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Sample GSM2417570 Query DataSets for GSM2417570
Status Public on Dec 31, 2017
Title BCY.D100h.rep3
Sample type SRA
 
Source name Whole seedling
Organism Arabidopsis thaliana
Characteristics transgenic-line: BCY
replicate: 3
Treatment protocol Seedlings were grown for 100h in the dark, and harvested under dim green light using liquid nitrogen.
Growth protocol Arabidopsis thaliana seeds were stratified for 5 days at 4 degree celcius in the dark, followed by a 3h far-red light (10 µmol m-2 s-1) treatment and then wrapped in the dark for another 97h in a growth chamber maintained at 21 degree celcius.
Extracted molecule polyA RNA
Extraction protocol 100 mg 100h dark-grown seedlings were collected under dim green light, flash frozen in liquid nitrogen, and total RNA was extracted using Zymo Quick-RNA™ MiniPrep (R1055).
RNA libraries were prepared for sequencing using the standard protocol of NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (#E7420S) 
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Transgenic line overexpressing PHYB C-terminal module fused to YFP in phyB-9 null mutant background
Data processing Illumina Casava1.7 software used for basecalling??
Sequenced reads were de-multicomplexed according to the barcodes.
Paired-end reads were mapped to the Arabidopsis TAIR10 genome and transcriptome using Tophat/v2.0.14 (Kim et al., 2013).
Gene expression was estimated using Cufflinks/v2.2.1 (Trapnell, Williams et al. 2010), and then differential gene expression between BCY and phyB-9 was determined by Cuffdiff/v2.2.1 (Trapnell, Hendrickson et al. 2013) using a q-value cutoff of 0.05 and a fold-change equal to or greater than 1.5. Since the RNA-seq libraries were constructed using the NEBNext Ultra Directional RNA library prep kit for Illumina and preserved information about the RNA strand orientation, the tophat and cufflinks parameter “--library-type fr-firststrand” was used to distinguish sense reads and anti-sense reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited gene_exp.diff txt file generated by cuffdiff software. The file contains differential gene expression FPKM values between BCY and phyB-9.
 
Submission date Dec 06, 2016
Last update date May 15, 2019
Contact name Meng Chen
E-mail(s) meng.chen@ucr.edu
Phone 951-827-5635
Organization name UC Riverside
Department Botany and Plant Sciences
Lab Chen
Street address 900 University Ave, 2150 Batchelor Hall
City Riverside
State/province CA
ZIP/Postal code 92521
Country USA
 
Platform ID GPL19580
Series (1)
GSE90925 Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B
Relations
BioSample SAMN06112623
SRA SRX2398180

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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