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Status |
Public on Jan 01, 2020 |
Title |
Sample 64_LC71 |
Sample type |
SRA |
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|
Source name |
dis2(UV10-4) F1
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Organism |
Fusarium graminearum |
Characteristics |
strain background: FMF384 strain: FMF860 genotype: dis2(UV10-4) F1 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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 3000 |
|
|
Description |
processed data file: LC68-75_fpkm.txt lane5-s048-indexRPI20-GTGGCC-LC71_S48_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
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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 |
SAMN11619437 |
SRA |
SRX5818477 |