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| Status |
Public on Nov 25, 2023 |
| Title |
SA_2 |
| Sample type |
SRA |
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| Source name |
Guy11
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| Organism |
Pyricularia oryzae |
| Characteristics |
cell line: Guy11
treatment: salicylic acid (SA)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) accordingtothemanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed usingtheAgilent2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructedusingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. Thetranscriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The libraries were sequenced on an llumina Novaseq 6000 platformand 150 bppaired-endreadswere generated.Rawreads of fastqformatwere firstly processed using fastp and the low quality reads were removed to obtainthecleanreads.Then the clean reads for each sample were retained for subsequent analyses. Thecleanreads were mapped to the reference genome using HISAT. FPKM of each gene was calculatedandthe read counts of each gene were obtained by HTSeq-count. PCA analysis were performedusingR(v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2 . Qvalue 2 or foldchange < 0.5 was set as the threshold for significantly differential expressiongene (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) todemonstratetheexpression pattern of genes in different groups and samples. The radar map of top 30 geneswasdrew to show the expression of up-regulated or down-regulated DEGs using R packet ggradar.
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome andWikiPathwaysenrichment analysis of DEGs were performed to screen the significant enriched termusingR(v3.2.0),respectively. R (v 3.2.0) was used to draw the column diagram, the chord diagramandbubblediagram of the significant enrichment term.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. Theanalysiswas www.oebiotech.com used a predefined gene set, and the genes were ranked according to the degreeof differentialexpression in the two types of samples. Then it is tested whether the predefinedgenesetwasenriched at the top or bottom of the ranking list.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Nov 20, 2023 |
| Last update date |
Nov 25, 2023 |
| Contact name |
Chi Zhang |
| Organization name |
Zhejiang Academy of Agricultural Sciences
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| Street address |
Deshengzhong Road No.298
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| City |
Hangzhou |
| ZIP/Postal code |
310021 |
| Country |
China |
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| Platform ID |
GPL32309 |
| Series (1) |
| GSE248232 |
Transcriptome of Magnaporthe oryzae treated with SA, ABA and sakuranetin |
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| Relations |
| BioSample |
SAMN38330341 |
| SRA |
SRX22582325 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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