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Sample GSM1226456 Query DataSets for GSM1226456
Status Public on Feb 27, 2014
Title RNA-seq; Sample 33_HTS586
Sample type SRA
 
Source name mycelium
Organism Fusarium graminearum
Characteristics strain number: FMF248
genotype: DELkmt6::neoR
nitrogen level: low
Extracted molecule total RNA
Extraction protocol mRNA was isolated using a Poly(A)Purist MAG kit (Ambion). We removed DNA by treatment with RNase-free DNAase (Qiagen), followed by column clean-up according to manufacturers instructions. We used Illumina TruSeq RNA Sample Preparation kits to make RNA-seq libraries
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Basecalls were made with RTA1.8_CASAVA1.7
ChIPSeq reads were trimmed of adapter sequence and mapped to the F. graminearum genome with BWA software using default options
RNASeq reads were trimmed of adapter sequence and mapped to the F. graminearum genome with Tophat software with options (-a 5 -m 1 -i 30 -I 2000)
samtools were used to convert BWA or Tophat output to sorted bam files
cufflinks v2.1.1 was used (--max-bundle-length 20000 -I 2000 --min-intron-length 30) to calculate FPKM values for Broad assembly 3 transcripts from sorted bam files of RNA-seq reads
Genome_build: Broad chromosome assembly 3
Supplementary_files_format_and_content: ChIP-seq processed files are tab delimited EpiChIP output containing gene name, NLCS value
Supplementary_files_format_and_content: RNA-seq processed files are tab delimited cufflinks output containing gene name, FPKM value
 
Submission date Sep 08, 2013
Last update date May 15, 2019
Contact name Kristina M Smith
E-mail(s) smitkris@science.oregonstate.edu
Organization name Oregon State University
Department Biochemisty and Biophysics
Lab Freitag
Street address ALS2011
City Corvallis
State/province OR
ZIP/Postal code 97331
Country USA
 
Platform ID GPL17573
Series (1)
GSE50689 The Fusarium graminearum Histone H3 K27 Methyltransferase KMT6 Regulates Development and Expression of Secondary Metabolite Gene Clusters
Relations
BioSample SAMN02361169
SRA SRX357575

Supplementary file Size Download File type/resource
GSM1226456_HTS586_FPKM.txt.gz 96.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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