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Sample GSM5962764 Query DataSets for GSM5962764
Status Public on Apr 02, 2022
Title Study participant 100-905
Sample type RNA
 
Source name Primary p16(+) oropharyngeal squamous cell carcinoma
Organism Homo sapiens
Characteristics age(years): 58
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): 1
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): 3
clin_m_stage(1=m0,2=m1): 1
clin_stage(1=stage i,2=stage ii,3=stage iii,4=stage iv): 2
recurrence(0=no recurrence,1=recurrence): 0
recurrence_time(days): 1089
vital_status(0=alive,1=dead): 0
os_time(days): 1089
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 2426.14
ACVR1C 30.81
ADAM12 1245.02
ADGRE1 29.67
ADM 912.94
ADORA2A 132.38
AKT1 2475.21
ALDOA 17040.06
ALDOC 494.13
ANGPT1 69.61
ANGPT2 92.44
ANGPTL4 118.68
ANLN 2076.94
APC 1546.3
APH1B 78.74
API5 3630.09
APLNR 222.53
APOE 2141.99
APOL6 3602.7
AQP9 209.98

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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