8.1- Characterization & DNA amplification
8.1.1-PCR
8.1.1.1-General PCR Methods & Guidelines
8.1.1.1.5-Guidelines for Primer Design [Updated by vg93 27Oct2016]
8.1.1.1.5.1-Primer Design Checklist [created by vg93 31Oct2016]
8.1.1.1.7-Primer Ordering and Reconstitution SOP [updated 2019-03-14 ram524]
8.1.1.1.9-Ten Things That Can Kill Your PCR Information Sheet [reviewed by mw16 07072016]
8.1.1.1.10-Submitting sequences to GenBank SOP [reviewed by mw16 07072016]
8.1.1.1.11-Primer Database Search Protocol.pdf SOP [updated 2Sept2016 nrs13]
8.1.1.1.12-rpoB sigB AT Assignment [MW]
8.1.1.1.17-pGEM Ladder for Size Determination of PCR Products Recipe [uploaded 17Jan2017 by sjr267]
8.1.1.1.18-Gel Electrophoresis of PCR Product SOP [updated 2019-10-11 by js2568]
8.1.1.1.19-PCR Product Purification and Sanger Sequencing Submission SOP [updated 2019-10-11 by js2568]
8.1.1.2-Listeria PCR
8.1.1.2.1-Ten Gene MLST for Listeria
8.1.1.2.1.1-10 gene MLST scheme.xls [reviewed by mw16 07072016]
8.1.1.2.1.2-addB PCR-GoTaq.xls [reviewed by mw16 07072016]
8.1.1.2.1.3-ldh PCR-GoTaq.xls [reviewed by mw16 07072016]
8.1.1.2.1.4-lmo0490 PCR-GoTaqhotstart.xls [reviewed by mw16 07072016]
8.1.1.2.1.5-lmo1555 PCR-GoTaq.xls [reviewed by mw16 07072016]
8.1.1.2.1.6-lmo2763 PCR-GoTaqhotstart.xls [reviewed by mw16 07072016]
8.1.1.2.1.7-pbpA PCR-GoTaqhotstart.xls [reviewed by mw16 07072016]
8.1.1.2.1.8-pbpA PCR-J1-208 GoTaqhotstart.xls [reviewed by mw16 07072016]
8.1.1.2.1.9-polC PCR-GoTaq.xls [reviewed by mw16 07072016]
8.1.1.2.1.10-prs PCR-GoTaq.xls [reviewed by mw16 07072016]
8.1.1.2.1.11-rarA PCR-GoTaq.xls [reviewed by mw16 07072016]
8.1.1.2.2-Listeria PCRs by Gene Name
8.1.1.2.2.1-actA PCR SOP [updated 2019-11-14 by js2568]
8.1.1.2.2.2-Gap PCR protocol for Listeria monocytogenes PCR Protocol [reviewed by mw16 07072016]
8.1.1.2.2.3-Hly a b gene PCR for Listeria monocytogenes PCR Protocol [reviewed by mw16 07072016]
8.1.1.2.2.4-inlA ORF and Gene Fragment PCR and Sequencing SOP [reviewed by mw16 07072016]
8.1.1.2.2.5-sigB PCR SOP [updated 2019-11-14 by js2568]
8.1.1.2.2.11-prs PCR Protocol for Listeria monocytogenes PCR Protocol [reviewed by mw16 07072016]
8.1.1.2.2.12-purM PCR Protocol for lineage II Listeria monocytogenes PCR Protocol [reviewed by mw16 07072016]
8.1.1.2.2.13-purM PCR Protocol for Listeria monocytogenes PCR Protocol [reviewed by mw16 07072016]
8.1.1.2.2.14-ribC PCR Protocol for Listeria monocytogenes PCR Protocol [reviewed by mw16 07072016]
8.1.1.2.2.16-PCRs For Quadruple sigma factor Mutant.pdf (Yichang and Veronica)
8.1.1.3-Salmonella PCR
8.1.1.3.4-7 Gene MLST for Salmonella Informational Document [reviewed by mw16 07072016]
8.1.1.3.4.1-7 gene MLST for Salmonella- Primers and PCR.xls (check)
8.1.1.3.4.2-Salmonella 7 gene MLST Template.xls (check)
8.1.1.3.6-InvA colony PCR for Salmonella PCR Protocol [updated 09Aug2016 ajh22]
8.1.1.3.7-PCR identification of common Salmonella serogroups SOP [reviewed by mw16 07072016]
8.1.1.3.8-PCR determination of H1 and H2-antigens for Salmonella SOP [reviewed by mw16 07072016]
8.1.1.4-PCRs for Other Organisms
8.1.1.4.1-E. coli 6-gene multiplex PCR.pdf
8.1.1.4.2-ipaH colony PCR for Shigella.pdf
8.1.1.4.3-SodA PCR Protocol for S. agalactiae.pdf
8.1.1.4.4-rpoB PCR and Sequencing SOP [updated 2019-10-11 by js2568]
8.1.1.4.5-PCR Amplification of Full Length 16s rDNA SOP [updated 18Nov2016 by sjr267]
8.1.1.4.5.1-PCR Amplification of 16s rDNA Internal Region SOP [updated 2019-11-14 by js2568]
8.1.1.4.6-ITS PCR for Yeast and Mold SOP [updated 2019-11-14 by js2568]
8.1.2-Phenotypic Characterization
8.1.2.2-Bacillus thuringiensis endotoxin crystal protein staining Protocol [reviewed by jk2739 2016-12-30]
[see archive below]
8.1.3-RFLP
[see archive below]
8.1.4-Southern Blot
[archive whole section]
8.2-DNA Labeling & Modification
[see archive below]
8.3-DNA preparation, Purification, & Quantification
8.3.3-Phenol Chloroform Listeria gDNA Extraction_1_28_2015.pdf
8.3.10-Quantification of Purified DNA by NanoDrop.pdf
8.3.12-Small-scale phenol-chloroform extraction of chromosomal DNA from Listeria monocytogenes.pdf
8.3.13-Genomic_DNA_Extraction_Qiagen SOP [updated by ajh22 4/28/16]
8.3.14-HighThroughput_gDNA_Extraction_Qiagen_1_28_15.pdf
8.3.15-Take3_NucleicAcid_96_well_Quantification_01_20_15 Protocol [reviewed by mw16 07072016]
8.3.16-DNA Preparation for Whole Genome Sequencing SOP [updated 27Oct2016 by sh988]
8.3.16.1-Step-by-step checklist for Gram+ bacteria Supplemental file [effective 2Sept2016 ajh22]
8.3.16.2-Step-by-step checklist for Gram- bacteria Supplemental file [effective 13Sept2016 ajh22]
8.3.16.3-CDC MiSeq Nextera XT Library Preparation Reference [reviewed 07Oct2016 by jk2739]
8.3.16.4-Example Nextera Library Sample Preparation Spreadsheet Template [reviewed 07Oct2016 by jk2739]
8.3.18-Preparing Cell Lysates for PCR SOP [updated 2019-10-11 by js2568]
8.4-DNA Sequencing Analysis
Sanger Sequencing
8.4.1-Automated Sequence Editing SOP [updated 2019-10-11 by js2568]
Whole Genome Sequencing
8.4.2-Quality Control and Assembly SOP [reviewed by jk2739 12/19/2016]
8.4.3-Short Read Submission (SRA) SOP [reviewed by jk2739 12/19/2016]
8.4.4-Assembly submission to NCBI SOP [reviewed by rho2 11/25/2016]
8.5-DNA Recombination & Mutagenesis
8.5.2-Cloning of DNA Fragments Protocol [reviewed 8Aug2016 mw16]
8.5.9-GUS promoter fusions in Listeria monocytogenes Protocol [reviewed 08Aug2016 mw16]
8.5.10-Integration of pPL2 derivatives into L. monocytogenes 10403S Protocol [reviewed 08Aug2016 mw16]
8.5.16-pMJG2 vector map.jpg Plasmid Map [reviewed 08Aug2016 mw16]
8.5.17-pMJG3 vector map.jpg Plasmid Map [reviewed 08Aug2016 mw16]
8.5.18-pMJG4 vector map.jpg Plasmid Map [reviewed 08Aug2016 mw16]
8.5.20-Whole Mutant-Soeing PCR for L. mono SOP [reviewed by bmb29 4/6/2016]
8.5.21-P22 Transduction of Salmonella Protocol [reviewed by ram524 28Jul2017]
8.5.22-Protocol for Lambda Red Recombinase in Salmonella Protocol [reviewed by ram524 28Jul2017]
8.6-Microarray
[see archive below]
8.7-Protein Methods
8.7.1-Assay for beta-galactosidase activity of B. subtilis transformed with lacZ reporter plasmid Protocol [mw16 checked07072016]
8.7.2-Beta Galactosidase Assay_general Protocol [mw16 checked07072016]
8.7.3-His tagged sigma factor protein purification protocol Protocol [mw16 checked07072016]
8.8-RNA Prep & Analysis
8.8.1 Qiagen RNA Midi Prep with RQ1 DNAse treatment Protocol [reviewed by vg93 Spring 2016]
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 [reviewed by vg93 Spring 2016]
8.8.10-Taqman- Quantitative Real-Time RT-PCR Protocol Protocol [Updated by vg93 Spring 2016]
8.8.11-RNA Extraction Using TriReagent SOP [reviewed by vg93 4/21/2016]
8.8.12-QuantStudio real time PCR Protocol [reviewed by vg93 Spring 2016]
8.8.13-Sybr Green qRT-PCR Protocol [reviewed by vg93 Spring 2016]
8.8.14_RNAextSalmonella.pdf SOP [created by arc326 2018-09-20]