title: Microdissected Hartig net-1

status: Public on Mar 01 2013

data_processing: Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA). For information on RMA see Biostatistics 2003 Apr; 4(2): 249-264

organism:
Corylus avellana
Tuber melanosporum

source_name: Microdissected Hartig net

extract_protocol: Total RNA from microdissected samples were isolated using the PicoPure RNA isolation kit (Arcturus, Mountain View, CA, USA). A DNase treatment (Qiagen) was included during RNA isolation procedure to remove traces of genomic DNA. Elution was performed with 12 μl of pre-warmed DEPC Water (65°C). Quality and quantity of RNA samples were assessed using the Bio-Rad Experion analyzer and Experion RNA High-sens analysis kit (Bio-Rad). Total RNA from each sample was subjected to two rounds of amplification using the MessageAmp™ II aRNA amplification kit (Ambion, Austin, USA) following manufacturer’s instructions. For each sample, amplified RNA (aRNA) profiles were verified using the Experion analyzer and Experion RNA Standard-sens analysis kit (Bio-Rad). Double-stranded cDNA were synthesized from 3 μg of aRNA using the Superscript™ Double-Stranded cDNA Synthesis Kit (Life Technologies SAS, Saint Aubin, France).

treatment_protocol: Seedlings of hazelnut tree inoculated with T. melanosporum were produced by ROBIN PEPINIERES SARL (France). For each biological replicate, 5 ECM root tips were collected 4 months after fungal inoculation. After harvesting, ECM root tips were immediately fixed on ice in Farmer’s solution containing 75% (v/v) ethanol and 25% (v/v) acetic acid. The fixative Farmer’s solution was 3 times 5 min vacuum-infiltrated (400 mm Hg) and then let in contact with the ECM root tips overnight at 4°C. After Farmer’s solution removal, samples were dehydrated in graded series of ethanol (45 min each on ice (v/v) 75%, 80%, 90% and 3 times in absolute ethanol), followed by ethanol:otix+ (Microm Microtech, Francheville, France) series (45 min each on ice (v/v) 75:25%, 50:50%, 25:75% and 3 times in 100% Otix+). Samples were then transferred in pre-warmed 37°C melting point wax (VWR, Fontenay-sous-Bois, France) 5 times and then embedded at 58°C in paraffin (Diapath, Martinengo, Italy). Fifteen μm-sections were cut on a rotary microtome (Microm Microtech, Francheville, France) and transferred onto a microscope membrane-slide (Zeiss, Bernried, Germany) without water bath impregnation of paraffin ribbons. In order to improve adhesion between microscope slide and ribbons, slides were kept at 45°C during 1 hour to spread out ribbons and stored at -20°C under dehydrating conditions as previously reported. Just before LCM, slides were deparaffinized once in Otix+ for 10 min and then in otix+:ethanol series (3 min each (v/v) 67:33%, 33:67% and 2 times in absolute ethanol).For each biological replicate, 80 transversal sections obtained from 5 ECM root tips were analysed. For each section, three areas corresponding to soil fungal interface (i.e. mantle, M), plant fungal interface (i.e. Hartig net, HN) and internal root cells (mainly containing vascular cells, VC) were isolated using LCM. A PALM® Robot-Microbeam system (P.A.L.M. Microlaser Technologies AG, Bernried, Germany) was used to microdissect cells from deparaffinized and dried tissue sections. For each of the three biological replicates, the three microdissected areas were collected in distinct adhesive caps of 500 μl tubes (Zeiss) for further nucleic acids isolation.

value: Hartig net


title: Microdissected mantle-2

type: RNA

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

hyb_protocol: Hybridization by NimbleGen Company

scan_protocol: Scanning by NimbleGen Company

data_processing: Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA). For information on RMA see  Biostatistics 2003 Apr; 4(2): 249-264

molecule: total RNA

organism: Tuber melanosporum

source_name: Microdissected mantle

label_protocol: Labelling by NimbleGen Company

tag: tissue

value: mantle


title: Microdissected mantle-3


title: Tibialis anterior muscle from WT mouse_rep 3

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

description:
replicate 3
WT_3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using the LumiExpresso function of the lumi Bioconductor package in R (R_v.2.15.2, lumi_2.10.0).

label: biotin

organism: Mus musculus

source_name: Tibialis anterior muscle from WT

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent (Invitrogen), following the manufacturer's instructions. Quality control was performed with Agilent Bioanalyzer

tag: strain background

value: mixed Sv129/Black Swiss

tag: genotype/variation

value: wild type

tag: gender

value: male

tag: age

value: 8 weeks

value: Tibialis anterior


title: Tibialis anterior muscle from Neb∆SH3 mouse_rep 3

description:
replicate 3
Neb∆SH3_3

source_name: Tibialis anterior muscle from Neb∆SH3

value: nebulin SH3 domain deleted (Neb∆SH3)


title: PtAIL1 over-expressing line T72-1

status: Public on Nov 01 2012

organism: Populus tremula x Populus tremuloides

source_name: Stem bases of PtAIL1 over-expressing line after 72h of rooting

growth_protocol: Cuttings of hybrid aspen (Populus tremula x tremuloides) clone T89 (wild type) and the transgenic lines were grown in half-strength Murashige/Skoog medium (½ MS) under sterile conditions for approximately 4 weeks and then used for In vitro rooting experiments.

extract_protocol:
RNA was extracted using the RNeasy micro kit (QIAGEN). We added a first clean-up step with QIAshredder Mini Spin Columns (QIAGEN) and an on-column DNA digestion step with DNAse I (Qiagen). RNA quality
was verified by Experion StdSens capillary gels (Bio-Rad). Total RNA preparations were amplified using the SMARTer PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions.

tag: clone

value: 2mm of the stem base from the base of excised shoots

value: PtAIL1 over-expressing line

tag: time

value: 72 hr


title: Tibialis anterior muscle from Neb∆SH3 mouse_rep 1

description:
replicate 1
Neb∆SH3_1


title: Microdissected Hartig net-3


title: Tibialis anterior muscle from WT mouse_rep 1

description:
replicate 1
WT_1


title: Tibialis anterior muscle from WT mouse_rep 2

description:
replicate 2
WT_2


title: PtAIL1 RNAi line T24-2

source_name: Stem bases of PtAIL1 RNAi line after 24h of rooting

value: PtAIL1 RNAi line

value: 24 hr


title: Microdissected mantle-1


title: PtAIL1 RNAi line T24-1


title: PtAIL1 over-expressing line T72-2


title: Populus tremula x Populus tremuloides T89 wild type T72-2

source_name: Stem bases of Populus tremula x Populus tremuloides T89 wild type after 72h of rooting


title: Populus tremula x Populus tremuloides T89 wild type T72-3


title: Populus tremula x Populus tremuloides T89 wild type T72-1


title: Tibialis anterior muscle from Neb∆SH3 mouse_rep 2

description:
replicate 2
Neb∆SH3_2


title: PtAIL1 RNAi line T72-2

source_name: Stem bases of PtAIL1 RNAi line after 72h of rooting


title: Microdissected Hartig net-2


title: PtAIL1 over-expressing line T24-2

source_name: Stem bases of PtAIL1 over-expressing line after 24h of rooting


title: PtAIL1 RNAi line T72-1


title: Populus tremula x Populus tremuloides T89 wild type T24-3

data_processing: Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA). For information on RMA see Biostatistic 2003 Apr; 4(2): 249-264

source_name: Stem bases of Populus tremula x Populus tremuloides T89 wild type after 24h of rooting


title: PtAIL1 over-expressing line T72-3


title: PtAIL1 RNAi line T24-3


title: PtAIL1 over-expressing line T24-1


title: PtAIL1 RNAi line T72-3


title: Populus tremula x Populus tremuloides T89 wild type T24-1


title: PtAIL1 over-expressing line T24-3


title: Populus tremula x Populus tremuloides T89 wild type T24-2


title: PtAIL1 RNAi line T0-2

source_name: Stem bases of PtAIL1 RNAi line at time 0


title: PtAIL1 over-expressing line T0-2

source_name: Stem bases of PtAIL1 over-expressing line at time 0


title: PtAIL1 RNAi line T0-3


title: PtAIL1 over-expressing line T0-3


title: PtAIL1 over-expressing line T0-1


title: Populus tremula x Populus tremuloides T89 wild type T0-2

source_name: Stem bases of Populus tremula x Populus tremuloides T89 wild type at time 0


title: PtAIL1 RNAi line T0-1


title: Casing 2

status: Public on Oct 01 2012

description: Casing, this zone consists of fine and stranded/corded mycelium, and developmental stages to fruitbody primordia (including aggregates and hyphal knots, undifferentiated and differentiated primordia).

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent arrays (ID 027120) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then 10 seconds in acetonitrile and 30 seconds in Stabilization and drying solution (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent's High-Resolution C Scanner (G2505C US94100321) using one color scan setting for 8x60k array slides (Scan resolution 3um).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 027120_D_F_20100129) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw array data were Robust multichip average normalized using the ARRAYSTAR software (DNASTAR, Inc. Madison, WI, USA).

organism: Agaricus bisporus var. bisporus H97

source_name: Colonised casing

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the Quick Amp Labelling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Casing compost were grown in standard conditions.

extract_protocol: RNA was extracted from casing samples using a method based on the FastRNA Pro Soil-Direct kit (MP Biochemicals). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain

tag: developmental stage

value: casing


title: Fruiting bodies 4

description: Fruiting bodies represent the mature mushroom fruitbody (including the stipe, cap and pilei pellis (skin) tissues).

source_name: mature mushroom

growth_protocol: Fruitbody samples were grown in standard conditions.

extract_protocol: RNA was prepared from fruitbody samples using the standard Trizol protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: fruiting body


title: Populus tremula x Populus tremuloides T89 wild type T0-1


title: Fruiting bodies 2


title: Casing 3


title: Compost 3

description: Compost represents the mycelium growing in wheat straw compost. This mycelium is both fine (likely to be nutritional) and strands or cords (some secondary structure and thicker (clearly visible to the naked eye)). All vegetative mycelium.

source_name: mycelium growing in wheat straw compost

value: compost


title: Populus tremula x Populus tremuloides T89 wild type T0-3


title: Casing 4


title: Compost 1

growth_protocol: Compost represents the mycelium growing in wheat straw compost.


title: Compost 2


title: Casing 1


title: Compost 4


title: Fruiting bodies 1


title: Fruiting bodies 3


title: Culture 4

description: Culture represents mycelium growing on compost extract medium in agar plates (Calvo-Bado et al., 2000).

growth_protocol: Culture samples were grown in axenic culture on Compost Extract Medium (Calvo-Baldo, 2000).

extract_protocol: RNA was prepared from culture samples using the standard Trizol protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: culture


title: Root primordium differentiation stage 2 2

data_processing:
Procedure for spot detection was performed by NimbleGen Company. Expression values
reflect across-array quantile normalization and gene calls generated using the Robust
Multichip Average (RMA). For information on RMA see Biostatistics 2003 Apr; 4(2): 249-264

organism: Populus trichocarpa

source_name: Root primordium differentiation of Populus trichocarpa

growth_protocol: For rooting leafless, hardwood dormant stems, the hardwood dormant stems from Populus trichocarpa Torr. & Gray (clone 101-74) were collected from stool beds in January 2010, then cut into 25 cm cuttings (6-7 nodes). These were sealed in polyethylene bags and kept in cold storage (0°C) until removed for rooting. Selected cuttings had a diameter range of 0.8 to 1.1 cm. For rooting and growth, cuttings were sub-irrigated. Stage 2 corresponds to the differentiation of the root primordium.

extract_protocol: RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer's instructions.

tag: stage


title: Root primordium differentiation stage 2 3

value: Stage 2 corresponds to the differentiation of the root primordium.


title: Organizing root primordium stage 1 2

source_name: Organizing root primordium of Populus trichocarpa

growth_protocol: For rooting leafless, hardwood dormant stems, the hardwood dormant stems from Populus trichocarpa Torr. & Gray (clone 101-74) were collected from stool beds in January 2010, then cut into 25 cm cuttings (6-7 nodes). These were sealed in polyethylene bags and kept in cold storage (0°C) until removed for rooting. Selected cuttings had a diameter range of 0.8 to 1.1 cm. For rooting and growth, cuttings were sub-irrigated. Stage 1 corresponds to the organizing root primordium.


title: Root primordium differentiation stage 2 1


title: Culture 2

source_name: mycelium growing on compost extract medium


title: Culture 3


title: Culture 1


title: Dormant Cutting Stage 0 2

source_name: Dormant Cutting of Populus trichocarpa

growth_protocol: For rooting leafless, hardwood dormant stems, the hardwood dormant stems from Populus trichocarpa Torr. & Gray (clone 101-74) were collected from stool beds in January 2010, then cut into 25 cm cuttings (6-7 nodes). These were sealed in polyethylene bags and kept in cold storage (0°C) until removed for rooting. Selected cuttings had a diameter range of 0.8 to 1.1 cm. For rooting and growth, cuttings were sub-irrigated. Stage 0 corresponds to dormant cuttings at time 0


title: Organizing root primordium stage 1 3

value: Stage 1 corresponds to the organizing root primordium.


title: Organizing root primordium stage 1 1

value: Stage 1 corresponds to the organizing root primordium


title: Dormant Cutting Stage 0 3

value: Stage 0 corresponds to dormant cuttings at time 0


title: Dormant Cutting Stage 0 1


title: Leaf disks compatible interaction 48h

status: Public on Sep 01 2012

data_processing: Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA). For information on RMA, see Biostatistics 2003 Apr; 4(2): 249-264.

organism: Populus trichocarpa x Populus deltoides

source_name: Leaf disks inoculated for 48h with M. larici-populina isolate 98AG31

extract_protocol: Total RNA extraction and quantity/quality control were performed as described in Rinaldi et al. 2007.  RNA quality was verified by Experion StdSens capillary gels (Bio-Rad). Double-stranded (ds) cDNA were synthesized using the SMARTer PCR cDNA Synthesis Kit (Clontech, Saint-Germain-en-Laye, France), following manufacturer's instructions, with 0,5 µg of starting total RNA and 19 cycles of PCR amplification in 25µL. PCR products were purified with the QIAquick PCR Purification Kit (Qiagen, Couteboeuf, France) and quantified with a NanoDrop 1000 spectrophotometer (Labtech, Palaiseau, France).

tag: cultivar

value: 'Beaupré'

value: 5 cm2 leaf disks

tag: treatment

value: inoculation with Melampsora larici-populina isolate 98AG31

tag: treatment duration


title: Heterobasidion irregulare grown in liquid medium amended with lignin 1

status: Public on Mar 15 2012

description: Procedure for spot detection was performed by NimbleGen Company

data_processing:
Expression values reflect across-array quantile normalization and gene calls generated
using the Robust Multichip Average (RMA). For information on RMA see Biostatistics
2003 Apr; 4(2): 249-264

organism: Heterobasidion irregulare

extract_protocol:
Total RNA was extracted using CTAB/phenol/chloroform and LiCl precipitation. The
RNA was DNase I treated and cleaned with Qiagen RNA cleanup Kit.

tag: sample type

value: Heterobasidion irregulare grown in liquid medium amended with lignin (Kraft Pine lignin B 471003-500G; SIGMA-Aldrich), cultures were harvested after 3 weeks of incubation 22°C in darkness

tag: substrate

value: liquid medium with lignin


title: Leaf disks incompatible interaction 21h

source_name: Leaf disks inoculated for 21h with M. larici-populina isolate 93ID6

value: inoculation with Melampsora larici-populina isolate 93ID6


title: Leaf disks incompatible interaction 24h

source_name: Leaf disks inoculated for 24h with M. larici-populina isolate 93ID6


title: H. irregulare grown on wood shavings from pine 3

value: H irregulare grown on wood shavings from pine, cultures were harvested after 3 weeks of incubation 22°C in darkness

value: wood shaving from pine


title: Heterobasidion irregulare grown in liquid medium amended with lignin 2

value: Heterobasidion irregulare grown in liquid medium amended with lignin Cultures were harvested after 3 weeks of incubation 22°C in darkness


title: H. irregulare grown on wood shavings from pine 2

extract_protocol: Total RNA was extracted using CTAB/phenol/chloroform and LiCl precipitation. The RNA was DNase I treated and cleaned with Qiagen RNA cleanup Kit.


title: H. irregulare grown on wood shavings from pine 4


title: Heterobasidion irregulare fruiting bodies collected in California 3


title: H. irregulare mycelium grown in liquid MMN medium 3

value: H irregulare mycelium grown in liquid MMN medium Cultures were harvested after 3 weeks of incubation 22°C in darkness

value: liquid MMN medium


title: H. irregulare mycelium grown in liquid MMN medium 2

value: H irregulare mycelium grown in liquid MMN medium, cultures were harvested after 3 weeks of incubation 22°C in darkness


title: Leaf disks compatible interaction 18h

source_name: Leaf disks inoculated for 18h with M. larici-populina isolate 98AG31


title: Leaf disks incompatible interaction 18h

source_name: Leaf disks inoculated for 18h with M. larici-populina isolate 93ID6


title: H. irregulare grown on wood shavings from pine 1


title: Heterobasidion irregulare fruiting bodies collected in California 2


title: H. irregulare mycelium grown in liquid MMN medium 1


title: Heterobasidion irregulare fruiting bodies collected in California 4


title: Heterobasidion irregulare fruiting bodies collected in California 1


title: Heterobasidion irregulare grown in liquid medium amended with cellulose from Spruce 2

value: Heterobasidion irregulare grown in liquid medium amended with cellulose from Spruce (22182-KG Fluka; SIGMA-Aldrich) Cultures were harvested after 3 weeks of incubation 22°C in darkness

value: cellulose from spruce


title: necrotic bark of pines inoculated with Heterobasidion irregulare 1

value: Necrotic bark of pines inoculated with H irregulare for 21 days

value: Necrotic bark of pines


title: Heterobasidion irregulare grown in liquid medium amended with cellulose from Spruce 1

value: Heterobasidion irregulare grown in liquid medium amended with cellulose from Spruce (22182-KG Fluka; SIGMA-Aldrich), cultures were harvested after 3 weeks of incubation 22°C in darkness


title: necrotic bark of pines inoculated with Heterobasidion irregulare 2

value: necrotic bark of pines inoculated with Heterobasidion irregulare for 21 days


title: Free-living mycelium of Laccaria bicolor S238N MMN 0.1x glucose 10d-3

status: Public on Mar 01 2012

data_processing:
Expression values reflect
across-array quantile normalization and gene calls generated using the Robust Multichip Average
(RMA). For information on RMA see Biostatistics 2003 Apr; 4(2): 249-264

organism: Laccaria bicolor

growth_protocol: For nutrient deprivation experiments, L. bicolor colonies (grown on cellophane membranes) were started on MMN media for 15 days after which they were transferred to fresh MMN with a 10 times reduction in the quantity of glucose. Samples were harvested after another 10d in liquid nitrogen.

extract_protocol:
RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA preparations
were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the
manufacturer's instructions.

value: Free-living mycelium of Laccaria bicolor S238N  precultured for 15 days on MMN medium was transferred to fresh MMN with a 10 times reduction in the quantity of glucose and grown for another 10 days

value: Free-living mycelium

tag: growth condition


title: Free-living mycelium of Laccaria bicolor S238N MMN 0.1x glucose 10d-2

value: precultured for 15 days on MMN medium was transferred to fresh MMN with a 10 times reduction in the quantity of glucose and grown for another 10 days


title: Free-living mycelium of Laccaria bicolor S238N 0.1x MMN 10d-3

growth_protocol: For nutrient deprivation experiments, L. bicolor colonies (grown on cellophane membranes) were started on MMN media for 15 days after which they were transferred to fresh MMN with a 10 times reduction in all major macro-elements. Samples were harvested after another 10d in liquid nitrogen.

value: Free-living mycelium of Laccaria bicolor S238N  precultured for 15 days on MMN medium was transferred to fresh  MMN with a 10 times reduction in all major macro-elements and grown for another 10 days


title: Free-living mycelium of Laccaria bicolor S238N Nut 10d-1

growth_protocol:
For nutrient deprivation experiments, L. bicolor colonies (grown on cellophane membranes) were started on MMN media for 15 days after which they were transferred onto agar medium
supplemented with the same nutrients used to fertilize our myco-
rrhization experiments (2.5 mM KNO3, 0.8 mM KH2PO4, 1mM
MgSO4x7H2O, 2.3 mM Ca(NO3)2x4H2O, 23 µM H3BO3, 4.6 µM
MnCl2x4H2O, 0.4 ZnSO4x7H2O, 0.09 µM (NH4)2MoO4, 0.18 µM CuSO4x5H2O, 20 µM FeNaEDTA, pH 5.8). Samples were harvested after another 10d in liquid nitrogen.

value: Free-living mycelium of Laccaria bicolor S238N  precultured for 15 days on MMN medium was transferred onto agar medium supplemented with the same nutrients used to fertilize our mycorrhization experiments  and grown for another 10 days


title: necrotic bark of pines inoculated with Heterobasidion irregulare 3


title: Free-living mycelium of Laccaria bicolor S238N Nut 10d-3

value: Free-living mycelium of Laccaria bicolor S238N  precultured for 15 days on MMN medium was transferred tonto agar medium supplemented with the same nutrients used to fertilize our mycorrhization experiments  and grown for another 10 days


title: Laccaria/Populus trichocarpa ECM greenhouse-3

status: Public on Dec 15 2011

data_processing:
Expression values reflect across-array quantile normalization and gene calls
generated using the Robust Multichip Average (RMA). For information on RMA see
Biostatistics 2003 Apr; 4(2): 249-264

organism:
Populus trichocarpa
Laccaria bicolor S238N-H82

source_name: three-month old Laccaria/Populus ectomycorrizal tissue

extract_protocol:
RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA
preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech)
according to the manufacturer’s instructions

value: L. bicolor/P.trichocarpa ectomycorrhizae were synthesized by growing cuttings of Populus trichocarpa for three month in pots containing Terragreen (Brenntag Lorraine, Toul, France) mixed with fungal inoculum in a peat-vermiculite mix (4:1,v/v). Mycorrhizal root tips were harvested and immediately frozen in liquid nitrogen.

value: 3 months


title: Free-living mycelium of Laccaria bicolor S238N 0.1x MMN 10d-2

value: precultured for 15 days on MMN medium was transferred to fresh  MMN with a 10 times reduction in all major macro-elements and grown for another 10 days


title: Free-living mycelium of Laccaria bicolor S238N Nut 10d-2

value: Free-living mycelium of Laccaria bicolor S238N  precultured for 15 days on MMN medium was transferred tonto agar medium supplemented with the same nutrients used to fertilize our mycorrhization experiments and grown for another 10 days


title: Laccaria/Pseudotsuga ECM greenhouse-2

organism:
Pseudotsuga menziesii
Laccaria bicolor S238N-H82

source_name: nine-month old Laccaria/Pseudotsuga ectomycorrizal tissue

value: Ectomycorrhizae of L. bicolor/Pseudotsuga menziesiia were synthesized by growing Pseudotsuga menziesii seedlings for nine month in polyethylene containers filled with a peat-vermiculite mix (1:1, v/v) and mixed with 2.5% (v/v) fungal inoculum.

value: 9 months


title: Laccaria/Populus deltoides ECM greenhouse-3

organism:
Populus deltoides
Laccaria bicolor S238N-H82

value: L. bicolor/P.deltoides ectomycorrhizae were synthesized by growing cuttings of Populus deltoides for three month in pots containing Terragreen (Brenntag Lorraine, Toul, France) mixed with fungal inoculum in a peat-vermiculite mix (4:1,v/v). Mycorrhizal root tips were harvested and immediately frozen in liquid nitrogen.


title: Free-living mycelium of Laccaria bicolor S238N 0.1x MMN 10d-1


title: Free-living mycelium of Laccaria bicolor S238N T0-3

growth_protocol: For nutrient deprivation experiments, L. bicolor colonies (grown on cellophane membranes) were started on MMN media for 15 days after which they were transferred to fresh MMN media. T0 samples were harvested immediately in liquid nitrogen.

value: Free-living mycelium of Laccaria bicolor S238N T0 precultured for 15 days on MMN medium

value: precultured for 15 days on MMN medium


title: Laccaria/Populus trichocarpa ECM greenhouse-2


title: Free-living mycelium of Laccaria bicolor S238N T0-1


title: Free-living mycelium of Laccaria bicolor S238N T0-2


title: Laccaria/Populus trichocarpa ECM greenhouse-1


title: Laccaria/Pseudotsuga ECM greenhouse-3

value: Ectomycorrhizae of L. bicolor/Pseudotsuga menziesiia were synthesized by growing Pseudotsuga menziesii seedlings for nine month in polyethylene containers filled with a peat-vermiculite mix (1:1, v/v) and mixed with 2.5% (v/v) fungal inoculum


title: Free-living mycelium of Laccaria bicolor S238N MMN 0.1x glucose 10d-1


title: Free-living mycelium of Laccaria bicolor S238N-2

data_processing:
Procedure for spot detection was performed by NimbleGen Company
Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA). For information on RMA see Biostatistics 2003 Apr; 4(2): 249-264

organism: Laccaria bicolor S238N-H82

source_name: three-weeks-old free-living mycelium of Laccaria bicolor S238N

growth_protocol: Free-living mycelium of L. bicolor S238N was grown onto cellophane-covered agar plates containing Pachlewski medium, and was grown for three weeks before harvesting the proliferating hyphal tips at the periphery.

value: 3 weeks


title: Free-living mycelium of Laccaria bicolor S238N MMN 10d-2

growth_protocol: For nutrient deprivation experiments, L. bicolor colonies (grown on cellophane membranes) were started on MMN media for 15 days after which they were transferred to fresh MMN media. Samples were harvested after another 10d in liquid nitrogen.

value: Free-living mycelium of Laccaria bicolor S238N  precultured for 15 days on MMN medium then transferred to fresh MMN medium for another 10 d


title: Laccaria/Pseudotsuga ECM greenhouse-1


title: Laccaria/Populus deltoides ECM greenhouse-2


title: Free-living mycelium of Laccaria bicolor S238N MMN 10d-3

value: Free-living mycelium

value: precultured for 15 days on MMN medium then transferred to fresh MMN medium for another 10 d


title: Free-living mycelium of Laccaria bicolor S238N MMN 10d-1


title: Free-living mycelium of Laccaria bicolor S238N-3

value: free-living mycelium of Laccaria bicolor S238N


title: Free-living mycelium of Laccaria bicolor S238N-1


title: G. intraradices-inoculated roots of M. truncatula 2

status: Public on Nov 01 2011

organism:
Medicago truncatula
Rhizophagus intraradices

source_name: G. intraradices-inoculated roots of M. truncatula (A17) 27dpi

extract_protocol: Total RNA was extracted from mycorrhizal roots with Trizol reagent (Invitrogen Corporation, Carlsbad, CA) with additional phenol (pH 6.6): chloroform (1:1, v/v) and chloroform purification steps. RNA from mycorrhizal roots was treated with Turbo DNase I (Ambion Inc., Austin, TX), and column purified with an RNeasy MinElute CleanUp kit (Qiagen). RNA quality and integrity were checked prior to cDNA synthesis using the Bio-Rad Experion analyzer and Experion RNA StdSens analysis kit. Total RNA preparations (three biological replicates) were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions.

tag: tag

value: M. truncatula (cv. A17) plants (two trifoliate leaf stage) were grown in pots with 10 plants per pot and inoculated with 1,000 G. intraradices spores per plant. The experiment included three pots (three biological replicates) of mock-inoculated plants and three pots of G. intraradices -inoculated plants. Plants were fertilized with 100 mL/pot of Hoagland solutions containing full strength nitrogen and low Pi (20uM), twice weekly. Roots were harvested at 27 days post inoculation and frozen in liquid nitrogen.


title: Extraradical mycelium 2

organism: Rhizophagus intraradices

source_name: ERM of G. intraradices grown on liquid M medium without sucrose for three weeks

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen) with RLT lysis buffer. RNA quality and integrity were checked prior to cDNA synthesis using the Bio-Rad Experion analyzer and Experion RNA StdSens analysis kit. Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions.

value: ERM of G. intraradices was grown on liquid M medium without sucrose (M-C) for three weeks before harvesting.


title: Laccaria/Populus deltoides ECM greenhouse-1

tag: tissue


title: G. intraradices-inoculated roots of M. truncatula 1

value: M. truncatula (cv. A17) plants (two trifoliate leaf stage) were grown in pots with 10 plants per pot and inoculated with 1,000 G. intraradices spores per plant. Plants were fertilized with 100 mL/pot of Hoagland solutions containing full strength nitrogen and low Pi (20uM), twice weekly. Roots were harvested at 27 days post inoculation and frozen in liquid nitrogen.


title: Serpula on wood 10d-1

status: Public on Jul 01 2011

organism: Serpula lacrymans var. lacrymans S7.9

source_name: Serpula was grown on wood for 10d

growth_protocol: serpula: Shavings of Pinus sylvestris (L.) sapwood were put on moist soil separated with a nylon net for a period of ten days at 20oC and 50% relative humidity.

extract_protocol:
The RNA was extracted from the culture isolates using a 2% cetyltrimethyl ammonium bromide (CTAB) protocol.
50-100ng total RNA was used to synthesize first strand cDNA. First and second stand cDNA synthesis and amplification was performed using the SMARTer™ pico PCR cDNA synthesis kit and Advantage ® 2 PCR kit from Clontech, according to the protocol from the manufacturer. The quantity of the cDNA was analyzed with NanoDrop and Qubit™ fluorometer from Invitrogen. The quality was determined using 2100 Bioanalyzer from Agilent Technologies.

tag: growth


title: Microdissected arbuscule-colonized cortical cells from Rice

organism:
Oryza sativa
Rhizophagus intraradices

extract_protocol: Total RNA was extracted from microdissected arbuscule-colonized cortical cells using the Ambion RNAqueous®-Micro Kit  according to the manufacturer's instructions.   Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions.


title: Microdissected arbuscule-colonized cortical cells from Medicago

extract_protocol: Total RNA were extracted from microdissected arbuscule-colonized cells using the Pico Pure Kit (Arcturus Engineering). DNase treatment of total RNA was performed using RNAse-free DNase Set (Qiagen). RNA quality and integrity were checked prior to cDNA synthesis using a Bio-Rad Experion analyzer and Experion RNA StdSens analysis kit. Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions.

value: For LMD, M. truncatula seedlings were inoculated with G. intraradices using the Millipore sandwich method described by Guether et al. (2009a). After about two months, mycorrhizal roots were dissected into 5 mm pieces and placed in RNase-free tubes containing freshly prepared Farmer's fixative (absolute ethanol/glacial acetic acid 3:1 v/v). After a step under vacuum at room temperature for 20 min, fixative solution was changed and root samples were incubated overnight at 4°C. Roots were then dehydrated in a graded series of ethanol (70, 90, 100 and 100 % in sterilized water) followed by two steps in Neoclear (Merck), with each step on ice for 30 min. Neoclear was gradually replaced with paraffin (Paraplast Plus; Sigma). About 10 Paraplast Plus chips were added to 20 ml of fresh Neoclear and samples were leaved for 2 h at room temperature and then for 3 h at 58 °C. Once the chips dissolved at 58 °C, the mixture was replaced with molten Paraplast Plus at 58 °C, and the medium was changed twice approximately at 4-5 h intervals before embedding in pure paraffin. Root samples were embedded in paraffin in Petri dishes and stored at 4 °C. A Leica AS LMD (Leica Microsystem, Inc) was used to collect 10,000 arbuscule-colonized cortical cells from paraffin root sections as described by Balestrini et al. (2007).


title: Serpula on wood 10d-2

value: Shavings of Pinus sylvestris (L.) sapwood were put on moist soil separated with a nylon net for a period of ten days at 20oC and 50% relative humidity.


title: Mycelium MMN medium 10d-1

source_name: Mycelium grown on liquid MMN medium for 10d

growth_protocol: mycelium: grown on liquid MMN medium for 10d

value: grown on liquid MMN medium for 10d


title: Serpula on wood 30d-3

source_name: Serpula was grown on wood for 30d

growth_protocol: serpula: Shavings of Pinus sylvestris (L.) sapwood were put on moist soil separated with a nylon net for a period of 30 days at 20oC and 50% relative humidity.


title: Mycelium MMN medium 10d-3


title: Germinating spores 3

source_name: Spores germinated in M medium at 30°C, 2% CO2 during 24 h

value: For control, 100,000 sterile spores were placed during 24 h in 6 ml of M medium at 30°C, 2% CO2 (Chabot et al., 1992). During this period, few emerging hyphae were formed. These germinated (control) spores corresponded to spores metabolically active without significant contamination by new hyphae.


title: Serpula on wood 30d-2

value: Shavings of Pinus sylvestris (L.) sapwood were put on moist soil separated with a nylon net for a period of 30 days at 20oC and 50% relative humidity.


title: Serpula on wood 10d-3


title: Extraradical mycelium 1


title: Germinating spores 2


title: G. intraradices-inoculated roots of rice

extract_protocol: Total RNA was extracted from mycorrhizal roots using the NucleoSpin Plant RNA extraction kit according to the manufacturer's instructions (Macherey-Nagel).  RNA quality and integrity were checked prior to cDNA synthesis using the Bio-Rad Experion analyzer and Experion RNA StdSens analysis kit. Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions.

value: Rice seeds were surface-sterilized twice with 3.5% sodium hypochloride solution for 15 min, washed extensively with sterile water, and pregerminated in sterile water for 5 d at 25°C in the dark. Germlings were transplanted into washed and autoclaved quartz sand and inoculated upon planting with ∼1000 Glomus intraradices spores per plant from a commercially available inoculum (Biorize). Plants were harvested at 6 wpi


title: Serpula on wood 30d-1


title: 2 hpi infected leaves 1

status: Public on Jun 10 2011

organism: Melampsora laricis-populina

source_name: infected leaves

extract_protocol:
RNA extraction was carried out using the RNeasy Plant Mini kit (Qiagen). Total RNA
preparations were subjected to a single round of amplification using the
MessageAmp™ II aRNA amplification kit (Ambion).

value: derived from infected leaves

value: 2h post infection


title: Extraradical mycelium 3


title: Mycelium MMN medium 10d-2


title: 12 hpi infected leaves 1

value: 12h post infection


title: G. intraradices-inoculated roots of M. truncatula 3


title: 6 hpi infected leaves 1

value: 6h post infection


title: Germinating spores 1


title: Leaf disks compatible interaction 24h

source_name: Leaf disks inoculated for 24h with M. larici-populina isolate 98AG31

value: 'Beaupré'

value: 5 cm2 leaf disks

value: inoculation with Melampsora larici-populina isolate 98AG31


title: 168 hpi infected leaves 3

data_processing:
Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA).
For information on RMA see Biostatistics 2003 Apr; 4(2): 249-264.

source_name: infected leaves, 168hpi

growth_protocol: Poplar leaves were infected by M. larici-populina 98AG31 strain and harvested 168 hours after urediniospores inoculation.

extract_protocol: RNA extraction was carried out using the RNeasy Plant Mini kit (Qiagen). Total RNA preparations were subjected to a single round of amplification using the MessageAmp™ II aRNA amplification kit (Ambion).

value: 168h post infection


title: 168 hpi infected leaves 2


title: 168 hpi infected leaves 1


title: 48 hpi infected leaves 3

source_name: infected leaves, 48hpi

growth_protocol: Poplar leaves were infected by M. larici-populina 98AG31 strain and harvested 48 hours after urediniospores inoculation.

value: 48h post infection


title: 48 hpi infected leaves 1


title: 48 hpi infected leaves 2


title: 24 hpi infected leaves 3

source_name: infected leaves, 24hpi

growth_protocol: Poplar leaves were infected by M. larici-populina 98AG31 strain and harvested 24 hours after urediniospores inoculation.

value: 24h post infection


title: Dried-urediniospores 1

status: Public on Apr 30 2011

data_processing:
Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA).
For information on RMA see Biostatistics 2003 Apr; 4(2): 249-264.
The normalized data were generated using ArrayStar (DNAStar) software.

source_name: urediniospores

growth_protocol: M. larici-populina urediniospores (98AG31 strain) were multiplicated on detached leaves of susceptible P. deltoides x Populus nigra ‘Robusta’, harvested and stored under dehydrating conditions.

value: urediniospores


title: Dried-urediniospores 3


title: Germlings 3

source_name: germlings

growth_protocol: M. larici-populina germlings were obtained from uredinispores (98AG31 strain) grown on water agar medium (2%) in petri dishes for 3 hours.

value: germlings


title: 96 hpi infected leaves 3

source_name: infected leaves, 96hpi

growth_protocol: Poplar leaves were infected by M. larici-populina 98AG31 strain and harvested 96 hours after urediniospores inoculation.

value: 96h post infection


title: Germlings 1


title: 24 hpi infected leaves 2


title: 24 hpi infected leaves 1


title: 96 hpi infected leaves 1


title: Dried-urediniospores 2


title: 96 hpi infected leaves 2


title: Germlings 2


title: Free-living mycelium 4°C 2

status: Public on Sep 15 2010

hyb_protocol: Hybridization by NimblGen Company

scan_protocol: Scanning by NimblGen Company

data_processing:
Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA).
For information on RMA, see Biostatistics 2003 Apr; 4(2): 249-264

organism: Tuber melanosporum

source_name: free-living mycelium, 4°C

label_protocol: Labelling by NimblGen Company

growth_protocol: The fungus was grown in flasks containing 50 ml of malt 1% liquid medium. The cultures were maintained in a dark room at 25°C. After four weeks, the flasks were moved to 4°C for 1 week.

extract_protocol: RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions

value: free-living mycelium


title: Free-living mycelium 4°C 3


title: Control roots 1h-1

status: Public on Jun 01 2011

scan_protocol: Scan by NimbleGen Company

data_processing: Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA). For information on RMA, see Biostatistics 2003 Apr; 4(2): 249-264

organism: Populus tremula x Populus alba

source_name: Mock-inoculated roots from P.tremula x alba INRA clone7171B4

extract_protocol: RNA was extracted using the RNAeasy kit (Qiagen) as per the manufacturer’s instructions with the addition of 20 mg PEG8000/mL to the extraction RLC buffer solution and an on-column DNA digestion step. with DNAse I (Qiagen). RNA quality was verified by Experion HighSens capillary gels (Bio-Rad). Total RNA preparations were amplified using the SMARTer PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions.

value: Poplar roots were exposed to a fluorescently treatmentged synthetic version of the MiSSP7 protein produced by Pi Proteomics (Huntsville, Alabama). Young roots of live 717-1B4 plants were acclimatized to new  MS medium for 30 minutes prior to the addition of the MiSSP7 peptide to a final concentration of 3.4 μM in DMSO or of DMSO alone (control). Rooted plants were incubated in this solution for one hour in the light at 24C.


title: MiSSP7 incubated roots 1h-2

source_name: MiSSP7 incubated roots from P.tremula x alba INRA clone7171B4

extract_protocol: RNA was extracted using the RNAeasy kit (Qiagen) as per the manufacturer’s instructions with the addition of 20 mg PEG8000/mL to the extraction RLC buffer solution and an on-column DNA digestion step with DNAse I (Qiagen). RNA quality was verified by Experion HighSens capillary gels (Bio-Rad). Total RNA preparations were amplified using the SMARTer PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions.

value: Poplar roots were exposed to a fluorescently treatmentged synthetic version of the MiSSP7 protein produced by Pi Proteomics (Huntsville, Alabama). Young roots of live 717-1B4 plants were acclimatized to new  MS medium for 30 minutes prior to the addition of the MiSSP7 peptide to a final concentration of 3.4 μM. Rooted plants were incubated in this solution for one hour in the light at 24C.


title: Free-living mycelium 4°C 1


title: MiSSP7 incubated roots 1h-3

value: Poplar roots were exposed to a fluorescently treatmentged synthetic version of the MiSSP7 protein produced by Pi Proteomics (Huntsville, Alabama). Young roots of live 717-1B4 plants were acclimatized to new MS medium for 30 minutes prior to the addition of the MiSSP7 peptide to a final concentration of 3.4 μM. Rooted plants were incubated in this solution for one hour in the light at 24C.


title: MiSSP7 incubated roots 1h-1

extract_protocol: RNA was extracted using the RNAeasy kit (Qiagen) as per the manufacturer’s instructions with the addition of 20 mg PEG8000/mL to the extraction RLC buffer solution and an on-column DNA digestion step with DNAse I (Qiagen). RNA qualityb was verified by Experion HighSens capillary gels (Bio-Rad). Total RNA preparations were amplified using the SMARTer PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions.

value: Poplar roots were exposed to a fluorescently treatmentged synthetic version of the MiSSP7 protein produced by Pi Proteomics (Huntsville, Alabama). Young roots of live 717-1B4 plants were acclimatized to new (hormoneless) MS medium for 30 minutes prior to the addition of the MiSSP7 peptide to a final concentration of 3.4 μM. Rooted plants were incubated in this solution for one hour in the light at 24C.


title: Control roots 1h-3


title: Uredinial stage spongy mesophyll 2

status: Public on Jul 22 2010

data_processing:
Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA).
For information on RMA, see Biostatistics 2003 Apr; 4(2): 249-264.

source_name: Uredinial stage spongy mesophyll

growth_protocol: Poplar leaves were infected by M. larici-populina strain 98AG31 and harvested at the uredinial stage 7 days after urediniospores inoculation.

extract_protocol: Laser Capture Microdissection was used to isolate uredinia tissues. RNA extraction was carried out using the PicoPure RNA isolation kit (Arcturus). Total RNA preparations were subjected to two rounds of amplification using the MessageAmp™ II aRNA amplification kit (Ambion).

value: uredinial stage spongy mesophyll


title: Control roots 1h-2

value: Poplar roots were exposed to a fluorescently treatmentged synthetic version of the MiSSP7 protein produced by Pi Proteomics (Huntsville, Alabama). Young roots of live 717-1B4 plants were acclimatized to new (hormoneless) MS medium for 30 minutes prior to the addition of the MiSSP7 peptide to a final concentration of 3.4 μM in DMSO or of DMSO alone (control). Rooted plants were incubated in this solution for one hour in the light at 24C.


title: Uredinial stage spongy mesophyll 3


title: Free-living mycelium 6

status: Public on Apr 01 2010

source_name: free-living mycelium

growth_protocol: Five-week-old liquid culture of Tuber melanosporum Mel 28 grown in 1% malt medium at 25°C.


title: Free-living mycelium 5


title: Free-living mycelium 2

description:
Six-month old liquid culture of Tuber melanosporum Mel 28 grown in 1% malt
medium
Procedure for spot detection was performed by NimbleGen Company

source_name: Tuber melanosporum free-living mycelium

value: Free-living mycelium


title: Uredinial stage palissade mesophyll 3

source_name: Uredinial stage palissade mesophyll

value: uredinial stage palissade mesophyll


title: Uredinial stage spongy mesophyll 1


title: Free-living mycelium 7

description:
Four-month old liquid culture of Tuber melanosporum Mel 28 grown in 1% malt
medium
Procedure for spot detection was performed by NimbleGen Company


title: Uredinial stage palissade mesophyll 2


title: Uredinial stage palissade mesophyll 1


title: Uredinial stage spores 2

source_name: Uredinial stage spores

value: uredinial stage spores


title: Ectomycorrhizal root tip 3

description:
Ectomycorrhizal root tips were harvested from hazelnut trees which were inoculated
five month before by AGRITRUFFE
Procedure for spot detection was performed by NimbleGen Company

organism:
Corylus avellana
Tuber melanosporum

source_name: Ectomycorrhizal root tip Tuber-Hazelnut tree

value: Ectomycorrhizal root tip


title: Fruiting body 3

description:
Fruiting body was harvested in December 2007 by Mr Matern in Lerouville/Meuse/France under hazelnut trees
Procedure for spot detection was performed by NimbleGen Company

source_name: Fruiting body Lerouville/Meuse/France

value: Fruiting body


title: Free-living mycelium 4


title: Ectomycorrhizal root tip P.trichocarpa 3

status: Public on Jan 15 2011

hyb_protocol: Hybridization by NimbleGen Company.

scan_protocol: Scanning by NimbleGen Company.

source_name: three-month-old Laccaria bicolor/Populus trichocarpa ectomycorrizal tissue

label_protocol: Labelling by NimbleGen Company.

growth_protocol: Populus trichocarpa ecm were synthesized by growing cuttings for three months in pots containing terragreen mixed with fungal inoculum (Laccaria bicolor) in a peat-vermiculite mix (4:1, v/v). Mycorrhizal root tips were harvested and immediately frozen in liquid nitrogen.

extract_protocol: RNA extraction was carried out using the RNeasy Micro Kit (Qiagen). Total RNA preparations were amplified using the SUPER SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer's instructions.

value: mycorrhizal root tips

value: 3 months


title: Free-living mycelium 3


title: Ectomycorrhizal root tip P.deltoides 3

organism: Populus deltoides

source_name: three-month-old Laccaria bicolor/Populus deltoides ectomycorrizal tissue

growth_protocol: Populus deltoides ecm were synthesized by growing cuttings for three months in pots containing terragreen mixed with fungal inoculum (Laccaria bicolor) in a peat-vermiculite mix (4:1, v/v). Mycorrhizal root tips were harvested and immediately frozen in liquid nitrogen.


title: Ectomycorrhizal root tip P.trichocarpa 2

organism: Populus trichocarpa


title: Ectomycorrhizal root tip P.trichocarpa 1


title: Uredinial stage spores 3


title: Uredinial stage spores 1


title: Free-living mycelium 1

description:
Four-month old liquid culture of Tuber melanosporum Mel 28 grown in 1% malt medium
Procedure for spot detection was performed by NimbleGen Company


title: Ectomycorrhizal root tip 4

description:
Ectomycorrhizal root tips were harvested from hazelnut trees which were inoculated
one year before by AGRITRUFFE
Procedure for spot detection was performed by NimbleGen Company


title: Ectomycorrhizal root tip 1

description:
Ectomycorrhizal root tips were harvested from hazelnut trees which were inoculated five month before by AGRITRUFFE
Procedure for spot detection was performed by NimbleGen Company


title: Fruiting body 1

description:
Fruiting body was collected by Ms Brechard in December 2006 in Auvergne/France, sample received from G Chevalier
Procedure for spot detection was performed by NimbleGen Company

source_name: Fruiting body Auvergne/France


title: Fruiting body 2

description:
Fruiting body was collected by Mr Matern in February 2008 in Lerouville/Meus/France under a hazelnut tree
Procedure for spot detection was performed by NimbleGen Company


title: Fruiting body 5

description:
Fruiting body was collected by Mr Raquillet in Ascoli Piceno/Italy
Procedure for spot detection was performed by NimbleGen Company

source_name: Fruiting body Ascoli Piceno/Italy


title: Ectomycorrhizal root tip 2


status: Public on Aug 01 2008

data_processing: Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA). For information on RMA see Biostatistics 2003 Apr; 4(2): 249-264.

source_name: free-living mycelium of Laccaria bicolor S238N; inoculated with a Pseudomonas fluoresecens BBc6R8 bacterial suspension in a 1.75cm distance

extract_protocol: Total RNA was extracted using Trizol as recommended by the manufacturer for small quantities of material (Invitrogen AB, Stockholm, Sweden). RNA was further purified using the RNA/DNA mini kit (Qiagen, Hilden, Germany).Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions.

tag: Laccaria bicolor S238N

tag: An in vitro confrontation bioassay was developed using 9-cm-diameter Petri dishes containing 20 ml per plate of a Pachlewski medium containing 0.5 g tartrate, 1 g KH2PO4, 0.5 g MgSO4, 1 g glucose, 1 ml 1/10 diluted Kanieltra microelement solution and 20 g agar l–1 at pH 5.5 (P20Th-). A plug of L. bicolor S238N was cut out from the edge of a colony grown on P5 medium and transferred into the centre of a P20Th– plate. Four 10 μl droplets of bacterial suspension (bacterial treatment) were distributed at 1.75 cm from the centre of the fungal plug. Plates were sealed with plastic tape and incubated at 10°C in the dark. Mycelium was harvested at day 14 before physical contact of the bacterial and fungal colonies (Deveau et al. 2007 New Phytol 175:743-755).


title: Ectomycorrhizal root tip P.deltoides 2

tag: age


title: free-living mycelium of Laccaria bicolor S238N; mock-inoculated

tag: An in vitro confrontation bioassay was developed using 9-cm-diameter Petri dishes containing 20 ml per plate of a Pachlewski medium containing 0.5 g tartrate, 1 g KH2PO4, 0.5 g MgSO4, 1 g glucose, 1 ml 1/10 diluted Kanieltra microelement solution and 20 g agar l–1 at pH 5.5 (P20Th-). A plug of L. bicolor S238N was cut out from the edge of a colony grown on P5 medium and transferred into the centre of a P20Th– plate. Four 10 μl droplets of sterile deionized water (control treatment) were distributed at 1.75 cm from the centre of the fungal plug. Plates were sealed with plastic tape and incubated at 10°C in the dark. Mycelium was harvested at day 14. (Deveau et al. 2007 New Phytol 175:743-755)


title: Laccaria/Pseudotsuga ECM greenhouse 2

status: Public on Feb 01 2008

description: Laccaria/Pseudotsuga ECM greenhouse 2

source_name: nine-month old Laccaria/Pseudotsuga ectomycorrizal tissue

growth_protocol: Ectomycorrhizae of L. bicolor/Pseudotsuga menziesii were synthesized by growing Pseudotsuga menziesii seedlings for nine month in polyethylene containers filled with a peat-vermiculite mix (1:1, v/v) and mixed with 2.5% (v/v) fungal inoculum. RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer's instructions.

tag: Laccaria and Pseudotsuga ectomycorrizal tissue

tag: Age

value: 9 month

tag: interaction with Douglas fir


title: Free-living mycelium Laccaria bicolor S238N 1

source_name: three-weeks-old free-living mycelium of Laccaria bicolor S238N

growth_protocol: Free-living mycelium of L. bicolor S238N was grown onto cellophane-covered agar plates containing Pachlewski medium, and was grown for three weeks before harvesting the proliferating hyphal tips at the periphery. RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer's instructions.

value: 3 weeks


title: Laccaria/Pseudotsuga ECM greenhouse 1

description: Laccaria/Pseudotsuga ECM greenhouse 1

extract_protocol: RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer's instructions.


title: Mature fruiting bodies

description: Mature fruiting bodies

source_name: mature fruiting bodies hat and stem

growth_protocol: Mature fruiting bodies of L. bicolor S238N were collected below Douglas fir seedlings grown in a greenhouse and inoculated using L. bicolor S238N. RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer's instructions.

tag: mature fruiting bodies hat and stem


title: Laccaria/Populus ECM greenhouse

description: Laccaria/Populus ECM greenhouse

source_name: three-month old Laccaria/Populus ectomycorrizal tissue

growth_protocol: L. bicolor/P.trichocarpa ectomycorrhizae were synthesized by growing cuttings of Populus trichocarpa for three month in pots containing Terragreen (Brenntag Lorraine, Toul, France) mixed with fungal inoculum in a peat-vermiculite mix (4:1, v/v). Mycorrhizal root tips were harvested and immediately frozen in liquid nitrogen. RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer's instructions.

tag: Laccaria and Populus ectomycorrizal tissue

tag: symbiosis with poplar roots


title: free-living mycelium of Laccaria bicolor S238N; inoculated-II


title: Young fruiting bodies

description: Young fruiting bodies

source_name: young fruiting bodies of Laccaria bicolor S238N

growth_protocol: Young fruiting bodies of L. bicolor S238N were collected below Douglas fir seedlings grown in a greenhouse and inoculated using L. bicolor S238N. RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer's instructions.


title: Free-living mycelium Laccaria bicolor S238N 2

tag: free-living mycelium of Laccaria bicolor S238N


title: Laccaria/Populus ECM in vitro

description: Laccaria/Populus ECM in vitro

organism:
Populus tremula x Populus alba
Laccaria bicolor S238N-H82

source_name: one-month old Laccaria/Populus ectomycorrizal tissue

growth_protocol: L. bicolor/P.tremula x alba ectomycorrhizae were synthesized by growing in vitro Populus tremula x alba (INRA clone 717-1B4) plantlets together with fungal inoculum for one month as described in (Handbook of Methods used in Rhizosphere research, 2006, editors Joerg Luster and Roger Finlay, p399, Swiss Federal Research Institute WSL). RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer's instructions.

value: 1 month


title: 3d indirect contact 1

status: Public on Nov 01 2009

description:
Populus tremula x alba INRA clone 717-1B4
Roots were in indirect contact with Laccaria bicolor for 3d.
Indirect contact was
made on cellophane on buffered P20 medium (12g/l agar, 1g/l MES).

source_name: Roots in indirect contact with Laccaria bicolor

growth_protocol:
Entire root systems of 4-6 weeks old poplar plants(Populus tremula x alba INRA clone
717-1B4) (6 plants/sample) from cuttings, grown in vitro on MS !. Plants were grown for
one week on MS with 2mg/l IBA to synchronize root development and then transferred for
three weeks to normal MS medium without IBA. Laccaria bicolor mycelium was grown on
carbon reduced Pachlewski medium (P20) (12g/l agar) for 10 days. Indirect contact was
made on cellophane on buffered P20 medium (12g/l agar, 1g/l MES). Control samples were
covered with cellophane membranes Samples were harvested after 3 days indirect contact,
which was realized in a phytotron (16hrs light/ 8hrs dark) at 24°C on 12x12 cm petri
dishes, half covered with a black plastic bag.

extract_protocol:
RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA
preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according
to the manufacturer's instructions.

value: root


title: Ectomycorrhizal root tip P.deltoides 1


title: 3d indirect contact 2

description:
Populus tremula x alba INRA clone 717-1B4
Roots were in indirect contact with Laccaria bicolor for 3d. Indirect contact was made on
cellophane on buffered P20 medium (12g/l agar, 1g/l MES).


title: 3d Control 1

description:
Populus tremula x alba INRA clone 717-1B4
Poplar control roots
Control samples were covered with cellophane membranes

source_name: Control roots


title: 3d Control 3

source_name: Control plant


title: 3d Control 2

growth_protocol:
Entire root systems of 4-6 weeks old poplar plants(Populus tremula x alba INRA clone 717-1B4) (6 plants/sample) from cuttings, grown in vitro on MS ½.
Plants were grown for one week on MS with 2mg/l IBA to synchronize root development and then transferred for three weeks to normal MS medium without IBA.
Laccaria bicolor mycelium was grown on carbon reduced Pachlewski medium (P20) (12g/l agar) for 10 days.
Indirect contact was made on cellophane on buffered P20 medium (12g/l agar, 1g/l MES).
Control samples were covered with cellophane membranes
Samples were harvested after 3 days indirect contact, which was realized in a phytotron (16hrs light/ 8hrs dark) at 24°C on 12x12 cm petri dishes, half covered with a black plastic bag.


title: 3d indirect contact 3


title: Fruiting body 4

description:
Fruiting body was collected by Mr Dessolas in October 2007 in St Front d'Alemps/Dordogne/France under oak trees
Procedure for spot detection was performed by NimbleGen Company

source_name: Fruiting body St Front d'Alemps/Dordogne/France

extract_protocol:
RNA extraction was carried out using the RNeasy Plant Mini Kit (Qiagen). Total RNA
preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech)
according to the manufacturer’s instructions