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Sample GSM1059889 Query DataSets for GSM1059889
Status Public on May 14, 2013
Title Magnaporthe infected rice leaf 96 hpi
Sample type SRA
 
Source name Infected rice leaf
Organism Pyricularia oryzae
Characteristics strain: 70-15
tissue: in planta tissues
treatment: Magnaporthe infected rice leaf 96 hpi
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
 
Description LMg96
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
 
Submission date Jan 03, 2013
Last update date May 15, 2019
Contact name Vidhyavathi Raman
E-mail(s) vidhya@udel.edu
Phone 302-831-7371
Organization name University of Delaware
Department Plant and Soil Sciences
Lab Donofrio Lab
Street address 531 S college Ave
City Newark
State/province DE
ZIP/Postal code 19716
Country USA
 
Platform ID GPL16451
Series (1)
GSE43277 Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae
Relations
SRA SRX214124
BioSample SAMN01882098

Supplementary file Size Download File type/resource
GSM1059889_LMg96_processed.txt.gz 107.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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