embryology study with ChIP-Seq, RNA-Seq data on dbGaP (19 participants)

phs001226 — Regulatory Genomics of Human Embryonic Development

We used epigenetic profiling to map active enhancers in the developing human limb and cortex as described in two published studies: <ul> <li>Cotney J, Leng J, Yin J, Reilly SK et al. The evolution of lineage-specific regulatory activities in the human embryonic limb. <a href="https://www.ncbi.nlm.nih.gov/pubmed/23827682">Cell 2013</a>;154(1):185-96. </li> <li>Reilly SK, Yin J, Ayoub AE, Emera D et al. Evolutionary changes in promoter and enhancer activity during human corticogenesis. <a href="https://www.ncbi.nlm.nih.gov/pubmed/25745175">Science 2015</a>;347(6226):1155-9.</li> </ul> We also used ChIP-seq to map binding sites for the chromatin modifier <a href="https://www.ncbi.nlm.nih.gov/gene/?term=CHD8">CHD8</a> in the developing human brain, as described in one published study: <ul> <li>Cotney J, Muhle RA, Sanders SJ, Liu L et al. The autism-associated chromatin modifier <a href="https://www.ncbi.nlm.nih.gov/gene/?term=CHD8">CHD8</a> regulates other autism risk genes during human neurodevelopment. <a href="https://www.ncbi.nlm.nih.gov/pubmed/25752243">Nat Commun 2015</a>;6:6404.</li> </ul> We are also depositing primary human sequence reads related to processed datasets in the Gene Expression Omnibus under the following accession numbers: <a href="https://www.ncbi.nlm.nih.gov/gds/?term=GSE42413">GSE42413</a> (Cotney et al. <a href="https://www.ncbi.nlm.nih.gov/pubmed/23827682">2013</a>); <a href="https://www.ncbi.nlm.nih.gov/gds/?term=GSE63649">GSE63649</a> (Reilly et al. <a href="https://www.ncbi.nlm.nih.gov/pubmed/25745175">2015</a>); <a href="https://www.ncbi.nlm.nih.gov/gds/?term=GSE57369">GSE57369</a> (Cotney et al. <a href="https://www.ncbi.nlm.nih.gov/pubmed/25752243">2015</a>).