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Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza development

ABSTRACT: Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza development

PROVIDER: PRJNA237653 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1165053.fastq.gz	Fastqsanger.gz
	SRR1165054.fastq.gz	Fastqsanger.gz
	SRR1165055.fastq.gz	Fastqsanger.gz
	SRR1165056.fastq.gz	Fastqsanger.gz
	SRR1165057.fastq.gz	Fastqsanger.gz

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Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza development

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Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza development

Project description:Illumina GAIIx technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after two, four and 12 weeks of contact in order to identify mycorrhiza-regulated transcripts. 37bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) and the Laccaria bicolor (http://genome.jgi-psf.org/Lacbi2/Lacbi2.home.html) reference genomes using CLC Genomics Workbench 6. mRNA profiles from Populus trichocarpa roots colonized by Laccaria bicolor for two, four and 12 weeks as well as from control roots and free-living mycelium were generated by using one lane of 37 bp Illumina GAIIx sequencing per sample.

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Project description:Illumina HiSeq2000 technology was used to generate mRNA profiles from the ectomycorrhizal fungi Laccaria bicolor colonizing roots of Populus trichocarpa. Samples were taken after 3 months of contact in order to identify mycorrhiza-regulated transcripts. 100bp reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) reference genome.

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Gene expression changes in leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering.

Project description:Illumina technology was used to generate mRNA profiles of leaves, roots and Laccaria bicolor mycorrhiza of Poplar treated with ozone or stopped watering. Total RNA was extracted separately from each plant and pooled to 4 biological replicates per condition.TruSeq mRNA Stranded libraries were constructed and and sequenced using Illumina HiSeq 3000 at the Genotoul sequencing facilities (Toulouse, France). Raw reads were filtered and trimmed using erne-filter command. Filtered reads from each library were aligned to P. trichocarpa (https://phytozome-next.jgi.doe.gov/info/Ptrichocarpa_v4_1) using TopHat2 v2.12.

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Laccaria-Poplar: A Timecourse of Mycorrhizal Root Tip Development

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Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza

Project description:Transcriptome analyses of the Laccaria bicolor-Populus trichocarpa mycorrhiza

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Poplar-Laccaria: A Timecourse of Mycorrhizal Root Tip Development

2014-10-09 | GSE62172 | GEO

Laccaria-Poplar: A Timecourse of Mycorrhizal Root Tip Development

Project description:This study characterizes the transcriptomic alterations of Laccaria bicolor S238N during interaction with P. trichocarpa. Four time-points were analyzed, two weeks, four weeks , six weeks and twelve weeks after inoculation and compared to the transcriptome of free-living mycelium from Laccaria bicolor S238N We performed 16 hybridizations (NimbleGen) with samples derived from P.trichocarpa/L.bicolor mycorrhizal root tips. Samples were taken after 2,4,6 and 12 weeks of interaction (four biological replicates). These samples were compared to free-living mycelium from Laccaria bicolor S238N (three biological replicates). All samples were labeled with Cy3.

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Laccaria bicolor S238N gene expression in different tissues

Project description:The Transcriptome of different tissues and developmental stages of Laccaria bicolor S238N was analyzed. The array probes were designed from gene models taken from the Joint Genome institute Laccaria bicolor genome sequence version1. One aim of this study was to verify the expression of the automatically annotated gene models in various tissues and to use this transcriptional information to confirm, to correct or to reject gene models. Another goal was to identify tissue-specific gene expression, e.g. mycorrhiza up-regulated transcripts or fruiting body up-regulated transcripts, or treatment specific gene expression for further detailed analyses. Keywords: Tissue comparison

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