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Blue Oyster Mushrooms Total Elapsed Time: ~10 days

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TWiki Administrator Group Set GROUP JeffreyBarrick Set ALLOWTOPICCHANGE TWikiAdminGroup (Note: Set the members of TWiki Administrator Group in GROUP...

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

Barrick Lab :: Reference Information Getting Started in Lab Getting Started with Lab Techniques Synthetic Biology 101 Background on what synthetic biology...

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...

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...

C1 Condition 1, C2 Condition 2, and BR# Biological Replicate Template Material Use cDNA dilution determined in cDNA Concentration qPCR Note: Once you...

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...

in vitro RNA synthesis(T7 RNA Polymerase ) T7 RNA Polymerase is used for in vitro mRNA synthesis and is highly specific for the T7 phage promoter. T7 in vitro transcription...

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...

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...

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...

Comparative 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...

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 symbiotica Serratia symbiotica is a secondary endosymbiont of the black bean aphid ( Aphis fabae ) gut microbiota that can be cultivated...

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...

Unix Commands Quick Reference Useful commands and flags that we get tired of looking up... Alphabetical Reference cat yourfile.txt Prints the contents of the given...

UV mutagenesis of Bacteria Determination of Optimal UV treatment This procedure is used to determine optimal treatment which will be used for library generation....

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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...

Checking Transformation Efficiency of Chemically Competent Cells Adapted from Molecular Cloning: A Laboratory Manual 3rd Ed. , Sambrook and Russell (2001) SUPPLIES...

Which polymerase is right for me? Types of polymerase NEB polymerases may be purchased from the NEB freezer, which is located in the Biomedical Research Supply Core...

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...

Barrick Lab Style Guide Writing a Scientific Paper Steps to Writing a Research Article (Original: Beth A. Fischer and Michael J. Zigmond, Survival Skills and...

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

Standard Polymerase Chain Reaction (PCR) PCR reactions produce an amplified double stranded DNA product from template DNA. In addition to the template, the reactions...

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...

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...

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...