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| Status |
Public on Oct 25, 2019 |
| Title |
SHZ-4 |
| Sample type |
SRA |
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| Source name |
hypha
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| Organism |
Verticillium dahliae |
| Characteristics |
tissue: hypha
strain: SHZ-4
culture days: 4
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| Growth protocol |
The SHZ-4, SHZ-5, and SHZ-9 strains was cultured in the Czapek liquid medium for 14 days at the conditions of 25℃, dark, and 180 rpm/min.
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| Extracted molecule |
total RNA |
| Extraction protocol |
The spore suspension was abtained through filtering the hyphae off. The spore suspension was then centrifuged to collect the concentrated spores. The total RNA were extracted using the Fungal RNA miniprep kit (Biomiga, San Diego, USA) according to the manufacturer’s instructions. Total RNA was sent to the Sangon Biotech Cooperation (Shanghai, China) for RNA examination and sequencing. The sequencing platform was a HiSeq-2500-Pe-125 of Illumina.
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 |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Cutadapt software with parameters O = 10, min_len = 35, a = adaptor sequence and Prinseq software with parameters trim_qual_left = 20, trim_qual_right = 20, trim_qual_window = 10, trim_qual_step = 1
All clean_reads were used to assembly the transcriptome sequence through the Trinity software with parameters --min_contig_length 200 --seqType fq.
The RSEM/bowtie program (version 1.2.8; Madison, WI, USA) with a cutoff defined at v =2 software was used for the mapping and the RSeQC (http://rseqc.sourceforge.net/) was used for the statistic of the mapping with default settings.
The expression level of unigenes (Fragment Per Kilo bases per Million mapped Reads, FPKM) was calculated by the RSEM/bowtie program with default settings. Since the transcriptome sequencing had no biological repetition, the analysis of differential unigene expression was conducted in reference to the Audic method (Audic and Claverie,1997).
Supplementary_files_format_and_content: FPKM
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| Submission date |
May 20, 2019 |
| Last update date |
Oct 25, 2019 |
| Contact name |
jin li |
| E-mail(s) |
1530804952@qq.com
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| Organization name |
Shihezi university
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| Department |
college of life science
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| Lab |
School Key Laboratory
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| Street address |
North Fourth Road
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| City |
Shihezi |
| State/province |
Xinjiang |
| ZIP/Postal code |
832000 |
| Country |
China |
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| Platform ID |
GPL26690 |
| Series (1) |
| GSE131467 |
Transcriptome sequencing of Verticillium dahliae with different virulence |
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| Relations |
| BioSample |
SAMN11783931 |
| SRA |
SRX5865764 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3781176_SHZ-4-FPKM.txt.gz |
444.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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