Data Downloads for "Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes"

These downloads include genome-wide fitness data for 32 bacteria (seven more than in the bioRxiv preprint). The easiest way to view the data is with the Fitness Browser (http://fit.genomics.lbl.gov) rather than with these downloads. These downloads include: an R image with all of the per-gene fitness values and analyses; metadata about the 32 bacteria; a gzipped tar file of genome sequences, protein sequences, and gene models; and a gzipped tar file of strain usage. See the README.txt file for more explanation.<br><br>Note added September 10, 2021: After publishing this data, Morgan Price and Adam Deutschbauer discovered that our stock solutions for sucrose and D-mannitol were problematic. In particular, Escherichia coli BW25113 is a K-12 strain (closely related to MG1655) and should not be able to grow on sucrose. In M9 media made with our original stock solution of sucrose, E. coli BW25113 grew, but in media made with a fresh stock solution, it did not. Similarly, growth of E. coli on mannitol should require the phosphotransferase uptake protein mtlA and the dehydrogenase mtlD. In our original fitness assays for E. coli, mtlA and mtlD were not important for growth on mannitol; instead, manX and manY, which encode the mannose phosphotransferase system, were important. When we repeated these experiments with a fresh stock solution for D-mannitol, we found that mtlA and mtlD were important for fitness, and manX and manY were not.<br>Please disregard the data regarding sucrose or D-mannitol. In the Fitness Browser (https://fit.genomics.lbl.gov), the problematic fitness experiments have been removed. As of September 2021, the data for these compounds in the Fitness Browser is from fresh stock solutions of sucrose and D-mannitol. We also checked that the data from these experiments is consistent with prior knowledge of the utilization of these compounds. Finally, we checked the gene re-annotations that were related to these sucrose or mannitol utilization.<br>