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Series GSE199039 Query DataSets for GSE199039
Status Public on Mar 01, 2023
Title RRC1 is required for epidermal phyB siganling by maintaining the circadian rhythm by suppressing the alternative splicing of core clock genes.
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Purpose : The goal of this study is to identify transcriptome changes induced by rrc1 mutation under red light. We compared the transcriptome of MLB (ML1pro::phyB-GFP/phyB-9) with EMS27 grown either in darkness or continuous red light to investigate the genes that the expression and the splicing patterns are regulated by epidermal phyB and/or RRC1. The transcriptome of Col-0 and rrc1-689 was further compared to enlarge the list of putative splicing targets of RRC1.
Methods : Seedlings grown under either monochromatic red light (19 ╬╝mol/m2s) or darkness for 60 hours on 1/2 MS agar plates were sampled. Total RNAs were extracted using the Spectrum Plant Total RNA Extraction Kit (Sigma-Aldrich). RNA libraries were generated and sequenced on the Illumina NextSeq 500 platform. The analysis was performed with three biological replicates. Roughly 90% of the sequencing reads were mapped to specific loci on the Arabidopsis TAIR10 reference genome using the TopHat pipeline. Mapped sequencing files were further processed with Aspli1.9 R package for Differentially Expressed Gene (DEG) analysis and Differentially Spliced Gene (DSG) analysis.
Overall design Epidermal phyB-induced gene expression change was identified by comparing Dark-grown MLB with Red-grown MLB, while RRC1-induced gene expression or splicing change was identified by comparing Red-grown control line (Col-0 or MLB) with Red-grown rrc1 mutant (rrc1-689 or EMS27). All samples in triplicates.
Contributor(s) Kim H, Kim J, Choi G
Citation(s) 36651061
BioProject PRJNA817881
Submission date Mar 21, 2022
Last update date May 31, 2023
Contact name hanim kim
Phone 82-010-4311-0332
Organization name KAIST
Department biological science
Street address Daehak-ro 291
City Daejeon
ZIP/Postal code 34141
Country South Korea
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (24)
GSM5962843 MLB_D60_rep1
GSM5962844 MLB_D60_rep2
GSM5962845 MLB_D60_rep3

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Supplementary file Size Download File type/resource
GSE199039_Supplementary_Data_Set1_DEG.xlsx 693.3 Kb (ftp)(http) XLSX
GSE199039_Supplementary_Data_Set2_DSG.xlsx 279.3 Kb (ftp)(http) XLSX
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