|
| Status |
Public on Sep 01, 2022 |
| Title |
TNBC1 |
| 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 |
| E-mail(s) |
jinyu.li.1@stonybrook.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN27018998 |
| SRA |
SRX14633680 |
