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| Status |
Public on Sep 12, 2024 |
| Title |
Leaves, Tre, 48h, repeat 1 |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Vitis vinifera |
| Characteristics |
tissue: leaf
treatment: Tre, 48h
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| Treatment protocol |
Collect grape leaves from the control group, trehalose, different stresses (low temperature (4 ℃), PEG6000, NaCl), and trehalose+different stress treatments for 48 hours, and perform RNA Seq analysis. The control group and the treatment group each contain three biological replicates. 8 samples examined: CK, 4C, NaCl，PEG6000，Tre，Tre-4C，Tre-NaCl，Tre-PEG6000.
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| Growth protocol |
The self-rooted cuttings of ‘Thompson Seedless’ were grown in a greenhouse (Henan Institute of Science and Technology) at 25–30℃ and 60%–75% relative humidity.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Polysaccharide Polyphenols Plant Total RNA Extraction Kit (genepioneer, R411). 1 ug of total RNA was used for the construction ofsequencing lilbraries
RNA libraries for RNA-seg were prepared using Hieff NGS® Ultima Dual-mode RNA Library Prep Kit (Yeasen, 12308ES) following manufacturer's protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Tre1
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| Data processing |
Use fastp (v0.20.0) to perform quality control on the raw data, with parameters set to - q 5 -n 5
Use HISAT2 (v2.1.0) to compare grape genome Vitis_vinifera.PN40024.v4 (http://ftp.ensemblgenomes.org/pub/plants/release-53/fasta/vitis_vinifera/), with parameters set to -- novelsplicesite-outfile XX.ss.. Compare the generated Sam files and use Samtools (version: 1.9) software to convert them to BAM format and sort them. Then use the rnaseq subroutine of qualimap (v2.2.1) software to calculate the comparison results and determine the comparison efficiency.
Use StringTie (stringtie-2.1.3b. Linux_x86_64) software to assemble transcripts based on the BAM file, with parameters set to - f 0.2 - a 30 - c 5 - j 5. Use StringTie to fuse all the reconstructed results of the samples to obtain the optimized transcript structure annotation file, and set the parameter -- merge.
Use StringTie to quantify gene expression based on the optimized annotation file of gene structure and the BAM file obtained from comparison, with parameters set to - e - p 4; Use Ballgown (R script) to organize the above results and obtain the readcount matrix of gene expression; Use your own script to obtain the FPKM matrix.
Assembly: Vitis_vinifera.PN40024.v4
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
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| Submission date |
Sep 05, 2024 |
| Last update date |
Sep 12, 2024 |
| Contact name |
Ling Wang |
| E-mail(s) |
[email protected]
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| Organization name |
Henan Institute of Science and Technology
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| Street address |
Eastern HuaLan Avenue, Xinxiang City , Henan Province , China
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| City |
Xinxiang |
| ZIP/Postal code |
453003 |
| Country |
China |
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| Platform ID |
GPL30515 |
| Series (1) |
| GSE276430 |
Transcriptome analysis of response to exogenous trehalose and abiotic stress in grapes |
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| Relations |
| BioSample |
SAMN43048605 |
| SRA |
SRX25666271 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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