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Sample GSM245004 Query DataSets for GSM245004
Status Public on Apr 01, 2008
Title D5_4(L-i)H210_52
Sample type RNA
 
Source name laser capture microdissected colorectal tissue; PATIENT: D5; HISTOLOGY: Tumor; MUTATION: APC
Organism Homo sapiens
Characteristics ARRAY: H210_52
PATIENT: D5
HISTOLOGY: Tumor
MUTATION: APC
Extracted molecule total RNA
Extraction protocol As described at Cardoso J, Molenaar L, de Menezes RX, van Leerdam M, Rosenberg C, Moslein G, Sampson J, Morreau H, Boer JM, Fodde R: Chromosomal instability in MYH- and APC-mutant adenomatous polyps, Cancer Res 2006, 66:2514-2519.
Label Cy5
Label protocol Each total RNA microdissected sample that passed the quality controls was linearly amplified with two rounds of amplification using the MessageAmp kit (Ambion, Huntingdon, UK), according to manufacturer’s protocol. One µg aliquots of target and reference aRNA were labeled with Cy5-dUTP and Cy3-dUTP respectively (Amersham Biosciences, Amersham, UK) by reverse transcription using the CyScribe First Strand cDNA Labeling kit (Amersham Biosciences, Amersham, UK).
 
Hybridization protocol Each labeling reaction was purified with the CyScribe GFX purification kit (Amersham Biosciences, Amersham, UK). Subsequently, both labeled cDNAs were hybridized on a human 18K cDNA microarray encompassing 19,200 spots (representing 18,432 independent cDNAs) produced and obtained from The Netherlands Cancer Institute Microarray Facility (Amsterdam, The Netherlands), according to manyfacturer´s protocol.
Scan protocol Sixteen-bit fluorescent images from the expression arrays were acquired with an Agilent DNA Microarray Scanner (Agilent Technologies, Inc., Palo Alto, CA).
Description D5_4
Data processing The resulting TIFF images were analyzed with the software GenePix Pro 4.0 (Axon Instruments, Union City, CA) and a unique .gpr file was generated for each sample. Each .gpr file was directly loaded into the R environment using the marray package to extract the background-corrected Cy3 and Cy5 median raw intensity per spot. Intensity data was normalized with the variance stabilization and normalization function implemented in the vsn package (http://www.R-project.org/).
 
Submission date Nov 26, 2007
Last update date Aug 14, 2011
Contact name Joana Cardoso
E-mail(s) joanacardoso@fm.ul.pt
Phone 351-21-7999519
Organization name Faculty of Medicine
Lab Biology of Chromatin Unit
Street address Av. Prof Egaz Moniz
City Lisbon
ZIP/Postal code 1700
Country Portugal
 
Platform ID GPL3408
Series (1)
GSE9689 Analysis of colorectal tissue from APC- and MYH-associated polyposis patients

Data table header descriptions
ID_REF
VALUE vsn normalized Cy5 signal intensity

Data table
ID_REF VALUE
1 0.283810163
2 0.43242985
3 -0.39290548
4 0.238338819
5 0.614815549
6 0.336001778
7 0.450132176
8 0.755465636
9 0.533784654
10 -0.185328052
11 0.088720415
12 -0.208429128
13 -0.017323915
14 0.5305145
15 0.268816773
16 0.45831341
17 0.088720415
18 0.293630037
19 0.283357094
20 0.223713005

Total number of rows: 19200

Table truncated, full table size 333 Kbytes.




Supplementary file Size Download File type/resource
GSM245004.gpr.gz 1.6 Mb (ftp)(http) GPR
Processed data included within Sample table

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