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| Status |
Public on Feb 28, 2021 |
| Title |
SSB_BPH_3 |
| Sample type |
SRA |
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| Source name |
Rice plant stems
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| Organism |
Oryza sativa |
| Characteristics |
tissue: Rice plant stems
age: 44–49 days after sowing
stress: SSB_BPH
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| Treatment protocol |
i) Control plants (Control), meaning that potted rice plants remained intact without insect infestation; (ii) SSB-infested plants (SSB), each potted rice plant was artificially infested with one 3rd instar SSB larva that had been starved for 3 hr for 48 hr; iii) BPH-infested plants (BPH), each potted rice plant was artificially infested with a mix of fifteen 3rd and 4th instars BPH nymphs for 48 hr; iv) SSB_BPH-infested plants (SSB_BPH), each potted rice plant was simultaneously infested with one SSB larva and 15 BPH nymphs for 48 hr. After 48h, the stems of the plants were harvested and frozen in liquid nitrogen. Samples from 5 individual plants of the same treatment were pooled together as one biological replicate, and three replicates were collected for each treatment.
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| Growth protocol |
Rice plants (Oryza sativa, cultivar Minghui63) were grown in a greenhouse at 27 ± 3 °C with 75 ± 10% RH (relative humidity) and a photoperiod of 16:8 hr L:D (light:dark).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from rice leaves samples was isolated using TRIzol Reagent (Life Technologies, Grand Island, NY, USA) following to the manufacturer’s instructions.
Libraries were prepared using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA USA) according to the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
For transcriptome data, raw Illumina data of fastq format were first processed using in-house perl scripts. After removing reads containing adaptors, reads containing poly-N and low-quality reads from raw data, we obtained the clean data. The Q20, Q30, GC (guanine-cytosine)-content and sequence duplication level of the clean data were calculated. The clean reads were aligned to the reference genome IRGSP-1.0 (https://rapdb.dna.affrc.go.jp)using HISAT2 tools (version 2.09)
Feature Counts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. Gene expression levels were estimated using fragments per kilobase of transcript per million mapped reads (FPKM) based on the length of the gene and reads count mapped to this gene. Differentially expressed genes analysis was performed using the DESeq2 R package.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each sample.
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| Submission date |
Feb 27, 2021 |
| Last update date |
Feb 28, 2021 |
| Contact name |
Qingsong Liu |
| E-mail(s) |
liuqingsong@xynu.edu.cn
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| Phone |
86-18537688228
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| Organization name |
Xinyang Normal University
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| Street address |
No. 237, Nanhu road
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| City |
Xinyang |
| State/province |
Henan |
| ZIP/Postal code |
464000 |
| Country |
China |
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| Platform ID |
GPL23013 |
| Series (1) |
| GSE167872 |
Cooperative herbivory between two important pests of rice |
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| Relations |
| BioSample |
SAMN18084049 |
| SRA |
SRX10185404 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5114362_SSB_BPH-3.txt.gz |
294.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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