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Sample GSM767199 Query DataSets for GSM767199
Status Public on Oct 10, 2012
Title HNSCC_primary_9005359
Sample type RNA
 
Channel 1
Source name HNSCC_primary_9005359
Organism Homo sapiens
Characteristics gender: male
tissue: head-neck
tumor type: HNSCC
age: 45
location: oral cavity
ct: 1
cn (clinical n-status = lymph node metastasis status): 0
pt: 1
pn (pathological n-status = lymph node metastasis status): 1
grade: 1
hpv: 0
Extracted molecule total RNA
Extraction protocol RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
Sample reference protocol: A reference sample was made by processing of the Universal Human Reference cell line (Stratagene) similarly as the test samples.
Label Cy3
Label protocol Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf] Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0 Last Updated: 2/2006 Number of Pages: 70
 
Channel 2
Source name UHR
Organism Homo sapiens
Characteristics sample type: Stratagene Universal human reference cell line (UHR)
Extracted molecule total RNA
Extraction protocol RNA isolation. We used 2-5 sections of 20-µm thickness for total RNA isolation. Total RNA was isolated with Trizol, and finally dissolved in RNase-free H2O and treated with DNase using the Qiagen RNase-free DNase kit and RNeasy spin columns.
Sample reference protocol: A reference sample was made by processing of the Universal Human Reference cell line (Stratagene) similarly as the test samples.
Label Cy5
Label protocol Low Input RNA Fluorescent Linear Amplification. Agilent's recommended procedures for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis 1). Convert mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT. 2) amplify sample using T7 RNA Polymerase [http://www.chem.agilent.com/temp/rad6D82C/00056953.pdf] Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0 Last Updated: 2/2006 Number of Pages: 70
 
 
Hybridization protocol Agilent recommended procedure for the preparation and labeling of complex biological targets and hybridization, washing, scanning, and feature extraction of Agilent 60-mer oligonucleotide microarrays for array-based two-color gene expression analysis. Publication Number: G4140-90050 V4.0 Last Updated: 2/2006 Number of Pages: 70
Scan protocol Scanned on an Agilent G2565AA scanner
Data processing Background subtracted data for the Cy5 (reference) and Cy3 (sample) channel were obtained using Agilent Feature Extraction software (version 9.5) based on MedianSignal calls. Lowess-normalization.
 
Submission date Jul 26, 2011
Last update date Oct 10, 2012
Contact name Paul Roepman
Organization name Agendia
Street address Science Park 406
City Amsterdam
ZIP/Postal code 1098 XH
Country Netherlands
 
Platform ID GPL13953
Series (1)
GSE30788 Validation of an expression signature for lymph node metastasis detection in oral cavity squamous cell carcinoma

Data table header descriptions
ID_REF
VALUE lowess-normalized, log2 (Cy3/Cy5) ratio

Data table
ID_REF VALUE
Agendia_HN_dedicated_probe_1 -0.3978
Agendia_HN_dedicated_probe_2 0.7028
Agendia_HN_dedicated_probe_3 -0.2482
Agendia_HN_dedicated_probe_4 -4.8263
Agendia_HN_dedicated_probe_5 -1.3855
Agendia_HN_dedicated_probe_6 -1.5741
Agendia_HN_dedicated_probe_7 1.0293
Agendia_HN_dedicated_probe_8 -0.034
Agendia_HN_dedicated_probe_9 -0.4953
Agendia_HN_dedicated_probe_10 -0.3523
Agendia_HN_dedicated_probe_11 -1.411
Agendia_HN_dedicated_probe_12 0.6738
Agendia_HN_dedicated_probe_13 -0.2191
Agendia_HN_dedicated_probe_14 -0.03
Agendia_HN_dedicated_probe_15 0.7638
Agendia_HN_dedicated_probe_16 -0.2488
Agendia_HN_dedicated_probe_17 -4.717
Agendia_HN_dedicated_probe_18 0.3311
Agendia_HN_dedicated_probe_19 -1.1617
Agendia_HN_dedicated_probe_20 0.9895

Total number of rows: 4096

Table truncated, full table size 156 Kbytes.




Supplementary file Size Download File type/resource
GSM767199_9005359.txt.gz 28.9 Kb (ftp)(http) TXT
Processed data included within Sample table

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