Vanessa cardui ChIP-seq of H3K27Ac and H3K4me3 in response to hostplant availability.
This experiment was performed to investigate the response to host plant availability in adult painted lady females (Vanessa cardui).  Offspring to one painted lady female whose grandparents were caught during spring 2021 in Catalonia were reared under controlled conditions, including constant temperature at 23?C, constant day length at 16 hours (h) light, 4 h ambient light and 4 h darkness, and ad libitum access to host plants (Malva sylvestris, pre-experimentally grown from seeds under controlled conditions in a common greenhouse). Upon pupation, the sex of each pupa was scored and when the imagines eclosed, they were immediately divided into two treatment cohorts (separate cages) using two replicate cages for each treatment. The first group was placed in one of two cages (40*40*40 cm) with five free-flying males and access to the host plant M. sylvestris. The individuals in the other treatment group were placed in one of two cages with five free-flying males and no host plants. All butterflies had ad libitum access to energy sources (20% sugar water). The females were sampled at noon five days after eclosure and immediately snap frozen in liquid nitrogen. The heads including antennae in each treatment/replicate (4 x 12 individuals) were pooled and used for ChIP-seq with SimpleChIP® Enzymatic Chromatin IP Kit (Cell Signaling Technology Inc.) acccording to protocol using Rabbit monoclonal H3K27Ac- and H3K4me3-antibodies. The purity and fragment distribution of the DNA was assessed with Nanodrop (Thermo Scientific Inc.) and a 2100 Bioanalyzer (Agilent Inc.). Library preparation with SMARTer ThruPLEX DNA-seq and sequencing of 2x150 bp reads was performed on a single Illumina NovaSeq6000 S4-300 lane at the National Genomics Infrastructure (NGI, see acknowledgements) in Stockholm.  The samples are marked 1 for access to hostplant and 0 for no host plant, with replicates A and B. 1A_ac, 1B_ac are samples with access to hostplant and precipitated with H3K27Ac. 1A_m3, 1B_m3 are samples with access to hostplant and precipitated with H3K4me3. 0A_ac, 0B_ac are samples without hostplant and precipitated with H3K27Ac. 0A_m3, 0B_m3 are samples without hostplant and precipitated with H3K4me3. 1A_input, 1B_input, 0A_input, 0B_input are the input samples for genomic baselines for each pool.