title: GSM3359523: Hoxa11_ChIPSeq_E11.5_rep1; Mus musculus; ChIP-Seq
library_construction_protocol: ChIP was performed according to a standard protocol (Cold Spring Harbor, NY) with the following modifications. Whole limb buds from E11.5 and the autopod from E11.0 wild type ICR mice were dissected in ice-cold PBS. Embryonic tissues were homogenized 13 times with a Dounce homogenizer, then fixed in 1% formaldehyde/PBS for 10minutes at 4C and quenched with 0.1 M glycine. The cross-linked material was sonicated to produce 200-1000 bp fragments with a DNA Shearing System S2 (Covaris). The immunoprecipitations were performed with 11 pairs of autopods from E11.0 embryos, whole limb buds from a litter of E11.5 embryos. PierceTM Protein A/G magnetic beads (Thermo Scientific) were conjugated to each antibody. Sonicated chromatin was incubated with the prepared protein A/G beads overnight at 4C with rotation. 10 ug of anti-Hoxa13 or 8 ug of anti-Hoxa11 were used for each experiment. E12.5 ChIP-Seq was performed as described previously (Beccari et al. 2016. Genes Dev. 30, 1172-1186). Anti-Hoxa13 antibody: Yamamoto et al. Development 125, 1325-1335 and Beccari et al. 2016. Genes Dev. 30, 1172-1186. Anti-Hoxa11 antibody: Yamamoto et al. Development 125, 1325-1335 and manuscript in preparation. The E11.0 and E11.5 libraries were prepared using NEB Next UltraTM DNA Library Prep kit for Illumina (NEB) according to the manufacturer's protocol. The E12.5 libraries were prepared as described previously (Beccari et al. 2016. Genes Dev. 30, 1172-1186).