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Sample GSM190830 Query DataSets for GSM190830
Status Public on Aug 01, 2007
Title Stage T1N1 NSCLC 8885065
Sample type genomic
 
Channel 1
Source name NSCLC_Resected
Organism Homo sapiens
Characteristics Gender: Male
Age: 64
Tissue: NSCLC
Histology: SCC
Stage: T1N1
Biomaterial provider VUMC, Amsterdam
Extracted molecule genomic DNA
Extraction protocol DNA isolation protocol available via the microarrays website of VU medisch centrum
Label Cy3
Label protocol DNA labeling protocol available via the microarrays website of VU medisch centrum
 
Channel 2
Source name Female reference DNA
Organism Homo sapiens
Characteristics Pooled DNA from the blood of 10 normal female individuals
Biomaterial provider VUMC, Amsterdam
Extracted molecule genomic DNA
Extraction protocol DNA isolation protocol available via the microarrays website of VU medisch centrum
Label Cy5
Label protocol DNA labeling protocol available via the microarrays website of VU medisch centrum
 
 
Hybridization protocol Hybridization protocol available via the microarrays website of VU medisch centrum
Scan protocol Microarray Scanner G2505B (Agilent Technologies), default settings
Description For preparation of the hybridization mixture 50 µl of Cy3-labeled test DNA, 50 µl of Cy5-labeled reference DNA and 10 µg Human Cot-1 DNA (Invitrogen) were mixed and precipitated using 0.1 volume of 3 M NaAc pH 5.2 and 2.5 volume of ice-cold absolute ethanol. After mixing by inversion the DNA was collected by centrifugation for 30 min at 20,000 g and 4°C, the supernatant aspirated and the pellet air-dried for approximately 5-10 min. The pellet was then dissolved in 13 µl Yeast tRNA (100 µg/µl, Invitrogen) and 26 µl 20% SDS taking care to prevent foam formation. After incubating at room temperature for 15 min 91 µl of Master mix (14.3 % (w/v) dextran sulphate (USB), 50% (v/v) formamide (Invitrogen), 2.9 X SSC pH 7.0 (Sigma)) was added and gently mixed. The hybridization solution was then incubated at 73°C for 10 min to denature the DNA and subsequently at 37°C for 60 min to allow the Cot-1 DNA to block repetitive sequences. Hybridization and washing was done automatically using a GeneTAC/HybArray12 hybstation (Genomic Solutions / Perkin Elmer). Hybridisation was for 38 h at 37°C. Subsequently slides were washed 6 cycles (flow for 10 s, hold for 20 s) with 50% (v/v) formamide, 2X SSC, 2 cycles with phosphate-buffer (0.1 M Na2HPO4/NaH2PO4, pH 8.0, 0.1% (v/v) Igepal CA630 (Sigma)), 2 cycles with 0.2 X SSC (Sigma) and 2 cycles with 0.1 X SSC. Slides were then taken out of the hybstation and briefly rinsed in 0.01 X SSC, dried by centrifugation for 3 min at 1000 g and scanned using a Microarray Scanner G2505B (Agilent Technologies).
Data processing Spot analysis and quality control was fully automated using BlueFuse version 3.1 (BlueGnome, Cambridge, UK). Spots were excluded when the quality flag was less than 1 or the Confidence value less than 0.1. Oligonucleotides from the human library were mapped to the human genome build NCBI35. Oligonucleotide sequences and mapping have been made accessible by Compugen (San Jose, CA, USA) and The Sanger Institute (Hinxton, Cambridge, UK), respectively, via www.ensembl.org. A unique chromosomal position was identified for 26845 of 28830 oligonucleotides in the human library. Oligonucleotides were excluded when they mapped to more than one position in the genome or showed one or more mismatches with regard to the current build. Log2ratios of spots that were not excluded after quality flagging and mapping were normalized to their mode value. Weighted moving average values were then calculated using a triangular function and a window of 250 kb as described (Barrett,M.T. et al. (2004) Proc.Natl.Acad.Sci.U.S.A, 101, 17765-17770.).
 
Submission date May 22, 2007
Last update date Aug 01, 2007
Contact name Daoud Sie
E-mail(s) d.sie@vumc.nl
Phone +31 20 4442428
Organization name Vrije Universiteit Medical Center
Department Pathology
Lab Microarray Core Facility
Street address De Boelelaan 1117
City Amsterdam
ZIP/Postal code 1081 HV
Country Netherlands
 
Platform ID GPL2827
Series (1)
GSE7878 Integrated genome-wide analysis of gene dosage and gene expression in Non Small Cell Lung Cancer

Data table header descriptions
ID_REF
AMPCH1 Total signal in channel 1 (Cy3)
AMPCH2 Total signal in channel 2 (Cy5)
LOG2RATIO CH1/CH2 Log, base 2, of the ratio of total signal in channel 1 divided by total signal in channel 2
CONFIDENCE The Confidence Estimate in the calculated ratio, between 0 and 1, calculated by BlueFuse
QUALITY A flag to highlight spots that suffer from poor printing and other experimental artefacts (1 acceptable; 0 not acceptable), estimated by BlueFuse
VALUE Mode normalized value of the log2ratio, replicates are fused by BlueFuse, features with confidenc < 0.1 or quality 0 are excluded
MOVING_AVERAGE weighted moving average with a window of 250 kb

Data table
ID_REF AMPCH1 AMPCH2 LOG2RATIO CH1/CH2 CONFIDENCE QUALITY VALUE MOVING_AVERAGE
1 361.27 521.985 -0.531 0.95 1 -0.253 -0.0255
2 163.564 209.192 -0.355 0.92 1 -0.077 0.040833333
3 190.27 232.721 -0.291 0.93 1 -0.013 0.049333333
4 862.518 1094.109 -0.343 0.97 1 -0.065 0.187
5 1386.184 1678.3 -0.276 0.98 1 0.002 0.184166667
6 703.336 852.589 -0.278 0.98 1 0 -0.0115
7 185.046 184.009 0.008 0.92 1 0.286 0.294
8 619.16 776.689 -0.327 0.95 1 -0.049 -0.049833333
9 114.577 152 -0.408 0.86 1 -0.13 0.2205
10 218.207 285.976 -0.39 0.94 1 -0.112 0.060666667
11 191.43 254.042 -0.408 0.92 1 -0.13 0.144833333
12 397.855 480.395 -0.272 0.93 1 0.006 0.1055
13 182.123 223.248 -0.294 0.92 1 -0.016 0.1145
14 251.273 218.591 0.201 0.93 1 0.479 0.392
15 244.499 289.173 -0.242 0.95 1 0.036 0.077333333
16 192.125 222.984 -0.215 0.92 1 0.063 0.371
17 239.015 274.768 -0.201 0.95 1 0.077 -0.02
18 232.648 285.264 -0.294 0.94 1 -0.016 0.380333333
19 141.892 191.56 -0.433 0.89 1 -0.155 0.203166667
20 201.785 170.486 0.243 0.91 1 0.521 0.514

Total number of rows: 30000

Table truncated, full table size 1415 Kbytes.




Supplementary file Size Download File type/resource
GSM190830.xls.gz 2.7 Mb (ftp)(http) XLS
Processed data included within Sample table

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