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Sample GSM1979145 Query DataSets for GSM1979145
Status Public on Dec 22, 2016
Title WT(Col0) rosette leaves
Sample type SRA
 
Source name Arabidopsis rosette leaves from 4-week old WT(Col0) plants.
Organism Arabidopsis thaliana
Characteristics tissue: rosette leaf
genotype: WT(Col0)
age: 4-week old plants
treatment/conditions: 22 degrees with light intensity of 80nmol quanta m-2s-1 in a 16-photoperiod
Treatment protocol 22 degrees with light intensity of 80nmol quanta m-2s-1 in a 16-photoperiod
Growth protocol Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to growth chambers at 22C, following a 16 h photoperiod.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the Spectrum Plant Total RNA kit (Sigma-Aldrich) with an on-column DNase treatment according to the manufacturer’s instructions.
RNA-seq libraries were generated using the TruSeq Stranded Total RNA with Ribo-Zero Plant kit according to manufacturer’s instructions (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description 3 replicates
Seeds were sown on MS media, statified at 4 C for 2-d before being transferred to growth chambers at 22C, following a 16 h photoperiod. At 5 day old seedlings were transferred to soil and rosette leaves collected at 4 weeks.
rosettes_col0vdko_tair.txt
Data processing Sequenced reads were trimmed for adaptor sequence, and filtered for low-quality sequence, then mapped to the tair10 whole genome using bowtie v2.2.0-beta7 and tophat v2.2.0 with the parameters:–b2-sensitive –r 0 –mate-std-dev 100 –g 1 –G .
Transcript abundance was estimated by FPKM (fragment per Kilobase of exon per million fragments mapped) using Cufflinks pipeline (version 2.2.0) and RNAseq data was analysed using Cuffdiff 2.2.0 under default parameters.
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample, as part of Cuffdiff output
 
Submission date Dec 23, 2015
Last update date May 15, 2019
Contact name Reena Narsai
Organization name La trobe University
Street address 5 Ring road
City Bundoora
ZIP/Postal code 3083
Country Australia
 
Platform ID GPL19080
Series (1)
GSE76287 Expression data for WT(Col0) and double mutants for AtTric1 (At3g49560) and AtTric2 (At5g24650) in Arabidopsis
Relations
BioSample SAMN04364429
SRA SRX1499207

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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