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Sample GSM1363399 Query DataSets for GSM1363399
Status Public on Sep 30, 2014
Title OSCC9N
Sample type RNA
 
Source name OSCC9N
Organism Homo sapiens
Characteristics uid: 6e7a5b24023f410194134c2911138d1a
filenumber: 4
disease state: late stage OSCC
tissue: surrounding normal margins
tumor stage: IV
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 7.965151063
7911320 8.853541081
7911319 6.729072072
7911318 8.548561779
7911317 10.60416832
7911316 8.011831233
7911315 8.09659454
7911314 9.985695593
7911313 7.808302328
7911311 9.128212571
7911330 7.506979107
7911334 7.767503498
7896743 7.229989133
7911336 11.49532105
7896747 9.444801939
7896749 7.224447252
7911338 11.87357278
7911340 11.67505712
7911342 11.3224336
7911344 10.32930931

Total number of rows: 108342

Table truncated, full table size 2104 Kbytes.




Supplementary file Size Download File type/resource
GSM1363399_OSCC9N.cel.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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