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Sample GSM7872937 Query DataSets for GSM7872937
Status Public on Jan 01, 2024
Title h64C_N
Sample type SRA
 
Source name Breast
Organism Homo sapiens
Characteristics tissue: Breast
age: adult
Sex: female
treatment: Pembrolizumab + Radiation
disease state: Triple-receptor negative breast cancer
Extracted molecule polyA RNA
Extraction protocol Human TNBC core needle biopsies were dissociated using the Miltenyi BiotecHuman Tumor Dissociation Kit, then CD45-positive cells were enriched using the Miltenyi Biotec anti-human CD45 microbeads and CD45-negative cells were obtained from the non-enriched portion
Single-cell gene expression and paired TCR (CD45-positive only) librarieswere prepared according to the 10X Genomics Single Cell 5’ v1 protocol.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing All immune cells following the single cell pipeline outlined in Methods
All non-immune cells following the single cell pipeline outlined in Methods
All TCR data
Assembly: hg38
Supplementary files format and content: H5AD file containing celltype, subtype, patient, batch, pCR and other metadata columns for each immune cell
Supplementary files format and content: H5AD file containing celltype, subtype, patient, batch, pCR and other metadata columns for each non-immune cell
Supplementary files format and content: CSV file containing TCR data
 
Submission date Oct 31, 2023
Last update date Jan 01, 2024
Contact name Simon Knott
E-mail(s) simon.knott@cshs.org
Organization name Cedars Sinai
Department BFG
Street address 8687 Melrose Ave
City West Hollywood
State/province California
ZIP/Postal code 90069
Country USA
 
Platform ID GPL24676
Series (1)
GSE246613 Single-cell and spatial profiling identify three response trajectories to pembrolizumab and radiation therapy in triple negative breast cancer
Relations
BioSample SAMN38001669
SRA SRX22243013

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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