<commit_before>---
layout: page
title: Station A.  Experimental Design
---
## Introduction to Genome Station A. Experimental Design

Naturally, there are no tools to help a researcher determine experimental intention, but this is the most critical station on the train ride to a reference genome. Here is a checklist of important things to consider:

  1. What is your Primary aim?

  Is there a specific hypothesis in mind, or is this an expedition to form new ones?
  A cluster of closely related species, or just a favourite one?

  2. Community resources
  
  Key advisors that can help along the way?
  Are there any existing community resources, such as ESTs, BAC libraries, frozen specimens or live cultures?
  Are there any closely related species with sequenced genomes?
  Are there any closely related species with sequenced AND well-annotated genomes?

  3. Any prior knowledge on the genomic architecture of the species (e.g. sex chromosomes, ploidy, genome size, number of chromosomes) and in particular the collected specimens (e.g. sex, heterozygosity levels).

  4. Acquiring high quality DNA and RNA material:
  
  Have established an optimum extraction protocols and best practices. Which specimens to use and how many?
  Which tissues for expression?
  Access to haploid tissues?
  Is it required (and possible) to establish an inbred line to reduce heterozygosity?

  5. Generating raw data
  
  How much data is needed and of what kind?
  What genome sequencing methods are available to you? Are they experimental or reliable and established?
  What are the library preparation options?
  Check whether DNA/RNA yields are compatible proposed library preparation and sequencing platforms
  What is affordable?
  What can be done commercially and what in-house?

  6. What are the personal aims that need to be achieved (e.g. a publication, specific downstream experiments etc)?
<commit_msg>Update intro.md<commit_after>---
layout: page
title: Station A.  Experimental Design
---
## Introduction to Genome Station A. Experimental Design

Naturally, there are no tools to help a researcher determine experimental intention, but this is the most critical station on the train ride to a reference genome. Here is a checklist of important things to consider:

**1. What is your Primary aim?

  Is there a specific hypothesis in mind, or is this an expedition to form new ones?
  A cluster of closely related species, or just a favourite one?

**2. Community resources

  Key advisors that can help along the way?
  Are there any existing community resources, such as ESTs, BAC libraries, frozen specimens or live cultures?
  Are there any closely related species with sequenced genomes?
  Are there any closely related species with sequenced AND well-annotated genomes?

**3. Any prior knowledge on the genomic architecture of the species (e.g. sex chromosomes, ploidy, genome size, number of chromosomes) and in particular the collected specimens (e.g. sex, heterozygosity levels).

**4. Acquiring high quality DNA and RNA material:

  Have established an optimum extraction protocols and best practices. Which specimens to use and how many?
  Which tissues for expression?
  Access to haploid tissues?
  Is it required (and possible) to establish an inbred line to reduce heterozygosity?

**5. Generating raw data

  How much data is needed and of what kind?
  What genome sequencing methods are available to you? Are they experimental or reliable and established?
  What are the library preparation options?
  Check whether DNA/RNA yields are compatible proposed library preparation and sequencing platforms
  What is affordable?
  What can be done commercially and what in-house?
  
**6. What are the personal aims that need to be achieved (e.g. a publication, specific downstream experiments etc)?

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