title: Volatiles_treated replicate 4

city: Campinas

first: Juliana

last: Oliveira

state: São Paulo

address: Giuseppe Máximo Scolfaro, 10.000

department: Brazilian Biorenewables National Laboratory (LNBR)

country: Brazil

institute: National Center for Research in Energy and Materials (CNPEM)

data_processing:
bcl2fastq-v2.18.0.12 was used for basecalling.
Low quality reads and adaptors were removed by Trimmomatic v 0.36 with SLIDINGWINDOW:4:15 MINLEN:50 parameters
Good quality reads were mapped against Thielaviopsis ethacetica genome by Hisat2 v. 2.0.4 with --rna-strandness RF parameter
GTF annotation file of the reference genome was generated by BRAKER v. 1.9 using the aligned reads as evidence of expression
Transcripts expression was obtained using featureCounts command from the R package Rsubread v. 1.16.1 with BAM files and GTF files generated in the previous steps as inputs. The following parameters were used: requireBothEndsMapped=FALSE checkFragLength=TRUE minFragLength=50 maxFragLength=800 strandSpecific=2 minMQS=0 readExtension5=0 readExtension3=0 minReadOverlap=1 countSplitAlignmentsOnly=FALSE countMultiMappingReads=FALSE countPrimaryAlignmentsOnly=FALSE countChimericFragments=FALSE ignoreDup=FALSE)
DESeq2 v. 1.6.3 was used to perform differential expression analysis. Transcripts with adjusted p-value < 0.05 and log2 fold-change > 1 or < -1 were considered as differentially expressed.
Genome_build: Thielaviopsis ethacetica (GCA_001599055)
Supplementary_files_format_and_content: Matrix table with raw counts for every transcript and sample
Supplementary_files_format_and_content: Matrix table with counts normalized by DESeq2 for every transcript and every sample
Supplementary_files_format_and_content: Table containing the results of differentially expressed transcripts obtained with DESeq2

organism: Thielaviopsis ethacetica

source_name: Phytopathogenic fungus

growth_protocol: Divided Petri dishes were used, where 100 µL of the antagonist (5x108 CFU/mL) were inoculated in one compartment  and five 1.5 mL Eppendorf tubes containing liquid MEX medium and 2x105 spores of T. ethacetica in a final volume of 200 µL were placed in the other compartment. For the control condition, plates without bacterial inocculum. The sealed plates were incubated at 28°C for two days.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen) according to manufacturer’s instructions.
The libraries were prepared using the TruSeq Stranded mRNA Sample Prep LS Kit (Illumina) according to manufacturer’s protocol and sequenced on the Illumina HiSeq 2500.

treatment_protocol: 4 replicates treated with bacterial VOCs

tag: treatment

tag: disease related

value: Sugarcane pineapple sett rot

tag: isolation site

value: Sertãozinho - SP


title: FFM_35

status: Public on Jul 22 2021

type: genomic

city: Frankfurt am Main

first: Patrick

middle: Nikolaus

last: Harter

address: Heinrich-Hoffmann Strasse 7

department: Edinger Institute

country: Germany

institute: Goethe University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing: Statistical analysis was performed using RnBeads software package, Methylation data was normalized using the “dasen” method from the wateRmelon R-package, deconvolution was performed using MeDeCom and MethylCIBERSORT

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: melanoma skin metastasis

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell FFPE DNA Purification Kit according to the manufacturer’s instructions.

tag: tissue

value: melanoma

tag: gender

value: male

tag: age

tag: brafmut (1 yes, 0 no)

tag: nrasmut (1 yes, 0 no)

tag: localization

value: Skin metastasis

tag: brain metastasis (1 yes, 0 no)

tag: tissue in relation to ici treatment

value: pre-ICI

tag: ici response (dc disease control, pd progressive disease, unk unknown)

value: PD


title: w1118_embryo_2_2.5h_rep_1

type: SRA

city: Cambridge

first: Martin

middle: Heinrich

last: Fabry

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson Way

department: Cancer Research UK, Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description: w1118_embryo_2_2.5h_rep_1 mRNA-Seq

library_source: transcriptomic

data_processing: Raw fastq files contained 50bp reads. The first and the last two bases of all reads were trimmed using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/). Reads from small RNA-Seq libraries were adapter clipped using fastx_clipper with settings -Q33 -l 15 -a AGATCGGAAGAGCACACGTCT. The first and last 4 bases of adapter clipped reads were trimmed using seqtk trimfq (https://github.com/lh3/seqtk). Reads were first aligned to the consensus sequence for all Drosophila melanogaster transposons using STAR (Dobin et al., 2013) allowing random allocation of multimappers. Unmapped reads were further uniquely aligned to Drosophila melanogaster genome release 6 (dm6). Generated bam files for RNA-Seq were split in reads originating from sense and antisense genomic strands using samtools view options -f 0x10 and -F 0x10 for sense and antisense reads respectively (Li et al., 2009). Indexes were generated using samtools index function. Coverage files were generated using bamCoverage with normalisation mode --normalizeUsing CPM (Ramirez et al., 2014) and applying a scaling factor (-- ScaleFactor). Scaling factors for individual files were calculated by dividing the sum of mapped reads contained in the file by the sum of all transposon and dm6 mapping reads of the corresponding library. Reads mapping to protein-coding genes were counted with htseq (Anders et al., 2015) using a feature file downloaded from Ensembl (https://www.ensembl.org/Drosophila_melanogaster/Info/Index). Reads mapping to individual transposons were counted with a custom script using samtools idxstats function to extract reads mapping to individual sequences of the reference genome/transposon consensus sequence. Count files generated as described above were normalised to reads per million (RPM) and plotted using ggplot2 (Wickham, 2016). Bar graphs displaying transposon expression profiles and heatmap during embryogenesis were calculated from collapsed replicates. Bar graphs and heatmaps were plotted using ggplot2 in R. Differential expression analysis was performed using DeSeq2 (Love et al., 2014). Metaplots flanking euchromatic transposon insertion sites were calculated using deepTools2?s computeMatrix scale-region function with bin size 10.

molecule: total RNA

organism: Drosophila melanogaster

source_name: embryo

growth_protocol: Flies were kept and grown at 25°C

extract_protocol:
RNA for mRNA-Seq and qRT-PCR experiments was isolated using the RNeasy Mini kit (Qiagen) with on-column DNA digestion (RNase-free DNase Set, Qiagen) according to the manufacturer’s recommendations.
NEBNext Poly(A) mRNA magnetic Isolation Module (NEB), followed by NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB)

treatment_protocol: Treatment of embryos for auxin-induced degradation:Embryos were collected for 1h and dechorionated. Control embryos were transferred into a fine mesh strainer placed in a plastic dish and submerged in PBS. 1M auxin solution was generated by diluting Indole-3-acetic acid (IAA) in water and stored at -20°C protected from light. Auxin-treated embryos were submerged in PBS with indicated auxin concentrations. Embryos were placed at 25°C for appropriate times and harvested for RNA experiments by transferring into 1ml Trizol followed by RNA extraction. Embryos used for ChIP-Seq were processed as described above.

tag: strain

value: embryo

tag: time after egg laying

tag: replicate number

tag: experiment

value: mRNA-Seq


title: w1118_embryo_0_2h_rep_2

description: w1118_embryo_0_2h_rep_2 mRNA-Seq


title: siHAND1_3

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
Illumina bcl2fastq (v2.17.14) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.15) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
HTSeq (v0.9.1) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
To normalized read counts, R (v3.6.1) and its package DESeq2 (v1.24.0) were performed.
For day 20 ventricular iRFP670+ subpopulations ex3 samples, two files after STAR mapping were combined to obtain enough reads.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file including DESeq2 nomalized count values for each sample.

source_name: siRNA transfected cardiomyotes derived from hiPSC

growth_protocol: For the standard ventricular protocol, on day 0, hiPSCs were aggregated and made into embryonic bodies (EBs) with 10 µM Y-27632 and 2 ng/ml BMP4 in each well of a 96-well plate coated with HEMA (Poly(2-hydroxyethyl methacrylate)) (2 × 10^4 cells/well). On day 1, cardiac mesoderm cells were induced by treatment with 18 ng/ml BMP4, 12 ng/ml Activin A and 10 ng/ml bFGF for 48 hours. On day 3, the EBs were dissociated and re-aggregated with day 3 medium: 10 ng/ml VEGF and 1 µM IWP-3 (8 × 10^4 cells/well). After day 7, the EBs were cultured with maintenance medium including 5 ng/ml VEGF in each well of a 6-well plate coated with HEMA until day 19. The EBs were incubated at 37℃ in a CO2 incubator (5% O2) from day 0 to day 12.   For the atrial differentiation, a standard protocol was followed except 0.5 µM all trans retinoic acid was appended to day 3 medium.

extract_protocol:
RNeasy Mini Kit / RNeasy micro kit
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold

tag: subpopulation

value: isolated iRFP670+

tag: differentiation protocol

value: Ventricular protocol, siRNA transfected

tag: day

value: Day 20


title: FFM_31

value: female

value: post-ICI


title: w1118_embryo_4_5h_rep_2

description: w1118_embryo_4_5h_rep_2 mRNA-Seq


title: Volatiles_treated replicate 3

molecule: polyA RNA

tag: treatment

tag: disease related

tag: isolation site


title: siLEF1_3


title: siHAND2_3


title: w1118_embryo_0_2h_rep_1

description: w1118_embryo_0_2h_rep_1 mRNA-Seq

tag: tissue


title: siNC_3


title: siLEF1_2


title: FFM_27

tag: gender

tag: age

tag: brafmut (1 yes, 0 no)

value: DC


title: IL18Rαhi-4

city: Goyang-si

first: Chungyong

last: Han

state: Gyeonggi-do

address: 323 Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National Cancer Center

data_processing:
Low quality reads were filtered according to the following criteria: reads containing more than 10% of skipped bases (marked as ‘N’s), reads containing more than 40% of bases whose quality scores were less than 20, and reads with average quality score less than 20.
The filtered reads were mapped to the reference genome related to Mus musculus using the aligner TopHat.
Gene expression level was determined using Cufflinks v2.1.1 of the gene annotation database of the species. To improve the accuracy of the measurement, multi-read-correction and frag-bias-correct options were applied. All other options were set to default values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files that includes FPKM values of all samples

organism: Mus musculus

source_name: CD8+ T cells

growth_protocol: On day 0, six- to eight-week-old C57BL/6 female mice were intradermally inoculated with B16F10 (2E+05). On day 3, pre-conditioning lymphodepletion was induced via intraperitoneal injection of 300 mg/kg cyclophosphamide. On day 5, Pmel-1 cells (2E+06) were isolated from the splenocytes of Thy1.1 Pmel-1 transgenic mice (Thy1a/Cy Tg(TcraTcrb)8Rest/J; expressing transgenic TCR specific for gp10025–33 and congenic Thy1.1 antigen) and injected into tumor-bearing mice. Starting on day 5, recombinant human IL-2 (10,000 IU) was intraperitoneally injected daily for 3 days. Starting from day 10, anti-CD4 treatment group involved weekly intraperitoneal injections of 200 μg anti-mouse CD4 monoclonal antibody (clone: GK1.5) for 3 weeks.

extract_protocol:
Total RNA was extracted from the isolated cells using Trizol reagent.
cDNA libraries were prepared for 150 bp paired-end sequencing using TruSeq Stranded mRNA sample preparation kit. In brief, the mRNA molecules were purified and fragmented from 1 μg total RNA using oligo (dT) magnetic beads. The fragmented mRNAs were synthesized as single-stranded cDNAs using random hexamer primers. Double-stranded cDNA was prepared using this as a template for second strand synthesis. After sequential end repair, A-tailing, and adapter ligation, the cDNA libraries were amplified via PCR. The quality of these cDNA libraries was evaluated using the Agilent 2100 BioAnalyzer and they were quantified using the KAPA library quantification kit according to the manufacturer’s protocol.

treatment_protocol: Four mice were used in the analysis. On day 25, the lymph nodes and spleen were gently disrupted and filtered through a 40 μm nylon cell strainer to make single-cell suspensions. Cells were treated with RBC lysis buffer before use. For each mice, Thy1.1-negative endogenous CD8+ T cells were isolated from the lymphoid cells with a CD8 isolation kit and Thy1.1 microbeads. Then, the IL-18Rαhi-enriched cells were positively selected with PE-labeled IL-18Rα antibody and PE microbeads. The cells that passed through the column were collected and used as a control for comparison with IL-18Rαhi-enriched cells.

value: Female

value: Six- to eight-week-old

value: Inguinal lymph nodes and spleen


title: FFM_29

tag: nrasmut (1 yes, 0 no)

tag: localization

tag: brain metastasis (1 yes, 0 no)


title: FFM_30

tag: tissue in relation to ici treatment

tag: ici response (dc disease control, pd progressive disease, unk unknown)


title: Volatiles_treated replicate 2

tag: strain

value: Sugarcane pineapple sett rot

value: Sertãozinho - SP


title: Volatiles_treated replicate 1


title: siHAND2_2


title: Control replicate 4

value: untreated


title: FFM_23

value: melanoma

value: male

value: Skin metastasis


title: IL18Rαhi-2


title: FFM_28

value: pre-ICI

value: PD


title: w1118_embryo_3_4h_rep_1

description: w1118_embryo_3_4h_rep_1 mRNA-Seq

value: embryo

tag: time after egg laying

tag: replicate number

tag: experiment

value: mRNA-Seq


title: siHAND1_2

tag: subpopulation

value: isolated iRFP670+

tag: differentiation protocol

value: Ventricular protocol, siRNA transfected

tag: day

value: Day 20


title: Control replicate 3

tag: treatment

tag: disease related

tag: isolation site


title: siNC_2


title: IL18Rαhi-1

tag: gender

tag: age

tag: tissue


title: Control-4

description: IL18Rαhi-depleted flowthrough-4


title: siLEF1_1


title: Control-3

description: IL18Rαhi-depleted flowthrough-3


title: Control replicate 1


title: siHAND1_4


title: Control replicate 2


title: GR+FABP4_dex_rep4

city: Parkville

first: Michelle

middle: L

last: Halls

state: VIC

address: 399 Royal Parade

department: Drug Discovery Biology

country: Australia

institute: Monash Institute of Pharmaceutical Sciences, Monash University

data_processing:
BGI used the DNBseq platform for basecalling
Reads mapped to rRNA and low-quality reads were removed. Clean reads were mapped to the reference genome using Bowtie2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated
Genome_build: Ensembl chlorocebus sabaeus (ChlSab1.1) release 99
Supplementary_files_format_and_content: Excel files contain FPKM values for each sample

organism: Chlorocebus sabaeus

source_name: COS-7 cells

growth_protocol: COS-7 cells were cultured in Dulbecco's modified Eagle's medium with 4 mM glutamine, 100 units/mL penicillin, 100 mg/mL streptomycin, and 10% (v/v) fetal bovine serum in a 95% air, 5% CO2 atmosphere at 37 °C. For transfections, cells were seeded into 6-well plates at a density of 2×10^5 cells/well in culture medium devoid of antibiotics. Transfections were carried out using X-tremeGENE 9 DNA transfection reagent according to the manufacturer's protocol. COS-7 cells were co-transfected with 0.1 μg of GR plasmid DNA and 0.6 μg of either empty vector (pSG5), FABP1 or FABP4 plasmid DNA in 6-well plates.

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen).
Transcriptome sequencing and bioinformatic analysis was performed by the Beijing Genomics Institute (BGI).

treatment_protocol: Twenty-four hours following transfection, cells were treated with vehicle (0.1% v/v DMSO) or 10 μM dexamethasone for 24 h.

tag: cell line

tag: transfection

value: glucocorticoid receptor and FABP4

value: 10 μM dexamethasone for 24 h

tag: biological repeat

value: experiment 4


title: siHAND2_1


title: Control-2

description: IL18Rαhi-depleted flowthrough-2

value: Female

value: Six- to eight-week-old

value: Inguinal lymph nodes and spleen


title: FFM_24

tag: brafmut (1 yes, 0 no)

tag: nrasmut (1 yes, 0 no)

tag: localization

tag: brain metastasis (1 yes, 0 no)

tag: tissue in relation to ici treatment

value: post-ICI

tag: ici response (dc disease control, pd progressive disease, unk unknown)

value: DC


title: FFM_25

value: melanoma

value: male


title: siHAND1_1

tag: subpopulation

tag: differentiation protocol


title: GR+FABP4_dex_rep3

tag: treatment

value: experiment 3


title: FFM_26

value: Skin metastasis

value: pre-ICI


title: Control-1

description: IL18Rαhi-depleted flowthrough-1

tag: strain


title: GR+FABP4_dex_rep2

value: experiment 2


title: Day0_3

source_name: Cells differentiated into cardimyocyts on day 0 from hiPSC

value: bulk

value: Ventricular protocol

tag: day

value: Day 0


title: FFM_22

tag: gender

value: PD


title: MeRIP-seq_GFP-IP-D4

city: Guangzhou City

first: Shujuan

last: Xie

state: China

country: China

institute: The Third Affiliated Hospital,Sun Yat-Sen University

data_processing:
Library strategy: MeRIP-Seq
The raw data (raw reads)were filtered by removing the joints at both ends of the reads and removing the fragment length <17nt;
Clean reads were compared with the reference genome (mm10) to obtain the distribution map of whole-genome reads.
Clean reads were classified and annotated for mRNA and ncRNA classification, and differential expression was analyzed between samples
For the m6A modification, R package exomePeak was used to identify significant m6A peaks and differential peaks.IGV software and HOMER were used for de novo motif discovery based on top 1k most-enrichment peaks.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: bw
Supplementary_files_format_and_content: log2FoldChange

source_name: GFP-overexpressing C2C12

growth_protocol: C2C12 cells were cultured in growth medium (GM), which consisted of Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum , 100 U/ml penicillin, and 100 ug/ml streptomycin (1×penicillin–streptomycin).When  cells grow up to about 90% confluency, the GM was subsequently replaced with differentiation medium (DM), which was DMEM containing 2% horse serum.

extract_protocol:
Total RNA was extracted from C2C12 cellswith TRIzol reagent according to the manufacturer’s instruction.
The total RNA or m6A-specific antibody immunoprecipated RNA fragments of the samples were extracted and connected to the 3-terminal and 5-terminal joints first and then reverse-transcribed into cDNA. PCR amplification was carried out and then the gel was cut to recover the target fragment library. Computer sequencing was performed on the library that passed the quality inspection

tag: time point


title: FFM_21

tag: tissue

tag: age


title: IL18Rαhi-3


title: GR+FABP4_dex_rep1

tag: cell line

tag: transfection

value: glucocorticoid receptor and FABP4

value: 10 μM dexamethasone for 24 h

value: experiment 1


title: siNC_1

value: isolated iRFP670+

value: Ventricular protocol, siRNA transfected

value: Day 20


title: Day0_2


title: GR+FABP4_vehicle_rep4

value: vehicle (0.1% v/v DMSO) for 24 h

tag: biological repeat

value: experiment 4


title: MeRIP-seq_GFP-IP-D0


title: Day0_1


title: FFM_20

value: melanoma

value: male

tag: brafmut (1 yes, 0 no)

tag: nrasmut (1 yes, 0 no)

value: DC


title: Day9_iRFP_Positive_2

source_name: Cells differentiated into cardimyocyts on day 9 from hiPSC

value: Day 9


title: MeRIP-seq_GFP-Input-D0


title: FFM_18

tag: localization

value: Skin metastasis

tag: brain metastasis (1 yes, 0 no)

value: pre-ICI


title: FFM_19

value: female

tag: tissue in relation to ici treatment

tag: ici response (dc disease control, pd progressive disease, unk unknown)


title: GR+FABP4_vehicle_rep3

value: experiment 3


title: GR+FABP4_vehicle_rep2

value: experiment 2


title: GR+FABP4_vehicle_rep1

value: glucocorticoid receptor and FABP4


title: FFM_17


title: Day9_iRFP_Negative_2

tag: subpopulation

value: isolated iRFP670-

tag: differentiation protocol

value: Ventricular protocol


title: Day9_iRFP_Positive_3

value: isolated iRFP670+


title: GR+FABP1_dex_rep4

value: glucocorticoid receptor and FABP1

tag: treatment

value: 10 μM dexamethasone for 24 h


title: FFM_16

value: PD


title: Day9_iRFP_Negative_3

tag: day


title: Lung - WT PBS_rep3

city: St. Louis

first: Michael

middle: J

last: Holtzman

state: MO

address: 4939 Childrens Pl

department: Pulmonary & Critical Care

country: USA

institute: Washington University in St. Louis School of Medicine

data_processing:
RNAseq was using a NovaSeq 6000 with S4 flow cell.
Gene and transcript levels were quantified using the RSEM (version 1.3.2) pipeline, and the estimated counts were stored as the appropriate raw data to feed into the edgeR (version 3.24.3), limma (version 3.38.3), and voom (version 3.38.3) pipeline.
The list of Ensemble gene ids was annotated by the biomaRt (version 2.38.0), which queried BioMart databases to retrieve additional information including entrezgene identifiers for gene symbol and chromosome.
A DGEList appropriate for our data was declared, and filterByExpr function in edgeR was used to maintain 35% of the genes in the gene list by filtering out lowly expressed genes automatically and in a principled way. The data were then normalized to account for variability in sequencing depth, library size, and other external factors that are not of biological interest.
After TMM normalization, unsupervised heirarchical clustering with the hclust function in base R (version 3.5.3) and principal component analysis with the prcomp function were conducted to identified treatment and control clusters. The correlations between replicate samples were also examined, with the lowest value of 0.94. We invoked voom software to compute precision weights and fitted linear models to the data using the lmFit function. Then, we refitted the model using the contrasts.fit function and computed moderated t- and F-statistics using the eBayes and treat functions, respectively. We chose the outputs from treat function for a more stringent definition of statistical significance to test against a fold change threshold.
Two heatmaps were generated with heatmap.2 function in gplots (version 3.1.0), based on subsets of the top 100 most significant genes sorted separately by the F-statistic and fold change. We also generated scatter plots with ggplot2 (version 3.3.2) with the top genes ranked by fold change labelled of our interest.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung - WT PBS

growth_protocol: Wild-type C57BL/6J mice (000664) were obtained from Jackson Laboratories (Bar Harbor, ME). All mice were maintained on a C57BL/6J background and were co-housed in a barrier facility using cages fitted with micro-isolator lids. Male and female mice (5-6 weeks of age) on a C57BL/6J genetic background were used for all experiments.

extract_protocol:
Lung tissue RNA was purified as described previously 11 from three mice per sample condition (12 or 21 d after SeV infection or PBS control challenge) and subjected to RNAseq using a NovaSeq 6000 with S4 flow cell (Illumina, San Diego, CA) in the Genome Technology Access Center in the McDonnell Genome Institute (Washington University, St. Louis).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were inoculated intranasally with Sendai virus (SeV strain 52) for 12 or 21 days or PBS as controls.

tag: strain

value: lung

value: PBS control

tag: genotype

value: wild type


title: GR+FABP1_dex_rep3


title: FFM_13

tag: tissue

value: melanoma

tag: gender


title: Lung - WT PBS_rep4


title: Day9_iRFP_Positive_1

value: Day 9


title: Lung - WT PBS_rep1


title: Patient26_MF33

type: RNA

city: Madrid

first: Alberto

last: Utrero-Rico

address: Av Cordoba s/n

country: Spain

hyb_protocol: 100 ng of RNA were hybridized to target-specific probes and controls in a single tube for 20h at 65ºC.

scan_protocol: Target-probe complexes were purified and immobilized on the nCounter prep station. Counts for each target RNA were acquired using the nCounter detection analyzer (NanoString).

data_processing:
nSolver software (NanoString) was used for normalization using housekeeping genes and for paired comparisons of gene expression.
software computed normalizes signal intensity

label: NanoString

source_name: Monocytes isolated from blood

label_protocol: Standard NanoString protocol

extract_protocol: RNA extraction was performed from > 1 million freshly isolated monocytes using RNeasy Plus Kit (Qiagen) according to manufacturer’s instructions. RNa concentration was determined using NanoDrop 1000 spectrophotometer and Qubit RNA HS Assay (Thermo Fisher Scientific). RNA quality and integrity was assessed by the Agilent RNA 6000 Nano Kit with the Agilent 2100 Bioanalyzer instrument (Agilent Technologies Inc.) RNA samples were used when the concentration was ≥20 ng/μL and RNA integrity Number (RIN) was >9.

tag: age

value: 58 years

tag: Sex

value: male

tag: cell type

value: Monocytes isolated from blood

tag: infection status

value: Acute COVID19

tag: status

value: Alive


title: Patient25_MF32

value: 56 years

value: female


title: GR+FABP1_dex_rep2

tag: cell line

tag: transfection

tag: biological repeat

value: experiment 2


title: Day9_iRFP_Negative_1

value: isolated iRFP670-

value: Ventricular protocol


title: GR+FABP1_dex_rep1

value: glucocorticoid receptor and FABP1

value: 10 μM dexamethasone for 24 h

value: experiment 1


title: FFM_14

tag: brafmut (1 yes, 0 no)

tag: nrasmut (1 yes, 0 no)

tag: localization

value: Skin metastasis

tag: brain metastasis (1 yes, 0 no)

tag: tissue in relation to ici treatment

value: post-ICI

tag: ici response (dc disease control, pd progressive disease, unk unknown)

value: PD


title: Lung - WT SeV d21_rep4

source_name: Lung - WT SeV d21

tag: strain

value: lung

tag: treatment

value: SeV for 21 days

tag: genotype

value: wild type


title: Lung - WT SeV d21_rep3

tag: tissue


title: Lung - WT PBS_rep2

value: PBS control


title: Patient24_MF31

tag: age

value: 78 years

tag: Sex

value: male

value: Monocytes isolated from blood

value: Acute COVID19


title: Day1_3

source_name: Cells differentiated into cardimyocyts on day 1 from hiPSC

tag: subpopulation

value: bulk

tag: differentiation protocol

tag: day

value: Day 1


title: Day1_2

value: Ventricular protocol


title: FFM_15

value: melanoma

tag: gender

value: female

value: pre-ICI


title: Lung - WT SeV d21_rep2


title: FFM_12

value: Skin metastasis

value: DC


title: Lung - WT SeV d21_rep1


title: GR+FABP1_vehicle_rep3

tag: cell line

tag: transfection

value: glucocorticoid receptor and FABP1

value: vehicle (0.1% v/v DMSO) for 24 h

tag: biological repeat

value: experiment 3


title: Day1_1


title: HC7_MF29

value: 59 years

tag: cell type

tag: infection status

value: Healthy Control

tag: status

value: Alive


title: Lung - WT SeV d12_rep4

source_name: Lung - WT SeV d12

value: lung

value: SeV for 12 days

value: wild type


title: GR+FABP1_vehicle_rep4

value: experiment 4


title: FFM_10

value: male

tag: brafmut (1 yes, 0 no)

tag: nrasmut (1 yes, 0 no)

tag: localization

tag: brain metastasis (1 yes, 0 no)

tag: tissue in relation to ici treatment

tag: ici response (dc disease control, pd progressive disease, unk unknown)


title: HC6_MF28

tag: age

value: 45 years

tag: Sex

value: Monocytes isolated from blood


title: FFM_11

tag: tissue

value: melanoma


title: GR+FABP1_vehicle_rep2

tag: treatment

value: experiment 2


title: Lung - WT SeV d12_rep3

tag: strain

tag: genotype


title: Patient22_MF27

value: 64 years

value: female

value: Acute COVID19


title: GR+vector_dex_rep4

tag: cell line

tag: transfection

value: glucocorticoid receptor and vector

value: 10 μM dexamethasone for 24 h


title: Day5_mCherry_Positive_3

source_name: Cells differentiated into cardimyocyts on day 5 from hiPSC

tag: subpopulation

value: isolated mCherry+

tag: differentiation protocol

value: Ventricular protocol

tag: day

value: Day 5


title: Lung - WT SeV d12_rep2

value: lung


title: Day5_mCherry_Negative_2

value: isolated mCherry-


title: GR+vector_dex_rep3

tag: biological repeat

value: experiment 3


title: Lung - WT SeV d12_rep1

value: SeV for 12 days

value: wild type


title: Patient20_MF25

value: 85 years

tag: cell type

tag: infection status

tag: status

value: Alive


title: Day5_mCherry_Positive_2


title: Patient23_MF30

value: 77 years

value: Monocytes isolated from blood


title: FFM_9

value: melanoma

tag: gender

value: male

tag: brafmut (1 yes, 0 no)

tag: nrasmut (1 yes, 0 no)

tag: localization

value: Skin metastasis

tag: brain metastasis (1 yes, 0 no)

tag: tissue in relation to ici treatment

value: pre-ICI

value: PD


title: Patient21_MF26

tag: age

value: 80 years

tag: Sex

value: Post COVID19


title: Patient19_MF24

value: 82 years

value: Acute COVID19


title: GR+vector_dex_rep2

tag: cell line

value: glucocorticoid receptor and vector

tag: treatment

value: 10 μM dexamethasone for 24 h

value: experiment 2


title: Day5_mCherry_Negative_1

tag: subpopulation

value: isolated mCherry-

value: Ventricular protocol

value: Day 5


title: Day5_mCherry_Positive_1

value: isolated mCherry+

tag: differentiation protocol


title: MED4_degron_6h_PCHi-C_2k_genes_Rep1

city: Los Angeles

first: Fei

last: Sun

state: California

address: 615 Charles E Young Drive South

department: Biological Chemistry

institute: UCLA

library_source: genomic

data_processing:
Base-calling was performed with RTA.
Sequence reads were processed by HiCUP with default options for mapping, pairing, filtering and de-duplication. .
The unique and valid read pairs were further processed by CHiCAGO. A CHiCAGO score > 5 was used as the cutoff for significant loops.
Genome_build: mm9
Supplementary_files_format_and_content: chinput files containing raw counts

growth_protocol: Degron cells were cultured on a MEF feeder layer (Invitrogen) in media containing DMEM-KO supplemented with 15% fetal bovine serum, 1000 U/ml LIF, 100 M nonessential amino acids, 2 mM L-gultamine and 8 nL/ml of 2-mercaptoethanol at 37oC in a humidified 5% CO2/95% air incubator.

extract_protocol:
Five million cells were harvested and formaldehyde-crosslinked as for ChIP-seq. Crosslinked cells were lysed for 15 min on ice in 10 mM Tris-HCl pH 8.0, 10 mM NaCl, and 0.2% NP-40 supplemented with cOmplete protease inhibitor. Nuclei were isolated by centrifugation and by removing the supernatant. Nuclei were gently resuspended in 50 μL of 0.5% SDS and incubated at 62°C for 5-10 min. SDS was quenched by adding 170 μl of 1.5% Triton X-100 and incubating at 37°C for 15 min. 25 μl of 10×NEBuffer2 and 100 U of MboI restriction enzyme were added and the sample was digested overnight on a thermo-mixer. MboI was inactivated by heating to 62°C for 20 min. After the sample was cooled down to room temperature, a fill-in master mix (37.5 μl of 0.4 mM biotin-14-dATP, 1.5 μl of 10 mM dCTP, 1.5 μl of 10 mM dGTP, 1.5 μl of 10 mM dCTP, 8 μl of Klenow Fragment) was added to the sample and incubated at 37°C for 1 hour. Proximity ligation was carried out by adding a ligation master mix (663 μl of H2O, 120 μl of 10X NEB T4 DNA ligase buffer, 100 μl of 10% Triton X-100, 12 μl of 10 mg/ml BSA, 5 μl of T4 DNA ligase) and incubating for 4 hours at room temperature. The sample was treated with Proteinase K before DNA purification with ethanol precipitation. Purified DNA was sheared on a Qsonica Q800R2 sonicator with 20% amplitude for 9 cycles at 10 s each with 30 s between cycles at 4°C. Size-selection of the sheared DNA was performed with KAPA pure beads to enrich fragments in the range of 300-500 bp. Size-selected biotinylated DNA was pulled down with Dynabeads MyOne Streptavidin T1 beads. After on-bead end repair and A-tailing, SureSelect Adaptor was added to the ends of DNA following Agilent’s protocol. The adaptor-ligated DNA was amplified directly off the beads with 6-8 PCR cycles. PCR products were purified and concentrated to 221 ng/μl using a vacuum concentrator. For capture, two 120-nt biotinylated RNA probes were designed to anneal specificity to the promoter region of one gene. In total, ~40,000 RNA probes targeting ~20,000 mouse genes were synthesized at Agilent. 3.4 μl (750 ng) of the concentrated PCR products were hybridized to the RNA probes following Agilent’s protocol. The hybridized library was captured by Dynabeads MyOne Streptavidin T1 beads and amplified off the beads with Agilent’s indexing primers.
Libraries were constructed using Agilent's SureSelect library prep kit

treatment_protocol: Degron cells were treated with auxin for 6 hours. For the degron controls and V6.5 cells, no treatment was performed.

value: embryonic stem cell

value: treated with auxin for 6 hours


title: MED4_degron_6h_PCHi-C_2k_genes_Rep2


title: GR+vector_dex_rep1

tag: transfection

value: experiment 1


title: Day3_3

source_name: Cells differentiated into cardimyocyts on day 3 from hiPSC

value: bulk

tag: day

value: Day 3


title: GR+vector_vehicle_rep4

value: vehicle (0.1% v/v DMSO) for 24 h

tag: biological repeat

value: experiment 4


title: Patient17_MF22

value: 45 years

value: male

tag: cell type

value: Monocytes isolated from blood

tag: infection status

value: Alive


title: MED4_degron_0h_PCHi-C_2k_genes_Rep2

value: untreated


title: MeRIP-seq_GFP-Input-D4

tag: time point


title: GR+FABP1_vehicle_rep1

value: glucocorticoid receptor and FABP1


title: GR+vector_vehicle_rep3

value: glucocorticoid receptor and vector

value: experiment 3


title: MED4_degron_0h_PCHi-C_2k_genes_Rep1


title: FFM_6

tag: tissue

value: melanoma

tag: gender

value: female

tag: brafmut (1 yes, 0 no)

value: Skin metastasis

value: post-ICI

tag: ici response (dc disease control, pd progressive disease, unk unknown)

value: PD


title: Day3_2

value: bulk

value: Ventricular protocol


title: Patient15_MF20

value: 89 years

value: Acute COVID19

tag: status

value: Dead


title: MED4_degron_6h_PCHi-C_20k_genes_Rep2

value: embryonic stem cell

value: treated with auxin for 6 hours


title: GR+vector_vehicle_rep1

value: vehicle (0.1% v/v DMSO) for 24 h

value: experiment 1


title: Patient14_MF19

tag: age

value: 35 years

value: male

value: Monocytes isolated from blood

value: Alive


title: Day20_Ventricular_CM_mCherry+EGFP+_3

description: day20_Ventricular_subpopulations.DESeq2.normalized.csv, day20_Ventricular_Atrial_populations.DESeq2.normalized.csv, day0_20.DESeq2.normalized.csv

source_name: Cardiomyocytes derived from hiPSC

value: isolated iRFP670+ mCherry+EGFP+

value: Day 20


title: GR+vector_vehicle_rep2

value: glucocorticoid receptor and vector

value: experiment 2


title: Patient16_MF21

value: 55 years

tag: Sex

value: Post COVID19


title: YO_P3_input

city: Lanzhou

first: Xingdong

last: Wang

state: 未选择

address: No.335 Jiangouyan, Qilihe District

institute: CAAS: Chinese Academy of Agricultural Sciences

description: m6A RIP-seq

data_processing:
raw data quality control performed using fastq 0.19.4.
HISAT2 2.0.4 software was used to compare the reference genome of valid data after preprocessing.
Using the peak calling software, R package exomepeak 1.9.1 performed peak scanning in the whole gene range.
Annotate these peaks using ChIPseeker 1.18.0.
Genome_build: Bos grunniens v101
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Bos grunniens

source_name: Yak ovary

growth_protocol: The ovarian tissues were collected from three healthy yaks of the same age during three different periods of the year. The samples were separately collected during the anestrus in April (A1, A2, A3), the follicular (also as estrus) phase in August (F1, F2, F3), and the pregnancy period in December (P1, P2, P3).

extract_protocol:
The total RNA was isolated and purified using the TRIzol reagent . The amount and purity of the RNA samples were quantified using the NanoDrop ND-1000.
The Poly (A) RNA was purified from 50 μg total RNA using Dynabeads Oligo (dT) 25-61005through two rounds of purification. Then the captured RNA was fragmented into small pieces using the Magnesium RNA Fragmentation Module for 7 min at 86°C. The fragmented RNA was premixed with the Dynabeads Antibody Coupling Kit and m6A antibody（No.202003, Synaptic Systems, Germany）  in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630) and incubated for 2 h at 4°C. The IP RNA was reverse-transcribed to synthesize the cDNA using the SuperScript™ II Reverse Transcriptase. Then the two-strand synthesis was performed with RNase H using the E. coli DNA polymerase I  to synthesize U-labeled second-stranded DNAs. At the same time, the dUTP Solution was incorporated into the two strands, and the ends of the double-stranded DNA were filled with blunt ends. An A-base was added at each end of the fragment to connect it to the T-base overhang, and the size of the fragment was screened and purified using the AMPureXP beads. The U-labeled second-stranded DNAs were digested using a heat-labile UDG enzyme , then amplified by PCR under the following conditions: Pre-denaturation at 95°C for 3 min, denaturation at 98°C (8 cycles) for 15 s, annealing at 60°C for 15 s, extending at 72°C for 30 s, and finally extending at 72°C for 5 min to form a cDNA library of 300 ± 50 BP. At last, the 2 × 150 bp paired-end sequencing (PE150) was performed on an Illumina Novaseq™ 6000.

treatment_protocol: The ovarian tissue  was immediately stored in liquid nitrogen for RNA isolation. All the ovarian samples were collected from the slaughtered yak within 1 h.

tag: developmental stage

value: pregnancy ovary

value: ovary


title: MED4_degron_0h_PCHi-C_20k_genes_Rep2

tag: treatment

value: untreated


title: Day20_Ventricular_CM_mCherry+EGFP-_3

tag: subpopulation

value: isolated iRFP670+ mCherry+EGFP-

value: Ventricular protocol


title: YO_P2_input

description: m6A RIP-seq


title: MED4_degron_6h_PCHi-C_20k_genes_Rep1

value: embryonic stem cell

value: treated with auxin for 6 hours


title: MED4_degron_0h_PCHi-C_20k_genes_Rep1


title: FFM_3

source_name: melanoma skin metastasis

value: melanoma

value: female

tag: nrasmut (1 yes, 0 no)

tag: localization

value: Skin metastasis

tag: brain metastasis (1 yes, 0 no)

tag: tissue in relation to ici treatment

value: pre-ICI

value: PD


title: Patient13_MF18

value: 64 years

tag: cell type

value: Monocytes isolated from blood

value: Acute COVID19

value: Alive


title: Day20_Ventricular_CM_mCherry-EGFP+_3

value: isolated iRFP670+ mCherry-EGFP+

tag: differentiation protocol

tag: day

value: Day 20


title: FFM_5

tag: tissue


title: FFM_4

tag: gender

value: male

value: post-ICI

value: DC


title: FFM_1

tag: brafmut (1 yes, 0 no)


title: Patient12_MF17

value: 76 years

tag: infection status

value: Dead


title: TAF12_degron_6h_PCHi-C_2k_genes_Rep2

value: embryonic stem cell

value: treated with auxin for 6 hours


title: YO_P1_input

description: m6A RIP-seq

value: pregnancy ovary

value: ovary


title: FFM_8

value: melanoma

value: female

value: Skin metastasis

value: pre-ICI

tag: ici response (dc disease control, pd progressive disease, unk unknown)


title: Day20_Ventricular_CM_mCherry-EGFP-_3

value: isolated iRFP670+ mCherry-EGFP-

value: Ventricular protocol


title: Patient11_MF16

tag: age

value: 77 years

value: Monocytes isolated from blood

value: Acute COVID19

tag: status

value: Alive


title: FFM_7

value: male

value: post-ICI

value: DC


title: TAF12_degron_6h_PCHi-C_2k_genes_Rep1

value: embryonic stem cell


title: YO_F2_input

description: m6A RIP-seq

tag: developmental stage

value: estrus ovary


title: YO_F3_input

description: m6A RIP-seq


title: Day20_Atrial_CM_mCherry-EGFP+_1

data_processing:
Illumina bcl2fastq (v2.17.14) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.15) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
HTSeq (v0.9.1) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
To normalized read counts, R (v3.6.1) and its package DESeq2 (v1.24.0) were performed.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file including DESeq2 nomalized count values for each sample.

extract_protocol:
RNeasy Mini Kit
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold

treatment_protocol: On day 19, the media were changed to collagenase typeⅠ. On day 20, the collagenase was removed, and the EBs were treated with Accumax (Innovative Cell Technologies) for 15 minutes at 37 ℃. The EBs were dissociated by pipetting gently and applied to a filter tube with 5% FBS-PBS including 0.5 µg/ml DAPI and 10 µg/ml DNaseⅠ.

value: cardiomyocytes derived from hiPSC

value: isolated iRFP670+ mCherry-EGFP+

value: Atrial protocol

value: Day 20


title: HC5_MF15

value: 60 years

tag: Sex

value: Healthy Control


title: TAF12_degron_0h_PCHi-C_2k_genes_Rep2

tag: treatment

value: untreated


title: HC4_MF14

value: 54 years


title: FFM_2

value: melanoma

value: female

tag: nrasmut (1 yes, 0 no)

value: Skin metastasis

value: pre-ICI

value: PD


title: YO_F1_input

description: m6A RIP-seq

value: ovary


title: TAF12_degron_0h_PCHi-C_2k_genes_Rep1


title: TAF12_degron_6h_PCHi-C_20k_genes_Rep2

value: treated with auxin for 6 hours


title: YO_A3_input

description: m6A RIP-seq

value: anestrus ovary


title: TAF12_degron_6h_PCHi-C_20k_genes_Rep1

value: embryonic stem cell


title: Day20_Ventricular_CM_mCherry+EGFP+_2

value: cardiomyocytes derived from hiPSC

tag: subpopulation

value: isolated iRFP670+ mCherry+EGFP+

value: Ventricular protocol


title: YO_A2_input

description: m6A RIP-seq


title: Day20_Ventricular_CM_mCherry-EGFP+_2

value: isolated iRFP670+ mCherry-EGFP+

value: Day 20


title: HC3_MF13

value: 48 years

value: male

value: Monocytes isolated from blood

value: Healthy Control

value: Alive


title: Patient10_MF11

value: 77 years

value: Post COVID19


title: Day20_Ventricular_CM_mCherry+EGFP-_2

value: isolated iRFP670+ mCherry+EGFP-


title: YO_A1_input

description: m6A RIP-seq

value: ovary


title: HC2_MF12

value: 56 years

value: female


title: Day20_Ventricular_CM_mCherry-EGFP-_2

value: isolated iRFP670+ mCherry-EGFP-


title: TAF12_degron_0h_PCHi-C_20k_genes_Rep2

value: embryonic stem cell

value: untreated


title: Day20_Atrial_CM_mCherry-EGFP+_2

value: cardiomyocytes derived from hiPSC

value: Atrial protocol


title: YO_P3

description: m6A RIP-seq

value: pregnancy ovary


title: Patient8_MF9

value: 87 years

value: Acute COVID19


title: Patient9_MF10

value: 26 years

value: Monocytes isolated from blood


title: Day20_Ventricular_CM_mCherry+EGFP+_1

value: isolated iRFP670+ mCherry+EGFP+

value: Ventricular protocol

value: Day 20


title: TAF12_degron_0h_PCHi-C_20k_genes_Rep1


title: YO_P2

description: m6A RIP-seq


title: Patient7_MF8

value: male

value: Dead


title: YO_P1

description: m6A RIP-seq

value: ovary


title: DIFF2-input

city: West Lafayette

first: Theresa

middle: M

last: Casey

state: Indiana

address: 175 S. University Street

department: Animal Sciences

institute: Purdue University

data_processing:
Sequence quality was assessed using FastQC (v 0.11.7) for all samples and quality trimming was done using Fastx toolkit to remove bases with Phred33 score of less than 30. The resulting reads of length at least 50 bases were retained. The quality trimmed reads were mapped against the reference genome (Mus_musculus.GRCm38.chr.fa) using bowtie2 (Version 2.2.9)
Peaks were called from mapped files (bam files) using ‘callpeaks’ script of HOMER (Version 4.10) to detect transcription factor associated peaks using default settings except for the following parameters: fold enrichment over input tag count (F) was set at 2, fold enrichment limit of expected unique tag positions (C) was set at 2 and fold enrichment over local tag count (L) was set at 2 and FDR was set at <0.01
Peaks were annotated using ‘annotate peaks’ script from HOMER using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: peak excel files

source_name: normal mouse mammary epithelial cells, HC11 line

growth_protocol: HC-11 cells were routinely cultured in complete growth medium: RPMI 1640 (50-020-PC, Mediatech Inc.) supplemented with 2 g/L sodium bicarbonate (S5761-500G, Sigma Life Science), 100 U/mL penicillin, 100 µg/mL streptomycin (15140-122, ThermoFisher Scientific), 10% heat inactivated calf serum (26170-043, Gibco), 5 µg/mL insulin ([Ins] IO516-5mL, Sigma-Aldrich), and 10 ng/mL epidermal growth factor ([EGF] E4127, Sigma-Aldrich) in 5% CO2 at 37°C. Cells were passaged 1:3 when they reached 80% confluence by harvesting cells with 0.25% trypsin EDTA (Gibco).   To induce differentiation, cells were plated at 100,000 cells/mL and grown to confluence.  At confluence cells were washed 2-times with PBS, and incubated for 48 h in RPMI media supplemented with 10% serum and Ins (no EGF in media).  Undifferentiated cultures (UNDIFF) were harvested for downstream analysis at this stage of culture.  For differentiated cultures (DIFF), media was changed to RPMI supplemented with 10% calf serum, dexamethasone (0.1 µM), insulin (5 µg/mL), and prolactin (5 µg/mL; ovine prolactin: L6520-250IU, Sigma-Aldrich), and incubated for 96 h, with media change every 2-days.  After 96 h in lactogen cocktail, differentiated cultures were collected.

extract_protocol:
Use of two independent biological replicates for ChIP-seq analysis to identify transcriptional targets is consistent with ENCODE (Encyclopedia of DNA Elements) guidelines. For ChIP-seq studies,  four independent ChIP experiments were performed, two with undifferentiated cultures and two for differentiated cultures, to enable analysis of the effect of differentiation on BMAL1 targets. Briefly, undifferentiated and differentiated HC11 cultures in 100 mm plates were treated with 1% formaldehyde to cross-link proteins to chromatin by adding 625 µl fresh 16% formaldehyde directly to the dishes containing cells and 10 mL media, and incubated at RT on a shaking platform for 7 min. To quench the formaldehyde, 500 µl of 2.5M glycine was added, and incubated at RT on the shaking platform for 5 min. Cells were washed twice with ice cold PBS, and removed from culture dish using a cell scraper.  Cells were pelleted by centrifugation and stored at the -80 °C. Samples were collected for ChIP assays in four replicate experiments (sample IDs UNDIFF6, UNDIFF8, DIFF1, DIFF2).    Nuclei were collected by resuspending each fixed-cell pellet in 10 mL of Rinse 1 (50mM Hepes pH 8.0, 140mM NaCl, 1mM EDTA, 10% glycerol, .5% NP40, .25% Triton x100), and incubating 10 min on ice. Samples were pelleted by centrifugation 1,200 X g at 4 °C for 5 min, and then resuspend in 10 mL CiA NP-Rinse 2 (10mM Tris pH 8.0, 1mM EDTA, 0.5mM EGTA, 200mM NaCl), and then centrifuged at 1,200 X g and 4 °C for 5 min.  Pellets were washed with 5 ml of CiA Covaris Shearing Buffer (0.1% SDS, 1mM EDTA pH 8.0, 10mM Tris HC1 pH 8.0) twice with centrifugation at 1,200 X g and 4 °C for 3 min after each wash. For sonication, pellets from approximately 3 million cells each were resuspended in 130 µl ofCiA Covaris Shearing Buffer with 10% protease inhibitor cocktail.  Pellets were sonicated in a Covaris E210 instrument (Covaris, Inc., Woburn, MA) using the following parameters: Duty Factor 5%, Peak power 105W, Cycles per burst 200, 10 min.  Following sonication sheared chromatin lysate was transferred to a new centrifuged at 20,000 X g and 4 °C for 15 min.  Supernatant (sheared chromatin stock) was divided into three aliquots for input DNA, mock-immunoprecipitation (IP) and IP and stored at -80 °C (-20C), after removal of an aliquot for analysis of product size in a 2% agarose gel and on the Agilent Bioanalyzer Nanochip. For immunoprecipitation step, cross-linked chromatin using anti-BMAL1 antibody and mock-IP aliquots were thawed on ice.  Samples were precleared by adding 50 µL resuspended A beads (DynaBeads Protein A, Invitrogen cat. # 10001D), and incubating at 4° C for 1.5 h with rotation.  Tubes were placed on a magnetic rack and liquid was transferred to a new microfuge tube.  One-quarter of the volume of 5X IP Buffer (250mM Hepes/KOH pH 7.5, 1.5M NaCl, 5mM EDTA, 5% TritonX 100, 0.5% DOC [4-chloro-2,5-dimethoxy-amphetamine], 0.5% SDS) was added, and 10 µL of BMAL1 antibody (Abcam ab 3350) was added to IP tube, and nothing was added to mock-IP tube.  Samples were rotated overnight at 4° C, and then 50 µL of resuspended A beads were added to each tube, and rotated for 3 h at 4° C.  Magnetic rack was used to remove A beads. Supernatant was collected transferred to a new tube, and washed with 1mL IP Buffer twice with rotation at RT for 3 min, and collection on magnetic rack following wash.  Supernatants were then washed with 1 mL of DOC buffer (10 mM Tris, pH8.0; 0.25 M liCl; 0.5% NP40, 0.5% DOC, 1 mM EDTA), followed by 1 mL of Tris EDTA (TE) buffer pH 8. Supernatant was removed and 150 µL elution buffer was added and samples were rotated at RT for 20 min. Supernatant was transferred to a new tube and store at -80 °C until DNA isolation. Chromatin was isolated from supernatant by adding 3 volumes of TE with 1% SDS and RNAse A (Sigma R6513), and vortexing to mix. Samples were incubated at 37° C for 30 min, and proteinase K was added, vortexed again to mix, and cross-linking was reversed by incubating at 55° C for ~2.5 h, and then overnight at 65° C in PCR tubes in the thermocycler.  DNA was extracted the next day by adding 230 µL TE and 330 µL phenol/chloroform, vortexing, followed by centrifugation for 1 min.  Aqueous layer was transferred into a new microfuge tube and 10 µL of commercial glycogen (ThermoScientific R0551) was added with 30 µL 3M NaCl.  One volume of 100% ethanol was added and samples vortexed to mix. Samples were incubated for two days at -20 ° C, and then centrifuged 1 h at 4 °C to pellet DNA. Pellet was washed twice by removing the supernatant and adding 500 µl 70% EtOH. Pellet was resuspended in 25 µL TE and concentration was measured with Qubit fluorometer (Thermo Fisher Scientific) and a Bioanalyzer 2100 (Agilent), and samples stored at -80° C until sequencing.
Libraries were prepared using NEXTFLEX® Rapid DNA-Seq Library Prep Kit for Illumina® Platforms (PerkinElmer, ) according to manufacturer’s protocol. Libraries were sequenced by paired ends reads on the Illumina Novaseq 6000 following the manufacturer's protocols.

treatment_protocol: To test the hypothesis that BMAL1 transcriptional targets changed with state of mammary epithelial differentiation we used ChIP-seq analysis to identify genes potentially regulated by BMAL1 in undifferentiated (UNDIFF) and lactogen hormone differentiated (DIFF) HC11 cultures.  Prior to beginning studies, specificity of the ChIP-grade antibody for the BMAL1 protein was confirmed with immunoprecipitation and western blot analysis (Supplemental Figure S1A).  Nanochip analysis of sonicated input DNA indicated that optimal size of sheared fragments was achieved for ChIP-seq analysis (Supplemental Figure S1B).  Moreover, ChIP-qPCR analysis of the promoter region of PER1, a transcriptional target of BMAL1:CLOCK, found that 70% of the input DNA sequence was captured by chromatin immunoprecipitation, with the q-PCR product being 9-fold higher in BMAL1-ChIP samples than mock samples (no primary antibody added). Q-PCR analysis of the exon region of MAGEA 1_2, a sperm specific gene that is not a BMAL1:CLOCK target was used as a negative control.  There was no difference in amount of  MAGEA 1_2 q-PCR between mock-ChIP and BMAL1-ChIP samples, thus further validating the BMAL1-ChIP assay.

value: mammary epithelial cells

tag: tag

value: lactogen differentiated


title: Patient6_MF7

value: 77 years

value: Post COVID19

value: Alive


title: Day20_Ventricular_CM_mCherry-EGFP+_1

value: cardiomyocytes derived from hiPSC

value: isolated iRFP670+ mCherry-EGFP+


title: DIFF1-input


title: Day20_Ventricular_CM_mCherry-EGFP-_1

value: isolated iRFP670+ mCherry-EGFP-


title: Patient5_MF6

value: 68 years

value: Acute COVID19


title: AICAR rep1

city: MIAMI

first: Julio

middle: C

last: Barredo

state: Florida

address: 1580 NW 10th ave room

institute: University of Miami

data_processing:
FASTQ data were processed with Trimmomatic v0.32 and aligned to the human genome hg19 using STAR aligner (ver 2.5.3a) and RSEM (ver 1.2.31)
Differential expression was determined between vehicle vs. AICAR conditions using DESeq2 and R (ver 3.2.3)
Genes with q-value < 0.05, fold change > 2 and FPKM (fragments per kilobase per million mapped fragments) >1 were considered significant.
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix table for all genes expreesion

source_name: B cell precursor leukemia

growth_protocol: NALM6 cells were grown in RPMI + 10% FBS

extract_protocol:
RNA was extracted from cells using the RNeasy plus kit (Qiagen)
Libraries were prepared using Illumina’s TruSeq Stranded Total RNA library preparation kit.Libraries were sequenced on a 75 bp single-end run using the NextSeq 500 High-Output Kit (75-cycle; 400 M flow cell).

treatment_protocol: For AICAR treatment, cells were firstly grown in no glucose medium for 24 hour and then treated with AICAR for 45min, for vehicle, cells were treated with DMSO for 45min.

tag: cell line

value: NALM6 cells

value: Glucose deprivation for 24h and then treated with 15mM AICAR for 45min


title: Patient3_MF4

value: 47 years

tag: cell type

value: Monocytes isolated from blood


title: UNDIFF8-ChIP

value: undifferentiated


title: AICAR rep2


title: YO_F2

description: m6A RIP-seq

value: estrus ovary


title: Patient4_MF5

value: 66 years

value: male


title: YO_A3

description: m6A RIP-seq

value: anestrus ovary

value: ovary


title: YO_F3

description: m6A RIP-seq


title: YO_F1

description: m6A RIP-seq


title: UNDIFF6-input

value: mammary epithelial cells


title: DIFF1-ChIP

value: lactogen differentiated


title: Patient2_MF3

value: 52 years

value: Alive


title: Day20_Ventricular_CM_mCherry+EGFP-_1

value: cardiomyocytes derived from hiPSC

value: isolated iRFP670+ mCherry+EGFP-

tag: differentiation protocol

value: Ventricular protocol

value: Day 20


title: vehicle rep1

value: NALM6 cells

value: Treated with DMSO for 45min


title: HC1_MF2

value: 54 years

value: Monocytes isolated from blood

value: Healthy Control


title: DIFF2-ChIP


title: vehicle rep2


title: YO_A1

description: m6A RIP-seq


title: UNDIFF6-ChIP

value: undifferentiated


title: Patient1_MF1

value: 75 years

value: female

value: Post COVID19


title: YO_A2

description: m6A RIP-seq

value: anestrus ovary

value: ovary


title: Patient18_MF23

value: 62 years

value: male


title: UNDIFF8-input

value: mammary epithelial cells


title: EV2

status: Public on Jul 21 2021

city: Madison

first: Mehdi

last: Kabbage

state: Wisconsin

address: Department of Plant Pathology, 583 Russell Labs 1630 Linden Dr

department: Department of Plant Pathology

institute: University of Wisconsin Madison

data_processing:
Quality control：trimmomatic；
Mapping：bowtie
Further: Self-written script to organize the results.
Supplementary_files_format_and_content: .xls, mapping and normalization
For the empty files (not archived), are you referring to the processed data? The data files that are empty are the alignments to our target sequence from the RNA of plants containing an empty silencing vector. There were zero alignments to the target sequence in plants containing our empty silencing vector (all processed files containing "EV") because the plants did not contain the silencing construct.
Under the files that say "normalized" in their name please look in the RPM column. These are the raw reads; They were multiplied by the conversion factor to get the small RNA count. We are not showing differentially expressed genes of soybean here. Instead, we are looking for genes that correspond to a fungus, Sclerotinia sclerotiorum, that were expressed from an RNAi silencing construct.

organism: Glycine max

source_name: EV

growth_protocol: The modified system, used in this work and developed by Zhang (2010), uses bean pod mottle virus (BPMV) which is bipartite. The two viral segments consist of a 6 kb RNA1 segment (pBPMV-IA-R1M) encoding viral proteins needed for genome replication and a 3.6 kb RNA2 segment (pBPMV-IA-V1) that encodes viral proteins needed for capsid assembly and movement and contains the cloning site where the silencing construct was inserted. As described in the protocol by Whitham et al. (2016), the RNA1 and RNA2 segments were co-bombarded into 10-day old Williams 82 (PI 518671) seedlings using gold particles coated with plasmid DNA. Two inoculations were made per plant, with one on each unifoliate leaf. Prior to inoculations, unifoliate seedlings were forced to etiolate in the dark for 24 h. After inoculations, plants were sprayed with water and kept in plastic bags for 24 h to maintain humidity. The inoculated plants were placed in a growth chamber at 22 °C during the day and 20 °C at night on a 16 h photoperiod. Soil was checked daily to determine if water was needed, and the plants were fertilized once weekly with Miracle-GroÒ (Scotts Miracle-Gro Co.).

extract_protocol:
A high concentration of total RNA was extracted from three leaves in three biological replicates from the pBPMV-OA and pBPMV-EV- containing plants. Leaves for RNA extractions were collected from the variety Traff, prior to inoculating soybeans symptomatic for BPMV with S. sclerotiorum in one experimental replicate of the expression experiment. The third trifoliate leaves were immediately frozen in liquid nitrogen. Two grams of leaf tissue per biological replicate was ground into fine powder using liquid nitrogen in a mortar and pestle and used in RNA extractions. A phenol chloroform extraction with a LiCl purification was performed as described in Aragão et al. (2013) to yield high RNA concentrations of 1.2-2.8 ug/ul.
A total amount of 2 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext® 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. Briefly, 3' SR Adaptor was directly and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double-stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for Illumina and index (X) primer. PCR products were purified on an 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips.

treatment_protocol: Inoculation of soybean plants with BPMV vectors targeting Ssoah1 (pBPMV-OA) first occurred in Williams 82 soybean. Symptomatic plants were then used to rub inocualte Traff.

value: leaves


title: EV3


title: EV1


title: OA3

source_name: OA


title: Day5_mCherry_Negative_3

value: isolated mCherry-

value: Ventricular protocol

tag: day

value: Day 5


title: TAK8_3

city: Uppsala

first: Magnus

last: Eklund

address: Norbyv. 18D

country: Sweden

institute: Uppsala University

data_processing:
Sequence reads were processed using the nf-core/rnaseq bioinformatics pipeline (https://github.com/nf-core/rnaseq)
Genome_build: version 5.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Marchantia polymorpha subsp. ruderalis

source_name: M. polymorpha thallus tissue

growth_protocol: Gemmae were grown aseptically on agar solidified Gamborg’s B5 medium53, pH 5.5, under cool white fluorescent light (50–60 µmol photons m−2 s−1) in 12: 12 hour, light: dark cycles at 20 °C before transfer to contiuous light (LL) for sampling.

extract_protocol:
Gemmae were  flash frozen in liquid nitrogen. RNA was extracted using RNeasy Plant Mini Kit (Qiagen) with on-column DNase treatment. Individual cDNA libraries for sequencing were prepared from 100 ng total RNA using the TruSeq stranded mRNA library preparation kit including polyA selection (Cat# 20020594/5, Illumina Inc.
The library preparation was accomplished according Illumina's protocol (#1000000040498)

treatment_protocol: Replicate samples (3) were sampled at 6 hour intervals starting 24 h after transfer to LL

tag: time point

value: 66 hours after shift to constant light

tag: accession

value: Takaragaike (Tak) -1

tag: tissue

value: young thallus


title: TAK8_2


title: TAK6_2

value: 54 hours after shift to constant light


title: TAK6_3


title: TAK7_1

value: 60 hours after shift to constant light


title: TAK8_1


title: OA1


title: TAK7_2


title: TAK6_1


title: TAK5_3

value: 48 hours after shift to constant light


title: OA2


title: TAK3_3

value: 36 hours after shift to constant light


title: TAK7_3


title: TAK5_2


title: Day3_1

value: bulk

value: Day 3


title: TAK4_2

value: 42 hours after shift to constant light


title: TAK4_3


title: Cornea Stage 49-51

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Fastq files were mapped the Xla 9.2 genome assembly using Cellranger software from 10X Genomics
Downstream analysis was performed using Seurat V3.1
Genome_build: Xenopus Laevis Build 9.2
Supplementary_files_format_and_content: Processed files are outputs from the Cellranger pipeline and are basically the matrixfiles with UMI values for genes in every cell

organism: Xenopus laevis

source_name: Cornea

extract_protocol:
A total of approximately 80 corneas in three separate glass depression dishes containing 400 ul 1X DPBS, on ice. Care was taken to ensure that corneas were carefully removed from the tip of the forceps and that they remained submerged in the 1X DPBS solution. Using a 200 ul pipette tip, most of the DPBS was gently removed without disturbing the corneas at the bottom of each glass dish. To dissociate the corneal epithelial tissue, ~350 ul of Accutase (CellnTec Advanced Cell Systems, Bern, Switzerland) was added to each dish, and the dishes were covered with plastic petri dish lids (35 X 10 mm, Corning, 351008) flat side down, and wrapped tightly with lab tape to secure them and prevent desiccation. Next, the dishes were incubated in a pre-hyb oven at 37 C for 35 minutes with intermittent trituration using a 200 l pipette tip. To stop the reaction, 200 ul of media containing 61% L-15 (Invitrogen, Carlsbad, CA), 0.5 M EDTA (Invitrogen, Carlsbad, CA) and 10% Fetal Bovine Serum (Invitrogen, Carlsbad, CA) was added to each dish. For mechanical dissociation, the suspension was finally triturated 8-10 times using the 200 ul pipette tip. The three cell suspensions were pooled in a 2ml LoBind microcentrifuge tube (Eppendorf, 022431048), spun at 325g for 5 minutes in a fixed-angle centrifuge, and resuspended in 200 ul L-15 with 10% FBS and 0.5 uM EDTA. Finally, the cells were passed through a 40 um FlowMi cell strainer (Bel-Art, Wayne, NJ; Cat 136800045) and collected in 2ml LoBind tube. Cell viability was assessed using a dual-fluorescence test by staining the cells with acridine orange (AO) and propidium iodide (PI)
The single-cell RNA-seq library was generated using the 10X Genomics Chromium Single Cell 3' Kit v3 (Location, Address) and sequenced with Illumina NovaSeq 6000 on a SP flow cell to obtain 150bp paired reads.

treatment_protocol: Tadpoles were anesthetized at room temperature by incubation for 30-60 seconds in  a 1:2000 dilution of MS222 (ethyl 3-aminobenzoate methanesulfonate, Sigma, St. Louis, MO) diluted in 1/20X NAM (Normal Amphibian Media). Anesthetized tadpoles were transferred to clay-lined dishes containing Ca++-Mg++ free Dulbecco’s Phosphate Buffered Saline (1X DPBS; Corning, NY, 21-031-CV). The corneal epithelial tissue was dissected using very fine microscissors (Henry et al., 2019), taking care not to include any surrounding skin.

tag: strain

value: WT

value: cornea


title: TAK3_2


title: TAK4_1


title: TAK3_1


title: TAK2_3

value: 30 hours after shift to constant light


title: TAK2_2


title: TAK2_1


title: TAK1_3

value: 24 hours after shift to constant light


title: TAK1_2


title: TAK5_1


title: TAK1_1


title: MDMs HIV3

city: wuhan

first: meirong

last: wang

address: donghuroad

institute: wuhan 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, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: monocyte derived macrophages (MDMs)

extract_protocol:
MDMs were extracted, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: monocyte derived macrophages (MDMs)

value: 7 days of HIV infection


title: MDMs HIV1


title: MDMs HIV2


title: D4-HSAPos-6days

city: Montreal

first: Eric

middle: A

last: Cohen

state: Quebec

address: 110 Ave des Pins Ouest

country: Canada

institute: IRCM

description:
processed data file:
rnaseq_raw_deseq.xlsx
tremblay_rnaseq_6dpos_vs_6dmock.xlsx

data_processing:
Raw reads were trimmed with Trimmomatic v0.30
Alignment was performed on hg19 human reference genome usign TopHat v2.0.8b
Gene quantification was performed using  htseq-count
Differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values obtained from differential analysis with DESEQ2.

source_name: Human monocyte-derived macrophages

extract_protocol:
Samples were resuspended in QIAzol lysis buffer and total RNA isolated from sorted cell populations using the miRNeasy kit from QIAGEN
RNA-seq libraries were prepared using the Scriptseq V2 complete gold kit (Epicentre) and the TrueSeq RNA Library Prep Kit V2 (Illumina)

tag: donor

value: Human monocyte-derived macrophages

tag: hiv infection

value: 6 days

tag: hsa+ or hsa-

value: HSA+


title: D2-HSANeg-36h

description:
processed data file:
rnaseq_raw_deseq.xlsx
tremblay_rnaseq_36neg_vs_36mock.xlsx

value: 36 hrs

value: HSA-


title: D4-HSAPos-36h

description:
processed data file:
rnaseq_raw_deseq.xlsx
tremblay_rnaseq_36pos_vs_36mock.xlsx


title: D1-HSANeg-6days

description:
processed data file:
rnaseq_raw_deseq.xlsx
tremblay_rnaseq_6dneg_vs_6dmock.xlsx


title: D3-HSAPos-36h


title: D3-HSANeg-36h


title: D1-MockNeg-6days

value: 6 days (MK)

value: Not infected


title: D4-MockNeg-6days


title: D2-MockNeg-6days


title: D3-MockNeg-36h

value: 36 hrs (MK)


title: D2-HSAPos-36h


title: D4-HSANeg-36h


title: D1-HSAPos-36h


title: D3-HSAPos-6days


title: D3-MockNeg-6days


title: D3-HSANeg-6days


title: D2-MockNeg-36h


title: D1-HSANeg-36h


title: D4-HSANeg-6days


title: D4-MockNeg-36h


title: D1-HSAPos-6days


title: MDMs NC3

value: Control


title: D2-HSAPos-6days


title: D2-HSANeg-6days


title: MDMs NC2


title: D1-MockNeg-36h


title: MDMs NC1


title: DIPG_NYU_LEDGF

city: Washington

first: Jia-Ray

last: Yu

state: DC

address: 7144 13th Pl Nw

institute: FBRI at Virginia Tech Carilion

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2/2.3.4.1
Duplicate reads were removed with picard/2.18.11
bigwigs were generated using deeptools/2.3.3
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: DIPG

growth_protocol: All DIPG cell lines were cultured and maintained in tumor stem media (TSM), which contains 1:1 mixture of Neurobasal-A and DMEM/F12 media (Life technologies), supplemented with 1% antibiotic/antimycotic solution (Life technologies), 2 mM GlutaMAX (Life technologies), 10 mM HEPES buffer (Life technologies), 1 mM sodium pyruvate (Sigma), 1% MEM non-essential amino acids solution (Sigma), B-27 supplement minus vitamin A (Gibco), human EGF (20 ng/ml) (Shenandoah biotech), and human FGF (20 ng/ml) (Shenandoah biotech). HEK293T and HEK293-FT cells were maintained in DMEM supplemented with 10% FBS,1 mM sodium pyruvate (Sigma), 2 mM L-glutamine (Sigma), and 1% penicillin/streptomycin solution (Sigma).

extract_protocol:
Cells were lysed in ChIP buffer (50 mM Tris-HCl pH 7.9, 150 mM NaCl, 1% Triron X-100, 0.5% NP-40, 5 mM EDTA pH 8.0, 1 mM PMSF and protease inhibitor) and chromatin was sonicated to ~200 bp with a Diagenode Bioruptor
Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters. Fragments of 300±100 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Q5 polymerase (NEB M0530).

tag: sample type

value: ChIP LEDGF


title: pcGBM_HDGF2

source_name: pcGBM

value: ChIP HDGF2


title: pcGBM_LEDGF


title: DIPG_4_LEDGF


title: DIPG_13_LEDGF


title: DIPG_4_HDGF2


title: DIPG_10_LEDGF


title: LysI_9 IKKβF/FLDLR-/- Peritoneal macrophages, HIV protein Tat

city: RIVERSIDE

first: ZHAOJIE

last: MENG

state: CA

address: 900 UNIVERSITY AVENUE

institute: UNIVERSITY OF CALIFORNIA, RIVERSIDE

data_processing:
The Sailfish tool was used to quantify the expression of each transcript.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample ...

source_name: Peritoneal macrophages

growth_protocol: Eight-week old IKKβF/FLDLR-/- and IKKβΔMyeLDLR-/- were intraperitoneally injected with 1 mL of 3% thioglycollate solution 3 days prior to the peritoneal macrophage collection.  The peritoneal macrophages were then collected from abdominal cavity and seeded to six-well plate.

extract_protocol:
Total RNA was isolated from cells using TRIzol Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Peritoneal macrophages were allowed to attach to cell culture plates for 4 hours and then treated with HIV protein Tat (100 nM) or PBS (control) for 12 hours.

value: Peritoneal macrophages (In vitro cultured)

tag: genotype

value: IKKbetaF/FLDLR-/-

value: HIV protein Tat

tag: treatment duration

value: 12 hr


title: DIPG_NYU_HDGF2


title: LysI_10 IKKβF/FLDLR-/- Peritoneal macrophages, HIV protein Tat

tag: treatment


title: DIPG_13_HDGF2


title: LysI_12 IKKβF/FLDLR-/- Peritoneal macrophages, HIV protein Tat


title: LysI_21 IKKβΔMyeLDLR-/- Peritoneal macrophages, HIV protein Tat

value: IKKbeta[delta]MyeLDLR-/-


title: LysI_5 IKKβF/FLDLR-/- Peritoneal macrophages, PBS (Control)

value: PBS (Control)


title: DIPG_10_HDGF2


title: LysI_23 IKKβΔMyeLDLR-/- Peritoneal macrophages, HIV protein Tat


title: LysI_19 IKKβΔMyeLDLR-/- Peritoneal macrophages, HIV protein Tat


title: LysI_20 IKKβΔMyeLDLR-/- Peritoneal macrophages, HIV protein Tat


title: LysI_8 IKKβF/FLDLR-/- Peritoneal macrophages, HIV protein Tat


title: LysI_6 IKKβF/FLDLR-/- Peritoneal macrophages, PBS (Control)


title: LysI_22 IKKβΔMyeLDLR-/- Peritoneal macrophages, HIV protein Tat


title: LysI_1 IKKβF/FLDLR-/- Peritoneal macrophages, PBS (Control)


title: LysI_2 IKKβF/FLDLR-/- Peritoneal macrophages, PBS (Control)


title: WT_42I_ctrl_EV

city: Hanover

first: Katja

last: Koeppen

state: NH

address: 504 Remsen

institute: Geisel School of Medicine at Dartmouth

data_processing:
fastq files were trimmed with trimmomatic
trimmed reads were aligned to the reference genome using bowtie
count tables were generated using samtools
Genome_build: hg19
Supplementary_files_format_and_content: csv count table of aligned reads

source_name: extracellular vesicles

growth_protocol: Primary human airway epithelial cells were grown in BronchiaLife basal medium (Lifeline Cell Technology, Frederick, MD, Cat. # LM-0007) supplemented with the BronchiaLife B/T LifeFactors Kit (Lifeline Cell Technology, Cat. # LS-1047) as well as 10,000 U/ml Penicillin and 10,000 μg/ml Streptomycin (Sigma-Aldrich, Cat. # P4333).

extract_protocol:
EVs were harvested from 15 ml cell culture supernatants using the ExoQuick-TC EV isolation kit. Total EV RNA was isolated with the SeraMir Exosome RNA Purification Column kit (System Biosciences, Cat. #RA808A-1) according to the manufacturer’s instructions. For each sample, 1 µl of the final RNA eluate was used for measurement of small RNA concentration by Agilent Bioanalyzer Small RNA Assay using the Bioanalyzer 2100 Expert instrument (Agilent Technologies, Santa Clara, CA, Cat. # 5067-1548).
Small RNA libraries were constructed with the CleanTag Small RNA Library Preparation Kit (TriLink Biotechnologies, San Diego, CA, Cat. # L-3206) according to the manufacturer's protocol. The final purified library was quantified with High Sensitivity DNA Reagents (Agilent Technologies, PO # G2933-85004) and High Sensitivity DNA Chips (Agilent Technologies, PO # 5067-4626). The libraries were pooled, and the 140 bp to 300 bp region was size selected on an 8% TBE gel (Thermo Fisher Scientific, Ref. # EC6215). The size selected library was quantified with High Sensitivity DNA 1000 Screen Tape (Agilent Technologies, PO # 5067-5584), High Sensitivity D1000 reagents (Agilent Technologies, PO # 5067-5585), and the TailorMix HT1 qPCR assay (SeqMatic, Fremont, CA, Cat. # TM-505).
Libraries were sequenced with Illumina NextSeq High Output single-end sequencing run at SR75 using NextSeq 500/550 High Output v2 kit (Illumina, San Diego, CA, Cat. # FC-404-2005) according to the manufacturer's instructions.

treatment_protocol: untreated controls

value: primary airway epithelial cells

value: wild type 42I


title: WT_25J_ctrl_EV

value: wild type 25J


title: LysI_3 IKKβF/FLDLR-/- Peritoneal macrophages, PBS (Control)


title: WT_10F_ctrl_EV

value: wild type 10F


title: LysI_11 IKKβF/FLDLR-/- Peritoneal macrophages, HIV protein Tat


title: LysI_7 IKKβF/FLDLR-/- Peritoneal macrophages, HIV protein Tat


title: HCC3_2DG_C0_288

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

description:
Plate3_IndexC
HCC3_2DG_C0_288_S288

data_processing:
Base calling was performed by bcl2fastq v 2.20.422
Quality trimming was performed using fastp v0.20.0
Alignment was performed using STAR v2.7.8a
Gene counts were performed with qCount in the QuasR R package v1.30.0
Normalization was performed with DESeq2 v1.30.1
Genome_build: Biospyder S1500 Gene Set
Supplementary_files_format_and_content: count_table.csv is a genes by samples count matrix of raw counts from the TempO-Seq data alignments.

source_name: Human Hepatoma HepaRG™ Cell Line

growth_protocol: Terminally differentiated human HepaRG™ cells, derived from a hepatocellular carcinoma, were seeded at approximately 4.0-5.0 x 10^4 viable cells per well in a collagen-coated 96-well CometChip® in William's E medium with TRL's Thawing and Plating Supplment. Cells were incubated for seven days following seeding to allow the cells to regain peak metabolic function.

extract_protocol:
RNA was not extracted from control and treated HepaRG™ cells, as TempO-Seq libraries were constructed directly from cell lysates according tp the TempO-Seq® Assay User Guide (Version 2.1, September 6, 2017).
Four hours following the last treatment, the media was aspirated from control (C0) and treated HepaRG™ cells (C1-C5). The cells were then washed with sterile PBS. Following aspiration of the PBS wash, 1X TempO-Seq lysis buffer was added to lyse the cells for 10 minutes at room temperature on a rocking plate. Lysed cells were then frozen at -80 degrees Celsius until library construction. The TempO-Seq® Assay User Guide (Version 2.1, September 6, 2017) was used to build the TempO-Seq libraries for panels with less than 5,000 probes using the TempO-Seq Reagent Kit with HumanTox+Surrogate Panel DO Kit in a 96-well format). Index Set A was used for plate 1, Index Set B for plate 2 and Index Set C for plate 3 (288 samples in total). Following amplification, libraries were pooled and purified using the Macherey-Nagel NucleoSpin Gel and PCR Cleanup Kit with modifications outlined in the TempO-Seq® User Guide. Pooled, purified libraires were quantified using the KAPA Biosystems qPCR library quantification kit and diluted to 4 nM for denaturation and dilution for sequencing.
Human TempO-Seq® Tox+ Surrogate (S1500+) kits - Index Sets A (plate 1), B (plate 2) & C (plate 3); sequenced using an Illumina NextSeq500.

treatment_protocol: Cells were then exposed in culture medium containing TRL's Pre-Induction/Tox Supplement to five concentrations of each DDI or non-DDI chemical plus matched vehicle controls daily for three days in a repeated exposure design (exposures at 0 hr, 24 hr, and 48 hr). Four hours following the last treatment (52 hr total time), one plate of cells was used for cell viability (n = 2 per treatment group alongside matched solvent controls) and CometChip® analysis and the second plate was used to generate cell lysates for gene expression analysis (n = 4 per treatment group per assay for CometChip® and TempO-Seq). The media was aspirated from exposed cells and they were washed with PBS, prior to adding 100 µl of TrypLE™ (for cell viability and CometChip® assays; ThermoFisher Scientific, Waltham, MA, USA) or 1X TempO-Seq Lysis Buffer in PBS (for TempO-Seq assay; BioSpyder Technologies, Carlsbad, CA, USA) to each well to lyse cells for 10 minutes at room temperature. Cell lysates were then frozen and stored at -80°C for subsequent TempO-Seq S1500+ transcriptome profiling. Samples used for the analysis of cell viability and DNA damage using CometChip® were neutralized with the addition of 100 µl of culture medium to each well and were processed as per manufacturer's User Guides.

value: Human Hepatoma HepaRG Cell Line

value: 2-Deoxy-D-Glucose (2DG)

tag: concentration

value: 0 µM

tag: index

value: GAATTGCTG

value: ATGCTCACA

tag: molecule source

value: Cell lysate (total RNA)


title: HCC3_2DG_C0_287

description:
Plate3_IndexC
HCC3_2DG_C0_287_S287

tag: cell line

value: AGACACAAT


title: HCC3_2DG_C0_285

description:
Plate3_IndexC
HCC3_2DG_C0_285_S285

value: GATTGTGTT


title: HCC3_CISP_C0_284

description:
Plate3_IndexC
HCC3_CISP_C0_284_S284

value: Cisplatin (Cisp)

value: GCCGTTACA


title: LysI_4 IKKβF/FLDLR-/- Peritoneal macrophages, PBS (Control)

value: Peritoneal macrophages (In vitro cultured)

value: IKKbetaF/FLDLR-/-

value: 12 hr


title: HCC3_2DG_C1_280

description:
Plate3_IndexC
HCC3_2DG_C1_280_S280

value: TGATTAAGC


title: HCC3_CISP_C0_283

description:
Plate3_IndexC
HCC3_CISP_C0_283_S283

value: TCTAACCAT


title: HCC3_CISP_C0_282

description:
Plate3_IndexC
HCC3_CISP_C0_282_S282

value: TAACGCGTC


title: HCC3_2DG_C1_279

description:
Plate3_IndexC
HCC3_2DG_C1_279_S279


title: HCC3_2DG_C1_277

description:
Plate3_IndexC
HCC3_2DG_C1_277_S277


title: HCC3_CISP_C1_276

description:
Plate3_IndexC
HCC3_CISP_C1_276_S276


title: HCC3_CISP_C1_273

description:
Plate3_IndexC
HCC3_CISP_C1_273_S273

value: ACGACTTGG


title: HCC3_CISP_C1_275

description:
Plate3_IndexC
HCC3_CISP_C1_275_S275

value: Human Hepatoma HepaRG Cell Line


title: HCC3_2DG_C1_278

description:
Plate3_IndexC
HCC3_2DG_C1_278_S278

value: 2-Deoxy-D-Glucose (2DG)

value: CGTAACTTA


title: HCC3_2DG_C2_270

description:
Plate3_IndexC
HCC3_2DG_C2_270_S270

value: ACACGTTAT


title: HCC3_2DG_C2_271

description:
Plate3_IndexC
HCC3_2DG_C2_271_S271


title: HCC3_CISP_C2_267

description:
Plate3_IndexC
HCC3_CISP_C2_267_S267


title: HCC3_CISP_C2_268

description:
Plate3_IndexC
HCC3_CISP_C2_268_S268


title: HCC3_2DG_C2_269

description:
Plate3_IndexC
HCC3_2DG_C2_269_S269


title: HCC3_CISP_C2_266

description:
Plate3_IndexC
HCC3_CISP_C2_266_S266


title: HCC3_CISP_C2_265

description:
Plate3_IndexC
HCC3_CISP_C2_265_S265


title: HCC3_2DG_C3_264

description:
Plate3_IndexC
HCC3_2DG_C3_264_S264

value: ATTGTTGCC

value: ATGCTCACA


title: HCC3_2DG_C3_262

description:
Plate3_IndexC
HCC3_2DG_C3_262_S262

value: Cell lysate (total RNA)


title: HCC3_2DG_C0_286

description:
Plate3_IndexC
HCC3_2DG_C0_286_S286

value: 0 µM

value: GAATTGCTG


title: HCC3_2DG_C3_261

description:
Plate3_IndexC
HCC3_2DG_C3_261_S261

value: GATTGTGTT


title: HCC3_CISP_C0_281

description:
Plate3_IndexC
HCC3_CISP_C0_281_S281

value: Cisplatin (Cisp)


title: HCC3_CISP_C1_274

description:
Plate3_IndexC
HCC3_CISP_C1_274_S274


title: HCC3_2DG_C2_272

description:
Plate3_IndexC
HCC3_2DG_C2_272_S272


title: HCC3_CISP_C3_260

description:
Plate3_IndexC
HCC3_CISP_C3_260_S260

value: GCCGTTACA


title: HCC3_CISP_C3_259

description:
Plate3_IndexC
HCC3_CISP_C3_259_S259


title: HCC3_CISP_C3_257

description:
Plate3_IndexC
HCC3_CISP_C3_257_S257


title: HCC3_CISP_C3_258

description:
Plate3_IndexC
HCC3_CISP_C3_258_S258


title: HCC3_2DG_C4_255

description:
Plate3_IndexC
HCC3_2DG_C4_255_S255

value: GGCAGACTT

value: AGACACAAT


title: HCC3_2DG_C4_256

description:
Plate3_IndexC
HCC3_2DG_C4_256_S256


title: HCC3_2DG_C3_263

description:
Plate3_IndexC
HCC3_2DG_C3_263_S263


title: HCC3_2DG_C5_248

description:
Plate3_IndexC
HCC3_2DG_C5_248_S248

value: ATTCGAATC


title: HCC3_2DG_C4_254

description:
Plate3_IndexC
HCC3_2DG_C4_254_S254


title: HCC3_CISP_C4_251

description:
Plate3_IndexC
HCC3_CISP_C4_251_S251

value: 25 µM

value: TCTAACCAT


title: HCC3_2DG_C4_253

description:
Plate3_IndexC
HCC3_2DG_C4_253_S253

value: Human Hepatoma HepaRG Cell Line


title: HCC3_2DG_C5_247

description:
Plate3_IndexC
HCC3_2DG_C5_247_S247

value: 2-Deoxy-D-Glucose (2DG)


title: HCC3_2DG_C5_245

description:
Plate3_IndexC
HCC3_2DG_C5_245_S245


title: HCC3_2DG_C5_246

description:
Plate3_IndexC
HCC3_2DG_C5_246_S246

value: CGTAACTTA


title: HCC3_CISP_C5_244

description:
Plate3_IndexC
HCC3_CISP_C5_244_S244

value: 50 µM


title: HCC3_CISP_C5_243

description:
Plate3_IndexC
HCC3_CISP_C5_243_S243


title: HCC3_CISP_C5_242

description:
Plate3_IndexC
HCC3_CISP_C5_242_S242

value: TAACGCGTC


title: HCC3_AraC_C0_239

description:
Plate3_IndexC
HCC3_AraC_C0_239_S239

value: Cytosine Arabinoside (AraC)

value: TGGAACGCT


title: HCC3_AraC_C0_240

description:
Plate3_IndexC
HCC3_AraC_C0_240_S240

value: 0 µM

value: ATGCTCACA

value: Cell lysate (total RNA)


title: HCC3_AraC_C0_237

description:
Plate3_IndexC
HCC3_AraC_C0_237_S237

value: GATTGTGTT


title: HCC3_AraC_C0_238

description:
Plate3_IndexC
HCC3_AraC_C0_238_S238


title: HCC3_AFB1_C0_236

description:
Plate3_IndexC
HCC3_AFB1_C0_236_S236

value: Aflatoxin B1 (AFB1)

value: GCCGTTACA


title: HCC3_AFB1_C0_235

description:
Plate3_IndexC
HCC3_AFB1_C0_235_S235


title: HCC3_AFB1_C0_234

description:
Plate3_IndexC
HCC3_AFB1_C0_234_S234


title: HCC3_AFB1_C0_233

description:
Plate3_IndexC
HCC3_AFB1_C0_233_S233

value: ACGACTTGG


title: HCC3_AraC_C1_232

description:
Plate3_IndexC
HCC3_AraC_C1_232_S232

value: TATCGCTCC


title: HCC3_CISP_C4_252

description:
Plate3_IndexC
HCC3_CISP_C4_252_S252

value: Cisplatin (Cisp)

value: 25 µM

value: GGCAGACTT


title: HCC3_AraC_C1_230

description:
Plate3_IndexC
HCC3_AraC_C1_230_S230

value: Human Hepatoma HepaRG Cell Line


title: HCC3_AraC_C1_231

description:
Plate3_IndexC
HCC3_AraC_C1_231_S231

value: AGACACAAT


title: HCC3_CISP_C4_250

description:
Plate3_IndexC
HCC3_CISP_C4_250_S250


title: HCC3_CISP_C4_249

description:
Plate3_IndexC
HCC3_CISP_C4_249_S249


title: HCC3_AraC_C1_229

description:
Plate3_IndexC
HCC3_AraC_C1_229_S229


title: HCC3_CISP_C5_241

description:
Plate3_IndexC
HCC3_CISP_C5_241_S241

value: 50 µM

value: ATTCGAATC


title: HCC3_AFB1_C1_227

description:
Plate3_IndexC
HCC3_AFB1_C1_227_S227

value: TCTAACCAT


title: HCC3_AFB1_C1_226

description:
Plate3_IndexC
HCC3_AFB1_C1_226_S226

value: TAACGCGTC


title: HCC3_AFB1_C1_225

description:
Plate3_IndexC
HCC3_AFB1_C1_225_S225


title: HCC3_AraC_C2_223

description:
Plate3_IndexC
HCC3_AraC_C2_223_S223

value: Cytosine Arabinoside (AraC)

value: TAATGGCTT


title: HCC3_AFB1_C2_218

description:
Plate3_IndexC
HCC3_AFB1_C2_218_S218

value: Cell lysate (total RNA)


title: HCC3_AFB1_C2_217

description:
Plate3_IndexC
HCC3_AFB1_C2_217_S217


title: HCC3_AraC_C2_224

description:
Plate3_IndexC
HCC3_AraC_C2_224_S224

value: ATGCTCACA


title: HCC3_AFB1_C2_220

description:
Plate3_IndexC
HCC3_AFB1_C2_220_S220

value: Aflatoxin B1 (AFB1)


title: HCC3_AFB1_C2_219

description:
Plate3_IndexC
HCC3_AFB1_C2_219_S219


title: HCC3_AraC_C3_214

description:
Plate3_IndexC
HCC3_AraC_C3_214_S214

value: TCGCCACTC

value: CGTAACTTA


title: HCC3_AraC_C2_222

description:
Plate3_IndexC
HCC3_AraC_C2_222_S222


title: HCC3_AFB1_C3_211

description:
Plate3_IndexC
HCC3_AFB1_C3_211_S211


title: HCC3_AFB1_C3_212

description:
Plate3_IndexC
HCC3_AFB1_C3_212_S212

value: GCCGTTACA


title: HCC3_AraC_C3_216

description:
Plate3_IndexC
HCC3_AraC_C3_216_S216


title: HCC3_AFB1_C3_210

description:
Plate3_IndexC
HCC3_AFB1_C3_210_S210


title: HCC3_AFB1_C3_209

description:
Plate3_IndexC
HCC3_AFB1_C3_209_S209

value: ACGACTTGG


title: HCC3_AFB1_C1_228

description:
Plate3_IndexC
HCC3_AFB1_C1_228_S228

value: TATCGCTCC


title: HCC3_AraC_C4_207

description:
Plate3_IndexC
HCC3_AraC_C4_207_S207

value: ATGTGTGCT


title: HCC3_AraC_C4_208

description:
Plate3_IndexC
HCC3_AraC_C4_208_S208

value: Human Hepatoma HepaRG Cell Line


title: HCC3_AraC_C4_205

description:
Plate3_IndexC
HCC3_AraC_C4_205_S205

value: GATTGTGTT


title: HCC3_AFB1_C4_204

description:
Plate3_IndexC
HCC3_AFB1_C4_204_S204

value: 15 µM


title: HCC3_AFB1_C4_203

description:
Plate3_IndexC
HCC3_AFB1_C4_203_S203


title: HCC3_AraC_C4_206

description:
Plate3_IndexC
HCC3_AraC_C4_206_S206


title: HCC3_AFB1_C4_202

description:
Plate3_IndexC
HCC3_AFB1_C4_202_S202


title: HCC3_AFB1_C4_201

description:
Plate3_IndexC
HCC3_AFB1_C4_201_S201


title: HCC3_AraC_C2_221

description:
Plate3_IndexC
HCC3_AraC_C2_221_S221

value: 25 µM


title: HCC3_AraC_C3_215

description:
Plate3_IndexC
HCC3_AraC_C3_215_S215

value: 50 µM

value: AGACACAAT


title: HCC3_AraC_C3_213

description:
Plate3_IndexC
HCC3_AraC_C3_213_S213

value: Cytosine Arabinoside (AraC)


title: HCC3_AraC_C5_200

description:
Plate3_IndexC
HCC3_AraC_C5_200_S200

value: ATGAGTTCC


title: HCC3_AraC_C5_199

description:
Plate3_IndexC
HCC3_AraC_C5_199_S199

value: Cell lysate (total RNA)


title: HCC3_AraC_C5_198

description:
Plate3_IndexC
HCC3_AraC_C5_198_S198


title: HCC3_AFB1_C5_195

description:
Plate3_IndexC
HCC3_AFB1_C5_195_S195

value: TCTAACCAT


title: HCC3_AFB1_C5_194

description:
Plate3_IndexC
HCC3_AFB1_C5_194_S194

value: Aflatoxin B1 (AFB1)

value: TAACGCGTC


title: HCC3_AFB1_C5_196

description:
Plate3_IndexC
HCC3_AFB1_C5_196_S196


title: HCC3_AFB1_C5_193

description:
Plate3_IndexC
HCC3_AFB1_C5_193_S193


title: HCC3_EUG_C0_191

description:
Plate2_IndexB
HCC3_EUG_C0_191_S191

value: Eugenol (Eug)

value: 0 µM

value: GTAGCTCCA

value: GGTCTAGCT


title: HCC3_EUG_C0_190

description:
Plate2_IndexB
HCC3_EUG_C0_190_S190

value: ATACCGGCA


title: HCC3_Urea_C0_186

description:
Plate2_IndexB
HCC3_Urea_C0_186_S186

value: Human Hepatoma HepaRG Cell Line

value: Urea

value: GCAGATGCA


title: HCC3_Urea_C0_187

description:
Plate2_IndexB
HCC3_Urea_C0_187_S187

value: AAGTAGGCT


title: HCC3_EUG_C0_189

description:
Plate2_IndexB
HCC3_EUG_C0_189_S189

value: GCACCTATT


title: HCC3_Urea_C0_185

description:
Plate2_IndexB
HCC3_Urea_C0_185_S185

value: TATGCTATG


title: HCC3_EUG_C1_184

description:
Plate2_IndexB
HCC3_EUG_C1_184_S184

value: TCAGCTAAT

value: TTGACGCTA


title: HCC3_EUG_C1_183

description:
Plate2_IndexB
HCC3_EUG_C1_183_S183

value: Cell lysate (total RNA)


title: HCC3_EUG_C1_182

description:
Plate2_IndexB
HCC3_EUG_C1_182_S182


title: HCC3_Urea_C1_180

description:
Plate2_IndexB
HCC3_Urea_C1_180_S180

value: ATACGCAGC


title: HCC3_Urea_C1_178

description:
Plate2_IndexB
HCC3_Urea_C1_178_S178


title: HCC3_Urea_C1_179

description:
Plate2_IndexB
HCC3_Urea_C1_179_S179


title: HCC3_EUG_C1_181

description:
Plate2_IndexB
HCC3_EUG_C1_181_S181


title: HCC3_Urea_C1_177

description:
Plate2_IndexB
HCC3_Urea_C1_177_S177


title: HCC3_EUG_C2_176

description:
Plate2_IndexB
HCC3_EUG_C2_176_S176

value: TGCTTATTC


title: HCC3_AraC_C5_197

description:
Plate3_IndexC
HCC3_AraC_C5_197_S197

value: Cytosine Arabinoside (AraC)

value: ATGAGTTCC

value: GATTGTGTT


title: HCC3_EUG_C2_175

description:
Plate2_IndexB
HCC3_EUG_C2_175_S175

value: Eugenol (Eug)


title: HCC3_EUG_C2_174

description:
Plate2_IndexB
HCC3_EUG_C2_174_S174


title: HCC3_EUG_C2_173

description:
Plate2_IndexB
HCC3_EUG_C2_173_S173


title: HCC3_Urea_C2_172

description:
Plate2_IndexB
HCC3_Urea_C2_172_S172


title: HCC3_Urea_C2_171

description:
Plate2_IndexB
HCC3_Urea_C2_171_S171


title: HCC3_Urea_C2_170

description:
Plate2_IndexB
HCC3_Urea_C2_170_S170


title: HCC3_Urea_C2_169

description:
Plate2_IndexB
HCC3_Urea_C2_169_S169


title: HCC3_Urea_C0_188

description:
Plate2_IndexB
HCC3_Urea_C0_188_S188

value: 0 µM

value: GTAGCTCCA


title: HCC3_EUG_C3_168

description:
Plate2_IndexB
HCC3_EUG_C3_168_S168

value: Human Hepatoma HepaRG Cell Line

value: GCGATAGTG


title: HCC3_EUG_C3_166

description:
Plate2_IndexB
HCC3_EUG_C3_166_S166

value: ATACCGGCA


title: HCC3_EUG_C3_165

description:
Plate2_IndexB
HCC3_EUG_C3_165_S165


title: HCC3_Urea_C3_163

description:
Plate2_IndexB
HCC3_Urea_C3_163_S163

value: Urea

value: AAGTAGGCT


title: HCC3_EUG_C0_192

description:
Plate2_IndexB
HCC3_EUG_C0_192_S192


title: HCC3_EUG_C3_167

description:
Plate2_IndexB
HCC3_EUG_C3_167_S167

value: GGTCTAGCT


title: HCC3_EUG_C4_160

description:
Plate2_IndexB
HCC3_EUG_C4_160_S160

value: TTCCGCACC


title: HCC3_Urea_C3_161

description:
Plate2_IndexB
HCC3_Urea_C3_161_S161

value: TATGCTATG


title: HCC3_Urea_C3_164

description:
Plate2_IndexB
HCC3_Urea_C3_164_S164

value: Cell lysate (total RNA)


title: HCC3_EUG_C4_159

description:
Plate2_IndexB
HCC3_EUG_C4_159_S159


title: HCC3_EUG_C4_158

description:
Plate2_IndexB
HCC3_EUG_C4_158_S158


title: HCC3_Urea_C4_155

description:
Plate2_IndexB
HCC3_Urea_C4_155_S155


title: HCC3_Urea_C4_156

description:
Plate2_IndexB
HCC3_Urea_C4_156_S156

value: ATACGCAGC


title: HCC3_EUG_C4_157

description:
Plate2_IndexB
HCC3_EUG_C4_157_S157

value: GCACCTATT


title: HCC3_Urea_C4_154

description:
Plate2_IndexB
HCC3_Urea_C4_154_S154

value: GCAGATGCA


title: HCC3_ctrl_UHRR_152

description:
Plate2_IndexB
HCC3_ctrl_UHRR_152_S152

value: No cells; Universal human +ve control

value: No cells; Universal human +ve control_0

value: ATCGCGACT

value: TTGACGCTA


title: HCC3_Urea_C4_153

description:
Plate2_IndexB
HCC3_Urea_C4_153_S153


title: HCC3_ctrl_UHRR_151

description:
Plate2_IndexB
HCC3_ctrl_UHRR_151_S151


title: HCC3_Urea_C3_162

description:
Plate2_IndexB
HCC3_Urea_C3_162_S162


title: HCC3_ctrl_neg_149

description:
Plate2_IndexB
HCC3_ctrl_neg_149_S149

value: No cells; Negative control

value: No cells; Negative control_0


title: F_4_q

city: Stockholm

first: Szabolcs

last: Éliás

address: Karolinska University Hospital

institute: Karolinska Institute

data_processing:
Base-calling was performed using Illumina HiSeq Control/Real Time Analysis software.
Base-call files were demultiplexed and converted to fastq files using bcl2fastq version 2.17.1.14.
Fastq files were adapter-trimmed using scythe version 0.991 and quality-trimmed using sickle version 1.33.
Trimmed fastq files were aligned to the human genome version hg38 using bowtie version 2.3.0 with the ‘--very-sensitive’ setting.
Bam files were sorted, indexed and filtered using samtools version 0.1.19 to remove duplicates, alignments with a mapping score below 10, and alignments not mapped to chromosomes 1-22, X or Y.
Peak-calling was performed using the ‘findPeaks’ script from the Homer suite version 4.9.1 with the '-style factor' setting.
A consensus peak-set containing genomic regions with reproducible accessibility was generated as described in the accompanying publication.
Reads in the genomic regions defined by the consensus peak-set were counted for each sample using the featureCounts version 1.5.2 with the settings ‘-s 0 –minOverlap 1 --fracOverlap 0.5’.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text file containing read counts at reproducibly accessible genomic regions (consensus peaks)

source_name: Peripheral Blood

growth_protocol: Primary cells from human peripheral blood.

extract_protocol:
Nuclear isolation was carried out according to Buenrostro et al. 2013 (PMID: 24097267).
Library construction including tagmentation and PCR amplification was performed according to Buenrostro et al. 2013 (PMID: 24097267) followed by additional gel size selection of DNA in the size range of 150-230 base pairs.

treatment_protocol: Peripheral blood mononuclear cell (PBMC) isolation by Ficoll gradient, followed by magnetic activated cell sorting (MACS) of given CD4 T cell sub-populations as follows. Naive, total (bulk) and memory CD4 T cells were isolated in parallel by negative magnetic isolation according to the manufacturer's protocol (Miltenyi Biotec). From an aliquot of total CD4 T cells, GM-CSF producing and GM-CSF negative cells were subsequently isolated without restimulation using the GM-CSF Secretion Assay - Cell Enrichment and Detection Kit (PE), human (Miltenyi Biotec), according to the manufacturer’s instructions. For each isolated cell type and donor, three technical replicates (denoted “p”, “q”, “r”; except donor A, two technical replicates) with 50000 cells each were further processed.

value: Peripheral Blood

tag: cell type

value: Bulk CD4 T cells

value: F

tag: gender

value: male


title: F_3_q

value: GM-CSF negative CD4 T cells


title: F_4_p


title: HCC3_ctrl_UHRR_150

description:
Plate2_IndexB
HCC3_ctrl_UHRR_150_S150

value: Human Hepatoma HepaRG Cell Line

value: ATACCGGCA


title: F_3_r


title: F_2_r

value: GM-CSF positive CD4 T cells


title: HCC3_Urea_C5_147

description:
Plate2_IndexB
HCC3_Urea_C5_147_S147

value: Urea

value: AAGTAGGCT

value: Cell lysate (total RNA)


title: F_3_p