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 - mikblack/wgsvar: Variant detection (SNV, InDel, CNV) in whole genome sequence (WGS) data.
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)
Mann Labs Cancer Genomics Resources
TempTrak Login (computer)
TempTrak Login (phone)
NCBI BioProject Datasets
Myeloid Leukemia Whole Genome Sequencing. Mus musculus (ID 285079) - BioProject - NCBI
Whole exome sequencing of murine SB|BrafV600E melanoma genomes. Mus musculus (ID 276299) - BioProject - NCBI
NIH Figshare Instance Datasets
- Supplementary Tables1-43 for 'Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression'
- SBCapSeq Protocol manuscript files for 'Quantifying tumor heterogeneity, clonal dynamics, and cancer driver gene evolution from Sleeping Beauty transposon mutagenesis models using SBCapSeq'
- Using intradermal injection of lentiviruses to functionally validate Cep350 as a haploinsufficient melanoma tumor suppressor gene in vivo | Datasets Supporting: Tumor Suppressive Functions of CEP350 in Cutaneous Melanoma Cells
- Bioinformatics analysis of CEP350 tumor suppression in human TCGA cutaneous melanoma | Datasets Supporting: Tumor Suppressive Functions of CEP350 in Cutaneous Melanoma Cells
- Phospho-proteomics tandem mass tag datasets from cells with CEP350 genetic alteration | Datasets Supporting: Tumor Suppressive Functions of CEP350 in Cutaneous Melanoma Cells
Figshare Datasets
- Supplementary Tables 1-24 for "Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation".
- Table 1: SB allele-specific tumor spectrum by whole-body, transposon-mediated mutagenesis in wild type mice.
- Supplementary Notes 1–3 for "Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation".
- SB-Onc2.3-Pan-TSG Trunk Driver SB insertion maps for "Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation".
- Onc2.3 pathology images for "Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation".
- SB-Onc2.3 multiplex PCR genotyping protocol.
- SB-Onc2.3 molecular cloning maps and files.
- Supplemental Figures Govindaraju et al 2020.
Useful Web sites
Moffitt Cancer Center Links
Department of Molecular Oncology
Cancer Biology and Evolution Program
Basic Science Research Division
Melanoma Research Center of Excellence
Moffitt-USF Cancer Biology Ph.D. Program
University of South Florida Links
USF Biosafety Education and Training
Professional Societies & Organizations
AACR | American Association for Cancer Research
SMR | Society for Melanoma Research
SID | Society For Investigative Dermatology
TSCF | The Skin Cancer Foundation
NCI | National Cancer Institute
GSA | Genetics Society of America
FASEB | Federation of American Societies for Experimental Biology
AAAS | American Association for the Advancement of Science
Scientific Journals
Preprints
Research Links
NCI-Frederick Mouse Repository
cBioPortal for Cancer Genomics
TCGA | The Cancer Genome Atlas
ICGC | International Cancer Genome Consortium
Human Skin Disease Resource Center
Canopy Scientific Python Environment
Professional Development Links
The Grant Application Writer’s Workbook - NIH