-SY5Y, HaCaT, and THP1 cells were stimulated with polyIC in the culture medium (25 μg/mL) for 6 h, and total RNA was isolated for analysis of IFNB and MXA transcripts by RT-qPCR (n = 3 biological replicates). c, SK-N-SH, SH-SY5Y, HaCaT, and THP1 cells were stimulated with IFNβ (25 ng/mL) for 6 h, and total RNA was isolated for analysis of MXA transcripts by RT-qPCR (n = 3 biological replicates). d-e, SK-N-SH, and THP1 cells were infected with HSV-1 (MOI 1) for 8 h, and total RNA was isolated for analysis of IFNB and MXA transcripts by RT-qPCR (n = 3 biological replicates). f, The number of sgRNAs with zero read counts following mapping and quantification with MAGeCK, displayed as log10(number of zero read count sgRNAs) for each sample in the screens (n = 2 independent screens). g, Gini index of each sample as a measurement of the sgRNA read count distribution. h-i, Boxplot visualization of sgRNA read counts from mock and GFPhigh samples of each screen. Q1 (25th percentile), median, Q3 (75th percentile); Whiskers defines as minima Q1 −1.5* interquartile range and maxima Q3 + 1.5* interquartile range. The sgRNA read count average/depth is denoted for each sample. USC, unsorted controls. j, SK-N-SH cells were treated with Cas9-gRNA RNPs targeting TMEFF1, NKX2-8, CTXN1, or AAVS1. Total RNA was isolated 36 h later, and levels of TMEFF1, NKX2-8, and CTXN1 mRNA expression relative to AAVS1 controls were determined by RT-qPCR (n = 3 biological replicates). Expression of mRNA transcripts was measured by RT-qPCR (a-e + j) and data is represented as means ± s.d. and analysed using unpaired two-tailed t-test; exact P-value shown. Data are representative of 3 independent experiments.
