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| Status |
Public on Mar 04, 2020 |
| Title |
rgs7-4h-3 |
| Sample type |
SRA |
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| Source name |
rgs7-4h
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| Organism |
Pyricularia oryzae |
| Characteristics |
sample type: Magnaporthe oryzae and rice leaves mixed sample
strain background: Guy11
genotype/variation: {deleta}Morgs7 mutants
timepoint: Conidia were inoculated onto rice leaves for 4 h
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| Extracted molecule |
total RNA |
| Extraction protocol |
The samples of the inoculated rice leaves with conidial suspensions were immediately frozen in liquid nitrogen, total RNA was extracted using an Invitrogen kit
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 |
Isolation of Poly (A) mRNA from total RNA and construction of cDNA libraries were preformed according to Dong et al. (Dong et al., 2015). Finally, the cDNA libraries were loaded onto the flow cell channels of an Illumina HiSeqTM 4000 platform for paired-end 151 bp x 2 sequencing at the Beijing Genomics Institute (BGI), Shenzhen, China (Zhang et al., 2013).
After discarding low-quality raw reads (contain the connectors and discarded the reads whose content had more than 5% unknown bases.), the clean reads from each library were assembled to M. oryzae. Gene expression levels were measured in the RNA-Seq analysis as reads per kb of exon model per million mapped reads (RPKM) (Mortazavi et al., 2008).
Differentially expressed genes and their corresponding P-values were determined using the DEG. Fold changes (Log2 Ratio) were estimated according to the normalized gene expression level in each sample. We used the absolute value of Log2Ratio>1, p-values<0.001, q-value<0.001 as the threshold to judge differentially expressed genes.
Genome_build: novel_coding_transcript.gtf
Supplementary_files_format_and_content: transcript.fpkm
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| Submission date |
Mar 13, 2019 |
| Last update date |
Mar 04, 2020 |
| Contact name |
Ying Li |
| E-mail(s) |
li1989ying0921@163.com
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| Organization name |
Nanjing Agricultural University
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| Department |
College of Plant protection
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| Street address |
weigang1#
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| City |
Nanjing |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platform ID |
GPL26294 |
| Series (1) |
| GSE128219 |
Magnaporthe oryzae Auxiliary Activity Protein MoAa91 Functions as Chitin-Binding Protein To Induce Appressorium Formation on Artificial Inductive Surfaces and Suppress Plant Immunity |
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| Relations |
| BioSample |
SAMN11111082 |
| SRA |
SRX5512664 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3667447_rgs7-4h-3.transcript.fpkm.txt.gz |
43.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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