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Series GSE176078 Query DataSets for GSE176078
Status Public on Jun 24, 2021
Title A single-cell and spatially resolved atlas of human breast cancers
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary This study presents a single cell and spatially resolved transcriptomics analysis of human breast cancers. We develop a single cell method of intrinsic subtype classification (scSubtype) to reveal recurrent neoplastic cell heterogeneity. Immunophenotyping using CITE-Seq provides high-resolution immune profiles, including novel PD-L1/PD-L2+ macrophage populations associated with clinical outcome. Mesenchymal cells displayed diverse functions and cell surface protein expression through differentiation within 3 major lineages. Stromal-immune niches were spatially organized in tumors, offering insights into anti-tumor immune regulation. Using single cell signatures, we deconvoluted large breast cancer cohorts to stratify them into nine clusters, termed ‘ecotypes’, with unique cellular compositions and clinical outcomes. This study provides a comprehensive transcriptional atlas of the cellular architecture of breast cancer.
Overall design We performed scRNA-Seq (Chromium, 10X Genomics) on 26 primary tumors from three major clinical subtypes of breast cancer, including 11 ER+, 5 HER2+ and 10 TNBC. We also performed bulk RNA-Seq on a total of 24 of these matched samples.
***Raw Data Disclaimer: Raw human data files are deposited to the EGA (EGAS00001005173) to adhere to ethics.***
Contributor(s) Swarbrick A, Wu S, Al-Eryani G, Roden D
Citation(s) 34493872, 35933466
Submission date Jun 03, 2021
Last update date Aug 24, 2022
Contact name Alexander Swarbrick
Organization name Garvan Institute of Medical Research
Street address 384 Victoria Street
City Darlinghurst
State/province NSW
ZIP/Postal code 2010
Country Australia
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (26)
GSM5354513 CID3586
GSM5354514 CID3838
GSM5354515 CID3921
BioProject PRJNA734812

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Supplementary file Size Download File type/resource
GSE176078_RAW.tar 532.4 Mb (http)(custom) TAR (of TAR)
GSE176078_Wu_etal_2021_BRCA_scRNASeq.tar.gz 532.9 Mb (ftp)(http) TAR
GSE176078_Wu_etal_2021_bulkRNAseq_raw_counts.txt.gz 5.3 Mb (ftp)(http) TXT
Raw data not provided for this record
Processed data provided as supplementary file
Processed data are available on Series record

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