RAINBOW-seq to capture the spatial transcriptome of bacterial biofilm

We developed a spatially resolved method to profile the spatial transcriptome of biofilm. In detail, we used fluorescent dyes to label the different regions of biofilm cultured in a microfluidic chip. After staining, the bacterial cells in biofilm were sorted into relevant bins according to their spatial information marked by the fluorescent pattern. Finally, miniBac-seq (RNA-seq) method was applied to capture the transcriptome of each bin. Overall design: We profiled the spatial transcriptome of five E. coli k12 BW25113 biofilms (b1~b5) as biological replicates. We sorted each sample into 3-7 bins, giving rise to totally 24 spatial transcriptome. Then we used the same strain to profile the temporal transcriptomes of the planktonic culture as a reference for comparison (two replicates, planktonic_r1/2).