|
| Status |
Public on Apr 06, 2022 |
| Title |
SJRHB013758_D1 |
| Sample type |
SRA |
| |
|
| Source name |
Patient tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: tumor
protocol: 10x genomics 3' snRNA-seq
|
| Extracted molecule |
total RNA |
| Extraction protocol |
single nucleus extraction
Nuclei were isolated from frozen tissue samples using a combination of detergent and mechanical separation in TST buffer. A detailed protocol is available on protocols.io at https://dx.doi.org/10.17504/protocols.io.bhbcj2iw
10x Genomics 3' single-cell gene expression kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
single nucleus RNA-sequence
|
| Data processing |
Single cell or nucleus RNA-seq reads from tumors or O-PDXs were aligned using the 10x Genomics Cell ranger Pipeline (v3.0.2) to the hg19 reference data v3.0.0 (for tumors) or hg19-and-mm10 v3.0.0 (for O-PDXs). In the case of single-nucleus datasets, a custom pre-mRNA reference was used to include intronic reads into expression matrices
Genome_build: hg19 or hg19-and-mm10
Supplementary_files_format_and_content: Cell Ranger output
|
| |
|
| Submission date |
Jun 17, 2021 |
| Last update date |
Apr 06, 2022 |
| Contact name |
Michael Dyer |
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Developmental Neurobiology
|
| Street address |
262 Danny Thomas Pl MS 324
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE174376 |
A single-cell/nucleus atlas of pediatric rhabdomyosarcoma |
|
| Relations |
| BioSample |
SAMN19763867 |
| SRA |
SRX11173048 |
