|
Status |
Public on Oct 11, 2024 |
Title |
Trabectedin-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: Trabectedin
|
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 |
Trabectedin-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 |
SAMN40200155 |
SRA |
SRX23792916 |