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Series GSE148842 Query DataSets for GSE148842
Status Public on Apr 18, 2020
Title Deconvolution of Cell Type-Specific Drug Responses in Human Tumor Tissue with Single-Cell RNA-seq
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Precision oncology requires the timely selection of effective drugs or drug combinations for individual patients. The ideal platform would enable rapid screening of cell type-specific drug sensitivities directly in patient tumor tissue and reveal strategies to overcome intratumoral heterogeneity. Here we combine multiplexed drug perturbation in acute slice culture from freshly resected tumors with single-cell RNA sequencing (scRNA-seq) to profile transcriptome-wide drug responses in individual patients. We applied this approach to glioblastoma (GBM) and demonstrated that acute slice cultures recapitulate the cellular and molecular features of the originating tumor tissue. Detailed investigation of etoposide, a topoisomerase poison, and the histone deacetylase (HDAC) inhibitor Panobinostat in acute slice cultures revealed cell type-specific responses across multiple patients, including unexpected effects on the immune microenvironment. We anticipate that this approach will facilitate rapid, personalized drug screening to identify effective therapies for solid tumors.
 
Overall design Performed single-cell RNA-seq on biopsies of human glioma surgical specimens and on acute slice cultures of human glioma surgical specimens treated with various drugs
 
Contributor(s) Zhao W, Dovas A, Spinazzi EF, Canoll P, Sims PA
Citation(s) 33975634
Submission date Apr 17, 2020
Last update date Sep 15, 2021
Contact name Peter A Sims
E-mail(s) pas2182@columbia.edu
Organization name Columbia University
Street address 3960 Broadway, Lasker 203AC
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (43)
GSM4483741 PW029-701
GSM4483742 PW029-702
GSM4483743 PW030-701
Relations
BioProject PRJNA625951
SRA SRP256920

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE148842_RAW.tar 341.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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