Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJNA661210: Transcriptome analysis of the rice response to Magnaporthe oryzae identified core genes involved in immunity

Source: NCBI / GSE157400
Submission Date: Sep 03, 2020
Release Date: Dec 31, 2022
Update Date: Dec 31, 2022

Summary: We carried out an time-series transcriptome study of susceptible rice cultivar Nipponbare and resistant cultivar Hui1586 in response to M. oryzae isolate Guy11 at 12, 24, 36 and 48 hpi. In total, 48 samples were subjected to RNA-seq, resulting in 6.8-gigabyte 100-bp paired-end reads per sample on average

Overall Design: mRNA of 14 days rice leaves infected by M. oryzae or water (mock) were subjected for RNA-sequcing and trancriptome profiling analysis.

GEN Datasets:
GEND000525
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Cell Line:
Development Stage:
Protocol
Growth Protocol: The rice plants were grown in a light incubator for 14 days with 12 h light and 12 h dark conditions.
Treatment Protocol: Spore concentration was adjusted to 5 × 105 spores/mL with 0.02% Tween-20, H2O with 0.02% Tween-20 was used as mock treatment. The fungal-inoculated rice seedlings were kept in a dark chamber at 25 ◦C with 85% humidity for 24 hours, then the plants were maintained in the growth chamber at 26/24 ◦C in a 14 h light/10 h dark cycle with 85% humidity.
Extract Protocol: Total RNA quality detection was performed with a Nanodrop for determining the RNA concentration; nondenaturing agarose electrophoresis for determining RNA integrity; and an Agilent 2100 Bioanalyser for determining the total RNA.
Library Construction Protocol: RNA libraries were prepared for sequencing using standard Illumina protocols
Sequencing
Molecule Type: rRNA- RNA
Library Source:
Library Layout: SINGLE
Library Strand: -
Platform: BGISEQ
Instrument Model: BGISEQ-500
Strand-Specific: Unspecific
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Condition Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate