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Sample GSM3674292 Query DataSets for GSM3674292
Status Public on Sep 02, 2020
Title card1_2_mock_4
Sample type SRA
 
Source name 7-day old liquid-grown seedlings
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
agent: mock (DMSO)
genotype/variation: card1-2
time point: 10 min
replicate: replicate 4
Treatment protocol Seedlings (7-day old) were treated with 5 µM DMBQ or DMSO (volume equivalent) for 10 minutes
Growth protocol Arabidopsis seedling (WT-expressing aequorin, card1-1 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 Extraction was carried out prepared as previously described in Townsley et al., 2015 Front. Plant Sci. (https://doi.org/10.3389/fpls.2015.00366)
Libraries were prepared as previously described in Townsley et al., 2015 Front. Plant Sci. (https://doi.org/10.3389/fpls.2015.00366)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description card1_2_control4
Data processing 50 bp single-ends reads were sequenced by Illumina Hiseq 4000 and basecalls performed using CASAVA bcl2fastq_v2.17
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 Arabidopsis genome (TAIR10) with Tophat2 v2.1.1 (http://ccb.jhu.edu/software/tophat) with the following settings: -i 20 -I 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 GPL21785
Series (2)
GSE128426 RNAseq of Arabidopsis wild-type (WT)-expressing aequorin, card1-1 mutant (WT-expressing aequorin background), card1-2 mutant (WT-expressing aequorin background) in response to 10 minute DMBQ or DMSO treatment
GSE128510 RNA-seq of Arabidopsis wild-type (WT)-expressing aequorin and card1 mutants (WT-expressing aequorin background) in response to DMBQ.
Relations
BioSample SAMN11164889
SRA SRX5540740

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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