|
| Status |
Public on Feb 26, 2019 |
| Title |
Patient derived xenograft 110 |
| Sample type |
SRA |
| |
|
| Source name |
mammary gland
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: total epithelium
number of cells: 10060
|
| Treatment protocol |
none
|
| Growth protocol |
none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Epithelial cells were isolated by FACS from each PDX. Freshly sorted cells were submitted to a 10X Genomics Chromium System for single cell capture.
cDNA synthesis and library preparation was done according to the protocol supplied by the manufacturer. Sequencing was carried out on Illumina NextSeq 500 platform using sequencing parameters recommended for Single Cell 3' V2.0 libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Read alignment and count summarization were performed using CellRanger v2.0.0 using the Illumina BCL files as input.
Genome_build: GRCh38
Supplementary_files_format_and_content: The matrix.mtx file contains genewise read counts for all cells in Matrix Market format. In this format, only cell-gene combinations with with one or more reads are included in the file. genes.tsv contains the corresponding Ensembl IDs and gene symbols as tab-delimited text and barcode.tsv contains the 10X barcodes used to identify cells.
A location-sorted BAM file is available from SRA.
|
| |
|
| Submission date |
Dec 17, 2018 |
| Last update date |
Oct 17, 2019 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE123926 |
Single cell RNA-seq of 25 thousand epithelial cells from xenografts of triple-negative breast cancers |
|
| Relations |
| BioSample |
SAMN10601953 |
| SRA |
SRX5139570 |
