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Sample GSM3425879 Query DataSets for GSM3425879
Status Public on Feb 20, 2020
Title Heat_3 (Degradome)
Sample type SRA
 
Source name Heat, plants leaves
Organism Solanum lycopersicum
Characteristics genotype: wild type
treatment: Heat
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 OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description Degradome sequencing
Data processing Degradome-Seq: Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
Degradome-Seq: The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
Degradome-Seq: The degradome reads were mapped to the mRNA database. Only the perfect matching alignment(s) for the given read would be kept for degradation analysis.
Degradome-Seq: All resulting reads (t-signature) were reverse- complemented and aligned to the miRNA identified in our study. No more than four alignment scores were allowed. Alignments where the degradome sequence position coincident with the tenth or eleventh nucleotide of miRNA were retained and scored. The target was selected and categorized as 0, 1, 2,3,or 4. category 0—over one raw read at the position, abundance at the position is equal to the maximum on the transcript, and there is only one maximum on the transcript; category 1—over one raw read at theposition, abundance at the position is equal to the maximum on the transcript, and there is more than one maximum position on the transcript; category 2—over one raw read at the position, abundance at position is less than the maximum but higher than the median for the transcript; category 3—over one raw read at the position, abundance at the position is equal to or less than the median for the transcript; and category 4—only one raw read at the position.
Genome_build: mRNA database (ftp://ftp.solgenomics.net/tomato_genome/assembly/build_3.00/ITAG3.2_cDNA.fasta)
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 SAMN10228528
SRA SRX4824967

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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