Project description:The purpose of this study was to make a single comparison between Cqf genes expressed during the vegetative stages of infection on the telial host (oak leaf) versus the aecial host (pine stem). A large proportion of genes were expressed in both hosts and significantly differentially expressed genes were enriched for candidate fungal effectors (small secreted proteins). These results suggest that the Cqf rust fungus uses a largely common set of genes to create two very different infection phenotypes. This study was based on hybridizations to custom microarrays containing features representing 8692 gene models from a Cqf genome sequencing project midpoint assembly. Two Agilent 4 X 44K microarray slides were populated with 60-mer probes (1 to 5 per transcript), designed using AgilentM-bM-^@M-^Ys web-based eArray software. Labeled target cRNA (complementary RNA) was generated using AgilentM-bM-^@M-^Ys Low Input Quick Amp Labeling Kit, such that oak and pine samples were labeled with either cy3 or cy5 an equal number of times across the experiment. Each microarray was hybridized with labeled cRNA target derived from a single oak sample and labeled cRNA target derived from a single pine sample. There were a total of eight oak sample replications and eight pine sample replications. Target hybridization and scanning were performed by the University of FloridaM-bM-^@M-^Ys Interdisciplinary Center for Biotechnology Research using standard procedures and an Agilent G250B Scanner.

2013-10-25 | E-GEOD-51655 | biostudies-arrayexpress

Conservation of small RNA pathways in platypus

Project description:Small RNA pathways play evolutionarily conserved roles in gene regulation and in defense from pathogenic and parasitic nucleic acids. The character and expression patterns of small RNAs show conservation throughout animal lineages, but specific animal clades also show variations on these recurring themes, including species-specific small RNAs. The monotremes, with only platypus and four species of echidna as extant members, represent the basal branch of the mammalian lineage. Here, we examine the small RNA pathways of monotremes by deep sequencing of six platypus and echidna tissues. We find that highly conserved microRNA species display their signature tissue-specific expression patterns. In addition, we find a large rapidly-evolving cluster of miRNAs on platypus chromosome X1 which is unique to monotremes. Platypus and echidna testes contain a robust piRNA system which appears to be participating in ongoing transposon defense. Keywords: piRNA

2008-05-21 | GSE10571 | GEO

Transcriptomic analysis of Phanerochaete chrysosporium mycelium in presence of oak acetonic extractives

Project description:The transcriptome of Phanerochaete chrysosporium control mycelium was compared to the transcriptome of mycelium grown on oak acetonic extractives containing medium. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Phanerochaete chrysosporium genome sequence version 1. The aim of this study was to determine gene expression changes in Phanerochaete chrysosporium grown on oak extract with a special focus on detoxification systems.

2014-08-13 | GSE54542 | GEO

Project description:Ornithorhynchus anatinus (platypus) genome assembly, mOrnAna1

| PRJNA513296 | ENA

Zacco platypus

Project description:Zacco platypus Genome sequencing and assembly

| PRJNA574044 | ENA