|
| Status |
Public on Apr 10, 2024 |
| Title |
Canine cutaneous histiocytoma, group 1 according to Cockerell & Slauson 1979, FFPE, 3 |
| Sample type |
RNA |
| |
|
| Source name |
FFPE tumor tissue, group 1
|
| Organism |
Canis lupus familiaris |
| Characteristics |
dv200: 71.2
pooled sample: no
breed: Terrier
age (years): n/s
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted utilizing the PureLink FFPE Total RNA Isolation Kit (Thermo Fisher Scientific Inc.). After DNase I treatment 150 to 250ng total RNA was used for library construction.
|
| Label |
n/a
|
| Label protocol |
n/a
|
| |
|
| Hybridization protocol |
150 to 250ng of total RNA were hybridized to the nCounter Canine IO Panel XT CodeSets (NanoString Technologies, Inc., Seattle, WA, USA). Hybridized samples were processed following the manufacturer’s protocols (protocol ID: MAN-10023-11, MAN-10056-06) and loaded onto the nCounter MAX Analysis System’s (NanoString) Prep Station for purification and immobilization on sample cartridges.
|
| Scan protocol |
These were transferred to the Digital Analyzer for data collection following the manufacturer’s user manual (protocol ID: MAN-C0035-08).
|
| Description |
n/s
|
| Data processing |
Following the workflow described in the manufacturer’s user manuals (MAN-C0019-08, MAN-C0011-04), the reporter library files (RLF) and reporter code count (RCC) files were imported into the nSolver 4.0 Analysis Software. Quality control and normalization followed default settings. DGE analysis was achieved using the R 3.3.2-based nCounter Advanced Analysis 2.0 plug-in (version 2.0.134) with recommended statistical settings.
Nanostring canine IO standard for normalization: 20220420_AL03_Standard_12.RCC
|
| |
|
| Submission date |
Mar 12, 2024 |
| Last update date |
Apr 10, 2024 |
| Contact name |
Alina Katharina Langenhagen |
| E-mail(s) |
Alina.langenhagen@fu-berlin.de
|
| Organization name |
Freie Universität Berlin
|
| Department |
Department of Veterinary Medicine
|
| Lab |
Institute of Veterinary Pathology
|
| Street address |
Robert-von-Ostertag Straße 15
|
| City |
Berlin |
| ZIP/Postal code |
14163 |
| Country |
Germany |
| |
|
| Platform ID |
GPL32796 |
| Series (1) |
| GSE261395 |
Immuno-Oncologic Profiling by Stage-Dependent Transcriptome and Proteome Analyses of Spontaneously Regressing Canine Cutaneous Histiocytoma [NanoString] |
|
| Relations |
| Reanalyzed by |
GSM8156118 |
