Transcriptome analysis of mouse stem cells and early embryos

The NIA Mouse Gene Index has recently made available to the public ( ). The web interface provides a view of transcripts and genes on the mouse genome sequence. Unique IDs ( U plus 6 digits, e.g., U018631 ) have been assigned to individual genes in the gene index. "U numbers" in the following Supplements have direct links to corresponding genes in the NIA Mouse Gene Index. Clicking the "U number" in the Supplements will lead to a web page of the NIA public web site.

Dataset S1 List of NIA Mouse cDNA Libraries and the number of ESTs generated.
Dataset S2 Summary of gene counts in NIA Mouse Gene Index.The web interface provides a view of transcripts and genes on the mouse genome sequence.
Dataset S3 List of 977 genes unique to NIA mouse cDNA collection (not found in RefSeq, Ensembl, and Riken). For sequence information, see Dataset S4.
Dataset S4 Sequence information of 977 genes in the FASTA format
Dataset S5 Primer sequences for RT-PCR analysis.
Dataset S6 Classification of cDNA libraries for the analysis of differentially expressed genes. This table describes how cDNA libraries were logically grouped for further EST analysis, where membership to a group is indicated with a '1' and non-membership is indicated with a '0'.
Dataset S7 List of genes overexpressed in preimplantation embryos and stem cells. This table identifies Genes overexpressed in each group of cells/tissues described in Dataset S6.
Dataset S8 Comparison of the gene lists identified in the Dataset S7 with the published data
Dataset S9 List of 2812 genes used for the Principal Component Analysis (PCA) to investigate the global feature of gene expression patterns.
Dataset S10 List of 88 genes correlated with developmental potential of cells.
Dataset S11 Comprehensive data about EST frequencies of genes in NIA mouse cDNA libraries and in public sequence databases.
Dataset S12 List of 10699 genes predominantly expressed in embryos and stem cells. These genes were identified by the analysis of NIA EST and public EST datasets.
Protocol S1 Supplemental Methods.
Video S1 (Read the footnote before loading!) 3D-view of results obtained by Principal Component Analysis (PCA) of log-transformed EST frequencies in NIA mouse cDNA Libraries. Red spheres represent libraries and yellow boxes represent genes. Gene names can be legible at closer distance. Genes are hyper-linked to the NIA Mouse Gene Index web site (mentioned in Supplement 3).
Publication Search Tool You can search by Gene Symbol, Gene Product Name or any other text. This tool will show occurences of your search term in the paper.
Note: To view results of Principal Component Analysis (PCA) in 3D you need a Cosmo Player plug-in for your web browser. Your browser should be open before you can view 3D picture.If you have problems installing the Cosmo Player, you can view a movie (AVI format. You can view it using Windows Media Player or Real Player).

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