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Series GSE229781 Query DataSets for GSE229781
Status Public on Dec 01, 2023
Title Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations [bulk DNA-Seq]
Organism Mus musculus
Experiment type Other
Summary Available genetically-defined cancer models are limited in genotypic and phenotypic complexity and underrepresent the heterogeneity of human cancer. Herein, we describe a combinatorial genetic strategy applied to an organoid transformation assay to rapidly generate diverse, clinically relevant models of bladder and prostate cancer. Importantly, the clonal architecture of the resultant tumors can be resolved using single-cell or spatially resolved next-generation sequencing to uncover polygenic drivers of cancer phenotypes.
 
Overall design 2-step PCR was performed on laser captured section of FFPF samples of bladder tumors generated by transducing the bladder urothelial cells with a pooled lentivirus containing candidate oncogenic events to amplify the oncogenic barcode region, helping deconvolute oncogenic events involved in initiating the tumors. The distributions of oncogenic barcode were retrieved in each sample. The overlapping enriched factors for different histology were identified to be potentially invovled in the histology initiation.
 
Contributor(s) Li S, Wong A, Sun H, Lee JK
Citation(s) 38424461
Submission date Apr 14, 2023
Last update date Mar 13, 2024
Contact name John K. Lee
E-mail(s) jklee5@fredhutch.org
Phone 2066673652
Organization name Fred Hutch Cancer Research Ctr
Street address 1100 Fairview Ave N Rm E2-430
City Seattle
State/province Washington
ZIP/Postal code 98101
Country USA
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (10)
GSM7177615 FHBT2_B1
GSM7177616 FHBT3_B2
GSM7177617 FHBT4a_B3_URO
This SubSeries is part of SuperSeries:
GSE229783 Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations
Relations
BioProject PRJNA955815

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE229781_RAW.tar 20.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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