|
| Status |
Public on Aug 31, 2015 |
| Title |
CK6h |
| Sample type |
SRA |
| |
|
| Source name |
Leaves
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Nipponbare
developmental stage: 40-day old
tissue: leaf
infection: water
time: 6hpi
|
| Treatment protocol |
The leaves of 40-day-old rice seedling were infected by Xoo PXO99 and water for experimental and control samples, respectively. Leaf tissues at 1 cm below the infected loci were collected at 2, 6, 12, and 24 hpi, respectively.
|
| Growth protocol |
Japonica rice varieties (Oryza sativa, Nipponbare) were grown in the experimental fields in Beijing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were collected from multiple plants and pooled together before use. Total RNAs of each sample were isolated using Trizol reagent (Invitrogen), and small RNAs were collected and sequenced by the Illumina’s sequencing technology.
Small RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Sample 2
small RNAs
|
| Data processing |
Raw sequence reads were first trimmed to remove adapter sequences. Sequences with low phred quality scores or shorter than 18 nucleotides were removed. The total number of reads for each data set was normalized to 10 million. Total sequences of the eight data sets were aligned to the rice genomic sequences and miRNA precursor sequences, respectively, using the BLASTN (Altschul et al., 1990) program.
Transposons and repeat regions in the rice genome were identified by the RepeatMasker software.
Target gene prediction for miRNAs and ta-siRNAs was performed as previously described (Zhao et al., 2012).
Statistical analysis and data plotting were carried out using R. Expression comparison of small RNAs was performed at each time point separately. Small RNAs with at least 10 reads in both the Xoo treated and control samples were included in the expression comparison analysis. Differentially expressed small RNAs were selected with at least 2 fold expression increment or decrease in the Xoo treated sample as compared to the control. fold change equal to or more than 2.
Original raw files unavailable: The *raw_reads.txt files are similar to FASTQ format but without phred quality score. In these files, the sequences with low phred scores have been removed.
Genome_build: rice genomic sequences version 6.1 [http://rice.plantbiology.msu.edu/ (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_6.1/)]
Supplementary_files_format_and_content: raw reads and normalized reads
|
| |
|
| Submission date |
Jun 11, 2014 |
| Last update date |
Aug 31, 2015 |
| Contact name |
Ying-Tao Zhao |
| E-mail(s) |
[email protected]
|
| Organization name |
New York Institute of Technology
|
| Department |
Biomedical Sciences
|
| Lab |
Jerry Zhao Lab
|
| Street address |
Riland building, Room 024 Northern Boulevard, P.O. Box 8000
|
| City |
Old Westbury |
| State/province |
NY |
| ZIP/Postal code |
11568 |
| Country |
USA |
| |
|
| Platform ID |
GPL15370 |
| Series (1) |
| GSE58385 |
Dynamic and coordinated expression changes of rice small RNAs in response to Xanthomonas oryzae pv. oryzae |
|
| Relations |
| BioSample |
SAMN02850079 |
