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>

本批次下载资源包含32种细菌的全基因组适应性数据（较bioRxiv预印本中的数据多7种）。查看该数据的最简途径为通过适应性浏览器（Fitness Browser，http://fit.genomics.lbl.gov），而非直接下载本次提供的文件。本次下载资源包含以下内容：内含所有单基因适应性数值及分析结果的R格式镜像文件、32种细菌的元数据、包含基因组序列、蛋白质序列与基因模型的gzip压缩tar归档文件，以及菌株使用情况的gzip压缩tar归档文件。详细说明请参阅README.txt文件。<br><br>2021年9月10日补充说明：本数据正式发布后，Morgan Price与Adam Deutschbauer发现，我们制备的蔗糖与D-甘露醇储备液存在质量问题。具体而言，大肠杆菌（Escherichia coli）BW25113属于K-12菌株（与MG1655亲缘关系密切），理论上无法在蔗糖培养基上生长。使用我们最初制备的蔗糖储备液配制的M9培养基中，大肠杆菌BW25113可正常生长，但更换为新鲜储备液配制的培养基后，该菌株无法生长。同理，大肠杆菌在甘露醇培养基上生长理论上需要磷酸转移酶摄取蛋白mtlA与脱氢酶mtlD。但在我们最初开展的大肠杆菌适应性实验中，mtlA与mtlD对大肠杆菌在甘露醇上的生长并非必需，反而编码甘露糖磷酸转移酶系统的manX与manY为关键基因。当我们使用D-甘露醇新鲜储备液重复该实验后发现，mtlA与mtlD对菌株适应性表型至关重要，而manX与manY则并非如此。<br><br>请忽略所有与蔗糖或D-甘露醇相关的实验数据。在适应性浏览器（https://fit.genomics.lbl.gov）中，存在问题的适应性实验数据已被移除。截至2021年9月，适应性浏览器中上述两种化合物的实验数据均已替换为使用新鲜储备液制备的结果。我们同时验证了上述实验数据与已知的该类化合物代谢利用知识相符。最后，我们核查了与蔗糖或甘露醇代谢相关的基因重新注释结果。