NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3760281 Query DataSets for GSM3760281
Status Public on Jan 01, 2020
Title Sample 62_LC69
Sample type SRA
 
Source name Δdis2::neo
Organism Fusarium graminearum
Characteristics strain background: PH-1 (FGSC#9075)
strain: FMF942
genotype: {delta}dis2::neo
tissue: mycelia
library construction: Illumina TruSeq RNA Sample Preparation kit
Treatment protocol Total RNA was isolated as described in Wu et al, 2014 G3
Growth protocol To generate Fusarium macroconidia, a small amount of frozen conidia or tissue was inoculated into 50 ml flasks containing CMC medium (Capellini, 1965, Mycologia) and shaken at 150 rpm for 3-4 days at room temperature (RT, ~22C). Conidia were collected by filtration through cheesecloth and stored at -80C in 25% glycerol. To isolate RNA, strains were inoculated into 50-100 ml YPD (0.3% yeast extract, 1% bacto-peptone, 2% dextrose) and incubated at 28C at 150 rpm for 24-36 hrs. Tissue was harvested by filtration and flash-frozen in liquid nitrogen until total RNA isolation.
Extracted molecule total RNA
Extraction protocol Total RNA was assessed with Agilent 2100 Bioanalyzer to determine RNA integrity; only high quality total RNA (integrity number between 9 - 10) were used. An Ribo-Zero rRNA removal Kit (Epicentre, #MRZY1324) was used for enrichment of transcripts.
For sample 1-60 The SOLiD total RNA-seq kit (ABI SOLiD, #4445374) was used to construct template cDNA.
For sample 61-68 Illumina TruSeq RNA Sample Preparation kits were used to make RNA-seq libraries.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description processed data file:
LC68-75_fpkm.txt
lane5-s046-indexRPI10-TAGCTT-LC69_S46_L005
Data processing Fastq files were input to Tophat and mapped to the F. graminearum genome with options -a 5 -m 1 -i 30 -I 2000
Cufflinks was used to quantify gene expression values as reads per kilobase of exon per million reads (RPKM) using gene annotation from MIPS ftp://ftpmips.gsf.de/fungi/Fusarium/F_graminearum_PH1_v32/.
cuffdiff was used to identify differentially expressed genes
Genome_build: GCA_000240135.3
Supplementary_files_format_and_content: processed data is cuffdiff output
 
Submission date May 10, 2019
Last update date Jan 01, 2020
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 GPL26651
Series (1)
GSE131036 Genetic dissection of gene silencing mediated by H3K27 methylation
Relations
BioSample SAMN11619439
SRA SRX5818475

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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