|
| Status |
Public on Oct 31, 2016 |
| Title |
Pid3.ZB13.8.2-RNAseq |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: leaf
age: 4 weeks old
inoculation type: ZB13 inoculation
phenotype: susceptible
interaction: compatible
|
| Treatment protocol |
Four-week seedlings were subjected to spray inoculation with conidial suspensions (for each strain) of 2.5 × 105 conidia/ml (suspended in 0.25% gelatin solution). For the mock control, the conidial suspensions were replaced with 0.25% gelatin solution. The inoculation was carried out under controlled conditions at 28℃ and 100% relative humidity for 24 h in darkness, then shifted to a 16/8 h light/dark regime.
|
| Growth protocol |
Rice seedlings were grown in 32°C day 16 hours and 28°C night 8 hours in greenhouse. Four-week seedlings were used for pathogen inoculation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated using TRIzol reagent (Life Technologies) and treated with RNase-free DNase I (Takara) to remove any contaminating genomic DNA.
mRNA extraction was performed using Dynabeads oligo(dT) (Dynal; Invitrogen Corp.). Double-stranded cDNAs were synthesized using reverse transcriptase (Superscript II; Invitrogen Corp.) and random hexamer primers. The cDNAs were then fragmented by nebulization, and the standard Illumina protocol was followed thereafter to create the mRNA-seq libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
For mRNA RNA-Seq data, TopHat for mapping, HTSeq for estimating their abundances
Genome_build: Reference genome sequences and annotations were downloaded from the rice genome website .(ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/).
Supplementary_files_format_and_content: The rpkm.txt.gz files include abundance measurements (RPKM values) for each mRNA RNA-Seq sample.
|
| |
|
| Submission date |
Oct 31, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Mengdi Liu |
| E-mail(s) |
liumengdi@novogene.cn
|
| Organization name |
Novogene institute
|
| Street address |
No.38 Xueqing Road, Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
| |
|
| Platform ID |
GPL13160 |
| Series (1) |
| GSE62911 |
The gene expression kinetics reveals a key role of jasmonic acid in rice disease resistance to Magnaporthe |
|
| Relations |
| BioSample |
SAMN03154679 |
| SRA |
SRX749100 |
