Multiregion Whole Exome and Smart-Seq3 single cell RNA sequencing of Breast Tumors

Multiple regions were cut out of each tumor extracted form breast cancer patients and two experiments were run: - Whole exome sequencing on each of the regions plus an adjacent normal tissue sample - Smart-Seq3 Single cell RNA sequencing on EPCAM+ CD45- sorted cells from different tumor regions

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 3 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001009781	Multiple regions were cut out of each tumor extracted form breast cancer patients and two experiments were run: - Whole exome sequencing on each of the regions plus an adjacent normal tissue sample - Smart-Seq3 Single cell RNA sequencing on EPCAM+ CD45- sorted cells from different tumor regions	Illumina NovaSeq 6000	1518

Publications	Citations
Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics. Jun SH, Toosi H, Mold J, Engblom C, Chen X, O'Flanagan C, Hagemann-Jensen M, Sandberg R, Aparicio S, Hartman J, Roth A, Lagergren J. Nat Commun 14: 2023 982	5
CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics. Kurt S, Chen M, Toosi H, Chen X, Engblom C, Mold J, Hartman J, Lagergren J. Bioinformatics 40: 2024 btae284	0
Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope. Shafighi S, Geras A, Jurzysta B, Sahaf Naeini A, Filipiuk I, Ra Czkowska A, Toosi H, Koperski Ł, Thrane K, Engblom C, Mold JE, Chen X, Hartman J, Nowis D, Carbone A, Lagergren J, Szczurek E. Nat Commun 15: 2024 9343	0