title: P18_ATAC-seq_Ino80cKO_rep3

data_processing:
Reads were trimmed using Trim Galore and aligned to mm10 using BWA. Duplicates were marked by Picard.
BigWig files were created from merged replicates scaled to 1 million mapped reads using BEDTools.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files for genomic tracks.

extract_protocol:
Seminiferous tubules from P18 testes were digested with collagenase and trypsin to obtain spermatogenic cells followed by filtration through 40 micron filter. Cells were prepared for ATAC-seq library preparation by Omni-ATAC protocol (Corces et al., 2017).
Libraries were generated by following Omni-ATAC protocol (Corces et al., 2017)

value: Mixed background


title: Leaf, bermudagrass heat treatment for 12h rep2

status: Public on Dec 21 2021

type: SRA

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

country: China

institute: Huazhong Agricultural University

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for base calling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed
Supplementary_files_format_and_content: raw counts and FPKMs

molecule: total RNA

organism: Cynodon dactylon

source_name: leaf

extract_protocol:
The leaves of control and heat treated bermudagrass plants were collected for RAN isolation following the standard Qiagen RNeasy mini kit protocol. RNA purity and integrity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: leaf

tag: treatment

value: heat

tag: time

tag: genotype

value: WT


title: Muscle_sham operated_1wk_Control2

type: RNA

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® ClariomS Mouse (LifeTechnologies) at 45°C for 17 hours.

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: The scanned images are then analyzed with Expression Console software (Thermofischer) to obtain raw data (cel files) and metrics for Quality Controls. The observations of some of these metrics and the study of the distribution of raw data show no outlier experiment.  RMA normalization is performed using R with CDF v22 of EntrezGene (Brian Array).

label: Biotin

organism: Mus musculus

label_protocol: 100 ng of total RNA is reverse transcribed following the GeneChip® WT Plus Reagent Kit (Thermofisher) .  Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA polymerase . After purification according to Affymetrix protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled.

extract_protocol: The muscles were collected and freezed in liquid nitrogen. 1ml of Trizol was added for each muscle and TRIzol™ Reagent experimental protocol for RNA isolation by Invitrogen/Thermo scientific was used. The samples were all treated with DNAsi.

value: adult plantaris muscle

value: wildtype


title: EVT-TSTerm #2

city: TauYau

first: Yun-Shien

last: Lee

state: Taiwan

address: TauYau

department: Dept. Biotechnology

country: Taiwan

institute: Ming Chuan Univ

description:
Total RNA by depleting ribosomal RNA.
RAWcount.txt
FPKM.txt

data_processing:
CLC Genomics Workbench v10 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, low quality sequence (QV³20), and ambiguous nucleotides, then mapped to Homo sapiens GRCh38 (hg38).
The expression value was calculated in FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) using a protocol from Mortazavi et al., Nature Methods, 2008.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: FPKM.txt: Matrix table with FPKM for every gene and every sample.
Supplementary_files_format_and_content: RAWcount.txt: Matrix table with raw gene counts for every gene and every sample.

organism: Homo sapiens

source_name: Placenta

extract_protocol:
Total RNA was extracted with the RNeasy mini Kit and RNase-free DNase (QIAGEN).
RNA libraries were prepared for sequencing using Universal RNA Seq Library Preparation Kit with NuQuant (Tecan Trading AG) according to the manufacturer's protocol.

tag: cell type

value: Extravillous trophoblast

tag: Stage

value: Differentiated into EVT


title: Leaf, bermudagrass heat treatment for 12h rep1


title: Post-secretory floral nectary B [J.procumbens 2_2]

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

country: USA

institute: University of Minnesota Duluth

description: RNA-Seq sample

data_processing:
Contigs assembled with Trinity v.2.12
Reads quantified using kallisto 0.46.1
Contigs mapped to Arabidopsis thaliana with NCBI’s blastn
Genome_build: N/A
Supplementary_files_format_and_content: Jaltomata_hp_tpms.xlsx

organism: Jaltomata procumbens

source_name: Nectary tissue

extract_protocol: Jaltomata procumbens and Jaltomata herrerae plants were grown in Sun Gro LC8 soil in the MAES/MDA Plant Growth Facilities at the University of Minnesota with typical daytime highs of 25C and nighttime lows of 15C. Three types of RNA samples were separately prepared in triplicate from the floral nectaries of both species, including: ‘pre-secretory’ (~24-48 hours prior to anthesis/nectar secretion), ‘secretory’ (full anthesis, at ~3-6 hours after dawn), and ‘post-secretory’ (after petal abscission). RNA from fully expanded leaf tissue was also isolated in triplicate for both species. All tissues were manually dissected by hand with the RNA being immediately extracted by mechanical disruption with a microcentrifuge pestle and using an RNAqueous® RNA isolation kit (Thermo Fisher) with Plant RNA Isolation Aid (Thermo Fisher). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for mRNA isolation, barcoded library creation and Illumina NovaSeq 6000 sequencing. Twenty-four TruSeq stranded mRNA libraries were created (triplicate samples for nectaries at three timepoints each, as well as leaf tissue, for each species) and sequenced via 150 bp, paired-end runs on the NovaSeq 6000 using Rapid chemistry. All libraries were pooled and sequenced. All expected barcodes were detected and mean depth for the libraries was ≥ 20 M reads. The average quality scores were all above Q30.

value: Post-secretory floral nectary


title: P18_ATAC-seq_Ino80cKO_rep2

city: Chapel Hill

first: Prabuddha

last: Chakraborty

state: NC

address: 120 Mason Farm Road5023 B, Genetic Medicine Building, CB#7264

department: Genetics

institute: University of North Carolina at Chapel Hill

library_source: genomic

molecule: genomic DNA

source_name: spermatogenic cells from Testes

tag: age

tag: strain

value: Spermatogenic cells

value: Testis


title: Post-secretory floral nectary A [J.procumbens 2_0]

description: RNA-Seq sample


title: EVT-TSTerm #1


title: P18_ATAC-seq_Ino80cKO_rep1


title: ST-TSTerm #2

value: Syncytiotrophoblast

value: Differentiated into STB


title: Pre-secretory floral nectary C [J.procumbens 0_2]

description: RNA-Seq sample

value: Pre-secretory floral nectary


title: LungD7_1

city: New York

first: Edwin

middle: Antonio

last: Rosado-Olivieri

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
The Cell Ranger (v.2.0.2) software pipeline was used to create FASTQ files which were aligned to the hg19 genome using default parameters.
Filtered gene expression matrices were generated using Cell Ranger and subsequently used for downstream analyses using Scanpy (v.1.6.0)
Data was filtered to have a minimum of 2000  and a maximum of 8000 detected genes per cell and genes were filtered to be expressed in at least 3 cells. Cells with over 10% mitochondrial genes were discarded. Clustering of cells was performed using the Leiden algorithm (resolution=0.4) and visualized using UMAP plots (n.neighbors = 50, PCA components= 50). Differential gene expression analysis was performed using the Wilcoxon rank-sum (Mann-Whitney-U) test to identify cluster markers.
Genome_build: hg19 genome
Supplementary_files_format_and_content: Processed cellranger matrix files with metadata file containing cell type classification.

source_name: lung organoids

growth_protocol: Lung organoids were derived from human embryonic stem cells using a standardized protocol described in this study.

extract_protocol:
Micropatterned coverslips with 225-μm diameter synthetic lung buds at day 7 of lung induction were dissociated with TrypLE Express (Gibco) for 10 min at 37 °C.
Samples were loaded for capture with the Chromium System using the Single Cell 3′ v3 reagents (10X Genomics). Following cell capture and lysis, cDNA was synthesized and amplified according to the manufacturer’s instructions (10X Genomics). The resulting libraries were sequenced on the Nova-seq platform.

value: lung organoids

value: Alveolar and airway tissue

tag: cell line


title: P18_CUT&RUN_H3K27me3_Ino80WT_rep3

data_processing:
Library strategy: CUT&RUN
CUT&RUN reads were aligned to the reference genome mm10 using Bowtie2 with very-sensitive setting allowing dovetail alignment.
Duplicates were marked by Picard and replicates were merged using Samtools.
Bigwig files were prepared from merged files with 1X normalization using Deeptools.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files for genomic tracks.

extract_protocol:
Seminiferous tubules from P18 testes were digested with collagenase and trypsin to obtain spermatogenic cells followed by filtration through 40 micron filter. Cells were prepared for CUT&RUN library by previously published protocol (Skene et al., 2018; Meers et al., 2019).
Libraries were generated using Kapa hyperprep DNA library kit for Illumina sequencing with modifications from CUT&RUN protocol (Skene et al., 2018; Meers et al., 2019).

tag: antibody

value: Rabbit anti-H3K27me3; Cell signaling (9733)


title: Secretory floral nectary A [J.procumbens 1_0]

description: RNA-Seq sample

value: Secretory floral nectary


title: Muscle_sham operated_1wk_Control1


title: P18_ATAC-seq_Ino80WT_rep1

value: Mixed background


title: Leaf, bermudagrass control rep2

value: leaf

value: control


title: ST-TSTerm #1


title: Pre-secretory floral nectary B [J.procumbens 0_1]

description: RNA-Seq sample


title: P18_ATAC-seq_Ino80WT_rep3


title: TSTerm #1

value: Trophoblast stem cell

value: Undifferentiated


title: P18_ATAC-seq_Ino80WT_rep2


title: TSTerm #2


title: Leaf, bermudagrass control rep1

value: WT


title: Leaf, bermudagrass heat treatment for 2h rep1

value: heat


title: Leaf, bermudagrass heat treatment for 2h rep2


title: 334441

status: Public on Dec 20 2021

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
miR-Neg1 vs miR-206
Date:2008/01/23

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 16 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

label_protocol: Ambion

extract_protocol: Trizol

tag: label

tag: extract

tag: sample

tag: subject

value: Human

value: Hela


title: 40_S6

city: Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 3

department: Department of Psychology and Logopedics

country: Finland

institute: University of Helsinki

data_processing:
Each sample was run mixed in all runs and lanes. RNA-sequencing reads for each sample were merged from three  Illumina NextSeq 500 runs totalling 12 lanes. Reads were aligned to mouse and human genomes using STAR aligner, version (Dobin et al. 2013) and annotated to genes using HTSeq (Anders et al. 2015).
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: Tab delimeted text file containing unnormalized (raw) read counts per feature.

organism:
Homo sapiens
Mus musculus

source_name: human iPSC-astrocyte progenitor transplanted RAG1 mouse cortical sample

growth_protocol: iPSC-astrocyte progenitors: The primary cells were reprogrammed with Cytotune 2.0 iPS Sendai Reprogramming Kit for Oct4, Sox2, Klf4, and c-myc. The emerged colonies were individually subcloned. For differentiation, iPSCs were cultured in feeder-free conditions with Matrigel-coating and Essential 8 culture medium. Astroglial differentiation was carried out as described (Stem Cell Reports. 2017;9:1885-1897) by maintaining neural progenitor spheres in astrocyte differentiation medium in suspension for 6–7 months before dissociation. Transplantation: hiPSC-astrocyte progenitors (100,000 cells/µl in PBS) dissociated from sphere cultures were transplanted into newborn Rag1 knockout mouse (B6.12957-Rag1tm1Mom/J, The Jackson Laboratory) forebrain using the published protocol  (Kim, et al., 2014). Cell transplantation was performed by injecting 300,000 cells into the brain at 5 locations: (0.8, 1.0, -1.5); (-0.8, 1.0, -1.5); (0.8, 2.0, -1.5); (-0.8, 2.0, -1.5); (0.0, -1.0, -1.5). The mice were killed when they were 11 months old and frontal cortex was separated.

extract_protocol:
Total RNA was extracted using Trizol and cleaned using RNeasy Mini Kit. The RNA quality was analyzed on the Agilent 2100 Bioanalyzer™ using an RNA6000 assay.
Sequencing libraries were prepared with Illumina NextSeq and SureSelect Strand Specific RNA Seq kits.

treatment_protocol: No treatment was applied.

tag: sample number

tag: mouse strand

tag: hipsc source

value: skin fibroblasts

tag: group status

value: healthy control

tag: mouse gender

value: female

tag: patient gender

tag: patient disease status

value: healthy

tag: sample type

value: Mouse cortex transplanted human iPSC-astrocyte progenitors from healthy control person


title: 334442

description:
miR-Neg1 vs miR-210
Date:2008/01/23

tag: tissue


title: 334443

description:
miR-Neg1 vs miR-122
Date:2008/01/23


title: 334503

description:
miR-Neg1 vs miR-122
Date:2008/01/21


title: 334659

description:
miR-34a vs miR-Neg1
Date:2008/01/21


title: 137_S17

tag: cell type

value: human iPSC-astrocyte progenitor transplanted RAG1 mouse cortical sample


title: 334410

description:
miR-Neg1 vs miR-34a
Date:2008/01/21


title: 334673

description:
miR-122 vs miR-Neg1
Date:2008/01/21


title: 334594

description:
miR-210 vs miR-Neg1
Date:2008/01/23


title: 334413

description:
miR-Neg1 vs miR-210
Date:2008/01/21


title: 334561

description:
miR-206 vs miR-Neg1
Date:2008/01/23


title: 334671

description:
miR-210 vs miR-Neg1
Date:2008/01/21


title: 334660

description:
miR-206 vs miR-Neg1
Date:2008/01/21


title: 334448

description:
miR-34a vs miR-Neg1
Date:2008/01/23


title: 46_S9

value: unaffected twin

value: Mouse cortex transplanted human iPSC-astrocyte progenitors from unaffected twin


title: 334415

description:
miR-Neg1 vs miR-34a
Date:2008/01/23


title: 334411

description:
miR-Neg1 vs miR-206
Date:2008/01/21


title: 334595

description:
miR-122 vs miR-Neg1
Date:2008/01/23


title: 45_S8


title: 145_S19

value: affected twin

value: schizophrenia

value: Mouse cortex transplanted human iPSC-astrocyte progenitors from affected twin with schizophrenia diagnosis


title: 24_S5


title: 41_S7


title: 150_S21


title: 146_S20


title: 133_S16


title: 16_S4


title: 124_S15


title: 138_S18


title: 103_S10


title: SMMh sample 8, 138P fraction

city: Boston

first: Irene

last: Ghobrial

state: MA

address: 4 Blackfan Circle, 2nd Floor, Suite 240

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: 3' barcoded RNA

data_processing:
cellranger mkfastq was used for extracting fastq files
cellranger count was used for sequence alignment and UMI counting
Genome_build: hg38
Supplementary_files_format_and_content: cellranger filtered gene barcode matrices

source_name: Bone Marrow

extract_protocol: Chromium Single Cell 3′ Library & Gel Bead Kit v3

tag: diagnosis

value: High Risk Smoldering Myeloma

tag: marker selection

value: Bone Marrow


title: SMMh sample 6, 138P fraction

description: 3' barcoded RNA


title: SMMl sample 1, 138P fraction

description: 3' barcoded RNA

value: Low Risk Smoldering Myeloma


title: SMMh sample 3, 138P fraction

description: 3' barcoded RNA


title: SMMh sample 2, 138P fraction

description: 3' barcoded RNA


title: SMMh sample 10, 138P fraction

description: 3' barcoded RNA


title: SMMl sample 3, 138P fraction

description: 3' barcoded RNA


title: SMMh sample 9, 138P fraction

description: 3' barcoded RNA


title: 112_S11


title: 113_S12


title: SMMl sample 2, 138P fraction

description: 3' barcoded RNA


title: SMMh sample 4, 138P fraction

description: 3' barcoded RNA


title: MDA-MB-231 WT DAXX OE

city: Gainesville

first: Daiqing

last: Liao

state: FL

address: 2033 Mowry Rd

department: Anatomy and Cell Biology

institute: University of Florida

data_processing:
ChIP-seq sequencing reads (Fastq files) were mapped to the human genome (GRCh37/hg19) using Bowtie2 (Langmead and Salzberg, 2012), where option –local was specified to trim or clip unaligned reads from one or both ends of the alignment. Genome browser BedGraph tracks and read density histograms were generated using SeqMINER. Peak finding and annotation to the nearest Refseq gene promoter was performed and de novo motif discovery was carried out using HOMER (Heinz et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: matrix table for peak distritbutions
Supplementary_files_format_and_content: matrix table for region distritbutions

source_name: Triple negative breast

growth_protocol: The panel of MDA_MB-231 derived cell lines (control and WT DAXX OE) were cultured in complete DMEM.

extract_protocol:
The cells were resuspended in a swelling buffer in the presence of the protease inhibitor cocktail (Sigma) and then pelleted and resuspended in the SDS lysis buffer. The lysates were transferred to a Covaris microTUBE and sonicated with an E220 Covaris Ultrasonicator. Chromatin fragmentation (~500 bps) was verified through agarose gel electrophoresis. DNA was extracted using Qiagen mini prep based on manufacturer instructions.
DNA libraries were prepared for sequencing using standard ChIP Illumina protocols

tag: strain

value: Triple negative breast

tag: age

tag: genotype

value: Overexpressiom


title: SMMh sample 5, 138P fraction

description: 3' barcoded RNA


title: NBM sample 7, 138P fraction

description: 3' barcoded RNA

value: Healthy Donor


title: NBM sample 8, 138P fraction

description: 3' barcoded RNA


title: NBM sample 4, 138P fraction

description: 3' barcoded RNA


title: NBM sample 6, 138P fraction

description: 3' barcoded RNA


title: 116_S14

value: skin fibroblasts


title: 115_S13


title: NBM sample 2, 138P fraction

description: 3' barcoded RNA


title: NBM sample 11, 138P fraction

description: 3' barcoded RNA


title: NBM sample 10, 138P fraction

description: 3' barcoded RNA


title: NBM sample 1, 138P fraction

description: 3' barcoded RNA


title: SMMh sample 1, 138P fraction

description: 3' barcoded RNA


title: MDA-MB-231 shControl

value: Control


title: MGUS sample 6, 138P fraction

description: 3' barcoded RNA

value: Monoclonal Gammopathy of Undetermined Significance


title: MM sample 1, 138P fraction

description: 3' barcoded RNA

value: Multiple Myeloma


title: MM sample 4, 138P fraction

description: 3' barcoded RNA


title: MM sample 3, 138P fraction

description: 3' barcoded RNA


title: MM sample 7, 138P fraction

description: 3' barcoded RNA


title: MM sample 5, 138P fraction

description: 3' barcoded RNA


title: MGUS sample 3, 138P fraction

description: 3' barcoded RNA


title: MGUS sample 4, 138P fraction

description: 3' barcoded RNA


title: MGUS sample 2, 138P fraction

description: 3' barcoded RNA


title: MM sample 2, 138P fraction

description: 3' barcoded RNA


title: MM sample 6, 138P fraction

description: 3' barcoded RNA


title: MM sample 8, 138P fraction

description: 3' barcoded RNA


title: MGUS sample 5, 138P fraction

description: 3' barcoded RNA


title: MGUS sample 1, 138P fraction

description: 3' barcoded RNA


title: Pre-secretory floral nectary A [J.procumbens 0_0]

description: RNA-Seq sample

value: Pre-secretory floral nectary


title: H05_JC_8

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

description: Gene expression from islets from 16-week C57BL/KsJ db/db mice.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Gene ST 2.0 or Affymetrix Mouse Gene ST 2.1 GeneChips. They were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Interrogating probes were imported, RMA normalized and RMA background corrected, Quantile normalization, Log probes using base 2 and Probeset summarization is Median Polish (Partek Genome Suite v6.6 (6.151022).

label: biotin

source_name: islet

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

growth_protocol: Mice were taken from the Garvan Institute breeding colonies. Animals were kept under conventional conditions with free access to food and water.

extract_protocol: Total RNA from islets was extracted using RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: Islets of C57BL/KsJ db/db and C57BL/6J ob/ob mice, and their age-matched lean control mice were isolated for RNA extraction.

value: C57BL/KsJ db/db

value: Pancreatic islets

value: 16 weeks


title: E05_JC_5

description: Gene expression from islets from 16-week C57BL/KsJ control mice.

value: C57BL/KsJ control


title: F05_JC_6


title: G07_JC_15

description: Gene expression from islets from 16-week C57BL/6J ob/ob mice.

value: C57BL/6J ob/ob


title: E07_JC_13

description: Gene expression from islets from 16-week C57BL/6J control mice.

value: C57BL/6J control


title: C07_JC_11

description: Gene expression from islets from 6-week C57BL/6J ob/ob mice.

value: 6 weeks


title: H07_JC_16


title: CON2

city: Beijing

first: Yujun

last: Wu

address: Yumingyuan West Road

institute: China Agricultrual University

data_processing:
After total RNA extraction and synthesized into double-stranded cDNA RNA-seq was performed on Illumina HiSeq platform to construct RNA libraries and generate reads of 150-bp long paired-end.
High-quality clean data were obtained by SeqPrep and Sickle with default parameters and then aligned to reference genome with orientation mode using HISAT2.
The mapped reads of each sample were assembled by StringTie.
Mus_musculus reference genome (GRCm39) and gene model annotation files were downloaded from the NCBI database.
Differentially expressed genes (DEGs) were identified through pairwise comparisons between every two stages by DESeq2. DEGs with |log2FC|>1.5 and Q value ≤0.05 were considered as significant.
Genome_build: GRCm39

source_name: macrophages

growth_protocol: Murine macrophage RAW264.7 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% inactivated fetal bovine serum (FBS) at 37℃ and 5% CO2

extract_protocol: Total RNA of colonic segments was extracted by Trizol (Invitrogen, California, USA), cDNA was obtained using Prime ScriptTM RT Kit (Takara, Shiga, Japan).

treatment_protocol: Murine macrophage RAW264.7 cells were seeded in six-well plates at a density of 10^6 cells. After ≈80% confluence, cells were treated with or without 1 mM ProNa for 24 h followed by LPS treatment (100 ng/mL) for 12 h.

tag: cell line

tag: treatment

value: CON


title: ProNa2

value: ProNa


title: ProNa1


title: CON3


title: LPS3

value: LPS


title: LPS1


title: LPS2


title: D05_JC_4

description: Gene expression from islets from 6-week C57BL/KsJ db/db mice.


title: C05_JC_3


title: CON1


title: D07_JC_12


title: A07_JC_9

description: Gene expression from islets from 6-week C57BL/6J control mice.


title: B05_JC_2

description: Gene expression from islets from 6-week C57BL/KsJ control mice.


title: ProNa3


title: A05_JC_1


title: RV.RNA.WT4

city: La Jolla

first: Ju

last: Chen

state: California

address: 9500 Gilman Drive 0613

institute: University of California San Diego

data_processing:
Sequencing reads were mapped to GENCODE mouse transcripts reference (release M22, GRCm38.p6)
Transcription levels were quantified using salmon (version: 1.2.1, parameters: -l A --validateMappings --seqBias --gcBias).
Gene expression levels were generated using tximport (version: 1.10.1) and differential expression analysis was carried out using DEseq2 (version: 1.22.2) in R.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM and reads count for each sample

source_name: Mouse heart right ventricle

extract_protocol:
E13.5 embryonic hearts or isolated ventricles were homogenized in TRIzol (Invitrogen) and total RNA was isolated according to the manufacturer’s instructions. The concentration and quality of purified RNA was assessed by TapeStation (Agilent). RNA integrity numbers (RIN) were in the range of 6.1 to 10. Libraries were sequenced with an Illumina HiSeq 4000 sequencer to a sequeencing depth of 20-70 million reads per sample.
cDNA libraries were prepared using an Illumina TruSeq stranded mRNA kit according to manufacturer’s instructions.

tag: genetic  manipulation

value: Mock

value: right ventricle


title: RV.RNA.WT2


title: 5_RNAseq_NPC_mutkdm2b_rep2

city: East Lansing

first: Jin

last: He

state: Michigan

address: 603 Wilson Road, Biochem Bldg. Rm. 410

institute: Michigan State Univeristy

description: NPC culture medium

data_processing:
For the RNA-Seq data analysis, all sequencing reads were mapped to NCBI build 37 (mm9) of the mouse genome using Tophat2.
The mapped reads were normalized to reads as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
The differential gene expression was calculated by Cuffdiff program and the statistic cutoff for identification of differential gene expression is q < 0.05 and 1.5-fold RPKM change between samples.
Genome_build: mm9
Supplementary_files_format_and_content: diff

source_name: Neural progenitor cells

growth_protocol: The neural tissues were isolated from the subventricular zone of E16 brains and dissociated with 0.05% trypsin-EDTA (Life Technologies) at 37 °C for 15 min. The reaction was stopped by trypsin inhibitor (10 mg/ml, Worthington Biochemical Corporation). The dissociated cells were washed with cold PBS for 3 times and plated onto the non-coated petri dishes in the proliferation medium [Neurobasal medium (Life Technologies) supplemented with 1× B27 supplement (Gibco), 1x GlutaMAX (Life Technologies), 20 ng/ml murine epithelial growth factor (Peprotech), 20 ng/ml basic fibroblast growth factor (Peprotech), and 100U/ml penicillin/streptomycin (Life Technologies).

extract_protocol:
RNA was extracted and purified from cells using QI shredder (Qiagen) and RNeasy (Qiagen) spin columns.
Total RNA (1 µg) was used to generate RNA-seq library using NEBNext Ultra Directional RNA library Prep Kit for Illumina (New England BioLabs, Inc) according to the manufacturer’s instructions. Adapter-ligated cDNA was amplified by PCR and followed by size selection using agarose gel electrophoresis. The DNA was purified using Qiaquick gel extraction kit (Qiagen) and quantified both with an Agilent Bioanalyzer and Invitrogen Qubit. The libraries were diluted to a working concentration of 10nM prior to sequencing. Sequencing on an Illumina HiSeq4000 instrument was carried out by the Genomics Core Facility at Michigan State University.

tag: modification

value: Kdm2b one allele mutant


title: 4_RNAseq_NPC_mutkdm2b_rep1

description: NPC culture medium


title: 6_RNAseq_NPC_mutkdm2b_rep3

description: NPC culture medium


title: 1_RNAseq_NPC_wt_rep1

description: NPC culture medium

value: wild-type


title: RV.RNA.WT3


title: 2_RNAseq_NPC_wt_rep2

description: NPC culture medium


title: B07_JC_10


title: G05_JC_7


title: RV.RNA.Prdm16cKO3

value: Prdm16 conditional knockout


title: RV.RNA.Prdm16cKO1


title: LV.RNA.WT1

source_name: Mouse heart left ventricle

value: left ventricle


title: LV.RNA.Prdm16cKO4


title: RV.RNA.Prdm16cKO2


title: LV.RNA.WT3


title: RV.RNA.Prdm16cKO4


title: LV.RNA.WT2


title: LV.RNA.WT4


title: LV.RNA.Prdm16cKO2


title: LV.RNA.Prdm16cKO1


title: LV.RNA.Prdm16cKO3


title: RV.RNA.WT1


title: Heart.RNA.WT2

source_name: Mouse heart

value: whole heart


title: Heart.RNA.Prdm16cKO1


title: RV.PRDM16.ChIP.WT2

data_processing:
Sequencing reads were aligned to the mouse genome (GRCm38, mm10) using bwa (version: 0.7.12-r1039)
ChIP-seq peaks were called using MACS2 (version: 2.1.1.20160309, default parameters). For WT samples, BED files were generated from merging reads from two WT replicates.
Motif analysis was carried out using Homer.
Differential binding analysis was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited WT and Prdm16cKO narrow peak files generated by MACS2 by combining reads from the same genotype.
Supplementary_files_format_and_content: tab-delimited diffbinding density between LV and RV was generated by DESeq2.

extract_protocol:
Isolated LV, RV or whole ventricles (atria removed) of E13.5 mouse hearts were dissected and tear to smaller pieces by forceps. Tissues were then dual crosslinked by EGS and formaldehyde and followed by sonication and immunoprecipitation with PRDM16 antibody.
For library preparation, ChIP or input DNA were end repaired, ligated with barcoded adaptors, amplified and purified using Kapa HyperPrep PCR-free Kit and Kapa Real Time Amplification Kit. DNA fragments in the range of 200-500 bp were selected using a PippinHT Size Selection System.

tag: chip antibody

value: PRDM16 antibody


title: Heart.RNA.Prdm16cKO2


title: Heart.RNA.WT1


title: Heart.RNA.Prdm16cKO3


title: RV.PRDM16.ChIP.WT1


title: RV.Input.ChIP.WT2


title: RV.Input.ChIP.WT1


title: LV.Input.ChIP.WT2


title: LV.Input.ChIP.WT1


title: Heart.PRDM16.ChIP.WT2


title: Heart.PRDM16.ChIP.Prdm16cKO1


title: Heart.Input.ChIP.WT1


title: Heart.Input.ChIP.WT2


title: LV.PRDM16.ChIP.WT1


title: LV.PRDM16.ChIP.WT2


title: Heart.RNA.WT3


title: 3_RNAseq_NPC_wt_rep3

description: NPC culture medium


title: SK07

city: Birmingham

first: Anindya

last: Dutta

state: AL

address: 720 20th Street South, Kaul 230

institute: University of Alabama at Birmingham

data_processing:
Paired end mRNA sequencing fastq files were mapped to the human genome version GRCh38 using kallisto 0.44.0. Abundance.h5 files were imported into R using tximport [39] and differential expression analysis conducted using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Additional file 'averageExpression_siE6Set8.csv' contains the average expression for each siRNA condition.

source_name: Control

growth_protocol: HeLa cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
RNA was extracted using the Qiagen RNA extraction kit
RNA samples were sent to Beijing Novogene Co., Ltd. (Beijing, China ) for library preparation and next generation RNA sequencing

treatment_protocol: HeLa cells were transfected with control siRNAs or HPV-E6 siRNA or HPV-E6 and Set8 siRNAs. Cells were collected 48 h after siRNA transfection.

value: HeLa

value: Control


title: SK04


title: SK05


title: SK08


title: SK09

value: HPV-E6 and Set8 siRNAs


title: SK06


title: SK01


title: SK02


title: Healthy-NBC24

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

data_processing:
Adapter sequences and low quality reads were trimmed using Trim Galore
Primary circRNA detection using CIRI2
circRNA detection using find_circ for secondary support
Genome_build: hg19
Supplementary_files_format_and_content: txt file with output from circRNA analysis, showing circRNA annotation. Also includes number of reads mapping to circRNA back-splice junctions and number of reads mapping to corresponding linear splice events

source_name: Isolated Naive B cells

extract_protocol: Samples were rRNA depleted and prepared using the SMARTer® Stranded Total RNA Sample RNA Prep Kit – HI mammalian (Takara) with 12 PCR cycles for amplification.

tag: Sex

value: M

tag: ki67 proliferation marker

value: Isolated Naive B cells

tag: disease state

value: Healthy


title: Heart.PRDM16.ChIP.WT1


title: Healthy-NBC21


title: TRV-GUS/TYLCCNV-IR-Bisulfite-seq_rep2

city: Beiing

first: Yijun

last: Qi

address: NO.1 Qinghuayuan

department: School of Life Sciences

institute: Tsinghua University

data_processing:
PCR duplicated reads were removed and the unique reads with read counts above 5 were retained for cytosine methylation analysis
Genome_build: TYLCCNV(AJ319675.1);BSCTV(U02311.1)
Supplementary_files_format_and_content: the processed data files contain the unique sequence and their counts

organism: Nicotiana benthamiana

source_name: leaves

growth_protocol: N. benthamiana plants were grown in a controlled growth chamber at 25°C under a 16 h light/8 h dark photoperiod and A. thaliana plants were grown in a growth room under long photoperiod conditions (16 h light, 22°C/8 h dark, 18°C).

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5012), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)60. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).

treatment_protocol: For TYLCCNV inoculation following VIGS, A. tumefaciens cultures carrying pCambia1300, pTRV1 plus pTRV2-GUS (TRV-GUS) or pTRV1 plus pTRV2-NbDMLs (TRV-NbDMLs) at an OD600 = 0.2 were inoculated into N. benthamiana plants at the eight-leaf stage. One week later, A. tumefaciens cultures harboring pBinPLUS (mock) or infectious clones of TYLCCNV or TYLCCNV plus TYLCCNB (TYLCCNV+B) at an OD600 = 1.0 were inoculated into pCambia1300-, TRV-GUS- or TRV-NbDMLs-infiltrated plants. For other TYLCCNV inoculation, N. benthamiana plants at the eight-leaf stage were directly agroinoculated with infectious clones of TYLCCNV, TYLCCNV+B or TYLCCNV+BV17A. Four-week-old A. thaliana were used for BSCTV inoculation as described before27. Symmetrically infected leaves were harvested at 10 days post inoculation.

value: Wild-type

tag: infection

value: TYLCCNV


title: TRV-GUS/TYLCCNV+B-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5014), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)62. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).

value: TYLCCNV+B


title: TRV-GUS/TYLCCNV-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5011), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)59. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: Healthy-NBC12

value: F


title: pCambia1300/TYLCCNV+B-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5010), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)58. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 16h00-80-C

city: Winnipeg

first: Olivia

last: Wilkins

state: Manitoba

address: 66 Chancellors Cir

department: Biological Sciences

country: Canada

institute: University of Manitoba

description: Okanese poplar (Populus×‘Okanese’)

data_processing:
Adaptors and low-quality bases removed with Trimmomtatic v. 0.36
Reads aligned to Populus trichocarpa v4.1 reference genome with HISAT2 v. 2.2.1
Converted to bam format with SAMtools v. 1.3.1
Genes quantified with featureCounts
Genome_build: Populus trichocarpa v4.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Populus sp. cv. 'Okanese'

source_name: First leaf developed in stress

growth_protocol: Okanese poplar clippings (~3in containing 2 lateral buds) were planted in 1 gallon pots of Sungro Sunshine Profressional Growing Mix, rewatered daily. Poplars were grown in a climate-controlled greenhouse (22-24°C during the day, 15-17°C, 15h photoperiod) for 42 days prior to treatment.

extract_protocol:
Leaves for transcriptome analysis were harvested at 10:00 (late morning) and 16:00 (early evening), flash frozen in liquid nitrogen, and stored at -80°C until further processing.
Leaf tissue was ground to a fine powder under liquid nitrogen and total RNA was extracted using RNeasy Plant MiniKits (Qiagen, Toronto, Canada). RNA was sent to Genome Québec (Montréal, PQ, Canada) where NEBNext stranded sequencing libraries were prepared according to manufacturer’s instructions (New England Biolabs, Whitby, ON, Canada) and single end 100 base pair reads were sequenced on an Illumina HiSeq4000. A minimum of 23 million reads were generated for each library.

treatment_protocol: Poplars were assigned a target weight (30, 50, or 80% of field capacity) and were withheld from watering until they reached their target weight, at which they were maintained at that weight by daily rewatering until 21 days after the treatment began.

value: First leaf developed in stress

tag: soil water content (g/g)

value: control

tag: time of day


title: pCambia1300/TYLCCNV+B-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5009), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)57. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: Heart.Input.ChIP.Prdm16cKO1

tag: tissue


title: pCambia1300/TYLCCNV+B-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5008), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)56. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 16h00-80-B

description: Okanese poplar (Populus×‘Okanese’)


title: pCambia1300/TYLCCNV-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5006), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)54. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: Healthy-Reactve-LN2

source_name: Lymph Node Specimen

value: Lymph Node Specimen


title: pCambia1300/TYLCCNV-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5007), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)55. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: SK03


title: TRV-GUS/TYLCCNV-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5013), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)61. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: pCambia1300/TYLCCNV-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5005), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)53. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 16h00-80-A

description: Okanese poplar (Populus×‘Okanese’)


title: Healthy-Reactve-LN1


title: 16h00-50-C

description: Okanese poplar (Populus×‘Okanese’)

value: moderate drought


title: DME-OX#6/TYLCCNV+B-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5073), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)121. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: DME-OX#6/TYLCCNV+B-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5072), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)120. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 16h00-50-B

description: Okanese poplar (Populus×‘Okanese’)


title: DME-OX#6/TYLCCNV+B-V17A-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5070), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)118. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: MCL-19

value: Mantle Cell Lymphoma (MCL)


title: DME-OX#6/TYLCCNV+B-V17A-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5068), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)116. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: DME-OX#6/TYLCCNV+B-V17A-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5069), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)117. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: DME-OX#6/TYLCCNV-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5067), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)115. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: Healthy-NBC11

extract_protocol: Samples were rRNA depleted and prepared using the SMARTer® Stranded Total RNA Sample RNA Prep Kit – HI mammalian (Takara) with 12 PCR cycles for amplification.


title: MCL-18


title: DME-OX#6/TYLCCNV-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5066), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)114. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: MCL-20


title: 16h00-50-A

description: Okanese poplar (Populus×‘Okanese’)


title: DME-OX#6/TYLCCNV-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5065), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)113. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 16h00-30-C

description: Okanese poplar (Populus×‘Okanese’)

value: severe drought


title: MCL-15


title: DME-OX#4/TYLCCNV+B-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5064), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)112. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 16h00-30-B

description: Okanese poplar (Populus×‘Okanese’)

extract_protocol:
Leaves for transcriptome analysis were harvested at 10:00 (late morning) and 16:00 (early evening), flash frozen in liquid nitrogen, and stored at -80°C until further processing.
Leaf tissue was ground to a fine powder under liquid nitrogen and total RNA was extracted using RNeasy Plant MiniKits (Qiagen, Toronto, Canada). RNA was sent to Genome Québec (Montréal, PQ, Canada) where NEBNext stranded sequencing libraries were prepared according to manufacturer’s instructions (New England Biolabs, Whitby, ON, Canada) and single end 100 base pair reads were sequenced on an Illumina HiSeq4000. A minimum of 23 million reads were generated for each library.


title: MCL-14


title: 16h00-30-A

description: Okanese poplar (Populus×‘Okanese’)


title: DME-OX#6/TYLCCNV+B-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5071), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)119. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: DME-OX#4/TYLCCNV+B-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5063), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)111. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: DME-OX#4/TYLCCNV+B-V17A-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5061), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)109. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: DME-OX#4/TYLCCNV+B-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5062), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)110. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 10h00-80-C

description: Okanese poplar (Populus×‘Okanese’)


title: MCL-13


title: DME-OX#4/TYLCCNV+B-V17A-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5059), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)107. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: NBM sample 3, 138P fraction

description: 3' barcoded RNA

extract_protocol: Chromium Single Cell 3′ Library & Gel Bead Kit v3

tag: diagnosis

value: Healthy Donor

value: Bone Marrow


title: DME-OX#4/TYLCCNV-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5058), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)106. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: DME-OX#4/TYLCCNV-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5057), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)105. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: DME-OX#4/TYLCCNV-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5056), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)104. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 10h00-80-B

description: Okanese poplar (Populus×‘Okanese’)


title: MCL-9


title: WT/TYLCCNV+B-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5055), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)103. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: MCL-12


title: MCL-8


title: WT/TYLCCNV+B-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5054), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)102. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 10h00-80-A

description: Okanese poplar (Populus×‘Okanese’)


title: WT/TYLCCNV+B-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5053), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)101. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: WT/TYLCCNV+B-V17A-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5052), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)100. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: MCL-6

extract_protocol: Samples were rRNA depleted and prepared using the SMARTer® Stranded Total RNA Sample RNA Prep Kit – HI mammalian (Takara) with 12 PCR cycles for amplification.


title: 10h00-50-A

description: Okanese poplar (Populus×‘Okanese’)


title: WT/TYLCCNV+B-V17A-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5050), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)98. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: WT/TYLCCNV-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5049), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)97. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: WT/TYLCCNV+B-V17A-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5051), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)99. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: MCL-7


title: MCL-5


title: WT/TYLCCNV-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5048), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)96. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 10h00-30-C

description: Okanese poplar (Populus×‘Okanese’)

extract_protocol:
Leaves for transcriptome analysis were harvested at 10:00 (late morning) and 16:00 (early evening), flash frozen in liquid nitrogen, and stored at -80°C until further processing.
Leaf tissue was ground to a fine powder under liquid nitrogen and total RNA was extracted using RNeasy Plant MiniKits (Qiagen, Toronto, Canada). RNA was sent to Genome Québec (Montréal, PQ, Canada) where NEBNext stranded sequencing libraries were prepared according to manufacturer’s instructions (New England Biolabs, Whitby, ON, Canada) and single end 100 base pair reads were sequenced on an Illumina HiSeq4000. A minimum of 23 million reads were generated for each library.


title: WT/TYLCCNV-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5047), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)95. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: DME-OX#4/TYLCCNV+B-V17A-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5060), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)108. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: MCL-1


title: 10h00-50-C

description: Okanese poplar (Populus×‘Okanese’)


title: MCL-3


title: TYLCCNV+B-V17A-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5031), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)79. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: TYLCCNV+B-V17A-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5029), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)77. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: TYLCCNV+B-V17A-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5030), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)78. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: 10h00-30-A

description: Okanese poplar (Populus×‘Okanese’)


title: 10h00-50-B

description: Okanese poplar (Populus×‘Okanese’)


title: Salt-IL22-3

city: Barcelona

first: Mireia

last: Bundó

state: Barcelona

address: C/ de la vall moronta, edifici CRAG, campus UAB

country: Spain

institute: CRAG-Centre for research in agricultural genomics

data_processing:
Base calling and demultiplexing. Processing raw data for both format conversion and demultiplexing by Bcl2Fastq 2.20 version of the Illumina pipeline.
Adapters masking. Adapter sequences are masked with Cutadapt v1.11 from raw fastq data using the following parameters: --anywhere (on both adapter sequences) --overlap 5 --times 2 --minimum-length 35 --mask-adapter
Quality check was performed on the raw sequencing data, removing low quality portions while preserving the longest high quality part of NGS reads. The minimum length was set to 35 bp and the quality score to 25. The software BBDuk was used for this scope.
The high quality reads were aligned against the Oryza sativa Japonica Group (IRGSP-1.0/Ensembl release 42) and the Oryza sativa Indica Group (ASM465v1/Ensembl release 42)with STAR aligner (version 2.5.2b).
FeatureCounts (version 1.5.1) was used to calculate gene expression values as raw fragment counts. Normalization was applied to the raw fragment counts by using the Trimmed Mean of M -values (TMM) normalization and Fragments Per Kilobase Million (FPKM) normalization
Statistical analysis of read counts was performed with R, with the HTSFilter package to remove low-expressed genes and the edge R package.
Genome_build: IRGSP-1.0
Genome_build: ASM465v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

organism: Oryza sativa

source_name: Leaves

growth_protocol: Rice seeds were pregerminated in water for 7 days and then transferred to hydroponic tanks with modified Yoshida solution for 7 days. Plants were grown at 28/26ºC day/night with a 14h/10h light/dark cycle.

extract_protocol:
Total RNA was extracted using the Maxwell RSC Plant RNA Kit (Promega).
TruSeq Stranded mRNA kit (Illumina, San Diego, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-firstrand).

treatment_protocol: Salt treatment was applied by supplementing the nutrient solution with 80 mM NaCl for 24 h. Control plants were not supplemented with NaCl. Leaves from salt-treated plants (80 mM NaCl, 24h of treatment) and untreated control plants were harvested (3 replicates per genotype and condition, 4 plants per replicate).

value: 24h of 80 mM NaCl

tag: line

value: Leaves


title: TYLCCNV+B-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5026), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)74. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: TYLCCNV+B-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5027), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)75. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: Salt-IL22-2


title: TYLCCNV-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5025), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)73. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: Salt-IL22-1


title: ksb024_upc2A∆ rox1∆ flu

city: Iowa City

first: Damian

middle: J

last: Krysan

state: IA

address: 25 South Grand, 2040 ML

department: Division of Pediatrics & Infectious Disease

institute: University of Iowa Hospitals and Clinics

data_processing:
Read quality was confirmed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).  Reads were mapped to the Candida glabrata CBS138 genome using HISAT2 in paired-end read mode. Kim, D., Paggi, J.M., Park, C. et al. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype, Nat Biotechnol 37, 907–915 (2019). Sorted and indexed bam files of mapped reads were prepared using Samtools (https://www.htslib.org). Mapped reads were assembled onto annotated CBS138 genes with Stringtie using the -eB parameter and raw gene count tables were generated using the prepDE.py script that is provided with Stringtie. Pertea M., Kim D., Pertea G.M., Leek J.T., Salzberg S.L. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nature Protocols 11, 1650-1667 (2016). Differential expression and statistical analysis were done from raw counts using the DESeq2 R package. The default negative binomial general linear model and Wald test were used. Correction for multiple hypothesis tests was done using the default Benjamini and Hochberg method. Love M.I., Huber W., Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 550 (2014).
Genome_build: s03-m01-r23 from Candida Genome Database on 2021 July 11
Supplementary_files_format_and_content: matrix table with relative abundance measurements to wild type

organism: Nakaseomyces glabratus

source_name: Exponential phase growth yeast cells with subsequent fluconazole treatment for 4 hours

growth_protocol: Growth in YPD to exponential phase with subsequent fluconazole treatment for 4 hours

extract_protocol:
Cells were collected via centrifugation from growth medium and RNA harvested according to manufacturer protocol for MasterPure Yeast RNA Purification Kit
Libraries were prepared with paired end adapters using Illumina chemistries per manufacturer’s instructions, and sequencing of libraries were performed with read lengths of approximately 150bp with at least 50 million reads per sample.

value: upc2A_delta rox1_delta


title: TYLCCNV-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5023), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)71. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: Salt-PL12-3


title: TRV-NbDMLs/TYLCCNV+B-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5022), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)70. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: TRV-NbDMLs/TYLCCNV+B-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5021), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)69. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: ksb021_rox1∆ flu


title: F07_JC_14

extract_protocol: Total RNA from islets was extracted using RNeasy Mini Kit according to the manufacturer's instructions.

tag: strain

value: C57BL/6J control

tag: cell type

value: Pancreatic islets

value: 16 weeks


title: 10h00-30-B

description: Okanese poplar (Populus×‘Okanese’)


title: TYLCCNV-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5024), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)72. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).

tag: genotype

value: Wild-type

value: TYLCCNV


title: TRV-NbDMLs/TYLCCNV+B-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5020), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)68. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).

value: TYLCCNV+B


title: Salt-PL12-1


title: ksb020_rox1∆ flu


title: TRV-NbDMLs/TYLCCNV-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5018), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)66. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: TRV-NbDMLs/TYLCCNV-IR-Bisulfite-seq_rep1

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5017), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)65. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: ksb019_rox1∆ flu


title: Salt-PL12-2


title: Control-IL22-3

value: Control


title: TRV-GUS/TYLCCNV+B-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5016), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)64. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: TYLCCNV+B-IR-Bisulfite-seq_rep3

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5028), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)76. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).


title: Control-IL22-2


title: ksb017_upc2A∆ flu


title: ksb018_upc2A∆ flu


title: ksb022_upc2A∆ rox1∆ flu


title: ksb023_upc2A∆ rox1∆ flu


title: TRV-GUS/TYLCCNV+B-IR-Bisulfite-seq_rep2

extract_protocol:
Total DNA was extracted from infected plant leaves using Plant Genomic DNA Kit (TIANGEN, DP305).Total DNA (500 ng) was subjected to bisulfite treatment using EZ DNA Methylation Gold TM Kit (Zymo Research, D5015), according to the manufacturer’s instructions.
The bisulfite-treated DNA was used as templates for amplification of the IR regions of TYLCCNV or BSCTV. Primer sequences are listed in Supplementary Table 1. The products were purified with AMPure XP beads (Beckman, A63880) and the purified DNA products were PCR amplified and the adapters were added using GXL DNA polymerase (Takara, R050Q) and primer F (5’-AATGATACGGCGACCACCGAGATCTACAC-Index-TCGTCGGCAGCGTC-3’) and primer R (5’-CAAGCAGAAGACGGCATACGAGAT-Index-GTCTCGTGGGCTCGG)63. The final products were purified with AMPure XP beads for sequencing on an Illumina HiSeqX-Ten platform by Annoroad Gene Technology (Beijing).