Methods
We host the protocols as Google Docs, so you see the most up to date version, the same one we are using. Please let if you find any errors, or have suggestions on how we can improve the protocols below please email us.
Laboratory protocols
DNA extraction
DNA extraction using silica magnetic beads
- Easily automatable procedure for DNA extraction.
High molecular weight DNA extraction
- Useful for large-insert libraries for de novo genome sequencing.
Sequencing library preparation
EcoRI RAD-tag using degraded DNA (v 1.0)
- This protocol can be used for degraded DNA
- Citation: Tin et al. PLoS ONE 2014, 9(5): e96793
Genomic shotgun sequencing using degraded DNA
- Related to the EcoRI RAD-tag protocol above, but used for whole genome shotgun sequencing.
- Citation: Tin et al. PLoS ONE 2014, 9(5): e96793
Version 2 PCR free genomic shotgun sequencing using degraded DNA
- Modification of original RAD-tag protocol to reduce error and bias due to PCR amplification.
RNA-seq library preparation from total RNA
- Citation: Aird et al. BMC Genomics 2013, 14:7907
FASSST ddRAD tag library preparation
- High-throughput protocol related to the EcoRI RAD-tag procedure above. Optimized for processing 96 samples at one using a liquid handling robot.
General protocols
Gel-free size selection and purification of library
- Useful for processing large numbers of samples at once.
Picogreen assay
- Most accurate measure of overall dsDNA concentration.