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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...

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 Combine in a 2 L flask the following: 1.5L Component 15 g Tryptone 7.5 g Yeast Extract...

LB: Lysogeny Broth / Luria Bertani Medium (Miller) Rich media used for routine culture of E. coli and other bacteria at high cell densities. 1L 5L...

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...

MOB: Mobility Media This media is useful for enhancing the mobility of ADP1, which moves across the plate by `twitching`. 1L Final Component...

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...

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...

Lithium Acetate Transformation This protocol is originally from the Spring Harbor Laboratory Yeast Genetics Genomics course manual. Making Competent S. cerevisiae...

Large scale Protein Expression in E. Coli: Notes: This can be applied to either soluble proteins (for a downstream prep in native conditions) or insoluble proteins...

Measuring Intracellular Reactive Oxygen Species (ROS) This procedure is commonly utilized to quantify ROS. For more information about limitations associated with this...

Tobacco hornworm (Manduca sexta) care The tobacco hornworm is the caterpillar stage of the five spotted hawk moth ( Manduca sexta ). They constitute a major pest of...

Barrick Lab Style Guide for Figures General Workflow Use a program (Excel, R, CIRCOS, matplotlib, etc.) to graph your data. Output a file in a vector graphics...

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...

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...

Genome Diff file Generation Overview This is a series of commands to automatically generate .gd files based on naming system present in .fastq files. This will typically...

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...

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...

Find Chemicals Often you come across a chemical structure or name in a publication and then you need to find a place to order some from for your research. Maybe you...

Dpn I digestion Purpose To digest (Adeno) methylated GATC sites. Useful for removing cell derived plasmid template from PCR samples. Use 1. Add 1...

Use of degenerate bases Spoke with IDT about some of their recommendations related to incorporation of degenerate bases in oligos. Machine Mix vs Hand Mix option...

This page is meant to include instructions on how to clone dcamp, and push back to the repository. It is not well tested. Standardized TACC DCAMP instructions. This...