NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM771192 Query DataSets for GSM771192
Status Public on Aug 03, 2011
Title HN05.187LP
Sample type RNA
 
Source name Left 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: left 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_SR11_HNO5 187LP

# 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 8.757131517
10002_at 2.115190777
10003_at 3.44886045
100048912_at 2.115190777
100049716_at 3.959666385
10004_at 3.597858588
10005_at 6.556954615
10006_at 10.69731236
10007_at 9.55801533
10008_at 2.536400988
100093630_at 10.44925426
10009_at 7.873642043
1000_at 3.044117704
100101467_at 3.35176676
10010_at 10.1111518
100113377_at 2.232077049
100113407_at 6.024401374
10011_at 8.875882491
100124700_at 2.115310088

Total number of rows: 17788

Table truncated, full table size 361 Kbytes.




Supplementary file Size Download File type/resource
GSM771192.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap