Whole Transcriptome RNA-seq of Planktonic and Biofilm PAO1

Whole transcriptome RNA-seq of PAO1 planktonic and biofilm cells was carried out using the ION Torrent Personal Genome System (Life Technologies)^{90 (link)}. Following depletion of rRNA using RiboZero (illumina), the cDNA libraries were constructed using the Ion Total RNA-Seq kit v2 (Life technologies) according to the manufacturer’s protocol. The cDNA libraries were used to prepare sequencing templates using the Ion PGM Template OT2 200 kit on the Ion OneTouch™2 instrument (Life Technologies), followed by Ion Sphere™ Quality Control Kit assessment and template-positive Ion Sphere™ Particle (ISP) enrichment using the Ion OneTouch™ ES instrument. Sequencing was carried out using the Ion Sequencing 200 Kit v2 and the Ion 316v2 Chip on the Ion Torrent PGM sequencing platform (Life Technologies). RNA-seq was performed in triplicate using biological replicates. The raw sequencing data are available in the NCBI short read archive (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi) with accession number SRP096901 under BioProject PRJNA362216.

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Kaleta M.F., Petrova O.E., Zampaloni C., Garcia-Alcalde F., Parker M, & Sauer K. (2022). A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria. NPJ Biofilms and Microbiomes, 8, 54.

Publication 2022

ION Torrent Personal Genome System RiboZero Ion Total RNA-Seq kit v2 Ion PGM Template OT2 200 kit Ion OneTouch™2 instrument Ion Sphere™ Quality Control Kit assessment Ion Sphere™ Particle ( Ion OneTouch™ ES instrument Ion Sequencing 200 Kit v2 Ion Torrent PGM sequencing platform

Biofilm Biological Cdna libraries Cells Chip Genome Planktonic Rna seq Rrna Total rna seq Transcriptome

Corresponding Organization :

Other organizations : Binghamton University, Roche (Switzerland)

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Variable analysis

independent variables

Planktonic growth condition
Biofilm growth condition

dependent variables

Whole transcriptome gene expression

control variables

Biological replicates (triplicate)

controls

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