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Making Presentations The purpose of this page is to provide a resource for how to make an effective presentation to a variety of different audiences. Considerations...

Lithium Acetate Transformation This protocol is originally from the Spring Harbor Laboratory Yeast Genetics Genomics course manual. Making Competent S. cerevisiae...

Large scale Protein Expression in E. Coli: Notes: This can be applied to either soluble proteins (for a downstream prep in native conditions) or insoluble proteins...

Measuring Intracellular Reactive Oxygen Species (ROS) This procedure is commonly utilized to quantify ROS. For more information about limitations associated with this...

Tobacco hornworm (Manduca sexta) care The tobacco hornworm is the caterpillar stage of the five spotted hawk moth ( Manduca sexta ). They constitute a major pest of...

Barrick Lab Style Guide for Figures General Workflow Use a program (Excel, R, CIRCOS, matplotlib, etc.) to graph your data. Output a file in a vector graphics...

iGEM Part Plasmid Assembly NOTE: The following page is under revision. The GGA procedures and protocols below may not be optimal for your experiments. If you are...

Gene Gorging Marker Mutations For competitive fitness assays, one must be able to distinguish two E. coli subpopulations in a mixed culture. One way this can be...

Genome Diff file Generation Overview This is a series of commands to automatically generate .gd files based on naming system present in .fastq files. This will typically...

Evolutionary Stability of Fluorescent Protein or Chromoprotein Expression This protocol is a work in progress This procedure is to monitor the decay of a genetic...

Find Strains, Plasmids, and Genes Reminder: Always revive new organisms according to an established protocol and archive a lab stock of the original freeze dried...

Find Chemicals Often you come across a chemical structure or name in a publication and then you need to find a place to order some from for your research. Maybe you...

Dpn I digestion Purpose To digest (Adeno) methylated GATC sites. Useful for removing cell derived plasmid template from PCR samples. Use 1. Add 1...

Use of degenerate bases Spoke with IDT about some of their recommendations related to incorporation of degenerate bases in oligos. Machine Mix vs Hand Mix option...

This page is meant to include instructions on how to clone dcamp, and push back to the repository. It is not well tested. Standardized TACC DCAMP instructions. This...

Working with Gilliamella apicola Gilliamella apicola is a gram negative bacterial member of the honey bee ( Apis mellifera ) gut core microbiota that can be cultivated...

Working with Lactobacillus `Firm 5` The Lactobacillus `Firm 5` clade are gram positive bacterial symbionts of the honey bee ( Apis mellifera ) gut core microbiota...

Working with Bartonella apis Bartonella apis is a gram negative bacterial member of the honey bee ( Apis mellifera ) gut core microbiota that can be cultivated...

Working with Arsenophonus nasoniae Arsenophonus nasoniae is symbiont of the wasp, Nasonia vitripennis, gut microbiota that can be cultivated in vitro . The isolation...

Colony Transformation This is a theoretical protocol that has not been tested! This protocol and be used for the rapid preparation of chemically competent E. coli...

Preparing Chemically Competent Cells using the Inoue Method 2 4H2O 10.88 g 55 mM CaCl2 2H2O 2.20 g 15 mM KCl 18.65g 250 mM PIPES (0....

Modular Cloning using CIDAR MoClo kit The lab recently acquired a CIDAR MoClo ( C ross disciplinary I ntegration of D esign A utomation R esearch lab Mo...

Measuring transcription in vitro Using Broccoli and Spinach Fluorescent RNA Aptamers: Background / Usage: Broccoli and Spinach are two versions of an RNA aptamer...

Breseq Results Reading the results files Look at the manual for information on output formats. Click around until you`re familiar with what everything means. First...

Step 1: Creating dsDNA encoding the part for cloning Two variations on preparing a dsDNA fragment with the proper restriction sites and Golden Gate overhangs are provided...

SeanLeonard 14 Sep 2017

Upon publication, this page will be updated with a full description of the BTK, parts list, and overhang types. SeanLeonard 14 Sep 2017

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...

SeanLeonard 14 Sep 2017

SeanLeonard 14 Sep 2017

The Arabinose (Ara) Genetic Marker Background The Escherichia coli B strain REL606 has a mutation in the araA gene that renders it unable to utilize the sugar...

Quick 3hr Antibiotic Rescue Verification Overview This short protocol describes a simple same day verification of antibiotic removal/`rescue` from counter selection...

Transforming Acinetobacter baylyi ADP1 About A. baylyi ADP1 Acinetobacter baylyi ADP1 is a naturally competent bacteria with enormous potential for genome engineering...

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

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...

Targeted PCR and Sanger Resequencing of Mutations Page in need of additional improvements. Descriptions here are particularly tailored for resequencing of evolved...

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...

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...

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...

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...

Protocol for Determining Mutation Rate to Phage (T5) resistance Day 2: Prepare Media/Revive/Titer Phage 1. If necessary, revive the frozen stock of each strain...