|
| Status |
Public on Mar 17, 2021 |
| Title |
D1 |
| Sample type |
SRA |
| |
|
| Source name |
Breast
|
| Organism |
Homo sapiens |
| Characteristics |
disease: healthy
tissue: Breast
|
| Treatment protocol |
No treatment
|
| Growth protocol |
These are normal human breast tissues
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells from the tissue were extracted using Tumor Dissociation kit human, cat# 130-095-929 from Miltenyl Biotec. Cells were extracted from either freshly collected tissues or cryopreserved using a procedure described in PMID: 26311223
10x Genomics protocol for chromium single cell 3' reagent kits V3
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
CellRanger 3.0.2 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Seurat 3.1.0 was used for hashtag demultiplexing, data normalization, data scaling, graph-based clustering, cluster marker genes idenfification, and integrative analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: HDF5 file of filtered gene-barcode matrices
|
| |
|
| Submission date |
Jan 15, 2021 |
| Last update date |
Mar 17, 2021 |
| Contact name |
Harikrishna Nakshatri |
| Organization name |
Indiana University School of Medicine
|
| Department |
General Surgery
|
| Street address |
980 W. Walnut St. R3C218C
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE164898 |
Single cell atlas of the healthy breast |
|
| Relations |
| BioSample |
SAMN17324027 |
| SRA |
SRX9856808 |
