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| Status |
Public on Jun 20, 2023 |
| Title |
Root-Rep3-WT-Salt-6h |
| Sample type |
SRA |
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| Source name |
root
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| Organism |
Oryza sativa |
| Characteristics |
genotype: Kitaake_WT
tissue: Root
treatment: Salt_6h
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| Treatment protocol |
Plants were either non-treated or exposed to 100 mM NaCl solution. 3 plants were used per biological replicate.
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| Growth protocol |
Plants were grown in hydroponic system at 28°C, 12h/12h photoperiod, with 60% relative humidity
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
RWNR3_6
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| 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
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| Submission date |
Jun 22, 2022 |
| Last update date |
Jun 20, 2023 |
| Contact name |
Thierry HEITZ |
| E-mail(s) |
theitz@unistra.fr
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| Organization name |
CNRS
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| Department |
IBMP
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| Street address |
12 rue du General Zimmer
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| City |
Strasbourg |
| ZIP/Postal code |
67000 |
| Country |
France |
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| Platform ID |
GPL23013 |
| Series (1) |
| GSE206706 |
Jasmonate signaling controls negative and positive effectors of salt stress tolerance in rice |
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| Relations |
| BioSample |
SAMN29251908 |
| SRA |
SRX15830688 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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