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| Status |
Public on Dec 30, 2015 |
| Title |
HHZ-ck-2 |
| Sample type |
SRA |
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| Source name |
leaves
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| Organism |
Oryza sativa |
| Characteristics |
genotype: recurrent parent
developmental stage: tillering phase
treatment: normal condition
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| Treatment protocol |
The Philippine’s representative strain of Xoo, PXO349, was used to artificially inoculate H471 and its parents. The strain was incubated on peptone sucrose agar at 30°C for 2 days, and the inoculum was prepared by suspending the bacterial mass in sterile water at a concentration of 108 cells mL-1. Five plants of each line were inoculated with PXO349 in the four to five uppermost leaves of each plant using the leaf-clipping method in three replications at the tillering stage (plant age of 65 days). LLs were measured on all inoculated leaves at 14 dpi when the lesions were stable.
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| Growth protocol |
Seeds of H471, HHZ, and P28 were sown in a seedling nursery and 30-day-old seedlings were transplanted into a screenhouse of the Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China. There were nine plants in each row, with a spacing of 20 × 17 cm.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For all RNA-seq samples, total RNA was extracted with TRIzol Reagent (Invitrogen, Carlsbad, California, USA), and quantified using a Qubit RNA assay kit (Applied Biosystems, Foster City, California, USA). RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California, USA). RNA samples from three independent replicates for each treatment were pooled.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
replicate 2
CP1
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| Data processing |
Primary data analysis and base calling was performed by the Illumina instrument software.
The raw reads were first filtered by removing adaptor sequences and low-quality sequences by using in-house perl script. Low quality nucleotides (< Q20) were trimmed from raw sequences for each sample, and then pair-end reads with either of both with length less than 30 bp were removed, and the retained high quality pair-end reads of rice for each sample were mapped to the rice genome of RGAP at MSU (Kawahara et al., 2013) by tophat (Trapnell et al., 2009) and then assembled with Cufflinks (Trapnellet al., 2010) to construct unique transcipts sequences, using the parameter:-g -b -u -o.
The retained high quality pair-end reads of each sample were mapped to the rice genome using Tophat2(v2.0.11) with default parameters. Then gene expression abundance was quantified by FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks(v2.1.1), and differentially-expressed genes (DEGs) between samples were identified by Cuffdiff, a component of the Cufflinks package.
Genome_build: MSU Release 7.0 (Os-Nipponbare-Reference-IRGSP-1.0)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Oct 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Fan Zhang |
| Organization name |
CAAS
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| Street address |
12 South Zhong-Guan-Cun St.
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
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| Platform ID |
GPL13160 |
| Series (1) |
| GSE62488 |
Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response |
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| Relations |
| BioSample |
SAMN03120592 |
| SRA |
SRX735428 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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