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1.  An in situ hybridization-based screen for heterogeneously expressed genes in mouse ES cells 
Gene expression patterns : GEP  2007;8(3):181-198.
We previously reported that Zscan4 showed heterogeneous expression patterns in mouse embryonic stem (ES) cells. To identify genes that show similar expression patterns, we carried out high-throughput in situ hybridization assays on ES cell cultures for 244 genes. Most of the genes are involved in transcriptional regulation, and were selected using microarray-based comparisons of gene expression profiles in ES and embryonal carcinoma (EC) cells versus differentiated cell types. Pou5f1 (Oct4, Oct3/4) and Krt8 (EndoA) were used as controls. Hybridization signals were detected on ES cell colonies for 147 genes (60%). The majority (136 genes) of them showed relatively homogeneous expression in ES cell colonies. However, we found that two genes unequivocally showed Zscan4-like spotted expression pattern (spot-in-colony pattern; Whsc2 and Rhox9). We also found that nine genes showed relatively heterogeneous expression pattern (mosaic-in-colony pattern: Zfp42/Rex1, Rest, Atf4, Pa2g4, E2f2, Nanog, Dppa3/Pgc7/Stella, Esrrb, and Fscn1). Among these genes, Zfp42/Rex1 showed unequivocally heterogeneous expression in individual ES cells prepared by the CytoSpin. These results show the presence of different types or states of cells within ES cell cultures otherwise thought to be undifferentiated and homogeneous, suggesting a previously unappreciated complexity in ES cell cultures.
PMCID: PMC2238805  PMID: 18178135
ES cells; EC cells; pluripotent stem cells; heterogeneous gene expression; homogeneous gene expression; Zscan4; Pou5f1; Oct4; Oct3/4; Krt8; EndoA; Whsc2; Nelfa; Rhox9; Zfp42; Rex1; Rest; Zfp42; Rex1; Rest; Atf4; Pa2g4; E2f2; Nanog; Dppa3; Pgc7; Stella; Esrrb; Fscn1
2.  High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridization 
Gene expression patterns : GEP  2005;6(2):213-224.
Mammalian preimplantation embryos provide an excellent opportunity to study temporal and spatial gene expression in whole mount in situ hybridization (WISH). However, large-scale studies are made difficult by the size of the embryos (∼60 μm diameter) and their fragility. We have developed a chamber system that allows parallel processing of embryos without the aid of a microscope. We first selected 91 candidate genes that were transcription factors highly expressed in blastocysts, and more highly expressed in embryonic (ES) than in trophoblast (TS) stem cells. We then used the WISH to identify 48 genes expressed predominantly in the ICM and to follow several of these genes in all seven preimplantation stages. The ICM-predominant expressions of these genes suggest their involvement in the pluripotency of embryonic cells. This system provides a useful tool to a systematic genome-scale analysis of preimplantation embryos.
PMCID: PMC1850761  PMID: 16325481
preimplantation embryo; whole mount in situ hybridization; High-throughput screen; hybridization chamber; ICM; TE

Results 1-2 (2)