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P1 Transduction in Escherichia coli This protocol is adapted from Thomason, L. C., Costantino, N. and Court, D. L. 2007. E. coli Genome Manipulation by P1 Transduction...

Retired Protocols Designing a new part Designing a new part for use in the BTK Bee Microbiome Toolkit (BTK) Golden Gate part kit for work in non model bacterial...

Electrocompetent E. coli Making Electrocompetent E. coli Cells (small batch) This procedure makes enough electrocompetent cells for 2 3 transformations. 1 Grow...

Checking Transformation Efficiency of Chemically Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES...

Isolating Phage Genomic DNA This protocol has been tested with phage T7. It has a double stranded genome that has a length of 40 kb. Materials 5...

Ethanol Precipitation Precipitating DNA/RNA from solution to remove salts and small nucleic acid fragments. Materials 3M Sodium Acetate, pH 5.2 (store at...

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Competence Assays This assay quantifies the ability of bacterial strains to uptake DNA in culture. The protocol below utilizes genomic DNA extracts obtained using...

`In plate` / solid medium transformation of Acinetobacter baylyi ADP1 The following protocol is for single colony `in situ` (in plate) transformation with minimal...

RNAseq Library Preparation Use RNA from RNASnap and Zymo column purification as outlined on wiki. rRNA Depletion Use the Ribozero (RZ) rRNA Removal Kit (Gram negative...

Plasmid copy number determination Plasmid copy number is known to vary depending on origin of replication and culture conditions refs . Typically, plasmids are referred...

Generating Illumina Sequencing Libraries for transposons created in A. baylyi ADP1 with the pBT20 vector. This protocol prepares Illumina sequencing libraries from...

Accessing Journal Articles from Off Campus PubMed PubMed is often the best practice for biology researchers to find and discover publications related to biological...

Aphid Care and Protocols Rearing and Caring for Aphid Species Protocols and Primers

Acinetobacter baylyi ADP1 Genome Manipulations Genome manipulations in Acinetobacter baylyi ADP1 can be performed without the need for exogenous recombinase expression...

Determining Phage Titer Phage Titering is a procedure used to quantify the density of plaque forming units (PFU, analogous to a bacterial culture...

Absolute QPCR for quantification of plasmid copy number in E. coli This protocol is based on methods described in Lee et al (2006), to paper. Designing primers...

Acinetobacter baylyi ADP1 Genome Manipulations by Overlap Extension PCR Overlap PCR Construct Generation The following is a standard procedure designing and constructing...

in vitro RNA synthesis(T7 RNA Polymerase ) T7 RNA Polymerase is used for in vitro mRNA synthesis and is highly specific for the T7 phage promoter. T7 in vitro transcription...

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What to do in case of workplace injury Notify senior lab personnel asap. If major medical treatment is necessary UT personnel are instructed to go to the...

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1 DPLYR 1 READR 1 GGPLOT, incl: 1 COWPLOT 1 GGREPEL 1 COLOR SCHEMES 1 (calculate growth rates) 1 SURVMINER (create survival curves) 1 SURVIVAL...

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Blue Oyster Mushrooms Total Elapsed Time: ~10 days

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asdasdf JeffreyBarrick 20 Jun 2009

Local TWiki Preferences favicon: Attach a favicon.ico to a web`s WebPreferences or add a FAVICON setting to WebPreferences Set FAVICON ///favicon...

These groups can be used to define fine grained .TWikiAccessControl in TWiki: TWikiAdminGroup Add your groups to this list and define new group topics similar...

TWiki Administrator Group Set GROUP JeffreyBarrick Set ALLOWTOPICCHANGE TWikiAdminGroup (Note: Set the members of TWiki Administrator Group in GROUP...

TGY Medium 1.5L Component 7.5 g Pancreatic digest of casein 7.5 g Yeast Extract 1.5g Glucose 1.5 g K2HPO4 24g Agar...

Predicting Riboswitch Regulation on a Genomic Scale This page describes how to install a set of Perl scripts designed to identify members of known classes in genomic...

Predicting Riboswitch Regulation on a Genomic Scale This page describes how to install a set of Perl scripts designed to identify members of known classes in genomic...

Subtle Grammatical Usage Notes aka Common mistakes when writing scientific papers and grants. Usage Alternate / Alternative Alternate means `every other...

Standard Microbiological Practices aka the approximately Ten Commandments of Microbiology 1 Thou shalt always include a media blank Otherwise you may contaminate...

Science Quotations The price of a metaphor is eternal vigilance. ...

Isolation of total RNA Reagents Materials Use filter tips, and designate all solutions, reagents and plastics as RNA only. Keep separate from other general stocks...

Commonly Used Plasmids plasmid markers origin host ref description pCA24N CamR Kitagawa2005 ASKA collection vector pKD...

References for Whole Genome Sequencing NCBI Short Read Archive (SRA) Documentation http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd show f doc m doc s doc...