geneticslab
Mike’s Genetics & Genomics Workbook
Preface
Disclaimers and copyright
Introduction to Experiments
General lab methods
Tips to reading science papers
Lab report write-up
Example – Student paper
Simulated student paper examples
Checklist — Lab report write-up
Polymerase Chain Reaction (PCR)
Overview of standard PCR
Overview of RTqPCR
PCR Troubleshooting
Agarose gel electrophoresis
Gel documentation
Basic stock solutions
About buffer solutions
TBE recipe
TAE recipe
Growth media
Growth media – Yeast
Model organisms
Tomato
Yeast
Arabidopsis
Brassica
Drosophila
Bioinformatics
Bioinformatics I: BLAST
Download sequences with BATCH Entrez
Bioinformatics II: Detecting designed sequences
Use of ORF Finder: Practice and Worked example
Bioinformatics III: Use of Primer BLAST and Primer3
Using BLAST to predict PCR product length
Use of Virtual Ribosome: Practice and worked example
Bioinformatics project: Evolutionary analysis of GWAS candidate genes
GWAS and essential genes
Explore essential genes
Identify phenotype and genotype of interest from PheGenI
Protocol: GWAS and the PheGenI Database
Find all SNP for your GOI
Evaluate possible citation bias
How to convert a distance matrix to a pairwise table with R
How to get the distances from a distance tree
Routine sequence analysis with R
Phylogenetics
How to read a phylogeny
Make a phylogenetic tree
Make a phylogeny from morphological characters
Use of NCBI Taxonomy page to retrieve phylogeny
Make a gene tree
Sequence alignment: Basics explained
Use of web services for building a gene tree
Change root for gene tree
Working with Newick file format
Tree reconciliation
Evolutionary rate tests
Molecular clock
An example consensus phylogenetic tree
Pairwise divergence times
Character Matrix to PHYLIP Converter
Systems Biology
Quick Tutorial: Building and Styling a Network in Cytoscape
Create network from csv file
Network of co-authors
NDEx Webapp example
List of of operations example
ImmPort gene list example
Gene Ontology database example
Checklist: Systems Biology Project Write-Up
App and software help
Help with imageJ
Simple gel documentation with imageJ
Install Cytoscape
Install and learn to work with UGENE
Alternatives to UGENE
Install and use the R statistical programming language
Digital literacy
Hidden files and directories
How to resize and convert image files
Please create good file names
Text files are data files
How to merge text files
Split column into multiple columns Google Sheets
Lab notebooks
Digital lab notebooks
Working folders
Spreadsheet pivot tables
Histogram from a spreadsheet pivot table
How to make a bar chart
How to obtain slope of the regression
How to make a scatterplot and obtain treddline
Make and submit video to YouTube
Culture methods
Culture methods
Tomato
Brassica
Arabidopsis
Yeast
Drosophila