GEO DataSets

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Cenococcum geophilum ectomycorrhizal poplar roots compared to free-living mycelium . Ectomycorrhizal poplar roots and control mycelium were harvested after 60 days and used for RNA extraction. Reads of 150bp were generated and aligned to the C. geophilum reference genome (https://genome.jgi.doe.gov/Cenge3/Cenge3.home.html).

Organism:

Cenococcum geophilum 1.58

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24474 GPL24473

6 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Cenococcum geophilum ectomycorrhizal Pine roots, sclerotia and extramatrical mycelium compared to free-living mycelium . Ectomycorrhizal pine roots, sclerotia, extramatrical mycelium and control mycelium were harvested after 90 days and used for RNA extraction. Reads of 150bp were generated and aligned to the C. geophilum reference genome (https://genome.jgi.doe.gov/Cenge3/Cenge3.home.html).

Organism:

Pinus sylvestris; Cenococcum geophilum 1.58

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24479 GPL24473 GPL24474

12 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Cenococcum geophilum ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 3 months, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Cenococcum geophilum (http://genome.jgi.doe.gov/Cenge3/Cenge3.home.html) reference transcripts using CLC Genomics Workbench 6.

Organism:

Cenococcum geophilum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22097

6 Samples

Download data: TXT

(Submitter supplied) To identify specific gene networks induced in host roots by C. geophilum, we inoculated seedlings of Scots pine simultaneously with C. geophilum and either Suillus granulatus or Rhizopogon roseolus, two common ECM fungi associated to pines. We then measured the differential expression of Scots pine genes in the respective mycorrhizas using oligoarrays.

Organism:

Pinus sylvestris; Cenococcum geophilum

Type:

Expression profiling by array

Platform:

GPL21757

14 Samples

Download data: PAIR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Piloderma croceum; Serendipita vermifera; Suillus luteus; Amanita muscaria; Hebeloma cylindrosporum; Oidiodendron maius; Tulasnella calospora; Paxillus involutus

Type:

Expression profiling by high throughput sequencing

10 related Platforms

42 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Suillus luteus ectomycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 40 days, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Suillus luteus (http://genome.jgi-psf.org/Suilu1/Suilu1.home.html) using CLC Genomics Workbench 6.

Organism:

Suillus luteus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19513

4 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Piloderma croceum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19512

6 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Paxillus involutus ectomycorrhizal roots compared to mycelium patches . Mycorrhizal roots were harvested after 4 weeks, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Paxillus involutus (http://genome.jgi-psf.org/Paxin1/Paxin1.home.html) using CLC Genomics Workbench 6.

Organism:

Paxillus involutus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19511

4 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Sebacina vermifera mycorrhizal roots compared to free-living mycelium . Mycorrhizal roots were harvested after 3, 7 and 14 days, pooled and used for RNA extraction. Reads of 2X100bp were generated and aligned to Sebacina vermifera (http://genome.jgi-psf.org/Sebve1/Sebve1.home.html) using CLC Genomics Workbench 6.

Organism:

Serendipita vermifera

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19510

6 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Oidiodendron maius mycorrhizal roots compared to free-living mycelium . Mycorrhizal roots and control mycelium were harvested after 45 days and used for RNA extraction. Reads of 2X100bp were generated and aligned to Oidiodendron maius transcripts (http://genome.jgi-psf.org/Oidma1) using CLC Genomics Workbench 6.

Organism:

Oidiodendron maius

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19509

6 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Tulasnella calospora mycorrhizal protocorms compared to free-living mycelium . Protocorms and control mycelium were harvested after 30 days and used for RNA extraction. Reads of 2X100bp were generated and aligned to Tulasnella calospora transcripts (http://genome.jgi-psf.org/Tulca1) using CLC Genomics Workbench 6.

Organism:

Tulasnella calospora

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19502

6 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Hebeloma cylindrosporum ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips and control mycelium were harvested after 3 weeks and used for RNA extraction. Reads of 150 bp were generated and aligned to Hebeloma cylindrosporum transcripts (http://genome.jgi-psf.org/Hebcy2) using CLC Genomics Workbench 7.

Organism:

Hebeloma cylindrosporum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19501 GPL19500

6 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Amanita muscaria ectomycorrhizal root tips compared to free-living mycelium . Ectomycorrhizal root tips and control mycelium were harvested after 6 weeks and used for RNA extraction. Reads of 150 bp were generated and aligned to Amanita muscaria transcripts (http://genome.jgi-psf.org/Amamu1) using CLC Genomics Workbench 7.

Organism:

Amanita muscaria

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19498 GPL19499

4 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Laccaria bicolor; Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17415 GPL21175

2 Samples

Download data: TXT

(Submitter supplied) 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.

Organism:

Laccaria bicolor; Populus trichocarpa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18263 GPL17579 GPL18265

7 Samples

Download data: TXT

(Submitter supplied) Illumina technology was used to generate mRNA profiles of Laccaria bicolor mycelium grown under different nutrien conditions. Total RNA was extracted.TruSeq mRNA Stranded libraries were constructed and and sequenced (2 x 150 bp Illumina HiSeq3000) at the Genotoul sequencing facilities (Toulouse, France). Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the L. more...

Organism:

Laccaria bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31043

20 Samples

Download data: TXT

(Submitter supplied) Illumina technology was used to generate mRNA profiles of three stages of L. bicolor basidiocarps. Total RNA was extracted separately from cap and stipe.TruSeq mRNA Stranded libraries were constructed and and 2 x 100 bp sequenced using Illumina HiSeq 2000 at the Genotoul sequencing facilities (Toulouse, France). Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the L. more...

Organism:

Laccaria bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19637

18 Samples

Download data: TXT

(Submitter supplied) Illumina technology was used to generate mRNA profiles of a time course of Laccaria bicolor S238N and Populus tremula x alba 717-1B4 in vitro ectomycorrhizal development. Total RNA was extracted, TruSeq mRNA Stranded libraries were constructed and and sequenced in triplicates (2 x 150 bp Illumina HiSeq3000) at the Genotoul sequencing facilities (Toulouse, France). Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the L. more...

Organism:

Laccaria bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31043

37 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq2000 technology was used to generate mRNA profiles from Hebeloma cylindrosporum pre-infectious stages (2 and 4 days) compared to control mycelium. Pre-infectious and control mycelia were harvested after 2 and 4 days and used for RNA extraction. Reads of 150 bp were generated and aligned to Hebeloma cylindrosporum reference transcripts (http://genome.jgi-psf.org/Hebcy2) using CLC Genomics Workbench 8.5.1.

Organism:

Hebeloma cylindrosporum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19500

12 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Laccaria bicolor S238N-H82; Populus trichocarpa; Laccaria bicolor; Populus tremula x Populus alba; Pseudotsuga menziesii

Type:

Expression profiling by array

Platform:

GPL6192

11 Samples

Download data: TXT