Additional file 1 of The molecular signatures of compatible and incompatible pollination in Arabidopsis

Additional file 1: Figure S1. Known gene expression information for sex-specifically expressed genes. Top 20 sex-specifically expressed genes were analysed with ThaleMine database ( https://apps.araport.org/thalemine/begin.do ). Heat maps of RNA-seq based gene expression levels (Cheng et al., 2016) for each list were derived (stigma: upper, pollen: lower). * genes analyzed by RT-PCR and sequencing in Fig. 3c. Figure S2. Depth coverage of Col-0/SRK14 and C24 reference genomes after variants calling. Distributions of depth coverage before filtering were obtained by using GATK Depth Of Coverage. After checking depth coverage, Col-0/SRK14 variants were filtered at depth 3 and C24 variants were filtered at depth 6. Table S1. Read length and depth of whole genome sequencing. Col-0/SRK14 and C24 genomes were sequenced with NextSeq500 platform (Illumina) applying paired-end sequencing (2×150 bp). Sequence quality was checked by FastQC ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc ). Read parts with quality score less than 26 were trimmed and reads shorter than 50bp were discarded. F = forward sequence, R = reverse sequence. Table S2. Length of sequenced RNA reads. Four RNA replicates selected from five samples at each pollination condition were sequenced with NextSeq500 platform (Illumina) applying paired-end sequencing (2×75 bp). Sequence quality was checked by FastQC ( http://www.bioinformatics.babraham.ac.uk/projects/fastqc ). Read parts with quality score less than 26 were trimmed and reads shorter than 40bp were discarded. F=forward sequence, R = reverse sequence. Table S6. Number of up- and down-regulated genes. Genes up-regulated (FC > 2.0, padj