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DBTMEE: a database of transcriptome in mouse early embryos.

Park SJ, Shirahige K, Ohsugi M, Nakai K - Nucleic Acids Res. (2014)

Bottom Line: Thereby, users can extensively investigate molecular characteristics among totipotent, pluripotent and differentiated cells while taking genetic and epigenetic characteristics into consideration.We have also designed user friendly web interfaces that enable users to access the data quickly and easily.DBTMEE will help to promote our understanding of the enigmatic fertilization dynamics.

View Article: PubMed Central - PubMed

Affiliation: Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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Screenshots of the web interfaces in DBTMEE. The front page (A) displays search boxes that handle a regular expression (A-1, 2) and gene catalog established by clustering of gene expression patterns (A-4). Users can access information of a gene or a set of genes on multiple tables in single web page (B) that contains hyperlinks (B-1) to each gene information page (C). Through the basic and advanced search options in browser interfaces (E) appearing to the left menu (A-3), users can handle more specific search results from a particular table (D).
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Figure 3: Screenshots of the web interfaces in DBTMEE. The front page (A) displays search boxes that handle a regular expression (A-1, 2) and gene catalog established by clustering of gene expression patterns (A-4). Users can access information of a gene or a set of genes on multiple tables in single web page (B) that contains hyperlinks (B-1) to each gene information page (C). Through the basic and advanced search options in browser interfaces (E) appearing to the left menu (A-3), users can handle more specific search results from a particular table (D).

Mentions: DBTMEE provides a searchable gene expression profile during normal and parthenogenetic early embryo developments that were established previously (6). In brief, we extracted high-quality metaphase II oocytes (Oo) and one-cell stage (1C), two-cell (2C) and four-cell (4C) stage embryos by in vitro fertilization. In addition, we collected mouse embryonic fibroblast cells (MEFs) and parthenogenetic 1C (p1C) and 4C (p4C) embryos. Total RNAs from ≥104 × 2 cells per stage were sequenced by SOLiD system and analyzed by Bioinformatics tools, detecting 17 486 genes that exhibited intriguing expression patterns (Figures 1 and 2). The gene expression patterns categorized by hierarchical clustering are browsable from the front page of DBTMEE (Figure 3A-4).


DBTMEE: a database of transcriptome in mouse early embryos.

Park SJ, Shirahige K, Ohsugi M, Nakai K - Nucleic Acids Res. (2014)

Screenshots of the web interfaces in DBTMEE. The front page (A) displays search boxes that handle a regular expression (A-1, 2) and gene catalog established by clustering of gene expression patterns (A-4). Users can access information of a gene or a set of genes on multiple tables in single web page (B) that contains hyperlinks (B-1) to each gene information page (C). Through the basic and advanced search options in browser interfaces (E) appearing to the left menu (A-3), users can handle more specific search results from a particular table (D).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383872&req=5

Figure 3: Screenshots of the web interfaces in DBTMEE. The front page (A) displays search boxes that handle a regular expression (A-1, 2) and gene catalog established by clustering of gene expression patterns (A-4). Users can access information of a gene or a set of genes on multiple tables in single web page (B) that contains hyperlinks (B-1) to each gene information page (C). Through the basic and advanced search options in browser interfaces (E) appearing to the left menu (A-3), users can handle more specific search results from a particular table (D).
Mentions: DBTMEE provides a searchable gene expression profile during normal and parthenogenetic early embryo developments that were established previously (6). In brief, we extracted high-quality metaphase II oocytes (Oo) and one-cell stage (1C), two-cell (2C) and four-cell (4C) stage embryos by in vitro fertilization. In addition, we collected mouse embryonic fibroblast cells (MEFs) and parthenogenetic 1C (p1C) and 4C (p4C) embryos. Total RNAs from ≥104 × 2 cells per stage were sequenced by SOLiD system and analyzed by Bioinformatics tools, detecting 17 486 genes that exhibited intriguing expression patterns (Figures 1 and 2). The gene expression patterns categorized by hierarchical clustering are browsable from the front page of DBTMEE (Figure 3A-4).

Bottom Line: Thereby, users can extensively investigate molecular characteristics among totipotent, pluripotent and differentiated cells while taking genetic and epigenetic characteristics into consideration.We have also designed user friendly web interfaces that enable users to access the data quickly and easily.DBTMEE will help to promote our understanding of the enigmatic fertilization dynamics.

View Article: PubMed Central - PubMed

Affiliation: Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

Show MeSH