*** This version of Confluence is for testing only and contains a copy of content from June 29th 2026. No changes will be preserved. ***
The following protocols are no longer used or updated by our labs. Please contact Martin Wiedmann, Nicole Martin, Ahmed Gaballa, Sam Reichler, or Jordan Skeens to request access to these these protocols.
8.1.1.1-General PCR Methods & Guidelines
8.1.1.1.1-16S rDNA PCR-Go Taq(1).pdf [archived 02Nov2016 by sjr267]
8.1.1.1.2-16S rDNA PCR-modified for Taq gold.pdf [archived 02Nov2016 by sjr267]
8.1.1.1.3-Basic GoTaq PCR Protocol.pdf Archived Protocol [archived 2019-10-30 by sjr267]
8.1.1.1.4-Colony PCR Archived Protocol Archived Protocol [archived 2019-10-30 by sjr267]
8.1.1.1.6-Primer Naming, Reconstitution and Storage Protocol.pdf
8.1.1.1.7-Primer Reconstitution.pdf
8.1.1.1.7-Primer_Ordering.pdf
8.1.1.1.8-Sample Submission to BRC.pdf
8.1.1.1.8-Singe-tube Sequencing Submission to BRC Archived Protocol Archived Protocol [archived 2019-10-30 by sjr267]
8.1.1.1.11-Primer Database Search Protocol.doc
8.1.1.1.11-Primer Database Search Protocol.pdf
8.1.1.1.13-PCR and Sanger Sequencing Reactions in 96-Well Plates (High-Throughput PCR and Sequencing) Archived SOP Archived SOP [archived 2019-10-30 by sjr267]
High Throughput PCR and Sequencing Reactions Protocol 10 Sep 15.pdf
High-Throughput Enzymatic Lysis of Bacterial Cells 2017-01-03.pdf
8.1.1.2.2-Listeria PCRs by Gene Name
8.1.1.2.2.6-Multiplex PCR for inlH screening.pdf Archived Protocol [archived 07July2016]
8.1.1.2.2.7-Nested hly PCR for Listeria monocytogenes.pdf Archived Protocol [archived 07July2016]
8.1.1.2.2.8-Protocol for sequencing actA gene most polymorphic region.pdf Archived Protocol [archived 07July2016]
8.1.1.2.2.9-Protocol for Sequencing actA gene region with best discrimination.pdf Archived Protocol [archived 07July2016]
8.1.1.2.2.10-Protocol for Sequencing inlA gene region with the best discrimination.pdf Archived Protocol [archived 07July2016]
8.1.1.2.2.15-SigB PCR Protocol GoTaq.pdf
8.1.1.3-Salmonella PCR
8.1.1.3.1-fimA PCR and DNA sequencing of Salmonella enterica for 3gene MLST.pdf Archived Protocol [archived 07July2016]
8.1.1.3.2-manB PCR and DNA sequencing of Salmonella enterica for 3gene MLST.pdf Archived Protocol [archived 07July2016]
8.1.1.3.3-mdh PCR and DNA sequencing of Salmonella enterica for 3gene MLST.pdf Archived Protocol [archived 07July2016]
8.1.1.3.4-Multiplex Serotyping Chart.xls
8.1.1.3.5-PCR detection of the presence or absence of antibiotic resistance genes in Salmonella.pdf Archived Protocol [archived 07July2016]
8.1.2-Phenotypic Characterization
8.1.2.1-Restriction Digest and Cloning of PCR amplified 16S rDNA.pdf
8.1.2.2-Semi-Quantitative Hemolysis Assay for Listeria.pdf Archived Protocol [archived 07July12016]
8.1.3-RFLP
8.1.3.1-Polymerase Chain Reaction- Restriction Fragment Length Polymorphism.pdf Archived Protocol [archived 07July2016]
8.1.4-Southern Blot [section archived 07July 2016]
8.1.4.1-Southern Blotting by Electrophoretic Transfer and non radioactive Detection.pdf Archived Protocol
8.1.4.2-Southern Blotting.pdf Archived Protocol
8.1.4.2-Southern Blotting.doc
8.1.4.3-SouthernBlot Hybridization.pdf Archived Protocol
8.1.5
8.1.5-Submitting sequences to GenBank.docx
8.2-DNA Labeling & Modification [section archived 07July2016]
8.2.1-3’ end labeling of oligonucleotides.pdf Archived Protocol
8.2.2-Kinasing and DIG labeling of LCR primer.pdf Archived Protocol
8.2.3-Poly-T tailing of oligonucleotides.pdf Archived Protocol
8.2.4-Protocol for Fluorescein labeling of oligonucleotides carrying an aminolink.pdf Archived Protocol
8.2.5-Protocol for Geneclean (USB).pdf Archived Protocol
8.3-DNA preparation, Purification, & Quantification
8.3.1-Chelex DNA extraction from blood.pdf Archived Protocol Protocol [archived on 07Jun2016]
8.3.2-Chelex DNA extraction from semen.pdf Archived Protocol Protocol [archived on 07Jun2016]
8.3.3-Detailed Preparation of Chromosomal Listeria DNA (5_05_2011).pdf
8.3.4-DNA Preparation from Listeria using Guanidinium Isothiocyanate.pdf Archived Protocol Protocol [archived on 07Jun2016]
8.3.5-Listeria Lysis Methods and Procedures_11_26_13 Archived Protocol Protocol [archived 2019-10-30 by sjr267]
8.3.6-PCR product purification using ExoSAP.pdf Archived Protocol Protocol [archived 2019-10-30 by sjr267]
8.3.7-PCR Purification Protocol for DNA Sequencing.pdf Archived Protocol Protocol [archived on 07July2016]
8.3.8-Preparation of chromosomal Listeria DNA according to Flamm et al..pdf
8.3.9-Preparation of chromosomal Listeria DNA.pdf
8.3.11-Single Stranded DNA preparation from M13.pdf Archived Protocol Protocol [archived on 07July2016]
8.3.16-WGS_SOP.pdf
WGS_SOP(June 2016).docx
8.3.17-High-Throughput Enzymatic Lysis of Bacterial Cells for PCR Archived Protocol Protocol [archived 2019-10-30 by sjr267]
8.5-DNA Recombination & Mutagenesis
8.5.1-Cloning of DNA Flanking Tn917-LTV3.pdf Archived Protocol [archived 08Aug2016]
8.5.3-Cloning PCR products for Sequencing using pCR 2.1.pdf Archived Protocol [archived 08Aug2016]
8.5.4-Cloning Protocol for Transformation of E. coli DH5aF.pdf Archived Protocol [archived 08Aug2016]
8.5.5-Electroporation L mono.pdf Archived Protocol [archived 08Aug2016]
8.5.6-Electroporation of E coli.pdf Archived Protocol [archived 08Aug2016]
8.5.7-Electroporation of Mycobacterium paratuberculosis.pdf Archived Protocol [archived 08Aug2016]
8.5.8-General Cloning DNA.pdf Archived Protocol [archived 08Aug2016]
8.5.11-Listeria Genomic Alterations.pdf Archived Protocol [archived 08Aug2016]
8.5.12-Overview-Making a mutant in Listeria monocytogenes.pdf Archived Protocol [archived 08Aug2016]
8.5.13-Part II-Making a mutant in Listeria monocytogenes.pdf Archived Protocol [archived 08Aug2016]
8.5.14-Part III-Making a mutant in Listeria monocytogenes.pdf Archived Protocol [archived 08Aug2016]
8.5.15-Part IV-Making a mutant in Listeria monocytogenes.pdf Archived Protocol [archived 08Aug2016]
8.5.19-Procedure for cloning with pDH32.pdf Archived Protocol [archived 08Aug2016]
8.6-Microarray
8.6.1-Analyzing Microarrays.pdf Archived Protocol Protocol [archived March 2016]
8.6.2-Creating Microarrays.pdf Archived Protocol Protocol [archived March 2016]
8.6.3-Labeling RNA with Cy3Cy5 and Hybridization for Microarrays.pdf Archived Protocol Protocol [archived March 2016]
8.6.4-Microarray Slide Blocking.pdf Archived Protocol Protocol [archived March 2016]
8.8-RNA Prep & Analysis
8.8.1-DNase treatment and phenolchloroform extractions for high purity RNA.pdf
8.8.2-Isolation of RNA from Listeria monocytogenes infected mammalian cells.pdf Archived Protocol Protocol [archived April 2016]
8.8.3-Preparation of infected tissue culture cells for bacterial RNA collection.pdf Archived Protocol Protocol [archived April 2016]
8.8.4-Preperation of Listeria RNA.pdf Archived Protocol Protocol [archived April 2016]
8.8.5-RNA extraction, clean-up and storage using Turbo DNase for TaqMan.pdf
8.8.6-RNA Prep with RNeasy Midi Kit instructions.pdf Archived Protocol Protocol [archived April 2016]
8.8.7-RNeasy kit total RNA isolation from Listeria monocytogenes with on-column DNase treatment.pdf Archived Protocol Protocol [archived April 2016]
8.8.8-RT-PCR for the detection of cytokine mRNA.pdf Archived Protocol Protocol [archived April 2016]
8.8.9-Synthesis of large amounts of RNA.pdf Archived Protocol Protocol [archived April 2016]