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Status |
Public on Feb 10, 2015 |
Title |
Col-0 ozone rep1 (control genotype for coi1-16 ein2 sid2) |
Sample type |
SRA |
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Source name |
whole rosette
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Organism |
Arabidopsis thaliana |
Characteristics |
genotype: Col-0 developmental stage: 3 weeks old plants treatment: 350 ppb ozone exposure for 2hr
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Treatment protocol |
Plants were exposed with 350 nL L-1 ozone for two hours.
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
control genotype for coi1-16 ein2 sid2
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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
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Submission date |
Feb 09, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Yuxin Hu |
E-mail(s) |
huyuxin@ibcas.ac.cn
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Organization name |
Institute of Botany, CAS
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Department |
Key Laboratory of Plant Molecular Physiology
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Street address |
No.20 Nanxincun, Xiangshan
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City |
Beijing |
ZIP/Postal code |
100093 |
Country |
China |
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Platform ID |
GPL17639 |
Series (1) |
GSE65740 |
Transcriptome analysis of apoplastic reactive oxygen species signaling and dissection of its regulatory pathways |
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Relations |
Reanalyzed by |
GSE117052 |
BioSample |
SAMN03333304 |
SRA |
SRX869002 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1603943_8_Col_ozone_old_htseq-counts.tsv.gz |
494.0 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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