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Which polymerase is right for me? Types of polymerase NEB polymerases may be purchased from the NEB freezer, which is located in the Biomedical Research Supply Core...

Working with Serratia symbiotica Serratia symbiotica is a secondary endosymbiont of the black bean aphid ( Aphis fabae ) gut microbiota that can be cultivated...

Custom Primer Design Overview While there are tools available for automatically designing primers (such as the Primer BLAST) often specialized PCR applications, such...

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

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

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

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

Allelic exchange using pKOV or pKOV style vectors Before beginning part 1: design primers 1 Insert should be ~1kb with approximately 500bp on either side of mutation...

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...

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...

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...

TA: Tetrazolium Sugar (TA, TM, TL, ...) Combine in a 1 L flask: 500 mL Component 5 g Tryptone 500 mg Yeast Extract 2.5 g NaCl 8 g...

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...

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...

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...

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

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 Medium (Miller) Rich media used for routine culture of E. coli and other bacteria at high cell densities. Add dH2O to desired...

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

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...

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...

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...

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

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...

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...

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...

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...

Dear internet, We don`t distribute this plasmid. If you want to purify your own enzymes to save money, here are some options to investigate: Bioeconomy Lab ...

Synthetic Biology 101 What is Synthetic Biology? Roughly, synthetic biology is the discipline that engineers cell and cell free systems to behave and produce products...

How to Create a Protocol Tips for Design You should generally organize a protocol to have sections that are relevant from this list: Supplies (materials, strains...