DNA Seq Prep - Revision history

Richard C. Cronn: /* Genomic DNA-Seq Notes */

2010-12-01T07:59:04Z

Genomic DNA-Seq Notes

←Older revision		Revision as of 07:59, 1 December 2010
Line 64:		Line 64:

	• Oligo note 4: PCR primers don't have to be phosphorylated, but they should be nuclease protected.		• Oligo note 4: PCR primers don't have to be phosphorylated, but they should be nuclease protected.
-
-
-	~~'''return to [[Cronn_Lab:Protocols]] page'''~~

	==Estimated Costs==		==Estimated Costs==

Richard C. Cronn: /* References */

2010-12-01T07:58:43Z

References

←Older revision		Revision as of 07:58, 1 December 2010
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		+
		+	'''return to [[Cronn_Lab:Protocols]] page'''

	[[Category:Protocol]]		[[Category:Protocol]]
	[[Category:DNA]]		[[Category:DNA]]
	[[Category:In vitro]]		[[Category:In vitro]]

Richard C. Cronn: /* Genomic DNA-Seq Notes */

2010-12-01T07:55:55Z

Genomic DNA-Seq Notes

←Older revision		Revision as of 07:55, 1 December 2010
Line 64:		Line 64:

	• Oligo note 4: PCR primers don't have to be phosphorylated, but they should be nuclease protected.		• Oligo note 4: PCR primers don't have to be phosphorylated, but they should be nuclease protected.
		+
		+
		+	'''return to [[Cronn_Lab:Protocols]] page'''

	==Estimated Costs==		==Estimated Costs==

Torsten Waldminghaus: /* Genomic DNA-Seq Notes */

2010-04-14T13:46:39Z

Genomic DNA-Seq Notes

←Older revision		Revision as of 13:46, 14 April 2010
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	• Phusion Flash DNA polymerase 2X mix (Finnzymes Oy). New England Biolabs #F-548S. This reagent is packaged for 100 - 20 μL reactions, but can be scaled up for 50 μL reactions (= 40 reactions total). List $78.00 (Nov. 2009).		• Phusion Flash DNA polymerase 2X mix (Finnzymes Oy). New England Biolabs #F-548S. This reagent is packaged for 100 - 20 μL reactions, but can be scaled up for 50 μL reactions (= 40 reactions total). List $78.00 (Nov. 2009).

-	• PCR Primer 1. See Cronn et al., 2008 for details.	+	• PCR Primer 1. See Cronn et al., 2008 <cite> Cronn-2008</cite> for details.

-	• PCR primer 2. See Cronn et al., 2008 for details.	+	• PCR primer 2. See Cronn et al., 2008 <cite> Cronn-2008</cite> for details.

Torsten Waldminghaus: /* Genomic DNA-Seq Notes */

2010-04-14T13:45:00Z

Genomic DNA-Seq Notes

←Older revision		Revision as of 13:45, 14 April 2010
Line 61:		Line 61:
	• Oligo note 2: Note that adapter 1 MUST be 5’ phosphorylated, and that adapter 2 must have one or two terminal phosphorthioate bonds to make the adapter nuclease resistant. Long barcodes are possible; see <cite>Craig-2008</cite> (see below)		• Oligo note 2: Note that adapter 1 MUST be 5’ phosphorylated, and that adapter 2 must have one or two terminal phosphorthioate bonds to make the adapter nuclease resistant. Long barcodes are possible; see <cite>Craig-2008</cite> (see below)

-	• Oligo note 3: If you synthesize your own oligonucleotides, the cost is about $100 per double-stranded adapter (= oligo pair). Consult <cite>Craig-2008 Parks-2009</cite> ~~or Bentley et al., 2008~~ for more information.	+	• Oligo note 3: If you synthesize your own oligonucleotides, the cost is about $100 per double-stranded adapter (= oligo pair). Consult <cite>Craig-2008 Parks-2009 Bentley-2008</cite> for more information.

	• Oligo note 4: PCR primers don't have to be phosphorylated, but they should be nuclease protected.		• Oligo note 4: PCR primers don't have to be phosphorylated, but they should be nuclease protected.

Torsten Waldminghaus: /* References */

2010-04-14T13:43:39Z

References

←Older revision		Revision as of 13:43, 14 April 2010
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	#Parks-2009 pmid=19954512		#Parks-2009 pmid=19954512
	#Craig-2008 pmid=18794863		#Craig-2008 pmid=18794863
		+	#Bentley-2008 pmid=18987734
	<biblio/>		<biblio/>

Torsten Waldminghaus: /* Genomic DNA-Seq Notes */

2010-04-14T12:21:11Z

Genomic DNA-Seq Notes

←Older revision		Revision as of 12:21, 14 April 2010
Line 59:		Line 59:
	• Oligo note 1: Paired-end (PE) adapters are compatable with single- or paired-end sample preparation methods and sequencing kits.		• Oligo note 1: Paired-end (PE) adapters are compatable with single- or paired-end sample preparation methods and sequencing kits.

-	• Oligo note 2: Note that adapter 1 MUST be 5’ phosphorylated, and that adapter 2 must have one or two terminal phosphorthioate bonds to make the adapter nuclease resistant. Long barcodes are possible; see <cite>Craig-2008</cite> (~~2008;~~ see below)	+	• Oligo note 2: Note that adapter 1 MUST be 5’ phosphorylated, and that adapter 2 must have one or two terminal phosphorthioate bonds to make the adapter nuclease resistant. Long barcodes are possible; see <cite>Craig-2008</cite> (see below)

	• Oligo note 3: If you synthesize your own oligonucleotides, the cost is about $100 per double-stranded adapter (= oligo pair). Consult <cite>Craig-2008 Parks-2009</cite> or Bentley et al., 2008 for more information.		• Oligo note 3: If you synthesize your own oligonucleotides, the cost is about $100 per double-stranded adapter (= oligo pair). Consult <cite>Craig-2008 Parks-2009</cite> or Bentley et al., 2008 for more information.

Torsten Waldminghaus at 15:15, 7 April 2010

2010-04-07T15:15:52Z

←Older revision		Revision as of 15:15, 7 April 2010
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-	[[Category:Protocol]][[Category:~~In vitro~~]][[Category:~~DNA~~]]	+	[[Category:Protocol]]
		+	[[Category:DNA]]
		+	[[Category:In vitro]]

Torsten Waldminghaus: /* References */

2010-04-07T15:13:27Z

References

←Older revision		Revision as of 15:13, 7 April 2010
Line 82:		Line 82:
	#Craig-2008 pmid=18794863		#Craig-2008 pmid=18794863
	<biblio/>		<biblio/>
		+
		+
		+
		+	[[Category:Protocol]][[Category:In vitro]][[Category:DNA]]

Torsten Waldminghaus: /* Genomic DNA-Seq Notes */

2010-04-07T15:11:31Z

Genomic DNA-Seq Notes

←Older revision		Revision as of 15:11, 7 April 2010
Line 59:		Line 59:
	• Oligo note 1: Paired-end (PE) adapters are compatable with single- or paired-end sample preparation methods and sequencing kits.		• Oligo note 1: Paired-end (PE) adapters are compatable with single- or paired-end sample preparation methods and sequencing kits.

-	• Oligo note 2: Note that adapter 1 MUST be 5’ phosphorylated, and that adapter 2 must have one or two terminal phosphorthioate bonds to make the adapter nuclease resistant. Long barcodes are possible; see Craig ~~et al.~~ (2008; see below)	+	• Oligo note 2: Note that adapter 1 MUST be 5’ phosphorylated, and that adapter 2 must have one or two terminal phosphorthioate bonds to make the adapter nuclease resistant. Long barcodes are possible; see <cite>Craig-2008</cite> (2008; see below)

-	• Oligo note 3: If you synthesize your own oligonucleotides, the cost is about $100 per double-stranded adapter (= oligo pair). Consult Craig ~~et al.,~~ 2008~~, Cronn et al. 2008,~~ or Bentley et al., 2008 for more information.	+	• Oligo note 3: If you synthesize your own oligonucleotides, the cost is about $100 per double-stranded adapter (= oligo pair). Consult <cite>Craig-2008 Parks-2009</cite> or Bentley et al., 2008 for more information.
-		+
-	~~• Oligo note 4: PCR primers don't have to be phosphorylated, but they should be nuclease protected~~.	+

		+	• Oligo note 4: PCR primers don't have to be phosphorylated, but they should be nuclease protected.

	==Estimated Costs==		==Estimated Costs==