|
| Status |
Public on May 09, 2020 |
| Title |
Gin-1 |
| Sample type |
RNA |
| |
|
| Source name |
hiPSC-derived DMD patient myoblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC-derived DMD patient myoblasts
treatment: ginsenoside Rd(5 micromolar) treated for 24 hours
|
| Treatment protocol |
Triplicate samples were used in microarray analysis. D2 hiPSC-derived myoblasts were treated with ginsenoside (5μM), fenofibrate (8μM) and DMSO for 24h in the differentiation medium.
|
| Growth protocol |
The DMD(D2325) hiPSC-derived myoblasts which carries mutation c.457 C->T were differentiated using the CHIR-DAPT protocol . Briefly, hiPSCs were plated as single cells on Geltrex (Gibco) treated dishes, at a density of 1.5 x 105 cells per well of a 24-well plate, in the presence of MEF-conditioned N2 media containing 10 ng/ml of FGF-2 (PeproTech) and 10 μM of Y-27632 (Cayman). The cells were induced to differentiate into myoblasts by adding CHIR99021 (3μM) in N2 medium for 4 days and by DAPT (10 μM) for the following 8 days. Afterwards cells continue to differentiate and mature in N2 medium for the next 13 days. Myoblasts were collected by FACS with the selection marker NCAM+/HNK1-. The NCAM+/HNK1- myoblasts were maintained in a humidified incubator containing 5% CO2 at 37°C, and grown in N2 media supplemented with 10% fetal bovine serum (FBS). To induce myotube formation, expanded NCAM+/HNK1- myoblasts were plated to confluence, and switched to N2 media without serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from Trizol-suspended cells with the QIAGEN RNeasy Mini Kit according to manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
RNA was labeled with the Affymetrix GeneChip WT PLUS Reagent Kit using the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
17 hours at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.
|
| Scan protocol |
Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.
|
| Description |
D2325 hiPSC-derived myoblasts treated with ginsenoside Rd-rep1
|
| Data processing |
Affymetrix CEL files were extracted with the Partek GS 6.6 platform and their data RMA and quantile-normalized to create log2 transcript signal values, which were used in subsequent ANOVA analysis.
|
| |
|
| Submission date |
Oct 09, 2018 |
| Last update date |
May 11, 2020 |
| Contact name |
Gabsang Lee |
| E-mail(s) |
glee48@jhmi.edu
|
| Phone |
443-287-8631
|
| Organization name |
The Johns Hopkins University
|
| Department |
School of Medicine
|
| Lab |
Institute for Cell Engineering
|
| Street address |
733 North Broadway
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL23159 |
| Series (1) |
| GSE121023 |
Gene expression data from DMD patient hiPSC-derived myoblasts treated with fenofibrate, ginsenoside Rd or DMSO |
|
