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| Status |
Public on Nov 05, 2020 |
| Title |
6h_3 |
| Sample type |
SRA |
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| Source name |
rice plant leaves
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| Organism |
Oryza sativa |
| Characteristics |
tissue: rice plant leaves
age: five weeks
time point: 6h
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| Treatment protocol |
A soft brush was used to place one 3rd-instar C. medinalis on the second leaf from the top. The larvae were starved for 2 h before experiments and confined within a small Parafilm bag. For the time-course bioassays, the larvae were transferred to rice leaves for the final 1, 6, 12, or 24 h of the experiment (Figure S1). Control rice plants were placed in the same type of Parafilm bags as in the herbivory treatment but without placement of insects. All leaf materials were harvested at the same time. The samples were immediately frozen in liquid nitrogen and stored at -80 °C for further use. Five leaf tissues collected from five independent plants within the same treatments were merged as one sample (i.e., biological replicate).
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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 |
Oct 08, 2020 |
| Last update date |
Nov 05, 2020 |
| 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) |
| GSE159259 |
Transcriptomic and metabolomic responses of rice plants to Cnaphalocrocis medinalis caterpillar infestation |
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| Relations |
| BioSample |
SAMN16398853 |
| SRA |
SRX9266291 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4824439_6h_3.txt.gz |
566.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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