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Sample GSM1444337 Query DataSets for GSM1444337
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

Supplementary file Size Download File type/resource
GSM1444337_wCot3h_b.txt.gz 1022.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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