GEO DataSets

(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:

Populus trichocarpa; Laccaria bicolor

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18263 GPL17579 GPL18265

7 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) To investigate which genes are affected by MiSSP7, a secreted effector protein of Laccaria bicolor, we analyzed the transcriptomes of poplar roots incubated with MiSSP7 protein.

Organism:

Populus tremula x Populus alba; Populus trichocarpa

Type:

Expression profiling by array

Platform:

GPL13485

6 Samples

Download data: PAIR

(Submitter supplied) This study characterizes the transcriptomic alterations of P. tremula x P. alba at three weeks after inoculation with the ectomycorrhizal fungus Laccaria bicolor.

Organism:

Populus trichocarpa; Populus tremula x Populus alba

Type:

Expression profiling by array

Platform:

GPL13485

6 Samples

Download data: PAIR

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

Organism:

Populus trichocarpa; Populus tremula x Populus tremuloides; Populus tremula x Populus alba

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL13485 GPL18583

40 Samples

Download data: PAIR, TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Populus tremula x alba INRA 717-1B4 roots treated with Methyl jasmonate. Samples were harvested after two weeks either from untreated control roots or from Methyl jasmonate treated roots. Paired-end (2X100bp) reads were generated and aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) using CLC Genomics Workbench 6.

Organism:

Populus tremula x Populus alba

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18583

4 Samples

Download data: TXT

(Submitter supplied) The Poplar transcriptome was analyzed in Populus tremulaxPopulus alba clone 717-1B4 control roots and in two poplar lines overexpressing MiSSP7.

Organism:

Populus trichocarpa; Populus tremula x Populus alba

Type:

Expression profiling by array

Platform:

GPL13485

9 Samples

Download data: PAIR, TXT

(Submitter supplied) The Poplar transcriptome was analyzed in mycorrhizal root tips in contact with Laccaria bicolor for 2 weeks. During mycorrhization the roots were treated with either 250µm ACC, 10nM JA or 500µM SA and compared to untreated mycorrhiza or control roots without contact to L. bicolor. In addition the poplar mutants 35S::PttACO1 and 35S::Atetr1 were used

Organism:

Populus tremula x Populus tremuloides; Populus trichocarpa; Populus tremula x Populus alba

Type:

Expression profiling by array

Platform:

GPL13485

27 Samples

Download data: PAIR, 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:

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

Type:

Expression profiling by array

Platform:

GPL6192

11 Samples

Download data: TXT

(Submitter supplied) The early phase of the interaction between tree roots and ectomycorrhizal (ECM) fungi, prior to symbiosis establishment, is accompanied by a stimulation of lateral root (LR) development. We set out to identify gene networks that regulate LR development during the early signal exchanges between Populus tremula x Populus alba (hereafter called poplar) and the ECM fungus Laccaria bicolor. A sandwich culture system was developed in order to bring plant and fungus into an indirect contact, which permits signal molecule exchange and LR stimulation (emergence after 4-5 days of contact) but prohibits root colonization. more...

Organism:

Populus trichocarpa; Populus tremula x Populus alba

Type:

Expression profiling by array

Platform:

GPL2699

6 Samples

Download data

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

Organism:

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

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:

GPL19500 GPL19501

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:

GPL19499 GPL19498

4 Samples

Download data: TXT