Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 16
Release date: Oct 25 2013
Last update date: Oct 30 2013
Access: Public
Taxon: Flavobacterium sp.
Dataset link Transcriptional profiling of the rust fungus Cronartium quercuum f. sp. fusiforme (Cqf) during vegetative growth on 2 different hosts.

Experimental Protocol


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 Agilent’s web-based eArray software. Labeled target cRNA (complementary RNA) was generated using Agilent’s 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 Florida’s Interdisciplinary Center for Biotechnology Research using standard procedures and an Agilent G250B Scanner.

Repositories


GEO

GSE51655

ArrayExpress

E-GEOD-51655

BioProject

PRJNA224236

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