AlanFung:LabNotes/CTCF/2011-4-25: Difference between revisions

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>Alan6017518
(Created page with '='''Nextera Methyl-Seq DNA Sample Prep on 100cells (600pg DNA)'''= ='''Low input transposase-based library preparation (Shendure's Protocol)'''= ==Objective== *Confirmation of …')
 
>Alan6017518
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*Increase yield from the bisulfite conversion using zymo methylation direct kit (works with 50pg starting amount)
*Increase yield from the bisulfite conversion using zymo methylation direct kit (works with 50pg starting amount)
*Test Kapa Hifi polymerase
*Test Kapa Hifi polymerase
==Samples & Materials==
*Nextera Sample Prep Kit_Epicentre_NMS072910B
NexteraTM Methyl-Seq Tagmentation Mix (Illumina-compatible)
5X Nextera Reaction Buffer (HMW)
50X Nextera Primer Cocktail (Illumina-compatible)
50X Nextera Adaptor 2 (Illumina-compatible)
2X Nextera Fill-in Buffer
2X Nextera PCR Buffer
200X Nextera Read 1 Primer
200X Nextera Read 2 Primer
200X Nextera Index Read Primer 
Nextera Methyl-Seq Polymerase
*Input DNA
*Bisulfite conversion kit (Methylation Direct Kit)

Revision as of 00:33, 26 April 2011

Nextera Methyl-Seq DNA Sample Prep on 100cells (600pg DNA)

Low input transposase-based library preparation (Shendure's Protocol)

Objective

  • Confirmation of the library prep with beta nextera methyl-seq kit with input DNA (100 cells, ~600pg DNA starting amount) with GM12878 gDNA.
  • Adapt Shendure's protocol for low input library preparation
  • Improve the yield from the bisulfite conversion step using suggestions made by zymo tech support
  • Increase yield from the bisulfite conversion using zymo methylation direct kit (works with 50pg starting amount)
  • Test Kapa Hifi polymerase

Samples & Materials

  • Nextera Sample Prep Kit_Epicentre_NMS072910B
NexteraTM Methyl-Seq Tagmentation Mix (Illumina-compatible) 
5X Nextera Reaction Buffer (HMW)
50X Nextera Primer Cocktail (Illumina-compatible) 
50X Nextera Adaptor 2 (Illumina-compatible) 
2X Nextera Fill-in Buffer 
2X Nextera PCR Buffer 
200X Nextera Read 1 Primer 
200X Nextera Read 2 Primer 
200X Nextera Index Read Primer  
Nextera Methyl-Seq Polymerase 
  • Input DNA
  • Bisulfite conversion kit (Methylation Direct Kit)