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Sample GSM136009 Query DataSets for GSM136009
Status Public on May 01, 2007
Title Primary Lung Adenocarcinoma Sample_A27
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 A27
Organism Homo sapiens
Characteristics Primary adenocarcinoma 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)
GSE5843 Expression profiling defines a recurrence signature in lung adenocarcinoma

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
1.1.1.1 0.15446007 0 2581 385 0 2534 400.5
1.1.1.2 -0.114614196 0 848 383.5 0 647 436
1.1.1.3 0.9822233 0 4280 382 0 7719 416.5
1.1.1.4 0.33111283 0 4186 400 0 4767 379
1.1.1.5 0.31517905 0 566 371 0 492 412.5
1.1.1.6 0.11016966 0 23484.5 463 0 26475 424
1.1.1.7 2 470 370 2 495 330
1.1.1.8 0.42398155 0 966 385 0 817 334
1.1.1.9 -0.022230135 0 1570 401 0 1313 396
1.1.1.10 -0.50204253 0 600 364 0 390 350
1.1.1.11 0.49987122 0 1336 365 0 1478 378
1.1.1.12 1.236378 0 3038 383 0 6145 385
1.1.1.13 -0.47045892 0 1066.5 422 0 650 401
1.1.1.14 3 33570.5 549.5 3 25400.5 498
1.1.1.15 0.3610872 0 3138.5 432 0 3533 396
1.1.1.16 2 419 377 2 448.5 408
1.1.1.17 2 323 396 2 314 351
1.1.1.18 2 459 363 2 485 365
1.1.1.19 2 392.5 366 2 384.5 352
1.1.1.20 2 315 353 2 513 346

Total number of rows: 23232

Table truncated, full table size 973 Kbytes.




Supplementary data files not provided

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