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Sample GSM771194 Query DataSets for GSM771194
Status Public on Aug 03, 2011
Title HN05.190P
Sample type RNA
 
Source name Posterior margin
Organism Homo sapiens
Characteristics patient identifier: 9
disease state: squamous cell carcinoma of the tongue
tissue location: upper alveolus
Stage: IV
grade: keratinizing mod diff
site: margin
site detail: posterior margin
recurrence: no
time.to.recurrence.or.last.follow-up.months: 19.63
site.of.recurrence: NA
outcome: ANED
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from all tissues using Trizol reagent (Life Technologies, Inc., Burlington, ON, Canada), followed by purification using the Qiagen RNeasy kit/DNase RNase-free set (Qiagen, Valencia, CA, USA), according to manufacturer’s instructions. RNA was quantified by spectrophotometry and its quality was assessed using the 2100 Bioanalyzer (Firmware v.A.01.16, Agilent Technologies, Canada). All samples were of sufficient quantity and quality for arrays and quantitative real-time PCR (QRT-PCR) analyses.
Label biotin
Label protocol Amplification and biotin labeling of antisense cRNA was performed using the Enzo BioArray High YieldTM RNA transcript labeling kit (Enzo Diagnostics, Farmingdale, NY, USA), according to the manufacturer’s instructions.
 
Hybridization protocol Labeling and hybridization to arrays were performed by The Centre for Applied Genomics, Medical and Related Sciences Centre (MaRS), Toronto, ON, Canada, using standard Affymetrix procedures.
Scan protocol Microarray slides were scanned using the GeneArray 2500 scanner (Agilent Technologies).
Description U133Plus2_073008L_SR13_HNO5 190P

# outcome: AWD (alive with disease); ANED (alive, no evidence of disease); DOD (dead of disease); DOC (dead of other causes).
Data processing Data were processed using the BrainArray Entrez-gene centric alternative CDF, with GC-RMA background correction and normalization.
 
Submission date Aug 02, 2011
Last update date Aug 03, 2011
Contact name Levi Waldron
E-mail(s) lwaldron.research@gmail.com
Organization name Harvard School of Publich Health
Department Biostatistics
Street address 655 Huntington Avenue
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL10526
Series (1)
GSE31056 A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence

Data table header descriptions
ID_REF
VALUE Log2 GC-RMA signal using Entrez-gene centered alternative chip definition file

Data table
ID_REF VALUE
10000_at 2.29242561
10001_at 7.850512102
10002_at 2.115190777
10003_at 5.060480825
100048912_at 2.115190777
100049716_at 4.999905726
10004_at 3.101465382
10005_at 7.403434802
10006_at 10.0523719
10007_at 8.807594556
10008_at 2.872149973
100093630_at 12.04859404
10009_at 8.829950924
1000_at 3.044117704
100101467_at 4.704264994
10010_at 9.223900896
100113377_at 2.856753866
100113407_at 5.728717811
10011_at 9.73141792
100124700_at 2.71494127

Total number of rows: 17788

Table truncated, full table size 361 Kbytes.




Supplementary file Size Download File type/resource
GSM771194.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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