|
| Status |
Public on Nov 22, 2011 |
| Title |
liver-mets-rep1 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-231 liver metatasis
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: MDA-MB-231 xenograft liver metastasis
age: 50 days
strain: MDA-MD-231
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cultured MDA-MB-231 cells, MDA-MB-231 liver metastases and mouse liver using Trizol Reagent (Invitrogen) according to the manufacturer’s instructions. Concentration and yield of RNA samples were determined using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). RNA integrity was determined by analysis on an Agilent 2100 Bioanalyzer (Agilent Technologies) following the manufacturer’s recommendations. Only samples with a RIN score >7.0 were used for microarray analysis.
|
| Label |
biotin
|
| Label protocol |
Samples were prepared according to the manufacturer’s instructions and analyzed using HumanHT-12 v4 Expression BeadChips (Illumina, Inc.)
|
| |
|
| Hybridization protocol |
Samples were prepared according to the manufacturer’s instructions and analyzed using HumanHT-12 v4 Expression BeadChips (Illumina, Inc.)
|
| Scan protocol |
Samples were prepared according to the manufacturer’s instructions and analyzed using HumanHT-12 v4 Expression BeadChips (Illumina, Inc.)
|
| Description |
Metastatic liver xenografts of MDA-MB-231 cells were harvested by gross surgical dissection ~50 days following implantation into the abdominal mammary fat pads of eight week old female NOD scid gamma mice (The Jackson Laboratory). Mice were injected unilaterally with 2.5 x 106 cells in 200 μL of 50:50 Matrigel/Collagen I into the fourth abdominal fat pad by subcutaneous injection at the base of the nipple. Tumor growth was monitored externally using vernier calipers for 50 days and animals sacrificed when tumors reached 10% of body weight. Necropsies were performed to identify liver macro-metastases.
|
| Data processing |
Raw expression data from BeadStudio software was background corrected, normalized, and VST transformed using the lumi package v. 2.2.0 in Bioconductor. Probes with detection p-values < 0.05 in all three independent replicates were considered 'present' and included in further analyses.
|
| |
|
| Submission date |
Jul 27, 2011 |
| Last update date |
Nov 22, 2011 |
| Contact name |
Jennifer Clarke |
| Organization name |
University of Miami
|
| Department |
Epidemiology and Public Health
|
| Lab |
Division of Biostatistics
|
| Street address |
1120 NW 14th Street
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE30993 |
Simultaneous analysis of tumor and stromal gene expression profiles from xenograft models |
|
