|
| Status |
Public on Apr 01, 2007 |
| Title |
C9029 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
C9029 tumor biopsy
|
| Organism |
Homo sapiens |
| Characteristics |
ERalpha Positive;ERbeta Positive
|
| Biomaterial provider |
Dept. of Oncology, Lund University, Sweden
|
| Treatment protocol |
n/a
|
| Growth protocol |
n/a
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue homogenization and RNA recovery using TRIzol reagent (Invitrogen), followed by 2nd round of purification using RNeasy kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
25 ug total RNA; anchored oligo-dT primers and CyScribe indirect amino-allyl cDNA synthesis and labeling protocol, with purification using GFX columns (all from Amersham Biosciences).
|
| |
|
| Channel 2 |
| Source name |
Stratagene Universal Human Reference
|
| Organism |
Homo sapiens |
| Characteristics |
See Stratagene product # 740000.
|
| Biomaterial provider |
Stratagene
|
| Treatment protocol |
See Stratagene product # 740000.
|
| Growth protocol |
See Stratagene product # 740000.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
See Stratagene product # 740000.
|
| Label |
Cy5
|
| Label protocol |
15 ug total RNA; anchored oligo-dT primers and CyScribe indirect amino-allyl cDNA synthesis and labeling protocol, with purification using GFX columns (all from Amersham Biosciences).
|
| |
|
| |
| Hybridization protocol |
Labeled targets were pooled and combined with blocking agents (12 ug poly-dA, 6 ug yeast tRNA, 20 ug Cot-1 DNA), and hybridized to microarray using the Pronto Universal Hybridization System (Corning) for 18 hours in a humidified chamber (Corning) submerged in a 42 C water bath. Slide was washing using the Pronto Universal Hybridization System.
|
| Scan protocol |
Scanned using the Agilent DNA Microarray Scanner at 10 micron resolution. The TIFF image was split and analyzed with GenePix 4.1.1.4. Result files were loaded into BioArray Software Environment. Cy3=channel 1, Cy5=channel 2.
|
| Description |
Human breast tumor sample
|
| Data processing |
Data was preprocessed in the BioArray Software Environment. For each channel, the Median FG - Median BG intensity value was used. Features flagged bad/missing during image analysis were removed. Data was normalized using pin-based LOWESS (6 groups of 8 pins/group). Filtering on median Signal-to-Noise ratio was applied, keeping only those datapoints with a ch1median or ch2median SNR>=3. Features that were present in at least 80% of the 88 tumors in the series were kept, all other features were removed. Features with a variation <0.45 SD of log2(ratio) were removed. Genes and arrays were then median centered 1X.
|
| |
|
| Submission date |
Dec 20, 2006 |
| Last update date |
Feb 26, 2007 |
| Contact name |
Sofia K Gruvberger-Saal |
| E-mail(s) |
sg2414@columbia.edu
|
| Phone |
212-851-5263
|
| Organization name |
Columbia University
|
| Department |
Institute for Cancer Genetics
|
| Street address |
1130 St. Nicholas Ave., ICRC 406
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL3883 |
| Series (1) |
| GSE6577 |
Estrogen receptor beta expression is associated with tamoxifen response in ER alpha-negative breast carcinoma |
|
