Transcriptional Diversification in a Human-Adapting Zoonotic Pathogen Drives Niche-Specific Evolution

Soma Ghosh, Chao-Jung Wu, Abraham G. Moller, Adrien Launay, Laina Hall, Bryan T. Hansen, Elizabeth R. Fischer, Jung-Ho Youn, Pavel P. Khil, John P. Dekker


You will find  the different script and data used for reproducing the results and figures from the paper in the corresponding directories:

1_EM_images:
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EM images and flagellar quantification for all 6 isolates. Data for Figure 3d and 3e 

2_R_script:
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R scripts for transcriptome data analysis. "Input" folder contain all the input files required to perform the DESeq2 analysis and the Output folder contains the results, including figures and supplementary data from the paper. 

3_Nanodisco_difference_files:
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Summarizes the difference in current traces between native and PCR-amplified genomic DNA for all the 22 isolates sequenced with an ONT GridIONs. 

4_CIRCOS:
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Input files and script required to generate the CIRCOS plot (Figure 4d).


Supplemental Data 8.pdf
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Supplemental Data 8.  Summary Nanodisco methylation motif analysis for all isolates. Isolate name followed by motif evidence dotplots and motif call confidence (k-nearest neighbors model) tables.