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Sample GSM7425746 Query DataSets for GSM7425746
Status Public on May 20, 2024
Title UKN1_SBAD2_Untreated_0_4
Sample type RNA
 
Source name SBAD2 iPS cells
Organism Homo sapiens
Characteristics cell type: SBAD2 iPS cells
Sex: male
Treatment protocol On days 0, 1 and 2, differentiating cells were incubated (5% CO2, 37 °C) with paraben concentrations ranging from 0.316 – 1000 µM and valproic acid at 600 µM for a total of 96 h, as well as the vehicle alone (0.1% DMSO).
Growth protocol The differentiation of SBAD2 hiPSCs to neuroepithelial precursor cells was performed using the UKN1 protocol (Chambers et al. 2009) with minor changes. Briefly, hiPSCs were seeded in 1 ml pluripotent stem cell (PSC) medium (spiked with a Rho-kinase inhibitor (ROCKi)) per well on extracellular matrix protein-coated 12-well-plates at a density of 12,000 - 24,000 cells/cm² on day -3. On day 2 and day 1, the PSC medium was refreshed. On days 0, 1 and 2, medium was changed to differentiation medium, which was spiked with 21.6 µM SB431542, 0.64 µM dorsomorphin, 35 ng/ml noggin and 0.1% DMSO to induce neural differentiation. On day 4, medium was changed to a mixed medium of 75% differentiation medium / 25% N2-S and the same concentrations of SB431542, dorsomorphin and noggin as given above. On day 6, cells were collected for RNA extraction. A more detailed method description is given in the supplemental information.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from sonicated cell lysates with the ExtractMe Total RNA-Kit (Blirt, Poland). The concentration and purity of the RNA were determined with a NanoDrop2000 (ThermoFisher Scientific, Germany).
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 4.2.1 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 May 24, 2023
Last update date May 20, 2024
Contact name Jan Georg Hengstler
E-mail(s) hengstler@ifado.de
Organization name Leibniz-Institut für Arbeitsforschung an der TU Dortmund
Department Toxikologie / Systemtoxikologie
Street address Ardeystraße 67
City Dortmund
ZIP/Postal code 44139
Country Germany
 
Platform ID GPL570
Series (1)
GSE233332 Risk assessment of parabens in a transcriptomics-based in vitro system

Data table header descriptions
ID_REF
VALUE Log2-transformed expression values

Data table
ID_REF VALUE
1007_s_at 9.4445947139726
1053_at 7.70440728124137
117_at 5.41866319919032
121_at 7.16885039825066
1255_g_at 6.82850637294719
1294_at 5.56734999539832
1316_at 6.28133173403972
1320_at 4.493590032817
1405_i_at 3.39655345869262
1431_at 3.81426833125531
1438_at 6.07827634360825
1487_at 7.04970753203123
1494_f_at 5.28786454701076
1552256_a_at 6.57213249929368
1552257_a_at 7.7382071380657
1552258_at 3.87224993247048
1552261_at 4.196897220485
1552263_at 6.33875962607899
1552264_a_at 7.71286378364014
1552266_at 3.48290171334933

Total number of rows: 54675

Table truncated, full table size 1479 Kbytes.




Supplementary file Size Download File type/resource
GSM7425746_81_Flo_HG-U133_Plus_2_.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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