Michael B. Mann Skin Oncogenomics Lab Resources

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. Take the SBCDDB tutorial (http://sbcddb.moffitt.org/doc/tutorial.html) to start using the SBCDDB for your research.

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 Protocols

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. We have published several Research Articles using the SBCapSeq method:

In work published in 2016 in Nature Biotechnology, we developed the SBCapSeq method to investigate intratumor heterogeneity, clonal driver gene dynamics, and cooperating driver pathways that control hematopoietic transformation in vivo using a new SB-driven mouse model of myeloid leukemia. Read the paper PMID: 27479497
In work published in 2021 in Cancers, we developed a new class of Promoterless SB alleles that can drive solid cancers via tumor suppressor inactivation. Read the paper PMID: 33435458.
In work published in 2021 in PLoS Genetics, we identified the cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression. Read the paper PMID: 34398873.

If you are interested in collaborating on an SBCapSeq project, please contact Dr. Mann.

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

Photo courtesy Houston Methodist (Original)

Soft Agar Assay Protocol

Prepared by Dr. Aziz Aiderus, this protocol describes the soft agar assay recently reported in work published in 2021 in PLoS Genetics, where we identified the cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression. Read the paper PMID: 34398873.

Download Soft agar assay protocol.pdf

Primary Cultures from Tumor Tissues Protocol

Prepared by Dr. Aziz Aiderus, this protocol describes the derivation of primary cell cultures from tumor tissues that will be reported in an upcoming manuscript.

Download Primary culture from tumor tissue.pdf

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!

If you would like to request a copy of the SBsplinkSeq protocol, please contact Dr. Mann.