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Sample GSM5974487 Query DataSets for GSM5974487
Status Public on Sep 01, 2022
Title TNBC2
Sample type SRA
Source name triple negative breast tumor tissue
Organism Homo sapiens
Characteristics tissue of origin for tumor: Breast
genetic alteration: NA
Extracted molecule total RNA
Extraction protocol The tumors were digested both mechanically and enzymatically (Collagenase/Hyaluronidase, and DNaseI) and single cell suspensions of viable cells were prepared. mRNA from each individual cell was captured and tagged with barcodes using 10X Genomics microfluidic platform.
Barcoded cDNA library was prepared using the manufacturer's instructions, 10X Genomics.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Single Cell sequencing data were pre-processed by cellranger 6.0.1 from 10X Genomics using default settings.
Downstreaming analysis was performed by Seurat 3.0
Assembly: mm10, GRCh38
Supplementary files format and content: gzipped file format containing "filtered_feature_bc_matrix" folder contents from cellranger outputs
Submission date Mar 28, 2022
Last update date Sep 01, 2022
Contact name Jinyu Li
Organization name Stony Brook University
Department Cancer Center
Street address 101 Nicolls Rd
City Stony Brook
State/province NY
ZIP/Postal code 11794
Country USA
Platform ID GPL24676
Series (1)
GSE199515 Comparative single-cell genomics uncovers evolutionarily conserved features and therapeutic targets in triple-negative breast cancer fibroblasts
BioSample SAMN27018997
SRA SRX14633681

Supplementary file Size Download File type/resource
GSM5974487_TNBC2.filtered_feature_bc_matrix.tar.gz 18.7 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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