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| Status |
Public on Apr 11, 2016 |
| Title |
03C6-2 rep3 |
| Sample type |
SRA |
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| Source name |
Appressorium_delta_vrf1
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| Organism |
Pyricularia oryzae 70-15 |
| Characteristics |
tissue: Appressorium
strain: 70-15
developmental stage: Appressorium at 5 hpi
genotype: delta_vrf1
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| Growth protocol |
The conidia were cultured on plasitc membranes in H2O at 28˚C for 5 h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from appressoria with RNeasy Plant mini kit (QIAGEN). Purified RNA was analyzed on a ND-8000 spectrophotometer (Nanodrop, Technologies, Wilmington, DE), agarose electrophoresis or a 2100-Bioanalyzer (Agilent Technologies, Santa Clara, CA), to determine the quantity. RNA samples were used if there was no smear on the agarose. RNA samples were also used if the 260/280 ratio was above 2.0 and the RIN (RNA integrity number) was greater than 7.0.
RNA libraries were prepared for sequencing using NEBNext RNA sample preparation kit (NEB) with standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Magnaporthe oryzae 70-15 (MG8) whole genome using tophat 2.0.8b with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.1.1
Genome_build: MG8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
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| Submission date |
Feb 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jianping Lu |
| E-mail(s) |
jplu@zju.edu.cn
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| Organization name |
Zhejiang University
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| Department |
College of Life Sciences
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| Street address |
866 Yuhantang Road
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL21479 |
| Series (1) |
| GSE78058 |
RNA-Seq Analysis of VRF1-dependent Genes in the appressoria of Magnaporthe oryzae 70-15 |
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| Relations |
| SRA |
SRX1591228 |
| BioSample |
SAMN04502975 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2065788_03C6-2_rep3.txt.gz |
85.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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