Cronn Lab:Protocols - Revision history

Richard C. Cronn: /* Illumina GA Data Management */

Richard C. Cronn — Tue, 05 Mar 2013 07:28:12 GMT

Illumina GA Data Management

←Older revision		Revision as of 07:28, 5 March 2013
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	{{Template:Cronn}}		{{Template:Cronn}}
	==Illumina GA Data Management==		==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.	+	[[Short read toolbox]]. Many of our projects use short-read data from Illumina Genome Analyzer and HiSeq. [[user: Brian J. Knaus \| Brian Knaus]] from our lab developed a number of scripts for managing and analyzing short-read files and data for the GA1 and GA2 platforms.

	==Illumina GA DNA-Seq==		==Illumina GA DNA-Seq==

Richard C. Cronn: /* Eliminating Illumina Adapter Dimers with Agilent AMPure Beads */

Richard C. Cronn — Wed, 17 Nov 2010 20:09:07 GMT

Eliminating Illumina Adapter Dimers with Agilent AMPure Beads

←Older revision		Revision as of 20:09, 17 November 2010
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	[[WGA Prep]]. We use phi29-based whole-genome amplification in a variety of different applications. Our standard phi29 WGA method is detailed here.		[[WGA Prep]]. We use phi29-based whole-genome amplification in a variety of different applications. Our standard phi29 WGA method is detailed here.

-	==~~Eliminating Illumina Adapter Dimers~~ with Agilent AMPure Beads==	+	==Purifying DNA with Agilent AMPure Beads==
-	[[AMPure_Mods]]. ~~We find that adapter dimers are frequently abundant in our Illumina libraries. This simple modification of~~ the ~~standard AMPure bead~~ DNA ~~isolation method makes~~ it possible to reduce or eliminate the adapters.	+	[[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==

Richard C. Cronn at 07:05, 14 November 2010

Richard C. Cronn — Sun, 14 Nov 2010 07:05:08 GMT

←Older revision		Revision as of 07:05, 14 November 2010
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	==Whole Genome Amplification==		==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.		[[WGA Prep]]. We use phi29-based whole-genome amplification in a variety of different applications. Our standard phi29 WGA method is detailed here.
		+
		+	==Eliminating Illumina Adapter Dimers with Agilent AMPure Beads==
		+	[[AMPure_Mods]]. We find that adapter dimers are frequently abundant in our Illumina libraries. This simple modification of the standard AMPure bead DNA isolation method makes it possible to reduce or eliminate the adapters.

	==Random Lab Methods==		==Random Lab Methods==
-	[[Random Lab Methods]]. ~~DNA~~ extraction, ~~RNA~~ extraction, gels, ~~and~~ short cuts... ~~all~~ here	+	[[Random Lab Methods]]. RNA extraction, DNA extraction, gels, short cuts... find it here

	==Important References on the Illumina GA Sequencer==		==Important References on the Illumina GA Sequencer==

Richard C. Cronn: /* Important References on the Illumina GA Sequencer */

Richard C. Cronn — Tue, 16 Feb 2010 08:26:53 GMT

Important References on the Illumina GA Sequencer

←Older revision		Revision as of 08:26, 16 February 2010
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	* Bentley DR, et al. ''Accurate whole human genome sequencing using reversible terminator chemistry''. Nature 2008 456:53-9.		* 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.		* 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.		* Quail MA, et al. ''A large genome center's improvements to the Illumina sequencing system.'' Nat Methods 2008 Dec;5:1005-10.

Richard C. Cronn: /* References on the Illumina GA Sequencer */

Richard C. Cronn — Tue, 16 Feb 2010 08:20:59 GMT

References on the Illumina GA Sequencer

←Older revision		Revision as of 08:20, 16 February 2010
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	[[Random Lab Methods]]. DNA extraction, RNA extraction, gels, and short cuts... all here		[[Random Lab Methods]]. DNA extraction, RNA extraction, gels, and short cuts... all here

-	==References on the Illumina GA Sequencer==	+	==Important References on the Illumina GA Sequencer==
	* ''Illumina support documentation'' [http://www.illumina.com/support/documentation.ilmn]		* ''Illumina support documentation'' [http://www.illumina.com/support/documentation.ilmn]
-
	* ''Illumina Paired-End Sequencing Sample Prep Instructions, Rev. A, April 2008.''		* ''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.		* 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.		* Craig DW, et al. ''Identification of genetic variants using bar-coded multiplexed sequencing''. Nat Methods 2008 Dec;5:887-93.
-
	* Quail MA, et al. ''A large genome center's improvements to the Illumina sequencing system.'' Nat Methods 2008 Dec;5:1005-10.		* Quail MA, et al. ''A large genome center's improvements to the Illumina sequencing system.'' Nat Methods 2008 Dec;5:1005-10.

Richard C. Cronn: /* References on the Illumina GA Sequencer */

Richard C. Cronn — Tue, 16 Feb 2010 08:19:50 GMT

References on the Illumina GA Sequencer

←Older revision		Revision as of 08:19, 16 February 2010
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	==References on the Illumina GA Sequencer==		==References on the Illumina GA Sequencer==
-	* Illumina support documentation [http://www.illumina.com/support/documentation.ilmn]	+	* ''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.
		+
		+	* Quail MA, et al. ''A large genome center's improvements to the Illumina sequencing system.'' Nat Methods 2008 Dec;5:1005-10.

Richard C. Cronn: Undo revision 379548 by Richard C. Cronn (Talk)

Richard C. Cronn — Wed, 06 Jan 2010 05:25:52 GMT

Undo revision 379548 by Richard C. Cronn (Talk)

←Older revision		Revision as of 05:25, 6 January 2010
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	==References on the Illumina GA Sequencer==		==References on the Illumina GA Sequencer==
-	*[http://www.illumina.com/support/documentation.ilmn]	+	* Illumina support documentation [http://www.illumina.com/support/documentation.ilmn]

Richard C. Cronn: /* References on the Illumina GA Sequencer */

Richard C. Cronn — Wed, 06 Jan 2010 05:23:53 GMT

References on the Illumina GA Sequencer

←Older revision		Revision as of 05:23, 6 January 2010
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	==References on the Illumina GA Sequencer==		==References on the Illumina GA Sequencer==
-	*[http://www.illumina.com/~~downloads~~/~~SS_DNAsequencing~~.~~pdf Illumina Sequencing Technology]~~	+	*[http://www.illumina.com/support/documentation.ilmn]
-	*[http://www.illumina.com/downloads/GenomicSeq_DataSheet.pdf Genomic Sequencing]	+
-	*[http://www.illumina.com/downloads/targetedresequencing.pdf Targeted Resequencing]	+

Richard C. Cronn at 06:40, 30 November 2009

Richard C. Cronn — Mon, 30 Nov 2009 06:40:01 GMT

←Older revision		Revision as of 06:40, 30 November 2009
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	==Illumina GA Hyb-Seq==		==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.		[[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.

	==Random Lab Methods==		==Random Lab Methods==
-	[[~~Lab_Methods~~]]. DNA extraction, RNA extraction, gels, and short cuts... all here	+	[[Random Lab Methods]]. DNA extraction, RNA extraction, gels, and short cuts... all here

	==References on the Illumina GA Sequencer==		==References on the Illumina GA Sequencer==

Richard C. Cronn at 08:08, 25 November 2009

Richard C. Cronn — Wed, 25 Nov 2009 08:08:45 GMT

←Older revision		Revision as of 08:08, 25 November 2009
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	{{Template:Cronn}}		{{Template:Cronn}}
-	==~~Genomic DNA Extraction~~==	+	==Illumina GA Data Management==
-	~~Add protocol here~~.	+	[[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.

-	==~~Gel Electrophoresis~~==	+	==Illumina GA DNA-Seq==
-	~~Add protocol here~~.	+	[[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.

-	==~~DNA Clean~~-up==	+	==Illumina GA RNA-Seq==
-	~~Add protocol here~~.	+	[[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.

-	==~~DNA Quantification~~==	+	==Illumina GA Hyb-Seq==
-	~~Add protocol~~ here.	+	[[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.

-	==~~Illumina DNA Sequencing~~==	+	==Random Lab Methods==
-	===Illumina ~~product literature=~~==	+	[[Lab_Methods]]. DNA extraction, RNA extraction, gels, and short cuts... all here
		+
		+	==References on the Illumina GA Sequencer==
	*[http://www.illumina.com/downloads/SS_DNAsequencing.pdf Illumina Sequencing Technology]		*[http://www.illumina.com/downloads/SS_DNAsequencing.pdf Illumina Sequencing Technology]
	*[http://www.illumina.com/downloads/GenomicSeq_DataSheet.pdf Genomic Sequencing]		*[http://www.illumina.com/downloads/GenomicSeq_DataSheet.pdf Genomic Sequencing]
	*[http://www.illumina.com/downloads/targetedresequencing.pdf Targeted Resequencing]		*[http://www.illumina.com/downloads/targetedresequencing.pdf Targeted Resequencing]