|
| Status |
Public on Aug 23, 2019 |
| Title |
Null rep2 |
| Sample type |
RNA |
| |
|
| Source name |
placenta, E13.5, Slc38a4 Null, B6N background
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
developmental stage: E13.5
slc38a4 allele: homozygous knockout
|
| Treatment protocol |
Whole placentas collected at E13.5 were cut into a half or quarter size.
|
| Growth protocol |
C57BL/6N (B6N) mice were purchased from Japan Slc Inc. The mutant mice for Slc38a4 allele were generated by using CRISPR/Cas9 system. They were housed under controlled lighting conditions (daily light period 07:00 to 21:00).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from E13.5 placentas using an RNeasy Mini Kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
Total RNA (200 ng) was amplified and labeled with a Low Input Quick Amp Gene Expression Labeling Kit (#5190-2305, Agilent Technologies).
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse Gene Expression v2 8x60K Microarray (G4852B) at 65°C for 17 h 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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).
|
| Data processing |
The scanned images of microarray slides were processed using Feature Extraction software (Agilent Technologies). All raw data were loaded into Gene Spring GX 14.5 (Agilent Technologies) and signal intensities were normalized by shift to 75 percentile. Baseline was set to the median of all samples. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Aug 22, 2019 |
| Last update date |
Aug 23, 2019 |
| Contact name |
Shogo Matoba |
| E-mail(s) |
[email protected]
|
| Organization name |
RIKEN BioResource Research Center
|
| Street address |
3-1-1, Koyadai
|
| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-0074 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21163 |
| Series (1) |
| GSE136212 |
Paternal knockout of Slc38a4/SNAT4 causes placental hypoplasia associated with intrauterine growth restriction in mice |
|
