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Sample GSM1363410 Query DataSets for GSM1363410
Status Public on Sep 30, 2014
Title OSCC25T
Sample type RNA
 
Source name OSCC25T
Organism Homo sapiens
Characteristics uid: 62836e2547554dcab7ebf9454a4300fb
filenumber: 15
disease state: late stage OSCC
tissue: tumor
tumor stage: III
Treatment protocol not applicable
Growth protocol Tumor samples and the surrounding normal margins were collected from the oral squamous cell carcinoma (OSCC) patients. The tissues collected were immediately placed in RNA later solution (Qiagen) and further stored at -80⁰C till further use.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the tissues using Qiagen Rneasy mini kit according to manufacturers protocol.
Label biotin
Label protocol labelling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual
 
Hybridization protocol microarrays were hybridized overnight with 5 mg biotin labelled ss-cDNA, and washed in fluidics station wash protocol: MES_EukGE-WS2v5_450
Scan protocol Genechip scanner 3000 7G
Data processing The input files were normalized with full quantile normalization (Irizarry et al 2003). For each input array, for each probe expression value, the array ith percentile probe value was replaced with the average of all array ith percentile points. Next, the 818,005 probes were manipulated into the analysis values as follows. Probes with GC count less than 6 and greater than 17 were excluded from the analysis. Probe scores were then transformed by taking the Base-2 Logarithm of 0 plus the probe score. Background CorrectionExon arrays do not use individual mis-match probes. Background is established from a pool of probes designed for that purpose. Background probes are stratified by CG content and are defined in the HumanGene10ST_antigenomic.bgp file. BGP files can also be downloaded from www.affymetrix.com. Each probe score was corrected for background by subtracting the median expression score of background probes with similar GC content. Probe-set Presence/Absence and the Removal of Non-expressed Probe-setsNon-expressed probes can cause tests for alternative splicing to find false positives (because they cause 'non-parallel' expression patterns across the gene). A probe-set is judged to be expressed above background if for any group: Integral from T0 to Infinity of the standard normal distribution < Significance (0.05) Where: T0 = Sqr(GroupSize) (T - P) / Sqr(Pvar), GroupSize = Number of CEL files in the group, T = Average of probe scores in probe-set, P = Average of Background probes averages of GC content, and Pvar = Sum of Background probe variances / (Number of probes in probe-set)^2,Hence we test that the average of probe-sets in a group is greater than the average expression of background probes of similar gc content as the probe-set probes as the center of background for the probe-set and derive its dispersion from the background probe-set variance.
 
Submission date Apr 05, 2014
Last update date Sep 30, 2014
Contact name sivapriya pavuluri
E-mail(s) pspriyamurthy@gmail.com
Organization name Deakin University
Department School of Medicine
Street address 75, Pigdons Road
City Waurnponds
State/province VIC
ZIP/Postal code 3216
Country Australia
 
Platform ID GPL10739
Series (1)
GSE56532 NORMALvs late stage OSCC

Data table header descriptions
ID_REF
VALUE quantile-normalized expression values

Data table
ID_REF VALUE
7911322 8.764063381
7911320 9.603871519
7911319 9.104820571
7911318 10.17330945
7911317 12.12979323
7911316 9.904681732
7911315 9.205793185
7911314 11.72263023
7911313 9.216951088
7911311 10.74868315
7911330 8.876201199
7911334 7.330555238
7896743 8.341446767
7911336 12.01985633
7896747 10.14774295
7896749 8.798205796
7911338 12.24654307
7911340 11.12990096
7911342 11.23055918
7911344 10.03396394

Total number of rows: 108342

Table truncated, full table size 2104 Kbytes.




Supplementary file Size Download File type/resource
GSM1363410_OSCC25T.cel.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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