|
| Status |
Public on Sep 12, 2023 |
| Title |
T342 [HA_014] |
| Sample type |
SRA |
| |
|
| Source name |
mammary carcinoma
|
| Organism |
Canis lupus familiaris |
| Characteristics |
cell type: mammary carcinoma
treatment: nanoparticle
time: P6-13
|
| Treatment protocol |
The largest tumor in each patient was the target tumor (injected) with eCPMV immunotherapy. In enrolled patients, a pretreatment incisional biopsy of the target injected tumor was taken before eCPMV immunotherapy, followed by intratumoral eCPMV injection immediately after obtaining the tumor biopsy sample. Two intratumoral doses of eCPMV immunotherapy were administered, the first on day 0 (D0) and the second between days six and nine (D6-D9; DTx2), followed by surgery on D12-D17 (DSx) at which time the injected tumor was resected and a surgical biopsy was collected for histopathology and research studies.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Snap-frozen tumor samples were used for rna isolation. RNA was extracted using the Rneasy Mini Kit (Qiagen, Redwood City, CA) after homogenization by beating with 2mm stainless steel beads in Qiagen RLT buffer.
RNA-seq libraries were prepared using the Lexogen QuantSeq Rev kit following manufacturer's protocols and sequencing as single-end, 100bp reads on a NextSeq2000 instrument.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
FastQC was used for quality control of raw sequences
Trimming of adapter sequences and poly-A tails was performed with cutadapt. Trimmed reads were aligned to the Canis lupus familiaris genome (RefSeq accession: GCF_000002285.5) using STAR.
Raw counts were generated for each gene using combat (v.3.42.0). Expression levels for each transcript were normalized using DESeq2's median of ratios. Differential gene expression analysis was conducted using the DESeq2 package.
Supplementary files format and content: comma separated value file includes counts for each sample
Assembly: canFam6
|
| |
|
| Submission date |
Sep 07, 2023 |
| Last update date |
Sep 12, 2023 |
| Contact name |
Hugo Arias-Pulido |
| E-mail(s) |
hugo.ariaspulido@dartmouth.edu
|
| Organization name |
Geisel School of Medicine at Dartmouth
|
| Department |
Department of Microbiology and Immunology
|
| Street address |
621 Rubin Building - HB 7936 1 Medical Center Drive
|
| City |
Hanover |
| State/province |
NH |
| ZIP/Postal code |
03756 |
| Country |
USA |
| |
|
| Platform ID |
GPL33053 |
| Series (1) |
| GSE242689 |
Neoadjuvant intratumoral immunotherapy with cowpea mosaic virus induces local and systemic antitumor efficacy in canine mammary cancer patients. |
|
| Relations |
| BioSample |
SAMN37319527 |
| SRA |
SRX21666914 |
