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Sample GSM3271489 Query DataSets for GSM3271489
Status Public on Jul 14, 2018
Title phyB full length red rep3
Sample type SRA
 
Source name Arabidopsis thaliana seedlings
Organism Arabidopsis thaliana
Characteristics ecotype/background: Col-0
genotype/variation: phyB full length
tissue: Seedlings
age: 3 days
treatment: 1h red light
Treatment protocol The seeds were surface sterilized and plated on the MS media without sucrose, cold stratified for three days before treated for 3 hours of white light and 21 hours of dark incubation to induce germination. After initial 24 hours, seeds were further treated with far-red light (10 µmole/s2/m2) to inactivate phytochrome activity. After additional two days in the dark, seedlings were either collected (dark sample) or treated with 1 hour of continuous red light (red sample) (8 µmole/s2/m2).
Growth protocol Total five genotypes: Col-0, cop1-4, spaQ, phyAphyB/phyB FL, and phyAphyB/phyB ΔC plants were used for mRNA sequencing analysis.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using sigma plant total RNA kit (Sigma, Cat.# STRN250).
NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB Cat.# E7370S) was used to generate mRNA sequencing library according to the manufacturer’s instruction.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description phyB_FL_R_3
Dark grown 3-day-old seedlings.
processed data file: Total_Count.txt
Data processing FastQC
Bowtie2
Tophat
HTseq
DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Total_Count.txt: Tab-delimited text file includes raw counts after HTseq.
 
Submission date Jul 13, 2018
Last update date Feb 05, 2019
Contact name Inyup Paik
E-mail(s) inyuppaik@gmail.com
Organization name UT Austin
Department Molecular Biosciences
Lab Enamul Huq lab
Street address NHB 2.616, Stop A5000 100 East 24th St.
City Austin
State/province TX
ZIP/Postal code 78712
Country USA
 
Platform ID GPL19580
Series (1)
GSE117114 Phytochrome B-SPA-COP1 regulation of red light induced gene expressions in Arabidopsis thaliana
Relations
BioSample SAMN09655945
SRA SRX4390365

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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