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RNA sequencing (RNA-seq) for identifing differentially expressed transcription factor genes during early plant growth

ABSTRACT: The purpose of this study is to identify differentially expressed transcription factor genes during early plant growth. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. We used an optimized data analysis workflow, and mapped about 45 million sequence clean reads per sample to the Arabidopsis genome and identified 33,685 transcripts in 2 and 6 dpg (day post germination) old wild type plant (Col-0). Among them, there are 9321 genes differentially expresses from 2- and 6-d-old plants, and 479 differentially expresses transcription factor (TF) genes. Of these genes, 344 TF genes up regulated and 135 down regulated in 6-d-old plants compared with 2-d-old plants, with a fold change ≥2, ≤0.6 and p value <0.05. The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression. This study will facilitate analysis related with developmental study in early plant growth stage.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE119325 | GEO | 2018/12/31

REPOSITORIES: GEO

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