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Sample GSM1429764 Query DataSets for GSM1429764
Status Public on Jul 09, 2014
Title mRNAs from F. graminearum fss1 overexpression mutant after 1 h after incubation in PDB
Sample type SRA
 
Source name Fungi culture
Organism Fusarium graminearum
Characteristics strain background: Z-3639
genotype/variation: fss1::gen-Pef1a-fss1; fss1 overexpression mutant
cultured in: potato dextrose broth for 1hr
Growth protocol Each fungal strain was grown in potato dextrose broth (PDB) with or wihtout 1 M NaCl supplementation for an hour
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from mycelia in liquid nitrogen using the Easy-Spin Total RNA Extraction Kit (Intron Biotech, Seongnam, Korea).
Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description PDB_OEFSS1
Data processing BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32 (manually proccessed version of 'ASM24013v3' accessible at http://mips.gsf.de/genre/proj/FGDB/)
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample
 
Submission date Jul 08, 2014
Last update date May 15, 2019
Contact name Hokyoung Son
E-mail(s) hogongi@gmail.com
Organization name Seoul National University
Department Center for Food and Bioconvergence
Street address Daehak-dong, Gwanak-gu
City Seoul
ZIP/Postal code 151-921
Country South Korea
 
Platform ID GPL17573
Series (1)
GSE59177 RNA-seq analysis of FSS1-dependent genes in Fusarium graminearum Z-3639
Relations
BioSample SAMN02904736
SRA SRX647719

Supplementary file Size Download File type/resource
GSM1429764_PDB_OEFSS1_processed.txt.gz 379.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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