|
| Status |
Public on Dec 01, 2023 |
| Title |
prostate_tumor_medium_cell |
| Sample type |
SRA |
| |
|
| Source name |
primary mouse prostate epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: primary mouse prostate epithelial cells
cell type: prostate tumor cells
phenotype: sorted cells with medium morphology
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Single cells (3,000 to 4,000 cells per μl) were resuspended in Tapestri cell buffer and encapsulated using a Tapestri microfluidics cartridge, lysed, and barcoded.
Libraries were generated either from cryopreserved or freshly dissociated tumor cells using the Mission Bio Tapestri Single-cell DNA Custom Kit according to the manufacturer’s recommendations
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw sequencing reads were trimmed to the amplicon regions using the awk command. Barcode sequences in the reads were filtered and extracted using UMI-tools
Processed reads were aligned to custom references containing all amplicon sequences using bwa-mem
Samtools was used to extract amplicon counts for each barcode
Assembly: custom built with reference amplicon
Supplementary files format and content: tab-delimited text files include raw count values for each amplicon
Library strategy: scDNA-seq
|
| |
|
| Submission date |
Apr 14, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
John K. Lee |
| E-mail(s) |
jklee5@fredhutch.org
|
| Phone |
2066673652
|
| Organization name |
Fred Hutch Cancer Research Ctr
|
| Street address |
1100 Fairview Ave N Rm E2-430
|
| City |
Seattle |
| State/province |
Washington |
| ZIP/Postal code |
98101 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE229782 |
Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations [scDNA-Seq] |
| GSE229783 |
Combinatorial genetic strategy accelerates the discovery of cancer genotype-phenotype associations |
|
| Relations |
| BioSample |
SAMN34193679 |
| SRA |
SRX19976566 |
