|
Status |
Public on Mar 01, 2023 |
Title |
EMS27_R60_rep1 |
Sample type |
SRA |
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|
Source name |
Whole Seedling
|
Organism |
Arabidopsis thaliana |
Characteristics |
ecotype background: Col-0 age: 60hr tissue: Whole Seedling genotype: EMS27 treatment: grown in continuous red light (19 μmol/m2s) for 60hr
|
Growth protocol |
Seeds were spotted on 1/2MS plate and cold stratified for 2 days. After 6hr of white light (50 μmol/m2s, 4°C) treatment for germination induction, seeds were kept in either darkness (4°C) or under red-light (19 μmol/m2s, 4°C) for 60hr.
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNAs were extracted using the Spectrum Plant Total RNA Extraction Kit (Sigma-Aldrich). RNA libraries were generated and sequenced on the Illumina NextSeq 500 platform.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
Supplementary Data Set1_DEG. Xlsx Supplementary Data Set2_DSG. Xlsx
|
Data processing |
Sequenced reads were trimmed for adaptor sequence, then mapped to TAIR10 Arabidopsis whole genome using Tophat v2.1.1 with parameters -p 8. Mapped BAM files were processed with Aspli1.9 R package for the expression and the splicing analysis Assembly: TAIR10 Supplementary files format and content: DEG analysis result including |log2(Fold-change)| value and FDR value for each genes. Supplementary files format and content: DSG analysis result including |delta(PSI/PIR)| value and FDR value for each genes.
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|
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Submission date |
Mar 21, 2022 |
Last update date |
Mar 01, 2023 |
Contact name |
hanim kim |
E-mail(s) |
qkfkvkvk93@gmail.com
|
Phone |
82-010-4311-0332
|
Organization name |
KAIST
|
Department |
biological science
|
Street address |
Daehak-ro 291
|
City |
Daejeon |
ZIP/Postal code |
34141 |
Country |
South Korea |
|
|
Platform ID |
GPL19580 |
Series (1) |
GSE199039 |
RRC1 is required for epidermal phyB siganling by maintaining the circadian rhythm by suppressing the alternative splicing of core clock genes. |
|
Relations |
SRA |
SRX14519193 |
BioSample |
SAMN26812245 |