|
| Status |
Public on Apr 04, 2018 |
| Title |
C3H_normal_3 |
| Sample type |
RNA |
| |
|
| Source name |
C3H_normal_3
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
gender: male
|
| Growth protocol |
pregnant F0 C3H/HeN mice were purchased from CLEA Japan (Tokyo, Japan) and F1 and F2 pups in the control group were given free access to a standard diet (CA-1; CLEA Japan) and tap water. C3H mice of 74~75 weeks were used in this analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
600 ng 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 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Ver 2.0Microarrays (G4858A) for 17 hours at 65℃ 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℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression of normal liver_3
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Oct 05, 2017 |
| Last update date |
Apr 04, 2018 |
| Contact name |
Keiko Nohara |
| E-mail(s) |
[email protected]
|
| Phone |
81-29-850-2500
|
| Organization name |
National Institute for Environmental Studies
|
| Department |
Center for Health and Environmental Risk Research
|
| Street address |
16-2 Onogawa
|
| City |
Tsukuba |
| ZIP/Postal code |
305-8506 |
| Country |
Japan |
| |
|
| Platform ID |
GPL13912 |
| Series (1) |
| GSE104627 |
Gene expression profiling in liver normal and tumor tissues in C3H mice |
|
