Genomic Analysis of C. difficile Agr Mutants

Genomic DNA was extracted from C. difficile WT, ΔagrB1, ΔagrD1, and ΔagrB1D1 strains using the Sigma bacterial genomic DNA extraction kit, following the manufacturer’s protocol. The genomic DNA was submitted to the Oklahoma Medical Research Foundation Genomics Core Facility and paired-end sequenced on an Illumina MiSeq. The data were aligned to the reference genome (GenBank accession number AM180355) using Geneious version 10.2.4 (39 (link)).

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Ahmed U.K., Shadid T.M., Larabee J.L, & Ballard J.D. (2020). Combined and Distinct Roles of Agr Proteins in Clostridioides difficile 630 Sporulation, Motility, and Toxin Production. mBio, 11(6), e03190-20.

Publication 2020

bacterial genomic DNA extraction kit

Bacterial dna Genome Strains

Corresponding Organization :

Other organizations : University of Oklahoma Health Sciences Center

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Variable analysis

independent variables

Genotype of C. difficile strain: WT, Δagrb1, ΔagrD1, ΔagrB1D1

dependent variables

Gene expression or transcriptional profile of C. difficile strains

control variables

Extraction of genomic DNA using Sigma bacterial genomic DNA extraction kit
Paired-end sequencing on Illumina MiSeq platform
Alignment of sequencing data to the reference genome (GenBank accession number AM180355)

controls

No positive or negative controls were explicitly mentioned in the input protocol.

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