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Series GSE137818 Query DataSets for GSE137818
Status Public on Aug 27, 2020
Title Mutations in homologous recombination genes BRCA1 and BRCA2 differentially affect the tumor microenvironment and response to checkpoint blockade immunotherapy
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary We report differential effects of mutations in genes of the homologous recombination (HR) pathway on response after ICB administration in mouse and human tumors, and show that truncating mutations in BRCA2 are associated with superior response to ICB compared to BRCA1-deficient tumors. Immunogenomic analyses demonstrated that mutations in BRCA1 and BRCA2 differentially modulate the tumor-immune microenvironment, with gene expression programs related to both adaptive and innate immune pathways enriched in BRCA2-deficient tumors. Single-cell RNA sequencing further revealed distinct T cell, NK, macrophage, and dendritic cell populations enriched in BRCA2 mutant tumors relative to BRCA1-deficient tumors.
Overall design Bulk RNA-sequencing from immunotherapy-naïve and immunotherapy-treated mouse 4T1 parental, Brca1 mutant, and Brca2 mutant tumors. Single cell RNA-sequencing from immunotherapy-naïve 4T1 parental, Brca1 mutant, and Brca2 mutant tumors
Contributor(s) Riaz N, Chan TA, Samstein R, Krishna C
Citation(s) 33834176
Submission date Sep 22, 2019
Last update date Jul 31, 2023
Contact name Vladimir Makarov
Organization name Cleveland Clinic
Department LRI
Street address 9500 Euclid Ave
City Cleveland
State/province OH
ZIP/Postal code 44195
Country USA
Platforms (2)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (40)
GSM4088892 Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 1
GSM4088893 Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 2
GSM4088894 Mouse 4T1 Brca2 KO Untreated bulk RNA-seq Rep 3
BioProject PRJNA573517
SRA SRP222890

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Supplementary file Size Download File type/resource
GSE137818_Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv.gz 994.2 Kb (ftp)(http) CSV
GSE137818_Mouse_TREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv.gz 291.1 Kb (ftp)(http) CSV
GSE137818_Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv.gz 908.3 Kb (ftp)(http) CSV
GSE137818_Mouse_UNTREATED_CELL_LINE_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv.gz 262.1 Kb (ftp)(http) CSV
GSE137818_Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_normcounts.csv.gz 1.2 Mb (ftp)(http) CSV
GSE137818_Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_BRCA1KO_rawcounts.csv.gz 346.1 Kb (ftp)(http) CSV
GSE137818_Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_normcounts.csv.gz 1.2 Mb (ftp)(http) CSV
GSE137818_Mouse_UNTREATED_bulkRNA_BRCA2KO_vs_WT_rawcounts.csv.gz 358.6 Kb (ftp)(http) CSV
GSE137818_scRNA_logcounts.csv.gz 608.0 Mb (ftp)(http) CSV
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