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| Status |
Public on May 14, 2013 |
| Title |
Mycelium grown in complete media for 16 h |
| Sample type |
SRA |
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| Source name |
Mycelium
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| Organism |
Pyricularia oryzae |
| Characteristics |
strain: 70-15
tissue: Mycelium
treatment: Mycelium grown in complete media for 16 h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using a standard TRIZOL-based method
Small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110) with modifications using standard Illumina sRNA adapters, followed by sequencing with Illumina's SBS method.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
MgCM01
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| Data processing |
Adapters were removed from the sequencing reads and matched to the M. oryzae genome (version 6 assembly) from the Broad Institute
Reads with sequencing errors were filtered out using PERL scripts
tRNA, rRNA, snRNA or snoRNAs -matched reads were removed from the total reads, and genome-matched reads were obtained using the program Bowtie, accepting only perfect matches
From the total genome matched reads, distinct genome matched reads were calculated and the abundance of each read was normalized to 5 million units of transcripts per 5 million (TP5M)
Genome_build: Magnaporthe oryzae genome assembly 6 from Broad Institute
Supplementary_files_format_and_content: tab-delimited text file including small RNA count
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| Submission date |
Jan 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Vidhyavathi Raman |
| E-mail(s) |
[email protected]
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| Phone |
302-831-7371
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| Organization name |
University of Delaware
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| Department |
Plant and Soil Sciences
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| Lab |
Donofrio Lab
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| Street address |
531 S college Ave
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| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19716 |
| Country |
USA |
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| Platform ID |
GPL16451 |
| Series (1) |
| GSE43277 |
Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae |
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| Relations |
| SRA |
SRX214117 |
| BioSample |
SAMN01882091 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1059882_MgCM01_processed.txt.gz |
233.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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