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Sample GSM7439177 Query DataSets for GSM7439177
Status Public on Jun 06, 2023
Title UKK2_hiPSC_VPA_Day1_R1
Sample type RNA
 
Source name IMR90 hiPSC cells
Organism Homo sapiens
Characteristics gender: female
state: proliferating state
agent: VPA
time point: Day1
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

Data table header descriptions
ID_REF
VALUE Log2-transformed expression values

Data table
ID_REF VALUE
1007_s_at 8.717843389
1053_at 9.122026438
117_at 5.388145544
121_at 7.657097476
1255_g_at 5.533589215
1294_at 5.960784652
1316_at 5.532135298
1320_at 4.393794663
1405_i_at 3.837069824
1431_at 3.487412097
1438_at 5.931435407
1487_at 7.300357326
1494_f_at 5.563705001
1552256_a_at 8.302489987
1552257_a_at 8.266754234
1552258_at 3.663843142
1552261_at 4.360851987
1552263_at 6.958732927
1552264_a_at 7.808372106
1552266_at 3.28388354

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM7439177_40.a_6.12.21_Anna_HG-U133_Plus_2_.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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