|
| Status |
Public on Sep 09, 2008 |
| Title |
FNA07_POST |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Post-operative, palpable invasive breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
Patient No.: FNA13
Tumor Type: IDC
Tumor Size(cm): 4
Tumor Grade: 2
LVI: +
EIC: -
ER: +
PR: +
ERBB2: -
Positive_Nodes: 2/20
palpable invasive breast cancer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNAeasy Micro kit (Qiagen) then amplified using the MessageAmp aRNA kit (Ambion) according to the manufacturer's instructions.
|
| Label |
Cy5, Cy3
|
| Label protocol |
The amplified RNA species from FNABs and an amplified Universal Human Reference RNA (Stratagene; La Jolla, CA) were directly labeled using cyanine 5 and cyanine 3 fluorescent dyes from 5 to 10μg of RNA according to the UHN Microarray Centre instructions. Dye-swap technical replicate was carried out for every FNABs.
|
| |
|
| Channel 2 |
| Source name |
Universal RNA
|
| Organism |
Homo sapiens |
| Characteristics |
Stratagene Universal RNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNAeasy Micro kit (Qiagen) then amplified using the MessageAmp aRNA kit (Ambion) according to the manufacturer's instructions.
|
| Label |
Cy3, Cy5
|
| Label protocol |
The amplified RNA species from FNABs and an amplified Universal Human Reference RNA (Stratagene; La Jolla, CA) were directly labeled using cyanine 5 and cyanine 3 fluorescent dyes from 5 to 10μg of RNA according to the UHN Microarray Centre instructions. Dye-swap technical replicate was carried out for every FNABs.
|
| |
|
| |
| Hybridization protocol |
The generated cDNA probes were then purified and denatured. The labeled targets were hybridized to UHN h19k cDNA microarrays.
|
| Scan protocol |
Scanned at 16 bits using the Genepix Axon Scanner 4000A (Molecular Devices Corp) at 635 nm (Cy5) and 532 nm (Cy3) using Genepix Pro 6.0 analysis software (Molecular Devices Corp).
|
| Description |
Two replicated (dye-swaped) data were combined for analysis
IDC, invasive ductal carcinoma; ILC, invasive lobular carcinoma; LVI, lymphovascular invasion; EIC, extensive intraductal component; ER, estrogen receptor; PR, progesterone receptor; ERBB2, HER2 status. ER, PR, and HER2 status as reported on standard surgical pathology reports were determined by immunohistochemistry, or by fluorescent in situ hybridization for HER2 according to our institutional standard of practice.
|
| Data processing |
Each quantified output file in GenePix report (GPR) format was directly transferred into Acuity 4.0 (Molecular Devices Corp.) for analysis. After Lowess slide normalization, any uninformative microarray data were flagged and filtered. The dye-swaped signal log2 ratios were inverted before the data of the replicate were combined, resulting in 16 PRE and 16 POST specimens for analysis finally. Probes with minimal changes in expression level (Log2 ratio >=1 or <=-1 in not more than 2 tumors) were removed, resulting in a list of 4,056 probes in the matrix dataset.
|
| |
|
| Submission date |
Jul 10, 2008 |
| Last update date |
Sep 09, 2008 |
| Contact name |
Dong-Yu Wang |
| Organization name |
UHN-PMH-OCI
|
| Street address |
610 University Ave
|
| City |
Toronto |
| ZIP/Postal code |
M5G 2M9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL7025 |
| Series (1) |
| GSE12072 |
The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers |
|
