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Sample GSM5962732 Query DataSets for GSM5962732
Status Public on Apr 02, 2022
Title Study participant 100-1026
Sample type RNA
 
Source name Primary p16(+) oropharyngeal squamous cell carcinoma
Organism Homo sapiens
Characteristics age(years): 66
sex (1=male,2=female): 1
race (1=white,2=asian): 1
tobacco (1=current,2=former,3=never): 3
subsite(1=tonsils and pillars,2=base of tongue,3=pharyngeal overlapping): 2
clin_t_stage(1=t0,2=t1,3=t2,4=t3,5=t4a,6=t4b): 3
clin_n_stage(1=n0,2=n1,3=n2,4=n3): 2
clin_m_stage(1=m0,2=m1): 1
clin_stage(1=stage i,2=stage ii,3=stage iii,4=stage iv): 1
recurrence(0=no recurrence,1=recurrence): 0
recurrence_time(days): 427
vital_status(0=alive,1=dead): 1
os_time(days): 427
disease state: human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma (OPSCC)
tissue: HPV(+) OPSCC tumor
Growth protocol NA
Extracted molecule total RNA
Extraction protocol RNA was extracted from samples using QIAGEN RNeasy kits
Label n/a
Label protocol Hybridized transcripts were purified and immobilized on a sample cartridge
 
Hybridization protocol Transcripts were hybridized to a panel of 770 probes (Nanostring IO360)
Scan protocol Counts of hybridized transcripts were read using the nCounter platform
Data processing Raw counts were normalized with the nSolver software (4.0) package using the geometric mean of both positive control probes and housekeeping probes. A background threshold count was set to 20.
 
Submission date Mar 20, 2022
Last update date Apr 02, 2022
Contact name Jose P Zevallos
E-mail(s) jpzevallos@wustl.edu
Organization name Washington University School of Medicine
Department Otolaryngology - Head and Neck Surgery
Street address 660 South Euclid Avenue, Campus Box 8115
City St Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL32069
Series (1)
GSE199029 Integrative genome analysis reveals low T cell infiltration as the primary feature of tobacco use in HPV(+) oropharyngeal cancer

Data table header descriptions
ID_REF
VALUE Normalized hybridization counts

Data table
ID_REF VALUE
A2M 4486.19
ACVR1C 172.86
ADAM12 406.87
ADGRE1 20
ADM 691.44
ADORA2A 90.51
AKT1 2132.21
ALDOA 17207.67
ALDOC 948.28
ANGPT1 61.97
ANGPT2 1188
ANGPTL4 1251.6
ANLN 1891.67
APC 2299.36
APH1B 110.08
API5 4945.25
APLNR 63.6
APOE 2844.84
APOL6 869.19
AQP9 94.58

Total number of rows: 760

Table truncated, full table size 9 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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