 |
 |
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
Processed data are available on Series record |
|
|
|
|
 |