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| Status |
Public on Apr 28, 2020 |
| Title |
Os15: Vegetative R1 |
| Sample type |
SRA |
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| Source name |
Vegetative R1
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| Organism |
Oryza sativa Indica Group |
| Characteristics |
strain: BRS Ligeirinho
tissue: Leaf tissue
genotype: Sensitive to salt stress
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| Treatment protocol |
I) control (C): plants received irrigation with water and nutrient solution throughout the experiment; II) vegetative (S V ), plants were exposed to saline shock only at the vegetative stage; III) reproductive (S R ) plants were exposed to saline shock only at the reproductive stage; and IV) vegetative + productive (S V+R ), plants were exposed to saline shock at the vegetative stage (first shock event) and at the reproductive stage (recurrent event)
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| Growth protocol |
Rice seeds, genotype BRS Ligeirinho (Oryza sativa L. ssp. Indica), were germinated in a paper roll in a BOD type growth chamber (Model 202, EletroLab, São Paulo, Brazil), with a photoperiod of 16 h of light and 8 h of darkness and a temperature of 25±2 °C, and they were kept there for seven days. After this period, the seedlings were transferred to 8-L plastic pots, drilled at the base to ensure perfect percolation of water. As substrate, sand previously washed with water and 1% hydrochloric acid was used. The plants were kept in a greenhouse with 70% relative humidity, a temperature of 25±2 oC, and daily irrigation, alternated with water and nutrient solution of Hoagland and Arnon (1950).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Collected leaf tissues were immediately frozen in liquid nitrogen. Total RNA was extracted using Trizol (Invitrogen Inc., Carlsbad, CA, USA) and treated with DNase I (Invitrogen Inc., Carlsbad, CA, USA). Illumina TruSeq RNA Sample Preparation® V2 (IlluminaTM) kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Plants were exposed to saline shock only at the vegetative stage (V4)
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| Data processing |
Illumina Casava1.7 software used for basecalling.
For quality analysis of the reads was used FastQC Ver. 0.11.7 software and later the Trimmomatic Ver. 0:35 program to remove adapters and poor quality bases in each library. The reads were mapped against the O. sativa cv. Nipponbare (IRGSP build 1.0) from the MSU Rice Genome Annotation Project (RGAP 7) Database using STAR Ver. 2.7 software (Default parameters). HTSeq Ver. 0.11.1 software was used to count mapped reads.
Identification of differentially expressed genes (DEGs) was performed in the R Ver. 3.5.2 statistical environment with the edgeR Ver. 3.8 package, obtained from the Bioconductor repository. The raw reads were transformed to counts per million (CPM), keeping the genes with CPM values >1, and then normalised by the trimmed mean of M values method (TMM), considering DEGs with false discovery rates (FDRs) of <0.05 by the edgeR test.
Genome_build: MSU Ver. 7
Supplementary_files_format_and_content: tab-delimited text files include count values by gene for each sample
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| Submission date |
Apr 27, 2020 |
| Last update date |
Apr 29, 2020 |
| Contact name |
Luis Willian Pacheco Arge |
| Organization name |
UFRJ
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| Department |
Genetica
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| Lab |
LGMBV
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| Street address |
Av. Carlos Chagas Filho, 373
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| City |
Rio de Janeiro |
| State/province |
Rio de Janeiro |
| ZIP/Postal code |
21941-590 |
| Country |
Brazil |
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| Platform ID |
GPL21027 |
| Series (1) |
| GSE149396 |
Long-term transcriptional memory in rice plants submitted to salt shock |
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| Relations |
| BioSample |
SAMN14734801 |
| SRA |
SRX8180586 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4498961_Os15_R1.count.txt.gz |
183.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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