|
| Status |
Public on May 26, 2024 |
| Title |
Diploid jujube under control environment (repeat 2) |
| Sample type |
SRA |
| |
|
| Source name |
Diploid jujube under control environment
|
| Organism |
Ziziphus jujuba var. spinosa |
| Characteristics |
ploidy/cultivar: Ziziphus jujuba Mill. var. spinosa
tissue: leaves
age: after tissue culture of 30 days, well-growing plants were cultured in the rooting medium for 45 days
genotype: wild type
treatment: control environment
|
| Treatment protocol |
Diploids and autotetraploid plants with uniform growth were transferred to 3% Hoagland and Arnon solution (pH 6.0 ± 0.2) with dark for 3 days and light for 7 days before treatment. The nutrient solution was replaced every two days and kept sterile. Following PEG6000 was gradually applied to the seedlings to avoid osmotic shock which is 5%, 10%, 15% and finally 20% over 1-day intervals under 16/8 h light/dark cycle at 25 ± 2 °C and 130μmolm-2s-1 illumination intensity.
|
| Growth protocol |
More than twenty generations diploid and its autotetraploid seedlings were tissue-cultured synchronously under 16/8 h light/dark cycle at 25 ± 2 °C and 130μmolm-2s-1 illumination intensity. After tissue culture of 30 days, well-growing plants were cultured in the rooting medium for 45 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaves under control and drought treatment of 6h, 12h and 48h were sampled from diploid and the autotetraploid for RNA-seq. Total RNA was extracted from 100mg sample with plant RNA kit (Omega Biotech, China) and purified with RNase-Free DNase set. Following, RNA concentration was measured on the NanoDrop 2000 spectrophotometer (Thermo Scientific, MA), and RNA integrity was assessed using an RNA Nano 6000 Assay kit supplied with the Agilent Bioanalyzer 2100 system (Agilent Technologies, USA).
A total of 1μg RNA was used to construct cDNA library and the library concentration and insert size was respectively assessed on the Qubit2.0 (Invitrogen, USA) and Agilent Bioanalyzer 2100 system, and then the effective concentration of the library was accurately quantified through Q-PCR.
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
DCK-2
DCK-2_ZiziphusjujubaMill_V198-01-T02
processed data file: DCK-1,DCK-2,DCK-3.txt
|
| Data processing |
Illumina Casava1.8 and Bcltofastq 1.8.4 software used for basecalling analysis.
Clean data were obtained after removing all adapter- and poly-Ncontaining sequences and low-quality reads from the raw data, and Q20 and Q30 values, GC content, and sequence duplication levels were then calculated. The clean reads were mapped to the Ziziphus jujuba Dongzao genome using HISAT2 software (Kim et al., 2015). Only reads with no more than one mismatch were further analyzed and annotated against the reference genome.
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated by StringTie. FPKM=cDNAs Fragments/(MappedFragment(millions)*Transcriptlength(kb)).CDNA fragments represent the number of fragments aligned to a certain transcript, i.e. the number of two terminal reads; Mapped fragments (millions) represents the total number of fragments compared to transcripts, in units of 10 ^ 6; Transcript length (KB): transcript length, in units of 10 ^ 3 bases.
Genome_build: Ziziphus jujuba cultivar:Dongzao
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample with 3 biological repeats.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| |
|
| Submission date |
May 26, 2021 |
| Last update date |
May 26, 2024 |
| Contact name |
Yingyue Li |
| Organization name |
Beijing Forestry University
|
| Street address |
Haidian District, Beijing
|
| City |
Beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
| |
|
| Platform ID |
GPL29421 |
| Series (1) |
| GSE175581 |
Multiple responses contribute to the enhanced drought tolerance of the autotetraploid Ziziphus jujuba Mill. var. spinosa |
|
| Relations |
| BioSample |
SAMN19355493 |
| SRA |
SRX11001659 |
