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Purifying 6xHis Tagged Proteins from E. Coli by Immobilized Metal Affinity Chromatograpy (IMAC) under Native Conditions SUPPLIES: Equipment: Nutator or Rocking...

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

Protocol Updates Needed this page on DNA sequencing needs to be updated and be made more for the general public than to the lab General guide for sorting...

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...

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....

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...

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...

Links to Product Manuals Molecular biology NEB DNA Polymerase HF DNA polymerase solution mix DNA Ligase DNA Ligase I, RNase free PNK Assembly Master Mix...

Veracode Golden Gate Genotyping How to process data from RTSF 1 Open GenomeStudio. 1 Create a new genotyping project. 1 Choose the option to `Load sample...

Total Alkaline Digest of Embedded RNA Linkages Materials 0.2 N Sodium Hydroxide (NaOH) Molarity and Normality are related by N nM For example...

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

topA Gene Sequencing The topA gene coordinates are 1329420 1332017. The topA mutation in the Ara 1 long term line is 1329516:C T. primer who coords...

Pulsed Field Gel Electrophoresis Mapping Purpose: To validate mutations predicted from whole genome re sequencing and possibly discover rearrangements through repetitive...

Primer Extension or Oligo Overlap Extension To stitch together large DNA templates from oligonucleotide fragments. Using Klenow Fragment (3 5 exo...

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...

Population Genetics Long Term Daily Procedure Supplies 1 13 x 50 ml flasks filled with 9.9 ml of DM500 (DM0 supplemented with 0.05% glucose). 1 12 x tetrazolium...

Polyacrylamide Gel Electrophoresis Our gel rigs and supplies are from Scientific. The Diagnostics Website has very helpful background on RNA/DNA polyacrylamide gels...

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...

Petri Dish Patch Templates The Full Template is for patching as many colonies as possible per petri plate. The 96 Well Format is for patching 48 colonies per plate...

Overlap PCR Background Before attempting this somewhat advanced PCR technique, be sure to read the PCR protocol and check out a reference describing PCR theory...

Strains Deleterious Mutations (UV Mutation Accumulation) Strain Fitness Ara relative to REL607 Marker Fitness Ara relative to Ara #8211; Designation...

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...

Label Templates Templates for printing labels...

Major version notes This is a protocol based on Kapa LTP Preparation Kit manual KR0453 v3.13 The main difference centers around the use of 1/2 volume in each reaction...

Genome Minimization Growth / Death Assays In order to be able to compare parameters uniformly between evolved and ancestor strains, all growth in these tests is done...

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...

Profiling Ribose Operon Deletions Day 1: Search strain databank for desired population. 1. Login to lab website, open lab databases. 1. Search under `strains...

Competition Assays for Evolvability Lines Serial transfer of 3.5 ...

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

Materials Description Cat # Price Qiagen RNeasy Protect Bacteria Mini Kit (50) 74524 $386.00 Invitrogen Superscript Plus Indirect cDNA Labeling...

ELUTION of OLIGOS FROM PAGE GEL Crush Soak Eluting DNA/RNA from PAGE or denaturing PAGE Materials Crush Soak Buffer (CSB) 200mM NaCl , 10 mM tris HCl (pH 7....

Competence Assays This assay quantifies the ability of bacterial strains to uptake DNA in culture. The protocol below utilizes genomic DNA extracts obtained using...

Changing Environment Long Term General Procedures Inoculating Tubes To start an experiment, obtain 98 test tubes. Split the test tubes into two racks, 49 in each...

Mutation Rates from Genome Resequencing Motivation: You have re sequenced several genomes after a mutation accumulation or adaptive evolution experiment. How do...

ASKA Collection Evolution Experiment Starting Lines 1 Revive each strain by inoculating a scrape of frozen culture from a well of a microplate into 3 ml of 0.1x...

Using Emulsions to Select by Yield Background Evolution in suspension culture proceeds by selecting for those strains that grow most rapidly, quickly depleting the...

Using the Deep 96 Well Pin Tool The 96 well pin tool can be used to transfer long term evolution experiments and to make dilutions when plating many samples. Although...

The Checklist for Plating Competitions Before plating, it is important to transfer and mix correctly from the competition plates. The following are guidelines...

The Checklist for Plating Competitions Before plating, it is important to transfer and mix correctly from the competition plates. The following are guidelines...

Packaging a Tool for Release You need these environmental variables set to work with the current CVS setup: export CVSROOT `:ext:local@barricklab.org:/bliss/cvs` export...

Lambda Red Protocol Lambda Red Plasmids These plasmids are available as part of the Lambda Red disruption kit from the E. coli Genetic Stock Center. pKD...

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...

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...

Day 1: Plating the Mixed Population 1. Find microsatellite containing strains in the 80...

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...

Bacterial Mutation Accumulation Experiments Background Mutation accumulation (MA) experiments involve periodically bottlenecking a population such that evolution...

(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...

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

Barrick Lab :: Previous Research Leafhoppers: Evolution and Biochemistry of Natural Nanoparticles Leafhopper and SEM image of brochosomes on its wing Leafhoppers...