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Sample GSM2065788 Query DataSets for GSM2065788
Status Public on Apr 11, 2016
Title 03C6-2 rep3
Sample type SRA
Source name Appressorium_delta_vrf1
Organism Pyricularia oryzae 70-15
Characteristics tissue: Appressorium
strain: 70-15
developmental stage: Appressorium at 5 hpi
genotype: delta_vrf1
Growth protocol The conidia were cultured on plasitc membranes in H2O at 28˚C for 5 h
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
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
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.
Submission date Feb 18, 2016
Last update date May 15, 2019
Contact name Jianping Lu
Organization name Zhejiang University
Department College of Life Sciences
Street address 866 Yuhantang Road
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310058
Country China
Platform ID GPL21479
Series (1)
GSE78058 RNA-Seq Analysis of VRF1-dependent Genes in the appressoria of Magnaporthe oryzae 70-15
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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