title: 192566_0_TCRB

status: Public on Jun 07 2021

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

data_processing:
Bulk repertoire data processing and analysis was carried out using tools from the Immcantation framework (http://immcantation.org).
Preprocessing was carried out using pRESTO v0.5.11 and the IMGT human germline IGHV reference database (IMGT/GENE-DB v3.1.19; retrieved May 30, 2019)
Genome_build: IMGT/GENE-DB v3.1.19
Supplementary_files_format_and_content: One annotation file in AIRR-C Rearrangement format was generated for each sample. The files are in tab-delimited format and gzip compressed.

source_name: PBMC

extract_protocol:
PBMCs were isolated by Ficoll-Paque PLUS (GE Healthcare) gradient centrifugation. Red blood cells (RBCs) were lysed using ACK buffer (ThermoFisher A1049201).
RNA was prepared from frozen PBMCs using the RNAEasy Mini kit (Qiagen) per the manufacturer’s instructions. BCR and TCR RNA libraries were prepared using reagents from New England Biolabs as part of the NEBNext® Immune Sequencing Kit (a kind gift of Drs. Eileen Dimalanta and Chen Song, Ipswich, MA). These steps were performed as described previously with the inclusion of an additional set of TCRB-specific primers on the 3’ end. Libraries were sequenced by 325 cycles for read 1 and 275 cycles for read 2 base-pair paired-end sequencing with a 20% PhiX spike on the Illumina MiSeq platform according to manufacturer’s recommendations.

value: PBMC

value: M

tag: age

tag: ethnicity

value: Not Hispanic or Latino

tag: disease stage

value: Acute/Recent onset Lyme disease


title: 192567_0_TCRB

type: SRA

city: New Haven

country: USA

institute: Yale University

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: Sex

value: F


title: 192564_0_TCRB


title: 192561_0_TCRB


title: 192565_0_TCRB


title: Subject 192566 EM Lesion (scTCR)

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function and aligned to the GCRhg38 genome supplied by 10X Genomics.
Sparse count matrices, barcode assignments and feature calls were made using the cellranger count subcommand.
Reconstructed V(D)J sequences from single cell sequencing were extracted using the cellranger vdj function from fastq reads.
V(D)J germline genes were re-assigned using IgBLAST v.1.6.1 also using the September 12, 2018 version of the IMGT gene database.
Following V(D)J annotation, non-functional sequences were removed from further analysis
Genome_build: GRCh38
Supplementary_files_format_and_content: Output files from Cell Ranger (10X Genomics) were archived and compressed into a tar.gz file, one per sample. Each compressed archive contains the tab-delimited text files filtered_contig_annotations.csv & filtered_contig.fasta.

source_name: skin

extract_protocol:
PBMCs and skin infiltrating cells were isolated by Ficoll-Paque PLUS (GE Healthcare) gradient centrifugation. Red blood cells (RBCs) were lysed using ACK buffer (ThermoFisher A1049201). Single cell suspensions were obtained from fresh human skin biopsies obtained with a Biopsy puncher using the Whole Skin Dissociation Kit (Miltenyi Biotec, San Diego, CA, 130-101-540), placed in MACS Tissue Storage Solution (Miltenyi Biotec, 130-100-008) and stored for less than 48 hrs at 4o Celsius.
Single cell preparations were loaded into the Chromium Controller (10x Genomics) for emulsion generation and libraries were prepared using the Chromium Single-cell 5′ Reagent Kit for version 1 chemistry per the manufacturer’s protocol. Libraries were sequenced on the NovaSeq 6000 with 2 x150 paired end reads.

value: Acute/Recent onset


title: Subject 192567 Unaffected Skin (scTCR)


title: Subject 192566 PBMC (scTCR)


title: EUF34

status: Public on Jul 01 2021

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

description:
Successful implantation after transfer
counts_exp2.txt.gz

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.36)
Retained reads were mapped to the reference human genome, GRCh38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts function in the Rsubread R package. Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode version 26 for samples 1-20;  Gencode version 27 for samples 21-93)
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: Uterine fluid derived Extracellular Vesicles

extract_protocol:
Endometrial tissue biopsies were obtained with the use of a Pipelle, immediately after UF sampling. Uterine fluid samples were obtained by lavage of the endometrial cavity with 2.5 of physiologic solution using a balloon hysterosonosonography catheter to avoid vaginal contamination. Extracellular vesicles were isolated- after mucus disgregation by vortexing- using standard ultracentrifugation protocol.  RNA was harvested using  RNase micro KIT of QIAGEN with DNAse treatment step in coloumn.
To compare the transcriptomic profile of tissues and UF-Evs (samples 1-20), cDNA libraries were generated from total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen GmbH, Vienna, Austria). To perform transcriptome sequencing on UF-EVs collected from fertile women and ART patients during the window of implantation (samples 21-93), cDNA libraries were prepared using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio Inc., Otsu, Shiga, Japan)

tag: population

value: Women undergoing ART and transfer of an euploid blastocyst

tag: menstrual cycle phase

value: secretory

tag: mentrual cycle day (counted from the first day of menstrual bleeding and expressed as n or from the day of urinary lh surge detection and expressed an lh+n)

value: LH+7 (within window of implantation)


title: Subject 192565 Unaffected Lesion (scTCR)


title: Subject 192564 EM Lesion (scTCR)


title: Subject 192564 Unaffected Skin (scTCR)


title: Subject 192565 EM Lesion (scTCR)


title: Subject 192563 EM Lesion (scTCR)


title: Subject 192561 Unaffected Skin (scTCR)


title: Subject 192561 EM Lesion (scTCR)


title: 192565SKN

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function and aligned to the GCRhg38 genome supplied by 10X Genomics.
Sparse count matrices, barcode assignments and feature calls were made using the cellranger count subcommand.
CellRanger output was analyzed using Seurat v.3.1.5.
Genome_build: GRCh38
Supplementary_files_format_and_content: Output files from Cell Ranger (10X Genomics) were archived and compressed into a tar.gz file, one per sample. Each compressed archive contains the tab-delimited text files barcodes.tsv & features.tsv. The tar.gz file also contains a feature-barcode matrix file named matrix.mtx, stored in the Market Exchange Format for sparse matrices. The matrix file contains indexes to barcodes and gene/features, as well as total UMI count per cell and gene/feature combination.

source_name: Subject 192565 Unaffected Lesion

extract_protocol:
PBMCs and skin infiltrating cells were isolated by Ficoll-Paque PLUS (GE Healthcare) gradient centrifugation. Red blood cells (RBCs) were lysed using ACK buffer (ThermoFisher A1049201). Single cell suspensions were obtained from fresh human skin biopsies obtained with a Biopsy puncher using the Whole Skin Dissociation Kit (Miltenyi Biotec, San Diego, CA, 130-101-540), placed in MACS Tissue Storage Solution (Miltenyi Biotec, 130-100-008) and stored for less than 48 hrs at 4o Celsius.
Single cell preparations were loaded into the Chromium Controller (10x Genomics) for emulsion generation and libraries were prepared using the Chromium Single-cell 5′ Reagent Kit for version 1 chemistry per the manufacturer’s protocol. Libraries were sequenced on the NovaSeq 6000 with 2 x100 paired end reads.

value: Acute/Recent onset Lyme Disease

value: skin


title: 192567SKN

source_name: Subject 192567 Unaffected Skin


title: 192566SKL

source_name: Subject 192566 EM Lesion


title: 192566

source_name: Subject 192566 PBMC


title: 192567SKL

source_name: Subject 192567 EM Lesion


title: 192563SKL

source_name: Subject 192563 EM Lesion


title: 192564SKN

source_name: Subject 192564 Unaffected Skin


title: 192564SKL

source_name: Subject 192564 EM Lesion


title: 192565SKL

source_name: Subject 192565 EM Lesion


title: 192566SKN

source_name: Subject 192566 Unaffected Skin


title: 192561SKN

source_name: Subject 192561 Unaffected Skin


title: 192561SKL

source_name: Subject 192561 EM Lesion


title: Subject 192566 Unaffected Skin (scTCR)


title: Subject 192567 EM Lesion (scTCR)


title: WT_NF_8_1

status: Public on Jun 01 2021

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

institute: IRCCS Humanitas Research Hospital

library_source: genomic

data_processing:
Raw single end reads were first quality checked with FastQC v0.11.8
Aligned to the UCSC Mus Musculus release mm9, available at https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/ using Bowtie2 v2.4.2
Mapped reads were then sorted using Samtools v1.9 and filtered with Sambamba v0.7.1 with the following settings (sambamba view -h -t 2 -f bam -F "[XS] == null and not unmapped and not duplicate").
ChIP-seq quality assessment was performed using ChIPQC v1.26.0 R Bioconductor package
Genome_build: UCSC Mus Musculus release mm9
Supplementary_files_format_and_content: Enriched regions relative to input DNA were assessed using the ENCODE recommended Irreproducibility Discovery Rate (IDR) framework. Peaks in both replicates were detected with MACS2 v2.2.7.1 with the following settings (macs2 callpeak -f BAM -g 1.87e9 -B -p 1e-3). Peak consistency between true replicates were detected with IDR v2.0.4.2 with the following settings (--input-file-type narrowPeak --rank p.value). Peak Annotation was assessed with ChIPseeker v1.26.0 R Bioconductor package using the pre-build annotation database TxDb.Mmusculus.UCSC.mm9.knownGene (tssRegion=c(-2000, 2000)). Coverage tracks for each sample was computed with Bedtools bamCoverage option, with the following settings (bamCoverage --binSize 20 --normalizeUsing BPM --smoothLength 60 --extendReads 150 –centerReads).

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

extract_protocol:
ChIP-seq for CEBPB was performed using the ChIP-IT high Sensitivity Kit (Active Motif)
Library construction was performed using the NEBNext® Ultra DNA Library Prep for Illumina® kit (E7370) according to the manufacturer's protocol. Samples were sequenced using the Illumina HiSeq2500.

treatment_protocol: Mice of the three genotypes were given ad libitum acess to food (AL) or feeding was restricted to 12 hours during the night (NF). Samples were collected at zeiteber times ZT8 and ZT20.

value: Liver

tag: genotype

value: WT

tag: feeding

value: Night feeding


title: WT_AL_8_2

value: Ad libitum


title: WT_NF_8_2


title: WT_AL_8_1


title: WT_AL_20_1


title: RE_NF_8_2

value: BMAL1 Liver-RE


title: WT_AL_20_2


title: RE_NF_8_1


title: KO_NF_8_2

value: BMAL1 KO


title: RE_AL_8_2


title: KO_NF_8_1


title: KO_AL_8_1


title: Input_WT_NF


title: RE_AL_8_1


title: Input_KO_NF


title: Input_WT_AL


title: Input_RE_NF


title: 192563_0_TCRB

value: PBMC


title: Input_KO_AL


title: Input_RE_AL


title: W10

description:
Primary hepatocyte WT_1
Primary hepatocytes treated with WT serum for 24 hours Replicate 1
Liver

data_processing:
Raw single end reads were first quality checked with FastQC v0.11.8.
Aligned to the Ensembl Mus musculus release GRC38, available at https://www.ensembl.org/Mus_musculus/Info/Index using STAR v 2.7.7a with the following settings (STAR --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD).
RNA-seq quality assessment was performed using RSeQC v3.0.1 tool.
Differential expression analysis was assessed with edgeR v3.30.0 R Bioconductor package.Only genes with a cut-off expression > 1 CPM in at least two samples were included in the analysis. TMM method was applied to normalize gene counts and glmQLFTest and decideTestsDGE functions were used to perform differential analysis, with a minimum cut-off of absolute fold change ≥ 1.2 and FDR ≤0.05.
Genome_build: Ensembl Mus musculus release GRC38
Supplementary_files_format_and_content: bigWig were generated with wigToBigWig command starting from Signal.Unique.str.out.wig file.
Supplementary_files_format_and_content: Tab file (number of reads mapping per Gene) were generated with STAR.
Supplementary_files_format_and_content: diff.all_set1.txt refers to the differential analysis of Primary hepatocyte mKO versus Primary hepatocyte WT.
Supplementary_files_format_and_content: diff.all_set2.txt refers to the differential analysis of AML12 siCEBPB versus AML12 siControl.

source_name: Primary hepatocytes

growth_protocol: AML12 cells were cultured in DMEM:F12 media supplemented with 10% FBS, ITS, Dexamethasone and antibiotics. Primary hepatocytes were cultured in DMEM low glucose supplemented with 10% FBs and antibiotics.

extract_protocol:
RNA was extracted using the Direct-zol RNA kit (Zymo Research).
Libraries were prepared using the NEBNext Ultra II RNA Library Prep (Illumina). Libraries were run on a NovaSeq 6000.
Paired-end 150x150bp.

treatment_protocol: AML12 cells were synchronized with 100nM DEX for 1 hour. Primary hepatocytes were treated with 25% serum from WT or mKO for 24 hours.

tag: cell type

value: Primary hepatocytes

tag: treatment

value: Serum from WT

tag: time point


title: W11

description:
Primary hepatocyte WT_2
Primary hepatocytes treated with WT serum for 24 hours Replicate 2
Liver


title: M6

description:
Primary hepatocyte mKO_5
Primary hepatocytes treated with mKO serum for 24 hours Replicate 5
Liver

value: Serum from muscle-specific BMAL1 KO (mKO)


title: M2

description:
Primary hepatocyte mKO_1
Primary hepatocytes treated with mKO serum for 24 hours Replicate 1
Liver


title: KD24_2

description:
AML12 siCEBPB CT24_2
Cebpb KD AML12 cells harvested 24h after dexamethasone synchronization Replicate 2
Liver

source_name: AML12 cells

tag: cell line

tag: sirna

value: siCebpb

value: Dexamethasone


title: M3

description:
Primary hepatocyte mKO_2
Primary hepatocytes treated with mKO serum for 24 hours Replicate 2
Liver


title: W12

description:
Primary hepatocyte WT_3
Primary hepatocytes treated with WT serum for 24 hours Replicate 3
Liver


title: M4

description:
Primary hepatocyte mKO_3
Primary hepatocytes treated with mKO serum for 24 hours Replicate 3
Liver


title: M5

description:
Primary hepatocyte mKO_4
Primary hepatocytes treated with mKO serum for 24 hours Replicate 4
Liver


title: C24_2

description:
AML12 siControl CT24_2
Control AML12 cells harvested 24h after dexamethasone synchronization Replicate 2
Liver

value: siControl


title: C24_1

description:
AML12 siControl CT24_1
Control AML12 cells harvested 24h after dexamethasone synchronization Replicate 1
Liver


title: C12_2

description:
AML12 siControl CT12_2
Control AML12 cells harvested 12h after dexamethasone synchronization Replicate 2
Liver


title: KO_AL_8_2


title: KD24_1

description:
AML12 siCEBPB CT24_1
Cebpb KD AML12 cells harvested 24h after dexamethasone synchronization Replicate 1
Liver


title: KD12_3

description:
AML12 siCEBPB CT12_2
Cebpb KD AML12 cells harvested 12h after dexamethasone synchronization Replicate 2
Liver


title: KD12_2

description:
AML12 siCEBPB CT12_1
Cebpb KD AML12 cells harvested 12h after dexamethasone synchronization Replicate 1
Liver


title: C12_1

description:
AML12 siControl CT12_1
Control AML12 cells harvested 12h after dexamethasone synchronization Replicate 1
Liver


title: PBSWT_545

status: Public on Apr 14 2021

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

institute: UTHSA-GCCRI

data_processing:
Illumina bcl2fastq software used for base-calling
All RNA-seq Fastq reads were aligned with the reference genome (UCSC mouse genome build mm9) using TopHat2 default settings (Trapnell et al., 2012).
The BAM files obtained after alignment were processed using htseq-count to obtain the counts per gene in all samples (Anders et al., 2015).
Genome_build: UCSC mouse genome build mm9
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: liver tissue from male mice

extract_protocol:
total RNA of liver tissue was isolated with RNeasy kit (Qiagen)
Approximately 500 ng Total RNA was used for RNA-seq library preparation by following kapa rRNA depletion Total RNA-se sample preparation kit

treatment_protocol: TRIM21 wild-type and knockout mice were treated with one dose of 200 mg/kg diethylnitrosamine (DEN) by intraperitoneal injection

tag: strain

value: 8-weeks old

value: Male

value: liver

value: PBS control


title: W9

description:
Primary hepatocyte WT_5
Primary hepatocytes treated with WT serum for 24 hours Replicate 5
Liver


title: Il-6 Treated

status: Public on May 13 2021

data_processing:
Raw sequencing data (bcl-files) were converted to fastq files with Illumina bcl2fastq tool, integrated into the CellRanger (10X Genomics) suite (version 2.1.1).
R1 = cellular barcode (CB) (16 bp) + molecular barcode (MB) (umi) 10bp
The CellRanger analysis pipeline was used to generate a digital gene expression matrix staring from raw data.
The raw digital gene expression matrix (UMI counts per gene per cell) was imported in R (version 3.5.0) using Seurat R package (version Seurat_2.3.4)
Genome_build: Pre-build mouse genome (version mm10-1.2.0) was used as genome reference.
Supplementary_files_format_and_content: UMI counts per gene per cell

source_name: primary cultured neurons

extract_protocol:
~5,000 cells were loaded into one channel of the Single Cell Chip A for each sample using the Single Cell 3’ v2 single cell reagent kit (10X Genomics) for Gel bead Emulsion generation into the Chromium system. Following capture and lysis, we synthesized cDNA and amplified it for 14 cycles following the manufacturer’s protocol (10X Genomics). 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries.
Sequencing was performed on the NextSeq500 Illumina sequencing platform following 10x Genomics instruction for reads generation; at least 50.000 reads per cell were produced.

treatment_protocol: IL-6 at 10ng/ml incubated at 1 and 4 days in vitro.

value: primary cultured hippocampal neurons


title: Control


title: W8

description:
Primary hepatocyte WT_4
Primary hepatocytes treated with WT serum for 24 hours Replicate 4
Liver


title: 2804

status: Public on May 20 2021

city: Boston

first: Christina

last: Codden

state: MA

address: 800 Washington Stree

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

data_processing:
Demultiplexing, read alignment, and read counting, and nuclei calls were done with Cellranger 3.0
Quality control (QC) filtering, clustering, dimensionality reduction, visualization, and differential gene expression was performed using the development version of the R package Seurat in R 3.5.0
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: tab separated values files with barcode sequences corresponding to column indices, features corresponding to row indices.  For each feature, its feature ID and names are stored in the first and second column of the features.tsv file.  The third column of this file indentifies that it is a gene expression feature.  The actual gene cell matrix, .mtx file, is stored in the Market Exchange Format (MEX) for sparse matrices.

molecule: nuclear RNA

source_name: Adult human myectomy tissue

extract_protocol:
Nuclei were released from the tissue via dounce homogenization and then nuclei were processed using 10x genomics Chromium Single Cell 3' reagent V2 kit
10x Genomics Chromium Single Cell 3' reagent v2 kit

value: adult heart IVS

tag: gender

value: Female


title: PBSWT_542

value: WT

tag: age


title: PBSKO_544

value: TRIM21 KO


title: PBSKO_549


title: PBSWT_541


title: PBSKO_154


title: DENWT_995

value: diethylnitrosamine (DEN)


title: DENWT_307


title: DENHET_136


title: WGA_M_DRG_n3

status: Public on Mar 19 2021

source_name: male DRG neurons innervating hindpaw skin and thigh muscle

growth_protocol: Normal development of mice; no treatments

extract_protocol:
Single cell suspension from DRG tissues. Sensory neuron fraction was isolated by using FACS sorting approach.
Approximately 1-5ng Total RNA was used for RNA-seq library preparation by following Smart Seq II protocol

treatment_protocol: Injection WGA AlexoFluor 488 into paw and thigh


title: WGA_M_DRG_n1


title: WGA_M_DRG_n4


title: WGA_M_DRG_n2


title: WGA_F_DRG_n4

source_name: female DRG neurons innervating hindpaw skin and thigh muscle


title: WGA_F_DRG_n1


title: DENWT_996


title: Wt_M_TG3

source_name: TG tissues from naïve males

extract_protocol:
Single cell suspension from TG and DRG tissues. Sensory neuron fraction was isolated by using Percoll gradient approach
Approximately 10-20ng Total RNA was used for RNA-seq library preparation by following kapa rRNA depletion Total RNA-se sample preparation kit

value: 3-4 month


title: tumor-associated macrophages F4/80low replicate 3

status: Public on Apr 01 2021

type: RNA

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C US91903683

data_processing: Agilent Feature Extraction Software was used for background subtraction and quantile normalization.

source_name: F4/80low tumor-associated macrophages (TAMs)

label_protocol: According to standard methods

extract_protocol: Total RNA was extracted from 1-5x10^6 PECs, F4/80high and F4/80low TAMs (RNeasy kit, Qiagen) according to standard methods

value: fibrosarcoma

value: macrophages

tag: cell subset


title: WGA_F_DRG_n2


title: tumor-associated macrophages F4/80high replicate 3

source_name: F4/80high tumor-associated macrophages (TAMs)


title: Wt_M_TG1


title: control peritoneal exudate cells replicate 2

source_name: peritoneal exudate cells (PECs)

value: peritoneum

value: control macrophages (PECs)


title: control peritoneal exudate cells replicate 1


title: tumor-associated macrophages F4/80low replicate 2

value: F4/80low tumor-associated macrophages (TAMs)


title: Wt_M_DRG1

source_name: DRG tissues from naïve males


title: DENKO_309


title: tumor-associated macrophages F4/80high replicate 1

value: F4/80high tumor-associated macrophages (TAMs)


title: tumor-associated macrophages F4/80high replicate 2


title: Wt_M_TG2


title: Wt_M_DRG3


title: Wt_M_DRG2


title: Wt_F_TG1

source_name: TG  tissues from naïve females


title: Wt_F_TG2


title: Wt_F_DRG3

source_name: DRG tissues from naïve females


title: Wt_F_DRG2


title: tumor-associated macrophages F4/80low replicate 1


title: Wt_F_TG3


title: Wt_F_DRG1


title: Trametes versicolor 1956-1252 4w-3

status: Public on Jan 15 2021

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

country: France

institute: INRAE

description: This sample is from 4 weeks old Trametes versicolor 1956-1252 mycelium. It is the third 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 Trametes versicolor (https://mycocosm.jgi.doe.gov/Trave1/Trave1.home.html) reference transcripts using CLC Genomics Workbench 7.5.1 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Trametes versicolor (https://mycocosm.jgi.doe.gov/Trave1/Trave1.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: Trametes versicolor

source_name: Trametes versicolor 1956-1252 4w

growth_protocol: Mycelium of Trametes versicolor BRFM1218 and Trametes versicolor 1956-1252 (NIBIO collection) were grown on 4% malt agar medium and harvested after 2 and 4 weeks of incubation.

extract_protocol:
Total RNA was extracted and purified from triplicate cultures using the RNeasy Plant Mini Kit
cDNA libraries were prepared for sequencing using standard Illumina protocols by Beckman Coulter Genomics

tag: age of culture

value: 4 weeks


title: Trametes versicolor 1956-1252 4w-2

description: This sample is from 4 weeks old Trametes versicolor 1956-1252 mycelium. It is the second of three biological replicates used in this experiment.


title: DENKO_141

value: 8-weeks old

value: Male

tag: tissue


title: WGA_F_DRG_n3

tag: Sex


title: control peritoneal exudate cells replicate 3


title: Trametes versicolor BRFM1218 4w-2

description: This sample is from 4 weeks old Trametes versicolor BRFM1218 mycelium. It is the second of three biological replicates used in this experiment.

source_name: Trametes versicolor BRFM1218 4w


title: Trametes versicolor BRFM1218 4w-1

description: This sample is from 4 weeks old Trametes versicolor BRFM1218 mycelium. It is the first of three biological replicates used in this experiment.


title: Trametes versicolor BRFM1218 2w-3

description: This sample is from 2 weeks old Trametes versicolor BRFM1218 mycelium. It is the third of three biological replicates used in this experiment.

source_name: Trametes versicolor BRFM1218 2w

value: 2 weeks


title: Trametes versicolor BRFM1218 2w-2

description: This sample is from 2 weeks old Trametes versicolor BRFM1218 mycelium. It is the second of three biological replicates used in this experiment.


title: Trametes versicolor 1956-1252 2w-3

description: This sample is from 2 weeks old Trametes versicolor 1956-1252 mycelium. It is the third of three biological replicates used in this experiment.

source_name: Trametes versicolor 1956-1252 2w


title: Trametes versicolor 1956-1252 2w-2

description: This sample is from 2 weeks old Trametes versicolor 1956-1252 mycelium. It is the second of three biological replicates used in this experiment.


title: Trametes versicolor 1956-1252 2w-1

description: This sample is from 2 weeks old Trametes versicolor 1956-1252 mycelium. It is the first of three biological replicates used in this experiment.


title: MW3 ECM-3

status: Public on Nov 18 2020

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

data_processing:
Illumina sofware was used by by the University of Western Sydney Next Generation Sequencing Facility to generate fastq raw data files
Raw reads were trimmed for low quality (quality score 0.05), Illumina adapters and sequences shorter than 15 nucleotides and aligned to the reference transcripts available at JGI (Pisolithus microcarpus 441; https://mycocosm.jgi.doe.gov/Pismi1/Pismi1.home.html) using CLC Genomics Workbench v12 (Qiagen).
Genome_build: Pisolithus microcarpus 441; https://mycocosm.jgi.doe.gov/Pismi1/Pismi1.home.html
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads and TPM values for each sample

organism:
Eucalyptus grandis
Pisolithus microcarpus

source_name: ECM

growth_protocol: For colonization experiments, individual 1 month old E. grandis seedlings were  transferred to ½ strength MMN medium with 0.1% glucose in a 9 cm Petri dish and a single  0.25 cm2 160 square of fungal mycelium (Pisolithus microcarpus Si-9, MW3, R4 or R10) was transferred directly on top of the plant root.  Inoculated plates were placed at a 45 degree angle in plant  growth chambers (GC20 BDAF; Biochambers; Canada). Plates were left to  incubate for 1 month. Root tissues were harvested frozen immediately at -80°C.

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

value: ectomycorrhiza

tag: colonization experiment

value: P. microcarpus MW3 fungal mycelium was transferred directly on top of the plant root


title: R10 ECM-3

value: P. microcarpus R10 fungal mycelium was transferred directly on top of the plant root


title: R10-ECM-2

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


title: R10 ECM-1

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


title: Trametes versicolor BRFM1218 2w-1

description: This sample is from 2 weeks old Trametes versicolor BRFM1218 mycelium. It is the first of three biological replicates used in this experiment.


title: R4 ECM-1

value: P. microcarpus R4 fungal mycelium was transferred directly on top of the plant root


title: R4 ECM-3


title: MW3-ECM-2


title: MW3 ECM-1


title: Si9 ECM-3

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

value: P. microcarpus Si9 fungal mycelium was transferred directly on top of the plant root


title: R4-ECM-2


title: Si9 ECM-1

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


title: MW3 Free-living mycelium-3

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

organism: Pisolithus microcarpus

source_name: Free-living mycelium

value: free-living mycelium

value: P. microcarpus MW3


title: Trametes versicolor 1956-1252 4w-1

description: This sample is from 4 weeks old Trametes versicolor 1956-1252 mycelium. It is the first of three biological replicates used in this experiment.


title: MW3 Free-living mycelium-2

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


title: R10 Free-living mycelium-1

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

value: P. microcarpus R10


title: R10 Free-living mycelium-2


title: R4 Free-living mycelium-3

value: P. microcarpus R4


title: R10 Free-living mycelium-3


title: MW3 Free-living mycelium-1


title: R4 Free-living mycelium-2


title: R4 Free-living mycelium-1


title: Trametes versicolor BRFM1218 4w-3

description: This sample is from 4 weeks old Trametes versicolor BRFM1218 mycelium. It is the third of three biological replicates used in this experiment.


title: Si9 Free-living mycelium-2

value: P. microcarpus Si9


title: Si9 Free-living mycelium-1


title: Si9 Free-living mycelium-3


title: NMP3

status: Public on Oct 21 2020

description:
This sample is from H. almeriense roots grown in pots for 5 months. Replicate 3
Lib_Truseq_RNA_181020B_NMP_3_P_171924_2_S9

data_processing:
Illumina software was used by LifeSequencing SL (Valencia, Spain) to generate fastq raw data files.
Raw reads were analyzed using FastQC for quality, paired, trimmed and mapped onto the assembled de novo transcriptome contigs with Bowtie2 version 2.3.0 and reads mapped onto the contigs were counted with SAMtools version 1.7. Only the contigs with more than 200 bases were selected for further steps and then they were annotated using BLAST on NCBI-nr (March 2018 version) and JGI Mycocosm annotation data (July 2018 version) using DIAMOND version 0.9.19.
Genome_build: H. almeriense de novo transcriptome was performed  with sequencing reads from NMP, WWMP and DSMP samples using Megahit version 1.1.3. (Assembly_plant_contigs.fasta)
Supplementary_files_format_and_content: Tab-delimited text files include relative read abundance after normalization using DESeq2.

organism: Helianthemum almeriense

source_name: H. almeriense non-mycorrhizal plant

growth_protocol: Vegetative mycelium of strain T7 from T. claveryi was grown in Erlenmeyer flasks containing MMNo medium. The cultures were shaken at 75 rpm and maintained in the dark at 23 °C for three months and then, mycelium was collected, snap frozen in liquid nitrogen and stored at -80 °C until later RNA extraction. H. almeriense seeds were collected in Zarzadilla de Totana (Murcia, Spain) and germinated in pots. After two months of growth, 36 plants were transferred to 300 mL individual pots where they were inoculated with T. claveryi spore solution. Twelve plants were left uninoculated to be used as non-mycorrhizal control plants (NMP).

extract_protocol:
RNA was extracted from 100 mg of each tissue and condition using CTAB Phenol:Cholroform method. Prior to sequencing, RNA was treated with  DNAse I (Thermofisher, US). In addition, potential bacterial contamination was assessed via 16S rDNA amplification and the quality and integrity of RNA was controlled by gel electrophoresis, fluorometric quantification (Qubit), 260/280 - 260/230 ratios and RNA electrophoresis bioanalyzer system (2100 Bioanalyzer, Agilent Technologies).
Lifesequencing SL (Valencia, Spain)

treatment_protocol: Three months after spore inoculation, the mycorrhizal status of plants was checked by microscopy methods and 12 of the inoculated plants were subjected to drought stress. Soil moisture was maintained over 75 % for the well-watered mycorrhizal plants (WWMP) and NMP, but it was lowered to 40 % and maintained until shoot water potential was less than -2 MPa in drought-stressed mycorrhizal plants (DSMP). From three replicates per treatment, secondary and tertiary roots were immediately snap frozen in liquid nitrogen and stored at -80 °C for for further RNA extraction.

value: Root

tag: condition

value: Well-watered


title: DSMP3 [re-analysis]

description:
This sample is from T. claveryi x H. almeriense inoculated for 3 months and submitted to dry conditions. Replicate 2
Lib_Truseq_RNA_181016B_DSMP_3_P_171924_2_S5

organism:
Terfezia claveryi
Helianthemum almeriense

source_name: T. claveryi x H. almeriense drought-stressed mycorrhizal plant

value: Mycorrhiza

value: Drought-stressed


title: WWMP6 [re-analysis]

description:
This sample is from T. claveryi x H. almeriense inoculated for 3 months and submitted to well watered conditions. Replicate 3
Lib_Truseq_RNA_181014B_WWMP_6_P_171924_2_S2

source_name: T. claveryi x H. almeriense well-watered mycorrhizal plant


title: DSMP2 [re-analysis]

description:
This sample is from T. claveryi x H. almeriense inoculated for 3 months and submitted to dry conditions. Replicate 1
Lib_Truseq_RNA_181015B_DSMP_2_P_171924_2_S4


title: DSMP3

description: This sample is from T. claveryi x H. almeriense inoculated for 3 months and submitted to dry conditions. Replicate 2

data_processing:
Illumina software was used by LifeSequencing SL (Valencia, Spain) to generate fastq raw data files.
Raw reads were analyzed using FastQC for quality, paired, trimmed and mapped against T. claveryi reference transcripts (https://mycocosm.jgi.doe.gov/Tercla1/Tercla1.home.html) using CLC genomics Workbench 11. For mapping, the minimum length fraction was 0.9, the minimum similarity fraction 0.9 and the maximum number of hits for a read was set to 10.
Genome_build: Terfezia claveryi v1 (https://mycocosm.jgi.doe.gov/Tercla1/Tercla1.home.html). H. almeriense de novo transcriptome was performed was performed with sequencing reads from NMP, WWMP and DSMP samples using Megahit version 1.1.3. Transcripts from each condition (NMP, WWMP and DSMP) were mapped onto the assembled contigs with Bowtie2 version 2.3.0  and reads mapped onto the contigs were counted with SAMtools version 1.7. Only the contigs with more than 200 bases were selected for further steps and then they were annotated using BLAST on NCBI-nr.  ) and JGI Mycocosm   annotation data  using DIAMOND version 0.9.19
Supplementary_files_format_and_content: Tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample.


title: DSMP2

description: This sample is from T. claveryi x H. almeriense inoculated for 3 months and submitted to dry conditions. Replicate 1


title: WWMP1 [re-analysis]

description:
This sample is from T. claveryi x H. almeriense inoculated for 3 months and submitted to well watered conditions. Replicate 1
Lib_Truseq_RNA_181012B_WWMP_1_P_171924_2_S1


title: WWMP6

description: This sample is from T. claveryi x H. almeriense inoculated for 3 months and submitted to well watered conditions. Replicate 3


title: WWMP4 [re-analysis]

description:
This sample is from T. claveryi x H. almeriense inoculated for 3 months and submitted to well watered conditions. Replicate 2
Lib_Truseq_RNA_181013B_WWMP_4_P_171924_2_S2


title: DSMP9 [re-analysis]

description:
This sample is from T. claveryi x H. almeriense inoculated for 3 months and submitted to dry conditions. Replicate 3
Lib_Truseq_RNA_181017B_DSMP_9_P_171924_2_S6


title: NMP2

description:
This sample is from H. almeriense roots grown in pots for 5 months. Replicate 2
Lib_Truseq_RNA_181019B_NMP_2_P_171924_2_S8


title: FLM7

description: This sample is from Terfezia claveryi grown for three months in vitro. Replicate 3

organism: Terfezia claveryi

source_name: T. claveryi free living mycellium

value: Free living mycellium


title: WWMP1

description: This sample is from T. claveryi x H. almeriense inoculated for 3 months and submitted to well watered conditions. Replicate 1


title: NMP1

description:
This sample is from H. almeriense roots grown in pots for 5 months. Replicate 1
Lib_Truseq_RNA_181018B_NMP_1_P_171924_2_S7


title: FLM6

description: This sample is from Terfezia claveryi grown for three months in vitro. Replicate 2


title: FLM1

description: This sample is from Terfezia claveryi grown for three months in vitro. Replicate 1


title: FBN-ARO-KO_GCI_2

status: Public on Oct 13 2020

description: Forebrain specific aromatase knock out mice

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: mm9
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: hippocampus

extract_protocol:
A forebrain neuron-specific aromatase knockout (FBN-ARO-KO) mouse model created previously by our group was utilized in this study. To conditionally delete locally synthesized aromatase in forebrain neurons, we generated Cyp19a1 Cre/LoxP conditional KO mice, under the control of the Ca2+-/calmodulin-dependent protein kinase II α (CaMKIIα) promoter, which expresses Cre exclusively in forebrain excitatory neurons. Ovariectomized female FLOX and FBN-ARO-KO mice were subjected to two-vessel occlusion GCI and reperfusion for 24 hours. Bilateral ovariectomy of female mice was conducted one week prior to GCI surgery. For GCI, mice were anesthetized under isoflurane, and both common carotid arteries (CCAs) were isolated and occluded with clips for 20 minutes. Blood flow through the arteries was verified when the clips were removed. Total RNA was isolated from the hippocampi and subjected to RNA-seq analysis.
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 the hippocampi of FLOX and FBN-ARO-KO mice that underwent 20 min CCA occlusion followed by 24 hours reperfusion and subjected to RNA-seq analysis.

value: Knockout


title: FBN-ARO-KO_GCI_1


title: FLOX-control_GCI_1

description: FLOX control mice

value: Control


title: DSMP9

description: This sample is from T. claveryi x H. almeriense inoculated for 3 months and submitted to dry conditions. Replicate 3


title: WWMP4

description: This sample is from T. claveryi x H. almeriense inoculated for 3 months and submitted to well watered conditions. Replicate 2


title: 5mC_TAC_MeDIPSeq

status: Public on Oct 10 2020

data_processing:
MeDIP-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 using findPeaks module in HOMER (v4.5) using -style "histone" parameter
Genome_build: mm10
Supplementary_files_format_and_content: bigWig were generated using makeUCSCfile module in HOMER (v4.5); bed files were generated using findPeaks module in HOMER (v4.5) using -style "histone" parameter

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

value: cardiomyocyte

value: 8 weeks

value: M

tag: medip antibody

value: Active Motif


title: Input DNA


title: FLOX-control_GCI_2

description: FLOX control mice


title: E11.5_XY-Sry-T-KO_NR5A1-Posi_PE150_rep1

status: Public on Oct 01 2020

city: Suita-shi, Osaka

first: Ryo

last: Maeda

address: Yamadaoka 1-3

country: Japan

institute: The University of Osaka

data_processing:
For SE50 or PE150 RNAseq, sequence reads were aligned using STAR (2.6.0a) with following parameters: --outFilterMultimapNmax 2 --outSAMattributes All --quantMode TranscriptomeSAM. The genomewide coverage data were generated with bamcoverage command (parameters: --normalizeUsing BPM -bs 25) in deepTools (3.2.0).
For long-read RNAseq, the reads were mapped using minimap2 (2.16-r922) with following parameter: -ax splice. Mapped reads with MapQ > 60 were extracted using samtools (1.9).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

source_name: E11.5 gonads

extract_protocol:
For SE50 RNA-seq, E11.5 gonadal somatic cells with high or low NR5A1 levels were isolated using fluorescent-activated cell sorting (FACS). For long-read RNA-seq and PE150 RNA-seq, magnetic-activated cell sorting (MACS) was applied for sorting NR5A1 positive cells.
Gonad/mesonephros complexes dissected from E11.5 embryos carrying the Nr5a1-hCD271-transgene were digested with Accutase (Nacalai Tesque, Kyoto, Japan) to obtain a single cell suspension. For FACS, cells were stained with FITC-labeled anti-LNGFR (hCD271) and collected according fluorescence intensity using FACS Aria 2 (BD Bioscience, San Jose, CA, USA). For MACS, hCD271-expressing cells were purified according to manufacturer’s instructions (Miltenyi Biotech, Bergisch gladbach, Germany).
Total RNA were isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany). For SE50 RNA-seq, Poly(A)+ RNA was converted to a library of cDNA fragments with adaptors at both ends using a TruSeq stranded mRNA Sample Preparation kit (Illumina, San Diego, California, USA). The libraries were then loaded into a flow cell for cluster generation using a TruSeq Rapid SR Cluster Kit (Illumina). Sequence was performed using a HiSeq2500 (Illumina) to obtain single-end 50-nt reads.
For PE150 RNA-seq, total RNA from NR5A1 expressed gonadal somatic cells was isolated as described above. A Ribogone kit (TaKaRa, Shiga, Japan) was used to deplete ribosomal and mitochondrial RNAs. cDNA was prepared and amplified into libraries using a SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (TaKaRa). Libraries were sequenced with Paired-end 150-nt reads using a HiSeq2500 (Illumina).
For long-read RNA-seq, Poly(A)+ RNA was purified from total RNA isolated from 27 pairs of E11.5 XY gonads through oligo(dT) selection. Libraries were prepared using a PCR-cDNA Sequencing Kit (SQK-PCS109; Oxford Nanopore Technologies, Oxford, UK). We amplified cDNA at an extension time of 10 min at 65 °C (15 cycles). The cDNA libraries are loaded onto the GridION Flow Cell (Oxford Nanopore Technologies).

tag: genotype

value: Nr5a1-hCD271; SryT-

tag: developmental stage

value: Gonad


title: 1week_Sham_shUhrf1_rep3

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was analyzed with lumi package, vst-transfromed and quantile normalized

label: biotin

source_name: mouse left ventricle isolated adult cardiomyocyte

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: Ten-day-old pups were infected with AAV9 encoding either a scrambled shRNA (AAV9-scr, control group) or sh-Uhrf1 #1 (AAV9-sh-Uhrf1 #1), and subjected them two months later to TAC

tag: infected

value: AAV9 encoding either a sh-Uhrf1 #1 (AAV9-sh-Uhrf1 #1)

tag: surgery

value: sham


title: 1week_TAC_shUhrf1_rep2

description: replicate 2

value: TAC


title: 1week_TAC_shUhrf1_rep3

description: replicate 3


title: 1week_Sham_shUhrf1_rep1

description: replicate 1


title: 1week_TAC_shUhrf1_rep1

description: replicate 1


title: 1week_Sham_shUhrf1_rep2

description: replicate 2


title: 1week_Sham_shctrl_rep2

description: replicate 2

value: AAV9 encoding either a scrambled shRNA (AAV9-scr, control group)


title: E11.5_XY_NR5A1-Posi_PE150_rep2


title: 5mC_Sham_MeDIPSeq

tag: cell type


title: E11.5_XX_NR5A1-Posi_PE150_rep2


title: 1week_TAC_shctrl_rep1

description: replicate 1


title: E11.5_XX_NR5A1-Posi_PE150_rep1


title: E11.5_XY-Sry-T-KO_NR5A1-Posi_PE150_rep2


title: E11.5_XY_NR5A1-Posi_PE150_rep1


title: E11.5_XY_NR5A1-High_SE50


title: 1week_Sham_shctrl_rep1

description: replicate 1


title: E11.5_XY_NR5A1-High_CAGE_rep2

data_processing:
Sequence reads were mapped using Bowtie (1.2.2) with following parameters: --best -k 1. The genomewide coverage data were generated with bamcoverage command (parameters: --normalizeUsing RPKM --filterRNAstrand forward or reverse -bs 25) in deepTools (3.2.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

extract_protocol:
E11.5 gonadal somatic cells with high NR5A1 levels were isolated using fluorescent-activated cell sorting (FACS).
Gonad/mesonephros complexes dissected from E11.5 embryos carrying the Nr5a1-hCD271-transgene were digested with Accutase (Nacalai Tesque, Kyoto, Japan) to obtain a single cell suspension. For FACS, cells were stained with FITC-labeled anti-LNGFR (hCD271) and collected according fluorescence intensity using FACS Aria 2 (BD Bioscience, San Jose, CA, USA).
For cap analysis gene expression (CAGE) sequence, library preparation and sequencing were performed by K.K. DNAFORM (Kanagawa, Japan). Briefly, we prepared total RNAs of NR5A1high and NR5A1low populations from seven pairs of E11.5 XY gonads. CAGE libraries were prepared using the CAGE Preparation Kit (DNAFORM). All libraries were sequenced on an Illumina HiSeq2500.


title: E11.5_XY_NR5A1-Low_CAGE_rep2


title: 1week_TAC_shctrl_rep2

description: replicate 2


title: 1week_TAC_shctrl_rep3

description: replicate 3


title: E11.5_XY_NR5A1-Posi_Long-read


title: E11.5_XY_NR5A1-Low_CAGE_rep1


title: Tgfbr2-/-Eomes-/- CD8+ regulatory T cells

status: Public on Sep 17 2020

source_name: CD8+ regulatory T cell

growth_protocol: CD8+ regulatory T cells were directly sorted from the spleens of naïve mice without further manipulation.

extract_protocol:
Total RNA was extracted from sorted cells using Quick-RNA miniprep kit from Zymo Research (Cat# 11-328)
Total RNA samples about 1-2 µg 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.

value: CD8+ regulatory T cell from the spleen


title: WT CD8+ regulatory T cells

value: WT


title: 1week_Sham_shctrl_rep3

description: replicate 3


title: P11_small_Macrophages

status: Public on Aug 05 2020

data_processing:
RNA-seq reads were aligned to the Ensembl GRCh38 genome assembly using STAR 020201 with the following parameters: --outFilterIntronMotifs RemoveNoncanonical --quantMode TranscriptomeSAM GeneCounts.
Differential expression analysis was performed using the GLM approach implemented in the R/Bioconductor package EdgeR.
Genome_build: Ensembl Homo Sapiens release GRCh38
Supplementary_files_format_and_content: bigWig were generated using bam2wig.py module in RSeQC v2.5

source_name: Macrophages

extract_protocol:
Total RNA was extracted using the Single Cell RNA Purification Kit (Norgen Biotek), following the manufacturer’s recommendations for extraction from low cell numbers.
Libraries were constructed by SMARTer Stranded Total RNA Kit (Clontech) according to manifacturer’s instructions
Paired-end sequence reads (75-bp in length) were generated on an Illumina NextSeq 500

tag: tumor

value: Colorectal liver metastasis


title: P10_small_macrophages


title: P12_large_Macrophages


title: P12_small_Macrophages


title: P10_large_Macrophages


title: P9_small_Macrophages


title: E11.5_XY_NR5A1-Low_SE50


title: P9_large_Macrophages


title: E11.5_XY_NR5A1-High_CAGE_rep1


title: P8_small_Macrophages


title: P8_large_Macrophages


title: Lung at DPI 7 [sample_1438]

status: Public on Jul 29 2020

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description: RNA extracted from mouse 7 days after SARS-CoV-2 infection

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the mouse Ensembl GRCh38.76 primary assembly and SARS-CoV-2 NCBI NC_045512 Wuhan-Hu-1 genome with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in at least four samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma6. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights
Genome_build: mouse Ensembl GRCh38.76 primary assembly
Supplementary_files_format_and_content: raw counts at gene level

source_name: mouse 7 days after SARS-CoV-2 infection

extract_protocol:
Total RNAs were extracted with the MagMax mirVana Total RNA isolation kit (Thermo Scientific) on the Kingfisher Flex extraction robot (Thermo Scientific).
cDNA libraries were constructed from 10 ng of total RNA from lung tissues of mice. Library construction was performed using 100 ng of cDNA undergoing end repair, A tailing, ligation of universal TruSeq adapters and amplification of 8 cycles to incorporate unique dual index sequences. Libraries were sequenced on the NovaSeq 6000 (Illumina, San Diego, CA) targeting 40 million read pairs and extending 150 cycles with paired end reads.

treatment_protocol: Eight-week-old mice of both sexes were administered 2.5 x 10^4 PFU of SARS-CoV-2 via intranasal administration.

tag: treatment

tag: days post-infection

value: lung


title: Lung at DPI 7 [sample_5323]

value: F


title: Lung at DPI 7 [sample_1427]


title: Lung at DPI 7 [sample_9159]


title: Lung at DPI 4 [sample_5235]

description: RNA extracted from mouse 4 days after SARS-CoV-2 infection

source_name: mouse 4 days after SARS-CoV-2 infection


title: Lung at DPI 4 [sample_5238]


title: Lung at DPI 7 [sample_5326]


title: Lung at DPI 4 [sample_5232]


title: Lung at DPI 4 [sample_1410]


title: Lung at DPI 2 [sample_5356]

description: RNA extracted from mouse 2 days after SARS-CoV-2 infection

source_name: mouse 2 days after SARS-CoV-2 infection


title: Lung at DPI 4 [sample_1407]


title: Lung at DPI 4 [sample_1415]


title: Lung at DPI 2 [sample_5340]


title: Lung at DPI 2 [sample_5338]


title: Lung at DPI 2 [sample_5329]


title: Lung at DPI 2 [sample_1412]


title: Lung at DPI 0 [sample_5198]

description: RNA extracted from mock-infected mouse

source_name: mock-infected mouse

value: NAÏVE


title: Lung at DPI 0 [sample_5228]

description: RNA extracted from mock-infected mouse


title: Lung at DPI 0 [sample_1402]

description: RNA extracted from mock-infected mouse


title: P3_DKO_Inp

status: Public on Jun 08 2020

data_processing:
Sequence reads were mapped to mouse mm10 genome using Bowtie2 (v 2.1.0) with default parameter. Only uniquely mapped and non-redundant reads were used for further analysis. The mapped reads were visualized using DeepTools (v.3.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage command in Deeptools

source_name: Postnatal male germ cells

extract_protocol:
Cells were suspended in 25 μl of 0.3 M sucrose-containing buffer 1 (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 0.5 mM DTT, 15 mM Tris-HCl pH 7.5, and protease inhibitor cocktail). The cells were then lysed following the addition of 0.3 M sucrose-containing buffer 1 (25 μl) with 0.8% NP40 on ice for 10 min; 1.2 M sucrose-containing buffer 1 (400 μl) was added and the chromatin was collected as pellets by centrifugation. The pellets were digested with micrococcal nuclease (0.05 U, Takara) in 10 μl of digestion buffer (0.32 M sucrose, 4 mM MgCl2, 1 mM CaCl2, 50 mM Tris-HCl pH 7.5) by vortexing at 37°C for 15 min; digestion was stopped with EDTA. The supernatant was obtained by centrifugation and incubated with anti-H3K9me2-conjugated magnetic beads (Dynabeads Protein G, Invitrogen) in 50 μl of incubation buffer (50 mM NaCl, 5 mM EDTA, 0.1% NP40, 20 mM Tris-HCl pH 7.5) at 4°C for 6 h. Then, DNA was extracted from the immune complex according to the standard protocol.
DNA from input and ChIP fractions was processed using SMARTer ThruPLEX DNA-seq Kit (TaKaRa) and sequenced using the Illumina HiSeq 1500 system according to the manufacturer’s instructions.

tag: strain background

value: Vasa-Cre; Jmjd1a-/-; Jmjd1b-/-

value: testis

value: Postnatal male germ cells

tag: chip antibody

value: Input


title: P3_DKO_H3K9me2

tag: age

value: H3K9me2; ab1220 (abcam)


title: P7_DKO_rep2

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to mm10 whole genome using TopHat2 v2.1.1 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were estimated using Cufflinks v2.1.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: P7_DKO_postnatal male germ cells

extract_protocol:
Total RNA was extracted using All Prep DNA/RNA Micro Kit (Qiagen). cDNA library was prepared from total RNA using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: P7_DKO_rep1


title: Lung at DPI 0 [sample_1432]

description: RNA extracted from mock-infected mouse

value: 8 weeks


title: P3_Ctrl_H3K9me2

value: Vasa-Cre; Jmjd1a-/+; Jmjd1b-/+


title: P3_WT_rep2

source_name: P3_WT_postnatal male germ cells


title: P3_Jmjd1aKO_rep2

source_name: P3_Jmjd1aKO_postnatal male germ cells

value: Vasa-Cre; Jmjd1a-/-; Jmjd1b-/+


title: P3_Jmjd1bKO_rep1

source_name: P3_Jmjd1bKO_postnatal male germ cells

value: Vasa-Cre; Jmjd1a-/+; Jmjd1b-/-


title: P7_Ctrl_rep2

source_name: P7_Ctrl_postnatal male germ cells


title: P7_Ctrl_rep1


title: P3_Jmjd1bKO_rep2


title: P3_Jmjd1aKO_rep1

source_name: P3_Jmjd1aKO_postinatal male germ cells


title: 15-Ctrl5

status: Public on Oct 02 2020

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 3.6.1 (2019-07-05). Beta-values were extracted from ‘idat’ files by using the ‘Load’ module of the ‘Champ’ R package (v. 2.16.2), with quality control options set as default. The quality control step retained 736048 probes, which were used for further analysis. Probes overlapped with SNP (96368) and with a detection pvalue < 0.01 (3456), beadcount <3 in at least 5% of samples in one or more samples (10453) were eliminated. X or Y chromosomes probes (16664), non-cg probes (2918), and probes aligning to multiple locations (11) and unannotated probes were also removed from analysis. No background correction was carried out. BMIQ normalisation was applied, with the deafult ‘method’ option”. The BMIQ normalized samples were assigned with respective genome coordinates based on probe name and manifest file B4 annotation (Illumina Inc., USA). Batch correction was performed using Combat function from sva package. The BMIQ normalized and batch corrected matrix has also been submitted here and are represented in the sample data tables. The file Matrix_processed.txt.gz includes the non-normalized Average Beta values.
Matrix_signal_intensities.txt.gz includes:Unmethylated signal (B) and methylated signal (A) intensities

label: Cy5 and Cy3

source_name: genomic DNA

label_protocol: Standard llumina Protocol

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

value: peripheral blood

tag: sample status

value: New Control

tag: gender

value: Female

tag: disease state

value: Control

tag: batch

value: Current study

tag: ethnicity

value: European


title: 3-FM

tag: tissue

value: BWS


title: 16-Ctrl6

value: Male


title: P3_Ctrl_rep2

source_name: P3_Ctrl_postnatal male germ cells

tag: genotype


title: P3_Ctrl_rep1


title: MID_KOrep2

status: Public on May 26 2020

city: Leicester

first: John

last: Schwabe

state: Leicestershire

address: Lancaster Road

department: Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

data_processing:
Fastq files trimmed, with reads smaller than 35bp excluded, using the Trimgalore!-0.4.5 wrapper for CutAdapt (v1.11), options: --paired -length35
Aligned to Mus musculus genome using STAR 2.5.2b options: --runMode alignReads --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Aligned files sorted with Samtools 1.3.2  options: sort -l 9 -O bam
Duplicates removed using (2.1) Picard's  markduplicates.jar, options: java -Xms1240m -Xmx30240m  REMOVE_DUPLICATES=true METRICS_FILE=metrics;
De-duplicated files indexed with Samtools 1.3.2 no options
DESeq2 was used to obtain raw counts and normalised counts for each data set and determine differentially regulated gene sets
Genome_build: mm10
Supplementary_files_format_and_content: excel file with normalised gene counts for each sample

source_name: Mouse embryonic fibroblast

growth_protocol: Mouse embryonic fibroblasts were isolated from e13.5 embryos using standard protocol and cultured in DMEM supplemented with 10% FCS 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted from MEF cell pellets using the Zymo quick RNA miniprep kit following the manufacturer's instructions and quality checked using a Bioanalyser. A total of 2 micrograms was sent to Novogene for sequencing
RNA libraries were prepared for sequencing using standard Illumina protocol

tag: strain

value: Fibroblast


title: MID_KOrep3


title: MID_KOrep1


title: 13-Ctrl3


title: DNT_KOrep2


title: 5-AA


title: MID_WTrep2


title: MID_WTrep3


title: DNT_KOrep1


title: 8-PA


title: 11-Ctrl1


title: 2-FS


title: DNT_WTrep1


title: VmRoot_Cd3

status: Public on Feb 12 2020

description: This sample is from  V.myrtillus roots treated with Cadmium. 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
Raw fastq file reads were trimmed for quality and adapter using CLC Genomics Workbench 8.   Trimmed reads were aligned to a Vaccinium myrtillus de novo transcriptome assembly (Vaccinium_myrtillus.transcriptome.fasta) as reference using CLC Genomics Workbench 8 and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Vaccinium myrtillus de novo transcriptome assembly (Vaccinium_myrtillus.transcriptome.fasta)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample

organism: Vaccinium myrtillus

growth_protocol: Oidiodendron maius Zn was grown on cellophane membranes 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. Final pH was adjusted to 4.7. Fungal colonies were removed after 45 days by peeling the biomass from the cellophane membrane. Fifteen plates were prepared in order to get enough fungal material to perform three separate RNA extractions for the RNASeq experiment. Endomycorrhizal plants were obtained aseptically in plastic petri plates (15 cm in diameter, 2.5 cm in height) containing the same medium described above for fungal cultures. Axenic V. myrtillus seedlings were obtained from surface-sterilized (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). 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).   For the Cd stressed condition, both O. maius Zn and V. myrtillus were grown on a modified MMN medium containing 1µM Cd (added as 3CdSO4*8H2O).  Fifteen plates, each containing ten plants, were prepared for each treatment in order to get enough root material to perform three separate RNA extractions for the RNASeq experiment. Roots were observed after a 1.5-month incubation period and the percentage of mycorrhization was evaluated.

extract_protocol:
RNA was extracted O. maius-inoculated V. myrtillus roots  and from control roots 45 days after cultures started.   Total RNA was extracted using the CTAB method.  Aliquots (100 mg) of V. myrtillus 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 was followed by 10 min centrifugation at 5000 rpm and room temperature. An overnight precipitation 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 NanoDrop (Thermo Scientific) specrophotometer and bioanalyzer (Agilent).
cDNA libraries were prepared for sequencing using standard Illumina protocols by the Joint Genome Institue (JGI)

value: roots


title: P3_DKO_rep2

source_name: P3_DKO_postnatal male germ cells

value: Vasa-Cre; Jmjd1a-/-; Jmjd1b-/-

value: testis

value: Postnatal male germ cells


title: U87_ control siRNA_1

status: Public on Apr 24 2020

description: U87 cells transfected with control siRNA.

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 (GRCh37)
Supplementary_files_format_and_content: *_Genes_ReadCount.txt: 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 transfected with control siRNA or PELP1 siRNA using oligofectamine transfection reagent and after 72 hours 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 transfected with control siRNA or PELP1 siRNA and subjected to RNA-seq analysis.

tag: cell line

tag: sirna


title: U87_ control siRNA_2


title: U87_ PELP1 siRNA_2

description: U87 cells transfected with PELP1 siRNA.

value: PELP1 Silencing


title: U87_ PELP1 siRNA_1

description: U87 cells transfected with PELP1 siRNA.


title: VmRoot_Cd2

description: This sample is from V.myrtillus roots treated with Cadmium. It is the second of three biological replicates used in this experiment.


title: VmRoot_Cd1

description: This sample is from  V.myrtillus roots treated with Cadmium. It is the first of three biological replicates used in this experiment.


title: VmRoot3

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


title: DNT_WTrep2


title: 14-Ctrl4


title: OmVmMyc_Cd3 (Vm dataset)

description: This sample is from O.maius-V.myrtillus mycorrhizal roots treated with Cadmium. It is the third of three biological replicates used in this experiment.

organism:
Vaccinium myrtillus
Oidiodendron maius Zn

value: mycorrhizal roots


title: VmRoot1

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


title: OmVmMyc_Cd2 (Vm dataset)

description: This sample is from O.maius-V.myrtillus mycorrhizal roots treated with Cadmium. It is the second of three biological replicates used in this experiment.


title: 12-Ctrl2


title: OmVmMyc_Cd1 (Vm dataset)

description: This sample is from O.maius-V.myrtillus mycorrhizal roots treated with Cadmium. It is the first of three biological replicates used in this experiment.


title: OmVmMyc1 (Vm dataset)

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


title: OmVmMyc2 (Vm dataset)

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


title: OmVmMyc3 (Vm dataset)

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


title: P11_large_Macrophages

source_name: Macrophages

value: Colorectal liver metastasis


title: OmVmMyc3

data_processing:
Illumina sofware was used by the JGI to generate fastq raw data files
Raw fastq file reads were trimmed for quality and adapter using CLC Genomics Workbench 8.   Trimmed reads were aligned to the Oidiodenron maius v1 (https://genome.jgi.doe.gov/Oidma1/Oidma1.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: Oidiodendron maius Zn v1 (https://genome.jgi.doe.gov/Oidma1/Oidma1.home.html)
Supplementary_files_format_and_content: tab-delimited text files include unique aligned reads, total aligned reads and RPKM values for each sample

extract_protocol:
RNA was extracted from O. maius Zn mycelia and from O. maius-inoculated V. myrtillus roots 45 days after cultures started. Aliquots (100 mg) of fungal 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). One phenol:chloroform:isoamyl alcohol (25:24:1) extraction and one chloroform extraction were then carried out. Each extraction was followed by 5 min centrifugation at 14000 rpm and 4°C. Isopropyl alcohol precipitation 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 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 NanoDrop (Thermo Scientific) specrophotometer and bioanalyzer (Agilent).   Total RNA was extracted from mycorrhizal V. myrtillus roots using the CTAB method.  Aliquots (100 mg) of V. myrtillus 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 was followed by 10 min centrifugation at 5000 rpm and room temperature. An overnight precipitation 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 NanoDrop (Thermo Scientific) specrophotometer and bioanalyzer (Agilent).
cDNA libraries were prepared for sequencing using standard Illumina protocols by the Joint Genome Institue (JGI)


title: OmVmMyc_Cd2


title: OmVmMyc_Cd1


title: OmVmMyc_Cd3


title: OmVmMyc2


title: OmVmMyc1


title: OmFLM_Cd3

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

organism: Oidiodendron maius Zn

value: free living mycelium


title: OmFLM_Cd1

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


title: OmFLM_Cd2

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


title: VmRoot2

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


title: OmFLM1

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


title: OmFLM2

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


title: OmFLM3

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


title: P3_WT_rep1

value: WT

tag: cell type


title: Chalo-10m-2

status: Public on Nov 28 2019

description: This sample is from Chalara longipesis mycelium grown on pine needles for 10 month. 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
Raw fastq file reads were trimmed for quality and adapter using CLC Genomics Workbench 9.   Trimmed reads were aligned to the Chalara longipesis v1 (https://mycocosm.jgi.doe.gov/Chalo1/Chalo1.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: Chalara longipesis v1 (https://mycocosm.jgi.doe.gov/Chalo1/Chalo1.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: Stipitochalara longipes

growth_protocol: A total of 24 microcosms were filled with 85g of sand and 11g of dry Scots pine needles (Pinus sylvestris) each and sterilised by gamma radiation. The needle litter contained 0.42% N, 50.6% C, had a C:N-ratio of 120 and a lignin concentration of approximately 25%. For each fungal species, twelve microcosms were inoculated through the addition of single needles that had been pre-colonized for 2 months on N-free agar cultures. After inoculation, 20 ml of 100 mM NH4Cl solution were added to all microcosms, to stimulate fungal growth. Sealed microcosms were incubated at 20 ºC and 4 replicates from each fungal species were harvested after 2, 5 and 10 months, shock frozen in liquid nitrogen, ground using mortar and pestle and stored at -80 ºC.

extract_protocol:
Total RNA was extracted from 800 mg of tissue per sample using the RNA PowerSoil Total RNA Isolation Kit (Mobio now 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: growth on pine needles 10 months


title: Chalo-10m-1

description: This sample is from Chalara longipesis mycelium grown on pine needles for 10 month. It is the first of three biological replicates used in this experiment.


title: Chalo-10m-3

description: This sample is from Chalara longipesis mycelium grown on pine needles for 10 month. It is the third of three biological replicates used in this experiment.


title: Chalo-5m1

description: This sample is from Chalara longipesis mycelium grown on pine needles for 5 months. It is the first of two biological replicates used in this experiment.

value: growth on pine needles 5 months


title: Chalo-2m1

description: This sample is from Chalara longipesis mycelium grown on pine needles for 2 months. It is the first of two biological replicates used in this experiment.

value: growth on pine needles 2 months


title: Gyman-10m-3

description: This sample is from  Gymnopus androsaceus mycelium grown on pine needles for 10 month. It is the third 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 Gymnopus androsaceus v1 (https://mycocosm.jgi.doe.gov/Gyman1/Gyman1.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: Gymnopus androsaceus v1 (https://mycocosm.jgi.doe.gov/Gyman1/Gyman1.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: Gymnopus androsaceus

value: mycelium

tag: growth medium

value: pine needles

tag: time

value: 10 months


title: Gyman-2m3

description: This sample is from Gymnopus androsaceus mycelium grown on pine needles for 2 months. It is the third of three biological replicates used in this experiment.

value: 2 months


title: TAC_4_weeks_repA

status: Public on Oct 12 2019

description:
TAC_4_weeks_repA+B_barcodes.tsv
TAC_4_weeks_repA+B_genes.tsv
TAC_4_weeks_repA+B_matrix.mtx

data_processing:
Raw sequencing data (bcl-files) were converted to fastq files with Illumina bcl2fastq tool, integrated into the CellRanger (10X Genomics) suite (version 2.1.1).
The CellRanger analysis pipeline was used to generate a digital gene expression matrix staring from raw data.
The raw digital gene expression matrix (UMI counts per gene per cell) was imported in R (version 3.5.0) using Seurat R package (version Seurat_2.3.3)
The I1 contains the sample index. The R1 = cellular barcode (CB) (16 bp) + molecular barcode (MB) (umi) 10bp. The R2 contains the transcript read.
Genome_build: Pre-build mouse genome (version mm10-1.2.0) was used as genome reference.
Supplementary_files_format_and_content: UMI counts per gene per cell
Dataset1-Average-clusters-conditions.xlsx: Average of normalized gene expression values were obtained using Seurat AverageExpression function with default parameters.
Dataset2-Markers-clusters-conditions.xlsx: List of positive and negative markers specific to each cluster obtained with Seurat FindAllMarkers function with default parameters and min.pct=0.2.

source_name: cardiac immune (CD45+) cells

extract_protocol:
~5,000 cells were loaded into one channel of the Single Cell Chip A for each sample using the Single Cell 3’ v2 single cell reagent kit (10X Genomics) for Gel bead Emulsion generation into the Chromium system. Following capture and lysis, we synthesized cDNA and amplified it for 14 cycles following the manufacturer’s protocol (10X Genomics). 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries.
Sequencing was performed on the NextSeq500 Illumina sequencing platform following 10x Genomics instruction for reads generation; at least 50.000 reads per cell were produced.

tag: condition

value: TAC

tag: time point


title: Gyman-10m-1

description: This sample is from Gymnopus androsaceus mycelium grown on pine needles for 10 month. It is the first of three biological replicates used in this experiment.


title: Gyman-10m-2

description: This sample is from  Gymnopus androsaceus mycelium grown on pine needles for 10 month. It is the second of three biological replicates used in this experiment.


title: Gtman-5m3

description: This sample is from Gymnopus androsaceus mycelium grown on pine needles for 5 months. It is the third of three biological replicates used in this experiment.

value: 5 months


title: Gyman-5m1

description: This sample is from Gymnopus androsaceus mycelium grown on pine needles for 5 months. It is the first of three biological replicates used in this experiment.


title: Gyman-2m1

description: This sample is from Gymnopus androsaceus mycelium grown on pine needles for 2 months. It is the first of three biological replicates used in this experiment.


title: TAC_4_weeks_repB

data_processing:
Raw sequencing data (bcl-files) were converted to fastq files with Illumina bcl2fastq tool, integrated into the CellRanger (10X Genomics) suite (version 2.1.1).
The CellRanger analysis pipeline was used to generate a digital gene expression matrix staring from raw data.
The raw digital gene expression matrix (UMI counts per gene per cell) was imported in R (version 3.5.0) using Seurat R package (version Seurat_2.3.3)
The I1 contains the sample index. The R1 = cellular barcode (CB) (16 bp) + molecular barcode (MB) (umi) 10bp. The R2 contains the transcript read.
Genome_build: Pre-build mouse genome (version mm10-1.2.0) was used as genome reference.
Supplementary_files_format_and_content: UMI counts per gene per cell


title: Sham_4_weeks_repB

description:
Sham_4_weeks_repA+B_barcodes.tsv
Sham_4_weeks_repA+B_genes.tsv
Sham_4_weeks_repA+B_matrix.mtx

value: Sham


title: Gyman-2m2

description: This sample is from Gymnopus androsaceus mycelium grown on pine needles for 2 months. It is the second of three biological replicates used in this experiment.


title: TAC_1_week_repA

description:
TAC_1_week_repA+B_barcodes.tsv
TAC_1_week_repA+B_genes.tsv
TAC_1_week_repA+B_matrix.mtx


title: TAC_1_week_repB


title: Sham_4_weeks_repA


title: Sham_1_week

description:
Sham_1_week_barcodes.tsv
Sham_1_week_genes.tsv
Sham_1_week_matrix.mtx


title: Chalo-5m2

description: This sample is from Chalara longipesis mycelium grown on pine needles for 5 months. It is the second of two biological replicates used in this experiment.


title: Chalo-2m2

description: This sample is from Chalara longipesis mycelium grown on pine needles for 2 months. It is the second of two biological replicates used in this experiment.


title: P3_Ctrl_Inp

tag: strain background

value: Vasa-Cre; Jmjd1a-/+; Jmjd1b-/+

value: testis

tag: chip antibody

value: Input


title: Gyman-5m2

description: This sample is from Gymnopus androsaceus mycelium grown on pine needles for 5 months. It is the second of three biological replicates used in this experiment.


title: Csf3r-/-_1_rep

status: Public on Jun 24 2019

description:
KO_rep1+2_barcodes.tsv
KO_rep1+2_genes.tsv
KO_rep1+2_matrix.mtx

data_processing:
Raw sequencing data (bcl-files) were converted to fastq files with Illumina bcl2fastq tool, integrated into the CellRanger (10X Genomics) suite (version 2.1.1).
R1 contains in the following order: cellular barcode (16bp) + molecular UMI (10bp).
R2 is the biological read.
The CellRanger analysis pipeline was used to generate a digital gene expression matrix starting from raw data.
The raw digital gene expression matrix (UMI counts per gene per cell) was imported in R (version 3.4.4) using Seurat R package (version Seurat_2.3.4)
Genome_build: Pre-build mouse genome (version mm10-1.2.0) was used as genome reference.
Supplementary_files_format_and_content: UMI counts per gene per cell

source_name: UTCαβ T cells

extract_protocol: UTCαβ cells of each sample were loaded into one channel of the Single Cell Chip A using the Single Cell 3’ v2 single cell reagent kit (10X Genomics) for Gel bead Emulsion generation into the Chromium system. Following capture and lysis, cDNA was  synthesized and amplified for 14 cycles following the manufacturer’s protocol (10X Genomics). 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries. Sequencing was performed on the NextSeq500 Illumina sequencing platform following 10x Genomics instruction for reads generation; at least 20.000 reads per cell were produced.

value: sarcoma

value: unconventional alpha beta T cells


title: Csf3r+/+_2_rep

description:
WT_rep1+2_barcodes.tsv
WT_rep1+2_genes.tsv
WT_rep1+2_matrix.mtx


title: Csf3r+/+_1_rep


title: KO_ab_gd_4

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


title: KO_ab_CD8_4


title: KO_ab_CD4_4


title: KO_ab_DN_4


title: KO_ab_gd_3


title: KO_ab_CD8_3


title: KO_ab_DN_3


title: KO_ab_gd_2


title: KO_ab_CD8_2


title: KO_ab_CD4_2


title: KO_ab_DN_1


title: KO_ab_CD4_3


title: Csf3r-/-_2_rep


title: KO_ab_gd_1


title: KO_ab_DN_2


title: KO_ab_CD8_1


title: KO_ab_CD4_1


title: WT_ab_DN_4


title: WT_ab_CD8_4


title: WT_ab_CD4_4


title: WT_ab_gd_3


title: WT_ab_CD4_3


title: WT_ab_CD8_3


title: MID_WTrep1

value: Fibroblast


title: WT_ab_gd_2


title: WT_ab_DN_2


title: WT_ab_CD8_2


title: WT_ab_gd_1


title: WT_ab_CD4_2


title: WT_ab_CD8_1


title: WT_ab_CD4_1


title: U87 ERβ FLAG_2

status: Public on May 02 2019

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

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: treatment

value: overexpression


title: WT_ab_DN_1


title: WT_ab_gd_4


title: P3_DKO_rep1

value: Vasa-Cre; Jmjd1a-/-; Jmjd1b-/-

tag: age

value: Postnatal male germ cells


title: U87 empty vector_1

description: U87 cells expressing empty vector

value: Control


title: KO3

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: KO2


title: KO1


title: Galls CAD mutant 3

status: Public on Jan 15 2019

description:
This sample is from CAD mutant galls. It is the third 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: Galls CAD mutant

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: Root-knot nematode Galls

tag: genotype/variation

value: CAD mutant


title: WT1


title: Roots CAD mutant 2

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

source_name: Roots CAD mutant

value: Roots


title: U87 empty vector_2

description: U87 cells expressing empty vector


title: Galls CAD mutant 2

description:
This sample is from CAD mutant galls. It is thesecond of three biological replicates used in this experiment.
Populus tremula x P. alba clone INRA 717-1B4


title: Roots WT 3

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

source_name: Wildtype roots

value: Wildtype


title: Galls WT 1

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

source_name: Wildtype galls


title: Roots WT1

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


title: CTRL02

status: Public on Oct 01 2019

description: methylation profiling using bisulfite converted

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

source_name: genomic DNA from CTRL02 Blood

value: blood

tag: gender

value: M

tag: disease state

value: Normal


title: Roots CAD mutant 1

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

tag: tissue


title: Galls WT 3

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


title: Galls WT 2

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


title: Galls CAD mutant 1

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