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Bee Functional Genomics Using Engineered Symbionts Welcome to the temporary website for our new NSF EDGE project! Insects are among the most widespread and diverse...

Co culture Competition Assays The instructions below include the basic protocol. Be sure to check whether there are variations needed for your specific samples! For...

Python snippets for biology Requires BioPython to be installed Open common formats: .gbk / .gbf / .gb import SeqIO with open(`/my/path/file.gb`,`r`) as file handle...

Generating Overhangs If generating overhangs for Golden Gate Assembly outside of YTK/BTK framework, NEB`s GETSET tool can be useful for generating a set of high fidelity...

Calculating Growth Rates with Grofit The following are instructions for calculating growth rates using Grofit, an R package that is no longer supported by the current...

Back to Golden Gate Protocols Second Stage Assembly Second Stage assemblies are used to build plasmids out of multiple transcriptional units (Protocol found here...

Back to Golden Gate Protocols First Stage Plasmid (Transcriptional Unit) Assembly Once you have all your desired part plasmids built you can assemble them into Transcriptional...

Golden Gate Assembly This page serves as the main repository for everything Golden Gate Assembly related. This page links to a number of protocol pages that will...

Leafhopper Care and Protocols Rearing and Caring for Leafhopper Species Leafhopper species are kept in BugDorms (BugDorm 4F3030 and 4F2222). We have the following...

Major version notes Runs prior to February 2020 had a variety of formats and sample submission requirements. Suggested that individual runs be consulted on utbox for...

Problem to be addressed: You have a set of compressed files that all need to be extracted, and you don`t want to manually extract each one. Steps 1 create a new...

Gibson Assembly Background and Design Gibson Cloning is a technique of DNA construct assembly that allows one to join multiple linear segments into either one large...

Preparing Chemically Competent Cells using the CaCl2/Glycerol Method Re engineering the ribosome for efficient selenoprotein synthesis Ross Thyer, 2012 http://docplayer...

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...

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...

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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