|
Status |
Public on Jul 15, 2017 |
Title |
wCot3h replicate-2 |
Sample type |
SRA |
|
|
Source name |
WT_cotyledon_high R:FR_3h
|
Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: Columbia genotype/variation: WT exposed to: high R:FR treatment time: 3h tissue: cotyledon
|
Treatment protocol |
5 day old white high R:FR grown seedlings were treated low R:FR or mock treated (high R:FR) for indicated times
|
Growth protocol |
Seeds of the indicated genotype was stratified for 2 days in the cold and then was grown on 0.5x Linsmaier and Skoog medium under 16hL 8hD conditions at 22°C.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNeasy Micro kit (Qiagen) Truseq RNA Sample prep kit v2 Cat# RS-122-2001 and RS-122-2002 (Illumina, CA)
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
base calling was done by RTA 1.17.20 (Illumina, CA) demultiplexing was done by CASAVA 1.8.2 (Illumina, CA) Sequenced reads were trimmed for adaptor sequence, then aligned to TAIR10 whole genome build using Tophat2 v2.0.8b (Kim et al. 2013 Genome Biology) on a Linux platform FPKM were calculated for each sample using Cufflinks 2.1.1 (Trapnell et al. 2012 Nature Protocols) with parameters -u --compatible-hits-norm -G parameters on a Linux platform Genome_build: TAIR10 Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
|
|
Submission date |
Jul 24, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Joanne Chory |
E-mail(s) |
chory@salk.edu
|
Phone |
8584534100
|
Organization name |
Salk Institute for Biological Studies
|
Department |
Plant Biology Laboratory
|
Lab |
Chory
|
Street address |
10010 N Torrey Pines RD
|
City |
La Jolla |
State/province |
California |
ZIP/Postal code |
92037 |
Country |
USA |
|
|
Platform ID |
GPL17639 |
Series (1) |
GSE59722 |
High-resolution tissue-specific analysis of the Arabidopsis transcriptome in response to shade |
|
Relations |
BioSample |
SAMN02937244 |
SRA |
SRX660670 |