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Sample GSM2080416 Query DataSets for GSM2080416
Status Public on May 13, 2016
Title mRNAs from Fusarium graminearum wild-type strain Z-3639 after 15 min incubation in complete media at 25 ºC, rep2
Sample type SRA
 
Source name Fungi culture
Organism Fusarium graminearum
Characteristics genotype: wild-type
strain: Z-3639
condition: normal temperature
Growth protocol Fungal strain was grown in complete medium (CM) for 15 min at 25 ºC and 37 ºC
Extracted molecule total RNA
Extraction protocol 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
 
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
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample …
 
Submission date Mar 04, 2016
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)
GSE78885 RNA-seq analysis of Fusarium graminearum Z-3639 in heat stress
Relations
BioSample SAMN04531880
SRA SRX1613193

Supplementary file Size Download File type/resource
GSM2080416_25-WT2_processed.txt.gz 371.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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