|
| Status |
Public on Sep 11, 2014 |
| Title |
Head_knockout_male_replicate1 |
| Sample type |
RNA |
| |
|
| Source name |
Head_knockout_male
|
| Organism |
Mus musculus |
| Characteristics |
gestational age: E14.5
strain: C57BL/6N ,C57BL/6J
tissue: Head
genotype: Peg3 knockout
gender: male
|
| Treatment protocol |
A litter of 14.5-dpc fetuses were harvested from a timed mating between a male heterozygote (-m/+) and wild-type female littermate. Three tissues were obtained from each fetus: embryo head, placenta and amnionic sac. The DNA from amnionic sac was used for determining the genotype and gender of each fetus.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol isolated total RNA from each sample was treated with DNAse I and later purified with columns to remove any genomic contaminations (Qiagen, RNeasy Mini-kit).
|
| Label |
biotin
|
| Label protocol |
400ng total RNA was labeled with Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit for Illumina system
|
| |
|
| Hybridization protocol |
750ng labeled RNA was hybridized to MouseRef-8 v2 BeadChip arrays (Illumina) according to manufacturer’s protocol.
|
| Scan protocol |
Chips were scanned using Illumina iScan system with default settings
|
| Description |
Two different types of heterozygotes were prepared for breeding experiment: male and female heterozygotes carrying the paternally (+/-p) and maternally (-m/+) transmitted targeted allele. These 4 heterozygotes were bred with their littermates: for Breeding 1, female wild-type littermates x male heterozygotes (+/-P); Breeding 2, female heterozygotes (+/-P) x male wild-type littermates; Breeding 3, female wild-type littermates x male heterozygotes (-m/+); for Breeding 4, female heterozygotes (-m/+) x male wild-type littermates.
|
| Data processing |
Raw data was analyzed using Illumina GenomeStudio with the Gene Expression Module v.1.0.6. Raw data were background-subtracted and normalized using the quantile normalization method (lumi software package). Normalized data were filtered for genes with significant expression levels compared to negative control beads. Selection for differentially expressed genes was performed on the basis of arbitrary thresholds for fold changes plus statistical significance according to the Illumina t-test error model (limma software). Pathway analyses were also performed with the EGAN (Explorative Gene Association Networks) package using up- and down-regulated gene sets.
Matrix normalized contains quantile normalized and background subtracted signal exported from GenomeStudio. Matrix non-normalized contains background subtracted non-normalized data exported from GenomeStudio
|
| |
|
| Submission date |
Sep 12, 2013 |
| Last update date |
Sep 11, 2014 |
| Contact name |
Joomyeong Kim |
| E-mail(s) |
[email protected]
|
| Phone |
225-578-7692
|
| Organization name |
Louisiana State University
|
| Department |
Biological Sciences
|
| Street address |
202 Life Sciences
|
| City |
Baton Rouge |
| State/province |
LA |
| ZIP/Postal code |
70803 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (1) |
| GSE50818 |
Peg3 mutational effects on reproduction and placenta-specific gene families |
|
