Computational protocol: Transcriptomic study of Salmonella enterica subspecies enterica serovar Typhi biofilm

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Protocol publication

[…] To acquire the counts data for differential expression analysis of the data generated, the two sample types, i.e. planktonic cells and biofilm cells, were mapped to the reference genome S. Typhi CT18 downloaded from the NCBI RefSeq database (Accession number: NC_003198.1). Data processing was done using the Tuxedo Suite program installed on a bioinformatics server at RIKEN. First Bowtie2 (Version 2.2.6) [] was used to align the transcripts against the reference genome to produce a SAM file. The SAM file was then converted to BAM format and sorted by genome coordinates using SAMtools (Version 0.0.18) []. After sorting, Cufflinks (Version 2.2.1) was used for calculating the differential gene expression levels between the planktonic cells and biofilm cells []. CummeRbund (Version 2.12.1), an R program written for Cufflinks, was used to view and tabulate the results in an Excel file []. Gene annotation was also done using CummeRbund. Gene function information was added to the tabulated Cuffdiff results using an in-house Perl script. […]

Pipeline specifications

Software tools Tuxedo, Bowtie2, SAMtools, Cufflinks, CummeRbund
Application Transcriptome data visualization
Organisms Salmonella enterica subsp. enterica serovar Typhi, Escherichia coli, Bacteria
Diseases Infection, Typhoid Fever