SBCDDB: Sleeping Beauty  Cancer Driver Database

SB Driver Analysis: A Sleeping Beauty cancer driver analysis framework for identifying and prioritizing experimentally actionable oncogenes and tumor suppressors

SBCDDB is an integrated SB data portal housing primary tumor models into an analysis and reporting framework, the Sleeping Beauty Cancer Driver DataBase (SBCDDB, http://sbcddb.moffitt.org), which identifies drivers in individual tumors or tumor populations. Newberg et al., Published online before print October 20, 2017. doi:10.1093/nar/gkx956. 

The SBCDDB is built using the SB Driver Analysis framework as reported in Newberg et al., Nucleic Acids Research. 2018. Published online before print May 26, 2018 doi:10.1093/nar/gky450. Learn more and download the source code from http://sbcddb.moffitt.org/software/.

Protocols

SBCapSeq Protocol

a method for selective cloning of Sleeping Beauty transposon insertions using liquid capture hybridization and Ion Torrent semiconductor sequencing. Mann et al., Published online 03 Aug 2016 at Protocol Exchange. doi:10.1038/protex.2016.053

Dr. Mann preparing SBCapSeq libraries on the Ion Torrent Sequencing platform

Photo courtesy Houston Methodist (Original)

SBsplinkSeq Protocol

a semi-quantiative splinkerette PCR and acoustic shearing method for selective cloning of Sleeping Beauty transposon insertions using multiplex Illumina sequencing. Coming soon!

 

In Silico Lab Tools

Cancer Genomics Data Analysis Tools (public)

GitHub - jynewberg/sbcapseq: SB capture sequencing workflow.

GitHub - jynewberg/sbfusion

GitHub - mikblack/wgsvar: Variant detection (SNV, InDel, CNV) in whole genome sequence (WGS) data.

SB Driver Analysis software 

 

Moffitt Community Tools (Moffitt network only)

 Gene Symbol Set Search — a cross-species gene symbol conversion tool

 CRISPRdb — human and mouse genome-wide CRISPR/Cas9 designs

 

Lab Member Tools (login required)

MannLabsWiki

Mann Labs Cancer Genomics Resources

Sleeping Beauty Cancer Driver Database

TempTrak Login

 

Useful Web sites