|
| Status |
Public on Nov 03, 2018 |
| Title |
Day0-1 |
| Sample type |
RNA |
| |
|
| Source name |
human ESC-MSCs, IFN-gamma nontreated, replicate 1
|
| Organism |
Homo sapiens |
| Characteristics |
agent: none
cell type: h1ESCs obtained from WiCell
|
| Treatment protocol |
human IFN-gamma treats the hESC-MSCs for 0, 1, 3 days respectively
|
| Growth protocol |
hESC-MSCs were kept in an undifferentiated state by using 10%FBS and 90%L-DMEM
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions
|
| Label |
Cy3
|
| Label protocol |
cDNA labeled with a fluorescent dye (Cy5 or Cy3-dCTP) was produced by Eberwine¡¯s linear RNA amplification method and subsequent enzymatic reaction
|
| |
|
| Hybridization protocol |
Labeled controls and test samples labeled with Cy5-dCTP and Cy3-dCTP were dissolved in 80 mL hybridization solution containing 3¡ÁSSC, 0.2% SDS, 5¡ÁDenhardt¡¯s solution and 25% formamide. DNA in hybridization solution was denatured at 95¡æ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42¡æ and washed with two consecutive solutions
|
| Scan protocol |
CapitalBio Technology Human LncRNA Array v4 was designed with four identical arrays per slide (4 x 180K format), with each array containing probes interrogating about 41,000 human lncRNAs and about 34,000 human mRNAs.
|
| Description |
Gene expression in IFN-gamma nontreated hESC-MSCs
|
| Data processing |
The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent). To select the differentially expressed genes, we used thresholdvalues of ¡Ý2 and ¡Ü_2-fold change and a Benjamini-Hochberg corrected p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998). Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).
|
| |
|
| Submission date |
Nov 02, 2018 |
| Last update date |
Nov 03, 2018 |
| Contact name |
Hua Liu |
| E-mail(s) |
liuhua@zju.edu.cn
|
| Organization name |
School of Medicine,Zhejiang University
|
| Department |
Li Dak Sum & Yip Yio Chin Center for Stem Cells and Regenerative Medicine Key Laboratory of Tissue Engineering and Regenerative Medicine of Zhejiang Province
|
| Street address |
#866 Yu Hang Tang Rd
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL20115 |
| Series (1) |
| GSE122091 |
human ESC-MSCs: IFN-γ-nontreated, IFN-γ-treated for 1 day, IFN-γ-treated for 3 days |
|
