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Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate...
Supplementary Scripts and Data Files Mutation rate inferred from synonymous substitutions in a long term evolution experiment with Escherichia coli Wielgoss, et...
Standard Polymerase Chain Reaction (PCR) PCR reactions produce an amplified product of a template DNA. In addition to the template the reactions include forward and...
Comparative Quantitative PCR (qPCR) Quantitative PCR (qPCR) is a tool routinely used for the quantitation of target nucleic acid sequences. If it is your first time...
Past Barrick Lab Members Sarah Bialik Julie Perreau Shireen Shah Eleanor Young Peng Geng Ginny Mortensen Spencer Hamrick Sean Leonard Gabriel Suarez Grace Stark Stratton...
Barrick Lab :: Team Past members of the Barrick lab Interested in our research? Join Us Principal Investigator Prof. Jeffrey E. Barrick...
Acinetobacter baylyi ADP1 Golden Transformation Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double stranded...
Reagent and Buffer Recipes General calculation resources Mass Molarity Calculator Solution Dilution Calculator 50x TAE Tris Acetate EDTA Used as a buffer...
Acinetobacter baylyi ADP1 Overview ADP1 Resources Genome Sequences type strain (GenBank Format) In general, use this genome as a reference when referring...
Barrick Lab :: Laboratory Protocols Creating Protocols How to Create a Protocol Best practices for designing a protocol and for putting it on the lab Wiki....
DNA Concentration Determination For many applications in cloning and genome editing, it is critical to accurately measure the concentration of DNA in a sample. This...
Sensaphone Protocol The sensaphone is the alarm monitor connected to both of the 80C freezers in MBB. Below is an overview of the current settings and the expected...
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...
The University of Texas at Austin :: iGEM Team Interested in joining the UT Austin iGEM Team? Participating in the iGEM competition is a unique opportunity for undergraduate...
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...
Barrick Lab Contact Research Publications Team Protocols Reference Computation Code UT Austin Mol Biosciences...
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...
Measuring Microbial Growth Rates in a Plate Reader The following protocol can be used to determine the growth rate of a bacterial culture using a plate reader by measuring...
Assembly Reactions Under Construction Protocols from NEB and https://www.neb.com/protocols/2020/01/15/golden gate assembly protocol for using neb golden gate assembly...
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...
Golden Gate Assembly Under Construction Refer to Bee Toolkit pages for design and assembly of parts and plasmids for use with Bee Toolkit Generating Overhangs Assembly...
Back to Golden Gate Protocols Old Golden Gate Assembly Protocols This page contains a collection of old protocols for Golden Gate Assembly. All these protocols should...
Back to Golden Gate Protocols Part Plasmid Assembly Once you have designed your part and either amplified with PCR or ordered the desired gBlock (as described here...
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...
Phenol/chloroform extraction Extracting genomic bacterial DNA from pellet with phenol/chloroform with a combined EtOH precipitation step for salt/SDS/small nucleic...
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...
Learn Biocomputing General Resources / Courses Software Carpentry https://software carpentry.org/lessons/ Code Academy https://www.codecademy.com/ edX Computer...
Getting Started with Lab Techniques
Barrick Lab :: Reference Information Getting Started in Lab Getting Started with Lab Techniques Templates and Spreadsheets Circular and Rectangular Tube...
Media amendments Antibiotic concentrations and stock solutions This table lists ...
FLP Recombination in E. coli Commonly used to eliminate the Kanamycin resistance cassette from E. coli strains from the Keio collection or produced by P1 transduction...
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...
breseq breseq is a computational pipeline for finding mutations relative to a reference sequence in short read DNA re sequencing data for haploid microbial sized...
Preparing Chemically Competent Cells using the CaCl2/Glycerol Method Re engineering the ribosome for efficient selenoprotein synthesis Ross Thyer, 2012 http://docplayer...
YPD Medium General media used for culturing Yeast. Adapted from spring harbor In 1 L bottle: 1L Component 20g Peptone 10 g Yeast Extract...
Back to Golden Gate Protocols Designing a new part Golden Gate Assembly Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA...
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...
SOB/SOC: Super Optimal Broth For SOB: 1L Final Component 5 g 0.5% yeast extract 20 g 2.0% tryptone 0.5 g...
Barrick Lab :: Home We are broadly interested in understanding evolution as a creative force. Our lab primarily uses experiments with microorganisms and molecules...
Barrick Lab :: Research https://barricklab.org/twiki/pub/Lab/ResearchInterests/collage.png See also: Previous Research Projects Engineering Insect Symbionts Many...
Checking Transformation Efficiency of Chemically Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES...
Back to Golden Gate Protocols Troubleshooting Golden Gate Assemblies Tips Screen Inserts for internal BsaI/BsmBI sites! Reactions with single off target sites...

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Topic revision: r2 - 2005-03-28 - 09:40:13 - Main.TWikiContributor
 
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