|
| Status |
Public on Sep 02, 2020 |
| Title |
WT_00.00_D_1 |
| Sample type |
SRA |
| |
|
| Source name |
7-day old liquid-grown seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
agent: 5 microM DMBQ
time point: 0 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 |
SAMN11164947 |
| SRA |
SRX5540765 |
