|
| Status |
Public on Apr 14, 2010 |
| Title |
TAX577656 [33K] |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Breast cancer (HER2+)
er: er_neg
osbin: 1
os: 2.115068493
age: 35.80835
ln: 1
size_mm: 20
primary: 1
grade: 3
|
| 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. Genomic DNA from FFPE tissue was extracted according to protocol from http://cancer.ucsf.edu/array/protocols/index.php. 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 DNA
|
| 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. Genomic DNA from FFPE tissue was extracted according to protocol from http://cancer.ucsf.edu/array/protocols/index.php. 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).
|
| Description |
n/a
|
| 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) spot diameter less than 40 um. 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 |
Apr 08, 2010 |
| Last update date |
Apr 14, 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 |
GPL7247 |
| Series (1) |
| GSE21259 |
High-resolution aCGH analyses of copy number alterations in HER2-amplified breast cancer |
|
