GEO DataSets

(Submitter supplied) Coccidioidomycosis (Valley Fever) is an emerging endemic fungal infection with a rising incidence and an expanding geographic range. It is caused by Coccidiodes, which are thermally dimorphic fungi that grow as mycelia in soil but transition in the lung to form pathogenic spherules. The regulatory mechanisms underlying this transition are not understood. Exploiting capped small (cs)RNA-seq, which identifies actively initiated stable and unstable transcripts and thereby detects acute changes in gene regulation with remarkable sensitivity, here we report the changes in architectural organization and key sequence features underlying phase transition of this highly pathogenic fungus. more...

Organism:

Agaricus bisporus; Coccidioides immitis; Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

7 related Platforms

27 Samples

Download data: GTF, TXT

(Submitter supplied) We investigated genome folding across the eukaryotic tree of life. We find four general manifestations of genome organization at chromosome-scale that each emerge and disappear repeatedly over the course of evolution. The submission represents chromosome-length Hi-C contact maps, architecture type and homolog separation analyses for 26 species across the tree of life, representing all subphyla of chordates, all 7 extant vertebrate classes, and 7 out of 9 major animal phyla, as well as plants and fungi.

Organism:

Triticum aestivum; Caenorhabditis elegans; Aplysia californica; Aedes aegypti; Culex quinquefasciatus; Homo sapiens; Muntiacus reevesi; Muntiacus muntjak; Strongylocentrotus purpuratus; Ciona intestinalis; Pleurobrachia bachei; Acropora millepora; Python bivittatus; Saccharomyces cerevisiae; Drosophila melanogaster; Gallus gallus; Hypsibius dujardini; Lethenteron camtschaticum; Arachis hypogaea; Agaricus bisporus; Branchiostoma lanceolatum; Xenopus laevis; Notamacropus eugenii; Pygocentrus nattereri; Cristatella mucedo; Clonorchis sinensis; Chiloscyllium punctatum

Type:

Other

30 related Platforms

32 Samples

Download data: BEDPE, FASTA, HIC, VCF, WIG

(Submitter supplied) Respiratory bursts were observed in A. bisporus. CO2 production and O2 consumption increased up to 3.5 fold during these 3 h bursts while compost temperature increased up to 3 °C. We set out to find which pathways were characteristic for these bursts and the interval between these bursts.

Organism:

Agaricus bisporus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26034

9 Samples

Download data: DIFF

(Submitter supplied) Cytosine methylation is a conserved base modification, but explanations for its interspecific variation remain elusive. Only through taxonomic sampling of disparate groups can unifying explanations for interspecific variation be thoroughly tested. Here we leverage phylogenetic resolution of cytosine DNA methyltransferases (DNA MTases) and genome evolution to better understand widespread interspecific variation across 40 diverse fungal species. more...

Organism:

Agaricus bisporus; Mixia osmundae; Sporobolomyces roseus; Cordyceps militaris; Wolfiporia cocos; Spinellus fusiger; Hesseltinella vesiculosa; Microbotryum lychnidis-dioicae; [Candida] auris; Heterobasidion irregulare; Phycomyces blakesleeanus; Fusarium fujikuroi; Neurospora crassa; Pleurotus ostreatus; Aureobasidium pullulans; Laccaria bicolor; Uncinocarpus reesii; Parasitella parasitica; Botrytis cinerea; Tilletiopsis washingtonensis; Plenodomus lingam; Candida albicans; Coemansia reversa; Postia placenta; Coemansia spiralis; Kirkomyces cordensis; Metarhizium robertsii; Pseudogymnoascus destructans; Saccharomyces cerevisiae; Aspergillus flavus; Coprinopsis cinerea; Clavispora lusitaniae; Lobosporangium transversale; Radiomyces spectabilis; Flammula alnicola; Cryptococcus neoformans var. grubii; Pyricularia oryzae KJ201; Syncephalis fuscata; Podospora anserina; Phanerodontia chrysosporium

Type:

Methylation profiling by high throughput sequencing; Third-party reanalysis

29 related Platforms

31 Samples

Download data: TSV, TXT, XLS

(Submitter supplied) The white button mushroom Agaricus bisporus is the most widely produced edible fungus with a great economical value. Its commercial cultivation process is often performed on wheat straw and animal manure based compost that mainly contains lignocellulosic material as a source of carbon and nutrients for the mushroom production. As a large portion of compost carbohydrates are left unused in the current mushroom cultivation process, the aim of this work was to study wild-type A. more...

Organism:

Agaricus bisporus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19762

16 Samples

Download data: TXT

(Submitter supplied) Drought is a stressor for many soil-inhabiting organisms. Although plants have been extensively investigated for drought-adaptive mechanisms, little information is available for fungi. Antioxidants are especially relevant, since desiccation is accompanied by an excessive intracellular production of reactive oxygen species. Riboflavin (vitamin B2) is one antioxidant regulating drought tolerance in plants. more...

Organism:

Agaricus bisporus

Type:

Expression profiling by array

Platform:

GPL20913

8 Samples

Download data: TXT

(Submitter supplied) The common edible mushroom Agaricus bisporus is a basidiomycete that thrives on decaying plant material in the forests and grasslands of North America and Europe. It is adapted to forest litter and contributes to global carbon recycling, degrading cellulose, hemicellulose and lignin in plant biomass to oligomers and monomers. A. bisporus is also an edible mushroom that is widely cultivated and economically important. more...

Organism:

Agaricus bisporus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19762

12 Samples

Download data: TXT

(Submitter supplied) Agaricus bisporus is a soil-inhabiting fungus which is cultivated for production of white button mushrooms. A disease of A. bisporus has been previously described with a range of disease symptoms (yield loss, pinning delay, cap distortions and cap browning) which has been given collective name of “Mushroom Virus X” (MVX). The causes of this disease are not clear however prior to this research an association was found between the disease and double-stranded RNA molecules in the mushroom fruitbodies. more...

Organism:

Agaricus bisporus

Type:

Expression profiling by array

Platform:

GPL20649

32 Samples

Download data: TXT

(Submitter supplied) Utilising a whole genome array, we have investigated the differential expression of genes across different developmental stages in the life cycle of Agaricus bisporus.

Organism:

Agaricus bisporus var. bisporus H97

Type:

Expression profiling by array

Platform:

GPL15836

16 Samples

Download data: TXT

(Submitter supplied) Microarrays have become established tools for describing microbial systems, however the assessment of expression profiles for environmental microbial communities still presents unique challenges. Notably, the concentration of particular transcripts are likely very dilute relative to the pool of total RNA, and PCR-based amplification strategies are vulnerable to amplification biases and the appropriate primer selection. more...

Organism:

Agaricus bisporus; Lentinula edodes; Fusarium oxysporum; Botrytis cinerea; Pleurotus eryngii; Schizophyllum commune; Trametes cinnabarina; Gelatoporia subvermispora; Trametes coccinea; Neurospora crassa; Pleurotus ostreatus; Heterobasidion annosum; synthetic construct; unidentified; Fusarium proliferatum; Cryphonectria parasitica; Phlebia radiata; Trametes versicolor; Coriolopsis gallica; Dichomitus squalens; Phanerodontia chrysosporium

Type:

Expression profiling by array

Platform:

GPL7797

68 Samples

Download data: TXT

(Submitter supplied) Arrays of this design have barcodes that begin with 16071199 or 2571199. Orientation: Features are numbered numbered Left-to-Right, Top-to-Bottom as scanned by an Agilent scanner (barcode on the left, DNA on the back surface, scanned through the glass), matching the FeatureNum output from Agilent's Feature Extraction software. The ID column represents the Agilent Feature Extraction feature number. more...

Organism:

Agaricus bisporus

1 Series

8 Samples

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(Submitter supplied) Agilent

Organism:

Agaricus bisporus

1 Series

32 Samples

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(Submitter supplied) Arrays of this design have barcodes that begin with 16027120 or 2527120. This is a condensed platform of the full array, which has probes designed from gene models taken from the Joint Genome Institute Agaricus bisporus H97 genome sequence version 2.0 (http://genome.jgi.doe.gov/Agabi_varbisH97_2/Agabi_varbisH97_2.home.html). Oligonucleotide sequences are available in the supplementary file 'GPL15836_027120_D_GEO_20100129_full_array.txt'. more...

Organism:

Agaricus bisporus var. bisporus H97

1 Series

16 Samples

Download data: TXT

(Submitter supplied) Probes were printed at 100 µM (in 100 mM Na2HPO4, 200 mM NaCl, 0.01% SDS print buffer) concentrations on epoxysilane-coated glass slides by a Microgrid II printing system (PerkinElmer Life And Analytical Sciences, Inc., Waltham, MA). Control spots were present as buffer, beacon, biotin, polyA and polyT oligonucleotides. The buffer spots were spots of blank print buffer (defined below) intended to ensure probe spots were well-spaced. more...

Organism:

Cryphonectria parasitica; Neurospora crassa; Phlebia radiata; Pleurotus ostreatus; Pleurotus eryngii; Trametes versicolor; Schizophyllum commune; Agaricus bisporus; Lentinula edodes; Fusarium oxysporum; Trametes cinnabarina; Heterobasidion annosum; synthetic construct; Botrytis cinerea; Gelatoporia subvermispora; Coriolopsis gallica; Dichomitus squalens; Trametes coccinea; Fusarium proliferatum; Phanerodontia chrysosporium

1 Series

68 Samples

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