|
| Status |
Public on Sep 30, 2014 |
| Title |
F. graminearum 48h |
| Sample type |
SRA |
| |
|
| Source name |
perithecia
|
| Organism |
Fusarium graminearum |
| Characteristics |
strain: PH-1, FGSC9075, NRRL31084
timepoints: 48h after induction of sexual development
cell type: perithecia
|
| Treatment protocol |
Material was flash frozen on dry ice, lyophilized and stored at -80 °C.
|
| Growth protocol |
Carrot agar (60 mm diam. Petri dish) was center-inoculated with 10 μl of F. graminearum strain PH-1 conidial stock solution and incubated under continuous light at room temperature (22–24 °C) until the mycelium reached the edge of the plate. Sexual development was induced by gently removing the surface mycelium and applying 900 μl of 2.5% Tween-60 to the surface of the plates. Development at each time-point was examined prior to sample collection to confirm that the cultures reached the appropriate stage of development. For later stages, where individual perithecia were visible, the representative cultures were checked by performing squash mounts of individually harvested perithecia.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from homogenized material with TRIzol reagent (Invitrogen) and mRNA was purified using Dynabeads oligo(dT) magnetic separation (Invitrogen).
Standard Illumina protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
replicate1
|
| Data processing |
The libraries were run on six lanes of an Illumina Genome Analyzer II, generating an average of 30 million single-end reads of 36 bases each.
The program Tophat v1.2.0 was used to perform spliced alignments of the tags against the F. graminearum genome, strain PH-1, obtained from the Broad Institute (http://www.broadinstitute.org/annotation/genome/fusarium_group/GenomesIndex.html).
We scored results only for tags that mapped to a single unique location in the genome (--max-multihits option was set to 1) with less than three mismatches (--splice-mismatches option was set to 2). We used the default settings for all other Tophat options. We tallied tags aligning to exons of genes with the program HTSeq v0.4.5p6
The data was normalized and differential expression was calculated by fragments per kilobase per million mapped reads (FPKM) using Cufflinks and Cuffdiff v.1.0.3
LOX v1.4 was applied to the tallies for each sample for each gene to estimate gene expression levels and credible intervals across developmental stages. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals
Genome_build: http://www.broadinstitute.org/annotation/genome/fusarium_group/GenomesIndex.html
Supplementary_files_format_and_content: Tables of FPKM values for all predicted genes at each time-point. Text file with LOX output.
|
| |
|
| Submission date |
Sep 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Frances Trail |
| E-mail(s) |
trail@msu.edu
|
| Organization name |
Michigan State University
|
| Department |
Plant Biology; Plant, Soil and Microbial Sciences
|
| Lab |
Plant Biology Laboratories
|
| Street address |
612 Wilson Road
|
| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48824 |
| Country |
USA |
| |
|
| Platform ID |
GPL19248 |
| Series (1) |
| GSE61865 |
Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology |
|
| Relations |
| BioSample |
SAMN03083857 |
| SRA |
SRX716768 |
