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Sample GSM1603944 Query DataSets for GSM1603944
Status Public on Feb 10, 2015
Title Col-0 ozone rep2 (control genotype for coi1-16 ein2 sid2)
Sample type SRA
 
Source name whole rosette
Organism Arabidopsis thaliana
Characteristics genotype: Col-0
developmental stage: 3 weeks old plants
treatment: 350 ppb ozone exposure for 2hr
Treatment protocol Plants were exposed with 350 nL L-1 ozone for two hours.
Growth protocol Seeds were sown on 1:1 peat: vermiculite, stratified for three days, and then grown at 22°C/19°C for a week. Subsequently the geminated seedlings were transplanted into new 1:1 peat: vermiculite mixture, one plants per pot (6cm x 6cm), and eight plants per genotype. All plants were randomly placed, grown in controlled chamber (Weiss Bio1300; Weiss Gallenkamp), at 22°C/19°C, and relative humidity of 70%/90%, under a 12-h light/12-h dark cycle for two weeks.
Extracted molecule total RNA
Extraction protocol Ten to 15 rosettes per genotype (Col-0 set1, coi1-16 ein2 sid2, Col-0 set2, tga2 tga5 tga6 ) from control and ozone treatment were pooled and frozen into liquid nitrogen. Three biological replicates of RNA were isolated with GeneJet Plant RNA purification Mini Kit (Fermentas, now part of Thermo Scientific). Quality and quantity of RNA was assessed using Agilent 2100 Bioanalyzer and NanoDrop.
Libraries were prepared from 100 ng of total RNA with Illumina TruSeq RNA Sample Prep Kit v2 according to the kit manual.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description control genotype for coi1-16 ein2 sid2
Data processing RNA-seq data analysis was performed with the JAVA-based client-server system Chipster
Quality of sequences was checked with FastQC package
First 13 reads were trimmed FRINSEQ package, then mapped to wild type Col-0 whole genome using TopHat2 with following settings:Do not ignore novel junctions, hits allowed=2, allowing 2 nucleotide mismatches, minimum anchor length=8, Maximum number of mismatches allowed in the anchor=0, minimum intron length=20, Maximu intron length=2000
Generated BAM files were sorted and indexed with SAMtools package
Number of Reads of each gene was counted and calculated with HTSeq package
Genome_build: Col-0 TAIR10.23
Supplementary_files_format_and_content: Tab-separated values files including AGI code, chromsomes, start, end, length and RPKM values for each Sample
 
Submission date Feb 09, 2015
Last update date May 15, 2019
Contact name Yuxin Hu
E-mail(s) huyuxin@ibcas.ac.cn
Organization name Institute of Botany, CAS
Department Key Laboratory of Plant Molecular Physiology
Street address No.20 Nanxincun, Xiangshan
City Beijing
ZIP/Postal code 100093
Country China
 
Platform ID GPL17639
Series (1)
GSE65740 Transcriptome analysis of apoplastic reactive oxygen species signaling and dissection of its regulatory pathways
Relations
Reanalyzed by GSE117052
BioSample SAMN03333308
SRA SRX869003

Supplementary file Size Download File type/resource
GSM1603944_22_Col_ozone_old_htseq-counts.tsv.gz 495.3 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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