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Sample GSM442624 Query DataSets for GSM442624
Status Public on Sep 21, 2009
Title Normal Lung_NL1
Sample type RNA
 
Channel 1
Source name Universal Reference RNA
Organism Homo sapiens
Characteristics sample type: Human Universal Reference RNA (Stratagene)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRizol following manufacturer's instructions
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 (Normal Lung) and incubating in the dark. The reactions were purified with Amersham GFX columns to remove the unincorporated/quenched dyes.
 
Channel 2
Source name Normal Lung Sample 1
Organism Homo sapiens
Characteristics gender: F
% predicted fev1: 107.5
% predicted kco: 85.39
age: 63
pack years: 59
age quit smoking: 62
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRizol following manufacturer's instructions
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 (Normal Lung) and incubating in the dark. The reactions were purified with Amersham GFX columns to remove the unincorporated/quenched dyes.
 
 
Hybridization protocol Amersham hybridization protocol was used
Scan protocol GMS418 confocal scanner was used according to manufacturer’s instructions
Description After the purification samples were combined for hybridization, the labeled cDNAs were co-hybridized to 22K oligo microarrays.
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) 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 50% 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 Aug 19, 2009
Last update date Sep 21, 2009
Contact name Santiyagu Mary Savarimuthu Francis
E-mail(s) ss.francis@uqconnect.edu.au
Phone 07-31394110
Fax 07-31394957
Organization name The University of Queensland
Department School of Medicine
Lab Thoracic Laboratory
Street address Level 1, Clinical Sciences Building, The Prince Charles Hospital, Rode Road
City Brisbane
State/province Queensland
ZIP/Postal code 4032
Country Australia
 
Platform ID GPL3877
Series (1)
GSE17770 Expression Profiling Identifies Genes Involved in Emphysema

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 -0.6917539 0 776 424.5 0 551 467
1.1.1.11 -0.06396842 0 1594 418 0 1498.5 437.5
1.1.1.12 0.27552167 0 5221 475 0 6500 392
1.1.1.13 -0.037531275 0 1295 524 0 1053 455
1.1.1.14 -0.32364592 0 25203 731 0 24569 668
1.1.1.15 -0.35909545 0 6003.5 550 0 5070 576.5
1.1.1.2 -0.663954 0 827.5 423.5 0 531 419
1.1.1.3 -0.2478157 0 6523.5 436.5 0 6047 569
1.1.1.4 -0.5154063 0 7980 482.5 0 6139 481
1.1.1.5 0.4217922 0 712.5 451 0 613 466
1.1.1.6 -0.42034203 0 11678 599.5 0 9970.5 631.5
1.1.1.7 0.8090885 0 876 474 0 920 505.5
1.1.1.8 0.027556434 0 1161 440 0 1032 469.5
1.1.1.9 -0.03348909 0 1529 447 0 1460.5 475
1.1.10.1 -1.3128034 0 1471 449.5 0 798 513.5
1.1.10.10 -0.48754054 0 1380 487 0 897 394
1.1.10.11 -0.18897836 0 5893 510 0 5502 494
1.1.10.12 0.20637126 0 5816.5 549 0 6949 448
1.1.10.13 0.084208906 0 1788.5 516.5 0 1762.5 474.5
1.1.10.14 -1.4694631 0 1609 556 0 805 547

Total number of rows: 21322

Table truncated, full table size 914 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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