|
| Status |
Public on Apr 23, 2008 |
| Title |
Decidua e17.0, biological rep1 (Series 2) |
| Sample type |
RNA |
| |
|
| Source name |
Mouse decidual tissue at embryonic day 17.0, biological replicate 1
|
| Organism |
Mus musculus |
| Characteristics |
Strain: Swiss Webster
Tissue: decidua (maternal origin)
|
| Treatment protocol |
For dissected samples, placentas were manually dissected into fetal placenta and decidual (maternal) portions, using fine forceps to separate the decidua from the spongiotrophoblast and trophoblast giant cells. Fetally derived placenta samples and maternally derived placenta samples were pooled separately for each litter, then flash frozen in liquid nitrogen and stored at –80° C until RNA isolation. Tissues from two to ten placentas from a single litter were combined for each sample except for two of the e8 samples, which were pooled from multiple litters after staging. For undissected samples, single undissected e17.0 placentas were flash frozen and stored at –80° C until RNA isolation.
|
| Growth protocol |
For all dissected samples, a minimum of two to three timed pregnant female Swiss Webster mice were sacrificed at each timepoint used in our analysis, generating two to three biological replicates at each stage. The one exception is e8.5: for this experiment (Series 2) only one of the placenta_e8.5 sample is used (see extract protocol below). For the two undissected samples, a single C57BL/6 female was sacrificed at e17.0 and two individual, undissected placentas were collected to generate two replicates. In all cases, fetal tissues were used to confirm staging of the embryos using Theiler’s morphological criteria.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each sample was homogenized in Trizol with a rotor homogenizer. RNA was isolated by chloroform extraction from the Trizol sample, purified using a Qiagen Rneasy column, then ethanol precipitated. Note: Due to limited tissue availability, two of the full timecourse e8.5 placenta samples (Placenta_e8.5-1 and Placenta_e8.5-2) included in Series 1 were homogenized in Ambion lysis buffer rather than Trizol and were purified with Ambion Rnaqueous rather than Quiagen Rneasy, so are not included in the Series 2 experiment.
|
| Label |
biotin
|
| Label protocol |
For each sample, labeled cRNA was prepared from 10 ug of starting RNA according to Affymetrix protocols. Briefly, RNA was reverse transcribed and the resulting double stranded cDNA was purified by phenol-chloroform extraction followed by ethanol precipitation. The cDNA was used as a template for a biotin labeling in vitro transcription. The resulting cRNA was purified using an Rneasy column, quantified, then fragmented using KOAc RNA fragmentation buffer.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA was hybridized for 16 hr at 45C on the Affymetrix Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000.
|
| Description |
Gene expression data from maternal decidua at e17.0
|
| Data processing |
In order to control for differences in overall strength of hybridization, all arrays were normalized to the same median intensity using the dCHIP invariant set method. Modeling was performed using the dCHIP Perfect Match (PM) modeling algorithm.
|
| |
|
| Submission date |
Apr 21, 2008 |
| Last update date |
Apr 22, 2008 |
| Contact name |
Kirstin Knox |
| Organization name |
Stanford Univeristy
|
| Department |
Genetics
|
| Lab |
Julie Baker
|
| Street address |
300 Pasteur Dr.
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE11222 |
Placental and decidual timecourse samples normalized and modeled with an undissected e17 sample |
| GSE11224 |
Expression data from developing mouse placenta |
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