|
| Status |
Public on Jan 01, 2021 |
| Title |
Root, salt rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Root, salt treated
|
| Organism |
Oryza sativa |
| Characteristics |
treatment: salt
|
| Treatment protocol |
In salt treatment, Oryza sativa seedlings were transferred to 300 mM NaCl solution for 8 h. In cold treatment, Oryza sativa seedlings were transferred to a cold room at 4ºC under continuous light for 8 h. The control and stress treated seedlings were collected and immediately frozen in liquid nitrogen and stored at -80ºC before RNA extraction.
|
| Growth protocol |
Arabidopsis thaliana plants were germinated in the soil and grown at 23 ºC under the standard long-day condition (16 hours of light followed by 8 hours of darkness). Oryza sativa seeds were germinated at 30ºC for 2 d. Uniformly germinated seeds were transferred to Yoshida’s nutrient solution and grown at 28ºC under long-day condition (14 hours of light followed by 10 hours of darkness). Yoshida’s solution were replaced every 3 d with pH adjusted to 5.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was conducted using TRIzol reagent (Invitrogen). Ethanol precipitation was performed overnight at -20ºC to maximize sRNA yield.
RNA pretreatment was conducted using rtStar tRF&tiRNA pretreatment kit (Arraystar). Pretreated RNAs were purified by Phenol:Chloroform extraction and ethanol precipitation. Pretreated RNAs were subjected to small RNA-seq library construction using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). Purification of PCR amplified cDNAs were conducted using VAHTS DNA Clean Beads (Vazyme).
tRNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
pretreated RNA
|
| Data processing |
tRNA-seq data were first processed to remove the 5’ and 3’ adaptor sequences using cutadapt with the parameters “-m 17 --trim-n -f fastq -a AGATCGGAAGAGCAC -A GATCGTCGGACTGTA -g TACAGTCCGACGATC -G GTGCTCTTCCGATCT -n 2”. Then, the trimmed data were analyzed by tRanalyzer, a self-designed pipeline for quantifications of tsRNAs and tRNAs.
Genome_build: TAIR10, TIGR7
Supplementary_files_format_and_content: Each excel format file includes four sheets. The tRNAID sheet includes the IDs, genomic coordinates and unique sequences of tRNAs. tRNA_expression sheet shows tRNA abundances. tRFs_from_each_tRNA sheet shows the abundance of tRFs from each tRNA. Each_tRF sheet shows the abundance of each tRF species.
|
| |
|
| Submission date |
Jan 03, 2019 |
| Last update date |
Jan 01, 2021 |
| Contact name |
Xuan Ma |
| E-mail(s) |
skyxma@tjnu.edu.cn
|
| Organization name |
Tianjin Normal University
|
| Department |
College of Life Sciences
|
| Street address |
Binshui West Road
|
| City |
Tianjin |
| ZIP/Postal code |
300387 |
| Country |
China |
| |
|
| Platform ID |
GPL23013 |
| Series (1) |
| GSE124608 |
Quantification of tRNA-derived fragments in Arabidopsis and rice |
|
| Relations |
| BioSample |
SAMN10689158 |
| SRA |
SRX5202441 |
