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Series GSE8555 Query DataSets for GSE8555
Status Public on Jul 25, 2007
Title Genome-wide analysis of Phgdh inactivation in murine embryonic head
Organism Mus musculus
Experiment type Expression profiling by array
Summary D-3-Phosphoglycerate dehydrogenase (Phgdh; EC is a necessary enzyme for de novo L-serine biosynthesis via the phosphorylated pathway. We demonstrated previously that Phgdh is expressed exclusively by neuroepithelium and radial glia in developing mouse brain and later mainly by astrocytes. Mutations in the human PHGDH gene cause serine deficiency disorders (SDD) associated with severe neurological symptoms such as congenital microcephaly, psychomotor retardation, and intractable seizures. We recently demonstrated that genetically engineered mice, in which the gene for Phgdh has been disrupted, have significantly decreased levels of serine and glycine, and exhibit malformation of brain such as microcephaly. The Phgdh null (KO) embryos exhibit lethal phenotype after gestational day 14, indicating that the phosphorylated pathway is essential for embryogenesis, especially for brain development. It is worth noting that the Phgdh knockout (KO) embryos primarily displayed microcephaly, which is the most conspicuous phenotype of patients with SDD. Thus, Phgdh KO mice are a useful animal model for studying the effect of diminished L-serine levels on development of the central nervous system and other organs. To better understand the mechanism underlying the molecular pathogenesis of SDD, we sought to examine whether gene expression is altered in the Phgdh KO mouse model. We identify genes that have altered expression in the head of the Phgdh KO embryos using the GeneChip array. Some of the genes identified by this method belong in functional categories that are relevant to the biochemical and morphological aberrations of the Phgdh deletion.
Keywords: genetic modification
Overall design Total RNA samples were prepared from head tissues from 2 embryos of Phgdh knockout and littermate wild-type controls.
RNA of 4 biological replicates was hybridized to Affymetrix Mouse Genome 430 2.0 arrays. Five microgram total RNA was labelled according to the ENZO-protocol, fragmented and hybridized according to Affymetrix's protocols.
Contributor(s) Furuya S, Yoshida K, Hirabayashi Y
Citation(s) 18228065
Submission date Jul 23, 2007
Last update date Feb 11, 2019
Contact name Shigeki Furuya
Organization name Kyushu University
Department Bio-Architecture Center
Lab Furuya Laboratory
Street address 6-10-1 Hakozaki, Higashiku
City Fukuoka
State/province Fukuoka
ZIP/Postal code 812-8581
Country Japan
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (8)
GSM212558 Gene expression profiling of Phgdh knockout embryo wild1
GSM212559 Gene expression profiling of Phgdh knockout embryo KO1
GSM212560 Gene expression profiling of Phgdh knockout embryo wild2
BioProject PRJNA101697

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Supplementary file Size Download File type/resource
GSE8555_RAW.tar 126.0 Mb (http)(custom) TAR (of CEL, CHP, EXP)
Processed data included within Sample table
Processed data provided as supplementary file
Raw data provided as supplementary file

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