NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM136011 Query DataSets for GSM136011
Status Public on May 01, 2007
Title Primary Lung Adenocarcinoma Sample_A29
Sample type RNA
 
Channel 1
Source name Universal Reference RNA
Organism Homo sapiens
Characteristics cell line: pool of 10 cell lines
sample type: reference
Extracted molecule total RNA
Extraction protocol The Universal Reference RNA was commercially available (Stratagene).
Label Cy3
Label protocol 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.
 
Channel 2
Source name Tumour sample A29, NARLC-AC
Organism Homo sapiens
Characteristics tissue: primary lung adenocarcinoma
lung cancer type: non-asbestos-related lung cancer-adenocarcinoma (NARLC-AC)
gender: female
age (yrs): 47.3
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from fresh-frozen tissue using Trizol (Invitrogen) and RNeasy (Qiagen) clean-up.
Label Cy5
Label protocol 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.
 
 
Hybridization protocol After the purification, the samples were combined for hybridization. The labeled cDNAs were co-hybridized to 22K oligo microarrays.
Scan protocol Slides were scanned on a GMS418 confocal scanner (Agilent).
Description Sample_A29
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 31, 2010
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 (2)
GSE5843 Expression profiling defines a recurrence signature in lung adenocarcinoma
GSE20875 ADAM-28: A potential oncogene involved in asbestos-related lung adenocarcinomas

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 0.22617462 0 6307 383 0 6670 347
1.1.1.2 0.5244637 0 642 358 0 623 363
1.1.1.3 0.10262425 0 4798 399 0 4739 415
1.1.1.4 0.1956205 0 4354.5 378.5 0 4570 406
1.1.1.5 -0.0891215 0 792 374 0 632 376
1.1.1.6 0.000536 0 21855 390 0 20695 387
1.1.1.7 1.7377081 0 461.5 354 0 597 379.5
1.1.1.8 -0.10474318 0 1624.5 371 0 1458 385
1.1.1.9 0.06748561 0 3158 366 0 3031 368
1.1.1.10 -0.13974571 0 609 386 0 433 334
1.1.1.11 -0.09012631 0 1719 394 0 1572 427
1.1.1.12 0.057597537 0 2206 367 0 2128 367
1.1.1.13 0.17776676 0 1556 382 0 1632 407
1.1.1.14 0.064628094 0 32342.5 379.5 0 33648 446.5
1.1.1.15 -0.009619696 0 3307 350 0 3034 363
1.1.1.16 2 321 367 2 391 348
1.1.1.17 2 404 349 2 435 340
1.1.1.18 2 427 340 2 369 308
1.1.1.19 2 415 342 2 236 267
1.1.1.20 2 331 340 2 351 350

Total number of rows: 23232

Table truncated, full table size 976 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap