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Sample GSM1363400 Query DataSets for GSM1363400
Status Public on Sep 30, 2014
Title OSCC10N
Sample type RNA
 
Source name OSCC10N
Organism Homo sapiens
Characteristics uid: 19002c8272ab43d1a933cd67be1a7718
filenumber: 5
disease state: late stage OSCC
tissue: surrounding normal margins
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 7.860415461
7911320 8.823022114
7911319 7.520301604
7911318 9.467055332
7911317 11.63371484
7911316 8.785533802
7911315 8.12639499
7911314 10.67233442
7911313 8.665858701
7911311 10.3225869
7911330 7.75420037
7911334 7.546583107
7896743 7.733869559
7911336 12.05261738
7896747 9.487896407
7896749 8.4056628
7911338 12.19357068
7911340 11.04573212
7911342 10.05242832
7911344 10.79378675

Total number of rows: 108342

Table truncated, full table size 2104 Kbytes.




Supplementary file Size Download File type/resource
GSM1363400_OSCC10N.cel.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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