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Status
Public on Apr 02, 2022
Title
Study participant 100-1164
Sample type
RNA
Source name
Primary p16(+) oropharyngeal squamous cell carcinoma
Organism
Homo sapiens
Characteristics
age(years): 60 sex (1=male,2=female): 2 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): 2 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): 539 vital_status(0=alive,1=dead): 0 os_time(days): 539 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
9606.58
ACVR1C
40.07
ADAM12
919.04
ADGRE1
20
ADM
470.51
ADORA2A
301.17
AKT1
3789.89
ALDOA
14703.28
ALDOC
557.11
ANGPT1
95.65
ANGPT2
85.31
ANGPTL4
209.4
ANLN
827.26
APC
1623.5
APH1B
250.76
API5
3266.39
APLNR
138.31
APOE
18873.2
APOL6
4339.25
AQP9
125.38
Total number of rows: 760 Table truncated, full table size 9 Kbytes .Supplementary data files not provided
Processed data included within Sample table