8.1- Characterization & DNA amplification
8.1.1-PCR
8.1.1.1-General PCR Methods & Guidelines
8.1.1.1.1-16S rDNA PCR-Go Taq.pdf [review rachel & Martin, make new 16S protocol]
8.1.1.1.2-16S rDNA PCR-modified for Taq gold.pdf [review Rachel and Martin, make new 16S protocol]
8.1.1.1.3-Basic GoTaq PCR Protocol.pdf [check with current users; keep]
8.1.1.1.4-Colony PCR Protocol.pdf [check with current users - Jeff??; keep]
8.1.1.1.5-Guidelines for Primer Design.pdf [Veronica]
8.1.1.1.7-Primer_Ordering.pdf [nancy]
8.1.1.1.8-singe_tube_Sequencing_Submission to BRC.pdf [alphina &]
8.1.1.1.9-Ten Things That Can Kill Your PCR [reviewed by mw16 07072016]
8.1.1.1.10-Submitting sequences to GenBank [reviewed by mw16 07072016]
8.1.1.1.11-Primer Database Search Protocol.pdf [nancy]
8.1.1.1.12-rpoB_sigB_ATassignment_User.pdf [MW]
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-Fact Sheet on ActA Differentiation PCR and Interpretation of Results.pdf [check with Shelley or sherry, should be superceeded by SOP; archived?]
8.1.1.2.2.2-Gap PCR protocol for Listeria monocytogenes[reviewed by mw16 07072016]
8.1.1.2.2.3-Hly a b gene PCR for Listeria monocytogenes.2013 [reviewed by mw16 07072016]
8.1.1.2.2.4-inlA ORF and Gene Fragment PCR and Sequencing [reviewed by mw16 07072016]
8.1.1.2.2.5-Modified SigB PCR Protocol-Taq Gold 10uM primers.pdf (MW)
8.1.1.2.2.6-Multiplex PCR for inlH screening.pdf (archive)
8.1.1.2.2.7-Nested hly PCR for Listeria monocytogenes.pdf (archive)
8.1.1.2.2.8-Protocol for sequencing actA gene most polymorphic region.pdf (arcive)
8.1.1.2.2.9-Protocol for Sequencing actA gene region with best discrimination.pdf (archive)
8.1.1.2.2.10-Protocol for Sequencing inlA gene region with the best discrimination.pdf (archive)
8.1.1.2.2.11-Prs PCR Protocol for Listeria monocytogenes [reviewed by mw16 07072016]
8.1.1.2.2.12-PurM PCR Protocol for lineage II Listeria monocytogenes [reviewed by mw16 07072016]
8.1.1.2.2.13-PurM PCR Protocol for Listeria monocytogenes [reviewed by mw16 07072016]
8.1.1.2.2.14-RibC PCR Protocol for Listeria monocytogenes [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
8.1.1.3.1-fimA PCR and DNA sequencing of Salmonella enterica for 3gene MLST.pdf (archive)
8.1.1.3.2-manB PCR and DNA sequencing of Salmonella enterica for 3gene MLST.pdf (archive)
8.1.1.3.3-mdh PCR and DNA sequencing of Salmonella enterica for 3gene MLST.pdf (archive)
8.1.1.3.4-7 Gene MLST for Salmonella [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)
8.1.1.3.5-PCR detection of the presence or absence of antibiotic resistance genes in Salmonella.pdf (archive)
8.1.1.3.6-InvA colony PCR for Salm 4-13-10.pdf (Jeff and Jasna - are we using this for Mars project???; update to reflect current protocol if needed)
8.1.1.3.7-PCR identification of common Salmonella serogroups [reviewed by mw16 07072016]
8.1.1.3.8-PCR determination of H1 and H2-antigens for Salmonella [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
8.1.2-Phenotypic Characterization
[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
8.3.5-Listeria Lysis Methods and Procedures_11_26_13.pdf
8.3.6-PCR product purification using ExoSAP.pdf
8.3.7-PCR Purification Protocol for DNA Sequencing.pdf (Archive)
8.3.10-Quantification of Purified DNA by NanoDrop.pdf
8.3.11-Single Stranded DNA preparation from M13.pdf (Archive)
8.3.12-Small-scale phenol-chloroform extraction of chromosomal DNA from Listeria monocytogenes.pdf
8.3.13-Genomic_DNA_Extraction_Qiagen.pdf 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 [reviewed by mw16 07072016]
8.3.16-DNA Preparation for Whole Genome Sequencing SOP [effective 13Jun2016 ajh22]
8.4-DNA Sequencing Analysis
8.4.1-Automated Sequence Editing SOP [reviewed by sjr267 03/23/2016]
8.5-DNA Recombination & Mutagenesis (MW to review)
8.5.1-Cloning of DNA Flanking Tn917-LTV3.pdf
8.5.2-Cloning of DNA Fragments.pdf
8.5.3-Cloning PCR products for Sequencing using pCR 2.1.pdf
8.5.4-Cloning Protocol for Transformation of E. coli DH5aF.pdf
8.5.5-Electroporation L mono.pdf
8.5.6-Electroporation of E coli.pdf
8.5.7-Electroporation of Mycobacterium paratuberculosis.pdf
8.5.9-GUS promoter fusions in Listeria monocytogenes.pdf
8.5.10-Integration of pPL2 derivatives into L. monocytogenes 10403S.pdf
8.5.11-Listeria Genomic Alterations.pdf
8.5.12-Overview-Making a mutant in Listeria monocytogenes.pdf
8.5.13-Part II-Making a mutant in Listeria monocytogenes.pdf
8.5.14-Part III-Making a mutant in Listeria monocytogenes.pdf
8.5.15-Part IV-Making a mutant in Listeria monocytogenes.pdf
8.5.19-Procedure for cloning with pDH32.pdf
8.5.20-Whole Mutant-Soeing PCR for L. mono [reviewed by bmb29 4/6/2016]
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.pdf (mw16 checked07072016)
8.7.2-Beta Galactosidase Assay_general.pdf (mw16 checked07072016)
8.7.3-His tagged sigma factor protein purification protocol.pdf (mw16 checked07072016)
8.8-RNA Prep & Analysis
8.8.1 Qiagen RNA Midi Prep with RQ1 DNAse treatment [reviewed by vg93]
8.8.5-RNA extraction using Qiagen Midi Kit and Turbo DNAse Protocol [reviewed by vg93]
8.8.10-Taqman- Quantitative Real-Time RT-PCR Protocol [Updated by vg93]
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]
8.8.13-Sybr Green qRT-PCR [reviewed by vg93]