We have been working on mouse and human projects by putting NCBI GEO Affymetrix data into GEB software/database system. We plan to release Gene Expression Browser for Mouse in Aug, 2009 and release Gene Expression Browser for Human in Dec, 2009. We are also developing Microarray Data Submission and Management System (MDSMS) that enables users to submit microarray raw data and experiment/sample annotation via web-based interfaces. The data submitted from users will finally go to GEB via our in-house high throughput data processing pipeline. We plan to release MDSMS by the end of 2009.
The mouse project uses Affymetrix Mouse Genome 430 2.0 Array (GEO GPL1261). GPL1261 has 11474 samples in 906 independent experiments. We have downloaded all the data and applied in-house normalization/QC and finally choose 8628 samples in 766 experiments. The human project uses Affymetrix Human Genome U133 Plus 2.0 Array (GEO GPL570). GPL570 has 24664 samples in 878 independent experiments. The human data have been downloaded and ready for further processing and QC.
We appreciate the excellent job of NCBI GEO for collecting, classifying and redistributing microarray expression data.