Supplementary Figure 7: Strategy used to make pools and superpools and their sequencing read content (millions).

(a) Strategy used to make pools and superpools. Strains (small yellow circles) were grouped to form 58 distinct pools (gray circles) by labeling total RNA extracted from each strain with unique barcoded oligoribonucleotides. RNA from 8 strains was mixed to create one pool, with the exception of pool 58, which contained RNA from only 5 strains. In total there were 58 pools. cDNAs from each pool were individually barcoded with Illumina P7 index oligonucleotides. Four different P7 oligonucleotides were used in this study. Four pools were mixed to form one superpool (large yellow circles). In total there were 15 superpools. Pool 58 contained cDNA from only five strains, and superpool 15 contained only two pools. The original number of strains we performed RNAtag-seq analysis on was 461, and here we present data for 442. Data from 19 strains were not included because of low sequence coverage. (b) Average number of sequence reads per pool for each of the 15 superpools is presented. Each circle represents mean and error bars represent standard deviation (SD). Median was calculated using data for superpools 1–14 (each comprised of four pools). Superpool 15 contained only two pools. (c) Graph depicts the median number of reads per sample per pool in millions. Median reads per sample for the pools 57 and 58 are larger due to the higher sequencing depth of these pools.