|
| Status |
Public on Jan 21, 2020 |
| Title |
LTH_12h_1 |
| Sample type |
SRA |
| |
|
| Source name |
leaves of three-week-old seedlings
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: LTH
genotype/variation: blast-susceptible
developmental stage: three-week-old seedlings
tissue: leaf tissue
|
| Treatment protocol |
Spores of each strain were mixed as the inoculum, and sprayed onto three-week-old seedlings of LTH and IR25. Leaves were collected at 0, 12, 24 hour post inoculation (hpi), immediately frozen in liquid nitrogen and stored at -80 ℃ until use
|
| Growth protocol |
All rice plants were grown at 26 ± 2 ℃ and 70% relative humidity under 12 h light : 12 darkness. M. oryzae strains (NC-24, NC-34, B9, Zhong8-10-14, 97-95-1, F1, NC-14, B13 and E37) were cultured in complete media at 28 ℃ under 12 h light : 12 darkness for two weeks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of each sample was isolated using TRIzol (Ambion) according to the manufacturer’s instructions.
For each sample, 25 µg of total RNA was used for circRNA-seq library preparation. Total RNA was depleted for ribosomal RNAs using the RiboMinus kit. The remaining RNAs were iron fragmented at 95℃ followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and subjected to PCR amplification. PCR products corresponding to 300-500 bp were purified and quantified, and then stored at -80 ℃ until used for sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Biological repeat 1 for LTH at 12 hpi with M.oryzae infection
|
| Data processing |
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2 and Qvalue <= 0.05
Reads were mapped using BWA
SAM files were then used to identify circRNAs with CIRI2
Reads were mapped to circRNAs using NovoAlign for calculating back-spliced reads
Genome_build: IRGSP v5.0
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample
|
| |
|
| Submission date |
May 30, 2019 |
| Last update date |
Jan 22, 2020 |
| Contact name |
Dong Chen |
| Organization name |
ABLife, Inc.
|
| Department |
Center for Genome Analysis
|
| Street address |
388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430075 |
| Country |
China |
| |
|
| Platform ID |
GPL21087 |
| Series (1) |
| GSE131641 |
CircRNAs function as a new layer of regulation in rice-Magnaporthe oryzae interaction |
|
| Relations |
| BioSample |
SAMN11891291 |
| SRA |
SRX5931283 |
