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Sample GSM3454784 Query DataSets for GSM3454784
Status Public on Nov 03, 2018
Title Day3-2
Sample type RNA
 
Source name human ESC-MSCs, IFN-gamma treated for 3days, replicate 2
Organism Homo sapiens
Characteristics agent: IFN-gamma
time point: 3days
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 Cy5
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 treated for 3day 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

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 4.040564039
DarkCorner -5.681092977
p42318_v4 -5.971567842
p117 3.423452548
p28737 -6.035350093
p17314 -6.078120355
A_33_P3310047 -1.549975587
p22477 -6.013715583
p8225 -2.805105868
p7095 -1.065640918
p19421 -6.047095892
p1301 -5.975831545
A_24_P58881 3.67500847
A_21_P0011890 -1.010731355
A_33_P3234550 -6.058825078
A_33_P3397840 -2.053030141
p35974_v4 -1.202875179
A_23_P217621 -4.992814118
A_21_P0008663 -3.01832023
p34840_v4 2.775242784

Total number of rows: 75217

Table truncated, full table size 1713 Kbytes.




Supplementary file Size Download File type/resource
GSM3454784_US10313827_256740610562_S01_GE2_1105_Oct12_1_4r.txt.gz 8.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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