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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...

Gel Electrophoresis Overview Gel electrophoresis separates DNA fragments based on size. Electric current moves the negatively charged DNA through the gel, which slows...

Reagent and Buffer Recipes General calculation resources Mass Molarity Calculator Solution Dilution Calculator Gel Electrophoresis 50 TAE (Tris Acetate...

RNA Structure Mutual Information Overview: What do these programs do? information between columns in a sequence alignment of structured RNAs can provide evidence...

WarningThese instructions and the associated scripts have not been tested with more modern versions of R / Perl / Matlab / etc. The procedure may require updates to...

16S rRNA Sequencing to Identify Unknown Microbes Ever wonder what that contaminant in your culture is? Need to accurately identify an environmental isolate? Overview...

Back to Golden Gate Protocols Troubleshooting Golden Gate Assemblies Tips Screen Inserts for internal BsaI/BsmBI sites! Reactions with single off target sites...

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...

FLP Recombination in E. coli This procedure is commonly used to eliminate the Kanamycin resistance cassette from E. coli strains from the Keio collection or produced...

Sanger DNA Sequencing Go to the UT DNA Sequencing Facility website. This page explains the pricing for various orders and the methods by which samples should be prepared...

(Numbers are PCR product dilution with `10` representing a 1:10 dilution of your 0.01ng/ul PCR product prepped as described above) Template Material Use PCR...

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...

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...

Ordering Primers 1 Go to ICMB`s IDT webpage ICMB`s IDT page 1 Click Set up new Account tab on bottom left. 1 Fill out all of your information, including...

Sequencing/Genotyping Primer Design This protocol is specifically for designing primers to PCR amplify a target region of interest from a genome and re sequencing...

CFU Counts This is an outline for a general protocol to assess the number of colony forming units in a sample using spot plating. This method cuts down on the number...

Phage Lysate Preparation We have used this protocol with phages T4, T5, T6 and T7. The general procedure should work with most lytic E. coli phages (although lysis...

Phenol/chloroform extraction Extracting genomic bacterial DNA from pellet with phenol/chloroform with a combined EtOH precipitation step for salt/SDS/small nucleic...

C1 Condition 1, C2 Condition 2, and BR# Biological Replicate Conditions If you want to be extra safe you should also include a negative control (usually...

C1 Condition 1, C2 Condition 2, and BR# Biological Replicate Template Material Use cDNA dilution determined in cDNA Concentration qPCR Note: Once you...

(Numbers are cDNA dilution with `5` representing a 1:5 dilution and so on) Template Material The cDNA used for this is a pool of all your cDNA samples i.e....

Fluctuation Tests Introduction This protocol is for doing a Luria Delbr...

YPD Medium General media used for culturing Yeast. Adapted from spring harbor In 1 L bottle: 1L Component 20g Peptone 10 g Yeast Extract...

Supplementary Scripts and Data Files Mutation rate inferred from synonymous substitutions in a long term evolution experiment with Escherichia coli Wielgoss, et...

Acinetobacter baylyi ADP1 Overview ADP1 Resources Genome Sequences type strain (GenBank Format) In general, use this genome as a reference when referring...

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...