 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 20, 2020 |
| Title |
Combination_3 (miRNA) |
| Sample type |
SRA |
| |
|
| Source name |
Combination, plants leaves
|
| Organism |
Solanum lycopersicum |
| Characteristics |
genotype: wild type
treatment: Combination
tissue: plants leaves
|
| Treatment protocol |
The 24-day-old seedlings were divided into two groups with one group irrigated by water and another group without irrigation. After three days, half of the seedlings from the group with/without irrigation were treated at a normal temperature (26°C, 48 h, day) as a control and drought stress treatment. The rest half of the seedlings from the group with/without irrigation were treated at high temperature (38°C, 48 h, day) as a heat and combined stress treatment. The 24-day-old and 27-day-old seedlings at control and heat stress treatment were subjected to two additional irrigations with water as compared to that at drought and combined stress.
|
| Growth protocol |
Single seeds were sown in a plug tray and then cultured in climate chambers (RDN-560E-4, Dongnan Instrument Co, Ltd, Ningbo, China). The air temperature was 26/18°C (14 h/10 h, 6:00-20:00/20:00-6:00, day/night) with a light intensity of 300 μmol m–2 s–1 photosynthetic photon flux density (PPFD) (LED light source, Dongnan Instrument Co, Ltd, Ningbo, China) and 50-60% relative humidity (RH). The seedlings were irrigated by water every five days. Then, the 15-day-old seedlings were irrigated by nutrient solution according to the Japanese Garden test formula [Ca(NO3)2.4H2O, 945mg/L; KNO3, 809 mg/L; NH4H2PO4, 153 mg/L; MgSO4.7H2O, 493 mg/L; FeSO4.7H2O, 13.9 mg/L; Na2-EDTA, 18.6 mg/L; H3BO3, 2.86 mg/L; MnSO4.4H2O, 2.13 mg/L; ZnSO4.7H2O, 0.22 mg/L; CuSO4.5H2O, 0.08 mg/L; (NH4)6Mo7O24.4H2O, 0.02 mg/L] every three days. The 21-day-old healthy and uniform seedlings were transferred to plastic plots (11 cm diameter, 9 cm height) and then cultured in the climate chambers under the same conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
The libraries were sequenced by Illumina Hiseq 2500/Hiseq 4000 at the LC-BIO following the vendor’s recommended protocol.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
miRNA sequencing
|
| Data processing |
miRNA-Seq: Unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
miRNA-Seq: Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
miRNA-Seq: The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
miRNA-Seq: The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
miRNA-Seq: The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: miRBase 21.0
Supplementary_files_format_and_content: normalized counts
|
| |
|
| Submission date |
Oct 10, 2018 |
| Last update date |
Feb 20, 2020 |
| Contact name |
Rong Zhou |
| E-mail(s) |
yanfliu@126.com
|
| Organization name |
Jiangsu Academy of Agricultural Sciences
|
| Street address |
50 Zhongling Street
|
| City |
Nanjing |
| ZIP/Postal code |
210014 |
| Country |
China |
| |
|
| Platform ID |
GPL19694 |
| Series (1) |
| GSE121089 |
Genome wide identification of circRNAs, miRNAs and their targets in tomatoes at heat, drought and their combination |
|
| Relations |
| BioSample |
SAMN10228505 |
| SRA |
SRX4824958 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
