|
| Status |
Public on Jan 01, 2015 |
| Title |
M3 tumor control, biological rep5 |
| Sample type |
RNA |
| |
|
| Source name |
MCF10CA1h (M3) tumor, control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast cancer xenograft tumor
treatment: control
|
| Treatment protocol |
refer to the summary for each study.
|
| Growth protocol |
MCF10CA1h (M3) cells were infected ex vivo with pLPCX retrovirus with no insert (M3-CON) or pLPCX expressing dominant negative type II TGF-b receptor (M3-dnTbRII) . Cells were selected in DMEM/F12 medium supplemented with 5% Horse serum and 4ug/ml puromycin for 5 days. 5x10e5 cells were implanted orthotopically into female athymic NCr nu/nu mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and purified by RNeasy Mini Kit (Qiagen) according to manufacturer's instructions. RNA quality was checked on Agilent Bioanalyzer. All samples used for microarray analysis have high quality score (RIN >9).
|
| Label |
Biotin
|
| Label protocol |
100 ng of RNA was reverse transcribed and amplified using Ambion WT expression kit following manufacturer’s suggested protocol. Sense strand cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit.
|
| |
|
| Hybridization protocol |
Three replicates of each group were hybridized to Affymetrix mouse (human) Gene ST 1.0 GeneChip in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs. Wash and stain were performed on Affymetrix Fluidics Station 450
|
| Scan protocol |
Genechips were scanned using an Affymetrix GeneChip Scanner 3000 and data was collected using Affymetrix AGCC software.
|
| Description |
RNA extracted by Rneasy
|
| Data processing |
Data were analyzed with Partek Genomics Suite (version 6.5) software using the RMA normalization algorithm with default format. More details needed here?
Original, Summarized, Difference, Filename, Chip Type, tumor, Scan Date, gene expression
|
| |
|
| Submission date |
Dec 08, 2011 |
| Last update date |
Jan 01, 2015 |
| Contact name |
Howard Yang |
| E-mail(s) |
[email protected]
|
| Phone |
2402765257
|
| Organization name |
NCI
|
| Street address |
9609 Medical Center Dr.
|
| City |
Rockville |
| State/province |
MD |
| ZIP/Postal code |
20850 |
| Country |
USA |
| |
|
| Platform ID |
GPL10739 |
| Series (2) |
| GSE34276 |
Global analysis of TGF-beta-regulated gene expression in MCF10Ca1h (M3) breast tumor xenografts |
| GSE34277 |
MCF10A-based xenograft model of breast cancer |
|
