Comment[ArrayExpressAccession] E-GEOD-43616 MAGE-TAB Version 1.1 Public Release Date 2016-03-16 Investigation Title Time-course transcriptome of wild-type Arabidopsis leaf Comment[Submitted Name] Time-course transcriptome of wild-type Arabidopsis leaf Experiment Description During the senescence stage, leaves undergo degeneration and relocate nutrients accumulated during the growth stage to sink parts such as seeds, critically contributing to plants’ productivity and fitness. Here, we asked how leaf transcriptome is regulated during the senescence stage by performing directional sequencing of total and small RNAs for the entire lifespan of Arabidopsis leaves. The total RNA and small RNA profiles of the Arabidopsis leaf along lifespan (14 and 7 time points, respectively) were generated by next-generation sequencing using Illumina Hiseq2000. Two independent biological replicates were used for each experiment. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Koo Woo Koo Jeong Kim Lim Hwang Nam Person First Name Hee Jung Hye Hee Hyobin Jeongsik Pyung Daehee Hong Person Email hooferlm@postech.ac.kr Person Affiliation Pohang University of Science and Technology Person Phone 82-10-90976741 Person Address Pohang University of Science and Technology, Hyojadong San 31, Pohang, South Korea Person Roles submitter Protocol Name P-GSE43616-2 P-GSE43616-1 Protocol Description Illumina Casava1.5 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and then mapped to TAIR10 whole genome using TopHat v1.4.0 (Trapnell et al., 2009) Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks (Trapnell et al., 2009) Genome_build: TAIR10 Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each sample RNA was isolated using WelPrepTM (WelGENE, Korea). Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer with an RNA Integrity Number (RIN) value greater than 8.5 RNA libraries were prepared for sequencing using standard Illumina protocols Protocol Type normalization data transformation protocol nucleic acid library construction protocol Experimental Factor Name days after emergence Experimental Factor Type days after emergence Comment[SecondaryAccession] GSE43616 Comment[GEOReleaseDate] 2016-03-16 Comment[ArrayExpressSubmissionDate] 2013-01-18 Comment[GEOLastUpdateDate] 2016-03-17 Comment[AEExperimentType] RNA-seq of coding RNA Comment[AEExperimentType] RNA-seq of non coding RNA Comment[AdditionalFile:Data1] GSE43616_smRNA_count_set1.txt Comment[AdditionalFile:Data2] GSE43616_smRNA_count_set2.txt Comment[AdditionalFile:Data3] GSE43616_total_RNA_FPKM_set1.txt Comment[AdditionalFile:Data4] GSE43616_total_RNA_FPKM_set2.txt Comment[SecondaryAccession] SRP018034 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR2079771-SRR2079812 SDRF File E-GEOD-43616.sdrf.txt