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Sample GSM1378088 Query DataSets for GSM1378088
Status Public on May 04, 2014
Title hAFSC before osteogenic induction
Sample type RNA
 
Source name hAFSC before osteogenic induction
Organism Homo sapiens
Characteristics cell type: Human amniotic fluid stem cells (hAFSC)
time point: before osteogenic induction
Treatment protocol The hAECs, hBMSCs and hAFMSCs were cultured in a classical osteogenic induction medium [α-MEM (Invitrogen, China) supplemented with 10% FBS (Gibico, China), 0.1 mM ascorbic acid (Sigma-Aldrich, USA), 10 mM β-glycerophosphate (Sigma-Aldrich, USA), 10-5 mM dexamethasone (Sigma-Aldrich, USA)]. After the 7-day osteogenic induction, total RNA was extracted with RNAiso Plus reagent (Takara, Japan).
Growth protocol The hAECs, hBMSCs and hAFMSCs were cultured in the expansion culture medium (ECM) with regular passaging. The ECM for hAECs was prepared with DMEM/F12 medium (Invitrogen, China) supplemented with 2 mM L-Glutamine (Invitrogen, China), 10 ng/ml rhEGF (Invitrogen, China), 20% fetal bovine serum (Gibco, China) and 1% antibiotic-antimycotic (Gibco, China). The ECM for hBMSCs and hAFMSCs was prepared with DMEM/F12 medium (Invitrogen, China) supplemented with 2 mM L-Glutamine (Invitrogen, China), 10 ng/ml rhFGF (Invitrogen, China), 20% fetal bovine serum (Gibco, China) and 1% antibiotic-antimycotic (Gibco, China).
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNAs integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).
Label biotin
Label protocol The sample labeling was performed based on the manufacturer’s standard protocols.
 
Hybridization protocol The microarray hybridization was performed based on the manufacturer’s standard protocols.
Scan protocol The arrays were scanned by the Affymetrix Scanner 3000(Affymetrix)
Description AFSC D0
Data processing Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Then the gene expression analysis and alternative splice analysis proceeded separately. [1] Gene expression analysis: Genesrping software (version 12.5; Agilent Technologies) was employed to finish the basic analysis. Differentially expressed genes were then identified through fold change. The threshold set for up- and down-regulated genes was a fold change>= 1.5 [2] Alternative splice analysis: Alternative splice analysis was conducted by Transcriptome Analysis Console (version1.0, Affymetrix). Differential exon or junction identified through splicing index. The threshold was splicing index >= 2.0 or < = -2.0 .
 
Submission date May 03, 2014
Last update date May 04, 2014
Contact name Jiawen Si
E-mail(s) dentarsjw@gmail.com
Organization name Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine
Department Department of Oral and Maxillofacial Surgery
Lab Shanghai Key Laboratory of Stomatology
Street address 639, Zhizaoju Road
City Shanghai
ZIP/Postal code 200011
Country China
 
Platform ID GPL17585
Series (1)
GSE57265 Expression data of hAEC, hAFSC and hBMSC before and after osteogenic induction in vitro

Data table header descriptions
ID_REF
VALUE Quantification
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
JUC01000001.hg.1 7.13922 0.0349806
JUC01000002.hg.1 4.29388 0.44915
JUC01000003.hg.1 6.4833 0.012195
JUC01000004.hg.1 5.73478 0.0812735
JUC01000005.hg.1 8.40499 0.000370247
JUC01000006.hg.1 6.56194 0.0458539
JUC01000007.hg.1 4.19543 0.647429
JUC01000008.hg.1 6.08747 0.00289434
JUC01000009.hg.1 3.54306 0.0261889
JUC01000010.hg.1 2.49642 0.0729334
JUC01000011.hg.1 10.7801 1.2733e-05
JUC01000012.hg.1 7.92815 0.0581187
JUC01000013.hg.1 10.5523 7.81118e-08
JUC01000014.hg.1 7.97729 1.08206e-07
JUC01000015.hg.1 5.56835 0.0144026
JUC01000016.hg.1 9.5664 1.00919e-06
JUC01000017.hg.1 5.94023 1.7947e-05
JUC01000018.hg.1 7.4357 0.0642251
JUC01000019.hg.1 9.58969 5.18896e-06
JUC01000020.hg.1 9.58969 5.18896e-06

Total number of rows: 914585

Table truncated, full table size 32001 Kbytes.




Supplementary file Size Download File type/resource
GSM1378088_AFSC_D0.CEL.gz 25.3 Mb (ftp)(http) CEL
GSM1378088_AFSC_D0.chp.gz 9.3 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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