A dual-core processor, composed of EIN3/EIL1 and PIFs, mediates both positive and negative regulation of apical hook development by multiple hormones and light signals. Overall design: Three-day-old etiolated seedlings of Col-0, hls1, pifq, ein3 eil1, and pifq ein3 eil1 plants (not including roots) were collected and ground into a fine powder in liquid nitrogen. Two biological replicates were prepared for each genotype. Total RNA was extracted using the RNeasy Plant Mini kit (QIAGEN). The RNA sequencing and differential gene expression analysis were performed at the Bionova company. RNA quality was evaluated on a Bioanalyzer 2100 instrument (Agilent, Santa Clara, CA). Sequencing libraries were prepared following the protocol for the Directional RNA Library Prep Kit (NEB), and 150 nt paired-end high throughput sequencing was performed on an Illumina Hiseq X Ten system. Low quality sequencing reads were removed.