Illumina HiSeq 4000 paired end sequencing; ChIP-seq for Hoxa2 on mouse second branchial arches at E11.5.
ChIP-seq for Hoxa2 on mouse second branchial arches at E11.5.
The preparation of the material was as described in Kutejova et al., 2008. Second branchial arches were dissected (the whole tissue), crosslinked and frozen in order to pool enough for ChIP. Kutejova E, Engist B, Self M, Oliver G, Kirilenko P, Bobola N. Six2 functions redundantly immediately downstream of Hoxa2. Development. 2008. 135(8):1463-70. PMID: 18321982. Diapure kit (Diagenode) ChIP-seq was performed as described in Donaldson et al., 2012.  'Rep1' used 20ug of a anti-Hoxa2 rabbit polyclonal antibody was generated by Biogenes (Berlin, Germany).  'Rep2' used 20ug of previously generated Ab detailed in Kutejova et al., 2009. 60 arches were used for 'rep1' and 'rep2'. Library preparation was performed using the Microplex Diagenode kit (Diagenode).  Donaldson I, Amin S, Hensman J, Kutejova E, Rattray M, Lawrence N, Hayes A, Ward C and Bobola N. Genome-wide occupancy links Hoxa2 to Wnt-beta-catenin signaling in mouse embryonic development. Nucleic Acids Res. 2012. 40(9):3990-4001  Kutejova et al, 2009 DOI:10.1242/dev.017624).