|
| Status |
Public on Feb 13, 2012 |
| Title |
wild-type_mycelium_CM |
| Sample type |
SRA |
| |
|
| Source name |
mycelium
|
| Organism |
Pyricularia oryzae |
| Characteristics |
strain: Guy11
medium: complete
tissue: mycelium
|
| Growth protocol |
Plugs of Guy11 mycelium grown on complete medium (CM) plates were used to innoculate liquid CM medium and were grown in shaking culture for 36 h at 25C, 200rpm. Mycelia were harvested by filtering through 3 layers of miracloth, washed 2-3 times with sterile distilled water (SDW) and blotted dry, before freezing in liquid nitrogen. Glucose minimal medium (GMM) samples were intially grown in CM as described above, but then transferred to GMM for 16 hours in shaking culture before being harvested.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Sequencing libraries were prepared using mRNA-Seq Sample Preparation kit from Illumina according to manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Tophat (http://tophat.cbcb.umd.edu/) was used to align short reads to the published genome (version 6) of Magnaporthe oryzae (http://www.broadinstitute.org/annotation/genome/magnaporthe_grisea/MultiHome.html) and to predict exon splice sites. Cufflinks (http://cufflinks.cbcb.umd.edu/) was used to analyse this data (only reads with a mapping quality > 30) using gene annotations from M. oryzae, resulting in normalised counts (expressed in fragments per kilobase of exon model per million mapped fragments - FPKM) for each gene.
|
| |
|
| Submission date |
Jun 30, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Darren Mark Soanes |
| E-mail(s) |
d.m.soanes@exeter.ac.uk
|
| Organization name |
University of Exeter
|
| Department |
College of Medicine and Health
|
| Street address |
RILD Building, RD&E Hospital Wonford, Barrack Road
|
| City |
Exeter |
| ZIP/Postal code |
EX2 5DW |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13743 |
| Series (1) |
| GSE30327 |
Comparison of transcript abundance in mycelium from the rice blast fungus Magnaporthe oryzae grown in rich medium and in minimal medium using RNA-Seq |
|
| Relations |
| SRA |
SRX081777 |
| BioSample |
SAMN00632028 |
