title: 319p.NOD2.5F

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted txt files were analyzed further using R and the associated BioConductor limma package. Background correction ( normexp) and normalization between arrays  (quantile) was used,control probe were removed. Within-array replicate features were condensed with their average by avereps.

source_name: HeLa NOD2 cells, 4hr, replicate 6

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: HeLa inducible NOD1 or NOD2 cells were grown in DMEM medium supplemented with 10% FBS, 1mM Sodium Pyruvate and 2mM L-Glutamine overnight. To induce NOD1 or NOD2 expression, HeLa NOD1 or NOD2 cells were treated in absence or presence of 0.5 µg/mL or 0.25 µg/mL doxycyclin overnight, respectively.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol: After doxycycline treatment, medium was replaced with fresh DMEM full medium. Then HeLa NOD1 or NOD2 cells were treated with various stimuli for 4 hrs.

value: HeLa

tag: inducible gene

tag: sample purification

value: phenol


title: gDNA from subject PARZYF

status: Public on Jan 01 2020

type: genomic

city: Little Rock

first: Jason

middle: Eli

last: Farrar

state: AR

address: 1 Children's Way, #512-10

department: Pediatrics/Hematology-Oncology

country: USA

institute: University of Arkansas for Medical Sciences

hyb_protocol: Bisulfite-converted genomic DNA was analyzed using the Infinium Human Methylation EPIC Beadchip Kit (Illumina). DNA amplification, fragmentation, array hybridization, extension and staining were performed with reagents provided in the kit according to the manufacturer’s protocol (Illumina Infinium II Methylation Assay). Briefly, 4 µl of bisulfite-converted genomic DNA at a minimum  concentration of 20 ng/µL) was added to 0.8 ml 96-well storage plate (Thermo Fisher Scientific), denatured in 0.014N sodium hydroxide, neutralized and then amplified for 20-24 hours at 37oC. Samples were fragmented at 37oC for 60 minutes and precipitated in isopropanol. Re-suspended samples were denatured in a 96-well plate heat block at 95oC for 20 minutes. 15 µl of each sample was loaded onto a 12-sample BeadChip, assembled in the hybridization chamber as instructed by the manufacturer and incubated at 48oC for 16-20 hours.  Following hybridization, the BeadChips were washed and assembled in a fluid flow-through station for primer-extension reaction and staining with reagents and buffers provided.

scan_protocol: Polymer-coated BeadChips were scanned in an iScan scanner (Illumina) using Inf Methylation mode.

data_processing:
Raw IDAT files were processed using R package SeSAMe (PMID: 30085201) with noob background correction (PMID: 23476028, 28035024), non-linear dye bias correction, SNP and non-detection (p-value) masking. Methylation beta values are computed as the fraction of total probeset intensity attributable to fluorescence from the methylated probe allele, with 0 indicating no methylation and 1 indicating full methylation. The SeSAMe/noob default offset of 15 was added to both unmethylated (U) and methylated (M) allelic intensities in each pair to avoid division by zero. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies (PMID: 27924034).
matrix_processed.csv: normalized (SeSAMe) Average Beta
matrix_signals.csv: Unmethylated and methylated signal intensities, and non-detection p-values

molecule: genomic DNA

organism: Homo sapiens

source_name: AML, pre-treatment

label_protocol: Bisulfite conversion of genomic DNA was performed with EZ DNA methylation Kit (Zymo Research, Irvine, CA, #D5002) following the manufacturer’s protocol with modifications for the Infinium Methylation Assay. Briefly, 250ng of genomic DNA was mixed with 5 µl of Dilution Buffer and incubated at 37oC for 15 minutes and then mixed with 100 µl of conversion reagent prepared as instructed in the protocol. Mixtures were incubated in a thermocycler for 16 cycles at 95oC for 30 seconds and 50oC for 60 minutes. Bisulfite-converted DNA samples were loaded onto the provided 96-column plates for desulphonation, washing and elution. The concentration of bisulfite-converted, eluted DNA was measured by UV-absorbance using a NanoDrop-1000 (Thermo Fisher Scientific, Waltham, MA).

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow (or if Bone Marrow unavailable, Peripheral Blood), cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.

treatment_protocol: Diagnostic (presentation) bone marrow or peripheral blood specimens were collected from patients prior to induction therapy. Additional genomic data types and clinical covariates are available for these specimens under the TARGET-AML study (phs000465), available through the database of genotypes and phenotypes (dbGaP) and the NCI Genomic Data Commons (GDC).

tag: group

value: tumor

tag: age at diagnosis (days)

tag: gender

value: Female


title: gDNA from subject PARBLP


title: gDNA from subject PARNTM

value: Male


title: gDNA from subject PASCBW


title: 320p.NOD2.6G

type: RNA

country: Germany

molecule: total RNA

tag: cell line

tag: treatment


title: Day10_Rep3_Vrip

type: SRA

city: Geneva

first: Alisson

last: Kovaleski

state: NY

address: 630 W. North Street

institute: Cornell University

library_source: transcriptomic

data_processing:
Barcode spltting: Fastx_Barcode_splitter.pl.  Raw data files were split based on custom 6bp nucleotides
Reads were quality filtered using fastq_quality_filter (-Q33 -q 25 -p 25)
Barcodes removed from each bin using fastx_trimmer  (-Q33 -f 7)
Adapter removal: cutadapt (--minimum-len 25 -O 3)
Alignment: STAR using default parameters, the 12xV2 grapevine genome and the V3 annotation file (Vitis_vinifera_gene_annotation_on_V2_v20.gff3)
Feature counting: ht-seq count (-f sam -s no -t gene)
Differential gene expression: DESeq2
Pathway Enrichment: VitisPathways
Genome_build: 12xV2 grapevine genome: https://urgi.versailles.inra.fr/Species/Vitis
Supplementary_files_format_and_content: Counts files are the output gene counts produced by htseq-count.

organism: Vitis riparia

growth_protocol: Two clonal vines of Vitis amurensis and Vitis riparia are maintained under standard vineyard conditions in the USDA cold hardy grapevine germplasm repository.  Vitis vinifera vines are grown in a commercial vineyard under standard vineyard conditions.

extract_protocol:
RNA was isolated from pulverized tissue using the Sigma Spectrum Plant total RNA isolation kit.
Libraries were constructed following a modified protocol based on Borodina et al 2011.  Methods were modified by adding 3% w/v PVP40 to the lysis buffer to help reduce extraction inhibitors.

treatment_protocol: Dormant canes were pruned from the vineyard.  Day0 buds (3 replicate buds) were cut from the cane and plunged into liquid nitrogen.  Canes were pruned to single node cuttings and placed in cups of water. Cups were placed at room temperature.  Each subsequent day, replicate buds were cut from the canes and flash frozen.  Five replicate collections were conducted on each collection day.  Buds were collected until evidence of budburst was observed for each genotype.

tag: tissue

value: Dormant Bud

tag: genotype

tag: replicate


title: ChIP_seq_H3K4ME3_PB_DJK_RS

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

country: Israel

institute: Bar-Ilan University

library_source: genomic

data_processing:
Reads were aligned to the GRCm38p2/mm10 genome assembly.
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 2 -m1 -l 50
Genome_build: GRCm38p2/mm10
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

organism: Mus musculus

source_name: Abelson-transformed pre-B cell

growth_protocol: Abelson pre-B cell lines were cultured DMEM supplemented 10% FBS, with 2 mM L-glutamine, 1 mM Sodium piruvate, non-essential amino acids, 0.05 mM β-mercaptoethanol, penicillin (100 U/ml) and streptomycin (100 U/ml) (Invitrogen).

extract_protocol:
Twenty million preB cells were used for ChIP-seq.
Rabbit monoclonal antibodies for RAG1 (mAb 23) and RAG2 (mAb 39) (Coster et al., 2012) and a polyclonal rabbit antibody for H3K4me3 (Millipore) were used. Cells were fixed by adding 37% formaldehyde (F1635, Sigma) to a final concentration of 1% and incubated at 37°C for 10 min. Fixation was quenched by addition of 1M glycine (Sigma) in PBS at a final concentration of 125 mM. Twenty million fixed cells were washed twice with cold PBS and pellets were snap frozen in dry ice and stored at -80°C. Fixed cell pellets of 20 million cells were thawed on ice and resuspended in 2 mL of cold RIPA buffer (10 mM TrisHCl pH 7.5, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1 Complete Mini EDTA free proteinase inhibitor (Roche)). Sonication was performed using the Covaris S220 sonicator at duty cycle 20%, peak incident power 175, cycle/burst 200 for 30 min at 4°C or using the Branson sonifier at amplitude 35%, 12 cycles of 20 s sonication and 30 s of pause at 4°C. Chromatin were clarified by centrifugation at 21,000 g at 4°C for 10 min and precleared with 80 ul prewashed Dynabeads protein A (ThermoFisher) for 30 min at 4°C. 40 μl prewashed Dynabeads protein A were incubated with 10 μg of each respective antibody in 100 μl of PBS for 10 min at room temperature in continuous mixing, washed twice in PBS for 5 min and added to 1 mL of chromatin followed by overnight incubation at 4°C on a rotator. Beads were then collected in a magnetic separator (DynaMag-2 Invitrogen), washed twice with cold RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (10 mM Tris pH 8.0, 1mM EDTA) plus 0.2% Triton X-100, and once with TE. Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1mg/mL of Proteinase K (Ambion). DNA was purified using Zymo ChIP DNA clean and concentrator kit (Zymo Research) and eluted in 20 μl. The entire ChIP DNA was used to prepare Illumina sequencing libraries. End-repair was performed in 75 μl of T4 ligase reaction buffer, 0.4 mM of dNTPs, 4 U of T4 DNA polymerase (NEB), 13.5 U of T4 Polynucleotide Kinase (NEB) and 1.5 U of Klenow fragment (NEB) at 24°C for 30 min in a ThermoMixer C at 400 rpm. End-repair reaction was cleaned using 2X Agencourt AMPure XP beads and eluted in 15 μl of EB that was used for A-tailing reaction in 30 μl of NEBNext dA-Tailing reaction buffer (NEB) with 7.5 U of Klenow fragment exo- (NEB) at 37°C for 30 min. The 30 μl of the A-tailing reaction was mixed with Quick Ligase buffer 2X (NEB), 3,000 U of Quick ligase and 5 nM of annealed adaptor (Illumina truncated adaptor) in a volume of 75 μl and incubated at 25°C for 20 min. The adaptor was prepared by annealing the following HPLC oligos: 5’-phosphate/GATCGGAAGAGCACACGTCT-3’ and 5’-ACACTCTTTCCCTACACGACGCT CTTCCGATC∗T-3’ (∗phosphorothioate bond). Ligation was stopped by adding 50mM of EDTA and cleaned with 1.8X Agencourt AM- Pure XP beads and eluted in 15ul of EB that was used for PCR amplification in a 50 uL reaction with 1 μM primers TruSeq barcoded primer p5, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC∗T, TruSeq barcoded primer p7, CAAGCAGAAGACGGCATACGAGANNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC∗T, (NNNNNNNN represents barcode and ∗ a phosphothiorate bond), and 2X Kapa HiFi HotStart Ready mix (Kapa Biosciences). The temperature settings during the PCR amplification were 45 s at 98°C followed by 15 cycles of 15 s at 98°C, 30 s at 63°C, 30 s at 72°C and a final 5 min extension at 72°C . PCR reactions were cleaned with Agencourt AMPure XP beads (Beckman Coulter), run on a 2% agarose gel and a smear of 200-500bp was cut and gel purified using QIAquick Gel Extraction Kit (QIAGEN). Library concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on the Illumina Nextseq500 (75bp single-end reads).

treatment_protocol: Pre-B cells were arrested in G1 by treatment with 3 mM imatinib for 48 hr.

tag: cell type

value: Abelson-transformed pre-B cell

value: DJK-RS

tag: strain

tag: chip antibody

value: Anti-Trimethyl-Histone H3 (Lys4)

value: rabbit polyclonal

tag: antibody vendor name

value: Millipore

tag: antibody vendor id


title: Day10_Rep2_Vrip


title: 317p.NOD2.Tm

value: Tunicamycin (5 µg/mL)


title: Day10_Rep1_Vrip


title: gDNA from subject PATKEA


title: 318p.NOD2.Tg

value: Thapsigargin (5 µM)


title: ChIP_seq_H3K4ME3_PB_WT

value: WT


title: ChIP_seq_H3K4ME3_PB_DJK

value: DJK


title: Day9_Rep3_Vrip


title: gDNA from subject PARPZP


title: ChIP_seq_RAG2_PB_DJK_RS


title: ChIP_seq_RAG2_PB_DJK


title: Day9_Rep2_Vrip


title: ChIP_seq_RAG2_PB_WT


title: lung adenocarcinoma sample_IFN-γ-PD-L1+ [PT 14571]

city: Wuhan

first: yi

last: gao

state: Hubei

address: No.1095 Jie Fang Avenue

department: Thoracic surgery

country: China

institute: Tongji Hospital

description: gene expression in IIIA lung adenocarcinoma with IFN-γ low expression and PD-L1 high expression

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: IIIA lung adenocarcinoma, IFN-γ low expression, PD-L1 high expression

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Lung adenocarcinoma specimens were obtained from patients, who underwent pulmonary resection for lung cancer between 2012 and 2015 in the Department of Thoracic Surgery, Tongji Hospital. Each tumor sample was divided into two parts. One part of the tumor tissue was stored in liquid nitrogen for RNA and Protein extraction. The other part was fixed in 10% formalin and embedded in paraffin wax for immunohistochemistry. None of these patients received either radiation or chemotherapy before surgical operation. Histological diagnosis of tumors was based on the World Health Organization criteria. The TNM stage was determined according to the revised 2010 AJCC staging guidelines.

value: lung adenocarcinoma

tag: ifn-gamma level

value: low

tag: pd-l1 level

value: high

tag: tumor stage

value: IIIA

value: male

tag: age


title: lung adenocarcinoma sample_IFN-γ-PD-L1+ [PT 14666]

value: female


title: lung adenocarcinoma sample_IFN-γ+PD-L1- [PT 14544]

description: gene expression in IIIA lung adenocarcinoma with IFN-γ high expression and PD-L1 low expression

source_name: IIIA lung adenocarcinoma, IFN-γ high expression, PD-L1 low expression


title: ChIP_seq_RAG1_PB_DJK_RS


title: Day8_Rep3_Vrip


title: lung adenocarcinoma sample_IFN-γ+PD-L1+ [PT 14634]

description: gene expression in IIIA lung adenocarcinoma with IFN-γ high expression and PD-L1 high expression

source_name: IIIA lung adenocarcinoma, IFN-γ high expression, PD-L1 high expression


title: 236.NOD2.AnisoM

value: HeLa

tag: inducible gene

value: Anisomycin (1 µM)

tag: sample purification

value: ok


title: lung adenocarcinoma sample_IFN-γ+PD-L1+ [PT 14495]

tag: gender


title: 235.NOD2.BFA

tag: cell line

value: BrefeldinA (0.2 µg/mL)


title: gDNA from subject PAPUSR

tag: group

value: tumor

tag: age at diagnosis (days)

value: Male


title: 234.NOD2.Lov

tag: treatment

value: Lovastatin (30 µM)


title: lung adenocarcinoma sample_IFN-γ+PD-L1+ [PT 14245]

tag: tissue


title: Day9_Rep1_Vrip

value: Dormant Bud

tag: genotype

tag: replicate


title: ChIP_seq_RAG1_PB_WT

tag: cell type

value: Abelson-transformed pre-B cell

tag: strain

tag: chip antibody

value: rabbit polyclonal


title: ChIP_seq_RAG1_PB_DJK

value: DJK


title: Day7_Rep3_Vrip


title: 312p.NOD2.2MC

value: phenol


title: Day7_Rep2_Vrip


title: END_seq_BMPB_BCL2TG

data_processing:
Library strategy: END-seq
mouse and human END-seq reads were aligned to the GRCm38p2/mm10 and  GRCh37/hg19 genome assemblies,respectively.
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 3 -k1 -l 50
END-seq peaks were called using MACS 1.4.3  with the parameters: --nolambda,-- nomodel and –keep-dup=all (keep all redundant reads). For Etoposide-treated END-seq data peak calling, we used the corresponding non-treated samples as control, keeping >10 fold-enriched peaks.
END-seq data from pre-B cells, where cells with ZFN break were spiked-in to the library at a 1:50 (2%) ratio, the RPKM value for each peak was divided by the signal around the spiked-in breaks and then multiplied by 2, to get values as cell-percentage. From this value, X, the #cells per lesion were calculated as 100/X.
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: bigwig files were made using Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

source_name: Primary BM pre-B cell

growth_protocol: Abelson pre-B cell lines and primary mouse bone marrow pre-B cells were cultured DMEM supplemented 10% FBS, with 2 mM L-glutamine, 1 mM Sodium piruvate, non-essential amino acids, 0.05 mM β-mercaptoethanol, penicillin (100 U/ml) and streptomycin (100 U/ml) (Invitrogen). Primary mouse bone marrow pre-B cells were cultured in the presence of recombinant IL-7 (ThermoFisher).

extract_protocol:
Single cell suspensions of pre-B cells (30 million per agarose plug), primary mouse bone marrow pre-B cells (10 million per agarose plug), and thymocytes (70 million per agarose plugs) were washed in PBS, embedded in agarose and transferred into plug molds (Bio-Rad CHEF Mammalian Genomic DNA plug kit) and processed as previously described (Canela et al., 2016).  Primary mouse bone marrow pre-B cells for END-Seq analyses were obtained from 6-12 week old Vavp-Bcl2-transgenic mice (Ortega-Molina et al., 2015) and cultured in the presence of recombinant IL-7 (ThermoFisher) for 7-10 days at 2 x 106 cells/ml in vitro. To induce cell cycle arrest, cells were resuspended in media without IL-7 and maintained at 2 × 106 cells/ml for 48 hours and harvested for END-seq.
END-seq was performed as described in Canela et al., 2017. Agarose plugs were made using the Bio-Rad CHEF Mammalian Genomic DNA plug kit. Embedded cells were lysed and digested using Proteinase K (50º C, 1 hour then  37ºC for 7 hours). Plugs were rinsed in TE buffer and treated with RNase A at 37ºC, 1 hour. The next enzymatic reactions were performed with the DNA in agarose plugs to prevent shearing. DNA ends were blunted for 1 hour at 25ºC with Exonuclease T (NEB). After blunting, A-tailing was performed, followed by ligation of “END-seq hairpin adaptor 1”, 5′-Phos-GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUU[Biotin-dT]U[Biotin-dT]UUACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3′ [*phosphorothioate bond], using NEB Quick Ligase.  Agarose plugs were then melted and dialyzed and DNA was sonicated to a median shear length of 170bp using Covaris S220 sonicator. DNA was ethanol-precipitated and dissolved in 70 ul TE buffer. Biotinylated DNA was isolated using MyOne Streptavidin C1 Beads (ThermoFisher #650-01), followed by end repair and dA-tailing. The second end was ligated to “END-seq hairpin adaptor 2”, 5′-Phos-GATCGGAAGAGCACACGTCUUUUUUUUAGACGTGTGCTCTTCCGATC*T-3′ [*phosphorothioate bond], using NEB Quick Ligase. Hairpins were digested using USER (NEB), and the resulting DNA fragments were PCR amplified using TruSeq barcoded primer p5, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC*T and TruSeq barcoded primer p7, CAAGCAGAAGACGGCATACGAGANNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T, (NNNNNNNN represents barcode and * a phosphothiorate bond).  PCR fragments were isolated by size selection from agarose gel, selecting 200-500 bp fragments followed by DNA purification using QIAquick Gel Extraction Kit. Libraries were quantified using KAPA Library Quantification Kit and sequenced using Illumina NextSeq 500 or 550.

treatment_protocol: Pre-cells were arrested in G1 by treatment with 3 mM imatinib for 48 hr.

value: Primary BM pre-B cell

value: Bcl2 Tg


title: END_seq_THY

source_name: Primary thymocyte

value: Primary thymocyte

value: WT


title: Day8_Rep2_Vrip


title: gDNA from subject PARYHR

value: Female


title: 231.NOD2.2BP

value: HeLa


title: Day7_Rep1_Vrip


title: Day8_Rep1_Vrip


title: 233.NOD2.LB42708


title: gDNA from subject PATGXE


title: 310p.NOD2.CCCP

value: CCCP (5 µM)


title: Day6_Rep3_Vrip


title: END_seq_PB_DELJK_RS_REP3

value: DJK-RS


title: END_seq_PB_DELJK_RS_REP2


title: END_seq_PB_DELJK_RS_REP1


title: END_seq_PB_RAG1


title: gDNA from subject PATMNY


title: Day6_Rep2_Vrip


title: 308p.NOD2.Etop

value: Etoposide (5 µM)


title: Day6_Rep1_Vrip


title: gDNA from subject PARDDY

value: tumor


title: Day6_Rep4_Vrip


title: END_seq_PB_DELJK_REP3


title: 229.NOD2.Actin

value: Actinonin (50 µM)

value: ok


title: END_seq_PB_DELJK_REP2


title: gDNA from subject PARFAL

value: Male


title: 227.NOD2.Nig

value: Nigericin (5 µM)


title: Day5_Rep1_Vrip

value: Dormant Bud


title: END_seq_PB_DELJK_REP1

value: Abelson-transformed pre-B cell

value: DJK


title: gDNA from subject PATIII


title: gDNA from subject PATIIM


title: Day5_Rep2_Vrip


title: 304p.NOD2.Vinbl

value: Vinblastine (10 µM)

value: phenol


title: 306p.NOD2.Nocad

value: Nocadazole (10 µM)


title: gDNA from subject PATFDF


title: gDNA from subject PATDFZ


title: 225.NOD2.CHX

value: Cycloheximide (50 µM)


title: 303p.NOD2.CytoD

value: Cytoclasin D (5 µM)


title: 222.NOD2.Jasp

value: HeLa

value: Jasplanokinolid (0.2 µM)


title: Day4_Rep5_Vrip


title: 221.NOD2.Control

value: Ctr (DMSO)


title: END_seq_PB_WT_REP9

value: WT


title: 299p.NOD1.5F

source_name: HeLa NOD1 cells, 4hr, replicate 6


title: END_seq_PB_WT_REP8


title: Day4_Rep4_Vrip


title: 218.NOD1.Tg

value: Thapsigargin (5 µM)


title: Day5_Rep3_Vrip


title: 215.NOD1.BFA

value: BrefeldinA (0.2 µg/mL)


title: END_seq_PB_WT_REP10


title: END_seq_PB_WT_REP7


title: 220.NOD1.6G

value: ok


title: gDNA from subject PATMCW

value: tumor

value: Female


title: 297p.NOD1.Tm

value: Tunicamycin (5 µg/mL)


title: Day4_Rep3_Vrip

value: Dormant Bud


title: END_seq_PB_WT_REP6

value: Abelson-transformed pre-B cell


title: END_seq_PB_WT_REP5


title: END_seq_PB_WT_REP4


title: Day4_Rep1_Vrip


title: gDNA from subject PATLVK

value: Male


title: END_seq_PB_WT_REP3


title: 293p.NOD1.LB42708

value: phenol


title: gDNA from subject PATLVC


title: 214.NOD1.Lov

value: Lovastatin (30 µM)


title: Day4_Rep2_Vrip


title: Day3_Rep3_Vrip


title: 296p.NOD1.AnisoM

value: Anisomycin (1 µM)


title: 211.NOD1.2BP


title: Day3_Rep2_Vrip


title: 212.NOD1.2MC


title: Day3_Rep1_Vrip


title: END_seq_PB_WT_REP1


title: Mouse 3 colon Nfil3(GFP)pos Treg

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

institute: University Medical Center of the Johannes Gutenberg-University Mainz

description:
scTCR-sequencing
clonotypes_summary2.tsv, consensus_summary2.tsv, metric_summary2.tsv

data_processing:
Fastq files were processed using Cell Ranger (version 2.2.0) based on 10xGenomics provided mm10 reference genome (refdata-cellranger-vdj-GRCm38-alts-ensembl-2.2.0). Clones were matched by TRA and TRB sequence and clonal diversity was estimated using the inverse Simpson index. Samples from each mouse were compared in a pairwise fashion using the Jaccard index. Clonal abundance pie charts were generated using ggplot2 (version 2.2.1) and R (version 3.4.2).
Genome_build: mm10

source_name: colon

growth_protocol: Mice were housed at UKR central animal facility

extract_protocol: Samples for scTCR-seq were loaded on the Chromium Single cell Controller using the Single Cell 5’ Library & Gel Bead Kit (10x Genomics #1000014) and the Single Cell V(D)J Enrichment Kit, Mouse T Cell (10x Genomics #1000071). TCR samples were sequenced on an Illumina NextSeq 500 with 300 cycles paired-end sequencing.

treatment_protocol: For scTCR-seq mouse 3, we sorted 800 CD25+Nfil3(GFP)+ Treg cells from the inguinal LN (mouse 3), 8000 CD25+Nfil3(GFP)+ Treg cells from the skin, 80000 CD25+Nfil3(GFP)+ Treg cells from the mesenteric LN and 11000 CD25+Nfil3(GFP)+ Treg cells from the colon. Samples were sorted from single male Nfil3(GFP) animals.

value: Nfil3(GFP)positive Treg

value: colon


title: Day2_Rep3_Vrip


title: gDNA from subject PATLKU


title: gDNA from subject PATLDB


title: END_seq_PB_WT_REP2


title: Day2_Rep2_Vrip


title: 289p.NOD1.Actin

value: HeLa

value: Actinonin (50 µM)


title: Day2_Rep1_Vrip


title: Mouse 3 inguinal LN Nfil3(GFP)pos Treg

source_name: inguinal lymph node

value: inguinal lymph node


title: Day1_Rep4_Vrip


title: 290p.NOD1.CCCP

value: CCCP (5 µM)


title: Day1_Rep3_Vrip


title: 288p.NOD1.Etop

value: Etoposide (5 µM)


title: Mouse 3 skin Nfil3(GFP)pos Treg

source_name: skin

value: skin


title: Lung_Klrg1-ST2- Treg_3 [ATAC-Seq]

data_processing:
Sequenced reads were trimmed for adaptor sequences using skewer v0.2.2
Reads were mapped to mm10 whole genome using bowtie2 v2.3.3 with the –very-sensitive parameter and a maximum insert size of 2000 bp
Duplicate and unpaired reads were removed using the sambamba (Tarasov et al., 2015) ‘markdup’ command, and reads with mapping quality >30 and alignment to the nuclear genome were kept.
Peak calling for each sample was performed using HOMER v4.10 (Heinz et al., 2010) with the following approach: Two different peak sets were called, once we used the options ‘-style factor -fragmentLength 150 -size 250 -minDist 250 –L 4 –fdr 0.0001’ parameters, to identify highly robust small regions of open chromatin, and in a second approach we used the parameters ‘-region -fragmentLength 150 -size 150 -minDist 250 -L 4 -fdr 0.0001’ to identify larger regions of open chromatin. The two peak sets were then merged using the mergePeaks function of HOMER to create the peak set that was used for downstream analysis.
For visualization purposes only, coverage files from filtered bam files were produced using bedtools (Quinlan and Hall, 2010) genomeCoverageBed, each position was normalized by dividing to the total library size and multiplying by 106, followed by conversion to a bigwig using the bedGraphToBigWig command from the UCSC genome browser tools.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain bed files (peaks) and bigWig files (for genome browser visuaizations)

source_name: lung

growth_protocol: Mice were housed at DKFZ or UKR central animal facility

extract_protocol: Chromatin accessibility mapping on purified cell populations was performed using the ATAC-seq method as previously described (Buenrostro et al., 2013; Corces et al., 2017), with minor adaptations. Briefly, in each experiment 2,000 - 15,000 sorted cells were pelleted by centrifuging for 10 min at 4 °C at 500 x g. After centrifugation, the pellet was carefully lysed in 50 µl resuspension buffer supplemented with NP-40 (Sigma), Tween-20 and Digitonin (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 % NP-40, 0.1 % Tween-20, 0.01 % Digitonin) and incubated for 3 minutes on ice. Then, 1 ml of ice-cold resuspension buffer supplemented with Tween-20 was added, and the sample was centrifuged at 4 °C at 500 x g for 10 minutes. The supernatant was discarded, and the cell pellet was carefully resuspended in the transposition reaction (25 µl 2 x TD buffer (Illumina), 2.5 µl TDE1 (Illumina), 16.5 µl PBS, 5 µl nuclease-free water, 0.5 µl 1% Digitonin (Promega), 0.5 µl 10% Tween-20 (Sigma)) for 30 min at 37 °C on a shaker at 1000 rpm. Following DNA purification with the Clean and Concentrator-5 kit (Zymo) eluting in 23 µl, 2 µl of the eluted DNA was used in a quantitative 10 µL PCR reaction (1.25 µM forward and reverse custom Nextera primers (Corces et al., 2017), 1x SYBR green final concentration) to estimate the optimum number of amplification cycles with the following program 72°C 5 min; 98°C 30 s; 25 cycles: 98°C 10 s, 63°C 30 s, 72°C 1 min; the final amplification of the library was carried out using the same PCR program and the number of cycles according to the Cq value of the qPCR. Library amplification using custom Nextera primers was followed by SPRI size selection with AmpureXP beads to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). The libraries were sequenced using the Illumina HiSeq3000/4000 or NextSeq platforms.

value: lung

value: Treg


title: gDNA from subject PATKMB

value: tumor


title: Mouse 3 mesenteric LN Nfil3(GFP)pos Treg

source_name: mesenteric lymph node

value: mesenteric lymph node


title: 286p.NOD1.Nocad

value: Nocadazole (10 µM)


title: Lung_Klrg1-ST2- Treg_2 [ATAC-Seq]


title: Lung_Klrg1-ST2- Treg_1 [ATAC-Seq]


title: 287p.NOD1.Nig

value: Nigericin (5 µM)


title: gDNA from subject PATKPC

value: Male


title: Day1_Rep1_Vrip

value: Dormant Bud


title: 285p.NOD1.CHX

value: Cycloheximide (50 µM)

value: phenol


title: Day0_Rep6_Vrip


title: Treg_R7_IL-2_BATF-WT [ATAC-seq]

extract_protocol: Chromatin accessibility mapping on purified cell populations was performed using the ATAC-seq method as previously described (Buenrostro et al., 2013; Corces et al., 2017), with minor adaptations. Briefly, in each experiment 2,000 - 15,000 sorted cells were pelleted by centrifuging for 10 min at 4 °C at 500 x g. After centrifugation, the pellet was carefully lysed in 50 µl resuspension buffer supplemented with NP-40 (Sigma), Tween-20 and Digitonin (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 % NP-40, 0.1 % Tween-20, 0.01 % Digitonin) and incubated for 3 minutes on ice. Then, 1 ml of ice-cold resuspension buffer supplemented with Tween-20 was added, and the sample was centrifuged at 4 °C at 500 x g for 10 minutes. The supernatant was discarded, and the cell pellet was carefully resuspended in the transposition reaction (25 µl 2 x TD buffer (Illumina), 2.5 µl TDE1 (Illumina), 16.5 µl PBS, 5 µl nuclease-free water, 0.5 µl 1% Digitonin (Promega), 0.5 µl 10% Tween-20 (Sigma)) for 30 min at 37 °C on a shaker at 1000 rpm. Following DNA purification with the Clean and Concentrator-5 kit (Zymo) eluting in 23 µl, 2 µl of the eluted DNA was used in a quantitative 10 µL PCR reaction (1.25 µM forward and reverse custom Nextera primers (Corces et al., 2017), 1x SYBR green final concentration) to estimate the optimum number of amplification cycles with the following program 72°C 5 min; 98°C 30 s; 25 cycles: 98°C 10 s, 63°C 30 s, 72°C 1 min; the final amplification of the library was carried out using the same PCR program and the number of cycles according to the Cq value of the qPCR. Library amplification using custom Nextera primers was followed by SPRI size selection with AmpureXP beads to exclude fragments larger than 1,200 bp. DNA concentration was measured with a Qubit fluorometer (Life Technologies). The libraries were sequenced using the Illumina HiSeq 4000 or NextSeq platforms.


title: Day0_Rep5_Vrip


title: gDNA from subject PATKYT

value: Female


title: Treg_R5_IL-4plusIL33_BATF-WT [ATAC-seq]


title: Day1_Rep2_Vrip


title: Day0_Rep4_Vrip


title: gDNA from subject PATJUT


title: 284p.NOD1.Vinbl

value: HeLa

value: Vinblastine (10 µM)


title: gDNA from subject PATJXZ


title: Day0_Rep3_Vrip


title: Treg_R5_IL-4plusIL33_BATF-KO [ATAC-seq]


title: 203.NOD1.CytoD

value: Cytoclasin D (5 µM)

value: ok


title: 202.NOD1.Jasp

value: Jasplanokinolid (0.2 µM)


title: Treg_R5_IL-2_BATF-WT [ATAC-seq]


title: Day0_Rep2_Vrip


title: Treg_R6_IL-4plusIL33_BATF-WT [ATAC-seq]


title: Treg_R5_IL-2_BATF-KO [ATAC-seq]


title: gDNA from subject PATJSP


title: Day10_Rep3_Vamu

organism: Vitis amurensis


title: 281p.NOD1.Control

value: Ctr (DMSO)


title: 160.NOD2.6G

source_name: HeLa NOD2 cells, 4hr, replicate 5


title: Treg_R4_IL-4plusIL33_BATF-KO [ATAC-seq]


title: Day10_Rep2_Vamu


title: Treg_R3_IL-4plusIL33_BATF-WT [ATAC-seq]


title: Treg_R3_IL-4plusIL33_BATF-KO [ATAC-seq]


title: 158.NOD2.Tg

value: Thapsigargin (5 µM)


title: 156.NOD2.AnisoM

value: Anisomycin (1 µM)


title: 159.NOD2.5F


title: Day0_Rep1_Vrip


title: 157.NOD2.Tm

value: Tunicamycin (5 µg/mL)


title: 155.NOD2.BFA

value: BrefeldinA (0.2 µg/mL)


title: 153.NOD2.LB42708


title: 150.NOD2.CCCP

value: CCCP (5 µM)


title: 154.NOD2.Lov

value: Lovastatin (30 µM)


title: 151.NOD2.2BP


title: Day9_Rep1_Vamu


title: 149.NOD2.Actin

value: Actinonin (50 µM)


title: Day10_Rep1_Vamu

value: Dormant Bud


title: Day9_Rep3_Vamu


title: gDNA from subject PATISV

value: tumor


title: Treg_R2_IL-4plusIL33_BATF-KO [ATAC-seq]


title: gDNA from subject PATIDY

value: Male


title: Day9_Rep2_Vamu


title: Treg_R3_IL-2_BATF-WT [ATAC-seq]


title: 152.NOD2.2MC


title: gDNA from subject PATIAB

value: Female


title: Day8_Rep2_Vamu


title: gDNA from subject PATIHH


title: Day8_Rep1_Vamu


title: Treg_R1_IL-4plusIL33_BATF-WT [ATAC-seq]


title: Treg_R2_IL-2_BATF-KO [ATAC-seq]


title: Treg_R2_IL-2_BATF-WT [ATAC-seq]


title: Treg_R3_IL-2_BATF-KO [ATAC-seq]


title: Day8_Rep3_Vamu


title: gDNA from subject PARBXE


title: Day7_Rep3_Vamu


title: 147.NOD2.Nig

value: HeLa

value: Nigericin (5 µM)


title: gDNA from subject PATHMB


title: D2_H3K27ac_input

city: San Francisco

first: Sheng

last: Ding

state: CA

address: 1650 Owens Street

institute: Gladstone Institute for Cardiovascular Disease

data_processing:
base-calling was done using CASAVA 1.8.4.
The alignment was done using bowtie2 with mouse genome build mm9. The result was then filtered by MAPQ scores  with smtools to only keep reads with MAPQ larger than 10 (version 0.1.19)
peak calling Macs (version 2.0: macs2 callpeak -t $treatment -c $control --broad -g mm -n $name)， for Klf4 ChIP seq, we used an additional parameter of  -p 0.05 to call the peaks.
Genome_build: mm9
Supplementary_files_format_and_content: peaks.narrowPeak bed files from the MACS2

source_name: SKM secondary MEF

growth_protocol: MEF cells are cultured in DMEM+10%FBS, and reprogramming cells were cultured in mouse ES medium in presence of doxycycline for 2 days.

extract_protocol:
Chromatins were cross-linked by 1% formaldehyde and extracted using EZ-ChIP Chromatin Immunoprecipitation kit (Millipore, 17-371). The chromatin was then sonicated to an average DNA fragment length of 100-500 bp on Covaris S2 .
Sequencing libraries were generated, according to the manufacturer’s instructions. Briefly, 4 ng of ChIP product was used for each library preparation. The NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645) was used to ligate adapters and for barcoding and amplification. Libraries was purified using SPRIselect® Reagent magnetic beads (Beckman Coulter, Inc. #B23317), quality-controlled by the Bioanalyzer, and quantified by qPCR.

tag: sample stage

value: Day 2 of SKM reprogramming


title: 145.NOD2.CHX

value: Cycloheximide (50 µM)

value: ok


title: Day7_Rep2_Vamu


title: Treg_R1_IL-2_BATF-KO [ATAC-seq]


title: 146.NOD2.Nocad

value: Nocadazole (10 µM)


title: gDNA from subject PATGXW


title: 148.NOD2.Etop

value: Etoposide (5 µM)


title: 144.NOD2.Vinbl

value: Vinblastine (10 µM)


title: D2_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: Day7_Rep1_Vamu


title: D0_H3K27ac

source_name: OG2 MEFs

value: Day 0 MEF


title: gDNA from subject PATGIY


title: Day5_Rep3_Vamu


title: D0_H3K27ac_input


title: Day5_Rep2_Vamu


title: Day5_Rep1_Vamu


title: D2_Klf4_input


title: 141.NOD2.Control

value: Ctr (DMSO)


title: Day4_Rep4_Vamu


title: gDNA from subject PATGDZ


title: D2_Klf4_1

value: Sox2 (Millipore, AB5603)


title: Day4_Rep3_Vamu


title: D2_Sox2_2_input


title: 143.NOD2.CytoD

value: Cytoclasin D (5 µM)


title: 142.NOD2.Jasp

value: Jasplanokinolid (0.2 µM)


title: gDNA from subject PATGAN

value: tumor


title: Day4_Rep1_Vamu

value: Dormant Bud


title: Day3_Rep3_Vamu


title: 137.NOD1.Tm

source_name: HeLa NOD1 cells, 4hr, replicate 5

value: Tunicamycin (5 µg/mL)


title: 138.NOD1.Tg

value: HeLa

value: Thapsigargin (5 µM)


title: D2_Sox2_1_input

value: Day 2 of SKM reprogramming


title: 140.NOD1.6G


title: Day3_Rep2_Vamu


title: D2_Sox2_1


title: gDNA from subject PATGBX

source_name: AML, pre-treatment

value: Female


title: D2_Klf4_2


title: gDNA from subject PATFNK

value: Male


title: Day3_Rep1_Vamu


title: Day3_Rep4_Vrip


title: gDNA from subject PATFMR


title: Day2_Rep3_Vamu


title: Dsn-2 (replicate 2)

city: Taipei

first: Na-Sheng

last: Lin

address: No.128, Sec. 2, Academia Rd, NaKang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica, Taiwan

description: Although the adjacent inoculated tissue were infected by CymMV and ORSV, both CymMV and ORSV infection was not detected in this area by using tissue blot. By using RT-PCR, both virus infection could be detected with low titers. Therefore the tissue is designated as at the early stage facing virus infection. (replicate 2)

data_processing:
Illumina HiSeq 2500 System used for basecalling.
The adaptor sequences were identified and removed by using a Perl script.
Small RNAs shorter than 18 nt or longer than 25 were removed.
Data matrix contains distinct small RNAs with their raw abundance after removing the adapter sequences.
Supplementary_files_format_and_content: tab-delimited text files include sequence and read counts for each Sample

organism: Phalaenopsis amabilis

source_name: Leaf

growth_protocol: Mericlone P. amabilis plants in 7.5-cm pots were purchased from local nursery. CymMV and ORSV-free plants were examined by multiplex RT-PCR and kept in walk-in chamber with day/night temperature of 28/25 oC and 16 h light. Challenged P. amabilis plants were grown in another walk-in chamber with constant 28 oC and 16 h light.

extract_protocol:
Total RNA from frozen leaves were purified using TriPure Reagent (Roche) following the manufacturer's instructions.
cDNA libraries of each sample were separately constructed by using Illumina small RNA kits and protocols. Indexed adaptors were used for multiplexed sequencing.
The 10 samples were sequenced as 2 batches. For batch 1 (Mi-1, Mn-1, Di, Dn), 4 cDNA libraries were equally pooled in the same lane and sequenced by standard Miseq chip. For batch 2 (Mi-2, Mn-2, Dsi-1, Dsi-2, Dsn-1, Dsn-2), 6 libraries were equally pooled. To share the 2 lanes of fast-mode Miseq chip, the pooled libraries were equally clustered on the lanes (i.e. each lane contains all the 6 libraries, therefore 2 fastq files were generated for 1 sample).

treatment_protocol: The uppermost two fully-expanded leaves were used as inoculated leaves and inoculated with CymMV and ORSV virion mixture (0.5 μg of each virus in 40 μL inoculation buffer, which containing 5 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 5 mM phosphate buffer (pH 8.0), and 1 g·L-1 bentonite). Only the tip-half was dusted with carborundum and the virions were rubbed-in by cotton-swabs. Mocked-inoculation with inoculation buffer only was parallelly conducted as controls. Virus infection was confirmed by tissue blot at 10 days post inoculation. Infection stages were assigned based on the tissue blot analysis. In brief, "D" stands for double infection, "M" stands for mock; "i" stands for "inoculated area" and "n" stands for "(adjacent) non-inoculated area". The double inoculated plants were further categorized as "Di/Dn" and "Dsi/Dsn" samples according to the infection status of CymMV. Di/Dn: Chlorotic lesions and ringspots appeared in inoculated area (Di) and CymMV infection spread through non-inoculated tissues (Dn). Dsi/Dsn: Leaves without virus invasion to the non-inoculated regions (Dsn) showed mild symptoms or even symptomless. We then collected the designated samples separately, and discriminated them as tissues representing late (Di), intermediate (Dsi), and early (Dsn) infection stages, respectively. Dn is uniquely specified as a transition stage of synergism since CymMV invasion was advanced but symptom formation was not yet elicited.

value: Leaf

tag: treatment/infection

value: Non-inoculated tissue adjacent to the inoculated tissue of CymMV and ORSV mixed inoculation

tag: batch of experiment


title: 135.NOD1.BFA

value: BrefeldinA (0.2 µg/mL)

value: ok


title: Dsi-2 (replicate 2)

description: Designated as late stage of infection (CymMV and ORSV infection was detected in this area). However, both CymMV and ORSV infection was not detected by tissue blot in the corresponding non-inoculated tissue. The virus titers were lower than in Di. (replicate 2)

value: Inoculated tissue of CymMV and ORSV mixed inoculation


title: gDNA from subject PATFYN


title: 133.NOD1.LB42708


title: gDNA from subject PATFGL


title: 139.NOD1.5F


title: Dsn-1 (replicate 1)

description: Although the adjacent inoculated tissue were infected by CymMV and ORSV, both CymMV and ORSV infection was not detected in this area by using tissue blot. By using RT-PCR, both virus infection could be detected with low titers. Therefore the tissue is designated as at the early stage facing virus infection. (replicate 1)


title: Day1_Rep3_Vamu


title: gDNA from subject PATESX


title: 131.NOD1.2BP


title: gDNA from subject PATEUF


title: 132.NOD1.2MC


title: 134.NOD1.Lov

value: Lovastatin (30 µM)


title: 130.NOD1.CCCP

value: CCCP (5 µM)


title: 129.NOD1.Actin

value: Actinonin (50 µM)


title: Day1_Rep2_Vamu


title: 128.NOD1.Etop

value: Etoposide (5 µM)


title: Mn-2

description: Corresponding non-inoculated tissue adjacent to the mock-inoculated area, used as controls of non-inoculated tissues

value: Mock, non-inoculated tissue adjacent to the inoculated tissue


title: gDNA from subject PATELV

value: tumor


title: Day0_Rep5_Vamu

value: Dormant Bud


title: Day2_Rep1_Vamu


title: Day1_Rep1_Vamu


title: D2_Sox2_2

value: Sox2 (Millipore, AB5603)


title: Dsi-1 (replicate 1)

description: Designated as late stage of infection (CymMV and ORSV infection was detected in this area). However, both CymMV and ORSV infection was not detected by tissue blot in the corresponding non-inoculated tissue. The virus titers were lower than in Di. (replicate 1)


title: Di

description: Designated as late stage of infection (CymMV and ORSV infection was detected in this area. In addition, CymMV infection was already spread to corresponding non-inoculated tissue as detected by tissue blot of the whole leaf)


title: Dn

description: Designated as intermediate stage of infection (with CymMV infection in this area as detected by tissue blot)


title: Day2_Rep2_Vamu


title: Mi-2

description: Mock samples without virus infection, used as controls of inoculated tissues

value: Mock, inoculated tissue


title: Day0_Rep3_Vamu


title: Day0_Rep4_Vamu


title: gDNA from subject PATEMV


title: gDNA from subject PATEID


title: Mn-1


title: gDNA from subject PATEIA


title: Mi-1


title: Day0_Rep2_Vamu


title: 127.NOD1.Nig

value: HeLa

value: Nigericin (5 µM)


title: gDNA from subject PATDVM

value: Female


title: ID23

city: Calgary

first: Chinju Therese

last: Johnson

state: Alberta

department: Production Animal Health

country: Canada

institute: University of Calgary

description: Low (12.2% CP, 62.9% TDN)

data_processing:
Base calling and demultiplexing was performed with CASAVA 1.9 (illumina) with default settings. Quality of the sequencing reads was assessed using FastQC software.
Sequencing reads were mapped to the bovine genome (Bos taurus, UMD3.1.87, downloaded from Illumina iGENOME website) using TopHat v2.0.10 and with bowtie v.1.1.2  used as an internal aligner.
Counts of reads mapping to genes were obtained using featureCounts software from Subread package
Count data was loaded into R, normalization and variance stabilizing transformation were applied using DESeq2 package. Normalized and variance stabilized data was used for the quality control and sample clustering analysis
Genome_build: Bos taurus, UMD3.1.87
Supplementary_files_format_and_content: rawcounts contain raw counts of reads mapping to features.

organism: Bos taurus

source_name: Bovine testes parenchyma

extract_protocol:
A small portion of testicular parenchyma (~75 mg) from each bull (n=24) was homogenised and total RNA extracted. Trizol reagent-mediated extraction was performed as per manufacturer’s instructions. For each sample (n=24) total RNA (1 µg) was used to create mRNA libraries using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diet

value: Low (12.2percent CP, 62.9percent TDN)

tag: breed

value: Holstein

tag: age at castration

value: 72 wk

value: testes


title: ID24

description: Low (12.2% CP, 62.9% TDN)


title: Si-TINCR-2 rep3

city: Harbin

first: Jian

last: Wang

address: 600 Changjiang Road

institute: Northeast Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Bowtie2 is used to map clean reads to the reference genome Homo sapiens GRCh38.p12 and to other sRNA databases. Bowtie2 : -q -L 16 --phred64 -p 6
The small RNA expression level is calculated by using Transcripts Per Kilobase Million  (TPM[14]). The TPM method eliminates the influence of sequencing discrepancy on the  calculation of small RNA expression level. Therefore, the calculated gene expression  level datacanbeuseddirectly tocomparethedifferenceingeneexpressionbetweenthe  samples. To calculate the TPM the following formula is used,C means miRNA counts  numberis asample,N means totalreads numberthatmappedtogenome:  TPM=C*1000000/N
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: text files include TPM values for each Sample

growth_protocol: Human breast cancer cell lines T47D was obtained from the Chinese Academy of Sciences Cell Bank and Cellbio (China) and cultured and stored according to their instructions.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human breast cancer cell lines T47D was seeded in 6-well dishes the night before to give 60-70% confluence for plasmid and 40-50% for miRNA or siRNA transfection. Cells were transfected using Lipofectamine 2000 (invitrogen), according to the manufacturer’s instructions in the following day. At 48 h post-transfection, cells were harvested for qRT-PCR analysis.

value: si-TINCR


title: gDNA from subject PATDRL

tag: gender

value: Male


title: 126.NOD1.Nocad

tag: cell line

tag: inducible gene

value: Nocadazole (10 µM)

tag: sample purification

value: ok


title: Si-TINCR-2 rep2

tag: treatment


title: Day0_Rep1_Vamu

tag: tissue


title: ID22

description: Low (12.2% CP, 62.9% TDN)


title: ID20

description: Low (12.2% CP, 62.9% TDN)


title: Si-TINCR-2 rep1


title: ID19

description: Medium (17.0% CP, 66.0% TDN)

value: Medium (17.0percent CP, 66.0percent TDN)


title: ID21

description: Low (12.2% CP, 62.9% TDN)


title: gDNA from subject PATDLZ

tag: group

tag: age at diagnosis (days)


title: 136.NOD1.AnisoM

value: Anisomycin (1 µM)


title: Si-TINCR-1 rep2


title: Si-TINCR-1 rep3


title: gDNA from subject PATDMY

value: tumor


title: 125.NOD1.CHX

value: Cycloheximide (50 µM)


title: 123.NOD1.CytoD

value: Cytoclasin D (5 µM)


title: 122.NOD1.Jasp

value: Jasplanokinolid (0.2 µM)


title: Si-TINCR-1 rep1


title: 121.NOD1.Control

value: HeLa

value: Ctr (DMSO)


title: 124.NOD1.Vinbl

value: Vinblastine (10 µM)


title: 200p.NOD2.6G

source_name: HeLa NOD2 cells, 4hr, replicate 4

value: phenol


title: gDNA from subject PATDLI

value: Female


title: 197p.NOD2.Tm

value: Tunicamycin (5 µg/mL)


title: 198p.NOD2.Tg

value: Thapsigargin (5 µM)


title: 195p.NOD2.BFA

value: BrefeldinA (0.2 µg/mL)


title: 199p.NOD2.5F


title: ID17

description: Medium (17.0% CP, 66.0% TDN)

value: Holstein

value: 72 wk

value: testes


title: 196p.NOD2.AnisoM


title: gDNA from subject PATCYP

value: Male


title: ID16

description: Medium (17.0% CP, 66.0% TDN)

value: Medium (17.0percent CP, 66.0percent TDN)


title: NC rep2

value: control


title: gDNA from subject PATDIC

value: tumor


title: ID14

description: High (20.0% CP, 67.9% TDN)

value: High (20.0percent CP, 67.9percent TDN)


title: MLL small RNA RIP-seq

city: shanghai

first: rui

middle: heng

last: wang

state: shanghai

address: ruijin two street

department: insitute of hematology

institute: shanghaijiaotong university

data_processing:
clean reads were obtained by removing reads containing adapter and filtering reads containg low quality base
Index of the hg38 was built using Bowtie2 and single-end reads were aligned to the reference genome by Hisat
FPKM and TPM of each gene and sRNA was calculated based on the length of the gene and reads count mapped to the gene by using RSEM
Genome_build: ftp://ftp.ensembl.org/pub/release-92/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: tab-delimited excel files include FPKM or TPM values for each sample

source_name: 293T cell line

growth_protocol: HEK293T cell line was cultured in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 10% fetal bovine serum and 1% 100×Pen Strep

extract_protocol:
using RIPA lysis buffer to extract RNAs
standard illumina protocols

treatment_protocol: no treatment

tag: cell type

value: human embryonic kidney cells

tag: cell line source gender

value: male

tag: cell line source tissue

value: embryonic kidney

tag: cell line source age

value: fetus

tag: rip antibody

value: customized antibody recognizing the MLLC180(aa2829-2883) [PMID  17908926]

tag: molecule subtype

value: small RNA


title: NC rep1


title: gDNA from subject PATCYY


title: ID15

description: Medium (17.0% CP, 66.0% TDN)

tag: diet


title: NC rep3


title: MLL total RNA RIP-seq


title: ID12

description: High (20.0% CP, 67.9% TDN)

tag: breed


title: ID11

description: High (20.0% CP, 67.9% TDN)

tag: age at castration


title: gDNA from subject PATBVJ

tag: gender


title: SR_CTC

city: Beijing

first: Qian

last: Bai

address: 35 East Qinghua Road

department: College of Forestry

institute: Beijing Forestry University

data_processing:
Basecalls performed using illumina Casava 1.8
Raw data of fastq format were processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’adaptercontaminants, without 3’adapteror the insert tag, containing poly A or T or G or C and low quality reads from raw data.
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al.,2009)without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0was used as reference, modified softwaremirdeep2(Friedlander et al., 2011)and srna-tools-cliwere used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to Repeat Masker, Rfam database or those types of datas from the specified species itself.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria(Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Genome_build: no suitable reference genome for Pistacia chinensis Bunge, so we used the all the known miRBases of plants, including: cre, cln, pab, pde, pta, ppt, smo, atr, pgi, cca, han, har, hci, hex, hpa, hpe, htu, aly, ath, bna, bol, bra, cpa, cme, hbr, mes, rco, aau, ahy, amg, gma, gso, lja, mtr, pvu, vun, ama, dpr, rgl, ssl, lus, gar, ghb, ghr, gra, tcc, aqc, bcy, bgy, mdm, ppe, ccl, crt, csi, ctr, peu, ptc, nta, sly, stu, vvi, ata, bdi, egu, far, hvu, osa, sbi, sof, ssp, tae, ttu, zma
Supplementary_files_format_and_content: A text file include readcount and TPM for each sample

organism: Pistacia chinensis

source_name: buds

extract_protocol:
The female, male, monoecious female and bisexual inflorescence buds during two sex differentiation stage were sampled. Total RNA was isolated from each sample using the EASYspin Plus Plant RNA Kit (Tiangen Biotech Co., Beijing, China). A total amount of 3 μg total RNA per sample was used as input material for the small RNA library.
Sequencing libraries were generated using NEB Next®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: strain

tag: sex type

value: monoeicous female

value: inflorescence buds

tag: developmental stage

value: stage C of floral development


title: 193p.NOD2.LB42708

tag: cell line

value: HeLa

tag: inducible gene

tag: treatment

tag: sample purification

value: phenol


title: 191p.NOD2.2BP


title: 194p.NOD2.Lov

value: Lovastatin (30 µM)


title: ID10

description: High (20.0% CP, 67.9% TDN)

value: Holstein

value: 72 wk

tag: tissue

value: testes


title: SR_CX


title: 190.NOD2.CCCP

value: CCCP (5 µM)

value: ok


title: 192p.NOD2.2MC


title: gDNA from subject PATBUR

tag: group

value: tumor

tag: age at diagnosis (days)

value: Female


title: ID9

description: High (20.0% CP, 67.9% TDN)

value: High (20.0percent CP, 67.9percent TDN)


title: SR_CC

value: female


title: ID13

description: High (20.0% CP, 67.9% TDN)


title: ID7

description: High (20.0% CP, 67.9% TDN)


title: SR_BTC

value: stage B of floral development


title: gDNA from subject PATBNP


title: SR_CTH

value: monoeicous bisexual


title: ID8

description: High (20.0% CP, 67.9% TDN)


title: gDNA from subject PATBIP


title: ID6

description: Medium (17.0% CP, 66.0% TDN)

value: Medium (17.0percent CP, 66.0percent TDN)


title: ID5

description: Medium (17.0% CP, 66.0% TDN)


title: SR_BC

value: inflorescence buds


title: ID4

description: Medium (17.0% CP, 66.0% TDN)


title: 189p.NOD2.Actin

value: Actinonin (50 µM)


title: gDNA from subject PATAST

value: Male


title: 186p.NOD2.Nocad

value: HeLa

value: Nocadazole (10 µM)

value: phenol


title: TM_14h3

city: guiyang

first: zhengting

last: yang

address: huaxi university town

institute: guizhou normal university

data_processing:
Illumina Casava1.7 software used for basecalling.
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, Q30, GC-content and sequence  duplication level of the clean data were calculated. All the downstream analyses were based on clean  data with high quality.
The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
To generate sequencing libraries for further Illumina® sequencing, a Next® Ultra™ RNA Library Prep Kit (NEB, USA) was used, and index parameters were applied to each sample to generate corresponding sequences
the parameter-programmed sample clustering was processed on a Cluster Generation (cBot) System using a Cluster Kit (TruSeq PE Cluster Kit v3-cBot-HS, Illumia). After the cluster was generated, the library was sequenced on an Illumina Hiseq apparatus and paired-end reads were developed.

organism: Cyclocarya paliurus

source_name: leaves

growth_protocol: in the nature

extract_protocol:
Leaf samples were kept in liquid nitrogen and submitted to company to determine the transcriptome sequence. Reverse transcription was performed using the method described for the Moloney Murine Leukemia Virus (M-MLV, Invitrogen) for qRT-PCR
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The 0.2 gram leaves from three individual trees were treated with tunicamycin (TM, 5 µg/mL) and Triton (0.5%, to improve leaf uptake) for 0 hours, 6 hours, and 14 hours(TM_0h, TM_6h, and TM_14h.

tag: genotype

value: wild type

tag: time point


title: 184p.NOD2.Vinbl

value: Vinblastine (10 µM)


title: 187p.NOD2.Nig

value: Nigericin (5 µM)


title: 183p.NOD2.CytoD

value: Cytoclasin D (5 µM)


title: TM_14h2


title: 188p.NOD2.Etop

value: Etoposide (5 µM)


title: ID2

description: Low (12.2% CP, 62.9% TDN)

value: Low (12.2percent CP, 62.9percent TDN)

value: Holstein

value: 72 wk

value: testes


title: ID3

description: Low (12.2% CP, 62.9% TDN)


title: TM_14h1


title: gDNA from subject PATAKC

value: tumor


title: 185p.NOD2.CHX

value: Cycloheximide (50 µM)


title: ID1

description: Low (12.2% CP, 62.9% TDN)


title: SR_BTH

value: monoeicous bisexual

value: inflorescence buds

value: stage B of floral development


title: Sample 68_LC75

city: Corvallis

first: Kristina

middle: M

last: Smith

state: OR

department: Biochemisty and Biophysics

institute: Oregon State University

description:
processed data file:
LC68-75_fpkm.txt
lane5-s052-indexRPI25-ACTGAT-LC75_S52_L005

data_processing:
Fastq files were input to Tophat and mapped to the F. graminearum genome with options -a 5 -m 1 -i 30 -I 2000
Cufflinks was used to quantify gene expression values as reads per kilobase of exon per million reads (RPKM) using gene annotation from MIPS ftp://ftpmips.gsf.de/fungi/Fusarium/F_graminearum_PH1_v32/.
cuffdiff was used to identify differentially expressed genes
Genome_build: GCA_000240135.3
Supplementary_files_format_and_content: processed data is cuffdiff output

organism: Fusarium graminearum

growth_protocol: To generate Fusarium macroconidia, a small amount of frozen conidia or tissue was inoculated into 50 ml flasks containing CMC medium (Capellini, 1965, Mycologia) and shaken at 150 rpm for 3-4 days at room temperature (RT, ~22C). Conidia were collected by filtration through cheesecloth and stored at -80C in 25% glycerol. To isolate RNA, strains were inoculated into 50-100 ml YPD (0.3% yeast extract, 1% bacto-peptone, 2% dextrose) and incubated at 28C at 150 rpm for 24-36 hrs. Tissue was harvested by filtration and flash-frozen in liquid nitrogen until total RNA isolation.

extract_protocol:
Total RNA was assessed with Agilent 2100 Bioanalyzer to determine RNA integrity; only high quality total RNA (integrity number between 9 - 10) were used. An Ribo-Zero rRNA removal Kit (Epicentre, #MRZY1324) was used for enrichment of transcripts.
For sample 1-60 The SOLiD total RNA-seq kit (ABI SOLiD, #4445374) was used to construct template cDNA.
For sample 61-68 Illumina TruSeq RNA Sample Preparation kits were used to make RNA-seq libraries.

treatment_protocol: Total RNA was isolated as described in Wu et al, 2014 G3

tag: strain background

value: mycelia

tag: library construction


title: gDNA from subject PATAER

value: Male


title: 182p.NOD2.Jasp

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

value: HeLa

value: Jasplanokinolid (0.2 µM)

value: phenol


title: TM_6h2

value: wild type


title: Sample 67_LC74

description:
processed data file:
LC68-75_fpkm.txt
lane5-s051-indexRPI23-GAGTGG-LC74_S51_L005

value: Illumina TruSeq RNA Sample Preparation kit


title: TM_6h3


title: TM_6h1


title: 180p.NOD1.6G

source_name: HeLa NOD1 cells, 4hr, replicate 4


title: Sample 66_LC73

description:
processed data file:
LC68-75_fpkm.txt
lane5-s050-indexRPI22-CGTACG-LC73_S50_L005


title: TM_0h3


title: 179p.NOD1.5F


title: 181p.NOD2.Control

value: Ctr (DMSO)


title: 177p.NOD1.Tm

value: Tunicamycin (5 µg/mL)


title: gDNA from subject PASZAF

extract_protocol: Starting with one vial of cryopreserved cells derived from Bone Marrow (or if Bone Marrow unavailable, Peripheral Blood), cells undergo a quick thaw and are adding to a tube containing PBS (to dilute the residual DMSO).  Cells are spun at 1000RPM and pelleted.  The pellet is vortexed and resuspended in lysis buffer from the Qiagen AllPrep DNA/RNA mini kit.  The lysate is added to an RNeasy spin column to isolate RNA while the flow through is added to the DNA spin column for subsequent DNA isolation.  After a series of washes on each column, DNA or RNA is eluted into a tube using elution buffer or RNase-free H20 respectively.  Both nucleic acids are evaluated on the NanoDrop for initial sample concentration and quality.  DNA quantification is then assessed using the Picogreen assay for better accuracy.  RNA quality and quantity is also assessed using the Agilent Bioanalyzer nanochip.

value: Female


title: gDNA from subject PASYWV


title: Sample 63_LC70

description:
processed data file:
LC68-75_fpkm.txt
lane5-s047-indexRPI11-GGCTAC-LC70_S47_L005


title: 176p.NOD1.AnisoM

value: Anisomycin (1 µM)


title: TM_0h1


title: Sample 62_LC69

description:
processed data file:
LC68-75_fpkm.txt
lane5-s046-indexRPI10-TAGCTT-LC69_S46_L005


title: SR_BX

value: male


title: TM_0h2


title: ECM_ES2_p26

city: Bron

first: Bertrand

middle: Pierre-Yves

last: PAIN

address: 18, Avenue du  Doyen Lépine

country: France

institute: U1208, INSERM

description:
ECM_ES2_p26
Reprogrammed with ECM gene cocktail.
Stranded mRNA library (Eurofins Genomics)
processed data file: Table1.xlsx
processed data file: Table2.xlsx

data_processing:
The raw files were converted into Fastq files and demultiplexed using bcl2fastq-1.8.4 software (Illumina).
Quality control was performed on Fastq files using the MultiQC 1.7 software aggregating data from fastp 0.19.6, FastQ Screen v0.13.0, kallisto v0.8.1.
fastq.gz files were pseudo-aligned using kallisto v0.8.1.
Normalized counts and DE genes were calculated using DESeq2 v1.24.0.
Genome_build: n/a
Supplementary_files_format_and_content: Table1.xlsx: kallisto
Supplementary_files_format_and_content: Table2.xlsx: ISG_PTC_vs_ES2_results

organism: Pteropus vampyrus

source_name: Reprogrammed cells derived from the somatic PTC cells

growth_protocol: Cells were maintained in culture at 37°C in 7.5% CO2 in different media in the presence of Doxycycline for the reprogrammed cells.

extract_protocol:
RNAs were obtained following Trizol extraction of frozen cell pellets.
Libraries were synthesized according to the Illumina procedure by Eurofins genomics from total RNAs.

treatment_protocol: Cells were dissociated, washed in PBS and immediately frozen at -80° before RNAs were extracted.

tag: cell type

tag: media

value: Seric medium


title: 175p.NOD1.BFA

data_processing: Microarray image data were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted txt files were analyzed further using R and the associated BioConductor limma package. Background correction ( normexp) and normalization between arrays  (quantile) was used,control probe were removed. Within-array replicate features were condensed with their average by avereps.

value: BrefeldinA (0.2 µg/mL)


title: 174p.NOD1.Lov

value: Lovastatin (30 µM)


title: gDNA from subject PASZUT

data_processing:
Raw IDAT files were processed using R package SeSAMe (PMID: 30085201) with noob background correction (PMID: 23476028, 28035024), non-linear dye bias correction, SNP and non-detection (p-value) masking. Methylation beta values are computed as the fraction of total probeset intensity attributable to fluorescence from the methylated probe allele, with 0 indicating no methylation and 1 indicating full methylation. The SeSAMe/noob default offset of 15 was added to both unmethylated (U) and methylated (M) allelic intensities in each pair to avoid division by zero. We excluded measurements from sub-optimally designed probes due to overlap with SNPs and repeat elements, as suggested by previous studies (PMID: 27924034).
matrix_processed.csv: normalized (SeSAMe) Average Beta
matrix_signals.csv: Unmethylated and methylated signal intensities, and non-detection p-values

value: tumor

tag: gender


title: Sample 65_LC72

description:
processed data file:
LC68-75_fpkm.txt
lane5-s049-indexRPI21-GTTTCG-LC72_S49_L005

tag: strain


title: ECM_ES2_p12

description:
EMC_ES2_p12
Reprogrammed with ECM gene cocktail.
Stranded mRNA library (Eurofins Genomics)
processed data file: Table1.xlsx
processed data file: Table2.xlsx

value: Reprogrammed cells derived from the somatic PTC cells


title: Sample 61_LC68

description:
processed data file:
LC68-75_fpkm.txt
lane5-s045-indexRPI9-GATCAG-LC68_S45_L005

value: mycelia


title: ECM_ES2_p22

description:
ECM_ES2_p22
Reprogrammed with ECM gene cocktail.
Stranded mRNA library (Eurofins Genomics)
processed data file: Table1.xlsx
processed data file: Table2.xlsx


title: ECM_E2_p18

description:
ECM_E2_p18
Reprogrammed with ECM gene cocktail.
Stranded mRNA library (Eurofins Genomics)
processed data file: Table1.xlsx
processed data file: Table2.xlsx

value: Non-seric medium


title: ECM_E2_p17

description:
ECM_E2_p17
Reprogrammed with ECM gene cocktail.
Stranded mRNA library (Eurofins Genomics)
processed data file: Table1.xlsx
processed data file: Table2.xlsx


title: Sample 64_LC71

description:
processed data file:
LC68-75_fpkm.txt
lane5-s048-indexRPI20-GTGGCC-LC71_S48_L005


title: gDNA from subject PASXWN


title: gDNA from subject PASXVC

value: Male


title: PTC_3_p28

description:
PTC_3_p28
Stranded mRNA library (Eurofins Genomics)
processed data file: Table1.xlsx
processed data file: Table2.xlsx

source_name: Primary trachea cells

value: Primary trachea cells


title: 172p.NOD1.2MC

value: HeLa

value: phenol


title: ECM_E2_p16

description:
ECM_E2_p16
Reprogrammed with ECM gene cocktail.
Stranded mRNA library (Eurofins Genomics)
processed data file: Table1.xlsx
processed data file: Table2.xlsx


title: 170p.NOD1.CCCP

value: CCCP (5 µM)


title: PTC_2_p29

description:
PTC_2_p29
Stranded mRNA library (Eurofins Genomics)
processed data file: Table1.xlsx
processed data file: Table2.xlsx


title: gDNA from subject PASXKT


title: gDNA from subject PASXNR


title: 168p.NOD1.Etop

value: Etoposide (5 µM)


title: 171p.NOD1.2BP


title: 166p.NOD1.Nocad

value: Nocadazole (10 µM)


title: PTC_1

description:
PTC_1
Stranded mRNA library (Eurofins Genomics)
processed data file: Table1.xlsx
processed data file: Table2.xlsx


title: HOXA10AS_2

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

institute: Goehte University Frankfurt

description: Gene expression data from CD11b+CD117-CD14- myeloid precursors transduced with HOXA10-AS

hyb_protocol: Hybridization was done for 16 hrs at conditions recommended by the manufacturer. Clariom™ S  chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: Image analysis was done by Affymetrix® GeneChip® Command Console® Software (AGCC) and  Affymetrix® Expression Console™ Software.

label: Biotin

source_name: CD34+ HSPC HOXA10-AS day 5 #2

label_protocol: 2-10 ng of total RNA were used for biotin labelling according GeneChip® Pico Kit (Affymetrix). 5.5 μg of biotinylated cDNA were fragmented and placed in a hybridization cocktail containing four biotinylated hybridization controls (BioB, BioC, BioD, and Cre) as recommended by the manufacturer. Samples were hybridized to an identical lot of Affymetrix Clariom™ S (400 Format) for 17 hours at 45°C.

growth_protocol: Three independent samples of human CD34+ HSPC from cord blood were transduced with lentiviral constructs containng HOXA10-AS or with a empty control vector. Transduced cells were FACS sorted for EGFP expression and cultured in conditions promoting myeloid differentiation. Total RNA was prepared of FACS-sorted CD11b+CD14-CD117- myeloid precursors on 5 of culture.  We analyzed early gene expression changes using Affymetrix Microarray Clariom™ S Pico Assay.

extract_protocol: Zymo Research Quick RNA Miniprep Kit according to manufacturers instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer.

value: CD34+ HSPC in monocytic differentiation medium

tag: lentiviral construct


title: 169p.NOD1.Actin

value: Actinonin (50 µM)


title: 167p.NOD1.Nig

value: Nigericin (5 µM)


title: Bull2_RNA_seq_3

first: Shengli

last: Zhang

address: 2rd, Yuanmingyuan West Road

department: Colledge of Animal Science and Techonology

institute: China Agricultural University

description: RNA-seq for Bull2

data_processing:
FASTQC (0.11.2) was used to assess the quality of sequence reads. Low quality reads and adapters were trimmed using Trimmomatic software (v0.35).
Trimmed reads were mapped to Bovine Reference Genome Assembly UMD3.1 using TopHat v2.0.12.
Read counts for each gene in each sample were then counted by HTSeq v0.6.0 for subsequent analyses of differentially expressed genes (DEGs) using DEGseq and edgeR. The expression levels of genes were also measured by FPKM using Cufflinks (v2.2.1) for subsequent analysis. DEGs were analyzed using Cuffdiff.
Genome_build: UMD3.1
Supplementary_files_format_and_content: excel files with FPKM of genes in each sample

source_name: Sperm

extract_protocol:
Fresh semen samples were carefully laid on a monolayer of 40% Percoll. Somatic cell contamination of the sperm cells was removed by centrifugation at room temperature for 20 min at 2000 rpm. After removal of the Percoll solution, sperm pellets were washed twice in 5 mL of warm-up phosphate-buffered saline for 20 min at 2000 rpm. Total RNA extraction of sperm pellets was performed using the standard TRIzol method.
We first preamplified extracted RNA using the Smart-seq2 protocol following the manufacturer’s instructions. A total of 20 ng of cDNA was subjected to library construction based on the manufacturer’s instructions. Sequencing was conducted in Hiseq2500 and 250-bp paired end reads were obtained.

tag: species

value: Holstein


title: HOXA10AS_3


title: 165p.NOD1.CHX

first: Hans-Joachim

last: Mollenkopf

institute: Max-Planck-Institute for Infection Biology

tag: cell line

value: Cycloheximide (50 µM)


title: gDNA from subject PASXLJ

first: Jason

last: Farrar

institute: University of Arkansas for Medical Sciences


title: Control_3

description: Gene expression data from CD11b+CD117-CD14- myeloid precursors transduced with ctrl vector

source_name: CD34+ HSPC ctrl day 5 #3

value: empty control vector


title: Bull2_RNA_seq_2

description: RNA-seq for Bull2


title: ID18

description: Medium (17.0% CP, 66.0% TDN)

tag: diet

value: Medium (17.0percent CP, 66.0percent TDN)

tag: breed

tag: age at castration

value: 72 wk

value: testes


title: HOXA10AS_1

source_name: CD34+ HSPC HOXA10-AS day 5 #1


title: 163p.NOD1.CytoD

tag: inducible gene

tag: treatment

value: Cytoclasin D (5 µM)

tag: sample purification


title: Control_2

source_name: CD34+ HSPC ctrl day 5 #2


title: Control_1

source_name: CD34+ HSPC ctrl day 5 #1


title: Bull2_RNA_seq_1

description: RNA-seq for Bull2


title: OATL4_MK-2048_25uM_16h_rep2

city: Musashimurayama-shi

first: Emi

last: Ikebe

state: Tokyo

address: 4-7-1, Gakuen

country: Japan

institute: National Institute of Infectious Diseases

hyb_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.

scan_protocol: We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.

data_processing: Data acquisition and normalization (SST-RMA) were used Affymetrix® Expression Console™ Software.

label: biotin

extract_protocol: RNeasy Mini Kit


title: 161p.NOD1.Control

city: Berlin

value: Ctr (DMSO)


title: 119p2.NOD2.5F

source_name: HeLa NOD2 cells, 4hr, replicate 3

value: ok


title: Bull1_RNA_seq_3

description: RNA-seq for Bull1


title: 164p.NOD1.Vinbl

value: HeLa

value: Vinblastine (10 µM)


title: OATL4_MK-2048_25uM_16h_rep3

label_protocol: We followed protocol of manual that is GeneChip® WT PLUS Reagent Kit User Manual.


title: 162p.NOD1.Jasp

value: Jasplanokinolid (0.2 µM)

value: phenol


title: gDNA from subject PASWTY

city: Little Rock

source_name: AML, pre-treatment

tag: group

value: tumor

tag: age at diagnosis (days)

value: Female


title: gDNA from subject PASWMP

value: Male


title: OATL4_MK-2048_25uM_16h_rep1


title: Bull1_RNA_seq_1

description: RNA-seq for Bull1


title: Bull1_RNA_seq_2

description: RNA-seq for Bull1


title: 117.NOD2.Tm

value: Tunicamycin (5 µg/mL)


title: 10_iWAT_300 ppb sodium-arsenite treated

city: Berkeley

first: Felicia

last: Castriota

address: 188 Li Ka Shing Center, Room 375E

institute: UC Berkeley

data_processing:
BGISEQ-500 instrumentation was used to perform the RNA sequencing. Primary sequencing data (raw reads) subjected to quality control (QC) to determine if resequencing step is needed.
After QC, raw reads filetered into clean reads to be aligned to the reference sequences, using Bowtie2 to mape clean reads to reference gene and HISAT to reference genome.
If alignment result passes QC, gene quantification is performed using RSEM, which quantifies maximum likelihood abundance estimates.
EBSeq method is then aopplied to detect differentially expressed genes under two biological conditions. EBSeq calculates two post-probability for each gene. EBSeq then calculates gene expression's fiold change between two groups (treatment vs control).
Gene Ontology (GO) is used as the standard gene functional classification system, filtering all GO terms that are significantly enriched in a list of differentially expressed genes (DEGs). The DEGs correspond to specific biological functions.
Pathway-analysis on KEGs is then performed using the KEGG pathway enrichment analysis. The analysis identifies significantly enriched metabolic pathways or signal transduction pathways in DEGs comparing with the whole genome background.
Supplementary_files_format_and_content: .xlsx file with gene length, average measures for treatment versus control, and log2fold ratios

source_name: iWAT_300 ppb sodium-arsenite treated

extract_protocol:
Inguinal white adipose tissues were removed, flash frozen using liquid nitrogen, and RNA was harvested. Qiagen Rneasy Lipid Tissue Mini Tissue Prep Kit (#74804) was used, with 5ng/uL of total RNA for processing.
RNA libraries were prepared for sequencing used standard approaches. The sequence was aligned with the Genome Reference Consortium Mouse Build 38 (GRCm38, mm10), generating 20M mapped reads per sample.

treatment_protocol: C57BL/6J male mice were administered drinking water prepared with either 300 ppb sodium arsenite or dH20, for a duration of 9 weeks

tag: genotype/variation

value: wild type

tag: age

value: 15 weeks

value: 300 ppb sodium-arsenite treated

tag: tissue

value: inguinal white adipose tissue


title: gDNA from subject PASWER


title: FC16_iWAT_300 ppb sodium-arsenite treated


title: 9_iWAT_300 ppb sodium-arsenite treated


title: 8_iWAT_dH2O-treated


title: 6_iWAT_dH2O-treated


title: gDNA from subject PASWPT


title: gDNA from subject PASVAN


title: LA+NTP2

city: Shanghai

first: Qinglan

address: 1200 Cailun Road

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
After filtering, clean reads are mapped to reference using HISAT/ Bowtie2 tool
Genes expression level is quantified by a software package called RSEM
Genome_build: mm10

source_name: primary hepatocyte

growth_protocol: DMEM with 10% FBS

extract_protocol: RNA was harvested using Trizol reagent.

treatment_protocol: Primary hepatocytes were pretreated with NTP for 1 h, followed by treatment with 200 uM palmitate (PA) or 12 uM linoleate (LA) for an additional 24 h.

tag: cell type

value: hepatocyte


title: 116.NOD2.AnisoM

address: Charitéplatz 1

value: Anisomycin (1 µM)


title: gDNA from subject PASVTP

address: 1 Children's Way, #512-10

tag: gender


title: OATL4_DMSO_16h_rep3

value: DMSO 16h


title: 118.NOD2.Tg

value: Thapsigargin (5 µM)


title: 4_iWAT_dH2O-treated

tag: strain


title: gDNA from subject PASUUP


title: 114.NOD2.Lov

value: Lovastatin (30 µM)

value: ok


title: OATL4_DMSO_16h_rep2


title: gDNA from subject PARXJW


title: LA+NTP1


title: 112.NOD2.2MC

value: HeLa


title: ED_DMSO_16h_rep2

value: ED


title: LA2


title: 110.NOD2.CCCP

value: CCCP (5 µM)


title: ED_MK-2048_25uM_16h_rep2


title: LA1


title: 108.NOD2.Etop

value: Etoposide (5 µM)


title: ED_MK-2048_25uM_16h_rep3


title: OATL4_DMSO_16h_rep1


title: PA+NTP2


title: 105p.NOD2.CHX

value: Cycloheximide (50 µM)

value: phenol


title: PA+NTP1


title: ED_DMSO_16h_rep3


title: 115.NOD2.BFA

value: BrefeldinA (0.2 µg/mL)


title: PA2


title: KK1_MK-2048_25uM_16h_rep2


title: ED_DMSO_16h_rep1


title: PA1


title: KK1_MK-2048_25uM_16h_rep1


title: 109.NOD2.Actin

value: Actinonin (50 µM)


title: 113.NOD2.LB42708


title: 106.NOD2.Nocad

value: Nocadazole (10 µM)


title: 111.NOD2.2BP


title: 103.NOD2.CytoD

value: Cytoclasin D (5 µM)


title: gDNA from subject PASTXM

value: tumor

value: Female


title: 104.NOD2.Vinbl

value: Vinblastine (10 µM)


title: 102.NOD2.Jasp

value: Jasplanokinolid (0.2 µM)


title: ED_MK-2048_25uM_16h_rep1


title: KK1_DMSO_16h_rep3

value: DMSO 16h


title: Vehicle2

value: hepatocyte


title: gDNA from subject PASTWE

value: Male


title: KK1_DMSO_16h_rep1


title: KK1_MK-2048_25uM_16h_rep3


title: Crypts_VEMD8

city: xiamen

first: hongda

last: li

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District, Xiamen, Fujian Province, China

institute: Xiamen University

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 sequencer or illumina X-TEN sequencer.
Clean reads were mapped onto the mouse genome (GRCm38/mm10) using hisat2 to obtain the aligned bam files.
The mouse ERVs annotation file was generated by RepeatMasker v4.0.7 comparing with Repbase consensus sequences (Edition-20181026)
The overlap reads for ERVs were summarized by featureCounts  and then quantified by EdgeR  with the Benjamini-Hochberg corrected p-value <0.05.
Genome_build: mm10

source_name: intestines

extract_protocol:
Crypts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries(WT, VEDM2, VEMD3, VEMD4, VEMD6, VEMD8) were prepared for sequencing using standard BGI-500 protocols. Besides this, purified total RNA from ISC cells isolated from Lgr5–EGFP–ires–CreERT2-mice was quantified by Qubit(invitrogen) and analyzed by an Agilent Bioanalyzer to evaluate RNA quality. rRNA-depleted was used to generate the cDNA library. cDNA library construction and sequencing were prepared for using illumina Hiseq X-TEN protocol.

treatment_protocol: For activation of CreERT2 mediated recombination, 8-10 weeks old Villin-CreERT2 mice and WT littermates were received one dose of tamoxifen (800 mg/kg) by gavage and harvested sacrificed as indicated in each figure. 8-10 weeks old Lgr5-EGFP-IRES-CreERT2;Setdb1fl/fl mice were received 200mg/kg tamoxifen every day for consecutive 3 days.

value: crypts

value: post natal 8 weeks

tag: genotype

value: setdb1 iIEC-KO


title: gDNA from subject PASTVM


title: 98p.NOD1.Tg

source_name: HeLa NOD1 cells, 4hr, replicate 3

value: HeLa

value: Thapsigargin (5 µM)


title: gDNA from subject PASTHA


title: SLB-1_MK-2048_25uM_16h_rep3


title: Crypts_VEMD6


title: 99p2.NOD1.5F

value: phenol


title: Vehicle1


title: KK1_DMSO_16h_rep2


title: Crypts_VEMD4


title: 97.NOD1.Tm

value: Tunicamycin (5 µg/mL)

value: ok


title: SLB-1_DMSO_16h_rep3


title: Crypts_VEMD2


title: 96.NOD1.AnisoM

value: Anisomycin (1 µM)


title: SCs from DPN rat7 [T7]

city: Wuhan

first: cheng

address: No. 1277 Jiefang Avenue

department: Union Hospital of Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
Illumina Xten software used for basecalling.
Transcriptome sequencing uses high-throughput sequencing technology to sequence the cDNA after total RNA reverse transcription, and obtains most transcripts of samples in this state.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome and FPKM were calculated using StringTie（Pertea et al., 2016)
Genome_build: rn6
Supplementary_files_format_and_content: FPKM values and counts.

organism: Rattus norvegicus

source_name: SCs from DPN

extract_protocol:
Schwann cell samples were randomly selected from control groups (n = 3) and diabetic groups (n = 3), rinsed with PBS twice and total RNA was isolated by using miRNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: Sprague-Dawley rats

tag: model

value: diabetic peripheral neuropathy (DPN) model

value: sciatic nerve

value: Schwann cells


title: SCs from DPN rat2 [T2]


title: SCs from DPN rat4 [T4]


title: gDNA from subject PASYJL

value: tumor


title: 93.NOD1.LB42708

tag: cell line


title: SCs from control rat10 [C10]

source_name: SCs from control

value: control rat


title: SCs from control rat6 [C6]


title: SLB-1_MK-2048_25uM_16h_rep2


title: CD44KO-Con

city: Chuncheon-si

first: Yoon Mee

last: Yang

state: Gangwon-do

address: 1 Kangwondaehak-gil

department: Pharmacy

country: South Korea

institute: Kangwon National University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using version 2.2.5 with parameters--phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Fragments Per Kilobase Million(FPKM) were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample.

source_name: Hepatic stellate cell

growth_protocol: Primary hepatic stellate cells were isolated from male wild-type, TLR4-/-, and CD44-/- mice. After, the isolated primary hepatic stellate cells were incubated in DMEM medium containing 10% FBS, and supplemented with Antibiotic-Antimycotic for 3 days, serum was deprived for 24 hr.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and purified using RNA isolation kit (Macherey-Nagel). Beijing Genomics Institute (BG) (Beijing, China) performed the RNA sequencing.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

treatment_protocol: 24-week-old male wild-type, TLR4-/-, and CD44-/- mice were used. All procedures were approvd by the Institutional Animal Care and Use Committee at Cedars-Sinai Medical Center. Hepatic stellate cells were isolated from the mice in a 2-step process: collagenase-pronase perfusion of mouse livers followed by Nycodenz 2-layer discontinuous density gradient centrifugation. We further depleted contaminated liver macrophages by magnetic antibody cell sorting (Miltenyi Biotec) using Cd11b-conjugated microbeads (Miltenyi Biotec).

tag: cell

value: Primary hepatic stellate cell


title: 91.NOD1.2BP

treatment_protocol: After doxycycline treatment, medium was replaced with fresh DMEM full medium. Then HeLa NOD1 or NOD2 cells were treated with various stimuli for 4 hrs.


title: gDNA from subject PASWAJ

treatment_protocol: Diagnostic (presentation) bone marrow or peripheral blood specimens were collected from patients prior to induction therapy. Additional genomic data types and clinical covariates are available for these specimens under the TARGET-AML study (phs000465), available through the database of genotypes and phenotypes (dbGaP) and the NCI Genomic Data Commons (GDC).

value: Female


title: SLB-1_MK-2048_25uM_16h_rep1


title: TLR4KO-Con


title: 92p.NOD1.2MC


title: WT-Con

value: wild-type


title: 90.NOD1.CCCP

value: CCCP (5 µM)


title: 94.NOD1.Lov

value: Lovastatin (30 µM)


title: 88.NOD1.Etop

value: HeLa

value: Etoposide (5 µM)


title: Crypts_VEMD3

value: crypts

value: post natal 8 weeks

value: setdb1 iIEC-KO


title: SCs from control rat5 [C5]


title: Crypts_WT


title: gDNA from subject PASWWD


title: 89.NOD1.Actin

value: Actinonin (50 µM)

value: ok


title: gDNA from subject PASPGA


title: 87.NOD1.Nig

value: Nigericin (5 µM)


title: 86.NOD1.Nocad

value: Nocadazole (10 µM)


title: Day1_Tg6

growth_protocol: Primary hepatic stellate cells were isolated from male aSMA-HAS2 Tg and HSC-specific Has2 knockout mice. The isolated primary hepatic stellate cells were incubated in DMEM medium containing 10% FBS, and supplemented with Antibiotic-Antimycotic for 4 hr. After cell attachment, the culture media was refreshed and incubated for another 14 hr.

treatment_protocol: 24-week-old male ASMA-human HAS2 transgenic mice and hepatic stellate cell-specific Has2 knockout mice generated by the Lrat-Cre/loxP system were used. All procedures were approvd by the Institutional Animal Care and Use Committee at Cedars-Sinai Medical Center. Hepatic stellate cells were isolated from the mice in a 2-step process: collagenase-pronase perfusion of mouse livers followed by Nycodenz 2-layer discontinuous density gradient centrifugation. We further depleted contaminated liver macrophages by magnetic antibody cell sorting (Miltenyi Biotec) using Cd11b-conjugated microbeads (Miltenyi Biotec).

value: ASMA-HAS2 Tg


title: Day1_Tg5


title: Day1_Tg4


title: Day1_KO7

value: HSC-specific Has2 KO


title: 84.NOD1.Vinbl

growth_protocol: HeLa inducible NOD1 or NOD2 cells were grown in DMEM medium supplemented with 10% FBS, 1mM Sodium Pyruvate and 2mM L-Glutamine overnight. To induce NOD1 or NOD2 expression, HeLa NOD1 or NOD2 cells were treated in absence or presence of 0.5 µg/mL or 0.25 µg/mL doxycyclin overnight, respectively.

value: Vinblastine (10 µM)


title: Transgenic line LCY3 (cv Money Maker) biological replicate 2 Breaker+10 stage

city: Rome

first: sarah

last: frusciante

address: Via Anguillarese 301

country: Italy

institute: ENEA Italian National Agency for New Technologies, Energy and Sustainable Development

description: not applicable

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit. It contains mix for target dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. Targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes incubated at 45 °C for 5 minutes and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® Eu-TOM3 (custom exon) was then hybridized with each biotin-labeled sense target. Hybridizations were performed for 16 h at 45 °C in a rotisserie oven. GeneChip® cartridges were washed and stained with GeneChip® Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0001 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 72 mixes/cycle with Wash Buffer A at 30 °C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50 °C; (3) stain of the probe array for 5 min in SAPE solution at 35 °C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30 °C; (5) stain of the probe array for 5 min in antibody solution at 35 °C; (6) stain of the probe array for 5 min in SAPE solution at 35 °C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35 °C; (8) fill the probe array with Array Holding buffer.

scan_protocol: Image acquisition, processing: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner3000 7G using default parameters.

data_processing:
Data were processed using RobiNA v2.0 software. Normalization method: rma; P-value correction method: fdr; Multiple testing strategy: global; P-value cut-off value for significant differential expression: 0.05; Genes that showed a log2-fold change smaller than two ignored: yes
probe group file: eutom3gene_v2_ucprobes
meta-probeset file: EUTOM3_funcion_GO.tsv

organism: Solanum lycopersicum

source_name: transgenic line mature fruit

label_protocol: Biotin-labeled cDNA targets were synthesized starting from 150 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with Ambion® WT Expression Kit (Ambion, Austin, TX). The sense strand cDNA was synthesized with the same kit, then it was fragmented and labeled with Affymetrix GeneChip® WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Plants were grown in a greenhouse under a long photoperiod (16-h light/24°C and 8-h dark/20°C) and irradiance (150 mmol m22 s21). Fruit were labeled at the Mature Green stage of ripening and collected at Mature Green, Breaker and 10 days later Breaker. Pericarps was frozen in liquid nitrogen and stored at -80°C for subsequent analyses.

extract_protocol: Briefly, total RNA isolation was performed using a Tris-Borate/phenol-chloroformisoamyl alcohol 25:24:1-based extraction followed by Potassium Acetate/Lithium Chloride/Sodium Chloride precipitation steps (Lopez-Gomez and Gomez-Lim, 1992) and DNAse I purification at 37°C for 20’. RNA quality was determined by using a Nanodrop ND-1000 (NanoDrop Technologies) and an Agilent 2100 Bioanalyzer: only RNAs showing A260/A280 and A260/230 ratios between, respectively, 1.8-2.0 and 2.0-2.2 and with a 28S/18S ratio between 1.5 and 2.0 were selected.

tag: Stage

value: breaker+10 stage

value: pericarp


title: Transgenic line LCY3 (cv Money Maker) biological replicate 3 Breaker+10 stage

description: not applicable


title: 85.NOD1.CHX

tag: inducible gene

value: Cycloheximide (50 µM)


title: gDNA from subject PASJEJ

value: tumor

value: Male


title: 83.NOD1.CytoD

value: HeLa

tag: treatment

value: Cytoclasin D (5 µM)


title: Transgenic line LCY1 (cv Money Maker) biological replicate 1 Breaker+10 stage

description: not applicable


title: gDNA from subject PASKFN


title: taur 3866 3

city: Memphis

first: Richard

middle: E

last: Lee

state: Tennessee

address: 262 Danny Thomas Place

department: Chemical Biology and Therapeutics

institute: St. Jude Children's Research Hospital

data_processing:
Ribosomal RNA sequences filtered out using BBDuk {https://jgi.doe.gov/data-and-tools/bbtools/}
Reads aligned to the reference Escherichia coli str. K-12 substr. MG1655 genome (NCBI) using Rockhopper {23716638} to generate the gene counts
DESeq2 analysis package {25516281} in the R statistical computing environment used for differential gene expression analysis
Genome_build: GenBank: U00096.3
Supplementary_files_format_and_content: CSV format containing locus tag and read count

organism: Escherichia coli

source_name: ATCC 2511 broth_taurine_TAT

growth_protocol: For each of three bioreplicates, a single colony of Escherichia coli K12 MG1655 was used to inoculate an overnight culture in either ATCC 2511 broth (M9) or the ATCC 2511 media with a molar equivalent of magnesium chloride used to replace magnesium sulfate and taurine used to as the sole sulfur source (M9T). The next day, overnight cultures were diluted 1:100 into fresh M9 or M9T.  The cultures were allowed to reach a mid-log OD600 and then treated.

extract_protocol:
10 mL RNAprotect Bacteria Reagent was immediately added and mixed with the drugged cultures and pelleted at 5,000XG for 10 minutes.  The supernatant was discarded and the pellets were flash frozen.  For RNA extraction, pellets of E. coli K12 were re-suspended in 100 µL of 1 mg/mL lysozyme and incubated at 37°C for 10 minutes with 5 seconds vortex every 2 minutes. Subsequent steps were carried out using the RNeasy extraction kit (Qiagen) according to protocol. RNA was eluted in 40-50 µL of supplied elution buffer. Residual genomic DNA contamination was depleted using RNA Clean and Concentrator kit (Zymo Research) following the manufacture’s protocol. Samples were eluted in 50 µL of DNase/Rnase-Free water. Quality of RNA samples were measured using an Agilent 2100 Bioanalyzer and RIN values were all > 7.0.
ScriptSeq™ v2 RNA-Seq Library Preparation Kit, standard protocol.

treatment_protocol: 50 μL of either DMSO or 50 μL of 1.56 mg/mL 2-((1H-1,2,3-triazol-4-yl)thio)-N-(2-fluorophenyl)acetamide was added to a 50 mL conical tube.  When E. coli cultures reached mid-log, 5 mL of culture was added to each tube and allowed to incubate with shaking at 37°C and 225 RPM.

tag: media

value: ATCC 2511 modified to have taurine as the sole sulfur source

value: 15.6 μg/mL 2-((1H-1,2,3-triazol-4-yl)thio)-N-(2-fluorophenyl)acetamide in 1% DMSO


title: 81p.NOD1.Control

value: Ctr (DMSO)

tag: sample purification

value: phenol


title: taur 3866 2


title: gDNA from subject PASFWI

tag: group

tag: age at diagnosis (days)

value: Female


title: Transgenic line LCY1 (cv Money Maker) biological replicate 2 Breaker+10 stage

description: not applicable

tag: genotype/variation


title: 79p.NOD2.5F

source_name: HeLa NOD2 cells, 4hr, replicate 2


title: taur 3866 1


title: 82.NOD1.Jasp

value: Jasplanokinolid (0.2 µM)

value: ok


title: Transgenic line LCY1 (cv Money Maker) biological replicate 3 Breaker+10 stage

description: not applicable

tag: tissue


title: Wild type (cv Money Maker)  biological replicate 3 Breaker+10 stage

description: not applicable

source_name: wild type mature fruit

value: wild type


title: M9 3866 3

source_name: ATCC 2511 broth_TAT

value: ATCC 2511 broth


title: 80.NOD2.6G


title: 78.NOD2.Tg

value: Thapsigargin (5 µM)


title: Transgenic line LCY3 (cv Money Maker) biological replicate 3 Breaker stage

description: not applicable

source_name: transgenic line breaker stage

value: breaker stage


title: Wild type (cv Money Maker)  biological replicate 2 Breaker+10 stage

description: not applicable

value: breaker+10 stage

value: pericarp


title: 77.NOD2.Tm

value: Tunicamycin (5 µg/mL)


title: Wild type (cv Money Maker) biological replicate 1 Breaker+10 stage

description: not applicable


title: gDNA from subject PARWXU

value: tumor

value: Male


title: 76.NOD2.AnisoM

value: HeLa

value: Anisomycin (1 µM)


title: gDNA from subject PARUTH


title: gDNA from subject PARUSN


title: M9 3866 1

value: 15.6 μg/mL 2-((1H-1,2,3-triazol-4-yl)thio)-N-(2-fluorophenyl)acetamide in 1% DMSO


title: M9 3866 2


title: Transgenic line LCY3 (cv Money Maker) biological replicate 2 Breaker stage

description: not applicable


title: taur 2

source_name: ATCC 2511 broth_taurine_DMSO

value: ATCC 2511 modified to have taurine as the sole sulfur source

value: 1% DMSO


title: gDNA from subject PARPVZ

value: Female


title: 75p.NOD2.BFA

value: BrefeldinA (0.2 µg/mL)

value: phenol


title: taur 1


title: 73.NOD2.LB42708

value: ok


title: M9 3

source_name: ATCC 2511 broth_DMSO

value: ATCC 2511 broth


title: gDNA from subject PARMME


title: gDNA from subject PASDGX


title: Transgenic line LCY1 (cv Money Maker) biological replicate 2 Breaker stage

description: not applicable


title: 74.NOD2.Lov

value: Lovastatin (30 µM)


title: Transgenic line LCY1 (cv Money Maker) biological replicate 1 Breaker stage

description: not applicable

value: breaker stage


title: M9 2


title: Transgenic line LCY1 (cv Money Maker) biological replicate 3 Breaker stage

description: not applicable


title: 71.NOD2.2BP