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The University of Texas at Austin :: iGEM Team Interested in joining the UT Austin iGEM Team? Participating in the iGEM competition is a unique opportunity for undergraduate...
Gibson Assembly Background and Design Gibson Cloning is a technique of DNA construct assembly that allows one to join multiple linear segments into either one large...
Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate...
Statistics for Lab Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and...
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...
Barrick Lab :: Team Past members of the Barrick lab Interested in our research? Join Us Principal Investigator Prof. Jeffrey E. Barrick...
Preparing Chemically Competent Cells using the CaCl2/Glycerol Method Re engineering the ribosome for efficient selenoprotein synthesis Ross Thyer, 2012 http://docplayer...
YPD Medium General media used for culturing Yeast. Adapted from spring harbor In 1 L bottle: 1L Component 20g Peptone 10 g Yeast Extract...
Media amendments Antibiotic concentrations and stock solutions This table lists ...
Past Barrick Lab Members Shireen Shah Eleanor Young Peng Geng Ginny Mortensen Beth Robinson Spencer Hamrick Sean Leonard Gabriel Suarez Grace Stark Stratton Georgoulis...
Back to Golden Gate Protocols First Stage Plasmid (Transcriptional Unit) Assembly Once you have all your desired part plasmids built you can assemble them into Transcriptional...
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...
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...
P1 Transduction in Escherichia coli This protocol is adapted from Thomason, L. C., Costantino, N. and Court, D. L. 2007. E. coli Genome Manipulation by P1 Transduction...
Barrick Lab :: Laboratory Protocols Creating Protocols How to Create a Protocol Best practices for designing a protocol and for putting it on the lab Wiki....
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...
Golden Gate Assembly This page serves as the main repository for everything Golden Gate Assembly related. This page links to a number of protocol pages that will...
Electrocompetent E. coli Making Electrocompetent E. coli Cells (small batch) This procedure makes enough electrocompetent cells for 2 3 transformations. 1 Grow...
SOB/SOC: Super Optimal Broth For SOB: 1L Final Component 5 g 0.5% yeast extract 20 g 2.0% tryptone 0.5 g...
Barrick Lab :: Home We are broadly interested in understanding evolution as a creative force. Our lab primarily uses experiments with microorganisms and molecules...
Barrick Lab :: Research https://barricklab.org/twiki/pub/Lab/ResearchInterests/collage.png See also: Previous Research Projects Engineering Insect Symbionts Many...
Checking Transformation Efficiency of Chemically Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES...
Reagent and Buffer Recipes General calculation resources Mass Molarity Calculator Solution Dilution Calculator 50x TAE Tris Acetate EDTA Used as a buffer...
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 Second Stage Assembly Second Stage assemblies are used to build plasmids out of multiple transcriptional units (Protocol found here...
Isolating Phage Genomic DNA This protocol has been tested with phage T7. It has a double stranded genome that has a length of 40 kb. Materials 5...
Ethanol Precipitation Precipitating DNA/RNA from solution to remove salts and small nucleic acid fragments. Materials 3M Sodium Acetate, pH 5.2 (store at...
Attach images that can be used throughout the Wiki here. Barrick Lab Overview is linked to on the UT CNS website, so don`t move it!
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...
Measuring Microbial Growth Rates in a Plate Reader Growing cells in plate reader and measuring OD600 All strains tested should at least have 3 replicates. Due to...
Competence Assays This assay quantifies the ability of bacterial strains to uptake DNA in culture. The protocol below utilizes genomic DNA extracts obtained using...
Acinetobacter baylyi ADP1 Golden Transformation Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double stranded...
Lab Notebook Best Practices Use a digital lab notebook that is backed up in the cloud. Currently we use Benchling. Assign each experiment an ID number...
`In plate` / solid medium transformation of Acinetobacter baylyi ADP1 The following protocol is for single colony `in situ` (in plate) transformation with minimal...
RNAseq Library Preparation Use RNA from RNASnap and Zymo column purification as outlined on wiki. rRNA Depletion Use the Ribozero (RZ) rRNA Removal Kit (Gram negative...
Barrick Lab Contact Research Publications Team Protocols Reference Computation Code UT Austin Mol Biosciences...
Media Recipes Liquid Media Included topic: ProtocolsRecipesSaline Included topic: ProtocolsRecipesLysogenyBroth Included topic: ProtocolsRecipesDavisMingioli...
Plasmid copy number determination Plasmid copy number is known to vary depending on origin of replication and culture conditions refs . Typically, plasmids are referred...
Generating Illumina Sequencing Libraries for transposons created in A. baylyi ADP1 with the pBT20 vector. This protocol prepares Illumina sequencing libraries from...
Accessing Journal Articles from Off Campus PubMed PubMed is often the best practice for biology researchers to find and discover publications related to biological...
Aphid Care and Protocols Rearing and Caring for Aphid Species Protocols and Primers
Fluctuation Tests Introduction This protocol is for doing a Luria Delbr...
Barrick Lab :: Computational Protocols Getting Started Learn Biocomputing Resources for learning the command line, R, Python, GitHub, etc. Useful Python...
Leafhopper Care and Protocols Rearing and Caring for Leafhopper Species Various leafhoppers species are kept in BugDorms and maintained on various plants (barley...
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...
Acinetobacter baylyi ADP1 Genome Manipulations Genome manipulations in Acinetobacter baylyi ADP1 can be performed without the need for exogenous recombinase expression...
Python snippets for biology Requires BioPython to be installed Open common formats: .gbk / .gbf / .gb import SeqIO with open(`/my/path/file.gb`,`r`) as file handle...
Determining Phage Titer Phage Titering is a procedure used to quantify the density of plaque forming units (PFU, analogous to a bacterial culture...
Absolute QPCR for quantification of plasmid copy number in E. coli This protocol is based on methods described in Lee et al (2006), to paper. Designing primers...
Acinetobacter baylyi ADP1 Genome Manipulations by Overlap Extension PCR Overlap PCR Construct Generation The following is a standard procedure designing and constructing...

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Topic revision: r2 - 2005-03-28 - 09:40:13 - Main.TWikiContributor
 
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