|
| Status |
Public on Jun 24, 2010 |
| Title |
TAX577387 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast tumor
hu subtype: Basal
familial status: sporadic
er: er_neg
osbin: 0
os: 14.4849315068493
pgr: pgr_neg
primary: 1
grade: 3
genomic subtype: amplifier
brca status: sporadic
pam50 classification: Basal
pam50 correlation: 0.61852
er: er_neg
brca1 methylation status: negative
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from fresh frozen breast tumor tissue was extracted using Trizol reagent (Invitrogen) followed by the RNeasy Midi Purification kit (Qiagen). RNA concentrations were measured using a Nanodrop (NanoDrop Technologies). RNA integrity was determined by an Agilent Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions from 5ug of total RNA using the Corning Pronto Plus System 6 kit as described (PMID:17334996).
|
| |
|
| Channel 2 |
| Source name |
Stratagene Universal reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
reference: Stratagene Universal reference RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from fresh frozen breast tumor tissue was extracted using Trizol reagent (Invitrogen) followed by the RNeasy Midi Purification kit (Qiagen). RNA concentrations were measured using a Nanodrop (NanoDrop Technologies). RNA integrity was determined by an Agilent Bioanalyzer.
|
| Label |
Cy5
|
| Label protocol |
Fluorescently labeled DNA targets for hybridization were prepared according to manufacturers' instructions from 5ug of total RNA using the Corning Pronto Plus System 6 kit as described (PMID:17334996).
|
| |
|
| |
| Hybridization protocol |
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. For spots, log ratio (M) was calculated as log2(Int1/Int2) and average intensity (A) was calculated as log10(Int1*Int2)/2. Prior to normalization only oligonucleotide probes without cross-hybridization to other genomic regions or transcripts were selected. Normalization was performed using block (print tip) based lowess. After normalization, a probe presence filter was applied to select only probes with suffcient presence, followed by imputation of missing values using weighted nearest-neighbor imputation (WENNI). Probes were subsequently merged on probe identifier and row-centered across the entire data set.
|
| |
|
| Submission date |
Jun 06, 2010 |
| Last update date |
Jun 25, 2012 |
| 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 |
GPL5345 |
| Series (2) |
| GSE22133 |
Genomic Subtypes of Breast Cancer Identified by Array Comparative Genomic Hybridization |
| GSE25307 |
The retinoblastoma gene is targeted for rearrangements in BRCA1-deficient basal-like breast cancer. |
|
