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Sample GSM3929461 Query DataSets for GSM3929461
Status Public on Jul 01, 2020
Title Whole seedlings, LowLight.bzip68.rep2
Sample type SRA
 
Source name LowLight.bzip68
Organism Arabidopsis thaliana
Characteristics tissue: whole seedlings
age: 14-day-old
genotype: bzip68
treatment: LowLight
Treatment protocol Lowlight treatment: seedlings of wildtype and bzip68 mutant were grown on 1/2 MS plates in presence of white light (30 umoles/m2 seg). Mock: seedlings of wildtype and bzip68 mutant were grown on 1/2 MS plates in presence of white light (125 umoles/m2 seg) for 14 days then sparyed with water supplied with 0.01% triton X-100. H2O2 treatment: seedlings of wildtype and bzip68 mutant were grown on 1/2 MS plates in presence of white light (125 umoles/m2 seg) for 14 days then sparyed with 5 mM H2O2 supplied with 0.01% triton X-100.
Growth protocol Arabidopsis seedlings were growth on 1/2 MS plates containing 3% sucrose and 0.8% agar for 14 days under 16h light/ 8h dark condition(with light 30 umoles/m2 seg )
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Agilent Plant RNA Isolation Mini kit according to the manufacturer’s instructions. Bar-coded mRNA libraries were constructed by BGI (Shenzhen, China) using the Illumina’s reagents and protocols according to the manufacturer’s instruction. Samples were sequenced on Illumina HiSeq 2500 system.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description 20190704.bzip.counts.xlsx
Data processing TopHat 2.1.0 software (Trapnell, Pachter and Salzberg, 2009) was used to map the reads to the Arabidopsis genome (TAIR10). RSEM 2.1.30 (Anders, Pyl and Huber, 2015) was used for statistical analysis of the read counts for each gene.
Genome_build: A. thaliana Ensemble 41 (TAIR10)
Supplementary_files_format_and_content: 20190704.bzip.counts.xlsx, Supplementary_Tables_S1_S2.BZIP68_CHIPSeq_peaks_v4.xlsx
 
Submission date Jul 06, 2019
Last update date Jul 01, 2020
Contact name Huan ZHONG
E-mail(s) zhdorothy5@gmail.com
Phone 91493987
Organization name HKBU
Department BIOLOGY
Street address T1012 CHA CHI-MING SCIENCE TOWER
City HONG KONG
State/province HONG KONG
ZIP/Postal code 00000
Country Hong Kong
 
Platform ID GPL17639
Series (1)
GSE133900 Redox-sensitive bZIP68 plays a role in balancing stress tolerance with growth in Arabidopsis
Relations
BioSample SAMN12226116
SRA SRX6410164

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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