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| Status |
Public on Feb 20, 2020 |
| Title |
Combination_2 (circRNA) |
| Sample type |
SRA |
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| Source name |
Combination, plants leaves
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| Organism |
Solanum lycopersicum |
| Characteristics |
genotype: wild type
treatment: Combination
tissue: plants leaves
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| 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.
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| 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.
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| 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.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
circRNA sequencing
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| Data processing |
circRNA-Seq: Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
circRNA-Seq: We used Bowtie2 and Tophat2 to map reads to the genome of species. Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion
circRNA-Seq: CIRCExplorer was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion and CIRCExplorer.
Genome_build: genome of species (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/188/115/GCF_000188115.3_SL2.50/GCF_000188115.3_SL2.50_genomic.fna.gz)
Supplementary_files_format_and_content: FPKMs
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| Submission date |
Oct 10, 2018 |
| Last update date |
Feb 20, 2020 |
| Contact name |
Rong Zhou |
| E-mail(s) |
yanfliu@126.com
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| Organization name |
Jiangsu Academy of Agricultural Sciences
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| Street address |
50 Zhongling Street
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| City |
Nanjing |
| ZIP/Postal code |
210014 |
| Country |
China |
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| Platform ID |
GPL25655 |
| Series (1) |
| GSE121089 |
Genome wide identification of circRNAs, miRNAs and their targets in tomatoes at heat, drought and their combination |
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| Relations |
| BioSample |
SAMN10228533 |
| SRA |
SRX4824981 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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