Euchromatic chromatin modifications on chromosome 2L

Chromosome-wide analysis of the distribution of H3K4me3, H3K36me2 and H3K36me3 on chromosome 2L. Keywords: ChIP-chip Input and antibody-bound DNA were separately amplified and labeled as described (Schübeler et al. 2004) except using indirect labeling via aminoallyl-modified nucleotides. Labeled DNA was co-hybridized to a chromosomal tiling array representing chromosome 2L of the Drosophila genome in a 2kb tiling resolution as described (Macalpine et al., 2004). Two repeats (including dye swap) starting from independent ChIP experiments were carried out. After hybridization and washing slides were scanned (Axon) and fluorescent reads were analyzed according to standard normalization and filtering criteria in the GenePix software package (Axon). Repeats showed high reproducibility (H3K4me3 R=0.98, H3K36me2 R=0.91, H3K36me3 R=0.92) so that average value from two experiments could be used in further analysis.