Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Uncultured fungus

ABSTRACT: Fungal microbiome of herbaceous plant roots collected on truffle grounds (Tuber melanosporum)

PROVIDER: PRJNA397712 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5930420.fastq.gz	Fastqsanger.gz
	SRR5930430.fastq.gz	Fastqsanger.gz
	SRR5930440.fastq.gz	Fastqsanger.gz
	SRR5930450.fastq.gz	Fastqsanger.gz
	SRR5930460.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 78

Similar Datasets

Bisulfite-Seq and RNA-seq profiling of truffle (Tuber melanosporum)

Project description:We investigated the ascomycete truffle Tuber melanosporum exploits DNA methylation and transcription to cope with the more than 45,000 repeated elements that are present in its genome. Whole-genome bisulfite sequencing and RNA-sequencing, were performed on different developmental stages of this symbiotic hypogeous fungus -fruitbody (FB), free-living mycelium (FLM), and ectomycorrhiza. Examination of DNA methylation and transcription of truffle in its free living mycelium (FLM), fruit body (FB), and ectomycorrhizal root tips (ECM)

2014-01-01 | E-GEOD-49700 | biostudies-arrayexpress

Bisulfite-Seq and RNA-seq profiling of truffle (Tuber melanosporum)

2014-01-01 | GSE49700 | GEO

Laser capture microdissection and microarray analysis of ectomycorrhizas formed by the ascomycete Tuber melanosporum reveal functional heterogeneity between mantle and Hartig net compartments

2013-03-01 | GSE36870 | GEO

Laser capture microdissection and microarray analysis of ectomycorrhizas formed by the ascomycete Tuber melanosporum reveal functional heterogeneity between mantle and Hartig net compartments

Project description:The aim of this analysis was to better understand the complex symbiotic stage of Tuber melanosporum by combining the use of laser capture microdissection and microarray gene expression analysis. We isolated the fungal/soil (i.e. the mantle) and the fungal/plant (i.e. the Hartig net) interfaces from transverse sections of T. melanosporum/Corylus avellana ectomycorrhizas and identified the transcriptional landscape associated with each compartment. We compared these data to the transcriptome of ectomycorrhizal root tips, free-living mycelium and fruiting bodies of Tuber melanosporum (Series GSE17529). The T. melanosporum custom-exon expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) contained five independent, nonidentical, 60-mer probes per gene model coding sequence. Included in the oligoarray were 12,232 annotated gene models, 3,913 random 60-mer control probes and labelling controls. Sequences used for the oligonucleotide design were from an early draft of the gene catalog containing several TE families. For 1,876 gene models, technical duplicates were included on the array. We performed 6 hybridizations (NimbleGen) with samples derived from microdissected mantles (3 biological replicates) and Hartig nets ((3 biological replicates each) from T. melanosporum/Corylus avellana ectomycorrhizal root tips . All samples were labeled with Cy3.

2013-03-01 | E-GEOD-36870 | biostudies-arrayexpress

The transcriptome of Oak roots associated with truffles

Project description:Illumina HiSeq technology was used to generate mRNA profiles from mycorrhizal Quercus robur roots. Tuber melanosporum, T. aestivum and T.magnatum mycorrhizal root tips were harvested and used for RNA extraction. Paired-end reads of 100 bp were generated and aligned to Quercus robur CDS using CLC Genomics Workbench 9.

2018-07-01 | GSE97122 | GEO

Quantitative Proteomics of different truffle species

Project description:Truffles of the Tuber species as expensive foods are predestined for food fraud. To find markers for distinguishing different truffle species the proteomes as phenotype determining basis were investigated. First, established sample preparation protocols subsequent to LC-MS/MS analysis for a bottom up proteomic approach were tested on a truffle sample. The sample preparation included protein extraction and in-solution tryptic digestion. For protein extraction sodium deoxycholate (SDC), sodium dodecylsulfate (SDS) and urea were tested, followed by direct tryptic digestion in solution (SDC extracted proteins) and a tryptic digestion utilizing the FASP approach with molecular cut-off filters (SDS and urea extracted proteins). By this approach the SDC sample preparation protocol was classified as the most suited one to prepare truffle samples. It resulted in a high protein identification rate, had a high reproducibility, was cost efficient and most easy to handle. By a quantitative proteomic approach using label-free and non-targeted bottom up LC-MS/MS the species T. magnatum (n=13), T. aestivum (n=16), T. uncinatum (n=4) and T. melanosporum (n=7) were compared and truffle species specific markers were identified.

2021-12-19 | PXD017901 | Pride

Project description:Soil fungal community of Tuber melanosporum

| PRJNA754366 | ENA

uncultured fungus

Project description:The fungal communities associating with the roots of dune grasses

| PRJNA322225 | ENA

Differential bottom-up proteomics of truffles

Project description:To compare truffles on protein level, samples of different truffle species (T. magnatum, T. indicum, T. melanosporum, T. aestivum and T. albidum Pico) were analysed by a LC-MS/MS based shotgun proteomics approach. First, different established bottom-up proteomics sample preparation approaches for in solution tryptic proteolysis were tested for a truffle sample. Then, a spectral library was generated by 2D LC-MS/MS and truffle samples were measured in data-independent acquisition (DIA) mode. We provide a comprehensive study on the proteomic differences between truffle species.

2021-12-19 | PXD027871 | Pride

Tuber melanosporum

Project description:Bisulfite-Seq and RNA-seq profiling of truffle (Tuber melanosporum)

| PRJNA214782 | ENA