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| Status |
Public on Jun 29, 2018 |
| Title |
Conidia rep2 |
| Sample type |
SRA |
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| Source name |
Conidia
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| Organism |
Colletotrichum fructicola |
| Characteristics |
tissue: Conidia
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted according to the instruction manual of the Trizol Reagent (Life technologies, California, USA).
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 4000 |
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| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to 1104-7 whole genome (GenBank accession no. MVNS00000000) using TopHat v. 2.1.0 with parameters --bowtie1 -p 8 -g 1
A gene expression profile was created using a combination of DESeq2 and edgeR packages.
Genes with a significant P-value (< 0.05) and a greater than threefold change (log2) in transcript level were considered to be differently expressed, and the different expression needs to be supported by both DESeq2 and edgeR. All P-values were corrected for false discoveries resulting from multiple hypothesis testing using the Benjamini-Hochberg procedure.
Genome_build: reference genome deposited at DDBJ/EMBL/GenBank under the accession MVNS00000000
Supplementary_files_format_and_content: tab-delimited text files include read counts and expression profiles with annotations.
Supplementary_files_format_and_content: 1104_genes-exp-annot.txt: Differently expressed genes with log2 fold changes and annotations.
Supplementary_files_format_and_content: 1104_genes.count.txt: Reads counts per gene.
Supplementary_files_format_and_content: 1104.transcripts.fasta: Transcript FASTA sequences.
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| Submission date |
Sep 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
bo wang |
| E-mail(s) |
bowang@nwsuaf.edu.cn
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| Organization name |
Northwest A&F University
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| Street address |
No. 3 Taicheng Road
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| City |
Yangling |
| State/province |
Shaanxi |
| ZIP/Postal code |
712100 |
| Country |
China |
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| Platform ID |
GPL24016 |
| Series (1) |
| GSE103878 |
Transcriptomic analysis reveals candidate genes regulating infection-related developments and host interactions of Colletotrichum fructicola |
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| Relations |
| BioSample |
SAMN07655938 |
| SRA |
SRX3189908 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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