|
| Status |
Public on Nov 22, 2011 |
| Title |
mouseliver-normal-rep3 |
| Sample type |
RNA |
| |
|
| Source name |
mouse liver
|
| Organism |
Mus musculus |
| Characteristics |
age: eight weeks
gender: female
strain: NOD scid gamma (The Jackson Laboratory)
|
| 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 MouseWG-6 v2 Expression BeadChips (Illumina, Inc.)
|
| |
|
| Hybridization protocol |
Samples were prepared according to the manufacturer’s instructions and analyzed using MouseWG-6 v2 Expression BeadChips (Illumina, Inc.)
|
| Scan protocol |
Samples were prepared according to the manufacturer’s instructions and analyzed using MouseWG-6 v2 Expression BeadChips (Illumina, Inc.)
|
| 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 |
GPL6887 |
| Series (1) |
| GSE30993 |
Simultaneous analysis of tumor and stromal gene expression profiles from xenograft models |
|
