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Sample GSM6813744 Query DataSets for GSM6813744
Status Public on Oct 01, 2023
Title Donor_S93_before_perfusion
Sample type RNA
Source name Human placenta prior to perfusion, donor S93
Organism Homo sapiens
Characteristics donor: S93
dose: 0 µg/ml
exposure time: 0 hours
treatment: untreated
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 Cy5
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 from donor S93 prior to perfusion
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
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

Data table header descriptions
VALUE Log2 transformed and quantile normalized values

Data table
1 15.00205637
2 5.646696041
3 5.537575337
4 11.34868361
5 6.870209158
6 5.656219804
7 5.708875982
8 6.20696607
9 12.42215792
10 7.997028538
11 6.444673414
12 11.86241294
13 9.459045444
14 5.78422599
15 5.656219804
16 5.682580535
17 12.83761439
18 8.858526911
19 8.509064807
20 11.97745449

Total number of rows: 62976

Table truncated, full table size 1087 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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