title: Bark of MIR15-2

status: Public on May 07 2015

description: This sample is from bark of MIR15 plants. It is the second of two biological replicates used in this experiment.

data_processing:
Illumina sofware was used by Beckman Coulter Genomics to generate fastq raw data files
Raw reads from two MIR15 and two WT samples were trimmed and aligned to Populus trichocarpa v3.0 reference transcripts (http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa; Ptrichocarpa_210_transcript_primaryTranscriptOnly) using CLC Genomics Workbench 7. For mapping, the minimum length fraction was 0.9, the minimum similarity fraction 0.8 and the maximum number of hits for a read was set to 10. The unique and total mapped reads number for each transcript were determined. A pair was counted as two, a single read as one. The DESeq software package (Anders et al. 2010) in Bioconductor in R was then used to normalize the total mapped reads and to identify differentially expressed transcripts (P <0.05).
Genome_build: http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa; Ptrichocarpa_210_transcript_primaryTranscriptOnly
Supplementary_files_format_and_content: tab-delimited text files including unique aligned reads, total aligned reads and DESEQ normalised values for each sample

organism: Populus tremula x Populus alba

growth_protocol: Wild type (WT) and transgenic poplars (Populus tremula x P. alba, clone INRA 717-1B4) were grown aseptically on Woody Plant Medium (Duchefa Biochemie) supplemented with 50 mg/l kanamycin when needed, at 24 ± 0.5°C under a 16h light photoperiod. Acclimatized plants were cultivated in soil in a growth chamber at 24 ± 0.5°C under a 16h light photoperiod.

extract_protocol:
Total RNA was extracted using Tri-Reagent (Sigma-Aldrich) according to the manufacturer’s instructions.
cDNA libraries were prepared for sequencing using standard Illumina protocols by Beckman Coulter Genomics (Danvers, MA, USA)

tag: clone id

value: clone INRA 717-1B4

value: MIR15 transgenic

value: bark


title: Bark of MIR15-1

type: SRA

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

description: This sample is from bark of MIR15 plants. It is the first of two biological replicates used in this experiment.

library_source: transcriptomic

molecule: total RNA

tag: genotype/variation

tag: tissue


title: Control grown in liquid medium 2

status: Public on Oct 01 2015

type: RNA

description: This sample is from liquid medium. It is the second of three  biological replicates used in this experiment.

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.

organism: Heterobasidion annosum

source_name: liquid medium

label_protocol: Labelling by NimbleGen Company

growth_protocol: Topsoil (organic layer) from the different sites was taken to the lab. 20g topsoil with one pine wood chip (1x1x1cm) in the flask was autoclaved followed by inoculation with H. annosum s.s (1x1cm agar plug). After 4 months incubation at 20°C, the total RNA was extracted from the topsoil. As control H. annosum was grown in liquid malt extract medium and harvested after  three weeks incubation at 20°C in the dark.

extract_protocol: Total RNA was extracted by using the CTAB/Chloroform and LiCl precipitation. The RNA was DNase I treated and cleaned with RNeasy® MinElute Cleanup kit (QIAGEN) according to the protocol. RNA concentration and quality were measured by using Agilent RNA 6000 Nano Kit and Bioanalyzer (Agilent Technologies). cDNA was synthesized by using the TransPlex® Complete Whole Transcriptome Amplification Kit (SIGMA) according to the protocol

value: mycelium

tag: developmental stage

value: three weeks


title: Bark of wildtype-2

description: This sample is from bark of wildtype plants. It is the second of two biological replicates used in this experiment.

value: wildtype


title: 3w ECM-2

status: Public on Jun 22 2015

description: This sample is from mycorrhizal root tips. It is the second of three biological replicates used in this experiment.

source_name: 3w ectomycorrhizal root tip

growth_protocol: Pre-rooted stem cuttings of P. tremula x P. alba (rooted for 4 weeks on in vitro agar half strength Murashig and skoog medium) were preparded. In parallel, Laccaria bicolor inoculum was grown on in vitro agar Pachlewski medium  (2.7 mM di-ammonium tartrate, 7.3 mM KH2PO4, 2.0 mM MgSO4·7 H2O, 13 mM maltose, 110 mM glucose, 2.9 µM thiamine-HCl, and 1 mL of a trace-element stock solution Kanieltra medium) for 10 days.   Roots were destructively harvested at 3 weeks after being put into contact with L. bicolor. Control roots without contact with the fungus were harvested at the same time points.

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: mycorrhizal root tip

tag: infection

value: Laccaria bicolor S238N


title: Control grown in liquid medium 1

description: This sample is from liquid medium. It is the first of three  biological replicates used in this experiment.


title: Whole leaves compatible interaction 24h

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: Entire detached leaves inoculated for 24h 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: entire detached leaves

tag: treatment

value: inoculation with Melampsora larici-populina isolate 98AG31

tag: treatment duration


title: 3w ECM-3

description: This sample is from mycorrhizal root tips. It is the third of three  biological replicates used in this experiment.


title: Bark of wildtype-1

description: This sample is from bark of wildtype plants. It is the first of two biological replicates used in this experiment.


title: Mycorrhizal roots-2

status: Public on Feb 06 2015

description: This sample is from  mycorrhizal roots. It is the second of three biological replicates used in this experiment.

data_processing:
Illumina sofware was used by IGA to generate fastq raw data files
Reads were aligned to Sebacina vermifera  (http://genome.jgi-psf.org/Sebve1/Sebve1.home.html)  reference transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Sebacina vermifera (http://genome.jgi-psf.org/Sebve1/Sebve1.home.html)
Supplementary_files_format_and_content: tab-delimited text files include transcript length,unique aligned reads, total aligned reads and RPKM values for each sample

organism: Serendipita vermifera

source_name: Mycorrhizal roots

growth_protocol: Arabidopsis thaliana seeds (Ecotype Columbia-0) were incubated for 5 min in 70%  ethanol, surface sterilized for 5 min with 6% sodium hypochlorite and washed 6 times  for 5 min in sterile water. After stratification for 3 days at 4°C in the dark on 1/10 PNM  medium, Arabidopsis seedlings were grown for 14 days under sterile conditions in a  phytochamber (Vötsch, Balingen-Frommern, Germany) at long day conditions (day: 16  h, 23°C, 350 μmol m-2 s-1; night: 8 h, 18°C). S. vermifera strain was grown on MYP (7  g malt extract, 1 g peptone, 0.5 g yeast extract and 12 g agar) agar plates or liquid MYP  with 120 rpm shaking at 25°C. Seven-day-old S. vermifera culture was filtered through  miracloth filter and the mycelium was washed with 0.9% NaCl. Mycelium was crushed  for 10 seconds in fresh MYP using a sterile blender (Microtron MB 550, Kinematica  AG). 20 ml of crushed mycelium was inoculated in 130 ml MYP and regenerated for 3  days at 25°C with 130 rpm shaking. For inoculation of S. vermifera with Arabidopsis,  fourteen-day-old germlings were inoculated with 5 g crashed fungal mycelium in 5 ml  0.9% NaCl solution for 2 h or 0.9% NaCl mock treated. S. vermifera inoculated plants,  of approximately the same size, were transferred to square petri dishes containing 1/10  PNM and the roots were treated with either 1 ml of crushed fungal biomass (1 g/ml in  0.9% NaCl solution) per 20 seedlings or mock treated. The first four cm of the roots  below the seed were excised and immediately frozen in liquid nitrogen for RNA  extraction at 3, 7 and 14 days post inoculation. For each time point roots from 80 to 100  plants were harvested and the experiments were performed in 3 independent biological  repetitions.

extract_protocol:
Total RNA from 200 mg of ground material was extracted using TRIzol  (Invitrogen, Karlsruhe, Germany) following the manufacturer’s instructions. Prior RNA  extraction, plant materials harvested at 3, 7 and 14 dpi from the same independent  biological experiment were pooled together. As control total RNA from 3 independent  biological replicates of seven-day-old S. vermifera grown in MYP medium was used.  RNA samples were additionally precipitated with ethanol. In brief, 1/10 volume of 3 M  NaOAc and 3 volumes of ethanol were added to RNA solution. After incubation at -  20°C overnight, the RNA pellet was centrifuged at 13000 rpm for 30 min and washed  once with 70% ethanol (diluted in DEPC ddH2O) and spin down for 10 min. The RNA  pellet was then air-dried and resuspended in RNase-free water with a final concentration  of 1 μg/μl. Purity and quantity of RNA samples were measured using the NanoDrop  ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and  Agilent RNA 6000 Nano Kit and Agilent 2100 Bioanalyzer following the  manufacturer’s protocol (Agilent, Santa Clara, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology Services (Udine , Italy)

tag: host

value: Arabidopsis thaliana

value: Mycorrhizal roots


title: Ectomycorrhizal roots-2

description: This sample is from  mycorrhizal roots. It is the second of two biological replicates used in this experiment.

data_processing:
Illumina sofware was used by IGA to generate fastq raw data files
Reads were aligned to Paxillus involutus (http://genome.jgi-psf.org/Paxin1/Paxin1.home.html) reference transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Paxillus involutus (http://genome.jgi-psf.org/Paxin1/Paxin1.home.html)
Supplementary_files_format_and_content: tab-delimited text files including transcript length,unique aligned reads, total aligned reads and RPKM values for each sample

organism: Paxillus involutus

source_name: Ectomycorrhiza

growth_protocol: Mycelium patches and mycorrhizas were prepared as described in Wright et al. In  brief, ECM association between birch and P. involutus was synthesized using a  cellophane-agar Petri-dish system. Seeds of birch were surface-sterilized and then  transferred aseptically to water agar plates until germination occurred. Nine-d-old  seedlings were aseptically transferred to the edge of 9-d-old colonies of P. involutus  growing on sheets of autoclaved cellophane placed over MMN agar containing 5.55 m  glucose. After 4 wk mycorrhizal seedlings were transferred to pots containing  unamended sphagnum peat to which four plugs of P. involutus mycelium were added.  These pots were enclosed within a propagator, to maintain high humidity, and placed in  a growth chamber at a day/night temperature of 18/15°C with a 16-h photoperiod and  80% relative humidity for 4 wk. After approximately 3 wk, once the extramatrical  mycelium had colonized approximately two-thirds of the microcosm, two nutrient  patches were placed into each chamber in advance (1 cm) of the mycelial front. Each  nutrient patch consisted of a shallow plastic dish filled with autoclaved fine quartz sand  (Sigma-Aldrich Sweden AB, Stockholm, Sweden) to which 1.5 ml of 1 mM  (NH4)2SO4 was applied initially. Subsequently, 0.5 ml of 1 mM (NH4)2SO4 was  applied weekly for 4 wk to allow extensive hyphal development within the patch and  the formation of mycelial rhizomorphs which link the mycelium within the nutrient  patch to the mycorrhizal root tips.In order to obtain a sufficient sample for total RNA  extraction, material of each tissue type was pooledfrom three microcosms to produce  one biological replicate. All material was immediately frozen in liquid N2 and stored  at−80°C until use.

extract_protocol:
Total RNA was immediately isolated from each sample using the  RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions, except  that PEG6000 (20 mg ml−1) (Merck KgaA, Darmstadt, Germany) and β-  mercaptoethanol (10 μl l−1) were added to the RLC buffer. Total RNA preparations  were inspected using a BioAnalyzer and the Total RNA Nano Series II kit (Agilent).
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology Services (Udine , Italy)

value: Betula pendula

value: Ectomycorrhiza


title: Mycelium patches-2

description: This sample is from free-living mycelium. It is the second of two biological replicates used in this experiment.

source_name: Mycelium patches

value: Mycelium patches


title: Ectomycorrhizal roots-1

description: This sample is from mycorrhizal roots. It is the first of two biological replicates used in this experiment.


title: Mycorrhizal roots-3

description: This sample is from  mycorrhizal roots. It is the third of three biological replicates used in this experiment.


title: Mycelium patches-1

description: This sample is from free-living mycelium. It is the first of two biological replicates used in this experiment.


title: Mycorrhizal roots-1

description: This sample is from mycorrhizal roots. It is the first of three biological replicates used in this experiment.


title: Free-living mycelium-1

description: This sample is from free-living mycelium. It is the first of tthree biological replicates used in this experiment.

source_name: Free-living mycelium

value: free-living mycelium


title: Mycorrhizal roots-2

data_processing:
Illumina sofware was used by IGA to generate fastq raw data files
Reads were aligned to Oidiodendron maius  (http://genome.jgi-psf.org/Oidma1) reference transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Oidiodendron maius  (http://genome.jgi-psf.org/Oidma1)
Supplementary_files_format_and_content: tab-delimited text files include transcript length,unique aligned reads, total aligned reads and RPKM values for each sample

organism: Oidiodendron maius

growth_protocol: O. maius strain Zn was grown on a modified MMN medium containing KH2PO4 0.5  gL-1, BSA (bovine serum albumin, SIGMA) 0.1 gL-1, CaCl2*2H2O 0.066 gL-1, NaCl  0.025 gL-1, MgSO4*7H2O 0.15 gL-1, thiamine-HCl 0.1 gL-1, FeCl3*6H2O 0.001 gL-  1, agar 10 gL-1. BSA and thiamine-HCl were added to the medium as filter sterilized  solutions just before plating. The final pH was 4.7. Prior to fungal inoculation, sterile  cellophane membranes were placed aseptically on the agar surface to provide a  convenient means of removing the mycelium from the plate. Plates (15 cm in diameter,  2.5 cm in height) were inoculated with 5 mm fungal plugs. Fungal colonies were  removed after 45 days by peeling the biomass from the cellophane membrane. Several  plates were prepared in order to get enough fungal material to perform three separate  RNA extractions for the RNASeq experiment. Endomycorrhizae were synthesized  aseptically in plastic petri plates (15 cm in diameter, 2.5 cm in height) containing the  same medium reported above for fungal cultures. Control, non-inoculated Vaccinium  myrtillus plants were grown on the same medium but (NH4)2HPO4 0,075 gL-1 was  added instead of the BSA. Axenic V. myrtillus seedlings were obtained from surfacesterilized  (70% ethanol, vol/vol, plus 0.2% Tween 20 for 3 min; rinsed twice with  sterile water and 0.25% sodium hypochlorite for 15 min, with three additional sterile  water rinses) bilberry seeds (obtained by Les Semences du Puy, Le Puy-En-Velay,  France) germinated on water and 1% agar petri plates in the dark for 2 weeks before  transfer to the growth chamber for 1 month. A conidia suspension in sterile deionised  water was prepared from 1 month-old fungal cultures grown on Czapek-glucose solid  medium (NaNO3 3 g L-1, K2HPO4*3H2O 1.31 g L-1, MgSO4*7H2O 0.5 g L-1,  FeSO4*7H2O 0.01 g L-1, KCl 0.5 g L-1, glucose 20 gL-1, agar 10 gL-1). All reagents  were purchased from Sigma. The medium was adjusted to pH 6 with the addition of 1M  HCl. The conidia suspension was distributed in the bottom half of the MMN petri  plates. Ten germinated V. myrtillus seedlings were then transferred aseptically in the  MMN plates at the upper limit of the surface covered by the conidia suspension. Finally  the plates were sealed and placed in a growth chamber (16-h photoperiod, light at 170  μmol m–2 s–1, temperatures at 23°C day and 21°C night). Several plates were prepared  in order to get enough root material to perform three separate RNA extractions for the  RNASeq experiment. The root systems were observed after a 1.5-month incubation  period and the percentage of mycorrhization was evaluated. Prior the observation, each  Vaccinium hair-root system from the synthesis plates was stained in 0.1 % (wt/vol)  cotton blue (methyl blue) overnight and distained with 80% lactic acid. Whole roots  were then mounted in the distaining solution, observed using a Nikon Eclipse E400  optical microscope, and photographed.

extract_protocol:
RNA was extracted from O. maius mycelia and from O. maius-inoculated V. myrtillus roots 45 days after cultures start.  100 mg aliquots of mycelium were collected, frozen in liquid nitrogen, mechanically ground and RNA was extracted in Tris-HCl extraction buffer (100 mM Tris-HCl pH 8, 100 mM NaCl, 20 mM Na-EDTA, 0.1% PVP, 1% Na-laurylsarcosine sodium salt dissolved in DEPC-treated deionised water), mixed 1:1 with phenol (pH 4.5-5; Roti-Phenol, Roth A980). A phenol:chloroform:isoamyl alcohol (25:24:1) extraction step and a chloroform extraction step followed. Each extraction step was followed by 5 min centrifugation at 14000 rpm and 4°C. A isopropyl alcohol precipitation step at -80°C for 30 min was than performed followed by 30 min centrifugation at 14000 rpm and 4°C. The pellet was then re-suspended in a 1:1 DEPC treated water:6M LiCl solution and precipitated over-night at 4°C. After 30 min centrifugation at 14000 rpm and 4°C the RNA was rinsed with 70% ethanol, centrifuged for 5 min at 14000 rpm and 4°C, air dried on ice, re-suspended in DEPC-treated water and quantified using the nanodrop and the bioanalyzer.   Total RNA was extracted from V. myrtillus mycorrhizal roots using the CTAB method.  100 mg aliquots of V. myrtillus mycorrhizal roots were collected, frozen in liquid nitrogen, mechanically ground and RNA was extracted in warm (65°C) CTAB buffer (2% CTAB, 2% PVP, 100 mM Tris-HCl pH 8.0; 25 mM EDTA pH 8; 2 M NaCl). 2% PVPP was added to the buffer 1 h before performing the extraction letting it to get hydrated and 2% β-mercaptoethanol was added to the buffer just before use. The extraction suspension was incubated at 65°C for 5 min. Two chloroform/isoamylalcohol (24:1) extraction steps followed.  Each extraction step was followed by 10 min centrifugation at 5000 rpm and room temperature. An overnight precipitation step in 10 M LiCl at 4°C followed. After a centrifugation at 10.000 rpm 4°C for 20 min, pellet was dissolved in SSTE buffer (1 M NaCl, 0.5% SDS, 10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8). Extraction steps with an equal volume of 1:1 phenol (pH 4.5-5; Roti-Phenol, Roth A980):chloroform/isoamyl alcohol (24:1) and of chloroform/isoamyl alcohol (24:1) followed. Each extraction step was followed by 10 min centrifugation at 10000 rpm and 4°C. Two volumes of ethanol 100% were then added and a precipitation step of 2 hours at -20°C followed. After a centrifugation of 20 min at 10000 rpm and 4°C, the pellet was washed with 80% ethanol, centrifuged 10 min at 10000 rpm and 4°C, air dried on ice, re-suspended in DEPC-treated water and quantified using the nanodrop and the bioanalyzer.
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology Services (Udine , Italy)

value: Vaccinium myrtillus


title: Mycorrhizal roots-1


title: 3w Control-1

description: This sample is from control roots. It is the first of three biological replicates used in this experiment.

source_name: 3w Control lateral root

value: control lateral root


title: 3w Control-3

description: This sample is from control roots. It is the third of three biological replicates used in this experiment.


title: Free-living mycelium-2

description: This sample is from free-living mycelium. It is the second of three biological replicates used in this experiment.


title: Free-living mycelium-2


title: 3w Control-2

description: This sample is from control roots. It is the second of three biological replicates used in this experiment.


title: Free-living mycelium-3

description: This sample is from free-living mycelium. It is the third of three biological replicates used in this experiment.


title: Free-living mycelium-1


title: Ectomycorrhizal roots-3

description: This sample is from ectomycorrhizal roots. It is the third of three biological replicates used in this experiment.

data_processing:
Illumina sofware was used by IGA to generate fastq raw data files
Reads were aligned to Piloderma croceum- (http://genome.jgi-psf.org/Pilcr1/Pilcr1.home.html) reference transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Piloderma croceum (http://genome.jgi-psf.org/Pilcr1/Pilcr1.home.html)
Supplementary_files_format_and_content: tab-delimited text files including transcript length,unique aligned reads, total aligned reads and RPKM values for each sample

organism: Piloderma croceum

growth_protocol: P. croceum (DSMZ 4824, ATCC MYA-4870) was cultivated at 23°C on MMN  (modified Melin-Norkrans medium) agar 102 with 10 g l−1 glucose, in the dark, or under  16:8 h day-to-night-cycle (photon flux density 100 μmol m-2s-1). For ECM synthesis, a  modified culture system of the oak clone DF159 (Quercus robur L.) established by  Herrmann et al. was used. After eight  weeks on agar or in ECM synthesis cultures, samples were submerged into liquid  nitrogen and stored at -80°C.

extract_protocol:
Total RNA was extracted from the samples using the  MasterPure Plant RNA Purification Kit (Epicentre, Hessisch Oldendorf, Germany)  according to the manufacturer’s instructions. In total, 50 mg of fungal mycelium or  ectomycorrhizas were used for each extraction. RNA quantity and quality were  estimated using a NanoDrop spectrophotometer (Thermo Scientific, Passau, Germany),  gel electrophoresis, and a Nano Chip in a Bioanalyzer 2100 (Agilent, Böblingen,  Germany).
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology Services (Udine , Italy)

value: Quercus robur


title: Ectomycorrhizal roots-2

description: This sample is from ectomycorrhizal roots. It is the second of three biological replicates used in this experiment.


title: 3w ECM-1

description: This sample is from mycorrhizal root tips. It is the first of three biological replicates used in this experiment.


title: Mycorrhizal roots-3


title: Ectomycorrhizal roots-1

description: This sample is from ectomycorrhizal roots. It is the first of three biological replicates used in this experiment.


title: Free-living mycelium-3

value: Free-living mycelium


title: Free-living mycelium-2


title: Free-living mycelium-3


title: Free-living mycelium-1

data_processing:
Illumina sofware was used by the JGI to generate fastq raw data files
Reads were aligned to the Hebeloma cylindrosporum (http://genome.jgi-psf.org/Hebcy2) reference transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Hebeloma cylindrosporum (http://genome.jgi-psf.org/Hebcy2)
Supplementary_files_format_and_content: tab-delimited text files include transcript length,unique aligned reads, total aligned reads and RPKM values for each sample

organism: Hebeloma cylindrosporum

growth_protocol: The wild-type diploid strain TV98 IV3 of Hebeloma cylindrosporum was used in this  work. Pure culture grown mycelia were six-day old thalli, obtained on the Melin-  Norkrans medium supplemented with 0.5 g l-1 fructose. Agar medium was covered  with a cellophane sheath to prevent mycelial growth inside the agar medium and to  make it easier mycelium recovery. Synthetic ectomycorrhizas and free-living mycelium were collected three weeks after inoculation.

extract_protocol:
H. cylindrosporum  total RNA from free living mycelia or ectomycorrhizas was extracted using the «  RNeasy Plant Mini Kit » (Qiagen). PEG 8000 (20mg/mL) and β-mercaptoethanol  (10μL/mL) were added in RLC buffer. Samples were subsequently purified using the «  Total RNA Purification, Nucleobond ARN/ADN 80 » (Macherey-Nagel) by following  the manufacturer’s recommendations
cDNA libraries were prepared for sequencing using standard Illumina protocols by the Joint Genome Institue (JGI)

tag: strain

value: TV98 IV3


title: Mycorrhizal protocorm-1

description: This sample is from mycorrhizal protocorm. It is the first of three biological replicates used in this experiment.

data_processing:
Illumina sofware was used by IGA to generate fastq raw data files
Reads were aligned to the Tulasnella calospora ( http://genome.jgi-psf.org/Tulca1 ) reference transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Tulasnella calospora ( http://genome.jgi-psf.org/Tulca1 )
Supplementary_files_format_and_content: tab-delimited text files include transcript length,unique aligned reads, total aligned reads and RPKM values for each sample

organism: Tulasnella calospora

source_name: Mycorrhizal protocorm

growth_protocol: The fungal isolate is T. calospora strain AL13, deposited at the Mycotheca Universitatis  Taurinensis collection (MUT4182) at the Department of Life Sciences and Systems  Biology, University of Turin, Italy. This strain was isolated from the roots of  Anacamptis laxiflora collected in a meadow in northern Italy (Festuco-Brometalia, at  410–450 m a.s.l.). The fungus was grown as a free living culture  for 14 days at 24°C on Oatmeal-agar medium (3% oat flakes, 1.5% agar); ten plugs of  0.5 cm of diameter were then aseptically collected from the actively growing margin of  the colony, and inoculated in 100mL Erlenmeyer flasks containing 50 mL of liquid  Oatmeal modified medium (0.75% oat flakes). Flasks were then incubated on an orbital  shaker at 150 rpm for 14 days at 24°C, and three separate RNA extractions were  performed. Symbiotic germination of Serapias vomeracea seeds was performed in  plastic petri plates (9 cm in diameter, 1.5 cm in height) containing Oatmeal-agar  medium (0.3% milled oat, 2.0% agar) inoculated with T. calospora. Protocorms were incubated at 20°C in darkness and collected 30 days after inoculation, immediately frozen in liquid nitrogen and stored at -80°C before RNA extraction.

extract_protocol:
Total RNA was extracted from 200 mg aliquots of T. calospora free living mycelia  grown in Oatmeal modified liquid medium. Mycelium was mechanically ground in  liquid nitrogen and RNA was extracted in Tris-HCl extraction buffer (100 mM Tris-HCl  pH 8, 100 mM NaCl, 20 mM Na-EDTA, 0.1% PVP, 1% Na-laurylsarcosine sodium salt  dissolved in DEPC-treated deionised water), mixed 1:1 with phenol (pH 4.5-5; Roti-  Phenol, Roth A980). A phenol: chloroform: Isoamyl alcohol (25:24:1, v/v/v) and a  chloroform extraction followed, with 5 min centrifugation at 14000 rpm and 4°C after  each extraction step. RNA was precipitated with isopropyl alcohol at -80°C for 30 min,  followed by 30 min centrifugation at 14000 rpm and 4°C. The pellet was then resuspended  in DEPC treated water: 6M LiCl solution (1:1, v/v) and precipitated  overnight at 4°C. After 30 min centrifugation at 14000 rpm and 4°C, the RNA was  rinsed with 70% ethanol, centrifuged for 5 min at 14000 rpm and 4°C, air dried on ice,  re-suspended in DEPC-treated water and quantified using Nanodrop 1000 (Thermo  Scientifics, USA) and Qubit 2.0 (Life Technologies, Italy). RNA integrity was checked  using a Bioanalyzer 2100 (Agilent Technologies, Italy).  Total RNA was extracted from mycorrhizal S. vomeracea protocorms using the  CTAB method. 100 mg aliquots of well-developed protocorms were mechanically  ground in liquid nitrogen and RNA was extracted in CTAB buffer (2% CTAB, 2%  PVP, 100 mM Tris-HCl pH 8.0; 25 mM EDTA pH 8; 2 M NaCl) at 65°C. 2% PVPP  was added to the buffer 1 h before the RNA extraction and 2% β-mercaptoethanol was  added to the buffer just before use. The homogenate was incubated at 65°C for 5 min  and extracted twice with chloroform: isoamylalcohol (24:1 v/v), each extraction  followed by 10 min centrifugation at 5000 rpm and room temperature. RNA was  precipitated overnight in 10 M LiCl at 4°C. After centrifugation at 10.000 rpm at 4°C  for 20 min, the pellet was dissolved in SSTE buffer (1 M NaCl, 0.5% SDS, 10 mM  Tris-HCl pH 8.0, 1 mM EDTA pH 8) and extracted with an equal volume of phenol (pH  4.5-5; Roti-Phenol, Roth A980): chloroform: isoamyl alcohol (25:24:1, v/v/v), followed  by chloroform: isoamyl alcohol (24:1, v/v). Each extraction step was followed by 10  min centrifugation at 10000 rpm and 4°C. Two volumes of 100% ethanol were then  added and RNA was precipitated for 2 hours at -20°C. After centrifugation for 20 min at  10000 rpm and 4°C, the pellet was washed with 80% ethanol, centrifuged 10 min at  10000 rpm and 4°C, air dried on ice, re-suspended in DEPC-treated water and  quantified using Nanodrop 1000 (Thermo Scientifics, USA) and Qubit 2.0 (Life  Technologies, Italy). RNA integrity was checked using a Bioanalyzer 2100 (Agilent  Technologies, Italy).
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology Services (Udine , Italy)

value: Serapias vomeracea

value: Mycorrhizal protocorm


title: Free-living mycelium-1


title: Mycorrhizal protocorm-3

description: This sample is from  mycorrhizal protocorm. It is the third of three biological replicates used in this experiment.


title: Free-living mycelium-3


title: Ectomycorrhizal roots-1

description: This sample is from ectomycorrhizal roots. It is the first of two biological replicates used in this experiment.

data_processing:
Illumina sofware was used by IGA to generate fastq raw data files
Reads were aligned toSuillus luteus (http://genome.jgi-psf.org/Suilu1/Suilu1.home.html) reference transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Suillus luteus (http://genome.jgi-psf.org/Suilu1/Suilu1.home.html)
Supplementary_files_format_and_content: tab-delimited text files including transcript length,unique aligned reads, total aligned reads and RPKM values for each sample

organism: Suillus luteus

growth_protocol: Suillus luteus was grown for 7 days at 23C on sterilized cellophane sheets sitting in  Fries medium plates (4 plugs/plate) and used further for inoculation. Free-living  mycelium was harvested after 7 days of growth in the same Fries medium by peeling  off the mycelium and immediately freezing it in an eppendorf in liquid N. Samples were  then stored at -80C. Pinus sylvestris seeds were kindly provided by Office National des  Forêts, France. Four hundred of them were rinsed in a sieve with sterile MQ water,  soaked in 34ml of a 12% TWEEN20 solution for 20min, rinsed with distilled water,  soaked in 10% H2O2 for 15 min, rinsed with distilled water, soaked in 70% ethanol for 5  min, rinsed with distilled water, and placed in a tray containing sieved, acid-washed  and moistened perlite. Seedlings were grown for four weeks in a growth chamber  (day:night regime of 18 h light at 22°C and 6 h dark at 15°C) and watered every week  with Ingestad’s nutrient solution slightly modified to induce P limitation in the pine  seedlings. The macronutrient weight proportions were 100 N:9 P:54 K:6 Ca:6 Mg:9 S. Suillus luteus was inoculated on Pinus sylvestris seedlings using the sandwich  technique described in Van Tichelen & Colpaert. Mycorrhizal root tips were  harvested on 40 days-old seedlings. Two sets of about 50 ECMs were harvested from  10 seedlings (5 seedlings each). Each tip was harvested with tweezers and immediately  frozen in an eppendorf floating in liquid N after separation from the root.

extract_protocol:
For ECMs, total RNAs were extracted from the frozen material using the protocol of  Chang et al. that is well adapted to high-polyphenol Pine  samples. http://ipmb.sinica.edu.tw/affy/document/Pine_Tree_Method.pdf. For  mycelium, 100 mg of frozen sample was extracted using the Plant RNA mini kit. RNA  quality was checked using Bioanalyzer.
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology Services (Udine , Italy)

value: Pinus sylvestris


title: Ectomycorrhizal roots-2

description: This sample is from ectomycorrhizal roots. It is the second of two biological replicates used in this experiment.


title: ECM-2

data_processing:
Illumina sofware was used by the JGI to generate fastq raw data files
Reads were aligned to the Amanita muscaria ((http://genome.jgi-psf.org/Amamu1) reference transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Amanita muscaria ((http://genome.jgi-psf.org/Amamu1)
Supplementary_files_format_and_content: tab-delimited text files include transcript length,unique aligned reads, total aligned reads and RPKM values for each sample

organism: Amanita muscaria

source_name: ECM

growth_protocol: Amanita muscaria ([L.] ex Fr.) Hooker strain MEII was isolated from fruiting bodies  collected under Norway spruce obtained in the Schönbuch forest near Tübingen,  Germany. Stock cultures were grown on MMN-agar at 8°C and were  used to inoculate 300 ml flasks containing 80 ml of modified MMN medium. Liquid  cultures were grown at 20°C on a rotary shaker (120 rpm) and were used as inoculum  for ectomycorrhiza formation in Petri dishes. Populus tremula x  tremuloides (clone T89) cuttings were rooted in MS-medium (Sigma, St. Louis, MI,  USA) under sterile conditions for about 2 month Rooted plants were transferred under  axenic conditions onto the agar surface of Petri dishes containing sugar-free modified  MMN medium with 300 μM ammonium as sole nitrogen source such that the root  system was inside and the shoot outside of the Petri dish. Inoculated and non-inoculated  control plants were grown in parallel in small plastic greenhouses for additional six  weeks at 18°C, 12 h day/night periods with 150 μE x m-2 x s-1 illumination.

extract_protocol:
Total RNA was isolated according to 99. In brief, frozen material was ground to a  fine powder in a mortar with pestle under liquid nitrogen and resuspended in five  volumes of 4 M guanidine isothiocyanate, 96 mM ß-mercaptoethanol, 25 mM sodium  acatate, pH 6.0 Insoluble material was removed by centrifugation (20 min, 20,000 x g,  20°C), and the supernatant was mixed with one volume of 5.7 M CsCl, 25 mM sodium  acatate, pH 6.0 in an ultracentrifuge tube. The RNA was sedimented by centrifugation  (20 h, 200,000 x g, 20°C) and the pellet was resuspended in 200 μl DEPC-treated H2O.  After transfer into an Eppendorf tube and the addition of 20 μl 3 M sodium acetate, 500  μl ethanol, the RNA was precipitated by centrifugation (40 min, 14,000 x g, 20°C), air  dried and resuspended in 50 μl DEPC-treated H2O. Aliquots were frozen in liquid  nitrogen and stored at -80 °C.
cDNA libraries were prepared for sequencing using standard Illumina protocols by the Joint Genome Institue (JGI)

value: ectomycorrhiza


title: ECM-1

value: Pinus pinaster


title: ECM-1

value: Populus tremula x tremuloides (clone T89)


title: ECM-3


title: Free-living mycelium-2


title: Free-living mycelium-3


title: Free-living mycelium-2

description: This sample is from free-living mycelium. It is the second of two biological replicates used in this experiment.

value: MEII


title: ECM-2


title: Free-living mycelium-1

description: This sample is from free-living mycelium. It is the first of two biological replicates used in this experiment.


title: Free-living mycelium-2


title: Free-living mycelium-1


title: Mycorrhizal protocorm-2

description: This sample is from  mycorrhizal protocorm. It is the second of three biological replicates used in this experiment.


title: Mycelium MMN medium 10d-2.

description: This sample is from control mycelium. It is the second of three  biological replicates used in this experiment.

organism: Serpula lacrymans var. lacrymans S7.9

source_name: Mycelium MMN medium 10d

growth_protocol: Mycelium was grown on liquid MMN medium for 10d. Two-week-old Picea sylvestris seedlings were aseptically inoculated with agar plugs from of S. lacrymans S7 in Petri dishes with growth substrate of sterilized fine sphagnum peat : vermiculite : 1/10 strength liquid MMN mixture in the ratio 1 : 4 : 2. Inoculated microcosms were incubated in a growth chamber at 20 ° C, with a 16 h light : 8 h dark photoperiod.

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

value: Mycelium


title: CMa H3K79me2_ChIPSeq

status: Public on Dec 22 2014

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

library_source: genomic

data_processing:
Sequencing reads were generated by the Lifetech analysis software on the SOLiD 5500™ sequencing machine
The .csfasta and .qual files were generated from the 5500 .xsq files with the convertFromXSQ Lifetech conversion utility
Mapping to the genome reference was performed with BOWTIE version 0.12.8, accepting only alignments with a QV > 10
Peak calling was performed using SICER version 1.1 with the following settings: windows size=200, gap size=600, redundancy threshold=1, FDR=0.05 and MACS version 1.4.2 with the following settings: effective genome size=1.87e+09, band width=300, model fold=5,30, p-value cutoff= 1.00e-05
Occupancy and differential binding affinity analysis were assessed with the R Bioconductor package DiffBind version 1.2.0
Genome_build: mm9
Supplementary_files_format_and_content: *_MACS bed file were generated after running MACS peak calling software
Supplementary_files_format_and_content: *_SICER bed file were generated after running SICER peak calling software

molecule: genomic DNA

organism: Mus musculus

source_name: CMa H3K79me2_ChIPSeq

extract_protocol:
Primary 1-day-old cardiomyocytes and 2-month-old cardiomyocytes have been isolated to single cells and purified after sequential enzymatic digestions using standard protocols. The chromatin obtained after nuclei isolation has been sonicated to obtain an average chromatin length of 300bp; immunoprecipitation was performed by incubating the chromatin at 4°C overnight with antibodies anti-H3K4me3, anti-H3K79me2, anti-H3K27me3 and anti-H3K9me3. After decrosslinking of the chromatin, the enriched DNA was extracted and control of quantity and quality was assessed before sequencing.
Sequencing libraries have been prepared and barcoded according to the Lifetech ChIP-Seq Alpha protocol and amplified with a total of 15 PCR cycles. All sequencing libraries have been quantified with the Qubit Fluorometer (Life Technologies), protocol DNA HS, and checked with the Agilent 2100 Bioanalyzer instrument, protocol DNA 1000

value: 2 month old

tag: cell type

value: left ventricle cardiomyocytes

tag: chip antibody

value: H3K79me2 (Abcam, ab3594)


title: Free-living mycelium-2


title: Mycelium MMN medium 10d-3.

description: This sample is from control mycelium. It is the third of three biological replicates used in this experiment.


title: PseudoECM-1

description: This sample is from pseudomycorrhiza. It is the first of three  biological replicates used in this experiment.

source_name: PseudoECM

value: Pseudomycorrhiza


title: CMa H3K9me3_ChIPSeq

source_name: CMa H3K9me3_ChIPSeq

value: H3K9me3 (Millipore-Upstate, 07-442)


title: PseudoECM-3

description: This sample is from  pseudomycorrhiza. It is the third of three biological replicates used in this experiment.


title: Mycelium MMN medium 10d-1.

description: This sample is from control mycelium. It is the first of three  biological replicates used in this experiment.


title: PseudoECM-2

description: This sample is from  pseudomycorrhiza. It is the second of three  biological replicates used in this experiment.


title: CMa Input_DNA

source_name: CMa Input_DNA


title: CMa H3K4me3_ChIPSeq

source_name: CMa H3K4me3_ChIPSeq

value: H3K4me3 (Active Motif, 39159)


title: CMp H3K27me3_ChIPSeq

source_name: CMp H3K27me3_ChIPSeq

value: 1 day old

value: cardiomyocytes

value: H3K27me3 (Millipore-Upstate, 07-449)


title: CMp H3K4me3_ChIPSeq

source_name: CMp H3K4me3_ChIPSeq


title: CMp Input_DNA_H3K4me3

source_name: CMp Input_DNA_H3K4me4


title: CMp H3K9me3_ChIPSeq

source_name: CMp H3K9me3_ChIPSeq


title: CMp H3K79me2_ChIPSeq

source_name: CMp H3K79me2_ChIPSeq


title: CMp Input_DNA

source_name: CMp Input_DNA


title: SI_12_ECM_650-2

status: Public on Oct 10 2014

description: This sample is from ectomycorrhizall roots. It is the second of three  biological replicates used in this experiment.

data_processing:
Illumina sofware was used by by the University of Western Sydney Next Generation Sequencing Facility to generate fastq raw data files
Reads were aligned to the Eucalyptus grandis (http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9) reference transcripts (primarytranscriptsonly) using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Eucalyptus grandis (http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9)
Supplementary_files_format_and_content: tab-delimited text files include transcript length,unique aligned reads, total aligned reads and RPKM values for each sample

organism:
Eucalyptus grandis
Pisolithus microcarpus

growth_protocol: For plant colonization experiments, individual 1 month old E. grandis seedlings were  transferred to ½ strength MMN medium with 0.1% glucose in a 9 cm Petri dish and a single  0.25 cm2 160 square of fungal mycelium (Pisolithus microcarpus SI-9 or SI-12) was transferred directly on top of the plant root. The  plates were closed using 2/3 electricians tape and 1/3 micropore tape. The micropore tape  was used to ensure free gas exchange. Contiguity between CO2 levels in the petri dishes and  the external environment was verified using a WMA-4 CO2 analyzer (PP Systems) according  to manufacturers instructions. Inoculated plates were placed at a 45 degree angle in plant  growth chambers (GC20 BDAF; Biochambers; Canada) under a temperature regime with a  daytime high of 30oC and a nighttime low of 22o166 C and constant level of either 400 ppm CO2  or 650 CO2. Non-mycorrhizal (NM) control E. grandis plants grown axenically were treated  identically for the same length of time and under the same conditions. Plates were left to  incubate for 1 month. Root tissues were harvested directly within the chambers to prevent a drop in CO2 levels and  were frozen immediately at -80°C.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Plant Kit  using the RLC lysis buffer supplemented with 25 mg/mL PEG 8000 and following  manufactuers instructions thereafter. RNA quantity was analyzed using the QuBit broad  spectrum RNA kit as per manufacturers instructions and RNA quality was verified using the  BioAnalyzer platform (Agilent Technologies Inc.).
cDNA libraries were prepared for sequencing using standard Illumina protocols by the University of Western Sydney Next Generation Sequencing Facility (Richmont,Australia)

value: Pisolithus microcarpus SI-12

tag: co2 concentration (ppm)


title: CMa H3K27me3_ChIPSeq

source_name: CMa H3K27me3_ChIPSeq


title: SI_12_ECM_400-3

description: This sample is from ectomycorrhizall roots. It is the third of three  biological replicates used in this experiment.


title: SI_12_ECM_650-3


title: SI_12_ECM_400-1

description: This sample is from ectomycorrhizall roots. It is the first of three  biological replicates used in this experiment.


title: SI_12_ECM_400-2


title: SI_12_ECM_650-1


title: SI_9_ECM_650-3

value: Pisolithus microcarpus SI-9


title: SI_9_ECM_400-2


title: undifferentiated mouse embryonic stem cell_rep3

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was normalized using LumiExpresso function of the lumi Bioconductor package in R

label: biotin

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

growth_protocol: primary cells purified and culture using standard protocols and conditions

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

treatment_protocol: no treatment applied

value: undifferentiated mouse embryonic stem cells

tag: Stage

value: undifferentiated


title: purified neonatal mouse cardiomyocytes_rep1

description: replicate 1

source_name: mouse heart

value: purified neonatal mouse cardiomyocytes


title: SI_9_ECM_400-1

value: ectomycorrhiza


title: purified adult mouse cardiomyocytes_rep1

description: replicate 1

source_name: mouse left ventricle

value: purified adult mouse cardiomyocytes


title: purified neonatal mouse cardiomyocytes_rep3

description: replicate 3


title: SI_9_ECM_650-1


title: SI_9_ECM_650-2


title: SI_9_ECM_400-3


title: purified adult mouse cardiomyocytes_rep2

description: replicate 2


title: undifferentiated mouse embryonic stem cell_rep1

description: replicate 1


title: purified neonatal mouse cardiomyocytes_rep2

description: replicate 2


title: purified adult mouse cardiomyocytes_rep3

description: replicate 3


title: undifferentiated mouse embryonic stem cell_rep2

description: replicate 2


title: 6W ECM-3

description: This sample is from mycorrhizal root tips. It is the third of three biological replicates used in this experiment.

organism:
Pseudotsuga menziesii
Laccaria bicolor S238N-H82

source_name: 6W ECM

growth_protocol: For colonization experiments Laccaria bicolor innoculum was grown on a substrate of peat moss:vermiculite (3:1) dampened with liquid Pachlewski medium medium (2.7 mM di-ammonium tartrate, 7.3 mM KH2PO4, 2.0 mM MgSO4·7 H2O, 13 mM maltose, 110 mM glucose, 2.9 µM thiamine-HCl, and 1 mL of a trace-element stock solution Kanieltra medium) for 3 months. One week old seedlings of Pseudotsuga menziesii were planted in a 9:1 mixture (v/v) of Terra-Green (a calcined attapulgite clay supplied by Turf-Pro, UK):L.  bicolor inoculum.   Each pot was given 20 mL of a dilute nutrient solution (0.8 mM KNO3, 0.8 mM Ca(NO3)2.4 H2O, 0.3 mM NaH2PO4, 0.3 mM MgSO4.7 H2O, and 20 μL trace elements solution Kanieltra per liter of solution) weekly. Roots were destructively harvested at 2, 4 and 6 weeks after being put into contact with L.  bicolor.

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.

tag: time

value: 6 w

value: mycorrhizal root tips


title: 4W ECM-3

source_name: 4W ECM

value: 4 w


title: 6W ECM-1

description: This sample is from mycorrhizal root tips. It is the first of three  biological replicates used in this experiment.


title: Free-living mycelium-1

source_name: Free-living mycelium

value: MEII

value: free-living mycelium


title: 6W ECM-2

description: This sample is from mycorrhizal root tips. It is the second of three  biological replicates used in this experiment.


title: 4W ECM-1


title: 2W ECM-2

source_name: 2W ECM

value: 2 w


title: 2W ECM-3


title: 2W ECM-1


title: 6wECM-3

description: This sample is from mycorrhizal root tips. It is the third of four  biological replicates used in this experiment.

organism:
Populus trichocarpa
Laccaria bicolor S238N-H82

growth_protocol: For colonization experiments Laccaria bicolor innoculum was grown on a substrate of peat moss:vermiculite (3:1) dampened with liquid Pachlewski medium medium (2.7 mM di-ammonium tartrate, 7.3 mM KH2PO4, 2.0 mM MgSO4·7 H2O, 13 mM maltose, 110 mM glucose, 2.9 µM thiamine-HCl, and 1 mL of a trace-element stock solution Kanieltra medium) for 3 months.   Pre-rooted stem cuttings of Populus trichocarpa (rooted for 1 week in a solution of: 2.5 mM KNO3, 0.8 mM KH2PO4, 1 mM MgSO4.7 H2O, 2.3 mM Ca(NO3)2.4 H2O, 23 μM H3BO3, 4.6 μM MnCl2.4 H2O, 0.4 μM ZnSO4.7 H2O, 0.09 μM (NH4)2MoO4, 0.18 μM CuSO4.5 H2O, 20 μM FeNaEDTA, pH 5.8) were planted in a 9:1 mixture (v/v) of Terra-Green (a calcined attapulgite clay supplied by Turf-Pro, UK):L.  bicolor inoculum.   Each pot was given 20 mL of a dilute nutrient solution (0.8 mM KNO3, 0.8 mM Ca(NO3)2.4 H2O, 0.3 mM NaH2PO4, 0.3 mM MgSO4.7 H2O, and 20 μL trace elements solution Kanieltra per liter of solution) weekly. Roots were destructively harvested at 2, 4, 6 and 12 weeks after being put into contact with L.  bicolor.


title: 6wECM-1

description: This sample is from mycorrhizal root tips. It is the first of four  biological replicates used in this experiment.


title: 4wECM-3


title: 4W ECM-2


title: 4wECM-4

description: This sample is from mycorrhizal root tips. It is the fourth of four  biological replicates used in this experiment.


title: 6wECM-2

description: This sample is from mycorrhizal root tips. It is the second of four  biological replicates used in this experiment.


title: Control root 650-3

description: This sample is from control roots. It is the third of five  biological replicates used in this experiment.

organism: Eucalyptus grandis

source_name: Control root 650

value: no fungus

value: control root


title: Control root 650-5

description: This sample is from control roots. It is the fifth of five biological replicates used in this experiment.


title: Control root 650-4

description: This sample is from control roots. It is the fourth of five  biological replicates used in this experiment.


title: Control root 650-2

description: This sample is from control roots. It is the second of five  biological replicates used in this experiment.


title: 4wECM-2


title: Control root 650-1

description: This sample is from control roots. It is the first of five  biological replicates used in this experiment.


title: 12wECM-2


title: 2wECM-4


title: 2wECM-3


title: Control root 400-5

description: This sample is from control roots. It is the fifth of six biological replicates used in this experiment.

source_name: Control root 400


title: 4wECM-1


title: Control root 400-6

description: This sample is from control roots. It is the sixth of six  biological replicates used in this experiment.


title: 12wECM-3


title: 2wECM-2


title: 12wECM-4


title: 12wECM-1


title: Control root 400-3

description: This sample is from control roots. It is the third of six  biological replicates used in this experiment.


title: 2wECM-1


title: Control root 400-2

description: This sample is from control roots. It is the second of six  biological replicates used in this experiment.


title: 6wECM-4


title: Control root 400-1

description: This sample is from control roots. It is the first of six  biological replicates used in this experiment.


title: Control root 400-4

description: This sample is from control roots. It is the fourth of six  biological replicates used in this experiment.


title: 6w ECM-3

status: Public on Oct 09 2014

organism: Populus trichocarpa

source_name: 6w ECM

growth_protocol: For colonization experiments Laccaria bicolor innoculum was grown on a substrate of peat moss:vermiculite (3:1) dampened with liquid Pachlewski medium medium (2.7 mM di-ammonium tartrate, 7.3 mM KH2PO4, 2.0 mM MgSO4·7 H2O, 13 mM maltose, 110 mM glucose, 2.9 µM thiamine-HCl, and 1 mL of a trace-element stock solution Kanieltra medium) for 3 months.   Pre-rooted stem cuttings of Populus trichocarpa (rooted for 1 week in a solution of: 2.5 mM KNO3, 0.8 mM KH2PO4, 1 mM MgSO4.7 H2O, 2.3 mM Ca(NO3)2.4 H2O, 23 μM H3BO3, 4.6 μM MnCl2.4 H2O, 0.4 μM ZnSO4.7 H2O, 0.09 μM (NH4)2MoO4, 0.18 μM CuSO4.5 H2O, 20 μM FeNaEDTA, pH 5.8) were planted in a 9:1 mixture (v/v) of Terra-Green (a calcined attapulgite clay supplied by Turf-Pro, UK):L.  bicolor inoculum.   Each pot was given 20 mL of a dilute nutrient solution (0.8 mM KNO3, 0.8 mM Ca(NO3)2.4 H2O, 0.3 mM NaH2PO4, 0.3 mM MgSO4.7 H2O, and 20 μL trace elements solution Kanieltra per liter of solution) weekly. Roots were destructively harvested at 2, 4, 6 and 12 weeks after being put into contact with L.  bicolor. Control roots without contact with the fungus were harvested at the same time points.

tag: agent

value: Laccaria bicolor S238N


title: 4w ECM-2

source_name: 4w ECM


title: 6w ECM-1


title: 4w ECM-4


title: 6w ECM-2


title: 4w ECM-1


title: 6w Control-3

description: This sample is from control roots. It is the third of four biological replicates used in this experiment.

source_name: 6w Control


title: 6w Control-4

description: This sample is from control roots. It is the fourth of four biological replicates used in this experiment.


title: 2w ECM-3

description: This sample is from mycorrhizal root tips. It is the third of four  biological replicates used in this experiment.

source_name: 2w ECM


title: 12w ECM-4

source_name: 12w ECM


title: 12w ECM-2


title: 4w Control-4

source_name: 4w Control


title: 4w Control-1

description: This sample is from control roots. It is the first of four  biological replicates used in this experiment.


title: 4w Control-3


title: 2w ECM-4

description: This sample is from mycorrhizal root tips. It is the fourth of four  biological replicates used in this experiment.


title: 2w ECM-2

description: This sample is from mycorrhizal root tips. It is the second of four  biological replicates used in this experiment.


title: 4w Control-2

description: This sample is from control roots. It is the second of four  biological replicates used in this experiment.


title: 6w Control-1


title: 2w Control-3

source_name: 2w Control


title: 12w ECM-3


title: 12w ECM-1

description: This sample is from mycorrhizal root tips. It is the first of four  biological replicates used in this experiment.


title: 2w Control-2


title: 4w ECM-3


title: 2w Control-4


title: 6w Control-2


title: 2w ECM-1


title: 12w Control-4

source_name: 12w Control


title: 2w Control-1


title: 6w ECM-4


title: 12w Control-3


title: 12w Control-1


title: Pf29ArpLaccaria_cy5/Pf29Arp_cy3 3

status: Public on Oct 01 2014

hyb_protocol: ChipHyb hybridization buffer (Ventana Medical Systems, Tucson, AZ,USA) was added to cDNA and hybridization was performed on a Ventana Discovery system for 8 h at 42°C. Washes were performed manually at room temperature in two successive 1× Ribowash solution (Ventana Medical Systems), followed by a wash in 0.1× SSC at room temperature

scan_protocol: Fluorescent images of the microarrays were generated with a Genepix 4000B scanner and Genepix Pro analysis software v6.0 (Axon Instruments, Molecular Devices Co., Sunnyvale, CA,USA)

data_processing: Raw data from microarray hybridization, exported from GenePix suites 6.0, was imported into LIMMA. Spots with a negative flag value, a signal-to noise  ratio (SNR) threshold ≤ 2 and an irregular aspect were assigned a weight of 0 in the subsequent analysis. Signal intensities were normalized using a print-tip group Loess normalization. Statistical values for gene expression of sample pairs were calculated after fitting a mixed model analysis of variance (LIMMA package) in R

organism: Pseudomonas fluorescens Pf29Arp

source_name: Bacterial cells + Laccaria

label_protocol: cDNA probe generation was performed with  the ChipSho Indirect Labeling and Clean-Up System (Promega) and the CyDye (Cy3/Cy5) Reactive Dye Protocols for Post-Labelling Aminoallyl-cDNA (Amersham Biosciences)

growth_protocol: The ectomycorrhizal basidiomycete L. bicolor S238N (Maire P. D. Orton) used as inoculum was maintained on Pachlewski agar medium P5 (Di Battista et al., 1996) at 25°C for three weeks. Pseudomonas fluorescens Pf29Arp was maintained at -80°C in Luria-Bertani Medium (Sambroock, Fritsch & Maniatis, 1989) with 20% glycerol added. To prepare the bacterial inocula for the in vitro bioassays with L. bicolor, the bacterial strains were first grown on 10 % TSA plates (Tryptic Soy Broth from Difco and 15 g.L-1 of agar) at 25°C for 65 hours. The bioassay was prepared as described in Deveau et al. (2007). Briefly, four droplets of bacterial solutions (OD600 nm 0.7 in sterile water) were distributed at 1.2 cm from the center of a fungal plug (Figure 1). Control treatments without fungus or in which bacteria were replaced by sterile water droplets were performed. Plates were incubated at 10°C in the dark to reproduce soil temperature.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen, Stockholm, Sweden) as recommended by the manufacturer.

value: cultivated with Laccaria bicolor S238N

source_name: Bacterial cells alone

value: cultivated alone


title: Pf29ArpLaccaria_cy3/Pf29Arp_cy5 1


title: 12w Control-2


title: Pf29ArpLaccaria_cy5/Pf29Arp_cy3 2


title: Pf29ArpLaccaria_cy5/Pf29Arp_cy3 1


title: Pf29ArpLaccaria_cy3/Pf29Arp_cy5 2


title: Laccaria alone 1

status: Public on Jun 12 2014

hyb_protocol: The nylon filters were pre-incubated in 30 ml of a hybridization solution (5x SSC solution, 5x Denhardtâ€™s solution, 0.5% SDS, 50Âµg/ml shared salmon sperm DNA) for 4h at 65°C in a HIR10M rotating hybridization incubator (Grant/Boekel, VWR international, Strasbourg, France). Then the filters were incubated in 20 ml of fresh hybridization solution containing the 33P-labelled probe at 65°C for 18h.  The hybridized filters were washed successively for 3x5 min in 2x SSC at room temperature, 2x20 min in 2x SSC containing 0.05% SDS (65°C), 2x20 min in 1x SSC containing 0.1% SDS (65°C) and 2x20 min in 0.1x SSC containing 0.1% SDS (65°C).

scan_protocol: Filters were then wrapped in plastic foils and exposed to a phosphor screen (Eastman Kodak Company, Rochester, NY, USA) for 24h, after which the imaging plate was scanned by a Personal Molecular Imager FX (Bio-Rad Laboratories, Hercules, CA, USA) at a resolution of 50Âµm per pixel.

data_processing: Phosphorimages of hybridized membranes were analyzed in XDOTREADER (Cose, Paris, France) to obtain raw spot intensity data. After background subtraction, the raw data were normalized by expressing individual spot intensities as a fraction of the sum of all spot intensities in each image and the data were analyzed using Microsoft EXCEL.

organism: Laccaria bicolor

source_name: Control

label_protocol: One µg of total RNA was reverse-transcribed using oligo-dT primers with the SMART cDNA synthesis kit (Clontech, Palo alto, CA, USA). Double strand cDNA were then synthesised using the Advantage 2PCR kit (Clontech, Palo alto, CA, USA). Labelling of the cDNA probes was done in the presence of 30ÂµCi 33P dCTP and  30ÂµCi 33P dATP, and random hexamers using the NonaPrimer Kit (Qbiogene, France) according to the manufacturerâ€™s instructions. The unincorporated labeled nucleotides were removed using QIAquick columns (QIAGEN, Hilden, Germany).

growth_protocol: The ectomycorrhizal basidiomycete L. bicolor S238N (Maire P. D. Orton) used as inoculum was maintained on Pachlewski agar medium P5 (Di Battista et al., 1996) at 25°C for three weeks. Collimonas fungivorans Ter331 was maintained at -80°C in Luria-Bertani Medium (Sambroock, Fritsch & Maniatis, 1989) with 20% glycerol added. To prepare the bacterial inocula for the in vitro bioassays with L. bicolor, the bacterial strains were first grown on 10 % TSA plates (Tryptic Soy Broth from Difco and 15 g.L-1 of agar) at 25°C for 65 hours. The bioassay was prepared as described in Deveau et al. (2007). Briefly, four droplets of bacterial solutions (OD600 nm 0.7 in sterile water) were distributed at 1.2 cm from the center of a fungal plug (Figure 1). Control treatments without fungus or in which bacteria were replaced by sterile water droplets were performed. Plates were incubated at 10°C in the dark to reproduce soil temperature.

extract_protocol: L. bicolor RNA were extracted using the RNeasy mini kit (Qiagen, Hilden, Germany) as recommended by manufacturer for fungal material

value: Mycelium

tag: bacterial inoculant


title: Laccaria alone 2


title: Control-2

status: Public on Aug 13 2014

description: This is a control sample. It is the second of three  biological replicates used in this experiment.

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: Phanerodontia chrysosporium

growth_protocol: Phanerochaete chrysosporium homocaryon RP78 was maintained in Malt Agar medium.  Fungal plugs were used to inoculate liquid minimal medium (5 mM sodium acetate pH 4.5, 1 % glucose, 1 mM ammonium tartrate, 1 % (v/v) base medium (20 g L-1 KH2PO4, 5 g Phanerochaete chrysosporium homocaryon RP78 was maintained in Malt Agar medium.    Fungal plugs were used to inoculate liquid minimal medium (5 mM sodium acetate pH  4.5, 1 % glucose, 1 mM ammonium tartrate, 1 % (v/v) base medium   (20 g L-1 KH2PO4, 5 g L-1 MgSO4, 1 g L-1 CaCl2), 7% (v/v) trace medium   (1.5 g L-1 Nitrilotriacetate, 3 g L-1 MgSO4, 1 g L-1 NaCl, 0.1 g L-1 FeSO4·7H2O,  0.1 g L-1 CoCl2, 0.1 g L-1 ZnSO4·7H2O, 0.1 g L-1 CuSO4, 10 mg L-1 AlK(SO4)·12H2O,  10 mg L-1 H3BO3, 10 mg L-1 NaMoO4·2H2O) and 225 μM MnCl2).   Cultures were performed at 37°C for 3 days.   Mycelial pellets were then transferred into fresh medium (30 ml)   with (TKCh) or without (TKT) extractives obtained from 200 mg of oak wood.

extract_protocol: Total RNA was extracted and purified from triplicate cultures using the RNeasy Plant mini Kit (Qiagen) according to the manufacturer. The RNA was treated twice with DNase I (during purification as recommended in manufacturer protocol and directly onto purified RNA) and cleaned with a Qiagen RNA Cleanup Kit.   An additional purification step was performed to remove residual phenolic compounds due to oak treatment by precipitating RNA with LiCl 2M. RNA was converted to double-strand cDNA using the SmarterTM PCR cDNA Synthesis Kit (Clontech) according to the manufacturer protocol and   purified using the Qiaquick PCR Purification Kit (Qiagen).An additional purification step was performed to remove residual phenolic compounds due to oak treatment by precipitating RNA with LiCl 2M. RNA was converted to double-strand cDNA using the SmarterTM PCR cDNA Synthesis Kit (Clontech) according to the manufacturer protocol and purified using the Qiaquick PCR Purification Kit (Qiagen).

value: homocaryon RP78

value: mycelium

tag: growth

value: control


title: Laccaria with Ter331 2

value: Collimonas fungivorans Ter331


title: Control-1

description: This is a control sample. It is the first of three  biological replicates used in this experiment.


title: Laccaria with Ter331 1


title: Laccaria with Pf29Arp 3

growth_protocol: The ectomycorrhizal basidiomycete L. bicolor S238N (Maire P. D. Orton) used as inoculum was maintained on Pachlewski agar medium P5 (Di Battista et al., 1996) at 25°C for three weeks. P. fluorescens BBc6R8 and P. fluorescens Pf29Arp  were maintained at -80°C in Luria-Bertani Medium (Sambroock, Fritsch & Maniatis, 1989) with 20% glycerol added. To prepare the bacterial inocula for the in vitro bioassays with L. bicolor, the bacterial strains were first grown on 10 % TSA plates (Tryptic Soy Broth from Difco and 15 g.L-1 of agar) at 25°C for 65 hours. The bioassay was prepared as described in Deveau et al. (2007). Briefly, four droplets of bacterial solutions (OD600 nm 0.7 in sterile water) were distributed at 1.2 cm from the center of a fungal plug (Figure 1). Control treatments without fungus or in which bacteria were replaced by sterile water droplets were performed. Plates were incubated at 10°C in the dark to reproduce soil temperature.

value: P. fluorescens Pf29Arp


title: Laccaria with Pf29Arp 2


title: Laccaria with Pf29Arp 1


title: Control-3

description: This is a control sample. It is the third of three  biological replicates used in this experiment.


title: Laccaria with Ter331 3


title: Pf29ArpLaccaria_cy3/Pf29Arp_cy5 3


title: Oak acetonic extractives-1

description: This is mycelium grown on Oak acetonic extractives . It is the first of three  biological replicates used in this experiment.

source_name: Oak acetonic extractives

value: oak acetonic extractives


title: Laccaria alone 3


title: Laccaria with BBc6R8 3

value: P. fluorescens BBc6R8


title: Oak acetonic extractives-2

description: This is mycelium grown on Oak acetonic extractives . It is the second of three  biological replicates used in this experiment.


title: PfBBc6R8-contact-1

description: PfBBc6R8-at the time of contact (16 days after inoculation)-co-culture with fungus Laccaria bicolor.

hyb_protocol: Hybridization by NimbleGen Company.

scan_protocol: Scanning by NimbleGen Company.

organism: Pseudomonas fluorescens BBc6R8

source_name: PfBBc6R8, at the time of contact with fungus

label_protocol: Labelling by NimbleGen Company.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen, Stockholm, Sweden) as recommended by the manufacturer. Total RNA preparations were amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer's instructions.

value: Laccaria bicolor fungus

tag: sampling time

value: 16 days after inoculation


title: Laccaria with BBc6R8 2

tag: tissue


title: Laccaria with BBc6R8 1


title: Oak acetonic extractives-3

description: This is mycelium grown on Oak acetonic extractives . It is the third of three  biological replicates used in this experiment.


title: PfBBc6R8-extended contact-1

description: PfBBc6R8-after an extended period of contact (21 days)-co-culture with fungus Laccaria bicolor.

source_name: PfBBc6R8, extended contact with fungus

value: 21 days after inoculation


title: PfBBc6R8-contact-2


title: Laccaria alone 3


title: PfBBc6R8-extended contact-3


title: Laccaria alone 2


title: PfBBc6R8-extended contact-2


title: PfBBc6R8-before contact-3

description: PfBBc6R8-before contact between the bacterial colonies and the fungus (14 days after inoculation)-co-culture with fungus Laccaria bicolor.

source_name: PfBBc6R8, before contact with fungus

value: 14 days after inoculation


title: Ter331 with Laccaria 2

organism: Collimonas fungivorans

source_name: Bacterial cells

tag: co-culture


title: PfBBc6R8-before contact-2


title: Ter331 alone 1

value: Control


title: Ter331 alone 2


title: Control root 2

status: Public on Apr 17 2014

description:
This sample is fromcontrol roots. It is the second of two biological replicates used in this experiment.
8Con

data_processing:
Illumina sofware was used by Beckman Genomics to generate fastq raw data files
Reads were aligned to the Populus trichocarpa (http://www.phytozome.net/poplar.php) reference transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Populus trichocarpa (http://www.phytozome.net/poplar.php)
Supplementary_files_format_and_content: tab-delimited text file including unique aligned reads, total aligned reads (Populus trichocarpa) and RPKM values for each sample

organism: Populus tremula x Populus alba

source_name: untreted root

extract_protocol:
Total RNA was isolated using RNaesy Plant Mini Kit (Qiagen). RNA integrity was checked using Experion RNA Analysis Kit (Biorad)
cDNA libraries were prepared for sequencing using standard Illumina protocols by Beckman Coulter Genomics (Danvers,MA, USA)

treatment_protocol: Plants were rooted according to Felten et al. (2009). After three weeks plantlets were placed onto MS medium supplemented with or without 10 nM methyl jasmonate (Sigma Aldrich) and cultivated under original growth conditions for additional ten days.For one biological replicate roots of six small plants were pooled.

value: INRA clone 717-1B4

value: root

tag: time of treatment

value: 10 days


title: Con 12w

status: Public on Feb 08 2014

data_processing:
Illumina sofware was used by IGA Technology services (Udine,Italy) to generate fastq raw data files
Reads were 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 transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Populus trichocarpa (http://www.phytozome.net/poplar.php), Laccaria bicolor (http://genome.jgi-psf.org/Lacbi2/Lacbi2.home.html)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample

source_name: root

growth_protocol: Cuttings of Populus trichocarpa (clone 101-74) were pre-rooted in nutrient hydroponic solution for two weeks before being potted in Terra-Green (a calcined attapulgite clay supplied by Turf-Pro, UK) dosed with 10% Laccaria bicolor S238N as a fungal inoculum.  Control plants were grown in pure, sterile, TerraGreen.  Samples were taken after two, four and 2 weeks. Short roots colonized byfungal mycelia (mycorrhizal root tips) were flash frozen in liquid nitrogen. Fine lateral roots of plants grown without fungal inoculum were used as a control.

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). Four total RNA preparations were pooled and amplified using the SMARTer PCR cDNA Synthesis Kit (Clontech) according to the manufacturer’s instructions.
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology services (Udine,Italy)

tag: pt clone

tag: time of contact

value: control 12 weeks


title: Ter331 with Laccaria 1

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.

value: Laccaria bicolor S238N


title: Methyl Jasmonate treated root 2

description:
This sample is from MeJA treated roots. It is the second of two biological replicates used in this experiment.
6MeJA10

source_name: MeJa treated root


title: Methyl Jasmonate treated root 1

description:
This sample is from MeJA treated roots. It is the first of two  biological replicates used in this experiment.
3MeJA10


title: PfBBc6R8-Control-1

description: PfBBc6R8-Control-single culture-no fungus.

source_name: PfBBc6R8, no fungus control

tag: treatment

value: no fungus

tag: sample type


title: PfBBc6R8-Control-2

tag: strain


title: PfBBc6R8-Control-3


title: PfBBc6R8-before contact-1-1

description:
Technical replicate 1 of 2.
PfBBc6R8-before contact between the bacterial colonies and the fungus (14 days after inoculation)-co-culture with fungus Laccaria bicolor.


title: Laccaria alone 1

value: Mycelium


title: Con 4w

value: control four weeks


title: Con 2w

value: control  two weeks


title: PfBBc6R8-before contact-1-2

description:
Technical replicate 2 of 2.
PfBBc6R8-before contact between the bacterial colonies and the fungus (14 days after inoculation)-co-culture with fungus Laccaria bicolor.


title: Populus tremulaxPopulus alba clone 717-1B4 MiSSP7 overexpressor LINE2-2

description:
This sample is from MiSSP7 overexpressor LINE2 roots. It is the second of three  biological replicates used in this experiment.
LINE2-2

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: P. tremula x P. alba clone 717-1B4  MiSSP7 overexpressor LINE2

growth_protocol: Transformation of P. tremula × P. alba with MiSSP7 lacking the secretion signal was performed using the pORE-E2 vector under the constitutive HPL promoter.The  mutant plants as well as Populus tremulaxPopulus alba clone 717-1B4  were propagated in 1/2 MS for 1 month at 24 degrees, 16hr light. The plants were then pulled gently out of the medium, the entire root system taken and frozen.

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.

tag: clone

value: clone 717-1B4

tag: line

value: MiSSP7 overexpressor LINE2

tag: developmental stage

value: one-month old roots


title: Populus tremulaxPopulus alba clone 717-1B4 MiSSP7 overexpressor LINE2-1

description:
This sample is from MiSSP7 overexpressor LINE2 roots. It is the first of three  biological replicates used in this experiment.
LINE2-1


title: Populus tremulaxPopulus alba clone 717-1B4 MiSSP7 overexpressor LINE1-3

description:
This sample is from MiSSP7 overexpressor LINE1 roots. It is the third of three  biological replicates used in this experiment.
LINE1-3

source_name: P. tremula x P. alba clone 717-1B4  MiSSP7 overexpressor LINE1

value: MiSSP7 overexpressor LINE1


title: Populus tremulaxPopulus alba clone 717-1B4 MiSSP7 overexpressor LINE2-3

description:
This sample is from MiSSP7 overexpressor LINE2 roots. It is the third of three  biological replicates used in this experiment.
LINE2-3


title: Populus tremulaxPopulus alba clone 717-1B4 MiSSP7 overexpressor LINE1-1

description:
This sample is from MiSSP7 overexpressor LINE1 roots. It is the first of three  biological replicates used in this experiment.
LINE1-1


title: Populus tremulaxPopulus alba clone 717-1B4 MiSSP7 overexpressor LINE1-2

description:
This sample is from MiSSP7 overexpressor LINE1 roots. It is the second of three  biological replicates used in this experiment.
LINE1-2


title: Populus tremulaxPopulus alba clone 717-1B4 control root 2

description:
This sample is from control roots. It is the secondof three  biological replicates used in this experiment.
CON-2

source_name: P. tremula x P. alba clone 717-1B4 control roots


title: ECM 12w

organism:
Populus trichocarpa
Laccaria bicolor

source_name: mycorrhizal root tip

tag: lb strain

value: mycorrhizal root tip

value: 12 weeks


title: Populus tremulaxPopulus alba clone 717-1B4 control root 3

description:
This sample is from control roots. It is the thirdt of three  biological replicates used in this experiment.
CON-3


title: Populus tremulaxPopulus alba clone 717-1B4 control root 1

description:
This sample is from control roots. It is the first of three  biological replicates used in this experiment.
CON-1


title: ECM 2w

value: two weeks


title: ECM 4w

value: four weeks


title: FLM

source_name: Free-living mycelium

value: Free-living mycelium

value: control


title: Control root 1

description:
This sample is from control roots. It is the first of two  biological replicates used in this experiment.
4Con

value: INRA clone 717-1B4

value: root

value: 10 days


title: 717-CON-3

status: Public on Dec 19 2013

description: This sample is from control roots. It is the thirdt of three biological replicates used in this experiment.

source_name: Populus tremula x Populus alba clone 717-1B4 control roots

growth_protocol: Populus tremula x Populus alba clone 717-1B4 was used for the mycorrhiza formation assays using chemicals to alter hormone signaling. The transgenic lines of 35S::PttACO1 and 35S::Atetr1-1 were in a Populus tremula x Populus tremuloides T89 background, and therefore this background was used as a control for these experiments. In all cases, 2-cm-long in vitro cuttings were rooted between two cellophane membranes on the surface of solid Murashige and Skoog (MS) medium. At the same time, fungal coloniesof L. bicolor were grown separately on a cellophane membrane onPachlewski solid medium. After the plants were rooted, either a  membrane bearing 10-d-old L. bicolor colonies (for fungal contacts) or a sterile membrane without fungus (for uncolonized root controls) was placed on top of the roots on low-glucose  Pachlewski solid medium (0.1% glucose) or low-glucose Pachlewski solid medium supplemented with 250 µM ACC, 10 nM JA or 500 µM SA. Roots were left in contact with the fungus for 2 weeks, at which point at least three lateral roots colonized by L. bicolor were harvested from each root system.

value: Two-week old control root

tag: mycorrhiza


title: 717-CON-2

description: This sample is from control roots. It is the secondof three biological replicates used in this experiment.


title: 717-MYC-1

description: This sample is from mycorrhizal root tips. It is the first of three biological replicates used in this experiment.

source_name: Populus tremula x Populus alba clone 717-1B4 mycorrhiza

value: Two week-old mycorrhizal root tips

value: Laccaria bicolor


title: 717-MYC-3

description: This sample is from mycorrhizal root tips. It is the third of three biological replicates used in this experiment.


title: ACC-MYC-2

description: This sample is from mycorrhizal root tips treated with 250 µM ACC. It is the second of three biological replicates used in this experiment.

source_name: Populus tremula x Populus alba clone 717-1B4 mycorrhiza treated with 250 µM ACC


title: ACC-MYC-3

description: This sample is from mycorrhizal root tips treated with 250 µM ACC. It is the third of three biological replicates used in this experiment.


title: SA-Myc-1

description: This sample is from mycorrhizal root tips treated with 500µM SA. It is the first of three biological replicates used in this experiment.

source_name: Populus tremula x Populus alba clone 717-1B4 mycorrhiza treated with 500µM SA


title: JA-MYC-3

description: This sample is from mycorrhizal root tips treated with 10nM JA. It is the third of three biological replicates used in this experiment.

source_name: Populus tremula x Populus alba clone 717-1B4 mycorrhiza treated with10nM JA


title: 717-MYC-2

description: This sample is from mycorrhizal root tips. It is the second of three biological replicates used in this experiment.


title: SA-Myc-2

description: This sample is from mycorrhizal root tips treated with 500µM SA. It is the second of three biological replicates used in this experiment.


title: ETR1-MYC-3

organism: Populus tremula x Populus tremuloides

source_name: Populus tremula x Populus tremuloides T89 35S::Atetr1-1 mycorrhiza


title: JA-MYC-2

description: This sample is from mycorrhizal root tips treated with 10nM JA. It is the second of three biological replicates used in this experiment.


title: 717-CON-1

description: This sample is from control roots. It is the first of three biological replicates used in this experiment.


title: ACO-MYC-2

source_name: Populus tremula x Populus tremuloides T89 35S::PttACO1 mycorrhiza


title: ETR1-MYC-1


title: T89-MYC-2

source_name: Populus tremula x Populus tremuloides T89 mycorrhiza


title: T89-CON-1

source_name: Populus tremula x Populus tremuloides T89 control roots


title: ACO-MYC-3


title: T89-MYC-3


title: ETR1-MYC-2


title: Ectopic endometrium_o

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

description:
ectopic endometrium
o.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were analysed with oneChannelGUI (1.16.2) Bioconductor (2.7) package: RMA + quantile normalization

organism: Homo sapiens

source_name: Endometrium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: donor

value: patient

value: endometrium

tag: disease state

value: Pathological (ectopic)


title: SA-Myc-3

description: This sample is from mycorrhizal root tips treated with 500µM SA. It is the third of three biological replicates used in this experiment.


title: ACC-MYC-1

description: This sample is from mycorrhizal root tips treated with 250 µM ACC. It is the first of three biological replicates used in this experiment.


title: Eutopic endometrium_z

description:
eutopic endometrium
z.CEL

value: Normal (eutopic)


title: T89-CON-2

description: This sample is from control roots. It is the second of three biological replicates used in this experiment.


title: JA-MYC-1

description: This sample is from mycorrhizal root tips treated with 10nM JA. It is the first of three biological replicates used in this experiment.


title: T89-MYC-1


title: ACO-MYC-1


title: Eutopic endometrium_v

description:
eutopic endometrium
v.CEL


title: Normal endometrium_b

description:
Normal endometrium
b.CEL

value: healthy donor

value: Normal (control)


title: Eutopic endometrium_r

description:
eutopic endometrium
r.CEL


title: Eutopic endometrium_u

description:
eutopic endometrium
u.CEL


title: Ectopic endometrium_p

description:
ectopic endometrium
p.CEL


title: Normal endometrium_e

description:
Normal endometrium
e.CEL


title: Eutopic endometrium_y

description:
eutopic endometrium
y.CEL


title: Ectopic endometrium_n

description:
ectopic endometrium
n.CEL


title: Eutopic endometrium_t

description:
eutopic endometrium
t.CEL


title: T89-CON-3

description: This sample is from control roots. It is the thirdof three biological replicates used in this experiment.


title: Ectopic endometrium_h

description:
ectopic endometrium
h.CEL


title: Eutopic endometrium_s

description:
eutopic endometrium
s.CEL


title: Normal endometrium_f

description:
Normal endometrium
f.CEL


title: Ectopic endometrium_m

description:
ectopic endometrium
m.CEL


title: Normal endometrium_c

description:
Normal endometrium
c.CEL


title: Ectopic endometrium_g

description:
ectopic endometrium
g.CEL


title: Normal endometrium_a

description:
Normal endometrium
a.CEL


title: Eutopic endometrium_q

description:
eutopic endometrium
q.CEL


title: Ectopic endometrium_i

description:
ectopic endometrium
i.CEL


title: Early telia 2

status: Public on Nov 01 2013

description: This sample is from telia. It is the second of three biological replicates used in this experiment.

organism: Melampsora laricis-populina

source_name: Early telia

growth_protocol: Poplar leaves were naturally infected by M. larici-populina (compatible strains from the environment) at Centre INRA Nancy Lorraine (Champenoux, 54, France) during summer 2010 and infected fallen leaves were harvested at the telial stage (with visible telia) in October 2010 corresponding to early telia before overwintering.

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: environmental sample

value: telia

value: early, before overwintering


title: Early telia 3

description: This sample is from telia. It is the third of three biological replicates used in this experiment.


title: Ectopic endometrium_l

description:
ectopic endometrium
l.CEL


title: H. annosum grown on secondary metabolites produced by Phlebiopsis gigantea-1

description: H. annosum grown on secondary metabolites produced by Phlebiopsis gigantea. Phlebiopsis gigantea was grown in liquid malt extract medium for ten days at 20°C and culture was filtered, heat killed any remnants of hyphae by incubating overnight at 70°C. H. annosum was inoculated in the filtrate and sample was harvested after 10 days incubation at 20°C in the dark.

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 annosum

extract_protocol: Total RNA was extracted by using the CTAB/Chloroform and LiCl precipitation. The RNA was DNase I treated and cleaned with RNeasy® MinElute Cleanup kit (QIAGEN) according to the protocol. RNA concentration and quality were measured by using Agilent RNA 6000 Nano Kit and Bioanalyzer (Agilent Technologies). cDNA was synthesized by using the TransPlex® Complete Whole Transcriptome Amplification Kit (SIGMA) according to the protocol.

value: growth on secondary metabolites produced by Phlebiopsis gigantea


title: H. annosum grown on liquid malt extract medium -3

description: H. annosum grown on liquid malt extract medium. H. annosum was grown in liquid malt extract medium and harvested after 10 days incubation at 20°C in the dark.

value: growth on liquid malt extract


title: H. annosum grown under nutrient starvation, rep3

extract_protocol: Total RNA was extracted by using the CTAB/Chloroform and LiCl precipitation. The RNA was DNase I treated and cleaned with the RNeasy® MinElute Cleanup kit (QIAGEN) according to the protocol. RNA concentration and quality were measured by using the Agilent RNA 6000 Nano Kit and Bioanalyzer (Agilent Technologies). cDNA was synthesized by using the TransPlex® Complete Whole Transcriptome Amplification Kit (SIGMA) according to the protocol.

treatment_protocol: H. annosum growth under nutrient starvation. H. annosum hyphae were harvested and washed with sterile MQ water after growth in liquid malt extract medium for twelve days. Thereafter, the hyphae was washed and cultured in 100 ml sterile MQ water supplied with final concentration of 0.0002g/ml glucose and harvested after 5 days incubation at 20°C in the darkness.

value: hyphae

tag: medium/substrate

value: sterile MQ water supplied with 0.0002g/ml glucose

tag: condition/stress

value: nutrient starvation for 5 days at 20°C in the dark


title: H. annosum grown on secondary metabolites produced by Phlebiopsis gigantea-3

treatment_protocol: H. annosum grown on secondary metabolites produced by Phlebiopsis gigantea. Phlebiopsis gigantea was grown in liquid malt extract medium for ten days at 20°C and culture was filtered, heat killed any remnants of hyphae by incubating overnight at 70°C. H. annosum was inoculated in the filtrate and sample was harvested after 10 days incubation at 20°C in the dark.


title: H. annosum grown on liquid malt extract medium -1

treatment_protocol: H. annosum grown on liquid malt extract medium. H. annosum was grown in liquid malt extract medium and harvested after 10 days incubation at 20°C in the dark.


title: H. annosum grown under nutrient starvation, rep1

tag: tissue


title: H. annosum grown under nutrient starvation, rep2


title: H. annosum grown on liquid malt extract medium -2


title: H. annosum grown on pulverized Scots pine sapwood shavings, rep3

treatment_protocol: H. annosum grown on autoclaved pulverized Scots pine sapwood shavings. Cultures were harvested after three months of incubation at 20°C in the dark.

value: pulverized Scots pine sapwood shavings

value: three months at 20°C in the dark


title: Necrotic xylem of Scots pine infected with H. annosum, rep1

source_name: necrotic xylem of Scots pine infected with H. annosum

treatment_protocol: Xylem tissues from mature (18-20 years old) Scots pine was harvested after three months inoculation with H. annosum.

value: necrotic xylem of mature Scots pine

value: three months


title: H. annosum grown on pulverized Scots pine sapwood shavings, rep1


title: H. annosum grown on pulverized Scots pine sapwood shavings, rep2


title: Necrotic xylem of Scots pine infected with H. annosum, rep3


title: H. annosum grown on secondary metabolites produced by Phlebiopsis gigantea-2


title: Necrotic xylem of Scots pine infected with H. annosum, rep2


title: H. annosum grown on liquid malt extract medium supplemented with NaCl, rep3

treatment_protocol: H. annosum grown on liquid malt extract medium. H. annosum was grown in liquid malt extract medium for 4 weeks. Thereafter, the fungus was exposed to a final concentration of 0.5 M NaCl and harvested after 60 min incubation at 20oC in the dark.

value: liquid malt extract

value: 0.5 M NaCl for 60 min at 20oC in the dark


title: PfBBc6R8-contact-3

description: PfBBc6R8-at the time of contact (16 days after inoculation)-co-culture with fungus Laccaria bicolor.

source_name: PfBBc6R8, at the time of contact with fungus

value: Laccaria bicolor fungus

tag: sampling time

value: 16 days after inoculation


title: H. annosum grown on liquid malt extract medium supplemented with hydrogen peroxide, rep3

treatment_protocol: H. annosum grown on liquid malt extract medium. H. annosum was grown in liquid malt extract medium for 4 weeks. Thereafter, the fungus was exposed to a final concentration of 5 mM hydrogen peroxide and harvested after 60 min incubation at 20oC in the dark.

value: 5 mM hydrogen peroxide for 60 min at 20oC in the dark


title: Necrotic phloem of Scots pine infected with H. annosum, rep2

source_name: necrotic phloem of Scots pine infected with H. annosum

treatment_protocol: Phloem of Scots pine was harvested after three months inoculation with H. annosum from mature (18-20 years old) Scots pine.

value: necrotic phloem of mature Scots pine


title: H. annosum grown on liquid malt extract medium supplemented with NaCl


title: Necrotic phloem of Scots pine infected with H. annosum, rep1


title: Necrotic phloem of Scots pine infected with H. annosum, rep3


title: H. annosum grown on liquid malt extract medium supplemented with NaCl, rep2


title: H. annosum grown on liquid malt extract medium supplemented with hydrogen peroxide, rep1


title: H. annosum grown on pulverized Scots pine heartwood shavings, rep2

treatment_protocol: H. annosum grown on autoclaved pulverized Scots pine heartwood shavings. Cultures were harvested after three months of incubation at 20°C in the dark.


title: H. annosum grown on pulverized Scots pine heartwood shavings, rep3


title: H. annosum grown on liquid malt extract medium supplemented with hydrogen peroxide, rep2


title: H. annosum grown on liquid malt extract medium, rep2

treatment_protocol: H. annosum grown on liquid malt extract medium. H. annosum was grown in liquid malt extract medium and harvested after three weeks incubation at 20°C in the dark.

value: three weeks at 20°C in the dark


title: H. annosum grown on liquid malt extract medium supplemented with CaCl2, rep1

treatment_protocol: H. annosum grown on liquid malt extract medium. H. annosum was grown in liquid malt extract medium for 4 weeks. Thereafter, the fungus was exposed to a final concentration of 0.5 M CaCl2 and harvested after 60 min incubation at 20oC in the dark.

value: 0.5 M CaCl2 for 60 min at 20oC in the dark


title: Normal endometrium_d

description:
Normal endometrium
d.CEL

value: healthy donor

value: endometrium

value: Normal (control)


title: H. annosum grown on liquid malt extract medium, rep1


title: H. annosum grown on pulverized Scots pine bark shavings, rep3

treatment_protocol: H. annosum grown on autoclaved pulverized Scots pine bark shavings. Cultures were harvested after three months of incubation at 20°C in the dark.

value: pulverized Scots pine bark shavings


title: H. annosum grown on liquid malt extract medium at +27°C, rep3

treatment_protocol: H. annosum grown on liquid malt extract medium. H. annosum was grown in liquid malt extract medium for 2 weeks at 20oC followed by three weeks incubation at +27°C.

value: +27°C for three weeks


title: H. annosum grown on liquid malt extract medium supplemented with CaCl2, rep2


title: H. annosum grown on pulverized Scots pine bark shavings, rep2


title: H. annosum grown on liquid malt extract medium at +27°C, rep2


title: H. annosum grown on liquid malt extract medium at +8°C, rep3

treatment_protocol: H. annosum grown on liquid malt extract medium. H. annosum was grown in liquid malt extract medium for 2 weeks at 20oC followed by three weeks incubation at +8°C.

value: +8°C for three weeks


title: H. annosum grown on liquid malt extract medium supplemented with CaCl2, rep3


title: H. annosum grown on pulverized Scots pine heartwood shavings, rep1

value: three months at 20°C in the dark


title: H. annosum grown on liquid malt extract medium at +27°C, rep1


title: H. annosum grown on liquid malt extract medium at +8°C, rep2


title: Early telia 1

description: This sample is from telia. It is the first of three biological replicates used in this experiment.

value: environmental sample

value: telia

value: early, before overwintering


title: H. annosum grown on liquid malt extract medium at +8°C, rep1

value: liquid malt extract


title: H. annosum grown on liquid malt extract medium, rep3


title: H. annosum grown on pulverized Scots pine bark shavings, rep1