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Sample GSM3674308 Query DataSets for GSM3674308
Status Public on Sep 02, 2020
Title WT_00.50_M_1
Sample type SRA
 
Source name 7-day old liquid-grown seedlings
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
agent: mock (DMSO)
time point: 0.5 hr
replicate: replicate 1
genotype/variation: WT
Treatment protocol Seedlings (7-day old) were treated with 5 µM DMBQ or DMSO (volume equivalent) for 0 hr, 0.5 hr, 1 hr and 6 hr
Growth protocol Arabidopsis seedling (WT-expressing aequorin and card1-2) were grown in liquid media containing half-strength Murashige-Skoog supplemented with 0.25 % sucrose. After 2 days stratification, seedlings were grown at 16 hr: 8 hr, light: dark, 22 C, 50 µE for 7 days
Extracted molecule total RNA
Extraction protocol RNA were extracted using Qiagen RNeasy Plant mini kit with DNaseI-digestion
Libraries were then prepared using KAPA mRNA HyperPrep Kit according to the manufacturer’s instructions
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing 50 bp single-ends reads were sequenced by Illumina NextSeq 500 and basecalls performed as described in Hasagawa et al., 2018 (doi:10.1038/s41598-018-25963-y)
Quality filtering was performed using the Fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Low Quality nucleotides (quality score < 30) were removed from the 3’end. Short reads (< 40 bp) and reads which showed at least 95 % nucleotides with low quality score (quality score < 20) were removed.
Filtered reads were mapped onto the Arabidopsis genome (TAIR10) with HISAT v2.1.0 (https://ccb.jhu.edu/software/hisat2/index.shtml) with a following setting: --max-intronlen 5000
Mapped reads were counted using HTseq v0.6.1 (13) (https://htseq.readthedocs.io/) with default settings.
Genome_build: TAIR10
Supplementary_files_format_and_content: comma separate values, HTseq read count values
 
Submission date Mar 18, 2019
Last update date Sep 02, 2020
Contact name Anuphon Laohavisit
E-mail(s) anuphon.laohavisit@riken.jp
Organization name RIKEN
Street address 1-7-22 Suehiro-cho
City Yokohama
State/province Kanagawa
ZIP/Postal code 230-0045
Country Japan
 
Platform ID GPL19580
Series (2)
GSE128427 RNAseq of Arabidopsis wild-type (WT)-expressing aequorin and card1-2 mutant (WT-expressing aequorin background) in response to DMBQ or DMSO treatment at 0 hr, 0.5 hr, 1 hr and 6 hr
GSE128510 RNA-seq of Arabidopsis wild-type (WT)-expressing aequorin and card1 mutants (WT-expressing aequorin background) in response to DMBQ.
Relations
BioSample SAMN11164910
SRA SRX5540756

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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