Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 12
Release date: Jun 20 2016
Last update date: Aug 9 2018
Access: Public
Dataset link Characteristic expression of MSX1, MSX2, TBX2, and ENTPD1 in dental pulp cells

Experimental Protocol


Dental pulp cells were isolated by the explant outgrowth method (Calcified tissue international (2000) 66:129-138.) from healthy teeth according to protocol approved by ethical authorities at Hiroshima University. Human skin fibroblasts were obtained from Kurabo (Osaka, Japan). Human gingival fibroblasts were isolated as described previously (Journal of periodontal research (2003) 38: 242-246.). Bone marrow-derived MSCs (BM-MSCs) were isolated13 from Hiroshima University with informed consent, or were obtained from Cambrex Bio Science Walkersville, Inc. (Walkersville, MD) and PromoCell Co., Ltd. (Heidelberg, Germany). Osteoarthritis and rheumatoid arthritis synovium-derived MSCs, and adipose tissue-derived MSCs, were obtained from Cell Applications Inc. (San Diego, CA) and Zen-Bio Inc. (Research Triangle Park, NC). Osteoblasts, adipocytes, and chondrocytes, which were derived from BM-MSC, were cultured with appropriate differentiation-inducing media for 28 days (Genes to cells (2009)14:407-424). Cells were cultured under similar conditions using the same batch of FBS. These cells were expanded with FGF-2 to maintain their multipotent nature throughout several mitotic divisions. We removed FGF-2 from the culture medium 72 h before the isolation of RNA to decrease a direct effect of the growth factor on gene expression. The total RNA was isolated, 24 h after the cultures reached confluency, using TRIzol (Life Technologies, Japan) and an RNeasy Mini Kit (Qiagen, Chatsworth, CA). DNA microarray analysis was performed by KURABO GeneChip Custom Analysis Service with Human Genome U133 Plus 2.0 chips(Affymetrix. Inc., Santa Clara, CA). The CHP data (Microarray Suite version 5.0, Scaling Factor = 1, Normalization Value = 1, Detection Call a1 = 0.05, a2 = 0.065, Tau = 0.015, Affymetrix Inc.) were standardized by the global median normalization method using GeneSpring (Silicon Genetics, Redwood City, CA). The normalization was limited by flag values, and the median was calculated using the genes that exceeded the Present or Marginal flag restriction.

Repositories


GEO

GSE66084

BioProject

PRJNA275856

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Contact


katsumi Fujimoto