Microarray databases slides, HTML, PDF, Rmd

Databases of genomic data, microarrays

https://www.ncbi.nlm.nih.gov/geo/ - Gene Expression Omnibus
https://www.ebi.ac.uk/arrayexpress/ - ArrayExpress
https://datamed.org/ - genomics database search engine
http://portals.broadinstitute.org/cgi-bin/cancer/datasets.cgi - Cancer program datasets from Broad Institute.
http://bioinformatics.mdanderson.org/main/Public_Datasets - MD Anderson public datasets
https://github.com/ramhiser/datamicroarray - A collection of small-sample, high-dimensional microarray data sets to assess machine-learning algorithms and models.

Selected GEO datasets

GSE62924 - Prenatal arsenic exposure and the epigenome: Identifying sites of 5-methyl cytosine alterations that predict functional changes in gene expression in newborn cord blood and subsequent birth outcomes. Illumina HumanMethylation450 BeadChip. Rojas D, Rager JE, Smeester L, Bailey KA et al. Prenatal arsenic exposure and the epigenome: identifying sites of 5-methylcytosine alterations that predict functional changes in gene expression in newborn cord blood and subsequent birth outcomes. Toxicol Sci 2015. PMID: 25304211

GSE48354 - Prenatal arsenic exposure and the epigenome: altered gene expression profiles in newborn cord blood. Affymetrix Human Gene 2.0 ST Array. Rager JE, Bailey KA, Smeester L, Miller SK et al. Prenatal arsenic exposure and the epigenome: altered microRNAs associated with innate and adaptive immune signaling in newborn cord blood. Environ Mol Mutagen 2014. PMID: 24327377

GSE47977 - Ozone Exposure Alters MicroRNA Expression Profiles in Humans. Agilent-016436 Human miRNA Microarray 1.0. Fry RC, Rager JE, Bauer R, Sebastian E et al. Air toxics and epigenetic effects: ozone altered microRNAs in the sputum of human subjects. Am J Physiol Lung Cell Mol Physiol 2014. PMID: 24771714

GSE21862 - Gene expression on 144 arrays representing 125 workers exposed to a range of benzene exposures. Illumina humanRef-8 v2.0 expression beadchip. McHale CM, Zhang L, Lan Q, Vermeulen R et al. Global gene expression profiling of a population exposed to a range of benzene levels. Environ Health Perspect 2011. PMID: 21147609

GSE1397 - the data on Down Syndrome Trisomy 21. Affymetrix GeneChipTM Human U133A. Mao R, Wang X, Spitznagel EL Jr, Frelin LP et al. Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart. Genome Biol 2005. PMID: 16420667

datamicroarray R package - A collection of small-sample, high-dimensional microarray data sets to assess machine-learning algorithms and models. https://github.com/ramhiser/datamicroarray

More GEO DataSets

136 datasets used by Hung, Jui-Hung, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, and Charles DeLisi. “Gene Set Enrichment Analysis: Performance Evaluation and Usage Guidelines.” Briefings in Bioinformatics 2012, Supplementary Data 1 http://bib.oxfordjournals.org/content/13/3/281/suppl/DC1

GDS1020 GDS1023 GDS1036 GDS1048 GDS1094 GDS1209 GDS1212 GDS1220 GDS1221 GDS1235 GDS1257 GDS1258 GDS1282 GDS1284 GDS1329 GDS1331 GDS1344 GDS1362 GDS1375 GDS1388 GDS1390 GDS1412 GDS1413 GDS1424 GDS1449 GDS1454 GDS1479 GDS1480 GDS1481 GDS1495 GDS1496 GDS1497 GDS1498 GDS1559 GDS1562 GDS1615 GDS1627 GDS1650 GDS1663 GDS1673 GDS1688 GDS1714 GDS1726 GDS1733 GDS1815 GDS1816 GDS1852 GDS1875 GDS1917 GDS1956 GDS1960 GDS1962 GDS1972 GDS1974 GDS1975 GDS1976 GDS1993 GDS2055 GDS2056 GDS2118 GDS2171 GDS2190 GDS2191 GDS2206 GDS2250 GDS2255 GDS2297 GDS2341 GDS2362 GDS2373 GDS2384 GDS2415 GDS2486 GDS2489 GDS2495 GDS2513 GDS2518 GDS2519 GDS2520 GDS2535 GDS2545 GDS2546 GDS2547 GDS2601 GDS2609 GDS2611 GDS2615 GDS2626 GDS2642 GDS2643 GDS2655 GDS2656 GDS2678 GDS2735 GDS2736 GDS2737 GDS2740 GDS274 GDS2767 GDS2771 GDS2772 GDS2785 GDS2819 GDS2822 GDS2824 GDS2831 GDS2835 GDS2842 GDS2855 GDS2922 GDS2926 GDS2935 GDS2942 GDS2960 GDS360 GDS395 GDS449 GDS495 GDS532 GDS534 GDS609 GDS610 GDS611 GDS612 GDS651 GDS690 GDS711 GDS724 GDS737 GDS806 GDS807 GDS841 GDS843 GDS946 GDS963 GDS987