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Sample GSM771227 Query DataSets for GSM771227
Status Public on Aug 03, 2011
Title HN04.137N
Sample type RNA
 
Source name Normal
Organism Homo sapiens
Characteristics patient identifier: 18
disease state: squamous cell carcinoma of the tongue
tissue location: tongue
Stage: IV
grade: invasive mod diff
site: margin
site detail: normal
recurrence: yes
time.to.recurrence.or.last.follow-up.months: 2.47
site.of.recurrence: regional and distant
outcome: DOD
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_091108_SR25_HN05-137N

# 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 3.068449862
10001_at 8.976807398
10002_at 2.115190777
10003_at 2.450607425
100048912_at 2.115190777
100049716_at 3.865537677
10004_at 3.982617193
10005_at 7.144301242
10006_at 11.08541633
10007_at 9.426190475
10008_at 2.931255606
100093630_at 10.43826612
10009_at 8.129185021
1000_at 3.044117704
100101467_at 4.162998812
10010_at 9.800134298
100113377_at 2.316233236
100113407_at 6.478969725
10011_at 9.049199975
100124700_at 2.115190777

Total number of rows: 17788

Table truncated, full table size 361 Kbytes.




Supplementary file Size Download File type/resource
GSM771227.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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