|
| Status |
Public on Sep 30, 2018 |
| Title |
E17.5 KO 3 |
| Sample type |
RNA |
| |
|
| Source name |
XX gonads at E17.5 (Elavl2 knockout)
|
| Organism |
Mus musculus |
| Characteristics |
gender: female
tissue: ovary
sample type: mixed
developmental stage: embryo
|
| Treatment protocol |
Embryonic and newborn gonads were disected in ice-cold PBS and were immeadiately frozen in RNAlater (Ambion). Frozen tissues were stored at -80 degree until total RNA extraction.
|
| Growth protocol |
Mice were housed in special pathogen free room
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted by QIAGEN (Rneasey Mini Kit) according to the manufacture's protocol
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.20 µg RNA using the One-Color Low RNA Input Linear Amplification 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 |
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 50 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) 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.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Mar 23, 2018 |
| Last update date |
Sep 30, 2018 |
| Contact name |
Yuzuru Kato |
| E-mail(s) |
yukato@nig.ac.jp
|
| Phone |
+81-55-981-6832
|
| Organization name |
National Institute of Genetics
|
| Department |
Division of Mammalian Development
|
| Lab |
Saga lab.
|
| Street address |
1111 Yata
|
| City |
Mishima |
| State/province |
Shizuoka |
| ZIP/Postal code |
411-8540 |
| Country |
Japan |
| |
|
| Platform ID |
GPL7202 |
| Series (2) |
| GSE112275 |
Microarray analysis of Elavl2 knockout ovaries |
| GSE113305 |
Primordial follicle formation involves dynamic conversion of RNA regulatory proteins |
|
