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Series GSE231542 Query DataSets for GSE231542
Status Public on Dec 01, 2023
Title Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations [DNA-seq_distribution]
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 prostate organoid cells transduced with a pooled lentivirus containing candidate oncogenic events to amplify the oncogenic barcode region, helping deconvolute distribution of each oncogenic event transduced in the cells. The distributions of oncogenic barcode were retrieved in each sample. Th distribution was used to determine if each oncogenic events were evenly distributed in the transduced cells.
Contributor(s) Li S, Wong A, Sun H, Lee JK
Citation(s) 38424461
Submission date May 02, 2023
Last update date Mar 13, 2024
Contact name John K. Lee
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)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (2)
GSM7290622 PE-pLVB1_cells
GSM7290623 PE-pLVB4_cells
This SubSeries is part of SuperSeries:
GSE229783 Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations
BioProject PRJNA966760

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

Supplementary file Size Download File type/resource
GSE231542_RAW.tar 10.0 Kb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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