NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2339344 Query DataSets for GSM2339344
Status Public on Oct 12, 2016
Title mRNAs from Fusarium graminearum mutant strain Fgdicer1 at 5 days after sexual induction
Sample type SRA
 
Source name Fungi culture
Organism Fusarium graminearum
Characteristics genotype: Fgdicer1 mutant
tissue: fungal culture
developmental stage: 5 days after sexual induction
Growth protocol Fungal strain was grown at 25 ÂșC under near UV light for 5 days after sexual induction
Extracted molecule total RNA
Extraction protocol Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol, and sequenced with Illumina HiSeq2000.
 
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 Oct 06, 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)
GSE87724 RNA-seq analysis of transcriptomes at 5 day after sexual induction in Fusarium graminearum strains
Relations
BioSample SAMN05877050
SRA SRX2225610

Supplementary file Size Download File type/resource
GSM2339344_deltaD1_processed.txt.gz 401.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap