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Items: 1 to 20 of 102

1.

Functional characterization of the transcription programs underlying phase transition in the BSL3 pathogen Coccidioides immitis

(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
Series
Accession:
GSE179468
ID:
200179468
2.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

(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
Series
Accession:
GSE169088
ID:
200169088
3.

Agaricus bisporus respiratory bursts

(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
Series
Accession:
GSE124976
ID:
200124976
4.

Diversity of cytosine methylation across the fungi tree of life

(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; 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; Plenodomus lingam; Candida albicans; Coemansia reversa; Postia placenta; Coemansia spiralis; Kirkomyces cordensis; Metarhizium robertsii; Pseudogymnoascus destructans
Type:
Methylation profiling by high throughput sequencing; Third-party reanalysis
29 related Platforms
31 Samples
Download data: TSV, TXT, XLS
Series
Accession:
GSE112636
ID:
200112636
5.

The physiology of Agaricus bisporus in semi-commercial compost cultivation appears to be highly conserved among unrelated isolates

(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
Series
Accession:
GSE99928
ID:
200099928
6.

Vitamin B2 and drought stress responses in Agaricus bisporus

(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
Series
Accession:
GSE73010
ID:
200073010
7.

Uncovering the abilities of Agaricus bisporus to degrade plant biomass throughout its life cycle

(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
Series
Accession:
GSE65800
ID:
200065800
8.

Gene expression changes with viral infection in Agaricus bisporus

(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
Series
Accession:
GSE70464
ID:
200070464
9.

Expression of lignin-degrading enzymes in soils using targeted microarrays

(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:
Cryphonectria parasitica; Phlebia radiata; Trametes versicolor; Coriolopsis gallica; Dichomitus squalens; Phanerodontia chrysosporium; Pleurotus eryngii; Schizophyllum commune; Trametes cinnabarina; Gelatoporia subvermispora; Trametes coccinea; Neurospora crassa; Pleurotus ostreatus; Heterobasidion annosum; synthetic construct; unidentified; Fusarium proliferatum; Agaricus bisporus; Lentinula edodes; Fusarium oxysporum; Botrytis cinerea
Type:
Expression profiling by array
Platform:
GPL7797
68 Samples
Download data: TXT
Series
Accession:
GSE13977
ID:
200013977
10.

Illumina HiSeq 4000 (Agaricus bisporus)

Organism:
Agaricus bisporus
1 Series
2 Samples
Download data
Platform
Accession:
GPL30350
ID:
100030350
11.

Illumina HiSeq 2500 (Agaricus bisporus)

Organism:
Agaricus bisporus
1 Series
9 Samples
Download data
Platform
Accession:
GPL26034
ID:
100026034
12.

Illumina NextSeq 500 (Agaricus bisporus)

Organism:
Agaricus bisporus
3 Series
7 Samples
Download data
Platform
Accession:
GPL24808
ID:
100024808
13.

Agilent-071199 Agbis_v1 040802

(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
Download data
Platform
Accession:
GPL20913
ID:
100020913
14.

018538_Agilent Agaricus bisporus array

(Submitter supplied) Agilent
Organism:
Agaricus bisporus
1 Series
32 Samples
Download data
Platform
Accession:
GPL20649
ID:
100020649
15.

Illumina HiSeq 2000 (Agaricus bisporus)

Organism:
Agaricus bisporus
2 Series
28 Samples
Download data
Platform
Accession:
GPL19762
ID:
100019762
16.

PNL mixed species lignin-degrading enzymes microarray

(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
Download data
Platform
Accession:
GPL7797
ID:
100007797
17.

Abisporus csRNA-input rep2

Organism:
Agaricus bisporus
Source name:
Agaricus bisporus fruiting body
Platform:
GPL24808
Series:
GSE179468
Download data
Sample
Accession:
GSM5418742
ID:
305418742
18.

Abisporus csRNA-input rep1

Organism:
Agaricus bisporus
Source name:
Agaricus bisporus fruiting body
Platform:
GPL24808
Series:
GSE179468
Download data
Sample
Accession:
GSM5418741
ID:
305418741
19.

Abisporus csRNA-seq rep3

Organism:
Agaricus bisporus
Source name:
Agaricus bisporus fruiting body
Platform:
GPL24808
Series:
GSE179468
Download data
Sample
Accession:
GSM5418740
ID:
305418740
20.

Abisporus csRNA-seq rep2

Organism:
Agaricus bisporus
Source name:
Agaricus bisporus fruiting body
Platform:
GPL24808
Series:
GSE179468
Download data
Sample
Accession:
GSM5418739
ID:
305418739
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