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Sample GSM1363406 Query DataSets for GSM1363406
Status Public on Sep 30, 2014
Title OSCC7T
Sample type RNA
Source name OSCC7T
Organism Homo sapiens
Characteristics uid: b5fa99552c434d42a4335c41fc93608c
filenumber: 11
disease state: late stage OSCC
tissue: tumor
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 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
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
VALUE quantile-normalized expression values

Data table
7911322 7.353650897
7911320 8.569816088
7911319 8.003291039
7911318 9.310673826
7911317 11.2512366
7911316 8.996469111
7911315 8.397891699
7911314 10.80968546
7911313 8.704196398
7911311 9.499017987
7911330 8.233126618
7911334 7.655241957
7896743 8.119086839
7911336 11.11490448
7896747 10.55243437
7896749 7.886564738
7911338 11.78977189
7911340 11.29653464
7911342 10.58204518
7911344 9.104818192

Total number of rows: 108342

Table truncated, full table size 2104 Kbytes.

Supplementary file Size Download File type/resource
GSM1363406_OSCC7T.cel.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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