Additional file 1: Table S1. of Combined physiological, transcriptome, and cis-regulatory element analyses indicate that key aspects of ripening, metabolism, and transcriptional program in grapes (Vitis vinifera L.) are differentially modulated accordingly to fruit size

Summary of RNA sequencing analysis metrics. RNA sequencing were carried in skins of small and large berries at four berry developmental stages namely 47 (before ripening, 4.9 °Brix), 74 (early ripening, 17.5 °Brix), 103 (ripening, 22.4 °Brix), and 121 (late ripening, 25.3 °Brix) days after anthesis (DAA). Table S2. Transcript abundance of the DE genes, reported as log2 (FPKM + 1) values, for each individual biological replicate (R1, R2, R3) in each treatment (small and large berry) at 47, 74, 103, and 121 days after anthesis. Table S3. Summary of differentially expressed genes between small and large berries at four berry developmental stages. All differentially expressed genes (Adj. P-value <0.05) and detailed description of the 12×V1 gene ID, log2 fold change values (small vs large), differential expression calls across four developmental stages, average log2 (FPKM + 1) values (3 replicates) of small and large berries together and individually, k-means assigned cluster (based on response and developmental stage), functional annotations based on Grimplet et al. [37] (including transcription factors), and MapMan pipeline. Table S4. Summary of PLACE- and PBM-curated cis-regulatory elements (CRE) analysis of k-means assigned clusters and selected group of genes. All information on the number of promoters with the specified CRE (match_in_sample), the number of genes within each group, number of promoters in the genome containing the specified CRE (match_in_genome), P-value and FDR of enriched CRE (FDR

RNA测序分析指标汇总。本研究针对大小浆果的果皮样本开展RNA测序实验，采样覆盖四个浆果发育阶段，分别为开花后天数（DAA, days after anthesis）第47天（成熟前，白利糖度4.9°Brix）、第74天（成熟初期，白利糖度17.5°Brix）、第103天（成熟期，白利糖度22.4°Brix）及第121天（晚熟期，白利糖度25.3°Brix）。
表S2：各处理组（大小果）在开花后第47、74、103、121天的单个生物学重复（R1、R2、R3）中，差异表达基因（DE genes, differentially expressed genes）的转录本丰度，以log₂(FPKM + 1)值表示，其中FPKM为每百万片段每千碱基转录本数（Fragments Per Kilobase of transcript per Million fragments mapped）。
表S3：四个浆果发育阶段大小果间差异表达基因汇总。包含所有校正后P值<0.05的差异表达基因，以及如下详细信息：12×V1基因ID的详细说明、log₂倍数变化值（小果vs大果）、四个发育阶段的差异表达状态注释、大小果单独及合并后的平均log₂(FPKM+1)值（3次生物学重复）、基于表达响应与发育阶段的k-means聚类分组、基于Grimplet等[37]的功能注释（含转录因子），以及MapMan分析流程。
表S4：针对k-means聚类分组及筛选基因集的、经PLACE与PBM手工注释的顺式调控元件（CRE, cis-regulatory element）分析汇总。包含以下信息：含指定CRE的启动子数量（match_in_sample）、每组基因数量、基因组中含指定CRE的启动子数量（match_in_genome）、富集CRE的P值及错误发现率（FDR）