|
| Status |
Public on May 08, 2024 |
| Title |
melanoma_FFPE_20 [20171109_Karen1_K09_09] |
| Sample type |
RNA |
| |
|
| Source name |
primary melanoma FFPE tissue
|
| Organism |
Homo sapiens |
| Characteristics |
gender: F
age at diagnosis: 31
cohort: Sinai
tnm: T2aN0M0
stage at original diagnosis: IB
ajcc thickness: 2
breslow thickness: 1.60
ulceration: Absent
os: 1
pfs: NA
dead or alive at last contact: Alive
tag: primary cutaneous melanoma tissue
|
| Treatment protocol |
None
|
| Growth protocol |
This cohort includes human tissue obtained from FFPE (n=205), fresh frozen human tissue (n=24), and human cell lines (n=12).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was obtained from the FFPE human tissue samples using the RecoverAll Total Nucleic Acid Isolation kit. RNA was obtained from the fresh frozen human tissue samples using the Qiagen Rneasy kit. Cell lines were pelleted and RNA was harvested using the Qiagen Rneasy kit.
|
| Label |
customized panel
|
| Label protocol |
Specimens were labeled with decode assignment which was linked to tumor origin.
|
| |
|
| Hybridization protocol |
200 ng RNA was hybridized to a custom NanoString panel code set according to the recommendations of the manufacturer (NanoString Technologies, Inc., Seattle, Washington, USA).
|
| Scan protocol |
Following hybridization, the target-probe complexes were purified and immobilized on the nCounter prep station. Digital counts for each gene-specific target RNA were then acquired on the nCounter detection analyzer and normalized to account for differences in tissue mRNA quantity as well as slight differences in assay efficiency.
|
| Description |
EPI1_3_C5626
|
| Data processing |
The nSolver analysis software version 4.0 (NanoString Technologies) was used for extraction of raw digital counts of expression, checking the quality of the data, normalizing expression values using housekeeping genes, and generating heatmaps.
|
| |
|
| Submission date |
Mar 11, 2022 |
| Last update date |
May 08, 2024 |
| Contact name |
Tiphaine Christiane Martin |
| E-mail(s) |
tiphaine.martin@mssm.edu
|
| Phone |
2128248403
|
| Organization name |
Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute
|
| Department |
Oncological Sciences
|
| Lab |
Parsons
|
| Street address |
1470 Madison Ave
|
| City |
New York |
| State/province |
75459 |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL32055 |
| Series (2) |
| GSE198429 |
An epigenetic gene signature underlies phenotype switching in early stage melanomas [Nanostring_sample1] |
| GSE198432 |
An epigenetic gene signature underlies phenotype switching in early stage melanomas. |
|
