Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

50 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dual transcriptomic analysis of the interaction between the ectomycorrhizal fungus Laccaria bicolor S238N and soil bacteria Pseudomonas fluorescens BB6cR8 and Pf29Arp

ABSTRACT: In order to get insights into the ability of ectomycorrhizal fungi to perceive their biotic environment as well as into the mechanisms of the interactions between ectomycorrhizal fungi and soil bacteria, we analysed the transcriptomic response of the ectomycorrhizal fungus L. bicolor and of two beneficial, and neutral soil bacteria during their interactions in vitro. We performed nine hybridizations (macroarray) with samples derived from Laccaria bicolor cultivated alone (3 biological replicates), with P. fluorescens BBc6R8 (3 biological replicates) and with Pf29Arp (3 biological replicates)

ORGANISM(S): Laccaria bicolor

SUBMITTER: Annegret Kohler

PROVIDER: E-GEOD-53608 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Dual transcriptomic analysis of the interaction between the ectomycorrhizal fungus Laccaria bicolor S238N and soil bacterium Collimonas fungivorans Ter331

Project description:In order to get insights into the ability of ectomycorrhizal fungi to perceive their biotic environment as well as into the mechanisms of the interactions between ectomycorrhizal fungi and soil bacteria, we analysed the transcriptomic response of the ectomycorrhizal fungus L. bicolor and one detrimental bacterial strain during their interactions in vitro. We performed six hybridizations (macroarray) with samples derived from Laccaria bicolor cultivated alone (3 biological replicates and with C. fungivorans Ter331 (3 biological replicates)

2014-06-12 | E-GEOD-53609 | biostudies-arrayexpress

Effect of 3,OC12-HSL on the transcriptome of the ectomycorrhizal fungus Laccaria bicolor S238N

Project description:Bacteria use small diffusible molecules to communicate and to coordinate population response by a cell density-depend mechanism named quorum sensing (QS). If such a cross-talk was first described between bacterial species, it was recently evidenced that bacterial QS signal molecules can also be sensed by eukaryotic organisms thus playing as inter-kingdom signalling molecules. Although ectomycorrhizal fungi interact physically and metabolically with myriads of bacterial species in soils, nothing is known about the ability of ectomycorrhiza-associated bacteria to produce QS molecules and the potential impact of these molecules in the interaction. While investigating the potential effect of these molecules on the physiology of the ectomycorrhizal fungus, we found that 3O,C12-HSL also induced an alteration of the transcriptome of L. bicolor S238N. This study used the microarray design as follows: cDNA libraries from pure culture of Laccaria bicolor S238N mycelium and from three stages of L. bicolor S238N sporocarp development (Lb2 library: stipes and caps of 5–10 mm growing sporocarps; Lb3 library: caps of 30– 40 mm mature sporocarps), collected under Douglas ﬁr seedlings grown in a glasshouse, were constructed in the λTriplEx2 vector. The cDNA inserts from bacterial clones were PCR-ampliﬁed and 4992 cDNAs were arrayed from 384-well microtitre plates on Nylon membranes. Three independent biological replicates were performed for the treatment (3,OC12-HSL) and for the control (ethyl acetate)

2010-11-23 | E-GEOD-18635 | biostudies-arrayexpress

Dual transcriptomic analysis of the interaction between the ectomycorrhizal fungus Laccaria bicolor S238N and soil Pseudomonas fluorescens Pf29Arp

Project description:In order to get insights into the ability of ectomycorrhizal fungi to perceive their biotic environment as well as into the mechanisms of the interactions between ectomycorrhizal fungi and soil bacteria, we analysed the transcriptomic response of the ectomycorrhizal fungus L. bicolor and the strain Pseudomonas fluorescens Pf29Arp during their interactions in vitro. We performed six hybridizations (shotgun DNA microarray) with samples derived from Pseudomonas fluorescens Pf29Arp cultivated alone or with Laccaria bicolor S238N in vitro (3 control biological replicates and 3 biological replicates with L. bicolor)

2014-10-01 | E-GEOD-55147 | biostudies-arrayexpress

Dual transcriptomic analysis of the interaction between the ectomycorrhizal fungus Laccaria bicolor S238N and soil Collimonas fungivorans Ter331

Project description:In order to get insights into the ability of ectomycorrhizal fungi to perceive their biotic environment as well as into the mechanisms of the interactions between ectomycorrhizal fungi and soil bacteria, we analysed the transcriptomic response of the ectomycorrhizal fungus L. bicolor and one detrimental bacterial strain during their interactions in vitro. We performed hybridizations (whole genome array) with samples derived from Collimonas fungivorans Ter331cultivated alone or with Laccaria bicolor S238N in vitro (2 control biological replicates and 2 biological replicates with L. bicolor)

2014-06-12 | E-GEOD-54533 | biostudies-arrayexpress

ChIP-chip of Spo14 and Mvp1

Project description:Genome-wide localization of two new RNA pol II interacting proteins. We use C-LYTAG to map binding sites of Spo14 and Mvp1 along the S. cerevisiae genome. Two biological replicates of each experiment were done. Keywords: ChIp-chip Two independent biological replicates of each IP. We used three macroarrays: V5R2-L1-20, V5R2-L1-21 and V5R2-L1-22 that were hybridized with Whole Cell Extract (WCE) and then with two biological samples of immunoprecipitated (IP) Mvp1 (V5R2-L1-20 and V5R2-L1-21) and Spo14 (V5R2-L1-20 and V5R2-L1-22)

2011-10-31 | E-GEOD-16905 | biostudies-arrayexpress

Distribution of elongating and total RNA polymerase II in xrn1 mutants using GRO and RPCC

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-05-22 | E-GEOD-43605 | biostudies-arrayexpress

Poplar-Laccaria: A Timecourse of Mycorrhizal Root Tip Development

Project description:This study characterizes the transcriptomic alterations of P. trichocarpa during interaction with the ectomycorrhizal fungus Laccaria bicolor S238N. Four time-points were analyzed, two weeks, four weeks , six weeks and twelve weeks after inoculation. We performed 32 hybridizations (NimbleGen) with samples derived from Populus trichocarpa control roots and P.trichocarpa mycorrhizal root tips. Samples were taken after 2,4,6 and 12 weeks of interaction (four biological replicates). All samples were labeled with Cy3.

2014-10-09 | E-GEOD-62172 | biostudies-arrayexpress

Identification of LEC1 target genes

Project description:The transcription factor (TF) LEAFY COTYLEDON1 (LEC1) acts as an essential regulator of Arabidopsis embryogenesis and seed development. It controls aspects of early embryogenesis such as cotyledon identity and suspensor morphology, as well as seed maturation processes such as storage compound accumulation, acquisition of desiccation tolerance and dormancy. To identify downstream components of the LEC1 regulon, dexamethasone-regulated expression of LEC1 and ChIP/chip were applied and revealed the enrichment of phytohormone- as well as elongation-related genes among LEC1 target genes. Two weeks old 35S::LEC1::GR seedlings were treated with DEX or ethanol for 24 hours before cross-linking and chromatin isolation. Four biological replicates were performed, using an ethanol-treated sample as control (LEC1_EtOH versus LEC1_DEX). After data normalization, statistical analysis and exclusion of putative false negatives, a number of 356 target promoter regions were identified.

2012-03-30 | E-GEOD-22352 | biostudies-arrayexpress

Gene expression changes in Piloderma croceum-Quercus robur ectomycorrhizal roots compared to Piloderma croceum free-living mycelium

Project description:Illumina HiSeq technology was used to generate mRNA profiles from Piloderma croceum ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 8 weeks, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Piloderma croceum (http://genome.jgi-psf.org/Pilcr1/Pilcr1.home.html) using CLC Genomics Workbench 6. mRNA profiles from Piloderma croceum ectomycorrhizal roots and free-living mycelium were generated by paired-end (2x100bp) Illumina HiSeq2000 sequencing. Three biological replicates were sequenced for mycorrhizal and mycelium samples.

2015-02-06 | E-GEOD-63925 | biostudies-arrayexpress

Distribution of total RNA polymerase II along the 5'/3' regions in xrn1 mutants

Project description:Determination of 3' or 5' intragenic RNA pol II occupancy. Maintaining the proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. Using a whole-genome analysis, we demonstrate that most yeast mRNAs are degraded by the 5'-to-3' pathway (the "decaysome"), as proposed previously. Unexpectedly, the level of these mRNAs is highly robust to perturbations in this major pathway, as defects in various decaysome components lead to transcription down-regulation. Moreover, these components shuttle between the cytoplasm and the nucleus, in a manner dependent on proper mRNA degradation. In the nucleus, they associate with chromatin - preferentially ~30bp upstream of transcription start-sites - and directly stimulate transcription initiation and elongation. Hence, the decaysome has a dual role in maintaining mRNA levels. Significantly, proper import of some decaysome components seems to play a key role in coupling the two functions. The gene expression process is therefore circular, whereby the hitherto first and last stages are interconnected. This study focuses on the distribution of RNA pol II in the 3' or 5' region of 377 S. cerevisiae ORFs. S. cerevisiae cells grown in YPD to exponential phase were subjected to chromatin immunoprecipitation (ChIP) with anti-Rpb3 antibody. Data were normalized using whole cell extract hybridized on the same array. Home-made macroarrays containing 300 bp from both the 5' or 3' ends of each ORF were used.

2013-05-22 | E-GEOD-43604 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data