|
| Status |
Public on Nov 03, 2015 |
| Title |
evt_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
evt_rep2
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: placenta
cell type: extravillous trophoblast
placenta_group: b
placental_gestation (weeks): 8.4
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Invitrogen PureLink mini-kit (Life Technologies, California) according to the manufacturer's instructions. RNA quality was assessed using Experion RNA HighSens chips (Biorad, Auckland) according to the manufacturer’s instructions. RNA was converted to cDNA and amplified using a NuGEN Ovation Pico WTA system V2 kit according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
Purified cDNA was biotin-labelled and hybridised to Affymetrix PrimeView microarrays (Affymetrix, California) according to the manufacturer's instructions
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Primeview Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Primeview Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Primeview Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Primeview Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Command Console software v3.2
|
| Data processing |
Data was RMA-normalised following background correction and log-transformation. The ‘limma’ package in the statistical language R was used to assess the evidence for differential abundance of RNA transcripts between each of the three cell types (EVT, CTP and SP). A blocked analysis was performed to correct for within-patient variance. Benjamini-Hochberg false-discovery rate control (FDR) was used to adjust p-values for differential expression.
|
| |
|
| Submission date |
May 20, 2014 |
| Last update date |
Nov 03, 2015 |
| Contact name |
Daniel Glyn Hurley |
| E-mail(s) |
daniel.hurley@unimelb.edu.au
|
| Organization name |
The University of Melbourne
|
| Department |
Systems Biology Laboratory
|
| Lab |
Systems Biology Laboratory
|
| Street address |
Level 4, Bldg 193, EEE
|
| City |
Melbourne |
| ZIP/Postal code |
3010 |
| Country |
Australia |
| |
|
| Platform ID |
GPL15207 |
| Series (1) |
| GSE57834 |
Isolation and Characterisation of a Novel Trophoblast Hoescht Side-Population with Stem Cell Properties from First Trimester Placentae |
|
