|
| Status |
Public on Nov 22, 2011 |
| Title |
cultured-MDA-MB-231-rep3 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: MDA-MB-231 cell line grown in vitro
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 |
MDA-MB-231 human breast carcinoma cell line was obtained from the American Type Culture Collection (ATCC) and maintained according to the supplier’s instructions. RNA was isolated from three independent cultures of sub-confluent MDA-MB-231 cells in the exponential phase of growth
|
| 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 |
|
