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Status
Public on Apr 02, 2022
Title
Study participant 100-162
Sample type
RNA
Source name
Primary p16(+) oropharyngeal squamous cell carcinoma
Organism
Homo sapiens
Characteristics
age(years): 54 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): 2548 vital_status(0=alive,1=dead): 0 os_time(days): 2548 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
6927.58
ACVR1C
138.88
ADAM12
3898.09
ADGRE1
20
ADM
5376.35
ADORA2A
143.59
AKT1
4244.11
ALDOA
18245.21
ALDOC
875.66
ANGPT1
193.02
ANGPT2
581.42
ANGPTL4
473.14
ANLN
800.33
APC
1329.96
APH1B
120.05
API5
4886.73
APLNR
506.09
APOE
6129.6
APOL6
2841.18
AQP9
84.74
Total number of rows: 760 Table truncated, full table size 9 Kbytes .Supplementary data files not provided
Processed data included within Sample table