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Bee Microbiome Toolkit The Bee Microbiome Toolkit (BTK) is a Golden Gate compatible toolkit of genetic parts designed for working with newly isolated, non model bacteria...

Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate...

Barrick Lab :: Team Past members of the Barrick lab Interested in our research? Join Us Principal Investigator Prof. Jeffrey E. Barrick...

The University of Texas at Austin :: iGEM Team What is synthetic biology? What is iGEM? `Synthetic biology is the design and construction of biological devices...

MG: Minimal Glucose agar, aka DM: Davis Mingioli agar Note: When making these plates it is necessary to prepare and autoclave the 3 main parts (salts, agar, and sugar...

Czapek Broth (CB) Combine in a flask: 500 mL 1 L Component 1.5 g 3 g sodium nitrate 0.5 g 1 g potassium phosphate dibasic 0.25 g...

Media Recipes Liquid Media Included topic: ProtocolsRecipesSaline Included topic: ProtocolsRecipesLysogenyBroth Included topic: ProtocolsRecipesDavisMingioli...

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...

General Conjugation Protocol Return to BTK Page Conjugation is a reliable, robust method to transfer plasmids between bacteria. This is a general purpose protocol...

SOB/SOC: Super Optimal Broth For SOB: 200mL 250mL 1L Final Component 1 g 1.25 g 5 g 0.5% yeast extract...

Media amendments Antibiotic concentrations and stock solutions This table lists ...

MOB: Mobility Media This media is useful for enhancing the mobility of ADP1, which moves across the plate by `twitching`. 1L Final Component...

DM: Davis Mingioli Growth medium used by the long term E. coli evolution experiment. 0.5L 1L 4.4L 5L Component MW 2.67 g...

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...

LB: Lysogeny Broth / Luria Bertani (Miller) Agar Add dH2O to full volume in an appropriately sized flask. Combine the following, making sure each component fully dissolves...

LB: Lysogeny Broth / Luria Bertani Medium (Miller) Rich media used for routine culture of E. coli and other bacteria at high cell densities. Add dH2O to desired...

Chemically Competent Cells Preparation of Chemically Competent Cells There are a few variations on the protocol for preparation of chemically competent cells. Choice...

Barrick Lab :: Home We are broadly interested in understanding evolution as a creative force. Our lab primarily uses experiments with microorganisms and molecules...

Past Barrick Lab Members Jack Dwenger Elizabeth Manriquez Dan Deathrage Victor Li Matt McGuffie Laurel Miller Aneesa Bhakta Braydin McReynolds Joseph Reitman Emmanuel...

Labeling Glassware and Other Containers All bottles, flasks, tubes, graduated cylinders, and beakers that contain liquid or any substance must be labeled with a description...

Evolution Experiments Introduction An evolution experiment typically consists of evolving one or more ancestor strains in laboratory culture and assessing the types...

Barrick Lab :: Reference Information Getting Started in Lab Getting Started with Lab Techniques Synthetic Biology 101 Background on what synthetic biology...

Computing Environment Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for...

Unix Commands Quick Reference Useful commands and flags that we get tired of looking up... Alphabetical Reference cat yourfile.txt Prints the contents of the given...

Coding 101: Best Practices for Writing Software Build Your Development Suite To code effectively, you need an appropriate development setup. We recommend at least...

Barrick Lab :: Laboratory Protocols Updating Protocols How to Create a Protocol Best practices for designing a protocol and for putting it on the lab Wiki....

Labeling Glassware and Other Containers All bottles, flasks, tubes, graduated cylinders, and beakers that contain liquid or any substance must be labeled with a description...

Commonly Used E. coli Strains OpenWetWare offers a comprehensive repository of the genotypes of the most commonly used E. coli strains. The following table points...

Computer Setup for Bioinformatics and Computational Biology So, you want to harness the immense power of bioinformatics and computational biology for your science...

Learn Biocomputing General Resources / Courses Software Carpentry https://software carpentry.org/lessons/ Code Academy https://www.codecademy.com/ edX Computer...

Creating animations for visualizing time resolved data. Rename files via command line How to use sed to rename multiple files in a single directory. Mass...

Barrick Lab Contact Research Publications Team Protocols Reference Software UT Austin Mol Biosciences...

Keio and ASKA collections Dear internet, Our lab is unable to distribute the Keio/ASKA strains to other institutions. We did not create them! If you want to use...

UV mutagenesis of Bacteria Determination of Optimal UV treatment This procedure is used to determine optimal treatment which will be used for library generation....

Golden Gate Assembly Golden Gate Assembly is a cloning method used to recombine multiple DNA components into a single linear piece or plasmid. It bears similarity...

Copying files to/from UT Box at the command line If you use SSO (through UT Box), you need to first up an external password. You will need LFTP installed on your system...

Barrick Lab :: Software Also check out our GitHub code repositories: http://plannotate.barricklab.org pLannotate (Plasmid Annotation)Automated annotation of engineered...

Lab Notebook Best Practices Notebook Setup Preferred Platform: Benchling Electronic Notebooks Have an administrator add you to the Barrick Lab organization on Benchling...

Isolation of dsRNA from bacteria Materials and Reagents This protocol can be used to validate expression of dsRNA in E. coli (e.g. E.coli HT115(DE3)) or in other...

Barrick Lab Style Guide Writing a Scientific Paper Steps to Writing a Research Article (Original: Beth A. Fischer and Michael J. Zigmond, Survival Skills and...

Microplate Reader Quick Start Best Practices 1 Follow typical best practice for experimental design. Utilize technical replicates from the same biological sample...

Working with Snodgrassella alvi Snodgrassella alvi is a member of the honey bee ( Apis mellifera ) gut core microbiota that can be cultivated in vitro . Its isolation...

CRISPR Associated Transposons (CASTs) The CRISPR Associated Transposon system allows for the targeted insertion of a large genetic cargo (up to 10 kb) into a bacterial...

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...

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...

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...

Acinetobacter baylyi ADP1 Golden Transformation Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double stranded...

Freezing Strains Supplies 1 Overnight liquid culture Several milliliters of overnight liquid culture grown in a suitable medium for each sample to be frozen...

Gene Gorging Evolved Alleles This procedure can be used to directly create unmarked mutations in the E. coli genome. Transform Gene Gorging and Donor Plasmid...