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.


 

In Silico Lab Tools


Cancer Genomics Data Analysis Tools (public)


SB Driver Analysis software 

GitHub - mbmann/SB-SCC-microarray-data: PLOS Genetics SB|cuSCC microarray shiny app

GitHub - jynewberg/sbcapseq: SB capture sequencing workflow.

GitHub - jynewberg/sbfusion

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

pT2/Onc2 sequence info

 

Moffitt Community Tools (Moffitt network only)


Sleeping Beauty Cancer Driver Database

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

TempTrak Login (computer)

TempTrak Login (mobile)

LabArchives Login

 

NCBI BioProject Datasets


Myeloid Leukemia Whole Genome Sequencing. Mus musculus BioProject: PRJNA285079 - NCBI

Transcriptome sequencing of murine myeloid leukemia genome. Mus musculus BioProject: PRJNA285082 - NCBI

Transcriptome analysis of mRNA samples from a cohort of mice with histopathologically diagnosed Undifferentiated Myeloid Leukemia. Mus musculus  BioProject: PRJNA285671 - NCBI

Sleeping Beauty capture-enrichment genome sequencing. Mus musculus BioProject: PRJNA325944 - NCBI

Whole exome sequencing of murine SB|BrafV600E melanoma genomes. Mus musculus BioProject: PRJNA276299 - NCBI

Whole transcriptome sequencing (WTS) of murine cutaneous squamous cell carcinoma (cuSCC) genomes. Mus musculus BioProject: PRJNA580460  - NCBI

Transcriptome analysis of mRNA samples from a cohort of mice with histopathologically diagnosed cutaneous Squamous Cell Carcinoma (cuSCC). Mus musculus BioProject: PRJNA580462 - NCBI 

 

Oncogenomic visualization using R Shiny


SB|cuSCC mciroarray data

NIH Figshare Instance Datasets


Michael Mann Lab Public Data

 

Figshare Datasets


Michael Mann Lab Public Data

Dryad Datasets


Michael Mann Lab Public Data

 

Useful Web sites