|
| Status |
Public on Jul 19, 2023 |
| Title |
Third Trimester Control_CTB1_38weeks |
| Sample type |
RNA |
| |
|
| Source name |
Placental Villi
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: Gestation-matched control
time point: 38 weeks
cell type: Cytotrophoblast
|
| Growth protocol |
Uncultured
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FACS sorting live MHC Class I negative Hoechst 33342-low side-population trophoblasts and bete4-integrin positive cytotrophoblasts
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
Affymetrix GeneChip PrimeView microarrays using the3' IVT PLUS kit
|
| Scan protocol |
Standard Affymetrix protocol
|
| Data processing |
Microarray data were quality checked and lacked obvious outliers (Bolstad et al. 2003; Irizarry et al 2003a; Irizarry et al 2003b). Preprocessing and normalaisation of the data using RMA was conducted using R package affy (Gautier et al. 2004). Side-population trophoblast gene expression was compared to that of cytotrophoblasts from the same placenta. In oder to determine differentially expressed transcripts, the statistical program R and the R package limma were used. (Ritchie et al 2015). Linear models were used to determine Log fold changes between side-population trophoblasts and cytotrophoblast populations from FGR and gestation-matched control placentae and an emperical Bayes method was used to moderate the standard deviation of the estimated Log fold changes. All data were cleaned and reanalysed using the method described to analyse the FGR and gestation-matched control samples to mitigate any bias in the data that may result from differences in the analysis pipelines used in the previous publication from which first trimester samples were obtained (James et al 2015).
|
| |
|
| Submission date |
Dec 10, 2018 |
| Last update date |
Jul 19, 2023 |
| Contact name |
Teena Gamage |
| E-mail(s) |
[email protected]
|
| Organization name |
Grafton
|
| Street address |
502-201, 85 Park Road
|
| City |
Auckland |
| State/province |
Scotland |
| ZIP/Postal code |
1023 |
| Country |
New Zealand |
| |
|
| Platform ID |
GPL16043 |
| Series (1) |
| GSE123555 |
Side-population trophoblasts from first and third trimester pregnancies |
|
