|
| Status |
Public on Jun 01, 2013 |
| Title |
MAS98.12 bevacizumab-doxorubicin day10 mouse No2 Right Side |
| Sample type |
RNA |
| |
|
| Source name |
Breast Cancer Xenograft MAS98.12 bevacizumab-doxorubicin day10
|
| Organism |
Homo sapiens |
| Characteristics |
xenograft model: MAS98.12
mouse #: 2
side graft: Right Side
treatment: Bevacizumab Doxorubicin
time (d): 10
intrinsic subtype: Basal
tissue: Basal breast cancer xenograft tumor
rna extraction date: 2009-03-14
rna concentration (ng/ul): 2045.3
a260/280: 1.98
a260/230: 2.28
rin value: NA
comment bioanalyzer: Bioanalyzer: looks good
amplification date: 2009-05-18
hybridization date: 2009-05-18
donor tissue: primary human breast cancer
|
| Growth protocol |
Two orthotopic xenograft models, MAS98.12 and MAS98.06, have been established by directly grafted orthotopic implantation of primary breast cancer tissue in SCID mice and are serially transplanted, as previously described. Locally bred athymic nude mice (NCr-Foxn1nu) were kept under pathogen-free conditions, at constant temperature (21.5 ± 0.5 °C) and humidity (55±5 %), 20 air changes/hr and a 12 hr light/dark cycle. The mice were fed RM3 diet (Scanbur BK, Norway) and distilled tap water ad libitum. The water was supplemented with 4 µg/ml 17-β-estradiol, ensuring growth in the luminal-like xenograft. Animals from the two xenograft models were randomly assigned to different treatment groups after the tumor diameter reached approximately 5 mm.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from all 60 tumor pieces was extracted using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol.
|
| Label |
Cy3
|
| Label protocol |
low-RNA input Linear Amplification RNA kit (Agilent Technologies)
|
| |
|
| Hybridization protocol |
One-Color Microarray-Based Gene Expression Analysis v5.5
|
| Scan protocol |
Agilent Technologies Microarray Scanner G2505C
|
| Data processing |
Data were extracted using Feature Extraction software (Agilent Technologies) version 10.1.1.1. The microarray data were detrended for multiplicative effects and log2 transformed. Data from control probes, probes with inferior quality for more than 20 percent of the arrays (such spots were defined as feature outliers from the FE file), and probes that were flagged as present on less than 20 percent of the arrays were omitted from the analysis. After setting spots flagged as outliers to NA, the average value of duplicate probes was used to represent each unique probe. Missing data were imputed using k-nearest neighbors with default k=1 [25], and data were normalized using quantile normalization. For transcripts (based on GeneName, as provided by Agilent Technologies) represented by multiple different probes, the probe with the highest interquartile range (IQR) was chosen to represent each transcript.
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| |
|
| Submission date |
Apr 24, 2012 |
| Last update date |
Jun 01, 2013 |
| Contact name |
Eldrid Borgan |
| E-mail(s) |
eldrid.borgan@gmail.com
|
| Organization name |
Oslo University Hospital Radiumhospitalet
|
| Department |
Genetics
|
| Street address |
Ullernchausseen 70
|
| City |
Oslo |
| ZIP/Postal code |
0310 |
| Country |
Norway |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE37543 |
Subtype-specific response to bevacizumab is reflected in the metabolome and transcriptome of breast cancer xenografts |
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