Assembly, Verification, and Initial Annotation of the NIA Mouse 7.4K cDNA Clone Set

Increasing interest in stem cells and early embryos requires a high-quality cDNA clone set for cDNA microarray experiments as well as downstream molecular biological studies of gene action. The application of DNA microarrays is strengthened when high-quality cDNA clones corresponding to array elements are readily available for further investigations. Genes that are uniquely expressed in these early embryonic cell types, however, are usually underrepresented in available cDNA clone sets (Ko 2001). To address this issue, we assembled and released the NIA mouse 15K cDNA clone set previously (Tanaka et al. 2000; Kargul et al. 2001), which was mainly derived from preimplantation and early postimplantation mouse embryos. The clone set has been used in over 200 cDNA microarray facilities worldwide. To complement this clone set and increase the coverage of genes, we have assembled and characterized an additional set of 7407 cDNA clones (NIA mouse 7.4K) from mouse cDNA libraries derived from various stem cell lines, preimplantation embryos, and newborn organs (Fig. ​(Fig.1A).1A). The combined sets therefore represent an estimated 19,000 genes (see below), including a large number of genes uniquely transcribed in stem cells, and embryonic and newborn organ cell types. Figure 1 Summary descriptions of the NIA mouse 7.4K clone set. (A) Library Composition of NIA mouse 7.4K. (B) Functional classification of 1490 clones with mouse gene identity in RefSeq (BLAST ≥400) or homology in NCBI nr (BLAST ≥100).