Chris:LabNotes/FateMapping/Calendar/2014/2014-7-30

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Revision as of 00:48, 31 July 2014 by >Cjwei (Created page with "=C1 DNA-seq experiment (done by Andrew and Chris)= ==Background== *We tried running the C1 DNA-seq chip for the first time using: neuN+ cortex AD patient 25-00 (sorted May 20,...")
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C1 DNA-seq experiment (done by Andrew and Chris)

Background

  • We tried running the C1 DNA-seq chip for the first time using: neuN+ cortex AD patient 25-00 (sorted May 20, 2014 into 1% BSA, spun down and resuspended in aliquots of 1% BSA+10% DMSO, frozen -80C)

Procedure

C1 DNA-seq

Nextera library construction

  • We tried two methods for Nextera library construction. The first method was to use a the same procedure as done for MIDAS (treating with ALS/NS + Pol1 prior to doing Nextera). In order to account for any DNA loss during ETOH precipitation, we used 3ng for each sample. The second method was to perform library construction without Pol1 treatment in order to test whether it's necessary for the amplicons created by the C1. Because this will go directly into Nextera, we inputted only 1ng of DNA for each sample.
  • The following is a table describing the samples and volume input from the C1 for each reaction:
rxn#     rxn sample           required mass     vol input (ul)            Idx
1        A12 (-.653ng/ul)     3ng               1.1895 + 0.3015 water     1

Results

  • Below are the gels from size selection