GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE186nnn/GSE186416/primaryOK200TranscriptomicsArabidopsis thalianaExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186416GEOGSEfalseMitochondrial Ca2+ homeostasis controls inter-compartmental proteostasis in Arabidopsis plants [mRNA]Purpose: The goals of this study are to determine the effects of mitochondrial Ca2+ homeostasis on nuclear gene expression. Methods: The mRNA profiles of 10-day-old WT, MCU2, MCU4, MCU6 overexpression and mcu sextuple mutation plants were generated by deep sequencing, in triplicate, using Illumina HiSeq2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped a minimum of 14 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified more than 33,000 transcripts. Data analysis revealed that perturbation of mitochondrial Ca2+ altered nuclear gene expression. Conclusions: Our study represents the first detailed analysis of Arabidopsis RNA transcriptomes in response to impaired mitochondrial Ca2+, with biologic replicates, generated by RNA-seq technology. Our results showed that perturbation of mitochondrial Ca2+ triggered nuclear gene expression response. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses of inter-compartmental communication at transcriptional level.2026/06/03GSE186416GSM5651402GSM5651385GSM5651386GSM5651383GSM5651384GSM5651400GSM5651389GSM5651401GSM5651387GSM5651388GSM5651381GSM5651382GSM5651380GSM5651374GSM5651396GSM5651397GSM5651375GSM5651394GSM5651373GSM5651395GSM5651378GSM5651379GSM5651376GSM5651398GSM5651377GSM5651399GSM5651392GSM5651393GSM5651390GSM565139117639SRP342724186416Arabidopsis thaliana[42207405]