|
| Status |
Public on Oct 01, 2007 |
| Title |
JR-915 placenta, non-smoking, XY |
| Sample type |
RNA |
| |
|
| Source name |
Full-term placenta from non-smoker
|
| Organism |
Homo sapiens |
| Characteristics |
Full term placenta. Non-smoking mother, boy-child.
|
| Biomaterial provider |
University of Oulu
|
| Treatment protocol |
Placentas were collected immediately after delivery. Connective tissue and coagulated blood were removed and placental tissue was rinsed in cold 0.9 % NaCl solution. Small pieces around the placenta were cut and frozen in liquid nitrogen and stored at -80°C.
|
| Growth protocol |
Full-time pregnancy.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with guanidium thiocyanate followed by centrifugation in cesium chloride (Magga et al. 1997).
|
| Label |
biotin
|
| Label protocol |
The biotinylated cRNA probes were prepared and hybridized according to manufacturer’s instructions (Affymetrix, Santa Clara, CA) as previously described (Rysä et al., 2005). Briefly, cDNA was reverse-transcripted from 5 ug of total RNA with a T7-(dT)24-primer by means of the One-cycle cDNA synthesis kit (Affymetrix). The DNA was purified using GeneChip Sample Cleanup Module (Qiagen). The cRNA was prepared and biotin-labeled by in vitro transcription (Affymetrix) and fragmented before hybridization.
|
| |
|
| Hybridization protocol |
The biotinylated cRNA was hybridized to the GeneChip Human Genome U133 Plus 2.0 Arrays, which represents over 47,000 human transcripts. After hybridization GeneChips were washed and stained with streptavidin-phycoerythrin (Molecular Probes). Staining signal was amplified by biotinylated anti-streptavidin (Vector Laboratories) and second staining with streptavidin-phycoerythrin by using Affymetrix Fluidics station according the standard protocol.
|
| Scan protocol |
GeneChip Scanner 3000 with GeneChip Operating Software (GCOS) v. 1.2 (Affymetrix) was used in scanning.
|
| Description |
JR-915 placenta, non-smoking, XY
|
| Data processing |
RMA-preprocessing was applied. Further normalized by dividing each measurement by the 50th percentile of all measurements in that sample.
|
| |
|
| Submission date |
Apr 04, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Markus Storvik |
| Organization name |
University of Eastern Finland
|
| Department |
Pharmacology
|
| Street address |
University of Eastern Finland
|
| City |
Kuopio |
| ZIP/Postal code |
70211 |
| Country |
Finland |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE7434 |
Full-term placenta, smokers and non-smokers |
|
| Relations |
| Reanalyzed by |
GSE64985 |
| Reanalyzed by |
GSE119087 |
