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Sample GSM5946715 Query DataSets for GSM5946715
Status Public on May 08, 2024
Title melanoma_FFPE_144 [20181219_Karen04_K01_09]
Sample type RNA
 
Source name primary melanoma FFPE tissue
Organism Homo sapiens
Characteristics gender: M
age at diagnosis: 75
cohort: Moffitt
tnm: T3bN0M0
stage at original diagnosis: IIB
ajcc thickness: 3
breslow thickness: 2.2
ulceration: Present
os: 88
pfs: 85
dead or alive at last contact: Dead
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_4_C6003
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) [email protected]
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)
GSE198430 An epigenetic gene signature underlies phenotype switching in early stage melanomas [nanotstring_sample2]
GSE198432 An epigenetic gene signature underlies phenotype switching in early stage melanomas.

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
NM_001029882.2 386
NM_001001655.2 161
NM_021926.3 139
NM_004925.3 9244
NM_000045.3 883
NM_006015.4 358
NM_020732.3 773
NM_005191.3 244
NM_175862.3 94
NM_015259.5 446
NM_001024736.1 1211
NM_024626.2 73
NM_022153.1 449
NM_001202439.1 142
NM_001282556.1 14
NM_004656.2 1016
NM_003658.4 219
NM_013449.3 918
NM_013450.2 456
NM_005180.5 328

Total number of rows: 194

Table truncated, full table size 3 Kbytes.




Supplementary file Size Download File type/resource
GSM5946715_20181219_Karen04_K01_09.RCC.gz 2.7 Kb (ftp)(http) RCC
Processed data included within Sample table

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