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| Status |
Public on Jun 27, 2020 |
| Title |
CK1: R. mucilaginosa |
| Sample type |
SRA |
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| Source name |
Citrus sinensis (L.) Osbeck
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| Organism |
Citrus sinensis |
| Characteristics |
tissue: Albedo
tissue: excised Albedo
age: 3 days after innoculation
treatment: R. mucilaginosa
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| Extracted molecule |
total RNA |
| Extraction protocol |
Using Illumina HiSeq 2500, subsequent sequencing was carried out after RNA extraction, library construction and sequencing, double-strand cDNA synthesis, terminal repair and ligation, and library quality control.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
After sequencing segmentation and quality control of the offline file was done using the reference genome reference genome version：GCF_000317415.1_Csi_valencia_1.0 reference genome site ads：https: //www.ncbi.nlm.nih.gov/genome/?term=Citrus+sinensis
To correct the significant P-value obtained from the original hypothesis test from the false discovery rate (FDR), the Benjamini-Hochberg correction method was used. The log2(fold change) I≥ 1 and FDR < 0.05 screening criteria was used to obtained the differentially expressed genes (DEGs). The function of the (DEGs) were annotated using gene database such as gene ontology (GO) (Young et al. 2010), cluster of original groups of protein (COG) (Darren et al. 2000), Kyoto encyclopaedia of genes and genes (KEGG) (Altermann et al. 2005), Swiss Prot (Pasquier et al. 1999) and National Center for Biotechnology Information (NCBI) (O’Leary et al. 2016).
Genome_build: Csi_valencia_1.0
Supplementary_files_format_and_content: FPKMs
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| Submission date |
Jun 26, 2020 |
| Last update date |
Jun 30, 2020 |
| Contact name |
Solairaj Dhanasekaran |
| E-mail(s) |
solaibt@hotmail.com
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| Organization name |
Jiangsu University
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| Department |
School of Food and Biological Engineering
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| Street address |
Jiangsu University
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| City |
Zhenjiang |
| State/province |
Jiangsu |
| ZIP/Postal code |
212013 |
| Country |
China |
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| Platform ID |
GPL21082 |
| Series (1) |
| GSE153334 |
Transcriptome defense response of orange fruit Induced with Rhodoturola mucilaginosa enhanced with salicylic acid |
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| Relations |
| BioSample |
SAMN15376963 |
| SRA |
SRX8622226 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4640688_CK1.t_data.ctab.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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