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Sample GSM4086309 Query DataSets for GSM4086309
Status Public on Mar 16, 2020
Title I-L20-1
Sample type SRA
 
Source name miR399f overexpressing line L20 infected with Magnaporthe oryzae 48 hpi
Organisms Oryza sativa; Pyricularia oryzae
Characteristics tissue: leaf
rice cultivar: Tainung67 (japonica)
m. oryzae strain: Guy11
Treatment protocol Soil-grown plants (3-4 leaf stage) were mock-inoculated or inoculated with M. oryzae spores for 48hours . Inoculation was done by spraying whole rice plants with a M. oryzae spore suspension (10E5 spores/ml; 0.2 ml/plant) by using an aerograph at 2 atmospheres of pressure
Growth protocol Rice plants were grown at 28ºC with a 14 h/10 h light/dark cycle. The fungus M. oryzae was grown in Complete Media Agar (CMA, 9 cm plates, containing 30 mg/L chloramfenicol) for 15 days at 28ºC under a 16 h/8 h light/dark photoperiod condition.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with the Maxwell 16 LEV Plant RNA Kit (Promega) following manufacturer's instructions.
Indexed libraries prepared from 1ug purified RNA with TruSeq Stranded mRNA Sample Prep Kit (Illumina). Samples pooled; each index-tagged sample present in equimolar amounts (final concentration of pooled samples at 2nm). Pooled samples subjected to cluster generation and sequencing using Illumina Hseq 2500. 2x100 paired-ennd at final concentration of 8pmol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Raw reads were checked for quality by using FastQC v0.11.3
Trimming and removal of adapters involved using Trimmomatic v0.33 (minimum quality score 35, minimum length 25).
The obtained reads were mapped against the Oryza sativa reference genome (MSU 7.0) by using STAR (v2.4.0j)
Alignment files were filtered to remove reads with mapping quality (MAPQ) <30. FeatureCounts (v1.4.5-p1)
Statistical analysis of read counts was performed with R, with the HTSFilter package to remove low-expressed genes and the edge R package
Genome_build: MSU 7.0
Supplementary_files_format_and_content: TXT
 
Submission date Sep 19, 2019
Last update date Mar 16, 2020
Contact name Blanca San Segundo
E-mail(s) blanca.sansegundo@cragenomica.es
Organization name Center for Research in Agricultural Genomics (CRAG)
Department Plant Responses to Stress
Street address Edifici CRAG - Campus UAB
City Bellaterra
State/province Barcelona
ZIP/Postal code 08193
Country Spain
 
Platform ID GPL27492
Series (1)
GSE137735 Phosphate excess increases susceptibility to pathogen infection in rice
Relations
BioSample SAMN12788355
SRA SRX6874257

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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