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Sample GSM551598 Query DataSets for GSM551598
Status Public on Jun 24, 2010
Title TAX577117
Sample type genomic
 
Channel 1
Source name Breast tumor
Organism Homo sapiens
Characteristics tissue: Breast tumor
hu subtype: LumA
familial status: familial
er: er_pos
osbin: 1
os: 7.876712329
pgr: pgr_pos
grade: 2
genomic subtype: Luminal-complex
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from fresh frozen breast tumor tissue was extracted using overnight digestion with proteinase K at 55C, followed by repeated phenol-chloroform purification steps. DNA concentrations were measured using a Nanodrop.
Label Cy3
Label protocol Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions using the Invitrogen Bioprime aCGH Genomic Labeling Module as described (PMID:17334996).
 
Channel 2
Source name promega male reference
Organism Homo sapiens
Characteristics reference: promega male reference
Extracted molecule genomic DNA
Extraction protocol Genomic DNA from fresh frozen breast tumor tissue was extracted using overnight digestion with proteinase K at 55C, followed by repeated phenol-chloroform purification steps. DNA concentrations were measured using a Nanodrop.
Label Cy5
Label protocol Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions using the Invitrogen Bioprime aCGH Genomic Labeling Module as described (PMID:17334996).
 
 
Hybridization protocol BAC aCGH microarrays were hybridized as described (PMID: 17334996)
Scan protocol Arrays were washed as described (PMID: 17334996) and fluorescence was recorded using an Agilent G2565AA microarray scanner (Agilent Technologies).
Data processing TIFF images were analyzed using the Gene Pix Pro software (Axon Instruments, Foster City, CA), and the quantified data matrix was loaded into a local installation of BioArray Software Environment (BASE) (http://base.thep.lu.se). Quantified intensities for tumor sample were stored as channel 1 (ch1) whereas quantified intensities for reference sample were stored as channel 2 (ch2). Median spot pixel values were used to calculate background corrected intensities (Int1 and Int2). Spots were removed and regarded as missing values if either: (1) flagged during image-analysis, (2) background corrected intensity value >64999 signal units, (3) background corrected intensity value <0 signal units, or (4) Signal to noise ratio <5 in either Int1 or Int2 channel. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Normalization was performed by applying popLowess (PMID: 17953745). Spots from dye-swap hybridization were merged using geometric mean of ratios after normalization.
 
Submission date Jun 06, 2010
Last update date Jun 24, 2010
Contact name Johan Staaf
Organization name SCIBLU - Swegene Centre for Integrative Biology at Lund University
Street address Medicon Village
City Lund
ZIP/Postal code SE-223 81
Country Sweden
 
Platform ID GPL4723
Series (2)
GSE22133 Genomic Subtypes of Breast Cancer Identified by Array Comparative Genomic Hybridization
GSE32578 Characterization of amplification patterns and target genes at chromosome 11q13 in CCND1-amplified sporadic and familial breast tumors

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio (tumor/reference male DNA)

Data table
ID_REF VALUE
1 0.0061
2 0.2399
3 -0.0082
4 0.0614
5 -0.1339
6 0.0258
7 0.1815
8 0.1203
9 0.0587
10 0.0631
11 -0.0681
12 -0.053
13 null
14 null
15 0.346
16 0.3391
17 0.431
18 0.0743
19 null
20 0.13

Total number of rows: 30120

Table truncated, full table size 379 Kbytes.




Supplementary file Size Download File type/resource
GSM551598_TAX577117_Cy3_1.gpr.gz 2.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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