|
| Status |
Public on Mar 31, 2014 |
| Title |
Mouse_embryonic_diploid_cell_clone1 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse embryonic diploid cell, clone1
|
| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic cells
genotype/variation: p53-/-
ploidy: diploid
|
| Treatment protocol |
Cells were not treated prior to RNA extraction.
|
| Growth protocol |
Mouse embryonic cells were cultured in Eagle’s Minimum Essential Medium (MEM) supplemented with 10% fetal bovine serum at 37℃ with 5% CO2 in a humidified environment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
500ng of Cy3 labelled aRNA were hybridized competitively for 17 hrs in a 65 C hybridization oven set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (One-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol including the Stabilization and Drying Solution step (One-Color Microarray-Based Gene Expression Analysis, Agilent)
|
| Scan protocol |
Arrays were scanned at 3um resolution on an Agilent DNA Microarray Scanner (G2565CA) using the default settings for 8x60K format one-color arrays.
|
| Description |
Gene expression in p53-/- mouse embryonic diploid cells.
Sample name: RRI2
RRI2 used for normalization during data processing.
|
| Data processing |
Data was analyzed with Agilent Feature Extraction and GeneSpring GX v11.5 softwares. Data was normalized to RRI2.
|
| |
|
| Submission date |
Sep 28, 2011 |
| Last update date |
Mar 31, 2014 |
| Contact name |
Hisakatsu Nawata |
| E-mail(s) |
chromosometransfer@yahoo.co.jp
|
| Organization name |
Kyoto University
|
| Department |
Medicine
|
| Lab |
Radiation Biology
|
| Street address |
2-1010
|
| City |
osaka |
| ZIP/Postal code |
590-0494 |
| Country |
Japan |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
| GSE32449 |
Triploid causes genome instability in tumorigenesis |
|
