|
| Status |
Public on Sep 24, 2022 |
| Title |
Patient 18 |
| Sample type |
RNA |
| |
|
| Source name |
tumor
|
| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from archived frozen and FFPE tumor and normal tissues using Qiagen RNeasy and Qiagen RNeasy FFPE kits, respectively. For the FFPE samples, five to seven tissue sections (5-10 µm thick) were cut from each block and pooled for RNA extraction. RNA was extracted from flash-frozen lymph node tumor tissues using the RNeasy Plus Mini Kit (QIAGEN) following manufacturer protocol. Depending on starting material, samples were eluted in 30-50uL and were initially checked for quantity and purity on a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher) prior to being stored at -80c until further processing. Samples were additionally quantity and quality checked using the RNA High Sensitivity assays on the Qubit 2.0 Fluorometer (Invitrogen/LifeTechnologies) and 5200 Fragment Analyzer Automated CE System (Agilent), respectively.
|
| Label |
n.a.
|
| Label protocol |
Depending on RNA qualities, up to 600ng total RNA was used in a multiplexed probeset hybridization reaction following manufacturer protocol
|
| |
|
| Hybridization protocol |
Sequence specific flurorescent reporter probes and biotinlyated capture probes were hybridized to target nucleic acid transcript sequences overnight at 65c for 19 h, followed by a a series of automated washes and immobilization onto a strepavidin lined cartridge for data collection
|
| Scan protocol |
Digital images from the cartridges were obtained over 4 h using the nCounter Digital Analyzer (CCD camera and microscope objective lens) using 555 FOV data resolution. Digital counts were tabulated and exported as comma separated values (CSV).
|
| Data processing |
Raw count data underwent positive contorl and housekeeping gene normalization and normalization quality control using the nSolver software.
|
| |
|
| Submission date |
Sep 19, 2022 |
| Last update date |
Sep 24, 2022 |
| Contact name |
Daniel Regan |
| Organization name |
Colorado State University
|
| Street address |
1678 Campus Delivery
|
| City |
Fort Collins |
| ZIP/Postal code |
80523 |
| Country |
USA |
| |
|
| Platform ID |
GPL32678 |
| Series (1) |
| GSE213726 |
Canine head and neck cancer as a spontaneous, translational model for radio-immunology research |
|
