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Method Article
Zoe Rogers
Winslow Lab
Corresponding Author
License:
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This protocol should be used in preparation from tumor barcode sequencing (Tuba-seq) with a goal of directly quantifying the tumor sizes within tissues. This protocol could also be used to quantify cells from culture, but here we only discuss genomic DNA extraction from whole tissues. The protocol begins with phenol-chloroform gDNA extraction of homogenized tissue. Once gDNA has been harvested, the barcode containing region is amplified with custom primers which allow attachment of Illumina adapters in a single step. Finally, we discuss how to pool samples before sending your library in for sequencing. The entire process takes 3-4 days. This protocol accompanies Rogers et al, Nature Methods, published online May 22, 2017 (nmeth.4297).
Keywords
Tuba-seq, barcoding, tumor suppressors, cancer
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Associated Publications
An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Zoe Rogers
Winslow Lab
Corresponding Author
Version History
CURRENT STATUS: Posted
Version 1
Posted 25 May, 2017
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
This protocol should be used in preparation from tumor barcode sequencing (Tuba-seq) with a goal of directly quantifying the tumor sizes within tissues. This protocol could also be used to quantify cells from culture, but here we only discuss genomic DNA extraction from whole tissues. The protocol begins with phenol-chloroform gDNA extraction of homogenized tissue. Once gDNA has been harvested, the barcode containing region is amplified with custom primers which allow attachment of Illumina adapters in a single step. Finally, we discuss how to pool samples before sending your library in for sequencing. The entire process takes 3-4 days. This protocol accompanies Rogers et al, Nature Methods, published online May 22, 2017 (nmeth.4297).
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