title: Shoot plants of col - 35 DAGs - Rep 1
design: To generate the libraries that were analyzed in this work, total RNA from two shoot and root repeats of 11 DAG and three shoot and root repeats of 35 DAG were previously extracted using the protocol described in method S7 and sent to Fasteris Life Sciences S.A for RNA sequencing. 8 libraries (11 DAG) and 8 libraries (35 DAG) were prepared according to the protocol available on the website and sequenced on the Illumina HISeq2OOO (11 DAG and NovaSeq 6000 (35 DAG) (single end). The raw reads were subjected to control quality (Q30 > 80%) and adapter trimming using Trimmomatic software. Mapping was performed using the TAIR10 genome as a reference using Bowtie software. Expression estimation, normalization and differential expression was performed using Cufflinks software.Libraries were normalized using the FPKM method with significance values at p-value <0.05. The differentially expressed genes (DEGs) were compared between the libraries, based on the difference in expression, generating FoldChange (FC) values classified as induced or repressed based on the Log calculation in base 2 of the FC values comparing the FPKM values of the library of interest against the control. All bioinformatics analyses, as well as sequencing, were performed by Fasteris Life Sciences S.A.