|
| Status |
Public on Dec 03, 2019 |
| Title |
hESCs, culturing medium for 6 days, D12_21 |
| Sample type |
RNA |
| |
|
| Source name |
hESCs have been incubated with culturing medium for 6 days
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
cell status: differentiated state
cell type: hESCs
incubated or treated with: culturing medium for 6 days
|
| Treatment protocol |
H9 hESCs were differentiated for 6 days in the presence and absence of the toxicants into neuroepithelia progenitors (NEP) (Krug AK et al. (2013) Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Arch Toxicol 87(1):123-43).
|
| Growth protocol |
According to Krug AK et al. (2013) Human embryonic stem cell-derived test systems for developmental neurotoxicity: a transcriptomics approach. Arch Toxicol 87(1):123-43).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from 6 days differentiated hESCs in the presence and absence of benchmark concentration (BMC) of toxicants has been isolated with Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen
|
| Label |
biotin
|
| Label protocol |
100ng total RNA was used for aRNA amplification with GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15µg of purified aRNA was fragmented with fragmentation buffer
|
| |
|
| Hybridization protocol |
12.5µg of fragmented aRNA was hybridized to the Human Genome U133 plus 2.0 microarrays in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.
|
| Scan protocol |
Arrays were washed and stained with phycoerythrin with Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions
|
| Data processing |
The quality control (QC) matrices were confirmed with expression console software (Affymertix, USA) and Partek genomics suite version 6.6 (Partek Inc.St.Louis,USA). QC passed CEL files were further analyzed using Partek genomics suite version 6.6. All CEL files were RMA background corrected, quantile normalized and all probe sets were summarized using median polish algorithm.
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| |
|
| Submission date |
Dec 02, 2019 |
| Last update date |
Dec 05, 2019 |
| Contact name |
Marcel Leist |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Konstanz
|
| Lab |
In vitro toxicology and biomedicine
|
| Street address |
Universitätsstraße 10
|
| City |
Konstanz |
| ZIP/Postal code |
78464 |
| Country |
Germany |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE141253 |
Development of a neural rosette formation assay (RoFA) to identify neurodevelopmental toxicants and to characterize their transcriptome disturbances |
|
| Relations |
| Reanalysis of |
GSM1827662 |
