Drosophila at different time points of development: ChIP-chip, ChIP-seq, RNA-seq. Drosophila at different time points of development: ChIP-chip, ChIP-seq, RNA-seq

This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for 6 Histone modifications (H3K9me3, H3K27me3, H3K4me3, H3K4me1, H3K27Ac, H3K9Ac), PolII and CBP/p300. Each factor has been studied for 12 different time-points of Drosophila development. This SuperSeries is composed of the following subset Series: GSE15422: ChIP-chip of H3K9me3 in Drosophila at different time points of development GSE15423: ChIP-chip of H3K27me3 in Drosophila at different time points of development GSE15424: ChIP-chip of H3K4me3 in Drosophila at different time points of development GSE15425: ChIP-chip of H3K4me1 in Drosophila at different time points of development GSE15426: ChIP-chip of H3K9Ac in Drosophila at different time points of development GSE15427: ChIP-chip of CBP/p300 in Drosophila at different time points of development GSE15430: ChIP-chip of H3K27Ac in Drosophila at different time points of development GSE16013: Genome-wide maps of chromatin state in staged Drosophila embryos, ChIP-seq GSE16702: ChIP-chip of PolII in Drosophila at different time points of development GSE18068: Genome-wide maps of chromatin state in staged Drosophila embryos, RNA-seq For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Overall design: ChIP-chip: For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays. ChIP-seq: For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. The hybridizations have been verified by sequencing one replicate of IP and one replicate of Input following Solexa sequencing procedure. RNA-seq: For each time-point (E-0-4h, E-4-8h, E-8-12h, E-12-16h, E-16-20h, E20-24h, L1, L2, L3, Pupae, Adult Males and Adult Females) a total RNA extraction has been performed. After conversion into double stranded DNA, the samples have been sequenced in duplicate on Solexa Genome Analyzer following Solexa sequencing procedure.