View source for Cronn Lab:Protocols

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==Illumina GA Data Management==
[[Short read toolbox]].  Many of our projects use short-read data from the Illumina Genome Analyzer 1 & 2. [[user: Brian J. Knaus | Brian Knaus]] in our lab has developed a number of scripts for managing and analyzing short-read files and data.

==Illumina GA DNA-Seq==
[[DNA_Seq Prep]]. Our research group has developed several methods for sequencing small genomes (mitochondria, chloroplasts, BACS) in multiplex using Illumina GA2. This page provides details on DNA-Seq library construction.

==Illumina GA RNA-Seq==
[[RNA_Seq Prep]]. We do mRNA-sequencing using methods developed by [http://www.cgrb.oregonstate.edu/faculty/mockler| Todd Mockler's] group at Oregon State University. This page provides details on RNA-Seq library construction.

==Illumina GA Hyb-Seq==
[[Hyb_Seq Prep]]. Like many groups, we've developed customized approaches to enrich rare genomic targets for high-throughput sequencing. Our method for isolating chloroplast genomes by Hyb-Seq is detailed here.

==Whole Genome Amplification==
[[WGA Prep]]. We use phi29-based whole-genome amplification in a variety of different applications. Our standard phi29 WGA method is detailed here.

==Purifying DNA with Agilent AMPure Beads==
[[AMPure_Mods]].  By altering the ratio of DNA:AMPure beads, it's possible to alter the size of the retained bands.  We use AMPure beads to clean DNA bands, as well as reduce or eliminate the abundance of small DNAs (oligos, double-stranded adapters, primer dimers).

==Random Lab Methods==
[[Random Lab Methods]]. RNA extraction, DNA extraction, gels, short cuts... find it here

==Important References on the Illumina GA Sequencer==
* ''Illumina support documentation'' [http://www.illumina.com/support/documentation.ilmn]
* ''Illumina Paired-End Sequencing Sample Prep Instructions, Rev. A, April 2008.''
* Bentley DR, et al. ''Accurate whole human genome sequencing using reversible terminator chemistry''. Nature 2008 456:53-9.
* Craig DW, et al. ''Identification of genetic variants using bar-coded multiplexed sequencing''. Nat Methods 2008 Dec;5:887-93.
* Cronn RC, et al. ''Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology''. Nuc Acids Res 2008 October 36:19:e122.
* Quail MA, et al. ''A large genome center's improvements to the Illumina sequencing system.'' Nat Methods 2008 Dec;5:1005-10.