title: Genome-wide  gene expression analysis of undifferentiated mouse embryonic stem cells (mES),  neonatal mouse cardiomyocytes (CMp) and adult mouse cardiomyocytes (CMa)

summary: Genome-wide  gene expression analysis at different stages of cardiomyocyte differentiation (undifferentiated mouse embryonic stem cells, neonatal mouse  cardiomyocytes and adult mouse cardiomyocytes). Results provide important information on the differential expressed genes between undifferentiated mouse embrionic stem cells (mES) and  mouse cardiomyocytes (CM) and also between cardiomyocytes from neonatal (CMp) and adult stages (CMa). This dataset allowed us to compare the expression profile of mES, CMp and CMa with the epigenetic profile of histone methylation generated with ChIP-seq experiments.

overall_design: Total RNA was obtained from biological triplicate of undifferentiated mouse embryonic stem cells (mES), neonatal mouse cardiomyocytes (CMp) and adult mouse cardiomyocytes (CMa)


title: Laccaria-Douglas fir: A Timecourse of Mycorrhizal Root Tip Development

status: Public on Oct 10 2014

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

summary: This study characterizes the transcriptomic alterations of Laccaria bicolor S238N during interaction with Pseudotsuga menziesii. Three time-points were analyzed, two weeks, four weeks and six weeks after inoculation and compared to the transcriptome of free-living mycelium from Laccaria bicolor S238N.

sample_organism:
Pseudotsuga menziesii
Laccaria bicolor
Laccaria bicolor S238N-H82

overall_design: We performed 9 hybridizations (NimbleGen) with samples derived from Pseudotsuga menziesii /L.bicolor mycorrhizal root tips. Samples were taken after 2,4 and 6 weeks of interaction (three biological replicates).  These samples were compared to free-living mycelium from Laccaria bicolor S238N (three biological replicates). All samples were labeled with Cy3.

first: J

middle: M

last: Plett

first: A

first: F

last: Martin


title: Elevated carbon dioxide alters the interaction between Eucalyptus grandis and Pisolithus microcarpus through a complex shift in the root transcriptome

type: Expression profiling by high throughput sequencing

summary: Illumina HiSeq technology was used to generate mRNA profiles from in vitro Eucalyptus grandis roots interacting with two different Pisolithus microcarpus strains (SI-9 and SI-12) and under two different CO2 concentrations (400 and 650 ppm) . Control roots or ectomycorrhizal root tips were harvested after 1 month and used for RNA extraction. Paired-end (2X150bp) reads were generated and aligned to Eucalyptus grandis transcripts (http://www.phytozome.net/; primarytranscripts only) using CLC Genomics Workbench 6.

sample_organism:
Eucalyptus grandis
Pisolithus microcarpus

overall_design: mRNA profiles from in vitro Eucalyptus grandis roots interacting with two different Pisolithus microcarpus strains (SI-9 and SI-12) and under two different CO2 concentrations (400 and 650 ppm) were generated by paired-end (2X110bp) Illumina HiSeq1500 sequencing. Three biological replicates were sequenced for mycorrhizal samples, five for CO2 650ppm control roots and six for CO2 400ppm control roots.

first: C

last: Janitz

last: Khachane

first: I

middle: C

last: Anderson


title: Laccaria-Poplar: A Timecourse of Mycorrhizal Root Tip Development

summary: 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

sample_organism:
Populus trichocarpa
Laccaria bicolor
Laccaria bicolor S238N-H82

overall_design: 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.

last: Brun


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

status: Public on Oct 01 2014

summary: 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.

overall_design: 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)

middle: G

last: Diédiou

first: M

last: Barret

first: P

last: Frey-Klett


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

status: Public on Jun 12 2014

summary: 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.

overall_design: 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)

last: Deveau

last: Leveau

first: W

last: de Boer


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

summary: 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.

overall_design: 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)

last: Sarniguet

last: Diedhiou


title: Transcriptomic analysis of Phanerochaete chrysosporium mycelium in presence of oak acetonic extractives

status: Public on Aug 13 2014

summary: The transcriptome of  Phanerochaete chrysosporium control mycelium was compared to the transcriptome of mycelium grown on oak acetonic extractives containing medium.   The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Phanerochaete chrysosporium genome sequence version 1.   The aim of this study was to determine gene expression changes in  Phanerochaete chrysosporium grown on oak extract with a special focus on detoxification systems.

overall_design: We performed 6 hybridizations (NimbleGen) with samples derived from control mycelium (3 biological replicates) and mycelium grown on oak acetonic extractives containing medium (3 biological replicates). All samples were labeled with Cy3.

last: Morel-Rouhier

last: Thuillier

first: E

last: Gelhaye


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

last: Kohler

overall_design: We performed six hybridizations (macroarray) with samples derived from Laccaria bicolor cultivated alone (3 biological replicates and with C. fungivorans Ter331 (3 biological replicates)


title: Effect of Methyl jasmonate of the Poplar root transcriptome

status: Public on Apr 17 2014

summary: 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.

overall_design: mRNA profiles from Populus tremula x alba INRA 717-1B4 roots treated with Methyl jasmonate as well as from control roots were generated by paired-end (2X100bp) Illumina HiSeq sequencing. Four samples were sequenced per lane, two biological replicates per treatment.

first: Sebastian

last: Wittulsky

first: Claire

last: Veneault-Fourrey

first: Francis

last: Martin


title: Effect of MiSSP7 overexpression on the Poplar root transcriptome

summary: The Poplar transcriptome was analyzed in Populus tremulaxPopulus alba clone 717-1B4 control roots and in two  poplar lines overexpressing MiSSP7.

overall_design: We performed 9 hybridizations (NimbleGen) with samples derived from Populus tremulaxPopulus alba clone 717-1B4 control roots, as well as from roots of LINE1 and LINE2 MiSSP7 overexpressor poplars (3 biological replicates each). All samples were labeled with Cy3.

last: Plett


title: Mechanisms of interaction between ectomycorrhizal fungi and the mycorrhiza helper bacterium Pseudomonas fluorescens BBc6R8

summary: Mycorrhiza helper bacteria (MHB) promote the formation of ectomycorrhizae between tree roots and ectomycorrhizal fungi. Despite the high relevance of MHB for forestry and for sustainable tree production in tree nurseries, little is known about the properties of the bacteria that contribute to their helper abilities. The MHB strain Pseudomonas fluorescens BBc6R8 is used as a model to study the mechanisms of the helper effect. We took advantage of new technologies to obtain, for the first time, the whole genome sequence of an MHB. Analyses reveal an important plasticity of the genome with numerous functions acquired by horizontal gene tranfer. Genome mining was combined with transcriptomic and mutagenesis approaches to reveal molecular determinants of the helper effect. The data suggest that the production of helper molecules is likely to be constitutive in vitro. The helper effect appears to be pleiotropic and to rely, for a substantial part, on trophic interactions. Despite its helper abilities, the bacterium is also able in specific conditions to outcompete ectomycorrhizal fungi and inhibit their growth. We conclude that the helper bacterium possess a broad range of properties whose expression depending on the biotic and abiotic conditions can result in either a beneficial, neutral or antagonistic interaction between the plant, the ectomycorrhizal fungus and the bacterium.

overall_design: The study was performed along a kinetic with three sampling times: before contact between the bacterial colonies and the fungus (14 days after inoculation), at the time of contact (16 days after inoculation) and after an extended period of contact (21 days). For each time, three independent replicates were performed. A control treatment without the fungus was performed in triplicate and sampled at 14 days.

first: Aurelie

first: Pascale

first: Abdala

last: Diédhiou


title: Ethylene and jasmonic acid act as negative modulators during mutualistic symbiosis between Laccaria bicolor and Populus roots

status: Public on Dec 19 2013

summary: 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

sample_organism:
Populus tremula x Populus tremuloides
Populus tremula x Populus alba

overall_design: We performed 27 hybridizations (NimbleGen) with samples derived from Populus tremula x Populus alba clone 717-1B4 control roots, untreated mycorrhiza, SA-treated mycorrhiza, ACC-treated mycorrhiza and JA-treated mycorrhiza (3 biological replicates each) as well as Populus tremula x Populus tremuloides T89 control roots, mycorrhiza, 35S::PttACO1 mycorrhiza and 35S::Atetr1-1 mycorrhiza (3 biological replicates). All samples were labeled with Cy3.


title: Melampsora larici-populina gene expression in telia, uredinia, urediniospores and in planta

status: Public on Nov 01 2013

summary: The transcriptome of Melampsora larici-populina was analysed in telia (in planta sample, early telia harvested before overwintering), uredinia (in planta sample, 168 hours post-inoculation, hpi), in planta during biotrophic growth (96 hpi) and in resting urediniospores. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. The aim of this study was to determine gene expression in early telia formed in decaying poplar leaves in autumn before the overwintering process and to compare this expression with other stages of the poplar rust life cycle that were previously described (i.e., resting urediniospores as pure fungal material, and uredinia and biotrophic growth stage as poplar leaf infecting fungal structures). This study should highlight telia-specific transcripts and contribute to the understanding of the poplar rust biological cycle.

overall_design: We performed 12 hybridizations (NimbleGen) with samples derived from resting urediniospores (3 biological replicates), infected poplar leaves harvested at 96 and 168 hpi (3 biological replicates each) and Telia (3 biological replicates). All samples were labeled with Cy3.

first: S

last: Duplessis

last: Hacquard

last: Frey


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

status: Public on Feb 08 2014

first: Annegret

summary: 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.

sample_organism:
Populus trichocarpa
Laccaria bicolor

platform_organism:
Populus trichocarpa
Laccaria bicolor

overall_design: 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.

first: Jonathan

first: Emilie

last: Tisserant


title: Heterobasidion annosum gene expression from mycelium grown on different substrates

summary:
Transcript profiles of H. annosum from  mycelium grown on different substrates and under different stresses were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) H. irregulare genome sequence version 1.

One aim of this study was to compare gene expression profiles  of H. annosum  pre-grown on secondary metabolites from the biocontrol agent Phlebiopsis gigantea.

overall_design:
We performed six hybridizations with samples derived from H. annosum grown in either liquid Malt Extract Medium (three biological replicates) or on secondary metabolite from Phlebiopsis gigantea (three biological replicates).
The Heterobasidion irregulare custom-exon expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained five independent, non-identical, 60-mer probes per gene model coding sequence. For 12,199 of the 12,299 annotated protein-coding gene models, probes could be designed. For 19 gene models, no probes could be generated, and 81 gene models shared all five probes with other gene models. Included in the array were 916 random 60-mer control probes and labelling controls. For 2032 randomly chosen gene models, technical duplicates were included on the array.

first: Anthony

last: Mgbeahuruike

first: T

last: Raffaello

first: H

last: Chen

first: F

middle: O

last: Asiegbu


title: Genome-wide gene expression analysis on tibialis anterior muscle from nebulin SH3 domain deleted (Neb∆SH3) mice

status: Public on Sep 23 2013

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

summary: Genome-wide gene expression analysis on tibialis anterior muscle from 2-month-old nebulin SH3 domain deleted (Neb∆SH3) mice compared to wildtype.

overall_design: Total RNA was obtained from biological triplicates of tibialis anterior muscle from 2-month-old nebulin SH3 domain deleted (Neb∆SH3) mice compared to wildtype.

first: Marie-Louise

last: Bang

first: Alessandra

last: Castaldi

first: Daniel

middle: L

last: Yamamoto

first: Paolo

last: Kunderfranco


title: Effect of Laccaria bicolor, MiSSP7 from L.bicolor and Jasmonic acid on the Poplar transcriptome

last: Kohler

summary: This SuperSeries is composed of the SubSeries listed below.

platform_organism:
Populus trichocarpa
Populus tremula x Populus alba

overall_design: Refer to individual Series


title: Endometriosis transcription profiling

status: Public on Nov 30 2013

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: Endometriosis is a complex pathological condition in which multiple components are involved in the disease development and clinical outcome. Endometriosis is mainly an inflammatory codition estrogen-dependent, with unknown pathogenesis, that is characterized by dissemination of edometrium tissue in ectopic position (ovary or pelvic peritoneum).  Two main theories rise the pathologic onset: the presence of retrograde menstruation and celomic metaplasia in the pelvic peritoneum, that can occur for development defects. Endometriosis is related not only to genetic or immunological changes and to environmental pollution factors, as the endocrine interferents.  The disease phenotype results from multiple events (genetics and enviromental), thus it is difficult to find a single gene as causative while is more probable that a gene network/s might involved in the onset and mantainement of the disease state.  The peculiarity of endometriosis rely on the tissue speificity manteinance in the ectopic position, where it responds to the hormone stimuli as the tissue in the eutopic position.

overall_design: In order to identify genes potentially involved in growth and mainteinance of the ectopic endometrium, we have profiled ectopic (8 samples g-p) and eutopic endometrium (8 samples q-z) from several affected woman in the proliferative phase. As control we used endometrium from normal health donors in the same phase (6 samples a-f).

first: Stefania

last: Crispi

first: Aldo

last: Donizetti

first: MariaTeresa

last: Piccolo

first: MariaRosaria

last: Boccellino

first: Lucio

last: Quagliuolo

first: Pietro

last: Signorile

first: Alfonso

last: Baldi


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

status: Public on Mar 01 2013

first: Annegret

summary:
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).

sample_organism:
Corylus avellana
Tuber melanosporum

overall_design: 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.

first: Stéphane

last: Hacquard

first: Emilie

last: Tisserant

first: Annick

last: Brun

first: Valérie

last: Legué

first: Francis

last: Martin


title: Human regulatory T cells induce lymphocyte senescence

status: Public on Oct 03 2012

city: St. Louis

first: Guangyong

last: Peng

state: MO

address: 1100 S Grand Blvd.

department: Internal Medicine

country: USA

institute: Saint Louis University

summary: Analysis of gene alternations during the process of senescence induced by human regulatory T cells at various time points.

overall_design: Total RNA obtained from isolated regulatory T (Treg) cell-treated responder CD8+ T cells  compared to the untreated T cells


title: Adventitious root formation in Populus trichocarpa involves complex cellular events

status: Public on Nov 01 2012

summary: Stem cuttings of P. trichocarpa (clone 101-74) were rooted in liquid medium without growth regulators (basal medium). The first emerging roots were observed on cuttings 6 days after the start of culture. The highest average root number per cutting (10 ± 2 roots/cutting) was obtained after 14 days. The first macroscopic evidence of root initiation was the appearance of root primordia, as lateral bulges observed at the stem surface 3 to 4 days after transfer to basal medium. Stem cross-sections showed intensely dividing cells forming root primordial. One to two days later the bark split and the organized sequence of cell division and differentiation steps in the primordium led to the establishment of the main root tissues, as well as the vascular connections of the incipient root with the pre-existing stem vasculature. Subsequently, the outgrowth and emergence of the adventitious root occurred. We refer to the dormant cutting as stage 0, the organizing primordium as stage 1, the primordium differentiation as stage 2. To examine changes in gene transcription associated with the development of adventitious roots, we monitored the transcript levels in differentiating primordia using microarrays. cDNA was prepared from replicate sets of P. trichocarpa rooted cuttings harvested at stages 0, 1 and 2.

overall_design:
The Populus whole-genome expression array version 2.0 manufactured by NimbleGen Systems
Limited (Madison, WI) contains in duplicates three independent, non-identical, 60-mer
probes per whole gene model plus control probes and labeling controls. Included in the
microarray are 65,965 probe sets corresponding to 55,970 gene models predicted on the P.
trichocarpa genome sequence version 1.0 and 9,995 aspen cDNA sequences (Populus
tremula, Populus tremuloides, and P. tremula x P. tremuloides). NimbleGen whole genome
microarray analyses were performed in triplicate as per manufacturers instructions. We
carried out nine hybridizations (NimbleGen) with samples derived from three early developmental stages of P. trichocarpa adventitious roots. cDNA was synthesized using CLONTECH Smart cDNA Synthesis kit containing an amplification step on
the cDNA level. All samples were labeled with Cy3.

first: Adeline

last: Rigal


title: Early infection of poplar leaves by the rust pathogen Melampsora larici-populina

status: Public on Sep 01 2012

summary: The identification of early-expressed pathogen effectors and early-modulated host functions is currently a major goal to understand the molecular basis of biotrophic lifestyle. Melampsora larici-populina isolates 98AG31 and 93ID6, respectively virulent and avirulent on the hybrid P. trichocarpa x P. deltoides poplar cultivar ‘Beaupré’ were used in this study. Inoculations were performed on 5 cm2 leaf disks. The following conditions were used for oligoarrays: Incompatible 18, 21 and 24 hpi, Compatible 18, 24 and 48hpi. One aim of this study was to compare RNA-Seq and hybridization-based approaches, therefore the cDNA templates were used for whole-genome poplar oligoarrays and 454-pyrosequencing.

overall_design: We performed 6 hybridizations (Nimblegen) with samples derived from incompatible (18, 21 and 24hpi) and compatible (18, 24 and 48hpi) interactions of Melampsora larici-populina with P. trichocarpa x P. deltoides poplar cultivar ‘Beaupré’ leaves. All samples were labeled with Cy3.

first: Benjamin

last: Petre

first: Pascal

last: Frey

first: Sébastien

last: Duplessis


title: Analysis of gene expression across developmental stages of Agaricus bisporus

status: Public on Oct 01 2012

last: Kohler

summary: Utilising a whole genome array, we have investigated the differential expression of genes across different developmental stages in the life cycle of Agaricus bisporus.

overall_design: Four biological replicates of each developmental stage (culture, casing, compost, fruiting body) were analysed.

first: Adam

middle: R

last: Baker

first: Kerry

middle: S

last: Burton

first: Emmanuelle

last: Morin

first: Mike

middle: P

last: Challen

first: Daniel

last: Eastwood


title: Gene expression of Laccaria bicolor S238N free-living mycelium grown on different media

status: Public on Mar 01 2012

summary: Transcript profiles of Laccaria bicolor S238N mycelium on various media were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Laccaria bicolor genome sequence version 1. One goal was to evaluate the effect of nutrient deprivation on the transcriptome of Laccaria bicolor.

overall_design: We performed 15 hybridizations (Roche-NimbleGen) with samples derived from Laccaria bicolor free-living mycelium grown on MMN medium, on MMN with a 10 times reduction in all major macro-elements, on MMN with a 10 times reduction in the quantity of glucose or onto agar medium supplemented with the same nutrients used to fertilize our mycorrhization experiments.

first: Jonathan

last: Plett


title: Laccaria bicolor gene expression in different tissues and with different host trees

status: Public on Dec 15 2011

first: Annegret

summary: Laccaria bicolor transcript profiles of different tissues and mycorrhizal root tips from different host trees were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Laccaria bicolor genome sequence version 1. One goal was to compare gene expression profiles from ectomycorrhizal root tips with different host plants.

sample_organism:
Pseudotsuga menziesii
Populus trichocarpa
Populus deltoides
Laccaria bicolor S238N-H82

overall_design: We performed 12 hybridizations (Roche-NimbleGen) with samples derived from Laccaria bicolor free-living mycelium and from Populus trichocarpa, P. deltoides and douglas fir ECM.

first: Eva

last: Lucic

first: Martina

last: Peter


title: Heterobasidion irregulare gene expression from different tissues and mycelium grown on different substrates

status: Public on Mar 15 2012

summary:
Transcript profiles of Heterobasion irregulare from different tissues and mycelium grown on different substrates were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI,
department of energy) Heterobasidion annosum genome sequence version 1. One aim of this study
was to verify the expression of the automatically annotated gene models under various
conditions. Another goal was to compare gene expression profiles from different tissues of Heterobasidion irregulare and from mycelium grown on liquid MMN medium, liquid medium amended with lignin or cellulose and on wood.

overall_design:
The Heterobasidion annosum custom-exon expression array (4 x 72K) manufactured byRoche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products
/exp/index.html) contained five independent, nonidentical, 60-mer probes per gene model
coding sequence. For 12,199 of the 12,299 annotated protein-coding gene models probes
could be designed. For 19 gene models no probes could be generated and 81 gene models
shared all five probes with other gene models. Included in the array were 916 random
60-mer control probes and labelling controls. For 2032 randomly chosen gene models,
technical duplicates were included on the array. We performed 18 hybridizations (NimbleGen)
with samples derived from Heterobasidion irregulare fruiting bodies (four biological replicates) , from necrotic bark of pines inoculated with H. irregulare (21dpi; three biological replicates), from H. irregulare mycelium grown in liquid MMN medium (three biological replicates) as well as from H. irregulare grown on wood shavings from pine (four biological replicates), grown in liquid medium amended with lignin  (2 biological replicates) and growth in liquid medium amended with cellulose from Spruce  (2 biological replicates). Cultures were harvested after 3 weeks of incubation 22°C in darkness. All samples were labeled with Cy3.

first: Åke

last: Olson

first: Kerstin

last: Dalman

first: Magnus

last: Karlsson

first: Carl

last: Fossdal

first: Matteo

last: Garbelotto

first: Emilie

last: Tisserant

first: Jan

last: Stenlid


title: Altered PtAIL1 expression is accompanied by significant transcriptome changes during adventitious rooting induction

summary: Oligoarray analysis was used to identify genes differentially expressed in 2 mm sections of the basal stem region of wild type T89, PtAIL1 over-expressing or PtAIL1 RNAi lines of P. tremula x Populus tremuloides 24h and 72h after adventitious rooting induction.

overall_design: The Populus trichocarpa custom-exon expression array (12x135K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained three independent, nonidentical, 60-mer probes per gene model coding sequence. Included in the oligoarray were 43,929 annotated gene models (Populus trichocarpa genome v2 ; Phytozome 5.0), 5,859 random 60-mer control probes and labelling controls. We performed 27 hybridizations from wildtype,  PtAIL1 over-expressing or PtAIL1 RNAi lines of P. tremula x Populus tremuloides at time 0, 24h and 72h after adventitious rooting induction. For each timepoint we performed three biological replicates.

first: Adeline

last: Rigal

first: Anna

last: Karlberg

first: Valérie

last: Legué

first: Rishi

last: Bhalerao

first: Francis

last: Martin


title: The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices

status: Public on Nov 01 2011

last: Kohler

summary: The virtual transcriptome of G. intraradices (based on >430,000 reads) served as the basis for the design of an EST expresson array and for a number of analyses of gene expression in germinating spores, extraradical mycelium (ERM) and symbiotic root tissues.

sample_organism:
Medicago truncatula
Oryza sativa
Rhizophagus intraradices

overall_design: The G. intraradices EST expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained three independent, non identical, 60-mer probes per sequence. Included in the oligoarray were 22,402 G. intraradices sequences, 5785 random 60-mer control probes and labeling controls. We performed 12 hybridisations with samples from germinating spores (three biological replicates), extraradical mycelium (three biological replicates), symbiotic root tissues from Medicago (three biological replicates) and rice (1 replicate) as well as from microdissected arbuscule-colonized cortical cells of Medicago and rice (1 replicate each).

first: Raffaella

last: Balestrini

first: S

middle: K

last: Gomez

first: Nuria

last: Ferrol

first: Uta

last: Paszkowski

first: Christophe

last: Roux

first: Maria

last: Harrisson

first: Pascale

last: Seddas


title: Heterobasidion annosum gene expression from different tissues and mycelium grown on different substrates and under different biotic and abiotic stresses

first: Annegret

summary:
Transcript profiles of H. annosum from different tissues and mycelium grown on different substrates and under different stresses were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) H. irregulare genome sequence version 1.

One aim of this study was to compare gene expression profiles of H. annosum grown on different substrates and under different biotic and abiotic stresses.

overall_design:
We performed  hybridizations (NimbleGen) with samples derived from H. annosum grown in either liquid Malt Extract Medium at 20°C (three biological replicates), under NaCl stress (three biological replicates), under CaCl2 stress (three biological replicates), at 8°C (three biological replicates), at 27°C (three biological replicates), saprotrophic growth on Scots pine sapwood (three biological replicates), bark (three biological replicates) or heartwood (three biological replicates). Additional hybridizations were performed with RNA from necrotrophic growth of Heterobasidion on Scots pine xylem (three biological replicates), necrotrophic growth on Scots pine phloem (three biological replicates), under nutrient starvation (three biological replicates) or under oxidative stress (three biological replicates).

The Heterobasidion irregulare custom-exon expression array (4 x 72K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained five independent, non-identical, 60-mer probes per gene model coding sequence. For 12,199 of the 12,299 annotated protein-coding gene models, probes could be designed. For 19 gene models, no probes could be generated, and 81 gene models shared all five probes with other gene models. Included in the array were 916 random 60-mer control probes and labelling controls. For 2032 randomly chosen gene models, technical duplicates were included on the array.

first: T

last: Raffaello

first: H

last: Chen

first: E

last: Jaber

first: A

first: F

last: Asiegbu


title: The transcriptome of poplar roots incubated with MiSSP7, a secreted effector protein of Laccaria bicolor

status: Public on Jun 01 2011

summary:
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.

overall_design: The Populus trichocarpa custom-exon expression array (12x135K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained three independent, nonidentical, 60-mer probes per gene model coding sequence. Included in the oligoarray were 43,929 annotated gene models (Populus trichocarpa genome v2 ; Phytozome 5.0), 5,859 random 60-mer control probes and labelling controls. We performed six hybridizations, three biological replicates from poplar roots inoculated with MiSSP7 peptide for one hour and three biological replicates from control roots.

first: Jonathan

last: Plett

first: Emilie

last: Tisserant


title: Melampsora larici-populina gene expression in different tissues and development stages

status: Public on Apr 30 2011

summary: The transcriptome of Melampsora-larici-populina was analysed in urediniospores, germlings and infected Poplar leaves. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. One aim of this study was to verify the expression of the automatically annotated gene models in various tissues and development stages. Another goal was to monitor gene expression at different developmental stages and to highlight tissue-specific transcripts, e.g. in planta up-regulated transcripts for further analyses.

overall_design: We performed 9 hybridizations (Nimblegen) with samples derived from urediniospores, germlings and infected Poplar leaves (three replicates each). Samples from infected leaves were harvested 96 hours post infection. All samples were labeled with Cy3.

first: Sébastien

last: Duplessis

first: Stéphane

last: Hacquard

first: Pascal

last: Frey


title: Serpula lacrymans gene expression on different substrates

status: Public on Jul 01 2011

last: Kohler

summary: Transcript profiles of Serpula lacrymans grown on different substrates were analyzed. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, department of energy) Serpula lacrymans genome sequence version 1. One aim of this study was to verify the expression of the automatically annotated gene models under various conditions. Another goal was to compare gene expression profiles from Serpula lacrymans grown on liquid MMN medium and on wood.

overall_design: We performed 9 hybridizations (NimbleGen) with samples derived fromfrom Serpula lacrymans grown on liquid MMN medium and on wood.

first: Nils

last: Högberg

first: Katarina

last: Ihrmark

first: Anna

last: Rosling

first: Jan

last: Stenlid

first: Francis

last: Martin


title: Comparison of gene expression in roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor

status: Public on Jan 15 2011

summary: The majority of trees live in association with symbiotic fungi, which facilitate their access to soil nutrients. The ectomycorrhizal symbiosis represents a complex biological system involving multifaceted interactions between the two partners. The establishment of the symbiosis depends on various conditions (e.g. climate), but also on the genetic traits of the partners. To evaluate the impact of the genetic predisposition on the development and functioning of ectomycorrhizas, we compared the transcriptome of roots from Populus trichocarpa and Populus deltoides colonized with Laccaria bicolor.

sample_organism:
Populus trichocarpa
Populus deltoides

overall_design: The Populus whole-genome expression array version 2.0 (S. DiFazio, A. Brunner, P. Dharmawardhana, and K. Munn, unpublished data) manufactured by NimbleGen Systems Limited (Madison, WI) contains in duplicates three independent, non-identical, 60-mer probes per whole gene model plus control probes and labeling controls. Included in the microarray are 65,965 probe sets corresponding to 55,970 gene models predicted on the P.trichocarpa genome sequence version 1.0 and 9,995 aspen cDNA sequences (Populus tremula, Populus tremuloides, and P. tremula x P. tremuloides). NimbleGen whole genome microarray analyses were performed in triplicate as per manufacturer's instructions. We carried out six hybridizations (NimbleGen) with samples derived from Populus trichocarpa  and Populus deltoides mycorrhizal root tips. Three samples (biological replicates) originated from Populus trichocarpa (GSM648401, GSM648403, GSM648405) and three biological replicates from Populus deltoides (GSM648408, GSM648411, GSM648414). cDNA was synthesized using CLONTECH Super Smart cDNA Synthesis kit containing an amplification step on the cDNA level. All samples were labeled with Cy3.

first: Eva

last: Lucic

first: Annick

last: Brun

first: Jessy

last: Labbé

first: Francois

last: Le Tacon


title: The black truffle of Perigord responds to a temperature shift with an extensive reprogramming of its transcriptional activity

status: Public on Sep 15 2010

first: Annegret

summary: Taking advantage of the availability of the Tuber melanosporum genome sequence and a whole-genome microarray, we wanted to test the hypothesis that the transition from a growth temperature of 24-25°C to a cold one (4°C) is perceived by the filamentous fungus at the transcriptomic level and we wanted to identify and characterize the genes involved in this stress response.

overall_design:
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 (3 control and 3 treated) with samples derived from liquid cultures of T. melanosporum Mel28. After a month, some flasks were moved to 4°C for 1 week. After this period, the mycelium was collected from the treated (from 25°C to 4°C) and the untreated (25°C) control cultures. All samples were labeled with Cy3.

first: Elisa

last: Zampieri

first: Raffaella

last: Balestrini

first: Simona

last: Abbà

first: Paola

last: Bonfante


title: Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations

status: Public on Jul 26 2011

city: Cambridge

first: Albert

middle: W

last: Cheng

state: MA

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

type:
Genome variation profiling by SNP array
Expression profiling by array

summary: This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series

first: Frank

last: Soldner


title: Poplar-Laccaria: A Timecourse of Mycorrhizal Root Tip Development

status: Public on Oct 09 2014

summary: 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.

overall_design: 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.

first: J

last: Plett

first: A

first: F


title: Identification of genes expressed in maize root cortical cells during lysigenous aerenchyma formation using laser microdissection and microarray analyses

status: Public on Aug 01 2010

city: Chikusa-ku

first: Mikio

last: Nakazono

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

summary:
Aerenchyma is a specialized tissue consisting of longitudinal gas spaces, which enables internal movement of gases (e.g., O2, CO2, ethylene and methane), in plant roots, petioles and stems. Especially, internal transport of oxygen via aerenchyma from shoots to roots is very important for adaptation or survival of plants under waterlogged condition.
To identify aerenchyma formation-associated genes expressed in maize root, we used LM combined with a microarray for monitoring genes expressed in root cortical cells under three conditions: under aerobic condition and under waterlogged condition with and without pretreatment with 1-MCP, an inhibitor of ethylene perception.

overall_design: For the waterlogging treatments, the primary root (but not the shoots) was waterlogged. Two and half day-old-seedlings were pre-treated with an inhibitor of ethylene perception 1-methylcyclopropene (1-MCP; 1 ppm) for 12 hours before the waterlogging treatment. Three-day-old seedlings were growing under aerated condition at the same time with other treatments as a control. Total RNA was extracted from root cortex cells from the segment of the primary root, 0.5 cm long: from 1.5 to 2 cm from the junction shoot-root derived from 3-days-old maize seedlings, and subjected to 44k oligo-DNA microarray (1. Aerated vs Hypoxia, 2. Hypoxia+MCP vs Hypoxia) with 3 biological replicates and color swaps.

first: Imene

last: Rajhi

first: Takaki

last: Yamauchi

first: Hirokazu

last: Takahashi

first: Shunsaku

last: Nishiuchi

first: Katsuhiro

last: Shiono

first: Yoshiaki

last: Nagamura

first: Nobuhiro

last: Tsutsumi

first: Naoko

last: Nishizawa


title: Tuber melanosporum gene expression in different tissues

status: Public on Apr 01 2010

first: Annegret

last: Kohler

summary:
The Transcriptome of different tissues and developmental stages of Tuber melanosporum was analyzed. The array probes were designed from gene models taken from the French Genoscope - Centre National de Séquençage Tuber melanosporum genome sequence version 1. 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 for further detailed analyses.

overall_design:
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 16 hybridizations (NimbleGen) with samples derived from various tissues. Four samples were originated from ectomycorrhizae, five samples derived
from fruiting bodies and seven samples from free-living
mycelium . All samples were labeled with Cy3.

first: Emmanuelle

last: Morin

first: Elisa

first: Gérard

last: Chevalier

first: Francis

last: Martin


title: Melampsora larici-populina gene expression in different tissues and developmental stages

status: Public on Jun 10 2011

summary: The transcriptome of Melampsora-larici-populina was analysed in urediniospores, germlings and during poplar leaf infection. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. One aim of this study was to verify the expression of the automatically annotated gene models in various tissues and development stages. Another goal was to monitor gene expression profiles during poplar leaf infection and to highlight tissue-specific transcripts, e.g. in planta up-regulated transcripts for further analyses.

overall_design: We performed 21 hybridizations (NimbleGen) with samples derived from urediniospores, germlings and infected poplar leaves. Samples from infected poplar leaves were harvested 2, 6, 12, 24, 48, 96, and 168 hours post infection (hpi). Three replicates each for 24, 48, 96 and 168 hpi. All samples were labeled with Cy3.

first: Sébastien

last: Duplessis

first: Stéphane

last: Hacquard

first: Emilie

last: Tisserant

first: Pascal

last: Frey


title: Expression profiling of in vitro Poplar roots during early interaction with the ectomycorrhizal fungus Laccaria bicolor

status: Public on Nov 01 2009

summary: 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. A NimbleGen full genome poplar oligo-array was used to investigate transcript profiles at three days of indirect poplar/L. bicolor contact, referring to the time point of LR initiation in response to the fungus.

overall_design: The Populus whole-genome expression array version 2.0 (S. DiFazio, A. Brunner, P. Dharmawardhana, and K. Munn, unpublished data) manufactured by NimbleGen Systems Limited (Madison, WI) contains in duplicates three independent, non-identical, 60-mer probes per whole gene model plus control probes and labeling controls. Included in the microarray are 65,965 probe sets corresponding to 55,970 gene models predicted on the P. trichocarpa genome sequence version 1.0 and 9,995 aspen cDNA sequences (Populus tremula, Populus tremuloides, and P. tremula x P. tremuloides). NimbleGen whole genome microarray analyses were performed in triplicate as per manufacturers instructions. We carried out six hybridizations (NimbleGen) with samples derived from each six pooled, entire in vitro grown root systems on MES-buffered medium. Three samples (biological replicates) originated from control roots in the absence of L. bicolor (GSM415421, GSM417830, GSM417831) and another serie of three biological replicates consisted of roots from a three days indirect contact with L. bicolor (GSM417832, GSM417833, GSM417856). cDNA was synthesized using CLONTECH Smart cDNA Synthesis kit containing an amplification step on the cDNA level. All samples were labeled with Cy3.

first: Judith

last: Felten

first: Benoit

last: Hilselberger

first: Valérie

last: Legué


title: Melampsora larici-populina gene expression in different tissues of uredinia

status: Public on Jul 22 2010

summary: Laser Capture Microdissection (LCM) was used for expression analysis of three contrasted fungal tissues of uredinia corresponding respectively to spores and sporogenous hyphae, fungal structures in the spongy mesophyll and fungal infection structures in the palisade mesophyll. The array probes were designed from gene models taken from the Joint Genome Institute (JGI, Department of Energy) Melampsora larici-populina genome sequence version 1. The aim of this study was to identify tissue-specific gene expression to gain insights into the genes specifically associated with the biotrophic phase and the sporulation phase of the rust fungus.

overall_design:
We performed 9 hybridizations (NimbleGen) with samples derived from Laser Capture Microdissection (LCM) of three contrasted fungal tissues of uredinia, corresponding respectively to spores and sporogenous hyphae, fungal structures in the spongy mesophyll and fungal infection structures in the palisade mesophyll. Three replicates per tissue.
All samples were labeled with Cy3.


title: Laccaria bicolor S238N gene expression in different tissues

status: Public on Feb 01 2008

summary:
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

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

overall_design: The Laccaria whole-genome expression array manufactured by NimbleGen (Madison, WI) contains in duplicates eight independent, non-identical, 60-mer probes per whole gene model (taken from the Joint Genome Institute Laccaria bicolor genome sequence version 1.0). We performed 11 hybridizations (NimbleGen) with samples derived from various tissues and treatments. Four samples were originated from ectomycorrhizae, two of them derived from the symbiosis with poplar roots (GSM245987 and GSM245992), the others from the interaction with Douglas fir (GSM245993 and GSM245994). Two samples  derived from fruiting bodies (GSM245995 and GSM245996) and two samples from free-living mycelium (GSM245997 and GSM247052). The two free-living mycelium (GSM245997 and GSM247052) as well as the two Douglas fir mycorrhizae samples (GSM245993 and GSM245994) were biological replicates. In addition, free-living mycelium inoculated with sterile deionized water (GSM292146) or a bacterial suspension (GSM292155 and GSM292658) were analyzed. All samples were labeled with Cy3.

first: Frédéric

last: Duchaussoy