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Sample GSM1413821 Query DataSets for GSM1413821
Status Public on Jun 15, 2016
Title WT-BL rep1
Sample type SRA
 
Source name seedling
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
genotype: WT
light condition: 15 μmol/m2/s blue light
growth time: 4.5 days
Growth protocol seeds were germinated in 1/2 MS plus 1% sucrose and placed at 4 degree centigrade for 3 days and then tranferred to white light for 12 h before placed in darkness or blue light for another 4 days
Extracted molecule total RNA
Extraction protocol RNA was extracted with RNAprep plant kit from TIANGEN, followed by DNase I (Takara) treatment. Quality control was performed with Agilent Bioanalyser. mRNA was purifed with Dynabeads® Oligo (dT)25(Life).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description replicate 1
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to primaryTranscript dataset obtained from primaryTranscript of Arabidopsis thaliana TAIR10 gene set using Bowtie 2 version 2.2.2 with parameters --very-fast-local
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.
 
Submission date Jun 16, 2014
Last update date May 15, 2019
Contact name Sheng-Bo He
Organization name Shanghai Jiao Tong University
Street address 800 Rd Dongchuan
City Shanghai
ZIP/Postal code 200240
Country China
 
Platform ID GPL17639
Series (1)
GSE58552 Analyses of blue light (BL) and CRY-regualted genes and genes dependent on auxin receptors by RNA-seq
Relations
BioSample SAMN02864793
SRA SRX608304

Supplementary file Size Download File type/resource
GSM1413821_WT-BL1.txt.gz 236.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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