|
| Status |
Public on Jun 06, 2023 |
| Title |
UKK2_hiPSC_untreated_Day 0_R2 |
| Sample type |
RNA |
| |
|
| Source name |
IMR90 hiPSC cells
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
state: pluripotent state
agent: untreated
time point: Day 0
|
| Treatment protocol |
Cells were incubated (5 % CO2, 37 °C) with the test compounds at different concentrations and a DMSO concentration of 0.1 % or 0.5 %.
|
| Growth protocol |
Cells were differentiated in RPMI 1640 GlutaMAX™ medium (Thermo Fisher Scientific, Germany) plus B-27™ Supplement, minus insulin (Thermo Fisher Scientific, Germany) supplemented with 10 µM Wnt activator small molecule CHIR99021 (R&D Systems, Minneapolis, USA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were homogenised with TRIzol lysis reagent (Thermo Fisher Scientific, Germany), and the total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.
|
| Label |
biotin
|
| Label protocol |
The samples were amplified and labelled with biotin using GeneChip 3′ IVT Express Kit per the manufacturer’s instructions (Affymetrix, High Wycombe, UK).
|
| |
|
| Hybridization protocol |
The samples were purified using magnetic beads and fragmented. 12,5 μg of fragmented RNA samples were hybridized on Affymetrix Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA, USA). The microarray hybridization step was performed in an Affymetrix GeneChip Hybridization Oven-645 for 16 h at 45 °C and 60 rpm. Washing and staining of the hybridized arrays was completed using the GeneChip HWS Kit (Affymetrix, High Wycombe, United Kingdom) and Affymetrix GeneChip Fluidics Station-450.
|
| Scan protocol |
Stained arrays were scanned with Affymetrix Gene-Chip Scanner-3000-7G and evaluated for quality control with Affymetrix GCOS software
|
| Data processing |
All analyses were conducted using the statistical software R, version 4.2.2. Pre-processing of the data consists of the three steps background correction, normalization, and summarization, using the frozen robust multi-array average (fRMA) algorithm. This yields expression values for 54675 probe sets. The R-packages affy, frma and hgu133plus2frmavecs were used.
|
| |
|
| Submission date |
Jun 01, 2023 |
| Last update date |
Jun 06, 2023 |
| Contact name |
Agapios Sachinidis |
| E-mail(s) |
a.sachinidis@uni-koeln.de
|
| Phone |
+492214787373
|
| Organization name |
University of Cologne
|
| Department |
Institute of Neurophysiology
|
| Street address |
Robert-Kochstr. 39
|
| City |
Cologne |
| State/province |
NRW |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE233924 |
Identification of cardiac developmental toxicants in differentiated human induced pluripotent stem cells [Toxicants] |
| GSE233926 |
Identification of cardiac developmental toxicants in differentiated human induced pluripotent stem cells |
|
