title: Aorta_Mouse_rep3

status: Public on Dec 05 2018

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using STAR v2.5
Detection and quantification of circRNAs was performed with DCC python package
Genome_build: mm10

molecule: polyA RNA

source_name: Aorta

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen), and treated with DNase according to the manufacture’s protocol.
Sample Validation:  -Standard RNA Reagent Kit (Perkin Elmer – Cat # CLS960010)  -HT DNA 5K/RNA/CZE LabChip (Perkin Elmer – Cat # 760435)  -LabChip GXTouch HT Instrument (Perkin Elmer)     -Sample Quantification  Qubit® RNA Assay Kit (LifeTechnologies – Cat# Q32852)  QUBIT 3.0 Fluorometer Instrument (LifeTechnologies – Cat# Q33216)     -Library Generation  TruSeq® Stranded mRNA Sample Prep Kit HT - (Illumina - Cat# RS-122-2103)   Purify and Fragment mRNA  Synthesize First/Second Strand cDNA  Adenylate 3' Ends  Ligate Adapters  - PCR Amplification  Plus: Agencourt AMPure XP (Beckman Coulter - Cat# A63881)    -Library Validation  HT DNA High Sens Reagent Kit (Perkin Elmer – Cat # CLS760672)  HT DNA 1K/12K/HI Sens Chip (Perkin Elmer – Cat # 760517)  LabChip GXTouch HT Instrument (Perkin Elmer)  Qubit® dsDNA HS Assay Reagent Kit (LifeTechnologies – Cat# Q32851)  Qubit® Assay Plastic Tubes (LifeTechnologies – Cat# Q32856)  QUBIT 3.0 Fluorometer Instrument (LifeTechnologies – Cat# Q33216)    -Normalization and Pool    -Denaturation and Dilution of Libraries    -Sequencing  NextSeq® 500/550 High Output v2 Reagent Kit (150 cycles) – Illumina – Cat# FC-404-2002)  NextSeq 500 Instrument
Paired end sequence reads (75-bp in length) were generated on an Illumina NextSeq 500

tag: strain

tag: genotype


title: Aorta_Mouse_rep1

type: SRA

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

library_source: transcriptomic

organism: Mus musculus


title: Aorta_Mouse_rep2


title: Adult 1 unfractionated

status: Public on Dec 22 2018

city: La Jolla

first: Miles

middle: F

last: Wilkinson

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 4811

department: Reproductive Medicine

country: USA

institute: University of California

data_processing:
De-multiplexing and FastQ file generation
Cell ranger based mapping and filtering
Seurat R package for QC filtering and normalization
pagoda2 and monocle for clustering and pseudotime trajectory
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix of genes, counts and cell barcodes

molecule: total RNA

organism: Homo sapiens

source_name: adult

extract_protocol:
Testis tissue was dissociated using two step enzymatic digestion with collagenase-IV and trypsin-EDTA. Single cell suspension was washed and enriched for ITGA6 expressing cells (MACS column) or was direclty used. Cells were diluted for loading on Chromium chip
Chromium Single Cell Kit [v2 chemistry]
10x single cell RNA sequencing

tag: tissue

value: Testis

tag: age

value: 37 yr

tag: sample


title: Adult 2 unfractionated

value: 42 yr


title: WT2

status: Public on Apr 21 2019

data_processing:
RNA-seq reads were aligned to the Ensembl GRC38 genome assembly using STAR v2.5 .1b
Differentially expressed genes were identified using the edgeR R Biocondutor package importing raw counts per gene calculated with featureCounts v1.5.2
Genome_build: Ensembll GRC38
Supplementary_files_format_and_content: bigWig were generated using bam2wig.py module in RSeQC v2.5
Supplementary_files_format_and_content: Normalized-count-table from edgeR

source_name: Mesenchymal Stem cells

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen), and treated with DNase according to the manufacture’s protocol.
Sample Validation:  -Standard RNA Reagent Kit (Perkin Elmer – Cat # CLS960010)  -HT DNA 5K/RNA/CZE LabChip (Perkin Elmer – Cat # 760435)  -LabChip GXTouch HT Instrument (Perkin Elmer)  -Sample Quantification  Qubit® RNA Assay Kit (LifeTechnologies – Cat# Q32852)  QUBIT 3.0 Fluorometer Instrument (LifeTechnologies – Cat# Q33216)  -Library Generation  TruSeq® Stranded mRNA Sample Prep Kit HT - (Illumina - Cat# RS-122-2103)   Purify and Fragment mRNA  Synthesize First/Second Strand cDNA  Adenylate 3' Ends  Ligate Adapters  - PCR Amplification  Plus: Agencourt AMPure XP (Beckman Coulter - Cat# A63881)  -Library Validation  HT DNA High Sens Reagent Kit (Perkin Elmer – Cat # CLS760672)  HT DNA 1K/12K/HI Sens Chip (Perkin Elmer – Cat # 760517)  LabChip GXTouch HT Instrument (Perkin Elmer)  Qubit® dsDNA HS Assay Reagent Kit (LifeTechnologies – Cat# Q32851)  Qubit® Assay Plastic Tubes (LifeTechnologies – Cat# Q32856)  QUBIT 3.0 Fluorometer Instrument (LifeTechnologies – Cat# Q33216)  -Normalization and Pool  -Denaturation and Dilution of Libraries  -Sequencing  NextSeq® 500/550 High Output v2 Reagent Kit (150 cycles) – Illumina – Cat# FC-404-2002)  NextSeq 500 Instrument
Single end sequence reads (75-bp in length) were generated on an Illumina NextSeq 500


title: L1

status: Public on Oct 01 2019

type: genomic

city: Naples

first: Ankit

last: Verma

state: Naples

address: Via Pietro Castellino, 111

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

description: methylation profiling using bisulfite converted

hyb_protocol: 800 nanograms of genomic DNA was treated with sodium bisulfite by using the EZ DNA Methylation Kit (D5001, Zymo Research) following the manufacturer’s protocol. The bisulfite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC 850K Bead Chip (WG-317-1001, Illumina) using Illumina standard protocol.

scan_protocol: Fluorescence intensities were captured using Illumina HiScan SQ (Illumina)

data_processing:
Data was analysed using R version 3.4.1 (2017-06-30). Beta-values were extracted from ‘idat’ files by using the ‘Load’ module of the ‘Champ’ R package (v. 2.12.0), with quality control options set as default. The quality control step retained 759772 probes, which were used for further analysis. Probes overlapped with SNP (79662) and with a detection pvalue < 0.01 (3447), beadcount <3 in at least 5% of samples in one or more samples (2582) were eliminated. X or Y chromosomes probes (17432), non-cg probes (2915), and probes aligning to multiple locations (46) and unannotated probes were also removed from analysis. No background correction was carried out. SWAN normalisation was applied, with the ‘method’ option set to “minfi”. The SWAN normalized samples were assigned with respective genome coordinates based on probe name and manifest file (Illumina Inc., USA).
The file 'matrix_signal_intensities.txt' includes: Unmethylated signal (B) and methylated signal (A) intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: genomic DNA from L1 Blood (proband)

label_protocol: Standard llumina Protocol

extract_protocol: Genomic DNA was isolated from peripheral blood lymphocytes by using the salting-out method.

value: blood

tag: gender

value: M

tag: disease state

value: Affected (Beckwith-Wiedemann syndrome)


title: CTRL01

source_name: genomic DNA from CTRL01 Blood

value: Normal


title: CTRL03

source_name: genomic DNA from CTRL03 Blood

value: F


title: CTRL05

source_name: genomic DNA from CTRL05 Blood


title: Tubma-ECM1

status: Public on Nov 01 2018

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

description:
Tubma_ECM1
This sample is from T.magnatum-Oak mycorrhiza. It is the first of three biological replicates used in this experiment.

data_processing:
Illumina software was used by GeT (Génopole Toulouse Midi-Pyrénées, Auzeville, France) to generate fastq raw data files
Raw fastq file reads were trimmed for quality and adapter using CLC Genomics Workbench 9.   Trimmed reads were aligned to the Tuber magnatum v1 (https://genome.jgi.doe.gov/Tubma1/Tubma1.home.html) reference transcripts using CLC Genomics Workbench 9 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Tuber magnatum v1 (https://genome.jgi.doe.gov/Tubma1/Tubma1.home.html)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample

organism:
Quercus robur
Tuber magnatum

source_name: Tuber magnatum_Quercus robur_mycorrhiza

growth_protocol: T.magnatum inoculated Oak (Quercus robur) plants were produced by ROBIN nurseries (http://www.robinpepinieres.com/fr/plants-truffiers/plants-truffiers-robin),  following their standard protocol. Mycorrhizal root tips were harvested from 6 months old plants.The free-living  mycelium of T. magnatum was isolated from a fruiting body collected in Città di Castello,  Perugia (Italy). It was grown in 100 ml liquid MNM medium supplemented with Bacto  Peptone (4 g per L), yeast extract (2 g per L), and malt extract (2 g per L) in the dark at 22-  24°C for 30 days. Mycelium was then sampled and snap frozen in liquid nitrogen before RNA  extraction. One T. magnatum fruiting body (631) was harvested in Assisi-  Valfabbrica (Perugia, Italy) in November 2005 and two (775, 765) in Pietralunga (Perugia, Italy) in  November 2006.

extract_protocol:
Total RNA from T. magnatum free-living mycelium and fruiting bodies was extracted  using the Spectrum Plant Total RNA kit (Sigma-Aldrich), following the protocol A and the  on-column DNase Digestion procedure. Total RNA was extracted from ectomycorrhizal root  tips of T. magnatum/Q.robur using the RNeasy Plant Mini Kit of Qiagen with DNase step and  addition of 20 mg/ml polyethylene glycol to the RLC extraction buffer.
cDNA libraries were prepared for sequencing using standard Illumina protocols by GeT (Génopole Toulouse Midi-Pyrénées, Auzeville, France)

value: oak mycorrhizal root tips


title: Tubma-FB3

description:
Tubma_FB_MA_765
This sample is from T.magnatum fruiting body. It is the third of three biological replicates used in this experiment.

organism: Tuber magnatum

source_name: Tuber magnatum_Fruiting_body

value: fruiting body


title: Tubma-ECM2

description:
Tubma_ECM2
This sample is from T.magnatum-Oak mycorrhiza. It is the second of three biological replicates used in this experiment.


title: Tubma-FB2

description:
Tubma_FB_MA_775
This sample is from T.magnatum fruiting body. It is the second of three biological replicates used in this experiment.


title: Tubma-ECM3

description:
Tubma_ECM3
This sample is from T.magnatum-Oak mycorrhizaa. It is the third of three biological replicates used in this experiment.


title: Tubma-FLM3

description:
Tubma_848_FLM_2
This sample is from T.magnatum free-living mycelium. It is the third of three biological replicates used in this experiment.

source_name: Tuber magnatum_free_living_mycelium

value: free living mycelium


title: Tubma-FLM2

description:
Tubma_848_FLM_1b
This sample is from T.magnatum free-living mycelium.. It is the second of three biological replicates used in this experiment.


title: KD1_rep2

type: RNA

description:
replicate 2
shUHRF1#3_repB

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was exported from GenomeStudio V2011.1 and analyzed with lumi package, vst-transfromed and quantile normalized

label: biotin

source_name: Primary VSMC

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

growth_protocol: no growth protocol

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

treatment_protocol: Primary VSMC were infected with lentivirus expressing Uhrf1-specific shRNA or scramble shRNA, selected with Puromicin for two days. RNA was collected after five days.

tag: shRNA

value: 8 weeks

tag: Sex


title: KD2_rep1

description:
replicate 1
shUHRF1#4_repA


title: ctr2_rep2

description:
replicate 2
shSCR#2_repB

value: shSCR


title: Tubma-FB1

description:
Tubma_FB_MA_631
This sample is from T.magnatum fruiting body. It is the first of three biological replicates used in this experiment.


title: ctr2_rep1

description:
replicate 1
shSCR#2_repA


title: ctr1_rep2

description:
replicate 2
shSCR#1_repB


title: KD2_rep2

description:
replicate 2
shUHRF1#4_repB


title: Donor3_scRNA-seq_rep1

status: Public on Oct 15 2018

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

data_processing:
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v1.2.1). Three types of fastq files were generated: I1 contains 8 bp sample index; R1 contains 26 bp (10 cell + 16 UMI) index and R2 contains 100 bp cDNA sequence. Fastq files were then run with count application (Cell Ranger v1.2.1) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: Donor3_testicular cells

extract_protocol:
Single testicular cells were generated using standard two step enzymatic digestion protocol as described before (Guo et al., Cell Stel Cell 2017). Cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 26 X 100 cycle paired-end run via a Illumina 2500 instrument. Samples from Donor 1 was sequenced in two separate sequencing lanes. For Donors 2 and 3, their libraries were mixed before sequencing, and seqenced by four different lanes.
10X Genomics single cell RNA sequencing

tag: subject status

value: healthy men of peak reproductive age

tag: subject id

value: donor 3

value: testicle

tag: cell type

value: testicular cells


title: Donor2_scRNA-seq_rep2

source_name: Donor2_testicular cells

value: donor 2


title: Donor3_scRNA-seq_rep2


title: Donor2_scRNA-seq_rep1


title: Tubma-FLM1

description:
Tubma_848_FLM_1A
This sample is from T.magnatum free-living mycelium. It is the first of three biological replicates used in this experiment.


title: Donor1_scRNA-seq_rep2

source_name: Donor1_testicular cells

value: donor 1


title: KD1_rep1

description:
replicate 1
shUHRF1#3_repA


title: ctr1_rep1

description:
replicate 1
shSCR#1_repA


title: U87 ERβ FLAG_1

status: Public on May 02 2019

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

description: U87 cells expressing ERβ FLAG vector

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: U87 MG glioblastoma cell line

growth_protocol: U87 cells were cultured in DMEM media supplemented with 10% FBS

extract_protocol:
U87 cells transduced with lentiviral particles carrying either empty vector or ERβ FLAG expression vector and total RNA was isolated using RNeasy mini kit using manufacturer’s protocol (Qiagen, Valencia, CA).
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from U87 cells expressing either empty vector or ERβ expression vector and subjected to RNA-seq analysis

tag: cell line

tag: treatment

value: overexpression


title: L3

source_name: genomic DNA from L3 Blood (brother of proband)

value: blood


title: CTRL04

source_name: genomic DNA from CTRL04 Blood


title: PhchrT6_1: Mycelium 6h-1

status: Public on Oct 01 2018

description: This sample is from Mycelium treated with Oak extractives for 6h. 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
Raw fastq file reads were trimmed for quality and adapter using CLC Genomics Workbench 9.   Trimmed reads were aligned to the P. chrysosporium reference transcripts (http://genome.jgi.doe.gov/Phchr2/Phchr2.home.html)  using CLC Genomics Workbench and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: P. chrysosporium v2.2 (http://genome.jgi.doe.gov/Phchr2/Phchr2.home.html)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample

organism: Phanerodontia chrysosporium

source_name: Mycelium extractives 6h

growth_protocol: Oak (Quercus petraea) heartwood samples were ground to a fine powder, passed through a   mesh sieve, and dried at 60ÅãC until minimal weight was obtained. Extraction was performed with high-performance liquid chromatography (HPLC)-grade acetone using a Soxhlet apparatus. The solvent was removed from the crude extracts by evaporation to dryness under vacuum. Phanerochaete chrysosporium homocaryon RP78 was maintained in malt agar medium. Fungal plugs were used to inoculate liquid minimal medium containing 5 mM sodium acetate pH 4.5,1% glucose, 1 mM ammonium tartrate, 1% (vol/vol) base medium (20 g liter-1 KH2PO4, 5 g liter-1 MgSO4, 1 g liter-1 CaCl2), 7% (vol/vol) trace medium (1.5 g liter-1 nitrilotriacetate, 3 g liter-1 MgSO4, 1 g liter-1 NaCl, 0.1 g liter-1 FeSO4 . 7H2O, 0.1 g liter-1 CoCl2, 0.1 g liter-1 294 ZnSO4 .7H2O, 0.1 g liter-1 CuSO4, 10 mg liter-1 AlK(SO4) . 12H2O, 10 mg liter-1 H3BO3, 10 mg liter-1 NaMoO4 . 2H2O), and 225 μM MnCl2 (Tien and Kirk, 1988). Static culturing in 20 ml of medium was performed at 37ÅãC for 4 days and oak extractives were then added at a final concentration of 100 μg/ml (from a stock solution at 200 mg/ml in DMSO). The treatments were done in triplicate at 37ÅãC for the control (T0), 1h (T1), 3h (T3) and 6h (T6). The mycelium was harvested, rinsed with distilled water and frozen in liquid nitrogen for further RNA extraction. For the control (T0), the treatment was done and the mycelium was harvested immediately.

extract_protocol:
Total RNA from P. chrysosporium was extracted using the RNeasy PowerSoil Total RNA Kit  305 (MoBio, Qiagen), following the standard protocol of the provider. Quantification and integrity check were conducted using an Experion Automated Electrophoresis Station (Biorad).
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology Services (Udine, Italy)

value: mycelium

value: Oak extractives 6h


title: PhchrT6_3: Mycelium 6h-3

description: This sample is from Mycelium treated with Oak extractives for 6h. It is the third of three biological replicates used in this experiment.


title: PhchrT1_3: Mycelium 1h-3

description: This sample is from Mycelium treated with Oak extractives for 1h. It is the third of three biological replicates used in this experiment.

source_name: Mycelium extractives 1h

value: Oak extractives 1h


title: CTRL06

source_name: genomic DNA from CTRL06 Blood

value: F

value: Normal


title: PhchrT3_1: Mycelium 3h-1

description: This sample is from Mycelium treated with Oak extractives for 3h. It is the first of three biological replicates used in this experiment.

source_name: Mycelium extractives 3h

value: Oak extractives 3h


title: PhchrT3_2: Mycelium 3h-2

description: This sample is from Mycelium treated with Oak extractives for 3h. It is the second of three biological replicates used in this experiment.


title: WT_ab_DN_3

status: Public on Jun 24 2019

data_processing:
RNA-seq reads were aligned to the Ensembl GRCm38 genome assembly using STAR v2.5.1b with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --quantMode TranscriptomeSAM GeneCounts.
Data was filtered accoring to a coefficient of variation calculated based on Trimmed Mean of M-Values in each group.
Differential expression analysis was performed using the GLM approach implemented in the edgeR R/Bioconductor package.
Genome_build: Ensembl release GRCm38
Supplementary_files_format_and_content: bigWig were generated using bam2wig.py module in RSeQC v2.5

source_name: T cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) following the manufacturer’s recommendations and purified with Maxwell 16 LEV SimplyRNA Cells Kit (Promega) using Maxwell 16 Instrument (Promega). Total RNA quality was evaluated using the Agilent Bioanalyzer: all samples had an average RIN greater than 5. For Poly(A) mRNA sequencing, libraries were constructed using the SMART Seq v4 Ultra Low Input RNA kit (Clontech) according to manufacturer´s instruction. Sequencing was performed with the NextSeq 500 in a single-end mode (75bp length) and with a coverage  >30M reads for each sample.
Single-end sequence reads (75-bp in length) were generated on an Illumina NextSeq 500

tag: tumor

value: sarcoma


title: PhchrT1_1: Mycelium 1h-1

description: This sample is from Mycelium treated with Oak extractives for 1h. It is the first of three biological replicates used in this experiment.


title: PhchrT0_3: Mycelium T0-3

description: This sample is from Mycelium Control T0. It is the third of three biological replicates used in this experiment.

source_name: Mycelium Control

value: Control T0


title: PhchrT0_1: Mycelium T0-1

description: This sample is from Mycelium Control T0. It is the first of three biological replicates used in this experiment.


title: Tubma_Qrob_mycorrhiza 2

status: Public on Jul 01 2018

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

data_processing:
Illumina software was used by GeT (Génopole Toulouse Midi-Pyrénées, Auzeville, France) to generate fastq raw data files
Reads were aligned to Quercus robur CDS using CLC Genomics Workbench 9 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Quercus robur cds (Qrob_H2.3_Genes_v2.2_20161004.CDS_nuc.txt)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample

organism: Quercus robur

source_name: Tuber magnatum

growth_protocol: Tuber melanosporum, T.aestivum (uncinatum) and T.magnatum inoculated Oak (Quercus robur) plants were produced by ROBIN nurseries (http://www.robinpepinieres.com/fr/plants-truffiers/plants-truffiers-robin), following their standard protocol. Mycorrhizal root tips were harvested from 1 year old plants.

extract_protocol:
Total RNA of 100 mg of tissue per sample was extracted using RNeasy Plant Mini Kit (Qiagen).   Quantification and integrity check were conducted using an Experion Automated Electrophoresis Station (Bio-Rad, Hercules, CA, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols by GeT (Génopole Toulouse Midi-Pyrénées, Auzeville, France)

value: mycorrhizal root tips


title: Tubmel_Qrob_mycorrhiza 3

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

source_name: Tuber melanosporum


title: Tubae_Qrob_mycorrhiza 3

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

source_name: Tuber aestivum


title: Tubae_Qrob_mycorrhiza 1

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


title: Tubma_Qrob_mycorrhiza 3

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


title: Tubae_Qrob_mycorrhiza 2

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


title: Tubma_Qrob_mycorrhiza 1

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


title: PhchrT3_3: Mycelium 3h-3

description: This sample is from Mycelium treated with Oak extractives for 3h. It is the third of three biological replicates used in this experiment.


title: Tubmel_Qrob_mycorrhiza 1

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


title: Poplar Mycorrhizal roots-late-3

status: Public on Mar 01 2018

description:
Cenococcum geophilum 1.58-Populus tremula x alba INRA 717-1B4
This sample is from 60d old mycorrhizal poplar rootss. It is the third of three biological replicates used in this experiment.
PoplarECMlate-3

data_processing:
Illumina sofware was used by the JGI to generate fastq raw data files
Raw fastq file reads were filtered and trimmed using the JGI QC pipeline. Filtered reads from each library were aligned to the reference genome using HISAT version 0.1.4-beta, featureCounts was used to generate the raw gene counts file using gff3 annotations. Only primary hits assigned to the reverse strand were included in the raw gene counts.Further  FPKM and TPM normalized gene counts were calculated.
Genome_build: Cenococcum geophilum 1.58 (https://genome.jgi.doe.gov/Cenge3/Cenge3.home.html)
Supplementary_files_format_and_content: tab-delimited text file including JGI Cenge3 Protein IDs, raw counts,FPKM and TPM normalised values

organism: Cenococcum geophilum 1.58

source_name: Mycorrhizal roots

growth_protocol: Populus tremula x Populus alba; INRA clone 717-1B4 was micropropagated in vitro in Murashige and Skoog (MS) medium, with hormone supplements to synchronize rhizogenesis. In parallel, MNM medium with low phosphorus and nitrogen was covered with cellophane membranes and inoculated with ten to twelve agar disks containing fungal mycelium at 25 °C for 20 days. Following this, two hybrid poplar plants per dish were transferred onto the fungal mycelium. The Petri dishes were incubated in a growth chamber at 25 °C with 16 h light/ day for 60 days. Pure cultures of C. geophilum grown in identical conditions were used as free-living mycelium controls.

extract_protocol:
Total RNA from mycorrhizal roots and fungal controls were extracted with the RNeasy Plant Mini kit (Qiagen, Courtaboeuf, France), including a DNase I (Qiagen) treatment, according to the manufacturer’s instructions to eliminate traces of genomic DNA. Assays for the quantification and integrity check were conducted using an Experion Automated Electrophoresis Station (Bio-Rad, Hercules, CA, USA) or Agilent 2100 Bioanalyzer system (Agilent, Santa Clara, CA, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols by the Joint Genome Institue (JGI)

value: Mycorrhizal roots


title: Roots WT 2

status: Public on Jan 15 2019

description:
This sample is from Wildtype roots. It is the second of three biological replicates used in this experiment.
Populus tremula x P. alba clone INRA 717-1B4

data_processing:
Illumina software was used by the GIGA genomic platform (Liege University, Liege, Belgium to generate fastq raw data files
Raw reads were trimmed for quality and mapped to the substituted genome sequence of P. tremula x P. alba 717-1B4 (http://aspendb.uga.edu/index.php/databases/spta-717-genome)
To identify differentially regulated Populus transcripts, the Linear Models for Microarray and RNA-Seq Data (LIMMA) package (Smyth, 2005) in R (R Core Team, 2013) and the raw counts from the CLC mapping were used.
Genome_build: substituted genome sequence of P. tremula x P. alba 717-1B4 (http://aspendb.uga.edu/index.php/databases/spta-717-genome)
Supplementary_files_format_and_content: tab-delimited text files include aligned reads (Counts_CLC) and normalised log2 expression values (norm log2_Limma) for each sample

organism: Populus tremula x Populus alba

source_name: Wildtype roots

growth_protocol: RKN infection and analysis were performed as described by Baldacci-Cresp et al. (2016). Cut apart galls at 21 dai and corresponding uninfected roots from the CAD and the WT lines (3 biological replicates) were frozen in liquid nitrogen.

extract_protocol:
Total RNA was extracted from galls at 21 dai and corresponding uninfected roots from the CAD and the WT lines  (3 biological replicates) using the Plant RNA Isolation Kit (Agilent) following standard procedures with a few  modifications: an incubation step (15 min, room temperature) and a centrifugation step (5 min, 20.000 g, 4°C) were added  before prefilter column application.   RNA quality controls were performed using a BioAnalyzer RNA Nano.   All samples presented a high quality with a RIN comprised between 9 and 10
TruSeq mRNA Stranded libraries were prepared by the GIGA genomic platform (Liege University, Liege, Belgium)

value: Roots

tag: genotype/variation

value: Wildtype


title: Sclerotia-2

description:
Sclerotia-2
11276.2.199279.AGTCTCA-GTGAGAC
This sample is from sclerotia. It is the second of three biological replicates used in this experiment.

data_processing:
Illumina sofware was used by the JGI to generate fastq raw data files
Raw fastq file reads were filtered and trimmed using the JGI QC pipeline. Filtered reads from each library were aligned to the Cenococcum reference transcriptome (https://genome.jgi.doe.gov/Cenge3/Cenge3.home.html) using BBmap with only unique mapping allowed (parameters: ambig=toss strictmaxindel=4 minid=0.9). If a read mapped to more than one location, it was ignored. Raw reads as well as  FPKM and TPM normalized gene counts were generated using bbmap.
Genome_build: Cenococcum geophilum 1.58 (https://genome.jgi.doe.gov/Cenge3/Cenge3.home.html)
Supplementary_files_format_and_content: tab-delimited text file including JGI Cenge3 Protein IDs, raw counts, FPKM and TPM normalised values

source_name: Sclerotia

growth_protocol: Pine seeds (P. sylvestris provenance VS/Leuk (31/10) WSL) were superficially disinfected in a laminar flux hood by immersion in H2O2 for 30 min, followed by three rinses with sterile distilled water. The seeds were germinated in modified MMN medium with low nitrogen and phosphorus during seven days for observation of contamination. After seed germination, the plants were transferred to Petri dishes containing modified MMN and covered with a cellophane membrane (135 mm). Approximately ten agar disks containing fungal mycelium of C. geophilum 1.58 were placed in the vicinity of the roots. The dishes were incubated in a growth chamber at 25 °C with 16 h light/ day for 90 days. Pure cultures of C. geophilum in identical conditions were used as experimental controls. Extramatrical mycelium surrounding roots and emanating from pine ECMs was scratched from the cellophane using a scalpel and if present, sclerotia formed in these dishes were separately collected and also immediately frozen in liquid nitrogen.

extract_protocol:
Total RNA from mycorrhizal roots, sclerotia, extramatrical mycelium and fungal controls were extracted with the RNeasy Plant Mini kit (Qiagen, Courtaboeuf, France), including a DNase I (Qiagen) treatment, according to the manufacturer’s instructions to eliminate traces of genomic DNA. Assays for the quantification and integrity check were conducted using an Experion Automated Electrophoresis Station (Bio-Rad, Hercules, CA, USA) or Agilent 2100 Bioanalyzer system (Agilent, Santa Clara, CA, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols by the Joint Genome Institue (JGI)

value: Sclerotia


title: Free-living mycelium-90-1

description:
FLM90-1
11276.8.199323.CTGACAC-TGTGTCA
This sample is from 90d old 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: Sclerotia-3

description:
Sclerotia-3
11307.8.200793.CCTCAGT-AACTGAG
This sample is from sclerotia. It is the third of three biological replicates used in this experiment.


title: Sclerotia-1

description:
Sclerotia-1
11276.2.199279.TCCGAGT-AACTCGG
This sample is from sclerotia. It is the first of three biological replicates used in this experiment.


title: PhchrT6_2: Mycelium 6h-2

description: This sample is from Mycelium treated with Oak extractives for 6h. It is the second of three biological replicates used in this experiment.


title: Free-living mycelium-90-3

description:
FLM90-3
11287.1.199512.TGTACAC-GGTGTAC
This sample is from 90d old free-living mycelium. It is the third of three biological replicates used in this experiment.


title: Extramatrical-mycelium-1

description:
Extramatrical-1
11287.5.199528.TTCGTAC-GGTACGA
This sample is from extramatrical mycelium. It is the first of tthree biological replicates used in this experiment.

source_name: Extramatrical mycelium

value: Extramatrical mycelium


title: Poplar Mycorrhizal roots-late-2

description:
Cenococcum geophilum 1.58-Populus tremula x alba INRA 717-1B4
This sample is from 60d old mycorrhizal poplar roots. It is the second of three biological replicates used in this experiment.
PoplarECMlate-2


title: Free-living mycelium-90-2

description:
FLM90-2
11287.1.199512.CCAGTGT-AACACTG
This sample is from 90d old free-living mycelium. It is the second of three biological replicates used in this experiment.


title: Poplar Mycorrhizal roots-late-1

description:
Cenococcum geophilum 1.58-Populus tremula x alba INRA 717-1B4
This sample is from 60d old mycorrhizal poplar roots. It is the first of three biological replicates used in this experiment.
PoplarECMlate-1


title: PhchrT0_2: Mycelium T0-2

description: This sample is from Mycelium Control T0. It is the second of three biological replicates used in this experiment.


title: PhchrT1_2: Mycelium 1h-2

description: This sample is from Mycelium treated with Oak extractives for 1h. It is the second of three biological replicates used in this experiment.


title: Free-living mycelium-late-3

description:
Cenococcum geophilum 1.58
This sample is from 60d old free-living mycelium. It is the third of three biological replicates used in this experiment.
FLMlate-3


title: Free-living mycelium-late-2

description:
Cenococcum geophilum 1.58
This sample is from 60d old free-living mycelium. It is the second of three biological replicates used in this experiment.
FLMlate-2


title: Tubmel_Qrob_mycorrhiza 2

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


title: Extramatrical-mycelium-3

description:
Extramatrical-3
11276.2.199279.GTAACGA-GTCGTTA
This sample is from extramatrical mycelium. It is the third of three biological replicates used in this experiment.


title: Pinus Mycorrhizal roots-90-3

description:
PinusECM90-3
11276.8.199323.GCCTTGT-AACAAGG
This sample is from 90d old mycorrhizal poplar roots. It is the third of three biological replicates used in this experiment.

organism:
Pinus sylvestris
Cenococcum geophilum 1.58


title: Pinus Mycorrhizal roots-90-1

description:
PinusECM90-1
11276.7.199319.CGGTTGT-AACAACC
This sample is from 90d old mycorrhizal poplar roots. It is the first of three biological replicates used in this experiment.


title: Pinus Mycorrhizal roots-90-2

description:
PinusrECM90-2
11276.7.199319.TACCAAC-GGTTGGT
This sample is from 90d old mycorrhizal poplar roots. It is the second of three biological replicates used in this experiment.


title: Extramatrical-mycelium-2

description:
Extramatrical-2
11276.7.199319.ACGGTCT-AAGACCG
This sample is from extramatrical mycelium. It is the second of three biological replicates used in this experiment.


title: Mycorrhizal roots-3

status: Public on Jan 01 2018

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

data_processing:
Illumina sofware was used by the JGI to generate fastq raw data files
Reads were aligned to Meliniomyces bicolor  (https://genome.jgi.doe.gov/Melbi2/Melbi2.home.html) reference transcripts using CLC Genomics Workbench 8 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Meliniomyces bicolor (https://genome.jgi.doe.gov/Melbi2/Melbi2.home.html)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample

organism: Hyaloscypha bicolor

source_name: Meliniomyces bicolor- Vaccinium myrtillus mycorrhizal roots

growth_protocol: Meliniomyces bicolor 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 113 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 113 days 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 M. bicolor mycelia and from M. bicolor-inoculated V. myrtillus roots 113 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 the Joint Genome Institue (JGI)


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.


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: 33925102: FB Stage III

status: Public on Jan 15 2018

description: This sampleis from stage III fruiting body (https://doi.org/10.1016/j.phytochem.2015.02.024)

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: Tuber melanosporum

source_name: Fruiting body stage III

label_protocol: Labelling by NimbleGen Company

growth_protocol: Samples of T. melanosporum FBs were collected at different developmental stages in the field near the city of L’Aquila (Italy), using the methods described by Pacioni et al. in addition to the traditional use of trained dogs. All of the ascocarps were analysed morphologically and microscopically and classified by maturation stage according to the criteria defined by Zarivi et al. 2015. For structural analysis and maturation stage assessment, 8-10 µm cryostat sections of each FB were observed after Giemsa staining (1 min).

extract_protocol: Total RNA were extracted from stages 3–6 (100 mg each) using TRIzol_ Reagent with the  PureLink_RNA Mini Kit (Ambion by Life Technologies Carlsbad, CA, USA).

value: fruiting body


title: 33647802: FB stage VI

description: This sampleis from stage VI fruiting body (https://doi.org/10.1016/j.phytochem.2015.02.024)

source_name: Fruiting body stageVI


title: Free-living mycelium-1

data_processing:
Illumina sofware was used by the JGI to generate fastq raw data files
Reads were aligned to Rhizoscyphus ericae UMAH 7357  (https://genome.jgi.doe.gov/Rhier1/Rhier1.home.html) reference transcripts using CLC Genomics Workbench 8 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Rhizoscyphus ericae UMAH 7357  (https://genome.jgi.doe.gov/Rhier1/Rhier1.home.html)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample

organism: Hyaloscypha hepaticicola

growth_protocol: Rhizoscyphus ericae UMAH 7357 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 75 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 75 days 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 Rhizoscyphus ericae UMAH 7357 mycelia and from Rhizoscyphus ericae UMAH 7357-inoculated V. myrtillus roots 75 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 the Joint Genome Institue (JGI)

value: UMAH 7357


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: Mycorrhizal roots-3

value: Mycorrhizal roots [Rhizoscyphus ericae UMAH 7357- Vaccinium myrtillus]


title: 33925202: FB Stage IV

description: This sampleis from stage IV fruiting body (https://doi.org/10.1016/j.phytochem.2015.02.024)

source_name: Fruiting body stageIV


title: 33924902: FB stage V

description: This sampleis from stage V  fruiting body (https://doi.org/10.1016/j.phytochem.2015.02.024)

source_name: Fruiting body stage V


title: Free-living mycelium-2


title: DIM

status: Public on Dec 08 2017

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using STAR v2.5
Differentially expressed genes were identified using the edgeR R Biocondutor package
Genome_build: mm10
Supplementary_files_format_and_content: bigWig were generated using bam2wig.py module in RSeQC v2.5

source_name: cardiomyocyte

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen), and treated with DNase according to the manufacture’s protocol.
Sample Validation:  -Standard RNA Reagent Kit (Perkin Elmer – Cat # CLS960010)  -HT DNA 5K/RNA/CZE LabChip (Perkin Elmer – Cat # 760435)  -LabChip GXTouch HT Instrument (Perkin Elmer)     -Sample Quantification  Qubit® RNA Assay Kit (LifeTechnologies – Cat# Q32852)  QUBIT 3.0 Fluorometer Instrument (LifeTechnologies – Cat# Q33216)     -Library Generation  TruSeq® Stranded mRNA Sample Prep Kit HT - (Illumina - Cat# RS-122-2103)   Purify and Fragment mRNA  Synthesize First/Second Strand cDNA  Adenylate 3' Ends  Ligate Adapters  - PCR Amplification  Plus: Agencourt AMPure XP (Beckman Coulter - Cat# A63881)    -Library Validation  HT DNA High Sens Reagent Kit (Perkin Elmer – Cat # CLS760672)  HT DNA 1K/12K/HI Sens Chip (Perkin Elmer – Cat # 760517)  LabChip GXTouch HT Instrument (Perkin Elmer)  Qubit® dsDNA HS Assay Reagent Kit (LifeTechnologies – Cat# Q32851)  Qubit® Assay Plastic Tubes (LifeTechnologies – Cat# Q32856)  QUBIT 3.0 Fluorometer Instrument (LifeTechnologies – Cat# Q33216)    -Normalization and Pool    -Denaturation and Dilution of Libraries    -Sequencing  NextSeq® 500/550 High Output v2 Reagent Kit (150 cycles) – Illumina – Cat# FC-404-2002)  NextSeq 500 Instrument
Paired end sequence reads (75-bp in length) were generated on an Illumina NextSeq 500

value: cardiomyocyte

tag: sub-population

value: FITCdim/FSChigh


title: Mycorrhizal roots-1

tag: strain


title: HIGH3-4

value: FITChigh/FSCdim


title: DIM3-4


title: DIM1-2


title: Free-living mycelium-late-1

description:
Cenococcum geophilum 1.58
This sample is from 60d old free-living mycelium. It is the first of tthree biological replicates used in this experiment.
FLMlate-1


title: HIGH


title: ECM 3month

status: Public on Apr 03 2017

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

organism:
Populus trichocarpa
Laccaria bicolor

source_name: mycorrhizal root tip

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 3 months. 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 Beckman Coulter Genomics (Danvers, MA, USA)

value: mycorrhizal root tip

tag: time of contact

value: mycorrhiza 3 months

tag: innoculant

value: Laccaria bicolor S238N


title: HIGH1-2


title: Control root 3month

organism: Populus trichocarpa

source_name: root

tag: tissue

value: root

value: control 3 months


title: Free spores 2

status: Public on Mar 01 2017

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

data_processing:
Illumina software was used by Beckman Coulter Genomics to generate fastq raw data files
Reads were aligned to the Pisolithus microcarpus (http://genome.jgi.doe.gov/Pismi1/Pismi1.home.html) reference transcripts using CLC Genomics Workbench 7 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Pisolithus microcarpus (http://genome.jgi.doe.gov/Pismi1/Pismi1.home.html)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample

organism: Pisolithus microcarpus

source_name: Free spores

growth_protocol: Intact P. microcarpus basidiocarps (UFV-VIC 26495) were collected in March 2013  from two commercial plantations of Eucalyptus sp. in Viçosa, Minas Gerais State (MG),  Brazil (with site location coordinates 20° 49’ 43.4”S, 42° 51’ 52.6”W and 20° 49’ 28.3”S, 42° 51’ 35.8”W).   The collected basidiocarps were immediately transported to the laboratory and superficially cleaned with 70% ethanol. The basidiocarps were opened and the gleba representative of the different stages of peridiole development were collected. The collected samples were then frozen in liquid nitrogen and stored at -80 ºC. A total of three basidiocarps were sampled, each representing one biological replication.

extract_protocol:
Total RNA of 100 mg of tissue per sample from unconsolidated, young, and mature peridioles, and from internal and free   basidiospores, was extracted using the lithium chloride (LiCl) method.   Assays for the quantification and integrity check were conducted using an Experion Automated Electrophoresis Station (Bio-Rad, Hercules, CA, USA).
cDNA libraries were prepared for sequencing using standard Illumina protocols by Beckman Coulter Genomics

value: Free spores


title: Free spores 3

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


title: Free spores 1

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


title: Mycorrhizal roots-2

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

value: Mycorrhizal roots


title: Internal spores 3

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

source_name: Internal spores

value: Internal spores


title: Free-living mycelium-3


title: Mycorrhizal roots-2


title: Internal spores 2

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


title: Internal spores 1

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


title: Mature peridioles 3

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

source_name: Mature peridioles

value: Mature peridioles


title: Mature peridioles 2

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


title: Young peridioles 3

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

source_name: Young peridioles

value: Young peridioles


title: Unconsolidated peridioles 1

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

source_name: Unconsolidated peridioles

value: Unconsolidated peridioles


title: Young peridioles 2

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


title: Inoculated_2d_2

status: Public on Feb 01 2017

description: This sample is from mycelium in contact with P.pinaster for 2 days. It is the second of three biological replicates used in this experiment.

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 8.5.1 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 unique aligned reads, total aligned reads and RPKM values for each sample

organism: Hebeloma cylindrosporum

source_name: Inoculated mycelium 2 days

growth_protocol: For experiments focusing on pre-infectious stages of the interaction,   seedling roots were inoculated by dipping them into a fast-growing mycelial homogenate in the Melin-Norkrans medium.  Two inoculated seedlings were placed in each Petri dish and inoculation was further improved by pouring 50µl  of fungal homogenate at the surface of each tap root. Control free-living mycelia were obtained by pouring,   in the absence of host plant, the homogenate used as inoculum in Petri dishes filled with the same Melin-Norkrans medium  as the one used for co-cultures. Inoculated seedlings were grown at 22 ± 1°C under 16 h photoperiodic illumination   (80 mmol photons.m-2.s-1). Roots were protected from direct illumination using a black plastic film.  After a two or four day co-culture, mycelia growing on the root surface were collected by gently scrubbing root surface   with a spatula. Mycelia collected from 40 roots were suspended in 8 mL of sterile water which were centrifuged for 10 min  at 10,800 g after adding 1 mL of 50% glycerol.   The pellet was subsequently rinsed with 1 mL of sterile water and again centrifuged for 10 min at 15,000 g.  The resulting pellet was frozen at -75°C and finally lyophilized before RNA extraction.

extract_protocol:
Lyophilized mycelia were ground in liquid nitrogen and total RNA was extracted using  the "RNeasy Plant Mini Kit" (Qiagen, Courtaboeuf, France).  PEG 8000 (20 mg.ml-1) and β-mercaptoethanol (10 µl.ml-1) were added in the RLC buffer (Qiagen).   Samples were subsequently purified using the "Total RNA Purification, NucleoBond® RNA/DNA 80" kit  (Macherey-Nagel, Hoerdt, France) by following the manufacturer’s recommendations.
cDNA libraries were prepared for sequencing using standard Illumina protocols by the Joint Genome Institue (JGI)

value: TV98 IV3

tag: protocol

value: in contact with Pinus pinaster rotts

tag: time point

value: 2 days


title: Inoculated_2d_3

description: This sample is from mycelium in contact with P.pinaster for 2 days. It is the third of three biological replicates used in this experiment.


title: Inoculated_4d_2

description: This sample is from mycelium in contact with P.pinaster for 4 days. It is the second of three biological replicates used in this experiment.

source_name: Inoculated mycelium 4 days

value: 4 days


title: Unconsolidated peridioles 2

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


title: Inoculated_2d_1

description: This sample is from mycelium in contact with P.pinaster for 2 days. It is the first of tthree biological replicates used in this experiment.


title: Young peridioles 1

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


title: Inoculated_4d_3

description: This sample is from mycelium in contact with P.pinaster for 4 days. It is the third of three biological replicates used in this experiment.


title: Control_4d_3

description: This sample is from control mycelium after 4 days. It is the third of three biological replicates used in this experiment.

source_name: Control mycelium 4 days

value: control mycelium


title: Inoculated_4d_1

description: This sample is from mycelium in contact with P.pinaster for 4 days. It is the first of tthree biological replicates used in this experiment.


title: Unconsolidated peridioles 3

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


title: Control_2d_2

description: This sample is from control mycelium after 2 days. It is the second of three biological replicates used in this experiment.

source_name: Control mycelium 2 days


title: Control_2d_1

description: This sample is from control mycelium after 2 days. It is the first of tthree biological replicates used in this experiment.


title: Control_4d_1

description: This sample is from control mycelium after 4 days. It is the first of tthree biological replicates used in this experiment.


title: Control_2d_3

description: This sample is from control mycelium after 2 days. It is the third of three biological replicates used in this experiment.


title: Control_4d_2

description: This sample is from control mycelium after 4 days. It is the second of three biological replicates used in this experiment.


title: Free-living myceliumM-3

status: Public on Dec 01 2016

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

data_processing:
Illumina sofware was used by the JGI to generate fastq raw data files
Reads were aligned to Tulasnella calospora ( http://genome.jgi-psf.org/Tulca1 ) reference transcripts using CLC Genomics Workbench 9 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 unique aligned reads, total aligned reads and RPKM values for each sample

organism: Tulasnella calospora

source_name: free-living mycelium N ammonium

growth_protocol: T. calospora free-living mycelium was grown on Modified Melin-Norkrans medium with two different N sources, ammonium (AL13 M) and glutamine (AL13 G), each added as 0.49g of N for 15 days. Symbiotic germination was obtained by co-inoculation of mycorrhizal fungi and orchid seeds in 9 cm Petri dishes, as described in Ercole et al. (2013). Seeds of S. vomeracea were surface sterilized in 1% sodium hypochlorite and 0.1% Tween-20 for 20 minutes on a vortex, followed by three 5-minutes rinses in sterile distilled water. Seeds were re-suspended in sterile water and dropped on strips of autoclaved filter paper (1.5 x 3 cm) positioned on solid oat medium (0.3% milled oats, 1% agar). Plates were inoculated with a plug of actively growing T. calospora mycelium and were incubated at 20°C in full darkness.  Symbiotic protocorms collected at stage P2 were  frozen immediately in liquid nitrogen and stored at -80 °C for RNA extraction

extract_protocol:
Total RNA was extracted  using the CTAB method. 100 mg aliquots  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 the Joint Genome Institue (JGI)

value: Free-living mycelium


title: Asymbiotic protocorm P2-2

description:
This sample is from asymbiotic, achlorophyllous protocorm. It is the second of three biological replicates used in this experiment.
P2A-2

data_processing:
Illumina sofware was used by the JGI to generate fastq raw data files
Reads were aligned to Serapias vomeracea reference contigs using CLC Genomics Workbench 9 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Serapias vomeracea reference (de novo transcript assembly)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample

organism: Serapias vomeracea

source_name: Asymbiotic protocorm

growth_protocol: Symbiotic germination was obtained by co-inoculation of mycorrhizal fungi and orchid seeds in 9 cm Petri dishes. Seeds of S. vomeracea were surface sterilized in 1% sodium hypochlorite and 0.1% Tween-20 for 20 minutes on a vortex, followed by three 5-minutes rinses in sterile distilled water. Seeds were re-suspended in sterile water and dropped on strips of autoclaved filter paper (1.5 x 3 cm) positioned on solid oat medium (0.3% milled oats, 1% agar). Plates were inoculated with a plug of actively growing T. calospora mycelium and were incubated at 20°C in full darkness. Asymbiotic seed germination was obtained on modified BM1 culture media at 20°C in darkness. Symbiotic and asymbiotic achlorophyllous protocorms collected at stage P2  were  frozen immediately in liquid nitrogen and stored at -80 °C for RNA extraction.

extract_protocol:
Total RNA was extracted using the CTAB method. 100 mg aliquots  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 the Joint Genome Institue (JGI)

value: Asymbiotic, achlorophyllous protocorm stage P2


title: Free-living myceliumG-3

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

source_name: free-living mycelium N glutamine


title: Free-living myceliumM-2

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


title: Asymbiotic protocorm P2-1

description:
This sample is from asymbiotic, achlorophyllous protocorm. It is the first of three biological replicates used in this experiment.
P2A-1


title: Mature peridioles 1

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


title: Free-living myceliumM-1

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


title: Free-living myceliumG-1

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


title: Free-living myceliumG-2

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


title: Mycorrhizal protocorm_plantP2-3

description:
This sample is from  mycorrhizal protocorm. It is the third of three biological replicates used in this experiment.
P2-3

organism:
Serapias vomeracea
Tulasnella calospora

source_name: Mycorrhizal protocorm

value: Mycorrhizal protocorm stage P2


title: Mycorrhizal protocorm_plantP2-2

description:
This sample is from  mycorrhizal protocorm. It is the second of three biological replicates used in this experiment.
P2-2


title: Mycorrhizal protocormP2-3

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

source_name: Mycorrhizal protocorm stage P2

value: Mycorrhizal protocorm


title: Mycorrhizal protocormP2-2

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


title: Mycorrhizal protocormP2-1

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


title: Mycorrhizal protocorm_plantP2-1

description:
This sample is from mycorrhizal protocorm. It is the first of three biological replicates used in this experiment.
P2-1


title: Asymbiotic protocorm P2-3

description:
This sample is from asymbiotic, achlorophyllous protocorm. It is thethird of three biological replicates used in this experiment.
P2A-3


title: sh-TET2_rep1

status: Public on Jun 21 2016

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using tophat v2.0.10
The mapped read files were then processed with bamtools API 2.2.3 tool with the following parameters: -isMapped true; -isPaired true; -isProperPair. Only reads with “mapQ” ≥ 20 retained for further analysis.
Reads were then processed by Cufflinks7 v2.1.1 with the following parameters: -b; -u; --library-type fr-firststrand; --max-bundle-frags 10000000; --compatible-hits-norm. The RNA expression level of a gene was represented by fragments per Kb of transcript per million mapped reads (RPKM) calculated using the Cufflinks package
Differentially expressed genes were identified using the Cuffdiff package with the following parameters: --compatible-hits-norm; -b; u; --library-type fr-firststrand; --max-bundle-frags 10000000
Genome_build: mm10
Supplementary_files_format_and_content: bigWig were generated using bam2wig.py module in RSeQC v2.5

organism: Mus musculus

source_name: sh-TET2 cardiomyocyte

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen), and treated with DNase according to the manufacture’s protocol.
Total RNA quality was evaluated using the 2100 Agilent Bioanalyzer and the RNA 6000 Nano kit: only samples with RIN score greater than 7 were further processed. RNA-Seq libraries were created using the Epicentre Script-Seq Complete Gold Kit-Low Input (Epicentre) composed of two modules: the Ribo-Zero Magnetic Kit depletion protocol for rRNA removal and the Script-Seq v2 Kit to prepare the libraries. 150 ng of total RNA was depleted and concentrated with RNeasy MinElute Cleanup Kit (Qiagen). Purified RNA was fragmented and first strand cDNA was synthesized using random hexamer with 5’ tagging sequences. After RNase digestion, a 3’ tag was introduced with random terminal tagging oligos. The obtained double tagged strand-specific cDNA was purified using AMPure XP beads (Beckman Coulter).  Libraries were enriched and indexed by 15 cycles of PCR amplification (ABI GeneAmp PCR system 9700) using FailSafe PCR enzyme and ScriptSeq Index PCR Primers for Illumina (Epicentre). After AMPure XP beads purification, library quality and size distribution were checked using an Agilent Bioanalyzer and DNA 1000 chip.  All libraries were quantified with a Qubit 2.0 Fluorometer (Life Technologies) using dsDNA BR Assay Kit (Life Technologies). RNA-Seq libraries were sequenced using TruSeq PE Cluster Kit v3 and TruSeq SBS Kit v3 (Illumina). According to index compatibility, the libraries were grouped into 2 pools and clustered on a TruSeq v3 flow cell at a concentration of 9pM to obtain > 50 million clusters for each sample.
Paired end sequence reads (50-bp in length) were generated on an Illumina HiSeq 2000 (Samples 1 to 8)     Paired end sequence reads (75-bp in length) were generated on an Illumina NextSeq 500 (Samples 9 to 12)

value: cardiomyocyte


title: Free-living mycelium-1

status: Public on Aug 01 2016

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

data_processing:
Illumina software was used by IGA to generate fastq raw data files
Reads were aligned to Cenococcum geophilum- (http://genome.jgi.doe.gov/Cenge3/Cenge3.home.html) reference transcripts using CLC Genomics Workbench 6 and Reads Per Kilobase of exon per Megabase of aligned reads (RPKM) were calculated.
Genome_build: Cenococcum geophilum (http://genome.jgi.doe.gov/Cenge3/Cenge3.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: Cenococcum geophilum

source_name: Free-living mycelium

growth_protocol: Free-living mycelium (FLM) was grown on agar Petri dishes containing Cg-Medium and covered by a cellophane membrane. ECM plants were produced after the protocol of Kipfer et al. 2012. Two-month-old P. sylvestris seedlings inoculated with C. geophilum were cultivated in pots (300ml, two plants per pot) in a growth chamber for 3 months before harvesting. To collect ECMs, the roots were washed under tap water, placed in cooled water and ECM root tips were sampled under a binocular loupe using forks and immediately put in tubes that were placed in liquid N. Tubes were stored at -80°C until RNA extraction.

extract_protocol:
Total RNA was extracted from free-living mycelium and from ectomycorrhizal root tips of C. geophilum/Pinus sylvestris using the RNAeasy Plant Mini Kit of Qiagen with DNase step and addition of 20 mg/ml polyethylene glycol to the RLC extraction buffer.
cDNA libraries were prepared for sequencing using standard Illumina protocols by IGA Technology Services (Udine , Italy)


title: Ectomycorrhizal roots-1

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

source_name: Ectomycorrhiza

tag: host

value: Pinus sylvestris

value: Ectomycorrhiza


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: Ectomycorrhizal roots-2

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


title: Ectomycorrhizal roots-3

description: This sample is from ectomycorrhizal roots. It is the third 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: CS_Suillus_3

description:
S_CS3_55781402
Suillus mycorrhiza from Pinus sylvestris, inoculated with both Cenococcum and Suillus.
It is the third of three biological replicates used in this experiment.

hyb_protocol: Hybridization by NimbleGen Company.

scan_protocol: Scanning by NimbleGen Company.

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: Pinus sylvestris

source_name: Pinus inoculated with Cenococcum/Suillus, Suillus-Pinus mycorrhiza

label_protocol: Labelling by NimbleGen Company.

growth_protocol: Double-mycorrhized P. sylvestris seedlings were produced using C. geophilum 1.58 and the abundant pine symbiotic ECM species Rhizopogon roseolus (Corda) Th. Fr. or Suillus granulatus (L.) Roussel. Four months after inoculation, three and two replicate plants were harvested for each fungal combination and for non-mycorrhizal plants, respectively. Single fine root tips were collected for each ECM species per plant and for non-mycorrhizal plants in separate tubes and were shock-frozen.

extract_protocol: Total RNAs were extracted using the NucleoSpin RNA Plant kit (MACHEREY-NAGEL) or the Power Plant RNA isolation kit (MOBIO), and cDNA was amplified using the SMART PCR cDNA Synthesis Kit (Clontech) according to the manufacturer's instructions.

tag: inoculated fungi

value: Cenococcum geophilum, Suillus granulatus

value: Suillus-Pinus mycorrhiza


title: CS_Suillus_1

description:
S_CS1_55782502
Suillus mycorrhiza from Pinus sylvestris, inoculated with both Cenococcum and Suillus.
It is the first of three biological replicates used in this experiment.


title: CS_Cenococcum_2

description:
Cg_CS2_55941702
Cenococcum mycorrhiza from Pinus sylvestris, inoculated with both Cenococcum and Suillus.
It is the second of three biological replicates used in this experiment.

source_name: Pinus inoculated with Cenococcum/Suillus, Cenococcum-Pinus mycorrhiza

value: Cenococcum-Pinus mycorrhiza


title: TAC_rep1

source_name: TAC cardiomyocyte


title: CR_Cenococcum_1

description:
Cg_CR1_55783602
Cenococcum mycorrhiza from Pinus sylvestris, inoculated with both Cenococcum and Rhizopogon.
It is the first of three biological replicates used in this experiment.

source_name: Pinus inoculated with Cenococcum/Rhizopogon, Cenococcum-Pinus mycorrhiza

value: Cenococcum geophilum, Rhizopogon roseolus


title: Non_mycorrhizal_2

description:
NM_2_55782402
Non-mycorrhizal control from Pinus sylvestris.
It is the second of two biological replicates used in this experiment.

source_name: Non-mycorrhizal Pinus roots

value: Non-mycorrhizal Pinus roots


title: Adult_rep1

source_name: Adult cardiomyocyte


title: TAC_rep2


title: Adult_rep2


title: Neonatal_rep2

source_name: Neonatal cardiomyocyte


title: CR_Rhizopogon_3

description:
R_CR3_55782102
Rhizopogon mycorrhiza from Pinus sylvestris, inoculated with both Cenococcum and Rhizopogon.
It is the third of three biological replicates used in this experiment.

source_name: Pinus inoculated with Cenococcum/Rhizopogon, Rhizopogon-Pinus mycorrhiza

value: Rhizopogon-Pinus mycorrhiza


title: CR_Rhizopogon_2

description:
R_CR2_55781802
Rhizopogon mycorrhiza from Pinus sylvestris, inoculated with both Cenococcum and Rhizopogon.
It is the second of three biological replicates used in this experiment.


title: CS_Suillus_2

description:
S_CS2_55942302
Suillus mycorrhiza from Pinus sylvestris, inoculated with both Cenococcum and Suillus.
It is the second of three biological replicates used in this experiment.


title: CR_Rhizopogon_1

description:
R_CR1_55941802
Rhizopogon mycorrhiza from Pinus sylvestris, inoculated with both Cenococcum and Rhizopogon.
It is the first of three biological replicates used in this experiment.


title: CS_Cenococcum_3

description:
Cg_CS3_55783202
Cenococcum mycorrhiza from Pinus sylvestris, inoculated with both Cenococcum and Suillus.
It is the third of three biological replicates used in this experiment.


title: CR_Cenococcum_2

description:
Cg_CR2_55781602
Cenococcum mycorrhiza from Pinus sylvestris, inoculated with both Cenococcum and Rhizopogon.
It is the second of three biological replicates used in this experiment.


title: CS_Cenococcum_1

description:
Cg_CS1_55783702
Cenococcum mycorrhiza from Pinus sylvestris, inoculated with both Cenococcum and Suillus.
It is the first of three biological replicates used in this experiment.


title: Non_mycorrhizal_1

description:
NM_1_55941902
Non-mycorrhizal control from Pinus sylvestris.
It is the first of two biological replicates used in this experiment.


title: sh-TET2_rep2


title: sh-control_rep2

source_name: sh-control cardiomyocyte


title: CR_Cenococcum_3

description:
Cg_CR3_55941602
Cenococcum mycorrhiza from Pinus sylvestris, inoculated with both Cenococcum and Rhizopogon.
It is the third of three biological replicates used in this experiment.


title: INPUT_DNA_sh-TET2

library_source: genomic

data_processing:
hMeDIP-seq reads were aligned to the mm10 genome assembly using bwa (v0.7.4-r385)
Duplicated aligned reads were filtered out with Picard MarkDuplicates tool (v1.87)
Reads with mapping quality ≤ 10 were removed with Bamtools (v2.2.3)
Peaks were called with HOMER Peaks -style histone
Genome_build: mm10
Supplementary_files_format_and_content: bigWig were generated using MEDIPS.mergeSets and MEDIPS.exportWIG modules of MeDIPS R package
Supplementary_files_format_and_content: bed files are the output of HOMER fndPeaks for each biological replicate

source_name: INPUT_DNA_sh-TET2 cardiomyocyte

extract_protocol:
DNA was isolated and immunoprecipitation was performed by Active Motif sequencing service
Libraries were prepared by Active Motif sequencing service

tag: hmedip antibody


title: INPUT_DNA_TAC_rep2

source_name: INPUT_DNA_TAC cardiomyocyte


title: INPUT_DNA_TAC_rep1


title: E14.5_rep2

source_name: E14.5 cardiomyocyte


title: INPUT_DNA_sh-control

source_name: INPUT_DNA_sh-control cardiomyocyte


title: E14.5_rep1


title: sh-control_rep1


title: INPUT_DNA_Adult_rep1

source_name: INPUT_DNA_Adult cardiomyocyte


title: INPUT_DNA_Adult_rep2


title: INPUT_DNA_Neonatal_rep1

source_name: INPUT_DNA_Neonatal cardiomyocyte


title: 5hmC_sh-control_rep2_hMeDIPSeq

source_name: 5hmC_sh-control cardiomyocyte

value: Active Motif


title: INPUT_DNA_E14.5_rep2

source_name: INPUT_DNA_E14.5 cardiomyocyte


title: INPUT_DNA_E14.5_rep1


title: 5hmC_sh-control_rep1_hMeDIPSeq


title: INPUT_DNA_Neonatal_rep2


title: 5hmC_sh-TET2_rep2_hMeDIPSeq

source_name: 5hmC_sh-TET2 cardiomyocyte


title: 5hmC_TAC_rep2_hMeDIPSeq

source_name: 5hmC_TAC cardiomyocyte


title: 5hmC_TAC_rep1_hMeDIPSeq


title: 5hmC_Neonatal_rep1_hMeDIPSeq

source_name: 5hmC_Neonatal cardiomyocyte


title: 5hmC_Neonatal_rep2_hMeDIPSeq


title: 5hmC_E14.5_rep1_hMeDIPSeq

source_name: 5hmC_E14.5 cardiomyocyte


title: 5hmC_E14.5_rep2_hMeDIPSeq


title: Donor1_scRNA-seq_rep1

data_processing:
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v1.2.1). Three types of fastq files were generated: I1 contains 8 bp sample index; R1 contains 26 bp (10 cell + 16 UMI) index and R2 contains 100 bp cDNA sequence. Fastq files were then run with count application (Cell Ranger v1.2.1) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

organism: Homo sapiens

source_name: Donor1_testicular cells

extract_protocol:
Single testicular cells were generated using standard two step enzymatic digestion protocol as described before (Guo et al., Cell Stel Cell 2017). Cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v2 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 26 X 100 cycle paired-end run via a Illumina 2500 instrument. Samples from Donor 1 was sequenced in two separate sequencing lanes. For Donors 2 and 3, their libraries were mixed before sequencing, and seqenced by four different lanes.
10X Genomics single cell RNA sequencing

tag: subject status

value: healthy men of peak reproductive age

value: donor 1

value: testicle

value: testicular cells


title: 5hmC_Adult_rep2_hMeDIPSeq

source_name: 5hmC_Adult cardiomyocyte


title: Neonatal_rep1

source_name: Neonatal cardiomyocyte


title: 5hmC_Adult_rep1_hMeDIPSeq


title: 5hmC_sh-TET2_rep1_hMeDIPSeq


title: H. annosum grown on Pine-dominant drained peatland forest topsoil (organic layer ) 2

status: Public on Oct 01 2015

description: This sample is grown on  Pine-dominant drained peatland forest topsoil. It is the second of three  biological replicates used in this experiment.

organism: Heterobasidion annosum

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: Four month


title: ECM-2 (II)

status: Public on Jul 01 2015

description: This sample is from ectomycorrhizal 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 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

source_name: ECM

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. For mycorrhizas obtained under greenhouse condition, P. pinaster seeds were germinated at 18°C on vermiculite watered with deionized water. Twenty-day old seedlings were inoculated by dipping their tap-root in a mycelial homogenate obtained as described above for proteomics studies. Inoculated plants were grown under greenhouse conditions in 0.5 l pots filled with sterilized organic matter rich (80%) "Easy growing TS 3 Argile" soil (Klasmann-Deilmann, France) made of moderately decomposed white peat, frozen through black peat and clay granules. Inoculation efficiency was further improved by injecting 3ml of the mycelial homogenate in the soil, in the close vicinity of tap-roots.

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 IGA Technology Services (Udine , Italy)

value: Pinus pinaster

value: greenhouse ectomycorrhiza


title: ECM-1 (II)

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


title: Free-living mycelium-2 (II)

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

source_name: Free-living mycelium

value: free-living mycelium

value: TV98 IV3


title: H. annosum grown on Pine-dominant drained peatland forest topsoil (organic layer ) 3

description: This sample is grown on  Pine-dominant drained peatland forest topsoil. It is the third of three  biological replicates used in this experiment.


title: Whole leaves compatible interaction 18h

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 18h 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

value: inoculation with Melampsora larici-populina isolate 98AG31

tag: treatment duration


title: Free-living mycelium-1 (II)

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


title: Whole leaves incompatible interaction 24h

source_name: Entire detached leaves inoculated for 24h with M. larici-populina isolate 93ID6

tag: treatment

value: inoculation with Melampsora larici-populina isolate 93ID6


title: H. annosum grown on Pine-dominant pristine peatland forest topsoil (organic  layer) 1

description: This sample is grown onPine-dominant pristine peatland forest topsoil. It is the first of three  biological replicates used in this experiment.


title: Control grown in liquid medium 3

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

source_name: liquid medium

value: three weeks


title: H. annosum grown on Pine-dominant mineral forest topsoil  (organic layer) 1

description: This sample is grown on Pine-dominant mineral forest topsoil. It is the first of three  biological replicates used in this experiment.

source_name: Pine-dominant mineral forest topsoil


title: H. annosum grown on Pine-dominant pristine peatland forest topsoil (organic  layer) 2

description: This sample is grown on Pine-dominant pristine peatland forest topsoil. It is the second of three  biological replicates used in this experiment.


title: H. annosum grown on Pine-dominant pristine peatland forest topsoil (organic  layer) 3

description: This sample is grown on Pine-dominant pristine peatland forest topsoil. It is the third of three  biological replicates used in this experiment.


title: Whole leaves incompatible interaction 18h

source_name: Entire detached leaves inoculated for 18h with M. larici-populina isolate 93ID6


title: H. annosum grown on Pine-dominant mineral forest topsoil  (organic layer) 2

description: This sample is grown on Pine-dominant mineral forest topsoil. It is the second of three  biological replicates used in this experiment.


title: Whole leaves compatible interaction 48h

source_name: Entire detached leaves inoculated for 48h with M. larici-populina isolate 98AG31


title: Whole leaves incompatible interaction 21h

source_name: Entire detached leaves inoculated for 21h with M. larici-populina isolate 93ID6


title: H. annosum grown on Pine-dominant drained peatland forest topsoil (organic layer ) 1

description: This sample is grown on  Pine-dominant drained peatland forest topsoil. It is the first of three  biological replicates used in this experiment.


title: H. annosum grown on Pine-dominant mineral forest topsoil  (organic layer) 3

description: This sample is grown on Pine-dominant mineral forest topsoil. It is the third of three  biological replicates used in this experiment.