|
| Status |
Public on Mar 16, 2020 |
| Title |
IRBB5_24h_2 |
| Sample type |
SRA |
| |
|
| Source name |
IRBB5_24h_leaves
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: IRBB5
developmental stage: at the tillering stage
treatment/infection: Xoo strain PXO86 infection
time point: 24 hpi
tissue: Leaf
|
| Treatment protocol |
Leaves were inoculated with Xoo strain PXO86 at the tillering stage by the leaf-clipping method. And leaf tissues loci were collected at 0, 8, 24 hpi, respectively.
|
| Growth protocol |
The Indica rice (Oryza sativa L.) cultivars, IR24 and IRBB5, were cultivated in the experimental fields in Beijing
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Every sample was pooled with infected leaves collected from twenty plants in one plot to diminish the individual environment differences.Total RNA were extracted from the mentioned samples using Trizol reagent (Invitrogen, USA) according to the manufacturer’s recommendation.
Small RNAs with 18~30 nt in length were isolated from the total RNA using a polyacrylamide gel electrophoresis gel, and then were sequenced by the BGISEQ-500.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Raw reads were processed into clean reads by trimming adapter sequence and the low-quality reads.
Then, clean reads were classified by aligning to rice genome(http://rise2.genomics.org.cn/page/rice/download.jsp) and non-coding RNA(http://rfam.janelia.org) using AASRA and cmsearch software, respectively.
Reads matching mature miRNA sequence in the miRBase Database (v20.0) were identified as known miRNAs, and novel miRNAs were predicted using ‘MIREAP’(https://sourceforge.net/projects/mireap/) in terms of the characteristic fold-back structure (Blake et al., 2008), and other small non-coding RNAs were also sorted out with related database.
MiRNAs with at least 20 M clean reads in three biological replicates were chosen to perform expression analysis, and the expression levels were quantified using the mean value. The criterion of DE miRNAs was set as |log2(fold change ratio)| ≥1.5.
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/Oryza_sativa_Japonica_Group/
Supplementary_files_format_and_content: abundance measurements
|
| |
|
| Submission date |
Dec 13, 2019 |
| Last update date |
Mar 16, 2020 |
| Contact name |
yanfeng jia |
| E-mail(s) |
yfjia@genetics.ac.cn
|
| Organization name |
Institute of genetics and developmental biology, Chinese academy of science
|
| Street address |
Beijing Beijing Chaoyang District Beichen West Road
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL27908 |
| Series (2) |
| GSE141995 |
Characteristic dissection of Xanthomonas oryzae pv. oryzae responsive microRNAs in rice [datatset 2] |
| GSE141996 |
Characteristic dissection of Xanthomonas oryzae pv. oryzae responsive microRNAs in rice |
|
| Relations |
| BioSample |
SAMN13558924 |
| SRA |
SRX7366924 |
