|
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 |