Tomato Transcriptome Dynamics During Fruit Set

To investigate the tomato transcriptome dynamics of fruit set, RNA were isolated from flower buds (Bud) and flowers at anthesis (Ant) and post-anthesis (Pos) stages. For each stage, cDNA libraries were generated from three biological replicates and subjected to Illumina mRNA-Seq technology sequencing. Then, after mapping reads to the tomato genome sequence, we obtained a table of raw counts with 34675 rows (genes) and 9 columns (3 stages and 3 replicates per stage). These technical procedures are described in Maza et al. (2013 (link)). In this paper, for sake of simplicity, the matrix (34675 × 9) containing raw counts is denoted by X.

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, & Maza E. (2016). In Papyro Comparison of TMM (edgeR), RLE (DESeq2), and MRN Normalization Methods for a Simple Two-Conditions-Without-Replicates RNA-Seq Experimental Design. Frontiers in Genetics, 7, 164.

Publication 2016

Biological Cdna libraries Flowers Fruit Genes Illumina sequencing technology Mrna Tomato Transcriptome

Corresponding Organization : Genomics and Biotechnology of the Fruits Laboratory

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Protocol cited in 17 other protocols

Variable analysis

independent variables

Developmental stage of tomato fruit (flower bud, anthesis, post-anthesis)

dependent variables

Tomato transcriptome dynamics

control variables

Biological replicates (3) for each developmental stage

controls

No positive or negative controls were explicitly mentioned in the provided information.

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