|
| Status |
Public on Feb 28, 2015 |
| Title |
metastatic 11 |
| Sample type |
RNA |
| |
|
| Source name |
metastatic 11
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary tumor
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ambion RecoverAll
|
| Label |
n/a
|
| Label protocol |
All sample preparations were performed according to the manufacturer’s instructions (NanoString Technologies). Preparation of small RNA samples involves the ligation of a specific DNA tag onto the 3’ end of each mature miRNA. These tags are designed to normalize the Tm’s of the miRNAs as well as to provide a unique identification for each miRNA species in the sample. Following the ligation reaction, excess tags and bridges were removed,
|
| |
|
| Hybridization protocol |
The samples were hybridized with a panel of miRNA:tag-specific nCounter capture and barcoded reporter probes. Hybridization reactions were performed with 5µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 64°C for a minimum of 18 h. Hybridized probes were purified using the nCounter Prep Station (NanoString Technologies) following the manufacturer’s instructions
|
| Scan protocol |
For each assay, a high density scan (600 fields of view) was performed.
|
| Data processing |
We identified approximately 225 miRNAs expressed in these samples and performed statistical analysis for the top 100 expressed miRNAs. Expression data for each sample was normalized to the entire miRNA dataset using the global sum through the nSolver software tool. Paired T-tests compared non-metastatic primary tumors to primary tumors or metastases. A heatmap of the top 100 expressed miRNAs was generated using Cluster 3.0 was able to cluster the majority of metastatic related tumors from non-metastatic cSCCs and normal tissues
|
| |
|
| Submission date |
May 17, 2014 |
| Last update date |
Feb 28, 2015 |
| Contact name |
Amanda Ewart Toland |
| E-mail(s) |
amanda.toland@osumc.edu
|
| Phone |
614-247-8185
|
| Organization name |
The Ohio State University
|
| Department |
MVIMG
|
| Street address |
460 W. 12th Ave
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43026 |
| Country |
USA |
| |
|
| Platform ID |
GPL17537 |
| Series (1) |
| GSE57768 |
MicroRNA Expression in Cutaneous Squamous Cell Carcinoma |
|
