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| Status |
Public on Jul 19, 2018 |
| Title |
CK_3 |
| Sample type |
SRA |
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| Source name |
Trichoderma_control
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| Organism |
Trichoderma asperellum |
| Characteristics |
strain: TJ01
treated with: 0 μg/mL (control) dichlorvos at 28°C and 180 rpm for 24 h
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| Treatment protocol |
Culturing in Burk broth containing 0 μg/mL (control), 100 μg/mL, 500 μg/mL, or 1000 μg/mL dichlorvos at 28°C and 180 rpm for 24 h
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| Growth protocol |
The spore suspension of T. asperellum TJ01 was transferred to PD medium. After culturing at 28°C and 180 rpm for 24 h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s instruction.
The mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
CK_3_FPKM
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| Data processing |
The original image data is transferred into sequence data via base calling
We use BWA to map clean reads to genome reference and use Bowtie to gene reference.
Genes and isoforms expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization).
Genome_build: http://genome.jgi.doe.gov/Trias1/Trias1.download.html
Supplementary_files_format_and_content: FPKM calculated using RSEM, FPKM values represent counting fragments, not reads.
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| Submission date |
May 09, 2018 |
| Last update date |
Jul 19, 2018 |
| Contact name |
Mi NI |
| E-mail(s) |
fannimi2001@163.com
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| Organization name |
Fuyang Normal Univ
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| Street address |
No.100 Qinghe West Road
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| City |
Fuyang |
| State/province |
Anhui |
| ZIP/Postal code |
236037 |
| Country |
China |
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| Platform ID |
GPL24979 |
| Series (1) |
| GSE114217 |
Transcriptome profile of Trichoderma asperellum challenged with Organophosphorus Pesticide Dichlorvos |
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| Relations |
| BioSample |
SAMN09097231 |
| SRA |
SRX4058796 |
| 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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