Transcriptomics

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Transcriptome analyses of Arabidopsis ldl1ldl2 (lysine-specific demethylase1 [LSD1]-like1 [ldl1]) double mutants as well as wild-type Columbia-0 plants via next-generation sequencing (NGS)

ABSTRACT: Purpose: The goals of this study are to compare transcriptome of ldl1ldl2 double mutants with that of wild-type Columbia-0 plants and to identify genes whose expression are tightly regualted by LDL1/LDL2 prtoeins in Arabidopsis. Methods: mRNA profiles of 3-week-old wild-type Col-0 and ldl1ldl2 mutant plants were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with a method : TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 27~31 million sequence reads per sample to the Arabidopsis genome (TAIR10). Conclusions: Our results show that LDL1 and LDL2 protein had significant effects on transcription of genes important for plant immune reponses against Pseudomonas infection.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE171433 | GEO | 2021/04/04

REPOSITORIES: GEO

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