|
| Status |
Public on Mar 15, 2012 |
| Title |
Heterobasidion irregulare gene expression from different tissues and mycelium grown on different substrates |
| Platform organism |
Heterobasidion annosum |
| Sample organism |
Heterobasidion irregulare |
| Experiment type |
Expression profiling by array
|
| Summary |
Transcript profiles of Heterobasion irregulare from different tissues and mycelium grown on different substrates were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI,
department of energy) Heterobasidion annosum genome sequence version 1. One aim of this study
was to verify the expression of the automatically annotated gene models under various
conditions. Another goal was to compare gene expression profiles from different tissues of Heterobasidion irregulare and from mycelium grown on liquid MMN medium, liquid medium amended with lignin or cellulose and on wood.
|
| |
|
| Overall design |
The Heterobasidion annosum custom-exon expression array (4 x 72K) manufactured byRoche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products
/exp/index.html) contained five independent, nonidentical, 60-mer probes per gene model
coding sequence. For 12,199 of the 12,299 annotated protein-coding gene models probes
could be designed. For 19 gene models no probes could be generated and 81 gene models
shared all five probes with other gene models. Included in the array were 916 random
60-mer control probes and labelling controls. For 2032 randomly chosen gene models,
technical duplicates were included on the array. We performed 18 hybridizations (NimbleGen)
with samples derived from Heterobasidion irregulare fruiting bodies (four biological replicates) , from necrotic bark of pines inoculated with H. irregulare (21dpi; three biological replicates), from H. irregulare mycelium grown in liquid MMN medium (three biological replicates) as well as from H. irregulare grown on wood shavings from pine (four biological replicates), grown in liquid medium amended with lignin (2 biological replicates) and growth in liquid medium amended with cellulose from Spruce (2 biological replicates). Cultures were harvested after 3 weeks of incubation 22°C in darkness. All samples were labeled with Cy3.
|
| |
|
| Contributor(s) |
Olson Å, Kohler A, Dalman K, Karlsson M, Fossdal CG, Garbelotto M, Tisserant E, Martin F, Stenlid J |
| Citation(s) |
22463738 |
| |
| Submission date |
Jun 27, 2011 |
| Last update date |
Jun 15, 2012 |
| Contact name |
Annegret Kohler |
| E-mail(s) |
annegret.kohler@inrae.fr
|
| Phone |
+33 (0)383 394072
|
| Organization name |
INRAE
|
| Department |
UMR 1136
|
| Lab |
Interactions Arbres/Micro-organismes
|
| Street address |
Centre INRAE Grand Est Nancy
|
| City |
Champenoux |
| ZIP/Postal code |
54280 |
| Country |
France |
| |
|
| Platforms (1) |
| GPL13772 |
Heterobasidion annosum 12K whole genome expression array |
|
| Samples (18)
|
| GSM748496 |
necrotic bark of pines inoculated with Heterobasidion irregulare 1 |
| GSM748497 |
necrotic bark of pines inoculated with Heterobasidion irregulare 2 |
| GSM748498 |
necrotic bark of pines inoculated with Heterobasidion irregulare 3 |
| GSM748499 |
Heterobasidion irregulare grown in liquid medium amended with cellulose from Spruce 1 |
| GSM748500 |
Heterobasidion irregulare grown in liquid medium amended with cellulose from Spruce 2 |
| GSM748501 |
Heterobasidion irregulare fruiting bodies collected in California 1 |
| GSM748502 |
Heterobasidion irregulare fruiting bodies collected in California 2 |
| GSM748503 |
Heterobasidion irregulare fruiting bodies collected in California 3 |
| GSM748504 |
Heterobasidion irregulare fruiting bodies collected in California 4 |
| GSM748505 |
H. irregulare grown on wood shavings from pine 1 |
| GSM748506 |
H. irregulare grown on wood shavings from pine 2 |
| GSM748559 |
H. irregulare grown on wood shavings from pine 3 |
| GSM748560 |
H. irregulare grown on wood shavings from pine 4 |
| GSM748572 |
Heterobasidion irregulare grown in liquid medium amended with lignin 1 |
| GSM748573 |
Heterobasidion irregulare grown in liquid medium amended with lignin 2 |
| GSM748574 |
H. irregulare mycelium grown in liquid MMN medium 1 |
| GSM748575 |
H. irregulare mycelium grown in liquid MMN medium 2 |
| GSM748576 |
H. irregulare mycelium grown in liquid MMN medium 3 |
|
| Relations |
| BioProject |
PRJNA143715 |
Less...
More...