|
| Status |
Public on Oct 01, 2023 |
| Title |
Control_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Human placenta perfused with perfusion medium only, replicate 1
|
| Organism |
Homo sapiens |
| Characteristics |
donor: S88
dose: 0 µg/ml
exposure time: 6 hours
treatment: perfusion medium
tissue type: human placenta derived from an uncomplicated pregnancy
slide position: 1_2
|
| Treatment protocol |
The perfusions of the placentas were performed using an ex vivo dual recirculating perfusion system described e.g. in Wick, P., et al., Barrier capacity of human placenta for nanosized materials. Environ Health Perspect, 2010. 118(3): p. 432-6. The perfusion medium consisted of M199 tissue culture medium, diluted 1:2 with Earl’s buffer and supplemented with glucose (1 g/L), bovine serum albumin (BSA; 10 g/L), dextran 40 (10 g/L), sodium heparin (2500 IU/L), amoxicillin (250 mg/L) and sodium bicarbonate (2.2 g/L). For the nanoparticle exposures, CuO or PS nanoparticles were added to the maternal chamber to reach a final concentration of 10 µg/mL (CuO, primary particle size 20 nm) and 25 µg/mL (PS, primary particle size 70 nm). Control samples were perfused with perfusion medium only. Tissue samples were collected from the villous region after 6 hours of exposure. Samples were stored in RNAlater (Thermo Fisher Scientific, Zurich, Switzerland) at -20 C.
|
| Growth protocol |
Human placentas were obtained from uncomplicated full term pregnancies after caeserean section. The donors provided written informed consent prior to delivery.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tissue lysates with miRNeasy Mini Kit (Qiagen, GmbH, Hilden, Germany) following the instructions of the manufacturer. RNA quantity and quality were assessed with NanoDrop (ND-1000, Thermo Fisher Scientific Inc., Wilmington, NC, USA) and Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), respectively. Samples with RNA integrity number > 7.5 were used for the analysis.
|
| Label |
Cy3
|
| Label protocol |
Samples (100 ng) were amplified using the T7 RNA polymerase method. cRNAs were labelled with Cy3 or Cy5 following the manufacturer's protocol (Agilent).
|
| |
|
| Hybridization protocol |
Labeled cRNA samples were hybridised onto the Agilent 2-colour 8x60k arrays according to the manufacturer's recommendations and hybridized for 17 hours at 65°C. After hybridization, slides were washed following the manufacturer's instructions (Agilent).
|
| Scan protocol |
Slides were scanned with Agilent microarray scanner G2505C and data were extracted using the Agilent Feature Extraction software (V11.5.1.1)
|
| Description |
US11263921_253949437527_S01_GE2_1105_Oct12_1_2.txt
Gene expression in the placenta after 6 hours of perfusion with the medium only
|
| Data processing |
Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and data were log2 transformed and normalized with quantile normalization. This experiment was performed as a two-colour experiment, but data were analyzed as single-channel arrays. Raw data files are available as a tar archive on the series record.
|
| |
|
| Submission date |
Dec 12, 2022 |
| Last update date |
Oct 01, 2023 |
| Contact name |
Dario Greco |
| E-mail(s) |
dario.greco@tuni.fi
|
| Organization name |
Tampere University
|
| Department |
Faculty of Medicine and Health Technology
|
| Lab |
Finnish Hub for Development and Validation of Integrated Approaches (FHAIVE)
|
| Street address |
Arvo ylpön Katu 34
|
| City |
Tampere |
| ZIP/Postal code |
33520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL16699 |
| Series (1) |
| GSE220756 |
Transcriptomic profiling reveals differential cellular response of copper oxide nanoparticles and polystyrene nanoplastics in perfused human placenta |
|
