Illumina HiSeq 4000 paired end sequencing; ChIP-seq for Meis on mouse branchial arches at E11.5.
ChIP-seq for Meis on mouse branchial arches at E11.5.
The preparation of the material was as described in Kutejova et al., 2008. First branchial arches, and posterior branchial arches connected to OFT 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, using 20ug of Meis antibody (Santa Cruz Biotechnology sc-10599X). 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. 70 arches were used for BA1 - 'rep1', the remaining samples used approximately 50. Library preparation was performed using different kits.  BA1 - 'rep1' used the TruSeq ChIP Sample Preparation kit (Illumina). BA1 - 'rep2' used the Rubicon ThruPlex kit (Takara Bio USA, Inc).  PBA 'rep3' and 'rep4' used the Microplex Diagenode kit (Diagenode).