|
| Status |
Public on May 25, 2010 |
| Title |
6_after |
| Sample type |
RNA |
| |
|
| Source name |
6_after_NR
|
| Organism |
Homo sapiens |
| Characteristics |
patient no: 6
tissue: Breast cancer tissue
gender: female
before/after chemotherapy: after
response: NR
initial cm: 3
post cht cm: 2.5
sinn: 1
ypt: 2
ypn: 0
grade: 3
er(%): 90
pr(%): 25
her2neu score: 0
|
| Treatment protocol |
A two-pass, high speed core biopsy, evaluated for a cancer cell content of >50% by fresh-frozen section analysis, was performed before and after four cycles neoadjuvant chemotherapy (epirubicine 90mg/m2 and cyclophosphamide 600mg/m2 every three weeks)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the RNA 6000 Nano LabChip kit (Agilent Technologies, Palo Alto, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression of patient 6 after neoadjuvant chemotherapy
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform, Saturated, and Population outlier were flagges A(bsent). Features flagged Not positive and significant and Not above background were flagged M(arginal). All other values were flagged P(resent).
|
| |
|
| Submission date |
May 24, 2010 |
| Last update date |
Jun 06, 2022 |
| Contact name |
Dietmar Pils |
| E-mail(s) |
dietmar.pils@meduniwien.ac.at
|
| Organization name |
Medical University of Vienna
|
| Department |
Dept. of Surgery
|
| Street address |
Waehringer Guertel 18-20
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE21974 |
Molecular Subtype Predicts Response to Neoadjuvant Chemotherapy in Breast Cancer |
|
| Relations |
| Reanalyzed by |
GSE205568 |
