|
| Status |
Public on Sep 02, 2020 |
| Title |
WT_DMBQ_4 |
| Sample type |
SRA |
| |
|
| Source name |
7-day old liquid-grown seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
agent: 5 microM DMBQ
genotype/variation: WT-expressing aequorin
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 |
WT_DMBQ4
|
| 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 |
SAMN11164885 |
| SRA |
SRX5540744 |
