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Sample GSM5962848 Query DataSets for GSM5962848
Status Public on Mar 01, 2023
Title MLB_R60_rep3
Sample type SRA
 
Source name Whole Seedling
Organism Arabidopsis thaliana
Characteristics ecotype background: Col-0
age: 60hr
tissue: Whole Seedling
genotype: MLB
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.
 
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.
 
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 SRX14519191
BioSample SAMN26812243

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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