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Sample GSM5962758 Query DataSets for GSM5962758
Status Public on Apr 02, 2022
Title Study participant 100-378
Sample type RNA
 
Source name Primary p16(+) oropharyngeal squamous cell carcinoma
Organism Homo sapiens
Characteristics age(years): 79
sex (1=male,2=female): 1
race (1=white,2=asian): 1
tobacco (1=current,2=former,3=never): 2
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): 6
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): 3
recurrence(0=no recurrence,1=recurrence): 1
recurrence_time(days): 312
vital_status(0=alive,1=dead): 0
os_time(days): 336
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 5863.13
ACVR1C 66.46
ADAM12 607.97
ADGRE1 20
ADM 1758.69
ADORA2A 153.84
AKT1 5450.84
ALDOA 36197.84
ALDOC 1313.17
ANGPT1 83.69
ANGPT2 428.29
ANGPTL4 594.44
ANLN 1800.54
APC 1518.7
APH1B 139.07
API5 3729.07
APLNR 190.76
APOE 3203.55
APOL6 3309.4
AQP9 150.15

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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