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Sample GSM7439162 Query DataSets for GSM7439162
Status Public on Jun 06, 2023
Title UKK2_hiPSC_Buspirone_Day4_R1
Sample type RNA
 
Source name IMR90 hiPSC cells
Organism Homo sapiens
Characteristics gender: female
state: proliferating state
agent: Buspirone
time point: Day4
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 8.812195114
1053_at 8.469779883
117_at 5.023329584
121_at 7.534972809
1255_g_at 5.458119769
1294_at 5.6019982
1316_at 6.091903018
1320_at 4.477070974
1405_i_at 3.576547634
1431_at 3.407341654
1438_at 7.642656419
1487_at 6.912398203
1494_f_at 5.184186257
1552256_a_at 7.172514843
1552257_a_at 8.069553096
1552258_at 3.782332088
1552261_at 4.861435471
1552263_at 6.646196297
1552264_a_at 7.209087789
1552266_at 3.200357188

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM7439162_25.a_6.12.21_Anna_HG-U133_Plus_2_.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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