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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 01, 2024 |
| Title |
B6 |
| Sample type |
SRA |
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| Source name |
Breast
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| Organism |
Mus musculus |
| Characteristics |
tissue: Breast
genotype: Female
treatment: Radiation + Pembrolizumab
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Murine TNBC tumors were minced and dissociated using the Miltenyi Biotec Mouse Tumor Dissociation kit, then CD45-positive cells were enriched using the Miltenyi Biotec anti-mouse CD45 microbeads
Single-cell gene expression librarieswere prepared according to the 10X Genomics Single Cell 3’ v2 protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Triple-receptor negative breast cancer
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| Data processing |
Demultiplexed fastq files for gene expression libraries were processed using Cellranger (version 4.0.0, GRCh38-3.0.0 transcriptome reference). Doublet cells were identified using Scrublet (Wolock et al., 2019) (version 0.2.1) from the filtered feature barcode matrices produced by Cellranger. Scrublet was run using the 10% highest variable genes, identified using the Scanpy2 scanpy.pp.highly_variable_genes function (scanpy version 1.5.1), with an expected doublet rate of 10%. Cells were scored as candidate doublets by Scrublet and removed if their doublet score exceeded 0.25. In addition, the top 1% of cells by UMI count per biopsy were filtered as presumed doublets. Remaining cells were finally filtered to have less than 10% of their UMI’s mapped to mitochondrial genes and to express greater than 100 genes.
Assembly: mm10
Supplementary files format and content: H5AD file containing celltype, subtype,batch, treatment and other metadata columns for each cell
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| Submission date |
Nov 06, 2023 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Simon Knott |
| E-mail(s) |
simon.knott@cshs.org
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| Organization name |
Cedars Sinai
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| Department |
BFG
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| Street address |
8687 Melrose Ave
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| City |
West Hollywood |
| State/province |
California |
| ZIP/Postal code |
90069 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE246613 |
Single-cell and spatial profiling identify three response trajectories to pembrolizumab and radiation therapy in triple negative breast cancer |
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| Relations |
| SRA |
SRX22256106 |
| BioSample |
SAMN38027297 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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