100 Recent Changes in Lab Web retrieved at 01:10 (GMT)

Main.TWikiGuest

Statistics for nop Lab Web Month: Topic views: Topic saves: File uploads: Most popular topic views: Top contributors for topic save and ...
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 ...
Main.KateElston

Barrick Lab :: Team Past members of the Barrick lab Interested in our research? Join Us Principal Investigator Prof. Jeffrey E. Barrick #128011 ...
Acinetobacter baylyi ADP1 Golden Transformation Overview The following protocol is to be used as a substitute for overlap extension PCR for constructing double stranded ...
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× phage precipitation ...
Main.JeffreyBarrick

Barrick Lab :: Publications Barrick Lab Publications on Google Scholar Barrick Lab researchers Equal contributions ^Corresponding author(s) Undergraduate ...
Main.JeffreyBarrick

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 ...
General Conjugation Protocol Return to BTK Page Conjugation is a reliable, robust method to transfer plasmids between bacteria. This is a general purpose protocol ...
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 ...
Main.JeffreyBarrick

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. ...
Main.JeffreyBarrick

Determining Phage Titer Materials Phage lysate or freezer stock (Procedure: Phage Lysate Preparation) Top Agar (LB Miller 0.8% agar) LB MIller (for ...
Main.JeffreyBarrick

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

Past Barrick Lab Members Gabriel Suarez Grace Stark Stratton Georgoulis Jenna McGuffey Dr. Simon D'Alton Dacia Leon Colin Brown Xue Zhang Michael Hammerling Brian ...
Main.JeffreyBarrick

Barrick Lab :: Contact Information Jeffrey E. Barrick, Ph.D. Associate Professor Department of Molecular Biosciences The University of Texas at Austin Office ...
Main.KateElston

C1 Condition 1, C2 Condition 2, and BR# Biological Replicate Template Material Use cDNA dilution determined in cDNA Concentration qPCR What you are looking ...
Competence Assays Day 0: Inoculation • Prepare n 1 tubes with 5ml LB (n samples and 1 uninoculated control) • Inoculate tubes with either 2uL of liquid culture or ...
Main.ElizabethRobinson

Autoclave Sterilization Overview Autoclaves heat their contents to 121°C, which is 21°C over the boiling point of water. To prevent the solutions from boiling over ...
(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 ...
(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. ...
Main.JeffreyBarrick

Barrick Lab ' '' " then "" else ""}% Contact Research Publications Team Protocols Reference Computation ...
Media amendments Antibiotic concentrations and stock solutions This table lists “standard” concentrations of antibiotics commonly used in microbiology laboratories ...
Unix Commands Quick Reference Useful commands and flags that we get tired of looking up... Disk Space The du command is verbose and confusing if you run it without ...
Main.JeffreyBarrick

Media Recipes Liquid Media Included topic: ProtocolsRecipesSaline Included topic: ProtocolsRecipesLysogenyBroth Included topic: ProtocolsRecipesDavisMingioli ...
Transforming Acinetobacter baylyi ADP1 About A. baylyi ADP1 Acinetobacter baylyi ADP1 is a naturally competent bacteria with enormous potential for genome engineering ...
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 ...
Main.MattMcGuffie

...in progress...
Main.MattMcGuffie

Barrick Lab :: Code Also check out our code repository: Github/BarrickLab Breseq (Bacterial Genome Resequencing)Determine mutations in evolved bacteria from next ...
LB: Lysogeny Broth / Luria Bertani (Miller) Agar Combine in a 2 L flask the following: 1.5L Component 15 g Tryptone 7.5 g Yeast Extract ...
Main.MattMcGuffie

Copying files to/from UT Box at the command line Follow the directions here to set up an additional Box password that you will use for connecting: https://uisapp2 ...
Main.SarahBialik

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 ...
Main.JeffreyBarrick

Barrick Lab :: Computational Protocols Command line Unix Commands Quick Reference Collection of useful Unix commands. SSH Public Key Authentication How ...
Main.JeffreyBarrick

Working with Git Setup GitHub Ask to be granted access to see private repositories Learning Git it – App for teaching you to use command line Git on ...
Main.JeffreyBarrick

Interested in research in the Barrick lab? We are always looking for outstanding undergraduate students, graduate students, and postdocs who are interested in experimental ...
Working with Vibrio natriegens (Vmax) Vibrio natriegens has the fastest doubling time of any known organism and has the potential to shorten experimental timelines ...
Main.JeffreyBarrick

ABMS: Acinetobacter Minimal Succinate Courtesy of the Averhoff lab, with modifications for available reagents. To make standard ABMS, combine the following pre sterilized ...
Back to Golden Gate Protocols Troubleshooting Golden Gate Assemblies Tips Screen Inserts for internal BsaI/BsmBI sites! Reactions with single off target sites ...
Protocol for harvesting Pfu Sso7d polymerase This protocol is for expressing and purifying the Pfu Sso7d polymerase from E. coli 1 . A variant of this protein with ...
P1 Transduction in Eschericha coli This protocol is adapted from Thomason, L. C., Costantino, N. and Court, D. L. 2007. E. coli Genome Manipulation by P1 Transduction ...
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 ...
Freezing Strains Supplies 1 Overnight liquid culture Several milliliters of overnight liquid culture grown in a suitable medium for each sample to be frozen ...
Main.KateElston

Quantitative real time PCR for differential gene expression THIS PAGE IS CURRENTLY UNDER CONSTRUCTION APOLOGIES FOR ANYTHING THAT'S STILL A BIT MESSY! Quantitative ...
RCV Medium RCV is a complex media consisting of 3 different sub components that must be prepared ahead of time if they are not already made. Main recipe 1L ...
Main.KateElston

1 2 3 4 5 6 7 8 9 A C1BR1 C1BR1 C1BR1 C1BR1 C1BR1 C1BR1 C1BR1 C1BR1 C1BR1 B C1BR2 C1BR2 ...
TA: Tetrazolium Sugar (TA, TM, TL, ...) Combine in a 2 L flask: 1.5L Component 15 g Tryptone 1.5 g Yeast Extract 7.5 g NaCl 24 ...
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 ...
Fluctuation Tests Introduction This protocol is for doing a Luria Delbrück fluctuation test to measure the rate at which mutations occur that enable growth on selective ...
Main.JeffreyBarrick

SOB/SOC: Super Optimal Broth For SOB: 1L Final Component 5 g 0.5% yeast extract 20 g 2.0% tryptone 0.5 g 10 ...
MOB: Mobility Media This media is useful for enhancing the mobility of ADP1, which moves across the plate by "twitching". 1L Final Component ...
Transforming Electrocompetent Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES: Equipment: ...
Chemically Competent Cells Preparation of Chemically Competent Cells There are a few variations on the protocol for preparation of chemically competent cells. Choice ...
Electrocompetent E. coli Making Electrocompetent E. coli Cells (small batch) This procedure makes enough electrocompetent cells for 2 3 transformations. 1 Grow ...
Main.JeffreyBarrick

Barrick Lab :: Links Advice for graduate students (Saw this linked by Cooper) for Young Scientists (Andrew Hendry) Serial Mentor (Claus Wilke's Blog ...
Main.SimonDAlton

Isolation of total RNA Reagents Materials Use filter tips, and designate all solutions, reagents and plastics as RNA only. Keep separate from other general stocks ...
Main.JeffreyBarrick

Barrick Lab :: Reference Information Templates and Spreadsheets Circular and Rectangular Tube Labels Templates for printing cryotube labels. Petri Dish ...
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. pKD46 ...
M9 Minimal Medium 1L Component 6 g Sodium phosphate dibasic (anhydrous), Na2HPO4 3 g Potassium phosphate monobasic, KH2PO4 0.5 g ...
Denaturing Formaldehyde Gels for Verifying RNA size RNA can be sized correctly on an agarose gel. However, it needs to be denatured and then remain denatured during ...
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 ...
Checking Transformation Efficiency of Chemically Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES ...
Main.JeffreyBarrick

Barrick Lab :: Research /collage.png Active Projects #PreventingEvolutionaryFailure Preventing Evolutionary Failure in Synthetic Biology Evolutionary half lives ...
Read trimming with trimmomatic Download and Install Download the "binary" version of trimmomatic from the lab. It's helpful to a create a shortcut so that you ...
Introduction to Experimental Design Motivation Whether for just a summer or for the duration of an entire Ph.D project, working on a scientific problem is a process ...
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 ...
Accessing Journal Articles from Off Campus PubMed PubMed is often the best practice for biology researchers to find and discover publications related to biological ...
Targeted PCR and Sanger Resequencing of Mutations Page in need of additional improvements. Descriptions here are particularly tailored for resequencing of evolved ...
Main.MattMcGuffie

Site directed mutagenesis protocol (adapted from QuickChange) A protocol for changing one (or a few) bases on a plasmid SUPPLIES: Primer Design: Use the following ...
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 ...
Protocol Updates Needed (as of 2016 Dec 15) Protocols needed or flagged for updates Flow protocol updates (Dan and Dacia) P1 transduction; FLP/FRT recombination ...
Working with Snodgrassella alvi Snodgrassella alvi is a member of the honey bee ( Apis mellifera ) gut core microbiota that can be cultivated in vitro . Its isolation ...
Main.SimonDAlton

Isolation of Total RNA Materials and Reagents Use filter tips. Keep all solutions, reagents and plastics to be used for RNA work separate from general supplies. Solutions ...
Introduction This protocol was inspired (after failed site directed mutagenesis attempts using Quikchange) by the protocol listed here at the Colgate website here ...
Main.SeanLeonard

Megaprimer whole plasmid cloning aka nop MEGAWHOP cloning aka Overlap Extension PCR cloning We describe two approaches to MEGAWHOP in this protocol page. Approach ...
Preparing Chemically Competent Cells using the CaCl2/Glycerol Method Adapted from: Re engineering the ribosome for efficient selenoprotein synthesis Ross Thyer, 2012 ...
Main.JeffreyBarrick

Commonly Used Plasmids plasmid markers origin host ref description pCA24N CamR Kitagawa2005 ASKA collection vector pKD46 ...
Main.JeffreyBarrick

Barrick Lab :: Home We are broadly interested in understanding evolution as a creative force. Our lab primarily uses experiments with microorganisms and molecules ...
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 ...
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 ...
Retired Protocols Designing a new part Designing a new part for use in the BTK Retired on May 23, 2014 Crush Soak ElutionRecover DNA or RNA samples from ...
Main.JeffreyBarrick

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 ...
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 ...
Working with Pseuodmonas syringae (PSY) Pseudomonas syringae (PSY) comprises many species of bacteria that live on or within different plant species, as noted ...
Main.DanielDeatherage

This information is a stub to be added into a reworked NGS protocol as an alternative. Follows the duplex seq method developed by the Loeb lab This protocol is for ...
Gel Electrophoresis In order to analyze PCR results, the products are run on an agarose gel, which is then analyzed in UV light to ascertain the length of DNA fragments ...
Measuring Lysis Timing of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates for protocol Overnight stock of permissive bacterial ...
Measuring Adsorption Rate of T7 Phage Reagents / Materials: Fresh phage lysate (no more than one day old) see Preparing Phage Lysates for protocol ...
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 ...
Working with Serratia symbiotica Serratia symbiotica is a secondary endosymbiont of the black bean aphid ( Aphis fabae ) gut microbiota that can be cultivated ...
Quick 3hr Antibiotic Rescue Verification Overview This short protocol describes a simple same day verification of antibiotic removal/"rescue" from counter selection ...
Measuring transcription in vitro Using Broccoli and Spinach Fluorescent RNA Aptamers: Background / Usage: Broccoli and Spinach are two versions of an RNA aptamer ...
M9 Minimal Media Plates As with DM and MG media, make sure to autoclave the agar and phosphate separately. For 1 liter of media: 1L Component 6 g ...
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 ...
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 ...
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 ...
Back to Golden Gate Protocols Second Stage Assembly Second Stage assemblies are used to build plasmids out of multiple transcriptional units (Protocol found here ...
Restriction Enzyme Cloning Restriction enzyme cloning is a bread and butter technique in molecular biology for modifying plasmids to contain genes or other DNA sequences ...
Standard Microbiological Practices aka the approximately Ten Commandments of Microbiology 1 Thou shalt always include a media blank Otherwise you may contaminate ...
Main.JeffreyBarrick

Barrick Lab Style Guide Writing a Scientific Paper Steps to Writing a Research Article (Tomorrow's Professor Mailing List Archive #1176) General Formatting ...
Main.SimonDAlton

Isolation of Total RNA from Plant Material Plant tissues can be tough (roots), impenetrably waxy, or contain large amounts of RNase activity (leaves). Flash freezing ...
Main.SimonDAlton

RNAseq Library Preparation Use RNA from RNASnap and Zymo coumn purification as outlined on wiki. rRNA Depletion Use the Ribozero (RZ) rRNA Removal Kit (Gram negative ...
Number of topics: 100

See also: rss-small RSS feed, recent changes with 50, 100, 200, 500, 1000 topics, all changes

 Barrick Lab  >  WebChanges

Contributors to this topic edittopic TWikiContributor, PeterThoeny
Topic revision: r2 - 28 Mar 2005 - 09:40:13 - Main.TWikiContributor
 
This site is powered by the TWiki collaboration platformCopyright ©2020 Barrick Lab contributing authors. Ideas, requests, problems? Send feedback