|
| Status |
Public on Jan 15, 2013 |
| Title |
Liver_CC_2 |
| Sample type |
RNA |
| |
|
| Source name |
Somatic cell clone CC-2
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
gender: female
age: neonate
cell type: Somatic cell clone CC-2
genetic background: (C57BL/6 x DBA2) x 129/Sv
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the Trizol kit (Lifetech) following the manufacturer's recommendations. Total RNA was then clean-up by RNAeasy column purification (QIAGEN). 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 the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100% and 10% (XDR)).
|
| Description |
Gene expression of neonatal liver from cumulus cell derived clone mouse.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v1_91-BETA and Grid: 014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.
Signals below background in the process of normalization and analysis. Thus removed values were indicated as null. Omitted null data from the normalized data leaving 34,140 probes. Signal for duplicated probes were represented by the mean value of them.
|
| |
|
| Submission date |
Jan 14, 2013 |
| Last update date |
Jan 18, 2013 |
| Contact name |
Takashi Kohda |
| E-mail(s) |
tkohda.epgn@mri.tmd.ac.jp
|
| Organization name |
Tokyo Medical and Dental University
|
| Department |
Medical Research Institute
|
| Lab |
Epigenetics
|
| Street address |
1-5-45 Yushima, Bunko-ku
|
| City |
Tokyo |
| ZIP/Postal code |
113-8510 |
| Country |
Japan |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE43476 |
Genomic Reprogramming Errors Do Not Accumulate with Serial Recloning in the Mouse |
|
