|
| Status |
Public on Nov 30, 2013 |
| Title |
mouse_mammary_irradiated_10cGy_Si_Wk1-post-IR_Rep3 |
| Sample type |
RNA |
| |
|
| Source name |
total RNA of mammary tissue, BALB/c, 1WK post-IR, 10cGy High-LET Si Particle Radiation (350 MeV/amu)
|
| Organism |
Mus musculus |
| Characteristics |
gender: female
strain: BALB/c
stress: 10cGy High-LET Si Particle Radiation (350 MeV/amu)
time: 1 week
tissue: mammary tissue
|
| Treatment protocol |
Mice were either irradiated or not with high-LET silicon particles (350MeV/amu) or low-LET gamma-radiation
|
| Growth protocol |
3 week old BALB/cJ female mice were purchased from Jackson Laboratory and housed in the Berg Animal Facility at NYUMC. After acclimation, mice were cleared of the inguinal mammary gland on one side while the contra lateral inguinal mammary gland was kept intact. The mice were allowed to recover and aged 6 additional weeks at the Berg Animal Facility at NYUMC. Mice were given food and water ad libitum. At 9 weeks of age, all mice were transported by courier to the Brookhaven National Lab Animal Facility. After acclimation for one week, mice were irradiated or sham irradiated at 10 weeks of age. Tissues are harvested 1 week, 4 weeks, and 12 weeks post IR. The 4 and 12 week time points are collected after the mice are transported back to NYUMC. This data submission is for the mammary tissue that was kept intact. All procedures were done under protocols reviewed and approved by both IACUC committees at NYUMC and Brookhaven National Laboratories.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Rneasy kit from Oiagen, according to manufacturer's instructions
|
| Label |
biotin
|
| Label protocol |
250 ng of total RNA is first amplified into cRNA and then made into cDNA using the Ambion WT Expression Kit. 5.5 ug of the cDNA is then fragmented using the Affymetrix GeneChip WT Terminal Labeling kit. Fragmentation is confirmed by running each sample on the Agilent Bioanalyzer using the RNA 6000 kit. The fragmented cDNA is then labeled using the Affymetrix GeneChip WT Terminal Labeling kit.
|
| |
|
| Hybridization protocol |
The labeled cDNA is added to the hybridization cocktail that is prepared according to the protocol included in the Affymetrix GeneTitan Hybridization Wash, and Stain kit. The samples are then put onto a hybridization tray and loaded into the Affymetrix GeneTitan MC for hybridization, washing, and scanning. The samples are hybridized for 60 degrees C for 16 hours once all plates are loaded.
|
| Scan protocol |
Arrays are scanned in the Affymetrix GeneTitan MC using a xenon light bulb and the image is captured using a camera.
|
| Description |
Si_10cGy_Wk1_Rep3
mouse_mammary_irradiated_10cGy_Si_Wk1-post-IR
|
| Data processing |
Raw CEL file data were imported into R for background subtraction and normalization using the Robust Multichip Average algorithm from the Bioconductor package oligo.
|
| |
|
| Submission date |
Jun 28, 2013 |
| Last update date |
Nov 30, 2013 |
| Contact name |
Jonathan Tang |
| E-mail(s) |
[email protected]
|
| Organization name |
Lawrence Berkeley National Laboratory
|
| Department |
Cancer and DNA Damage Response
|
| Street address |
1 Cyclotron Road, MS-977
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL11533 |
| Series (1) |
| GSE48392 |
Response of mammary tissue to high-LET HZE particle (Silicon ions) radiation or low-LET gamma-rays |
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