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8.1- Characterization & DNA amplification
8.1.1-PCR
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8.1.1.1-General PCR Methods & Guidelines
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8.1.1.1.1-16S rDNA PCR-Go Taq(1).pdf [archived 02Nov2016 by sjr267]
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High-Throughput Enzymatic Lysis of Bacterial Cells 2017-01-03.pdf
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8.1.1.2-Listeria PCRPCR
8.1.1.2.1-Ten Gene MLST for Listeria
8.1.1.2.1.1-16S rDNA PCR-Go Taq(1).pdf [archived 02Nov2016 by sjr26710 gene MLST scheme.xls [archived 10April2020]
8.1.1.2.1.2-16S rDNA addB PCR-modified for Taq gold.pdf GoTaq.xls [archived 02Nov2016 by sjr26710April2020]
8.1.1.2.1.3-ldh PCR-Basic GoTaq PCR Protocol.pdf Archived Protocol xls [archived 2019-10-30 by sjr26710April2020]
8.1.1.2.1.4-Colony PCR Archived Protocol [archived 2019-10-30 by sjr267lmo0490 PCR-GoTaqhotstart.xls [archived 10April2020]
8.1.1.2.1.5-lmo1555 PCR-GoTaq.xls [archived 10April2020]
8.1.1.2.1.6-Primer Naming, Reconstitution and Storage Protocol.pdflmo2763 PCR-GoTaqhotstart.xls [archived 10April2020]
8.1.1.2.1.7-Primer Reconstitution.pdfpbpA PCR-GoTaqhotstart.xls [archived 10April2020]
8.1.1.2.1.7-Primer_Ordering.pdf8-pbpA PCR-J1-208 GoTaqhotstart.xls [archived 10April2020]
8.1.1.2.1.8-Sample Submission to BRC.pdf9-polC PCR-GoTaq.xls [archived 10April2020]
8.1.1.2.1.810-Singe-tube Sequencing Submission to BRC Archived Protocol [archived 2019-10-30 by sjr267prs PCR-GoTaq.xls [archived 10April2020]
8.1.1.2.1.11-Primer Database Search Protocol.docrarA PCR-GoTaq.xls [archived 10April2020]
8.1.1.2.2-Listeria PCRs by Gene Name
8.1.1.2.2.2-Gap PCR protocol for Listeria monocytogenes PCR Protocol [archived 10April2020]
8.1.1.2.2.6-Multiplex PCR for inlH screening.pdf Archived Protocol [archived 07July2016]11-Primer Database Search Protocol.pdf
8.1.1.2.12.137-PCR and Sanger Sequencing Reactions in 96-Well Plates (High-Throughput PCR and Sequencing) 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
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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]
8.1.1.2.2.11-prs PCR Protocol for Listeria monocytogenes PCR Protocol [archived 10April2020]
8.1.1.2.2.12-purM PCR Protocol for lineage II Listeria monocytogenes PCR Protocol [archived 10April2020]
8.1.1.2.2.13-purM PCR Protocol for Listeria monocytogenes PCR Protocol [archived 10April2020]
8.1.1.2.2.14-ribC PCR Protocol for Listeria monocytogenes PCR Protocol [archived 10April2020]
8.1.1.2.2.15-SigB PCR Protocol GoTaq.pdf
actA PCR Assay to Differentiate Listeria monocytogenes.pdf
8.1.1.3-Salmonella PCR
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8.1.1.3.1-fimA PCR and DNA sequencing of Salmonella enterica for 3gene MLST.pdf Archived Protocol [archived 07July2016]
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8.1.1.3.5-PCR detection of the presence or absence of antibiotic resistance genes in Salmonella.pdf Archived Protocol [archived 07July2016]
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8.1.1.4-PCRs for Other Organisms
8.1.1.4.2-ipaH colony PCR for Shigella.pdf [archived 10April2020]
8.1.1.4.3-SodA PCR Protocol for S. agalactiae.pdf [archived 10April2020]
8.1.2-Phenotypic Characterization
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8.1.2.1-Restriction Digest and Cloning of PCR amplified 16S rDNA.pdf
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8.1.2.2-Bacillus thuringiensis endotoxin crystal protein staining Protocol [archived 10April2020]
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
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8.1.4.3-SouthernBlot Hybridization.pdf Archived Protocol
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8.1.5
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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
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8.2.5-Protocol for Geneclean (USB).pdf Archived Protocol
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8.3-DNA preparation, Purification, & Quantification
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8.3.1-Chelex DNA extraction from blood.pdf Archived Protocol [archived on 07Jun2016]
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8.3.17-High-Throughput Enzymatic Lysis of Bacterial Cells for PCR Archived Protocol [archived 2019-10-30 by sjr267]
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8.5-DNA Recombination & Mutagenesis
8.5.1-Cloning of DNA Flanking Tn917-LTV3.pdf Archived Protocol [archived 08Aug2016]
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8.5.19-Procedure for cloning with pDH32.pdf Archived Protocol [archived 08Aug2016]
8.6-Microarray
8.6.1-Analyzing Microarrays.pdf Archived Protocol [archived March 2016]
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8.6.4-Microarray Slide Blocking.pdf Archived Protocol [archived March 2016]
8.8-RNA Prep & Analysis
8.8.1-DNase treatment and phenolchloroform extractions for high purity RNA.pdf
8.8.1 Qiagen RNA Midi Prep with RQ1 DNAse treatment Protocol [archived May 2020]
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
8.8.5-RNA extraction using Qiagen Midi Kit and Turbo DNAse RNA extraction, clean-up and storage using Turbo DNase for TaqMan.pdf Protocol [archived May 2020]
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]
8.8.10-Taqman- Quantitative Real-Time RT-PCR Protocol Protocol [archived May 2020]
8.8.12-QuantStudio real time PCR Protocol [archived May 2020]