|
| Status |
Public on Aug 04, 2015 |
| Title |
WT.M.21 |
| Sample type |
RNA |
| |
|
| Source name |
Placenta, WT, M, day 18.5pc
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: B6.129S4-Vdrtm1Mbd/J
genotype/variation of offspring: wild-type
sex of offspring: M
tissue: placenta
developmental stage: day 18.5pc
litter_id: 21
|
| Treatment protocol |
Whole placentas were collected at day 18.5pc and fixed in RNAlater before RNA isolation.
|
| Growth protocol |
Male and female mice heterozygous for the Vdr allele (Vdr knockout strain B6.129S4-Vdrtm1Mbd/J - The Jackson Laboratory) were mated at 10-12 weeks of age to generate offspring of the three genotype combinations: Vdr knockout, Vdr heterozygotes and Wild-type. Placentae from pregnant females were collected at day 18.5pc for gene expression analyses. Mice were raised on a standard chow diet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA following the Manual Target Preparation Guidelines for GeneChip® Whole Transcript (WT) Expression Arrays.
|
| |
|
| Hybridization protocol |
3.5 ug of fragmented and labeled single-stranded cRNA were hybridized on Affymetrix MoGene 2.1 ST arrays and washed and stained following the Manual Target Preparation Guidelines for GeneChip® Whole Transcript (WT) Expression Arrays.
|
| Scan protocol |
Arrays were scanned using the Affymetrix GeneChip scanner by the Ramaciotti Centre for Genomics, Sydney, Australia.
|
| Description |
A18
Gene expression data from placental tissue collected at day 18.5pc.
|
| Data processing |
The data were preprocessed, background subtracted and quantile normalised at the probe level using the Oligo package in R. Probesets were annotated using the Bioconductor mogene21sttranscriptcluster.db: Affymetrix mogene21 annotation data (chip mogene21sttranscriptcluster) package.
|
| |
|
| Submission date |
Sep 19, 2014 |
| Last update date |
Aug 04, 2015 |
| Contact name |
Sam Buckberry |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Western Australia
|
| Street address |
35 Stirling Highway, Crawley
|
| City |
Perth |
| State/province |
WA |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17400 |
| Series (1) |
| GSE61583 |
The effect of Vdr gene ablation in the mouse placenta |
|
