|
| Status |
Public on Jan 01, 2015 |
| Title |
M3 cell, minus at 6h, biological rep3 |
| Sample type |
RNA |
| |
|
| Source name |
MCF10CA1h (M3), vehicle treated, 6h
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: vehicle treated
time: 6h
cell line: MCF10Ca1h (M3)
cell line origin: Breast epithelium
tumor stage represented: Malignant, low grade
|
| Treatment protocol |
Cells were grown to 50-60% confluence and then serum-starved in DMEM/F12 supplemented with Serum Replacement 1 for 16 hours prior to TGF-beta treatment with 5ng/ml or vehicle for 1 hour or 6 hour.
|
| Growth protocol |
M1 and M2 cells were grown in DMEM/F12 medium supplemented with 10ug/ml, insulin, 20ng/ml EGF, 0.5ug/ml hydrocortisone, 100ng/ml cholera toxin and 5% horse serum. M3 and M4 cells were grown in DMEM/F12 medium supplemented with 5% Horse serum.
|
| 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.
Original, Summarized, Difference, Filename, Chip Type, Attribute, cell, treatment, time, group, 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 |
GPL6244 |
| Series (2) |
| GSE34270 |
In vitro gene expression profile of TGFbeta-regulated genes in MCF10A-based xenograft model of breast cancer progression |
| GSE34277 |
MCF10A-based xenograft model of breast cancer |
|
