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Series GSE49171 Query DataSets for GSE49171
Status Public on Sep 01, 2013
Title Comparative gene expression analyses using post-implanted E6.5 cloned embryos
Organism Mus musculus
Experiment type Expression profiling by array
Summary The great majority of embryos generated by somatic cell nuclear transfer (SCNT) display defined abnormal phenotypes after implantation, such as an increased likelihood of death and abnormal placentation. To gain better insight into the underlying mechanisms, we analyzed genome-wide gene expression profiles of day 6.5 postimplantation mouse embryos cloned from three different cell types (cumulus cells, neonatal Sertoli cells and fibroblasts). The embryos retrieved from the uteri were separated into embryonic (epiblast) and extraembryonic (extraembryonic ectoderm and ectoplacental cone) tissues and were subjected to gene microarray analysis. Genotype- and sex-matched embryos produced by in vitro fertilization (IVF) were used as controls. Principal component analysis revealed that whereas the gene expression patterns in the embryonic tissues varied according to the donor cell type, those in extraembryonic tissues were relatively consistent across all groups. Within each group, the embryonic tissues had more differentially expressed genes (DEGs) (> 2-fold vs. controls) than did the extraembryonic tissues (P < 1.0 × 10–26). In the embryonic tissues, one of the common abnormalities was upregulation of Dlk1, a paternally imprinted gene. This might be a potential cause of the occasional placenta-only conceptuses seen in SCNT-generated mouse embryos (1–5% per embryo transferred in our laboratory), because dysregulation of the same gene is known to cause developmental failure of embryos derived from induced pluripotent stem cells. There were also some DEGs in the extraembryonic tissues, which might explain the poor development of SCNT-derived placentas at early stages, although these alterations were not always statistically significant for all three SCNT groups because of variability. These findings suggest that SCNT affects the embryonic and extraembryonic development differentially and might cause further deterioration in the embryonic lineage in a donor cell-specific manner. This could explain donor cell-dependent variations in cloning efficiency using SCNT.
 
Overall design Comparative gene expression analyses using post-implanted E6.5 cloned embryos were performed by microarray. Cloned embryos were produced with three different types of donor cells (cumulus cells, neonatal Sertoli cells and fibroblasts). As controls, sex- and genotype-matched embryos produced by in vitro fertilization were used. Each embryos were mechanically dissected into the embryonic and extraembryonic parts at E6.5 and were subjected to gene expression microarray.
 
Contributor(s) Hirawasa R, Matoba S, Inoue K, Ogura A
Citation(s) 24146866
Submission date Jul 24, 2013
Last update date Jan 12, 2017
Contact name Kimiko Inoue
E-mail(s) kimiko.inoue@riken.jp
Organization name BRC, RIKEN
Department Bioresource Engineering Division
Street address 3-1-1 Koyadai
City Tsukuba
State/province Ibaraki
ZIP/Postal code 305-0074
Country Japan
 
Platforms (1)
GPL7202 Agilent-014868 Whole Mouse Genome Microarray 4x44K G4122F (Probe Name version)
Samples (30)
GSM1194932 Cumulus_clone_embryonic_E6.5_rep1
GSM1194933 Cumulus_clone_embryonic_E6.5_rep2
GSM1194934 Cumulus_clone_embryonic_E6.5_rep3
This SubSeries is part of SuperSeries:
GSE49173 Donor cell type-specific gene expression in embryonic but not extraembryonic tissues of postimplantation embryos cloned from somatic cells
Relations
BioProject PRJNA213218

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE49171_RAW.tar 65.7 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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