Category Archives: Protocols
Detection of differentially expressed genes using RNA-Seq and CyVerse
Detection of differentially expressed genes using RNA-Seq Introduction In this tutorial we will analyze an RNA-Seq data set to detect differences in gene expression between two experimental conditions. We will use a program called Tophat to align the RNA-Seq reads … Continue reading
Pathogen Identification using DNA Barcoding
Background DNA Barcoding is a technique for identifying species using DNA sequences. Short DNA sequences are used like barcodes on items at the supermarket to uniquely identify each product. Read more about DNA Barcoding on Wikipedia and the website of the … Continue reading
DNA cleaning RT-PCR
WAV, 07/10/10 DNA Cleaning DNAFree from Ambion RNA 5 µl (10-20 µg) 10 X Buffer 2 µl DNAse 1µl RNAse free Water 12 µl Incubate for 30 min at 37o C Add 5 µl of DNAse inhibiting … Continue reading
SOP
Standard Operating Procedures for the Handling of Transgenic Plant Pathogenic Fungi Michael Thon July 19, 2006 Laboratory Handling Procedures: 1. All work with transgenic isolates of Colletotrichum spp. are done in strict adherence to NIH BL1/BL2-P containment procedures (see … Continue reading
Media
LB (Luria-Bertani) medium Commercially available: or use the following recipe: To 950 mls of ultrapure water, add 10g bacto-tryptone 5g bacto-yeast extract 10g NaCl. 15g bacto-agar, to solidify. Mix, autoclave. PH to … Continue reading
Recipes
Stock solutions 70% Ethanol (1L) 736 ml 95% ethanol. Bring up to 1 L with nanopure water.Don’t autoclave. EDTA 0.5 M To prepare 500 ml, 0.5M EDTA pH 8.0: Add 84 g of disodium EDTA•2H2O to 300 ml … Continue reading
Primer Preparation
Primers are delivered as dry pellets and can be storage at 4C. -Use sterile 1.5ml centrifuge tubes, add to each primer tube received 1ml nuclease free water using filter tips. -Adjust the concentration of your primers to a final of … Continue reading
Working with RNA
When working with RNA: Nucleases (RNases) can destroy RNA and ARE EVERYWHERE, so you should: Prepare an RNAse free working environment. Wear gloves while handling reagents and RNA samples to prevent RNase contamination from the surface of the … Continue reading
How to make Solutions
| simple dilution | serial dilution | VC=VC method | molar solutions | percent concentrations | molar – % conversions 1. Simple Dilution (Dilution Factor Method) A simple dilution is one in which a unit volume of a … Continue reading
Basic PCR
Basic PCR, 25 ul Use tips and tubes nuclease free VOL … Continue reading