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| Status |
Public on Jun 24, 2021 |
| Title |
CID3838 |
| Sample type |
SRA |
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| Source name |
Mammary Tumor
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| Organism |
Homo sapiens |
| Characteristics |
clinical_subtype: HER2+
gender: female
tissue: Primary Breast Tumor
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single-cell sequencing was performed using the Chromium Single-Cell v2 3’ and 5’ Chemistry Library, Gel Bead, Multiplex and Chip Kits (10X Genomics) according to the manufacturer's protocol. A total of 5,000 to 7,000 cells were targeted per well.
Libraries were sequenced on the NextSeq 500 platform (Illumina) with pair-ended sequencing and dual indexing. A total of 26, 8 and 98 cycles were run for Read 1, i7 index and Read 2, respectively.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
***Raw Data Disclaimer: Raw human data files are deposited to the EGA (EGAS00001005173) to adhere to ethics.***
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| Data processing |
Raw bcl files were demultiplexed and mapped to the reference genome GRCh38 using the Cell Ranger Single Cell v2.0 software (10X Genomics). The EmptyDrops method from the DropletUtils package (v1.2.2) was applied for cell filtering with additional cutoffs for cells with a gene and unique molecular identifier (UMIs) count greater than 200 and 250, respectively, and a mitochondrial percentage less than 20%.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data files in MM matrix format (*.mtx), genes and barcode IDs (*.tsv)
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| Submission date |
Jun 03, 2021 |
| Last update date |
Jun 26, 2021 |
| Contact name |
Alexander Swarbrick |
| E-mail(s) |
a.swarbrick@garvan.org.au
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| Organization name |
Garvan Institute of Medical Research
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| Street address |
384 Victoria Street
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| City |
Darlinghurst |
| State/province |
NSW |
| ZIP/Postal code |
2010 |
| Country |
Australia |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE176078 |
A single-cell and spatially resolved atlas of human breast cancers |
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| Relations |
| BioSample |
SAMN19546316 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5354514_CID3838.tar.gz |
21.5 Mb |
(ftp)(http) |
TAR |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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