|
| Status |
Public on Sep 30, 2013 |
| Title |
JH_100927_Tweak_MDA-MB-436_219_TWEAK_0_25hrs |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-436 cells, treated with 100ng_per_ml TWEAK for 0.25hours
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-436
cell line origin: mammary
cell type: ductal carcinoma
gender: female
race: caucasian
|
| Treatment protocol |
100 ng/ml TWEAK or media control was added on day 2 to subconfluent cells. For each time point and treatment, five replicates were generated. One replicate from each treatment group was used for QC as assessed with immunoblotting for Fn14 expression. Samples were collected in all cell lines after 4 h, 8 h or 24 h of stimulation or control treatment with five replicates. For the U2OS and MDA-MB-436 arrays, 15 min and 1 h time points were also collected.
|
| Growth protocol |
Cells were seeded in appropriate media with 2% heat-inactivated FBS in humidified 95% air, 5% CO2 overnight in 6-well plates at 37oC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using Qiagen Rneasy Minikit.
|
| Label |
biotin
|
| Label protocol |
5'IVT Express kit was followed according to manufacturer's recommendations
|
| |
|
| Hybridization protocol |
Hybridization followed manufacturer's recommendations
|
| Scan protocol |
GC_scanner3000 Affymetrix scanner was utilized with AGCC
|
| Data processing |
Statistical analysis was done by simple linear modeling using Partek Genomics Suite software. A model containing fixed effects for treatment and time and their interaction was calculated, and contrasts were constructed for the overall TWEAK vs. vehicle treatment comparison and for each individual time point. Relevant gene lists of interesting genes and patterns of genes were created. Lists were generated for probesets where treatment induced changes had significance p values of <0.05 and which change at least 1.8-fold at 2 time points.
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| |
|
| Submission date |
Nov 05, 2012 |
| Last update date |
Sep 30, 2013 |
| Contact name |
Mary Simcox |
| E-mail(s) |
msimcox@formatherapeutics.com
|
| Phone |
857-209-2853
|
| Organization name |
Forma Therapeutics
|
| Street address |
500 Arsenal St
|
| City |
Watertown |
| State/province |
MA |
| ZIP/Postal code |
02472 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE42045 |
TWEAK-treated time course in MDA-MB-436 cells |
| GSE42050 |
Blocking TWEAK inhibits tumor growth through inhibition of tumor cell proliferation and survival and by enhancing the host antitumor immune response |
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