Arichard:Notebook/bulkNxt2014Jul30

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Bulk Nextera libraries from neuronal nuclei[edit]

Neuronal nuclei were sorted May 20, 2014 by Gwen Kaeser from AD patient 25-00 and control patient 703. Both were females in their 80s. Both cortex and cerebellum were sorted for each patient. Nuclei were sorted from the Hi DCV (Hi PI staining for DNA) fraction of each peak. Sort conditions were +/- for NeuN.

  • 25-00 Ctx+
  • 25-00 Ctx-
  • 25-00 Cbl+
  • 7-03 Ctx+
  • 7-03 Ctx-
  • 7-03 Cbl+

~1200 nuclei were used for each sample. Hypotonic lysis buffer was used. TO BE CONTINUED.

Gels after Nextera PCR[edit]

13 total cycles.

File:BulkNxt2014Jul30GelsSlide1.JPG File:BulkNxt2014Jul30GelsSlide2.JPG File:BulkNxt2014Jul30GelsSlide3.JPG File:BulkNxt2014Jul30GelsSlide4.JPG

Sequencing statistics[edit]

Sequencing statistics for bulk Nextera libraries from May 20 sort

Coverage, bias, and CNVs for 50K bins[edit]

703CblPos File:703CblPos.jpg 703CtxNeg File:703CtxNeg.jpg

703CtxPos File:703CtxPos.jpg 2500CblPos File:2500CblPos.jpg

2500CtxNeg File:2500CtxNeg.jpg 2500CtxPos File:2500CtxPos.jpg