Additional file 2 of Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size

Additional file 2: Table S1. Summary of reads obtained from total RNA sequencing of 36 cDNA libraries from the five seed developmental stages (S1-S5) and flag leaf (L) of SN and LGR. Table S2. Pearson’s correlation between biological replicates of the five seed developmental stages (S1-S5) and flag leaf (L) of SN and LGR. Table S3. FPKM values of all rice genes (transposable elements removed) in flag leaf and five seed development tissues of SN and LGR. The higlighted ones indicate significant DEGs in at least one seed stage. Table S4. Log2fold change values in seed development stages, of significant DEGs (Log2FC≥1, q value≤0.05, p value ≤0.05, FPKM≥1). Non-significant differential expression is indicated by ‘-’. Table S5. Stage-specific DEGs common between SN and LGR. Log2 fold change values of DEGs which are specific (log2FC≥1 in that stage and <1 in rest) to the same stage of SN and LGR. Table S6. FPKM values of cell cycle related genes specifically up regulated in seeds of SN and LGR. Table S7. List of DEGs preferential to S3 stage of LGR by comparison with SN S3/LGR S2 and SN S2/LGR S2. Genes which are LGR S3 preferential in both analyses have been highlighted. Table S8. List of TF encoding genes (with their log2fold changes), significantly differentially expressed at log2fc≥1 in at least one seed developmental stage of SN and/or LGR. “-” indicates non-significant values. Table S9. FPKM values of phytohormone encoding genes, which were present in different expression clusters (variation in expression pattern) and had higher expression values (difference in log2FPKM≥0.5; variation in expression level) in a stage in either SN or LGR. Table S10. Summary of grain size QTLs identified using a mapping population (Sonasal x LGR) in rice. Table S11. Log2 fold change values of genes which are significantly differentially expressed amongst SN and LGR seed development stages and are located within QTLs associated with a seed size-related trait. Table S12a. Summary of reads obtained from small RNA sequencing of each library from the five seed developmental stages (S1-S5) and flag leaf (L) of SN. In all samples, _1, _2, _3 represent biological replicates. Table S12b. Summary of reads obtained from small RNA sequencing of each library from the five seed developmental stages (S1-S5) and flag leaf (L) of LGR. In all samples, _1, _2, _3 represent biological replicates. Table S13. Pearson's correlation between biological replicates of the five seed developmental stages (S1-S5) and flag leaf (L) of SN and LGR obtained from small RNA sequencing. Table S14. Expression of all miRs in seed and flag leaf of SN and LGR. The TPM values of 604 miRs detected in at least one of the tissues used has been mentioned. The TPM values ≥50 have been highlighted in gray. Table S15. Comparison of DEMs between SN and LGR. The orange colored cells indicate the log2 fold changes of 467 DEMs for each stage of seed development. The yellow color indicates comparison between similar stages (by developmental event) of SN and LGR. The grey color indicates comparison between same stage (by DAP) of SN and LGR. U implies 'up regulation' while D implies 'down regulation' in the respective stage mentioned. - indicates non-significant differential expression. The up regulated genes have been marked in green while down regulated ones are in red. Table S16. List of miRNA-target modules for miRNAs up and down-regulated in all five seed developmental stages of either SN or LGR. Table S17. List of primers for validation. Table S18. Details of replicate data.