NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM771172 Query DataSets for GSM771172
Status Public on Aug 03, 2011
Title HN08.424N
Sample type RNA
 
Source name Normal
Organism Homo sapiens
Characteristics patient identifier: 4
disease state: squamous cell carcinoma of the tongue
tissue location: tongue
Stage: unknown
grade: unknown
site: margin
site detail: normal
recurrence: no
time.to.recurrence.or.last.follow-up.months: 13.8
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_060508L_SR04_HNO8-424

# 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) [email protected]
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 2.321786167
10001_at 9.385171182
10002_at 2.115190777
10003_at 3.633774601
100048912_at 2.115190777
100049716_at 3.865537677
10004_at 3.2581475
10005_at 7.164133686
10006_at 11.21392612
10007_at 9.130797433
10008_at 2.536400988
100093630_at 11.39615762
10009_at 8.249934359
1000_at 2.496443089
100101467_at 4.210055726
10010_at 9.773207792
100113377_at 2.237920491
100113407_at 5.356287677
10011_at 8.117731612
100124700_at 2.115310088

Total number of rows: 17788

Table truncated, full table size 361 Kbytes.




Supplementary file Size Download File type/resource
GSM771172.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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