Bacterial-MERFISH measurements of E. coli in various media and B. thetaiotaomicron in the mouse colon

Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based, transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial mRNA. To overcome this challenge, we combine 1000-fold volumetric expansion with multiplexed error robust fluorescence in situ hybridization (MERFISH) to create bacterial-MERFISH. This method enables high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. Using bacterial-MERFISH, we dissect the response of E. coli to carbon starvation, systematically map subcellular RNA organization, and chart the adaptation of a gut commensal, B. thetaiotaomicron, to micron-scale niches in the mammalian colon. 

This deposition contains raw data and final analysis structures associated with the benchmarking of bacterial-MERFISH in E. coli in LB medium, profiling of E. coli through a glucose-xylose diauxic shift, mapping of the internal organization of the E. coli transcriptome in LB, and measurements of the spatial-niche-adaptation of B. theta to the mouse colon. 

Methods
Raw data provided here were collected using a version of multiplexed error robust fluorescence in situ hybridization (MERFISH) adapted for the measurement of the bacterial transcriptome. The detailed protocols used for sample preparation and MERFISH measurements are provided in the methods of the associated publication. 

Some MERFISH data were analyzed using the single-cell analysis package, scanpy, and the intermediate and final data analysis objects created by this program are also provided. 

Analysis of the intracellular organization of the E. coli transcriptome was performed with custom scripts described in the methods of the associated publication. These results are provided here with an example script illustrating the access of data within these custom files.