Extended Data Fig. 3: HCR-FlowFISH and CASA enhance selectivity of CRISPRi screens at the GATA1 locus.

a, HCR-FlowFISH and PrimeFlow-CRISPRi individual guide score comparison for shared guides. Guides are grouped by overlap with CASA-nominated CREs. We find using HCR-FlowFISH improves separability between guide scores inside and outside of designated CREs compared to PrimeFlow. We also note guide score variability is reduced in HCR-FlowFISH. The minima, centers, and maxima of the boxes indicate the 25th, 50th, and 75th percentiles of the data distributions. Whiskers capture all remaining data, excluding outliers extending beyond 1.5 times the interquartile range below or above the 25th or 75th percentiles, respectively. n = 2,897 (grey boxes) and n = 88 (green boxes) shared guides analyzed outside and inside CRE boundaries, respectively. b, CASA CRE identification on simplified ABC data and comparison to HCR data. CASA only considers the highest and lowest expression bins from the first PCR replicate of each CRISPRi-FlowFISH screen replicate, yet distinguishes CREs from non-specific scores induced by perturbing the GATA1 gene body, in contrast to the original analysis.