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

References for Whole Genome Sequencing NCBI Short Read Archive (SRA) Documentation http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd show f doc m doc s doc...

Characteristics of the E. coli Genome The Origin of DNA Replication ( oriC ) is not at position zero (0...

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...

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...

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...

Animations Saves a series of generated images to GIF, Flash, video, HTML, or PDF (LaTeX) formats. Installation install.packages(`animation`) library(animation)...

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 performing...

Publicly Archiving Data These locations can give you accession numbers for data that may not be easily communicated as supplementary information for a research report...

Working with Vibrio natriegens (Vmax) Vibrio natriegens has the fastest doubling time of any known organism and has the potential to shorten experimental timelines...

Working with Serratia marcescens Serratia marcescens is a gram negative pathogenic bacteria known for its distinctive red pigmentation. While it is not found in...

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

Using APE If APE is not currently installed on this computer, search APE plasmid on google, and download the software for the appropriate system. APE can open the...

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...

Which polymerase is right for me? Types of polymerase Our lab stocks two main types of polymerase: Type Vender Cost per unit Product Information...

TGY Medium 1.5L Component 7.5 g Pancreatic digest of casein 7.5 g Yeast Extract 1.5g Glucose 1.5 g K2HPO4 24g Agar...

Strain Database Table Description Barrick lab strains are stored in a database on UT Box, accessible after login via this link. column example description...

red mediated ssDNA gene modification Background Protocol designed based on 3/16/11 Court Lab Protocol (which is available here) with Barrick lab specific modifications...

Large Scale Metagenomic Soil Prep This is a protocol developed to extract large quantities of metagenomic DNA from large soil samples. Note that this preparation technique...

Setting up Autotools http://sourceware.org/autobook/autobook/autobook toc.html http://www.gnu.org/software/autoconf/ http://www.gnu.org/software/automake/ http://www...

Setting up SSH Public Key Authentication These instructions will allow you to connect as user1 on machine FROM to user2 on machine TO without typing your password...

Running an SDS PAGE Gel: Note that the following uses pre cast gels and pre made running buffer, see accessory protocols NotDoneYetDudez for casting gels and making...

Running breseq on TACC Installing breseq on stampede for mac Open a new terminal window and use the following commands: 1 ssh into stampede and set up folder...

Resuspending Primers 1 Your primers will arrive as a lyophilized film at the bottom of a cryo tube. To use them, you must resuspend them in autoclaved dH2O....

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...

YPS Medium 1L 1.5L Component 3.0 g 4.5 g Yeast Extract 3.0 g 4.5 g Peptone 2.0 mL 3.0 mL 1 M Magnesium sulfate 2....

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...

TGY Medium 1L 5L Component 5 g 25 g Pancreatic digest of casein 5 g 25 g Yeast Extract 1g 5 g Glucose 1 g 5 g...

Stab Agar Making agar stabs for storage and transport of bacterial strains. 1L Component 10 g Tryptone 5 g Yeast extract 10 g Sodium...

Special Media

Sterile Saline Purpose: Used make dilutions of viable cells for plating or transfer to new media. This saline concentration of 0.85% w/v (145 mM) is suitable for...

S2 Used for Acinetobacter Recipe for 900mL (Autoclave in three separate bottles 300mL each) Bottle 1 (Erlenmeyer flask: 300mL) 300mL Component...

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...

R2A R2A is a medium that can be used to grow a wide variety of soil microbes. 1L 5L Component 0.5 g 2.5 g Yeast Extract 0.5 g...

MC: Minimal Citrate Prepared the same as MG: Minimal Glucose with the following changes: No glucose 4.5 g/L Sodium Citrate (trisodium, dihydrate)

M9 Minimal Medium 1L Component 6 g Sodium phosphate dibasic (anhydrous), Na2HPO4 3 g Potassium phosphate monobasic, KH2PO4 0.5 g...

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...

DR: Defined minimal media for D. radiodurans 250 ml 500 ml Component 50 ml 100 ml 5x M9 salts 250 ul 500 ul 5mM MnCl2 250 ul...

Blood Heart Infusion Agar Heart Infusion Agar supplemented with sterile Sheep`s Blood. Used for the cultivation of fastidious organisms (Bee gut microbiome species...

ABMS: Acinetobacter Minimal Succinate Courtesy of the Averhoff lab, with modifications for available reagents. To make standard ABMS, combine the following pre sterilized...

1416: 4 hydroxybenzoic acid medium (for JJ 1b, Bacillus sp.) 1L 4L Component 4.25 g 17.0 g Potassium Phosphate (dibasic) K2HPO4 trihydrate...

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...

Overview Lab protocol for using the pSLTS plasmid method of scarless genome editing developed by the Copley lab. If you use this protocol, you should cite: Kim, J...

Measuring Lysis Timing of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates for protocol Overnight stock of permissive bacterial...

Measuring Burst Size of T7 Phage Reagents / Materials: Phage lysate see Preparing Phage Lysates Overnight stock of permissive bacterial host...

Measuring Adsorption Rate of T7 Phage Reagents / Materials: Fresh phage lysate (no more than one day old) see Preparing Phage Lysates for protocol...

PA: Lac Papillation Agar Make 10 Minimal A Salts. 10 Minimal A Salts 1L Component MW 80 g Potassium Phosphate (dibasic) K2HPO...

Introduction This protocol was inspired (after failed site directed mutagenesis attempts using Quikchange) by the protocol listed here at the Colgate website here...

Overview This is an example command for renaming multiple files at once. Ideally it is presented as a method for shortening file names by removing common elements...