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Sample GSM135973 Query DataSets for GSM135973
Status Public on May 01, 2007
Title Primary Lung SCC Carcinoma Sample_S3
Sample type RNA
 
Channel 1
Source name Universal Reference RNA
Organism Homo sapiens
Characteristics The reference sample used for this experiment was commercially available Universal Reference RNA (Stratagene)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Tumour sample S3
Organism Homo sapiens
Characteristics Primary SCC carcinoma of the lung. Total RNA extracted from fresh-frozen tissue using Trizol and RNeasy clean-up.
Extracted molecule total RNA
Label Cy5
 
 
Description Synthesis of the labelled first strand cDNA was conducted using Amersham CyScribe Post-Labelling kit with starting material of 20 ug of total RNA. The amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA. Following the hydrolysis reaction, single-stranded cDNA probes were purified using Amersham GFX columns. Dye coupling reactions were performed by mixing the cDNA samples with Amersham Cy3 (reference) or Cy5 (tumour) and incubating in the dark. The reactions were purified with Amersham GFX columns to remove the unincorporated/quenched dyes. After the purification samples were combined for hybridization, the labeled cDNAs were co-hybridized to 22K oligo microarrays. Slides were scanned on GMS418 confocal scanner (Agilent).
Data processing Raw images were imported into Imagene V5.1 (BioDiscovery, CA, USA) to extract pixel intensities and to flag spots with poor/absent signal. The raw background subtracted signal median for each probe was imported into GeneSpring GX V7.3 (Agilent Technologies, Inc., CA, USA) for analysis. Data was normalized (Lowess: per spot and per chip; per chip to the 50th percentile) and probe signals filtered on pixel intensity (for both red and green channels any spots less than 20 units or greater than 65,000 units were excluded) and consistent spot morphology. Only spots flagged present in at least 80% of samples were included. For each probe, the logarithm to the base 2 of the ratio between the intensity in the tumor sample (red) channel and the reference (green) channel was used as the expression value for the probe.
 
Submission date Sep 13, 2006
Last update date Mar 20, 2007
Contact name Jill Everland Larsen
E-mail(s) j.larsen@uq.edu.au
Phone +61731394110
Fax +61731394957
Organization name The Prince Charles Hospital
Department Thoracic Medicine
Lab Thoracic Research Lab
Street address Rode Road, Chermside
City Brisbane
State/province Queensland
ZIP/Postal code 4032
Country Australia
 
Platform ID GPL3877
Series (1)
GSE5828 Gene expression profiling classifies lung squamous cell carcinomas with N1 positive lymph nodes

Data table header descriptions
ID_REF
VALUE Log2 Ratio Cy5/Cy3 Background subtracted, Lowess normalised
CH1_FLAG Cy3 flag (0=good)
CH1_SIG_MED Cy3 signal median
CH1_BKD_MED Cy3 background median
CH2_FLAG Cy5 flag (0=good)
CH2_SIG_MED Cy5 signal median
CH2_BKD_MED Cy5 background median

Data table
ID_REF VALUE CH1_FLAG CH1_SIG_MED CH1_BKD_MED CH2_FLAG CH2_SIG_MED CH2_BKD_MED
1.1.1.10 1.9786361 0 333.5 273 0 192.5 28
1.1.1.11 0.22906758 0 1489 276 0 1413 47
1.1.1.12 0.23365086 0 3279 302 0 3416 91
1.1.1.13 0.6311961 0 1067 320 0 1262.5 137
1.1.1.14 0.071948044 0 22182 453 0 23464 214
1.1.1.15 -0.29918957 0 5300 300 0 4019 127
1.1.1.2 0.07179846 0 641 275 0 398 92
1.1.1.3 0.3170412 0 4759.5 300.5 0 5479 153
1.1.1.4 -0.016815936 0 9828 301 0 9113 56
1.1.1.5 0.5352622 0 578.5 302 0 376 63
1.1.1.6 0.47180405 0 16001 358 0 21655 175
1.1.1.7 -0.83664346 0 836 290 0 379 138
1.1.1.8 0.13226824 0 863 280 0 687 93
1.1.1.9 0.044214956 0 1360 277 0 1155 81
1.1.10.1 0.45955053 0 865 274 0 860 78
1.1.10.10 -0.19577785 0 905 316 0 532 72
1.1.10.11 0.24248078 0 6630.5 317.5 0 7220 90
1.1.10.12 -0.03032043 0 10158 340 0 9357 110
1.1.10.13 0.57262754 0 1199 294 0 1355.5 54
1.1.10.14 0.35533184 0 1905 278 0 2042.5 63.5

Total number of rows: 21322

Table truncated, full table size 908 Kbytes.




Supplementary data files not provided

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