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Transcriptome analysis of mouse stem cells and early embryos.

Sharov AA, Piao Y, Matoba R, Dudekula DB, Qian Y, VanBuren V, Falco G, Martin PR, Stagg CA, Bassey UC, Wang Y, Carter MG, Hamatani T, Aiba K, Akutsu H, Sharova L, Tanaka TS, Kimber WL, Yoshikawa T, Jaradat SA, Pantano S, Nagaraja R, Boheler KR, Taub D, Hodes RJ, Longo DL, Schlessinger D, Keller J, Klotz E, Kelsoe G, Umezawa A, Vescovi AL, Rossant J, Kunath T, Hogan BL, Curci A, D'Urso M, Kelso J, Hide W, Ko MS - PLoS Biol. (2003)

Bottom Line: Principal component analysis identified a set of 88 genes whose average expression levels decrease from oocytes to blastocysts, stem cells, postimplantation embryos, and finally to newborn tissues.This can be a first step towards a possible definition of a molecular scale of cellular potency.The nonrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine.

View Article: PubMed Central - PubMed

Affiliation: National Institute on Aging, Baltimore, Maryland, USA.

ABSTRACT
Understanding and harnessing cellular potency are fundamental in biology and are also critical to the future therapeutic use of stem cells. Transcriptome analysis of these pluripotent cells is a first step towards such goals. Starting with sources that include oocytes, blastocysts, and embryonic and adult stem cells, we obtained 249,200 high-quality EST sequences and clustered them with public sequences to produce an index of approximately 30,000 total mouse genes that includes 977 previously unidentified genes. Analysis of gene expression levels by EST frequency identifies genes that characterize preimplantation embryos, embryonic stem cells, and adult stem cells, thus providing potential markers as well as clues to the functional features of these cells. Principal component analysis identified a set of 88 genes whose average expression levels decrease from oocytes to blastocysts, stem cells, postimplantation embryos, and finally to newborn tissues. This can be a first step towards a possible definition of a molecular scale of cellular potency. The sequences and cDNA clones recovered in this work provide a comprehensive resource for genes functioning in early mouse embryos and stem cells. The nonrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine.

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Related in: MedlinePlus

PCA Analysis of EST FrequencyThe results were obtained by analyzing 2,812 genes that exceeded 0.1% in at least one library. (A) 3D biplot that shows both cell types (red spheres) and genes (yellow boxes). (B) 2D PCA of cell types. EST frequencies were log-transformed before the analysis. Names of some cells and tissues are abbreviated as follows: 6.5 EP, E6.5 whole embryo (embryo plus placenta); 7.5 EP, E7.5 whole embryo (embryo plus placenta); 8.5 EP, E8.5 whole embryo (embryo plus placenta); 9.5 EP, E9.5 whole embryo (embryo plus placenta); 7.5 E, E7.5 embryonic part only; 7.5 P, E7.5 extraembryonic part only; NbOvary, newborn ovary; NbBrain, newborn brain; NbHeart, newborn heart; NbKidney, newborn kidney; 13.5 VMB, E13.5 ventral midbrain dopamine cells; 12.5 Gonad (F), E12.5 female gonad/mesonephros; 12.5 Gonad (M), E12.5 male gonad/mesonephros; HS (Kit−, Sca1−), hematopoietic stem/progenitor cells (Lin−, Kit−, Sca1−); HS (Kit−, Sca1+), hematopoietic stem/progenitor cells (Lin−, Kit−, Sca1+); HS (Kit+, Sca1−), hematopoietic stem/progenitor cells (Lin−, Kit+, Sca1−); HS (Kit+, Sca1+), hematopoietic stem/progenitor cells (Lin−, Kit+, Sca1+); and NS-D, differentiated NS cells.
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pbio.0000074-g004: PCA Analysis of EST FrequencyThe results were obtained by analyzing 2,812 genes that exceeded 0.1% in at least one library. (A) 3D biplot that shows both cell types (red spheres) and genes (yellow boxes). (B) 2D PCA of cell types. EST frequencies were log-transformed before the analysis. Names of some cells and tissues are abbreviated as follows: 6.5 EP, E6.5 whole embryo (embryo plus placenta); 7.5 EP, E7.5 whole embryo (embryo plus placenta); 8.5 EP, E8.5 whole embryo (embryo plus placenta); 9.5 EP, E9.5 whole embryo (embryo plus placenta); 7.5 E, E7.5 embryonic part only; 7.5 P, E7.5 extraembryonic part only; NbOvary, newborn ovary; NbBrain, newborn brain; NbHeart, newborn heart; NbKidney, newborn kidney; 13.5 VMB, E13.5 ventral midbrain dopamine cells; 12.5 Gonad (F), E12.5 female gonad/mesonephros; 12.5 Gonad (M), E12.5 male gonad/mesonephros; HS (Kit−, Sca1−), hematopoietic stem/progenitor cells (Lin−, Kit−, Sca1−); HS (Kit−, Sca1+), hematopoietic stem/progenitor cells (Lin−, Kit−, Sca1+); HS (Kit+, Sca1−), hematopoietic stem/progenitor cells (Lin−, Kit+, Sca1−); HS (Kit+, Sca1+), hematopoietic stem/progenitor cells (Lin−, Kit+, Sca1+); and NS-D, differentiated NS cells.

Mentions: The global expression patterns of 2,812 relatively abundant genes (see Materials and Methods; Dataset S9) were further analyzed by principal component analysis (PCA), which reduces high-dimensionality data into a limited number of principal components. The first principal component (PC1) captures the largest contributing factor of variation, which in this case corresponds to the average EST frequency in all tissues, and subsequent principal components correspond to other factors with smaller effects, which characterize the differential expression of genes. As we were interested in the differential gene expression component, we plotted the position of each cell type against the PC2, PC3, and PC4 axis in three-dimensional (3D) space by using virtual reality modeling language (VRML) (Figure 4A; Video S1; a full interactive view is available on http://lgsun.grc.nia.nih.gov/Supplemental-Information). Genes were also plotted in the same 3D space (a version of PCA called a biplot) (Chapman et al. 2002) to see their association with cell/tissue types. Close examination of the 3D model identified PC2 and PC3 as the most representative views of the 3D model (Figure 4B). A two-dimensional (2D) plot of PC2 and PC3 is therefore used for the following discussion, with references to the 3D model. It is important to keep in mind that the distance between cell types along principal components has a substantial error associated with randomness of clone counts in EST libraries. The estimated error range (2*SE) in the PC3 scale is about 7%–9% based on Poisson distribution (Figure 4B). Nonetheless, PCA identifies major trends and clusters in gene expression among these cell types.


Transcriptome analysis of mouse stem cells and early embryos.

Sharov AA, Piao Y, Matoba R, Dudekula DB, Qian Y, VanBuren V, Falco G, Martin PR, Stagg CA, Bassey UC, Wang Y, Carter MG, Hamatani T, Aiba K, Akutsu H, Sharova L, Tanaka TS, Kimber WL, Yoshikawa T, Jaradat SA, Pantano S, Nagaraja R, Boheler KR, Taub D, Hodes RJ, Longo DL, Schlessinger D, Keller J, Klotz E, Kelsoe G, Umezawa A, Vescovi AL, Rossant J, Kunath T, Hogan BL, Curci A, D'Urso M, Kelso J, Hide W, Ko MS - PLoS Biol. (2003)

PCA Analysis of EST FrequencyThe results were obtained by analyzing 2,812 genes that exceeded 0.1% in at least one library. (A) 3D biplot that shows both cell types (red spheres) and genes (yellow boxes). (B) 2D PCA of cell types. EST frequencies were log-transformed before the analysis. Names of some cells and tissues are abbreviated as follows: 6.5 EP, E6.5 whole embryo (embryo plus placenta); 7.5 EP, E7.5 whole embryo (embryo plus placenta); 8.5 EP, E8.5 whole embryo (embryo plus placenta); 9.5 EP, E9.5 whole embryo (embryo plus placenta); 7.5 E, E7.5 embryonic part only; 7.5 P, E7.5 extraembryonic part only; NbOvary, newborn ovary; NbBrain, newborn brain; NbHeart, newborn heart; NbKidney, newborn kidney; 13.5 VMB, E13.5 ventral midbrain dopamine cells; 12.5 Gonad (F), E12.5 female gonad/mesonephros; 12.5 Gonad (M), E12.5 male gonad/mesonephros; HS (Kit−, Sca1−), hematopoietic stem/progenitor cells (Lin−, Kit−, Sca1−); HS (Kit−, Sca1+), hematopoietic stem/progenitor cells (Lin−, Kit−, Sca1+); HS (Kit+, Sca1−), hematopoietic stem/progenitor cells (Lin−, Kit+, Sca1−); HS (Kit+, Sca1+), hematopoietic stem/progenitor cells (Lin−, Kit+, Sca1+); and NS-D, differentiated NS cells.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC300684&req=5

pbio.0000074-g004: PCA Analysis of EST FrequencyThe results were obtained by analyzing 2,812 genes that exceeded 0.1% in at least one library. (A) 3D biplot that shows both cell types (red spheres) and genes (yellow boxes). (B) 2D PCA of cell types. EST frequencies were log-transformed before the analysis. Names of some cells and tissues are abbreviated as follows: 6.5 EP, E6.5 whole embryo (embryo plus placenta); 7.5 EP, E7.5 whole embryo (embryo plus placenta); 8.5 EP, E8.5 whole embryo (embryo plus placenta); 9.5 EP, E9.5 whole embryo (embryo plus placenta); 7.5 E, E7.5 embryonic part only; 7.5 P, E7.5 extraembryonic part only; NbOvary, newborn ovary; NbBrain, newborn brain; NbHeart, newborn heart; NbKidney, newborn kidney; 13.5 VMB, E13.5 ventral midbrain dopamine cells; 12.5 Gonad (F), E12.5 female gonad/mesonephros; 12.5 Gonad (M), E12.5 male gonad/mesonephros; HS (Kit−, Sca1−), hematopoietic stem/progenitor cells (Lin−, Kit−, Sca1−); HS (Kit−, Sca1+), hematopoietic stem/progenitor cells (Lin−, Kit−, Sca1+); HS (Kit+, Sca1−), hematopoietic stem/progenitor cells (Lin−, Kit+, Sca1−); HS (Kit+, Sca1+), hematopoietic stem/progenitor cells (Lin−, Kit+, Sca1+); and NS-D, differentiated NS cells.
Mentions: The global expression patterns of 2,812 relatively abundant genes (see Materials and Methods; Dataset S9) were further analyzed by principal component analysis (PCA), which reduces high-dimensionality data into a limited number of principal components. The first principal component (PC1) captures the largest contributing factor of variation, which in this case corresponds to the average EST frequency in all tissues, and subsequent principal components correspond to other factors with smaller effects, which characterize the differential expression of genes. As we were interested in the differential gene expression component, we plotted the position of each cell type against the PC2, PC3, and PC4 axis in three-dimensional (3D) space by using virtual reality modeling language (VRML) (Figure 4A; Video S1; a full interactive view is available on http://lgsun.grc.nia.nih.gov/Supplemental-Information). Genes were also plotted in the same 3D space (a version of PCA called a biplot) (Chapman et al. 2002) to see their association with cell/tissue types. Close examination of the 3D model identified PC2 and PC3 as the most representative views of the 3D model (Figure 4B). A two-dimensional (2D) plot of PC2 and PC3 is therefore used for the following discussion, with references to the 3D model. It is important to keep in mind that the distance between cell types along principal components has a substantial error associated with randomness of clone counts in EST libraries. The estimated error range (2*SE) in the PC3 scale is about 7%–9% based on Poisson distribution (Figure 4B). Nonetheless, PCA identifies major trends and clusters in gene expression among these cell types.

Bottom Line: Principal component analysis identified a set of 88 genes whose average expression levels decrease from oocytes to blastocysts, stem cells, postimplantation embryos, and finally to newborn tissues.This can be a first step towards a possible definition of a molecular scale of cellular potency.The nonrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine.

View Article: PubMed Central - PubMed

Affiliation: National Institute on Aging, Baltimore, Maryland, USA.

ABSTRACT
Understanding and harnessing cellular potency are fundamental in biology and are also critical to the future therapeutic use of stem cells. Transcriptome analysis of these pluripotent cells is a first step towards such goals. Starting with sources that include oocytes, blastocysts, and embryonic and adult stem cells, we obtained 249,200 high-quality EST sequences and clustered them with public sequences to produce an index of approximately 30,000 total mouse genes that includes 977 previously unidentified genes. Analysis of gene expression levels by EST frequency identifies genes that characterize preimplantation embryos, embryonic stem cells, and adult stem cells, thus providing potential markers as well as clues to the functional features of these cells. Principal component analysis identified a set of 88 genes whose average expression levels decrease from oocytes to blastocysts, stem cells, postimplantation embryos, and finally to newborn tissues. This can be a first step towards a possible definition of a molecular scale of cellular potency. The sequences and cDNA clones recovered in this work provide a comprehensive resource for genes functioning in early mouse embryos and stem cells. The nonrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine.

Show MeSH
Related in: MedlinePlus