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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...

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....

YPD Medium General media used for culturing Yeast. Adapted from spring harbor In 1 L bottle: 1L Component 20g Peptone 10 g Yeast Extract...

TA: Tetrazolium Sugar (TA, TM, TL, ...) Combine in a 1 L flask: 500 mL Component 5 g Tryptone 500 mg Yeast Extract 2.5 g NaCl 8 g...

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...

SOB/SOC: Super Optimal Broth For SOB: 200mL 250mL 1L Final Component 1 g 1.25 g 5 g 0.5% yeast extract...

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...

MG: Minimal Glucose agar, aka DM: Davis Mingioli agar Note: When making these plates it is necessary to prepare and autoclave the 3 main parts (salts, agar, and sugar...

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...

LB: Lysogeny Broth / Luria Bertani (Miller) Agar Add dH2O to full volume in an appropriately sized flask. Combine the following, making sure each component fully dissolves...

LB: Lysogeny Broth / Luria Bertani Medium (Miller) Rich media used for routine culture of E. coli and other bacteria at high cell densities. Add dH2O to desired...

DM: Davis Mingioli Growth medium used by the long term E. coli evolution experiment. 0.5L 1L 4.5L 5L Component MW 2.67 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...

Czapek Broth (CB) Combine in a flask: 500 mL 1 L Component 1.5 g 3 g sodium nitrate 0.5 g 1 g potassium phosphate dibasic 0.25 g...

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...

Dear internet, We don`t distribute this plasmid. If you want to purify your own enzymes to save money, here are some options to investigate: Bioeconomy Lab ...

Reagent and Buffer Recipes General calculation resources Mass Molarity Calculator Solution Dilution Calculator Gel Electrophoresis 50 TAE (Tris Acetate...

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...

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...

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...

Plasmid copy number determination Plasmid copy number is known to vary depending on origin of replication and culture conditions refs . Typically, plasmids are referred...

Determining Phage Titer Phage Titering is a procedure used to quantify the density of plaque forming units (PFU, analogous to a bacterial culture...

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

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...

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