|
| Status |
Public on Oct 30, 2012 |
| Title |
hiPSCs, 24h after DMSO treatment |
| Sample type |
RNA |
| |
|
| Source name |
hiPSCs_24h_0.1% DMSO treatment
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hiPSCs (IMR90-1)
cell type: hiPSCs at day3 after cardiac differentiation onset
|
| Treatment protocol |
The medium was changed to cardiac differentiation medium with 10μM KY02111 or 0.1% DMSO at day3 after cardiac differentiation onset.
|
| Growth protocol |
hiPSCs (IMR90-1) were maintained on mitomycin C-treated mouse embryonic fibroblasts (MEF) in Primate ES Cell Culture Medium (ReproCell Inc., Japan) with 5ng/ml bFGF. Then, hiPSC colonies were harvested by digestion, and hiPSCs were cultured in 6 well plate (3-10×105 cells/cm3) in cardiac differentiation medium, which is IMDM (Sigma) containing 20% FBS (Gibco), 1% MEM non-essential amino acid solution (Sigma), 1% Penicillin-Streptomycin (Gibco), 2 mM L-glutamine (Sigma), 0.001 % 2-Mercaptoethanol (Gibco) and 0.005N NaOH, with 10ng/ml BMP4 (R&D).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Synthesis of cDNA, in vitro transcription and biotin labeling cRNA, and hybridization to the Human Gene 1.0 ST array (Affymetrix) were performed according to Affymetrix protocols.
|
| |
|
| Hybridization protocol |
Synthesis of cDNA, in vitro transcription and biotin labeling cRNA, and hybridization to the Human Gene 1.0 ST array (Affymetrix) were performed according to Affymetrix protocols.
|
| Scan protocol |
Hybridized arrays were scanned using an Affymetrix GeneChip Scanner.
|
| Description |
Gene expression data from hiPSCs at day3 after cardiac differentiation onset, 24h after control DMSO treatment
|
| Data processing |
Data normalization and further analysis were performed with GeneSpring GX (Agilent Technologies). The genes ,whose GCRMA normalized values of 0h sample were less than 300, were excluded from further analysis. Ratios of gene expression relative to control samples (KY02111/DMSO) were calculated in each time point . The down-regulated and up-regulated genes in response to KY02111 were identified by more than 25 % changes of KY/DMSO ratios at both 12 hr and 24hr after KY02111 treatment (down-regulated genes = KY12h/DMSO12h < 0.75 and KY24h/DMSO24h < 0.75, up-regulated genes = KY12h/DMSO12h > 1.25 and KY24h/DMSO24h > 1.25) [ratio_data.txt available as a Series Supplementary file].
|
| |
|
| Submission date |
Nov 11, 2011 |
| Last update date |
Oct 30, 2012 |
| Contact name |
Itsunari Minami |
| E-mail(s) |
[email protected]
|
| Organization name |
iCeMS
|
| Lab |
Nakatsuji G
|
| Street address |
Yoshida Ushinomiya-cho
|
| City |
Kyoto, Sakyo-ku |
| ZIP/Postal code |
606-8501 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE33622 |
Expression data from human iPS cells treated by a small molecule KY02111 |
|
