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Sample GSM1001213 Query DataSets for GSM1001213
Status Public on Mar 04, 2015
Title Head and neck Squamous cell carcinomas_OROPHARYNX_46
Sample type RNA
 
Source name Head and neck Squamous cell carcinomas_OROPHARYNX_pretreatmeant_46
Organism Homo sapiens
Characteristics tissue type: head and neck squamous cell carcinoma (HNSCC)
anatomic site: OROPHARYNX
gender: F
hpv status: pos
Treatment protocol All the patients were treated with concurrent chemoradiotherapy. Samples with microscopic tumor or tumor content <60% were excluded from further analysis.
Extracted molecule total RNA
Extraction protocol Guided by H&E stained slides, the region with the highest tumor content was cut from OCT blocks, pulverized using CryoPrep (Covaris, Woburn, MA) and homogenized in a lysis buffer from an AllPrepRNA/DNA/Protein Mini kit (Qiagen, Valencia, CA) or from a RNA/DNA/Protein Purification Kit (Norgen Biotek, Thorold, Canada) using an Ultrasonicator (Covaris, Woburn, MA). DNA, RNA and protein were isolated from each sample using the respective kit and following manufacturer’s protocol. RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). If DNA contamination was seen, RNAs were treated with TURBO DNA-free (Ambion, CA) to remove genomic DNA, and subsequently quantitated using a spectrophotometer. Only RNAs with integrity number (RIN) ≥7.5, a 260/280 ratio ≥1.8 and a 260/230 ratio ≥1.8 (≥1.1 for a few RNAs) were labeled for expression arrays.
Label Cy3
Label protocol Labeling for Agilent 4x44K v2 expression arrays was done using a Quick Amp Labeling Kit one-color according to the manufacturer’s protocol using 200ng of starting material.
 
Hybridization protocol Expression arrays were performed at the Argonne National Laboratory in an ozone-controlled atmosphere.
Scan protocol Expression arrays were performed at the Argonne National Laboratory in an ozone-controlled atmosphere.
Description 8146623
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.3.1. Raw data were background corrected, quantile normalized and log2 transformed.
 
Submission date Sep 11, 2012
Last update date Mar 04, 2015
Contact name Tanguy Seiwert
E-mail(s) tseiwert@medicine.bsd.uchicago.edu
Organization name University of Chicago
Street address 900 E. 57th street
City chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL13497
Series (1)
GSE40774 Integrative genomic analysis identifies clinically relevant subtypes of head and neck cancer characterized by hypoxia, T-cell infiltration, and EMT

Data table header descriptions
ID_REF
VALUE normalized log2 signal intensity

Data table
ID_REF VALUE
A_23_P42935 8.91
A_23_P117082 12.56
A_23_P2683 8.55
A_24_P358131 8.34
A_23_P157316 6.37
A_32_P14850 13.05
A_23_P158596 7.04
A_23_P350107 8.90
A_23_P388190 8.80
A_23_P106544 10.97
A_32_P85539 8.90
A_23_P94998 8.80
A_23_P103905 9.06
A_24_P497186 9.15
A_23_P118536 7.46
A_23_P434289 7.31
A_33_P3326898 7.30
A_24_P67898 10.94
A_24_P28657 8.93
A_33_P3344292 6.79

Total number of rows: 18255

Table truncated, full table size 327 Kbytes.




Supplementary file Size Download File type/resource
GSM1001213_US80900103_252665214270_S01_GE1_107_Sep09_1_4.txt.gz 9.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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