|
| Status |
Public on Jan 01, 2020 |
| Title |
Sample 30_LC28 |
| Sample type |
SRA |
| |
|
| Source name |
dat18(UV11-2) F1
|
| Organism |
Fusarium graminearum |
| Characteristics |
strain background: FMF384
strain: FMF493
genotype: dat18(UV11-2) F1
tissue: mycelia
library construction: SOLiD total RNA-seq 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 |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
processed data file:
LC1-35_fpkm.txt
|
| 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 |
GPL26650 |
| Series (1) |
| GSE131036 |
Genetic dissection of gene silencing mediated by H3K27 methylation |
|
| Relations |
| BioSample |
SAMN11619471 |
| SRA |
SRX5818443 |
