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Sample GSM1338999 Query DataSets for GSM1338999
Status Public on Mar 05, 2014
Title Analysis 3: HPV Negative - Biological replicate 3
Sample type RNA
 
Source name HPV Negative - Oropharyngeal squamous cell carcinoma
Organism Homo sapiens
Characteristics gender: Male
race: European American
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from fresh frozen tumor samples using a miniaturized mortar and pestle system (CryoGrinder™, CryoCooler™, OPS diagnostics LLC) and TRIzol® Reagent (Ambion®, by Life Technologies).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.
 
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >8.6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray (G4858A-039494) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immersed in acetonitrile and dried immediately by slowly removing the slide.
Scan protocol Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green at 20 bit).
Description re-analysis of US10130359_253949410163_S01_GE1_107_Sep09_1_3 sample in analysis 1, 2, 4, 6, 8
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Data was uploaded into Genespring version 11.5.1 where it was log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filted by flags in a way that at least 75% of the samples in any of the experimental groups had DETECTED flags. Then, differentially expressed genes were determined.
 
Submission date Mar 04, 2014
Last update date Apr 23, 2018
Contact name Diego Altomare
Organization name University of South Carolina
Department Department of Drug Discovery and Biomedical Sciences
Lab Functional Genomics Core
Street address 715 Sumter Street, Room 617
City Columbia
State/province SC
ZIP/Postal code 29208
Country USA
 
Platform ID GPL17077
Series (2)
GSE55544 Gene expression profiling of European American HPV-active, HPV-inactive and HPV-negative oral and oropharyngeal cancers
GSE55550 Gene expression profiles of oral and oropharyngeal cancers from European American and African American patients
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE Normalized signal intensity (Background corrected, log2 transformed, quantile normalized and base line transformed using the median of all samples).

Data table
ID_REF VALUE
GE_BrightCorner -0.42783165
DarkCorner -0.14510155
A_23_P117082 -0.20783424
A_33_P3246448 -0.41631365
A_33_P3318220 -0.03093481
A_33_P3236322 -0.61960196
A_33_P3319925 0.4108057
A_21_P0000509 -2.4627256
A_21_P0000744 -0.19589615
A_24_P215804 -0.016386986
A_23_P110167 0
A_33_P3211513 -0.39230728
A_23_P103349 -0.038375616
A_32_P61480 -0.19153476
A_33_P3788124 -0.051707268
A_33_P3414202 0.21549034
A_33_P3316686 0.6067343
A_33_P3300975 1.6271639
A_33_P3263061 0.12563896
A_33_P3261373 -0.056872606

Total number of rows: 50739

Table truncated, full table size 1205 Kbytes.




Supplementary file Size Download File type/resource
GSM1338999_US10130359_253949410163_S01_GE1_107_Sep09_1_3.txt.gz 3.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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