|
| Status |
Public on Oct 11, 2024 |
| Title |
PBS-treated K7M2 flank tumor |
| Sample type |
SRA |
| |
|
| Source name |
flank tumor (subQ)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: flank tumor (subQ)
cell line: K7M2
cell type: Osteosarcoma
treatment: PBS (control)
|
| Treatment protocol |
The Ewing sarcoma human xenografts were treated with either oHSV (1e7 pfu/mL) or PBS (as a control) intratumorally on Days 0 and 2 and/or trabectedin (0.15 mg/kg) on Day 0. Osteosarcoma mouse models were treated with either oHSV (1e8 pfu/mL) or PBS (as a control) intratumorally on Days 0 and 2 and/or trabectedin (0.15 mg/kg) on Day 0. Tumors were harvested on Day 3.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Following dissociation into single cell suspension, single-cell 3’ RNA-Seq libraries were prepared using Chromium Single Cell 3′RNA-sequencing system (10x Genomics) with the Reagent Kit v3.1 (10XGenomics, PN-1000120) according to the manufacturer's instructions.
Libraries were constructed per 10x protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
PBS-treated K7M2 flank tumor
|
| Data processing |
BCL files were converted to fastq files using cellranger mkfastq
Fastq files were processed using cellranger count
Further processing and analyses performed are outlined on GitHub (https://github.com/kidcancerlab/oHSV-trabectedin)
Assembly: The reference genome was built from mm10, hg19, and HSV-1 strain 17 (concatenated into one reference genome).
Supplementary files format and content: Tar files for each sample include the contents of the filtered_feature_bc_matrix folder output by Cellranger count (barcodes.tsv.gz features.tsv.gz matrix.mtx.gz)
|
| |
|
| Submission date |
Feb 29, 2024 |
| Last update date |
Oct 11, 2024 |
| Contact name |
Emily M. Ringwalt |
| Organization name |
Nationwide Children's Hospital
|
| Department |
Center for Childhood Cancer
|
| Street address |
575 Children's Xrd
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43215 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE260551 |
Trabectedin Promotes Oncolytic Virus Antitumor Efficacy, Viral Gene Expression, and Immune Effector Function in Models of Bone Sarcoma |
|
| Relations |
| BioSample |
SAMN40200157 |
| SRA |
SRX23792914 |
