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Sample GSM529615 Query DataSets for GSM529615
Status Public on May 28, 2010
Title Primary Lung Adenocarcinoma_Sample_A68
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 A68, ARLC-AC
Organism Homo sapiens
Characteristics tissue: primary lung adenocarcinoma
lung cancer type: asbestos-related lung cancer-adenocarcinoma (ARLC-AC)
gender: male
age (yrs): 70.9
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_A68
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 Mar 31, 2010
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 (1)
GSE20875 ADAM-28: A potential oncogene involved in asbestos-related lung adenocarcinomas

Data table header descriptions
ID_REF
VALUE Log2 Cy5/Cy3 ratio (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 0.284967 0 6845 86.5 0 8333.5 132
1.1.1.2 0.5007468 0 372 70 0 385 118
1.1.1.3 0.17543897 0 4331 61 0 4715 114
1.1.1.4 -0.10671309 0 4507.5 58.5 0 4023 103
1.1.1.5 0.27214965 0 346 61 0 262 57
1.1.1.6 3 23571 103 3 21955 115
1.1.1.7 -0.57553536 0 440 80 0 218 85
1.1.1.8 -0.1371572 0 762 77 0 523 60
1.1.1.9 0.28609425 0 1289 62 0 1346 54
1.1.1.10 0.35234123 0 173 63 0 145 79
1.1.1.11 0.25427502 0 1362 71 0 1386.5 54
1.1.1.12 0.5474114 0 2578 67 0 3410 40
1.1.1.13 0.18996365 0 951.5 101.5 0 921 112
1.1.1.14 3 47403 237 3 36292 243
1.1.1.15 0.12945524 0 3115 112 0 3120.5 97.5
1.1.1.16 2 77 82 2 37 75
1.1.1.17 2 58 56 2 89.5 64
1.1.1.18 2 125 50 2 81 26
1.1.1.19 2 78 56 2 76 14
1.1.1.20 2 70 56 2 113 30

Total number of rows: 23232

Table truncated, full table size 941 Kbytes.




Supplementary file Size Download File type/resource
GSM529615_Cy3.txt.gz 4.0 Mb (ftp)(http) TXT
GSM529615_Cy5.txt.gz 3.9 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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