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Sample GSM6261053 Query DataSets for GSM6261053
Status Public on Jun 20, 2023
Title Shoot-Rep3-WT-Control-0h
Sample type SRA
 
Source name Shoot
Organism Oryza sativa
Characteristics genotype: Kitaake_WT
tissue: 2nd leaf
treatment: none
Treatment protocol Plants were either non-treated or exposed to 100 mM NaCl solution. 3 plants were used per biological replicate.
Growth protocol Plants were grown in hydroponic system at 28°C, 12h/12h photoperiod, with 60% relative humidity
Extracted molecule total RNA
Extraction protocol Root total RNA was extracted with Rneasy Plant Mini Kit (Quiagen) and 2nd leaf total RNA extracted with Tri-Reagent. After DNAse treatment, RNA was purified using NucleoSpin RNA Clean-up kit (Macherey-Nagel).
After analysis with an Agilent 2 100 Bioanalyzer, all samples had a RIN value ≥ 6.
illumina PE150 platform, performed by NOVOGENE (Cambridge, UK)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description SWCR3_0
Data processing Raw data were first processed through fastp then filtered by removing reads containing adapters, reads containing N > 10% (N = base that could not be determined), low quality reads (Qscore of over 50% bases of the read)
Mapping to the Os-Nipponbare-Reference-IRGSP-1.0 reference genome with Hisat2
We estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to gene expression level, gene length and sequencing.
Differentially expression analysis was performed with DESeq2 (package R)
Assembly: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary files format and content: csv files with differentially expressed genes between the different conditions
 
Submission date Jun 22, 2022
Last update date Jun 20, 2023
Contact name Thierry HEITZ
E-mail(s) theitz@unistra.fr
Organization name CNRS
Department IBMP
Street address 12 rue du General Zimmer
City Strasbourg
ZIP/Postal code 67000
Country France
 
Platform ID GPL23013
Series (1)
GSE206706 Jasmonate signaling controls negative and positive effectors of salt stress tolerance in rice
Relations
BioSample SAMN29251934
SRA SRX15830662

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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