title: blood_covid+_CB0106_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0106-05

tag: participant id


title: MYC_NoTrp, 108

status: Public on Sep 30 2023

type: SRA

city: Dallas

first: Jiwoong

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern Medical Center

library_source: transcriptomic

data_processing:
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality and adapter trimming. STAR (v2.7.2b) (Dobin et al., 2013) was employed to align the reads onto the mouse genome, SAMtools (v1.9) (Li et al., 2009) was employed to sort the alignments, and HTSeq Python package (Anders et al., 2015) was employed to count reads per gene.
The mouse reference genome sequence and gene annotation data, mm10, were downloaded from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). The qualities of RNA sequencing libraries were estimated by mapping the reads onto mouse transcript and ribosomal RNA sequences (Ensembl release 89) using Bowtie (v2.3.4.3). STAR (v2.7.2b) was sed to align the reads onto the mouse genome. SAMtools (v1.9) was used to sort the alignments, and HTSeq Python package was used to count reads per gene. DESeq2 R Bioconductor package was used to normalize read counts and identify differentially expressed (DE) genes. KEGG pathway data was downloaded using KEGG API (https://www.kegg.jp/kegg/rest/keggapi.html) and gene ontology (GO) data was downloaded from NCBI FTP (ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz). The enrichment of DE genes to pathways and GOs were calculated by Fisher's exact test in R statistical package. The reads were aligned to mouse RefSeq RNA sequences using Burrows-Wheeler Aligner (BWA, v0.7.17) with MEM algorithm and the options, -T 19 -h 200 -Y, and primary alignments with proper read pairs were selected by SAMtools with the options, -f 3 -F 2316, to count the reads aligned to ribosomal RNA sequences defined by the sequence descriptions containing the keyword of ribosomal RNA or rRNA. The reads were aligned to human MYC RNA isoform 1 sequence (NM_002467.6) using BWA with MEM algorithm. The alignments were compared with the alignments to mouse genomic and RNA sequences from NCBI Assembly, GRCm38.p6, using a custom Perl script named REMOCON (https://github.com/jiwoongbio/REMOCON) and the reads with better alignments to human MYC were counted.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include gene read counts for each sample
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Mus musculus

source_name: liver

growth_protocol: MYC-driven liver tumor model was generated by crossing TRE-MYC with LAP-tTA mouse. Male breeders with 2 copies of LAP-tTA and single copy of TRE-MYC was crossed with WT FVB females to generate LAP-tTA/TRE-MYC mice used for experiments. The breeders were maintained on doxycycline water (1 mg/mL). The females with the litters were transferred to a fresh cage on the day of birth to activate MYC overexpression. Animals were maintained on a regular chow diet. For comparison between WT and MYC overexpression, FVB WT males were used. Both the WT males and MYC overexpression males were 45 days old.

extract_protocol: RNA-seq was performed by Genewiz and the data processing was done using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for quality and adapter trimming

treatment_protocol: For the experiments with different Trp diet, the mice were transferred to either the control diet, or No-Trp diet for 21 days

tag: tissue

value: liver

tag: injected cell_type

tag: host mouse_genotype

tag: cancer cell_genotype

value: FVB MYC ON

tag: treatment

value: No Trp Diet


title: NC.D2_Plate1.D3

city: Sendai

first: Kota

last: Sato

state: Miyagi

address: 1-1, Seiryo-machi, Aoba-ku

department: Ophthalmology

country: Japan

institute: Tohoku University

library_source: transcriptomic single cell

data_processing:
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software. Trimmed reads were then mapped to the mouse GRCm38.p6 (mm10) genome with STAR software (version 2.7.2b). Reads on annotated genes were counted using featureCounts (version 1.6.1). FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

molecule: total RNA

source_name: retina

extract_protocol:
Total RNA were directly extracted with lysis buffer inculding Rnase inhibitor from single cell sorted with FACS.
RNA sequence library preparation, sequencing, mapping, gene expression, and gene ontology (GO) enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). cDNA synthesis and amplification of RNA derived from lysed cell was sequentially conducted in a same PCR tube. After purification, amplified cDNA was validated and quantified. Following tagmentation of cDNA, adapter addition and PCR amplification were conducted using Nextera XT DNA Library Prep Kit (Illumina).

tag: cell type

value: microglia

value: retina

tag: strain

tag: age

value: 16 weeks old

value: nerve crush day 2


title: NC.D2_Plate1.D2


title: MYC_NoTrp, 107


title: Donor 3 pRNA stimulated BDCA3

type: RNA

city: Nijmegen

first: Johannes

last: Textor

address: Geert Groteplein 26-28

country: Netherlands

institute: Radboud University Medical Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: According to the standard Affymetrix protocol by ThermoFisher (Clariom D Expression Analysis Technical Manual revision B.0, ThermoFisher).

data_processing: Expression intensities from CEL files were converted to an expression matrix using the bioconductor packages affycoretools, version 1.70.0, and oligo, version 1.62.2.

label: biotin

organism: Homo sapiens

source_name: Blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol by ThermoFisher (Clariom D Expression Analysis Technical Manual revision B.0, ThermoFisher).

growth_protocol: Cells were obtained from aphaeresis of 5 different donors. Peripheral blood mononuclear cells (PBMCs) were isolated by using Ficoll density centrifugation (Lymphoprep; Axis-Shield PoC AS, Oslo, Anti-Human Lineage Cocktail 1 in FITC (LIN1) (BD Bioscience Pharmingen, San Jose, CA) containing antibodies for CD3, CD14, CD16, CD19, CD20, CD56 receptors, together with the anti-FITC conjugated magnetic microbeads of Miltenyi Biotec (Bergisch-Gladbach, Germany) were used to deplete the LIN1+ cell fraction, by following manufacturer’s instructions. Next, CDC1were further purified by sorting (flowcytometry) using anti–BDCA-3–APC combined with anti-HLA-DR-PE-Vio770 (Miltenyi Biotec) to a purity of 99.9%. DCs were cultured in X-VIVO-15 medium (Lonza, Basel, Switzerland) supplemented with 2% human serum (Sanquin).

extract_protocol: RNA was harvested using Trizol (Invitrogen, MA, USA), following the standard protocol. Quality control of the isolated RNA (concentration, RIN, 28S/18S and size) was performed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

treatment_protocol: DCs were stimulated with: pRNA (15μg/ ml) and Hiltonol (10 μg/ml) for 16 hours.

value: cDC1 (BDCA3+ DC)

value: pRNA


title: Donor 3 Hiltonol stimulated BDCA3

value: Hiltonol


title: Donor 3 unstimulated BDCA3


title: NC.D2_Plate1.D1


title: blood_covid+_CB0106_timepoint 4

city: Seattle

first: Fang Yun

last: Lim

state: WA

address: 1100 Eastlake Ave E

department: Vaccine and Infectious Disease Division

institute: Fred Hutchinson Cancer Center

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0106-04

data_processing: nCounter RCC files of all samples were pre-processed on the nSolverTM software (nanoString) to obtain normalized expression counts. Quality control (QC) measures were applied to all participant samples.  Imaging QC was assessed by measuring the percent field of view (FOV) successfully scanned within each sample. Samples with scanned FOV < 75% were flagged for removal. Binding density QC was assessed by measuring the density of the reporter probe on the cartridge surface within each sample. Samples with binding density outside of 0.1 - 2.25 spots/square micron were flagged for removal. The correlations between the observed counts for all six positive ERCC control probes (Positives A – F) and their spike-in synthetic nucleic acids (0.125 fM – 128 fM) were used to determine a sample’s positive control linearity. Samples with positive control linearity of < 0.95 were flagged for removal. Gene expression count normalization was performed on all samples that passed the QC metrics above. For normalization, all samples were subjected to i) positive control normalization, ii) codeset content normalization, and iii) panel standard normalization. Nine reference genes (ABCF1, GUSB, HRPT1, MRPS7, NMT1, NRDE2, PGK1, SDHA, TBP) were used in codeset content normalization.

label: Molecular barcode with using 4 fluorophores (Alexa 488, Alexa 594, Alexa 647, Cy3) in 7 positions: https://www.nature.com/articles/nbt1385

source_name: acute phase COVID-19+ participants-longitudinal

label_protocol: color-coded reporter and capture probes from manufacturer (nCounter codeset chemistry): https://nanostring.com/wp-content/uploads/MAN-10056-05-Gene-Expression-Hybridization-Protocol.pdf

growth_protocol: Capillary blood was self-collected and immediately stabilized using a home-use blood collection kit (homeRNA). Stabilized blood were mailed back to the lab and samples stored at -80ºC until ready for RNA extraction.

tag: disease status

tag: Sex

value: male

tag: covid-19 vaccination history

value: unvaccinated

tag: day post symptom onset

tag: study day

tag: ncounter host response codeset


title: blood_covid+_CB0106_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0106-02


title: blood_covid+_CB0106_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0106-03


title: MYC_control, 103

value: Complete diet


title: blood_covid+_CB0106_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0106-01


title: MYC_NoTrp, 105


title: blood_covid+_CB0104_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0104-07

value: female

value: vaccinated


title: Donor 2 pRNA stimulated BDCA3


title: NC.D0_Plate3.C6

value: no treatment


title: MYC_control, 102


title: Donor 2 Hiltonol stimulated BDCA3


title: NC.D0_Plate3.C5


title: Donor 1 Hiltonol+pRNA stimulated BDCA3

value: Hiltonol+pRNA


title: Donor 2 unstimulated BDCA3


title: blood_covid+_CB0104_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0104-06


title: RNA-Seq - Vero-Spike-1

city: Boston

first: Jonathan

middle: David

last: Lee

state: MA

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

data_processing:
Raw sequencing reads were aligned to a reference transcriptome generated from the Ensembl v104 GRCh38 or ChlSab1.1 databases with salmon v1.4.0 using options “--seqBias --useVBOpt --gcBias --posBias --numBootstraps 30 --validateMappings”.
Assembly: hg38 or ChlSab1.1
Supplementary files format and content: ".sf files from salmon v1.4.0. The columns represent the following: Name: the name of the target transcript provided in the input transcript database (FASTA file). Length: the length of the target transcript in nucleotides. EffectiveLength: the computed effective length of the target transcript. TPM: the estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM). NumReads: the estimate of the number of reads mapping to each transcript that was quantified."

organism: Chlorocebus sabaeus

growth_protocol: VeroE6 (ATCC, CRL-1586) cells were maintained in DMEM (Gibco) supplemented with 10% FBS (Sigma) and 1% penicillin/streptomycin (Thermo). A549 (ATCC, CCL-185) and A549 TP53ko cells (a gift from Dr. William Hahn) were cultured in DMEM/F-12 (Gibco) supplemented with 10% FBS (Sigma) and 1% penicillin/streptomycin (Thermo). Cells were incubated at 37 °C and 5% CO2.

extract_protocol:
Cells were lysed using Trizol reagent (Thermo Fisher) and RNA was extracted by phase separation. Total RNA was quantified by nanodrop (DeNovix DS-11) and TapeStation 4200 (RNA Screen Tape; Agilent Technologies, Inc) or 2100 Bioanalyzer (Total RNA Nano; Agilent Technologies, Inc).
500 ng of total RNA was used for library preparation via the KAPA mRNA HyperPrep kit (Roche) according to the manufacturer’s recommendations. Briefly, mature mRNA was isolated from total RNA using mRNA Capture Beads. Following elution in Fragment, Prime and Elute buffer (FPE), RNA was fragmented using heat (6 min at 94oC) in the presence of Mg2+. First and second strand synthesis and A-tailing were performed according to manufacturer’s recommendations. 7 μM KAPA Unique Dual-Indexed (UDI, Roche) adapters were ligated to the second strand synthesis product in the presence of a ligation master mix in a reaction that was performed at 20 oC for 15 min. Following cleanup, all libraries underwent 11 cycles of amplification. Successful library production, quality control, and quantification was assessed using Tapestation (High sensitivity D1000 Screen Tape, Agilent). Libraries were pooled together and subjected to NovaSeq 6000.

treatment_protocol: Doxycycline (Sigma, D9891) induction of gene expression was performed with 1 μg/mL treatment in media for 48 hours.

tag: cell line

value: Ancestral (WA1) spike expression, doxycycline induction, 48h


title: MYC_control, 101

value: liver

value: FVB MYC ON


title: NC.D0_Plate3.C1

value: microglia


title: RNA-Seq - Vero-Spike-2


title: NC.D0_Plate3.C4

value: retina


title: NC.D0_Plate3.C3

value: 16 weeks old


title: rHSC + [SO3] HMGB1#3

city: Chicago

first: Xiaodong

last: Ge

state: IL

address: 909 South Wolcott Ave, COMRB 6140

department: Pathology

institute: The University of Illinois at Chicago

description: XG#14 4-3

data_processing:
Data were aligned using RNA-Seq Alignment v.2.0.1 in basespce
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count for each sample

organism: Rattus norvegicus

extract_protocol:
Total liver RNA was isolated with illustra™ RNAspin Mini RNA Isolation Kit; HSC RNA was isolated with Qiagen miRNeasy micro kit.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA library prep

treatment_protocol: Mice were injected with MO or CCl4 for 4 weeks and or regressed for 1 week, HSC was administrated with different HMGB1 isoforms for 6 hours

value: Hepatic Stellate cell

tag: genotype

value: WT

tag: time

value: 6 hours

value: [SO3] HMGB1

tag: gender

value: Male


title: RNA-Seq - Vero-EGFP-2

value: EGFP expression, doxycycline induction, 48h


title: NC.D0_Plate3.C2

tag: tissue


title: Donor 1Hiltonol stimulated BDCA3

value: cDC1 (BDCA3+ DC)

value: Hiltonol


title: rHSC + [SO3] HMGB1#1

description: XG#14 4-1


title: Donor 1 pRNA stimulated BDCA3

value: pRNA


title: rHSC + [SO3] HMGB1#2

description: XG#14 4-2


title: blood_covid+_CB0104_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0104-02

tag: participant id

value: female

value: vaccinated


title: blood_covid+_CB0104_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0104-05


title: blood_covid+_CB0104_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0104-03


title: rHSC + [O] HMGB1#3

description: XG#14 3-3

value: [O] HMGB1


title: NC.D0_Plate3.B6

value: no treatment


title: RNA-Seq - Vero-Delta-2

value: Delta (B.1.617.2) spike expression, doxycycline induction, 48h


title: RNA-Seq - Vero-EGFP-1


title: RNA-Seq - Vero-Delta-1


title: blood_covid+_CB0104_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0104-01


title: rHSC + [O] HMGB1#2

description: XG#14 3-2


title: NC.D0_Plate3.B5

value: microglia


title: Donor 1 unstimulated BDCA3


title: RNA-Seq - Vero-Alpha-2

value: Alpha (B.1.1.7) spike expression, doxycycline induction, 48h


title: rHSC + [O] HMGB1#1

description: XG#14 3-1


title: NC.D0_Plate3.B4

value: retina

value: 16 weeks old


title: blood_covid+_CB0102_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0102-07

value: unvaccinated


title: rHSC + [H] HMGB1#3

description: XG#14 2-3

value: Hepatic Stellate cell

value: WT

value: 6 hours

value: [H] HMGB1


title: NC.D0_Plate3.B3


title: rHSC + [H] HMGB1#1

description: XG#14 2-1

value: Male


title: rHSC + [H] HMGB1#2

description: XG#14 2-2


title: RNA-Seq - Vero-Alpha-1


title: NC.D0_Plate3.B2


title: blood_covid+_CB0104_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0104-04


title: rHSC + BSA#3

description: XG#14 1-3

value: BSA


title: NC.D0_Plate3.B1


title: ATAC-Seq - Vero-Nutlin-1

library_source: genomic

data_processing:
Paired-end sequencing reads were trimmed with TrimGalore v0.4.5 to remove adaptor sequence CTGTCTCTTATACACATCT, which arises at the 3’ end due to sequenced DNA fragments being shorter than the sequencing length (75 bp). For plasmid-transfected ATAC-seq datasets, trimmed reads were first aligned to plasmid DNA sequences using bowtie2 v2.2.9 with options “--no-mixed --dovetail --un-conc -X 2000”. Unaligned reads or reads from other experiments were aligned to either the hg38 or ChlSab1.1 reference genomes using bowtie2 v2.2.9 with options “--no-unal --no-discordant --no-mixed -X 2000”. Reads mapping to the mitochondrial genome were subsequently removed, and duplicate reads were removed with Picard v2.8.0.
Reads were downsampled to approximately 5 million paired-end fragments. Visualization was performed by mapping insertions to a genome-wide sliding 150 bp window with 20 bp offsets with bedops v2.4.30, followed by conversion to bigwig format with wigToBigWig from UCSC tools v363.
Assembly: hg38 or ChlSab1.1
Supplementary files format and content: BAM (.bam) file of aligned reads after filtering mitochondrial reads and duplicates
Supplementary files format and content: Bigwig (.bw) file of read pileups mapping to a 150 bp genomic window with 20 bp offsets for visualization

molecule: genomic DNA

extract_protocol:
ATAC-seq with iDAPT-MS profiling: VeroE6 cells were washed and suspended in 1xPBS. Cells were pelleted (500 x g, 5 min, 4 °C), incubated in 500 μL nuclei extraction buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton X-100, 20% glycerol, and 1x EDTA-free protease/phosphatase inhibitors [Thermo] in ultrapure water) per ~5e6 cells for 10 min on ice, and 50 μL DMSO mixed into the nuclear suspension prior to freezing cells at -80 °C. We found these lysis conditions to inactivate live SARS-CoV-2 virus for downstream handling and be compatible with high-quality ATAC-seq/iDAPT-MS profiling. 1.25 nmol MEDS-A/B, corresponding recombinant transposase (TP [transposase-peroxidase] or T [Tn5 transposase]) enzyme, and 0.5 nmol hemin chloride per sample were incubated at room temperature for 1 hr. Nuclei were thawed on ice, pelleted (1000 x g, 10 min, 4 °C), and resuspended in tagmentation buffer (20% dimethylformamide, 10 mM MgCl2, 20 mM Tris-HCl pH 7.5, 33% 1xPBS, 1% BSA, 0.01% digitonin, 0.1% Tween-20, 500 μM biotin-phenol, and 1x protease/phosphatase inhibitor) without transposome. Nuclei were counted with trypan blue (Thermo) with a Countess 3 (Thermo), and 5e6 nuclei per condition was resuspended in tagmentation buffer and 1 nmol transposome equivalent in a total volume of 500 μL, followed by incubation at 37 °C for 30 min with agitation on a thermomixer (1,000 rpm). 10 μL of tagmentation mix was saved for quality assessment as described below for ATAC-seq sample preparation.  ATAC-seq only: The OmniATAC sample preparation protocol was used as previously described with modifications where indicated below. Normalized transposase enzyme (in 2xDB) was mixed with 12.5 pmol MEDS-A/B (1.25 μL in water) and incubated at room temperature for 1 hr. In the meantime, 100,000 cells were centrifuged at 500 x g for 5 min at 4°C. Cells were resuspended in 50 μL lysis buffer 1 (LB1: 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.01% digitonin, 0.1% Tween-20, and 0.1% NP-40) with trituration, incubated on ice for 3 min, and then further supplemented with 1 mL lysis buffer 2 (LB2: 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20). Nuclei were pelleted (500 x g, 10 min, 4 °C), resuspended with 50 μL tagmentation reaction mixture (20% dimethylformamide, 10 mM MgCl2, 20 mM Tris-HCl pH 7.5, 33% 1xPBS, 0.01% digitonin, 0.1% Tween-20, and transposome complex in 50 μL total volume), and incubated at 37 °C for 30 min with agitation on a thermomixer (1,000 rpm). After tagmentation, DNA libraries were extracted with DNA Clean and Concentrator-5 (Zymo) and eluted with 21 μL water.
To determine optimal PCR cycle number for library amplification, quantitative PCR was performed similarly as previously reported on a StepOnePlus Real-Time PCR (Applied Biosystems) with the StepOne v2.3 software. 2 μL of each ATAC-seq library was added to 2x NEBNext Master Mix (NEB) and 0.4x SYBR Green (Thermo Fisher) with 1.25 μM of each primer (Primer 1.1: 5’-AATGATACGGCGACCACCGAGATCTACACTAGATCGCTCGTCGGCAGCGTCAGATGTGTAT-3’; Primer 2.1: 5’-CAAGCAGAAGACGGCATACGAGATTCGCCTTAGTCTCGTGGGCTCGGAGATGT-3’) in a final volume of 15 μL, and quantification was assessed using the following conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. Optimal PCR cycle number was determined as the qPCR cycle yielding fluorescence between 1/4 and 1/3 of the maximum fluorescence. The remaining DNA library was then amplified accordingly by PCR using previously reported barcoded primers for library multiplexing, purified with DNA Clean and Concentrator-5 (Zymo), and eluted into 20 μL final volume with water. Libraries were then subject to TapeStation 2200 High Sensitivity D1000 fragment size analysis (Agilent), MiSeq Nano v2 sequencing for library normalization, and NovaSeq 6000 paired-end sequencing for deep sequencing (Illumina).

treatment_protocol: Coronaviruses were added to cells at an MOI 0.5 for 48 hours. All work with infectious virus was performed in a Biosafety Level 3 laboratory and approved by the Yale University Biosafety Committee.  Plasmid transfections: 1e6 VeroE6 cells were reverse transfected with expression plasmids via TransIT-X2 (Mirus) at a 1:3 ratio (2.5 μg plasmid, 7.5 μL TransIT-X2, and 250 μL OptiMEM). Cells were harvested 48 hr after transfection. After 8 hr post-transfection, puromycin was added at a final concentration of 5 μg/mL to enrich for positively transfected cells.   Doxycycline (Sigma, D9891) induction of gene expression was performed with 1 μg/mL treatment in media for 48 hours.   Nutlin-3a (Selleckchem, S8059) was diluted in DMSO and added to cells at 10 uM for 24 hours.

tag: enzyme

value: 1 uM nutlin-3a treatment, 24 h


title: blood_covid+_CB0102_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0102-06

value: female


title: NC.D0_Plate3.A5

tag: treatment


title: blood_covid+_CB0102_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0102-05


title: ATAC-Seq - Vero-DMSO-1

value: DMSO treatment, 24 h


title: blood_covid+_CB0102_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0102-01


title: blood_covid+_CB0102_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0102-03


title: blood_covid+_CB0102_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0102-02


title: ATAC-Seq - Vero-iDAPT-Spike-TP-2

value: Ancestral (WA1) spike expression, doxycycline induction, 48h


title: ATAC-Seq - Vero-DMSO-2


title: ATAC-Seq - Vero-Nutlin-2


title: NC.D0_Plate3.A6

tag: cell type

value: no treatment


title: rHSC + BSA#2

description: XG#14 1-2


title: blood_covid+_CB0101_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0101-06


title: blood_covid+_CB0101_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0101-07


title: NC.D0_Plate3.A3

tag: strain


title: NC.D0_Plate3.A4

tag: age


title: NC.D0_Plate3.A2


title: RIP-seq GFP control D35 rep2

city: Vienna

first: Ruben

last: Gutzat

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute GmbH

data_processing:
Reads were trimmed to 21 - to 24-nt in length (cutadapt v 1.18) with parameters "cutadapt -a AACTGTAGGCACCATCAAT -g GTTCAGAGTTCTACAGTCCGACGATC -m 21 -M 24 --discard-untrimmed"
Trimmed reads are aligned to Arabidopsis TAIR 10 Genome using bowtie2 (v 2.3.5.1) with parameters "bowtie2 -k 1000 --no-unal"
Raw count table was achieved by using featureCounts from subread (v 2.0.1) with parameter "featureCounts -s 0 -M --fraction -t pseudogene,gene,transposable_element"
Raw counts were normalized to read per million (RPM)
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix table with normalized read per million for every gene and transposon for every sample. The table contains GeneID, Chr, Start, End, Strand, Length, from 21 to 24nt RPM count of sample A, 21nt RPM count of sample A, 22nt RPM count of sample A, 23nt RPM count of sample A, 24nt RPM count of sample A, from 21 to 24nt RPM count of sample B,  21nt RPM count of sample B, 22nt RPM count of sample B, 23nt RPM count of sample B, 24nt RPM count of sample B, and so on

organism: Arabidopsis thaliana

source_name: infloresence meristem, floral meristems and young flower buds

growth_protocol: Seedlings were grown on soil at standard growth conditions (16h light/8h dark). Shoot apices harvested at 7 days and inflorescence meristem, flower meristems and young flower buds at 35 days after germination

extract_protocol:
GFP-AGO5 and GFP-AGO9 were immo-precipitated and trizol reagent were used to extract AGO5- and AGO9-bound sRNAs
Libraries were prepared according to Qiagen miRNA library Kit (Cat. No. 331502)

tag: genotype/variation

value: p35S::GFP in col-0

value: 35 days after germination

value: meristem and young flower buds

tag: molecule subtype

value: RNA extract from immuno-precipitation


title: ATAC-Seq - Vero-iDAPT-Spike-TP-1


title: ATAC-Seq - Vero-iDAPT-Spike-T-2


title: RIP-seq Input D35 rep1

value: pAGO5::GFP-AGO5 in col-0


title: NC.D0_Plate3.A1

value: microglia

value: retina

value: 16 weeks old


title: ATAC-Seq - Vero-iDAPT-EGFP-TP-2

value: EGFP expression, doxycycline induction, 48h


title: RIP-seq GFP control D35 rep1


title: NC.D0_Plate2.C6


title: ATAC-Seq - Vero-iDAPT-EGFP-TP-1


title: blood_covid+_CB0101_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0101-04

tag: disease status

tag: Sex

tag: covid-19 vaccination history

value: unvaccinated


title: ATAC-Seq - Vero-iDAPT-Spike-T-1


title: blood_covid+_CB0101_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0101-05

tag: day post symptom onset

tag: study day

tag: ncounter host response codeset


title: blood_covid+_CB0101_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0101-02


title: blood_covid+_CB0101_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0101-03


title: NC.D0_Plate2.C5


title: ATAC-Seq - Vero-iDAPT-EGFP-T-2

tag: cell line


title: rHSC + BSA#1

description: XG#14 1-1

value: Hepatic Stellate cell

tag: genotype

value: WT

tag: time

value: 6 hours

tag: gender

value: Male


title: RIP-seq AGO9 D35 rep2

value: pAGO5::GFP-AGO9 in col-0

tag: tissue


title: RIP-seq AGO9 D35 rep1


title: NC.D0_Plate2.C4

tag: treatment


title: ATAC-Seq - Vero-iDAPT-EGFP-T-1

tag: enzyme


title: RIP-seq AGO5 D35 rep2


title: blood_covid+_CB0101_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0101-01

tag: participant id

value: female


title: leaf, treatment with biocontrol agent and fungal pathogen, rep3 [Cl_3CPT3]

city: Catania

first: Angela Roberta

last: Lo Piero

state: CT

address: Via S. Sofia 98

country: Italy

institute: University of Catania

data_processing:
Base calling, base quality and Phred score relationship performed with the Illumina CASAVA v1.8 software
Raw reads are filtered to remove reads containing adapters or reads of low quality
Clean reads have been assembled using Trinity software (2.6.6 version, minKmerCov= 3, min_glue=4). Corset software (4.6 version) was used for hierarchical clustering (parameter -m 10)
Seven databases have been applied for gene functional annotation: Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG and GO.
CDS prediction using blast and EST-scan
De novo transcriptome filtered by Corset (4.6 version) used as a reference for mapping reads back to transcriptome and quantify the expression level using RSEM.
DESeq2 (1.26.0 version) used for gene expression difference analysis
Assembly: FASTA assembled sequences
Supplementary files format and content: Microsoft excell file containing raw readcounts of all unigenes in each sample

organism: Citrus x limon

source_name: Leaf

growth_protocol: Potted lemon 'Femminello Siracusano 2Kr' plants grafted onto Citrus aurantium (sour orange) kept in greenhouses at Agrobiotech srl (Catania) were used for the inoculation tests. The bacterial inoculum was obtained from cultures of Pseudomonas mediterranea strain PVCT 3C grown overnight at 28°C in liquid substrate Luria Broth (LB) under stirring conditions (180 rpm). Bacterial cells were harvested by centrifugation at 7500 rpm for 15 minutes. The pellet was suspended in sterile water up to a concentration of 108 cfu ml-1 equal to an optical density (OD) OD600= 1.0 measured by a spectrophotometer at a wavelength of 600 nm. The inoculum of P. tracheiphilus consisted of vial phialoconidia of the PVCT Pt57 strain obtained in carrot broth (Dimaria et al., 2023). Briefly, two PDA plugs taken along the growing margins of 7-day-old fungal colonies were transferred into 250 mL breakwater indented flasks containing 150 mL of carrot broth. The flasks were incubated under continuous stirring (220 rpm) for four days, at 22°C in diffused light condition. Conidia were obtained by centrifugation (6,000 rpm for 15 minutes) of the culture broth previously filtered in order to remove the mycelial component. Phialoconidia were suspended in dH2O at the concentration of 106 ml-1.

extract_protocol:
On the seventh day after inoculation, three leaves were taken for each thesis (washed with RNase-free H2O to eliminate the excess of bacteria on the surface). The collected leaves were immediately frozen in situ with liquid nitrogen and stored at -80°C until DNA extraction. DNA extraction was performed with the CTAB protocol (Springer, 2010) after powdering the frozen samples with mortar and pestle using liquid nitrogen. On the seventh day after inoculation, three leaves were taken for each thesis (washed with RNase-free H2O to eliminate the excess of bacteria on the surface). The collected leaves were immediately frozen with liquid nitrogen in situ and stored at -80°C. RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Venlo, The Netherlands) according to the manufacturer's instructions as detailed in (Russo et al. 2021).
All samples passed through three steps before library construction: Nanodrop for preliminary quantitation, agarose gel electrophoresis to tests RNA degradation and potential contamination, Agilent 2100 to checks RNA integrity and quantitation. After the QC procedures, mRNA from is enriched from total RNA using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added, with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation and AMPure XP beads is used to purify the cDNA. The final cDNA library is ready after a round of purification, terminal repair, Atailing, ligation of sequencing adapters, size selection and PCR enrichment. Libraries are fed into Illumina machines according standard Illumina protocol.

treatment_protocol: The inoculations with the fungal pathogen were carried out by placing 10 µl of the vial suspension of P. tracheiphilus isolated PVCT Pt57 (see paragraph 2.2) on the secondary veins of young but fully expanded leaves; the droplets were then pierced until the leaf was incised with an awl with three entomological needles mounted at the end (Oliveri et al., 2022). Each leaf was inoculated in four spots. Plants have been treated by aerial spray of the foliage with the bacterium suspension, both at three days and at one day before fungal pathogen inoculation. 3C thesis,  plants treated with the biocontrol agent three days and one day before H2O inoculation; 3CPt thesis, plants treated with the biocontrol agent three days and one day before P. tracheiphilus inoculation; Pt thesis: plants treated with water three days and one day before P. tracheiphilus inoculation; CK thesis, plants treated and inoculated with dH2O. Six plants were inoculated for each thesis and, in each of these, three branches and at least six leaves per branch, for a total of about 18 leaves per plant.

value: Leaf

value: 'Femminello Siracusano 2Kr'

value: Pseudomonas mediterranea strain PVCT 3C + Plenodomus tracheiphilus phialoconida suspension


title: RIP-seq Input D35 rep2

tag: age

value: 35 days after germination

value: meristem and young flower buds


title: RIP-seq AGO5 D35 rep1

tag: genotype/variation

value: pAGO5::GFP-AGO5 in col-0

value: RNA extract from immuno-precipitation


title: NC.D0_Plate2.C3

tag: cell type

value: microglia

value: retina

tag: strain

value: no treatment


title: NC.D0_Plate2.C2

value: 16 weeks old


title: ATAC-Seq - Vero-iDAPT-Delta-TP-2

value: Delta (B.1.617.2) spike expression, doxycycline induction, 48h


title: RIP-seq GFP control D7 rep2

source_name: shoot apex

value: p35S::GFP in col-0

value: 7 days after germination

value: shoot apex

tag: molecule subtype


title: ATAC-Seq - Vero-iDAPT-Delta-TP-1


title: NC.D0_Plate2.C1


title: leaf, treatment with biocontrol agent and fungal pathogen, rep1 [Cl_3CPT1]


title: RIP-seq Input D7 rep2

value: pAGO5::GFP-AGO9 in col-0


title: NC.D0_Plate2.B6


title: leaf, treatment with biocontrol agent and fungal pathogen, rep2 [Cl_3CPT2]


title: ATAC-Seq - Vero-iDAPT-Delta-T-2


title: NC.D0_Plate2.B5


title: leaf, treatment with fungal pathogen, rep1 [Cl_PTM1]

value: Plenodomus tracheiphilus phialoconida suspension + H2O


title: leaf, treatment with fungal pathogen, rep2 [Cl_PTM2]

value: Leaf


title: RIP-seq Input D7 rep1


title: RIP-seq GFP control D7 rep1


title: leaf, treatment with fungal pathogen, rep3 [Cl_PTM3]

value: 'Femminello Siracusano 2Kr'


title: ATAC-Seq - Vero-iDAPT-Alpha-TP-2

value: Alpha (B.1.1.7) spike expression, doxycycline induction, 48h


title: RIP-seq AGO9 D7 rep2


title: ATAC-Seq - Vero-iDAPT-Delta-T-1


title: NC.D0_Plate2.B3


title: NC.D0_Plate2.B4


title: leaf, treatment with biocontrol agent, rep2 [Cl_3C2]

value: Pseudomonas mediterranea strain PVCT 3C + H2O


title: leaf, treatment with biocontrol agent, rep3 [Cl_3C3]


title: ATAC-Seq - Vero-iDAPT-Alpha-T-2


title: leaf, treatment with biocontrol agent, rep1 [Cl_3C1]


title: RIP-seq AGO9 D7 rep1


title: RIP-seq AGO5 D7 rep2


title: NC.D0_Plate2.B2


title: ATAC-Seq - Vero-iDAPT-Alpha-T-1


title: NC.D0_Plate2.B1


title: leaf, control, rep3 [Cl_M3]


title: ATAC-Seq - Vero-D-EF1a-orf10-2

value: EF1a-orf10 plasmid transfection, 48 hr post-transfection


title: NC.D0_Plate2.A6


title: ATAC-Seq - Vero-D-EF1a-orf9c-2

value: EF1a-orf9c plasmid transfection, 48 hr post-transfection


title: RIP-seq AGO5 D7 rep1

value: pAGO5::GFP-AGO5 in col-0

value: RNA extract from immuno-precipitation


title: leaf, control, rep1 [Cl_M1]


title: NC.D0_Plate2.A4

value: microglia

value: retina


title: NC.D0_Plate2.A5

value: 16 weeks old

value: no treatment


title: leaf, control, rep2 [Cl_M2]


title: NC.D0_Plate2.A2


title: ATAC-Seq - Vero-D-EF1a-orf8-2

value: EF1a-orf8 plasmid transfection, 48 hr post-transfection


title: 5 days post irradiation biol rep 3

city: Sagamihara

first: Makoto

last: Kashima

state: Kanagawa

address: 5-1-16, Fuchinobe

institute: Aoyama Gakuinn University

data_processing:
Read 1 reads were processed with fastp (version 0.21.0) (S. Chen et al. 2018) using the following command: “ fastp --trim_poly_x -w 20 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -l 31”. The trimmed reads were then mapped to a D. japonica transcriptome reference (An et al. 2018), using BWA mem (version 0.7.17-r1188) (W. Chen et al. 2013) with the default parameters. The read count for each gene was calculated with salmon using -l IU, which specifies the library type (version v0.12.0) (Patro et al. 2017).
Assembly: D. japonica transcriptome reference (An et al. 2018)
Supplementary files format and content: csv-delimited text file includes rawcnt values for each Sample

organism: Dugesia japonica

source_name: whole body

growth_protocol: A clonal strain of planarian D. japonica, sexualizing super planarian (SSP) (2n=16), was used in this study (Shibata et al. 2012). The planarians were maintained in deionized water containing 0.05 g/L Instant Ocean Sea Salt (Instant Ocean, Blacksburg, VA, USA) and fed with chicken liver once or twice a week. The planarians that are approximately 5 mm in length were starved for at least one week prior to the following experiments.

extract_protocol:
At the indicated time points, irradiated animals were lysed with ISOGEN-LS (Nippon gene, Tokyo, Japan), followed by extraction of their total RNA according to the manufacturer’s protocol.
3’ mRNA-Seq were conducted according to the Lasy-Seq ver. 1.1 protocol (https://sites.google.com/view/lasy-seq/) (Kamitani et al. 2019; Kashima et al. 2021). Briefly, total RNA was reverse transcribed using an RT primer with index and SuperScript IV reverse transcriptase (Thermo Fisher Scientific, Waltham, MA, USA). Then, all RT mixtures of the samples were pooled and purified using an equal volume of AMpure XP beads (Beckman Coulter, Brea, CA, USA) according to the manufacturer’s instructions. Second strand synthesis was conducted on the pooled samples using RnaseH (5 U/μL, Enzymatics, Beverly, MA, USA), and DNA polymerase I (10 U/μL, Enzymatics, Beverly, MA, USA). To avoid the carryover of large amounts of rRNAs, the mixture was subjected to Rnase treatment using Rnase T1 (Thermo Fisher Scientific, Waltham, MA, USA). Then, purification was conducted with a 0.8× volume of Ampure XP beads. Fragmentation, end-repair, and A-tailing were conducted using 5× WGS Fragmentation Mix (Enzymatics, Beverly, MA, USA). The Adapter for Lasy-Seq was ligated using 5× Ligation Mix (Enzymatics, Beverly, MA, USA), and the adapter-ligated DNA was purified twice with a 0.8× volume of Ampure XP beads. After optimisation of PCR cycles for library amplification by qPCR using Evagreen, 20× in water (Biotium, Fremont, CA, USA) and the QuantStudio5 Real-Time PCR System (Applied Biosystems, Waltham, MA, USA), the library was amplified using KAPA HiFi HotStart ReadyMix (KAPA BIOSYSTEMS, Wilmington, MA, USA) on the ProFlex PCR System (Applied Biosystems, Waltham, MA, USA). The amplified library was purified with an equal volume of Ampure XP beads. One microliter of the library was then used for electrophoresis using a Bioanalyzer 2100 with the Agilent High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA, USA) to check for quality. Then, sequencing of 150-bp paired-end reads was performed using HiSeq X Ten (Illumina, San Diego, CA, USA) by Macrogen, Inc. (Seoul, Korea).

treatment_protocol: Planarians were irradiated with 150 Roentgens X-ray by using a SOFTEX B-5 X-ray generator (SOFTEX, Tokyo, Japan).

value: SSP

value: whole body

value: 5 days post irradiation


title: WT-wounded, replicate 1

city: Lausanne

first: Karolina

last: Bojkowska

address: Unil, Genopode

country: Switzerland

institute: University of Lausanne

description:
WTw1
Col-0; wounded leave 8

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065).
Reads were aligned to the Arabidopsis thaliana.TAIR10.39 genome using STAR (v. 2.5.3a).
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1).
Genome_build: Arabidopsis thaliana, release TAIR10.39
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read count estimates, computed by the htseq-count software package.

source_name: Leave 13

growth_protocol: Arabidopsis Col-0 was used as wild type. isi1-2 (SALK_014032) were from the Nottingham Arabidopsis Stock Center (NASC). To work with 5-week-old plants, seeds were sown individually in 7 cm diameter pots. Plants were stratified at 4 °C for 2 days in the dark before transferring them to the growth room at 21°C under 150 μE m-2 s-1 light (10 h light, 14 h dark, 70% humidity).

extract_protocol:
Total RNA from all samples was purified with ReliaPrep TM RNA Tissue Miniprep System (Promega, Madison, WI). RNA quality was assessed with a Fragment Analyzer (Agilent, Santa Clara, CA).
RNA-seq libraries were prepared from 500 ng of total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina) using a unique dual indexing strategy, and following the official protocol automated on a Sciclone liquid handling robot (PerkinElmer). Libraries were quantified by a fluorometric method (QubIT, Life Technologies) and their quality assessed on a Fragment Analyzer (Agilent Technologies). Cluster generation was performed with 2 nM of an equimolar pool from the resulting libraries using the Illumina HiSeq 3000/4000 SR Cluster Kit reagents and sequenced on the Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit reagents for 150 cycles (single end).

treatment_protocol: 5-week-old Col-0 and isi1-2 plants were used. For wounding, 50%-60% of the apical lamina surface distal to the rossete centre of leaf 8 was crushed with a plastic forceps. Distal leaves 13 were harvested one hour after wounding leaves 8. As controls, leaves 13 from unwounded plants were also collected.

tag: ecotype/background

value: WT

value: 5 weeks

value: Wounded leaf 8

value: Leaf 13


title: ATAC-Seq - Vero-D-EF1a-orf9b-2

value: EF1a-orf9b plasmid transfection, 48 hr post-transfection


title: NC.D0_Plate2.A3


title: WT-wounded, replicate 3

description:
WTw3
Col-0; wounded leave 8


title: ATAC-Seq - Vero-D-EF1a-orf7a-2

value: EF1a-orf7a plasmid transfection, 48 hr post-transfection


title: 7 days post irradiation biol rep 3

value: 7 days post irradiation


title: 1 days post irradiation biol rep 3

value: 1 days post irradiation


title: 3 days post irradiation biol rep 3

value: 3 days post irradiation


title: NC.D0_Plate2.A1

value: microglia


title: WT-unwounded, replicate 2

description:
WTun2
Col-0; unwounded

value: Unwounded


title: WT-unwounded, replicate 3

description:
WTun3
Col-0; unwounded


title: ATAC-Seq - Vero-D-EF1a-orf7b-2

value: EF1a-orf7b plasmid transfection, 48 hr post-transfection


title: WT-unwounded, replicate 1

description:
WTun1
Col-0; unwounded


title: 0.5 days post irradiation biol rep 3

value: 0.5 days post irradiation


title: ATAC-Seq - Vero-D-EF1a-orf6-2

value: EF1a-orf6 plasmid transfection, 48 hr post-transfection


title: NC.D0_Plate1.C6

value: retina

value: 16 weeks old

value: no treatment


title: ATAC-Seq - Vero-D-EF1a-orf3b-2

value: EF1a-orf3b plasmid transfection, 48 hr post-transfection


title: WT-wounded, replicate 2

description:
WTw2
Col-0; wounded leave 8

value: WT

value: 5 weeks


title: isi-wounded, replicate 3

description:
isi-w3
isi1-2 mutant; wounded leave 8

value: isi1-2 mutant

value: Wounded leaf 8

value: Leaf 13


title: NC.D0_Plate1.C5


title: isi-wounded, replicate 2

description:
isi-w2
isi1-2 mutant; wounded leave 8


title: NC.D0_Plate1.C4


title: 7 days post irradiation biol rep 2

value: SSP

value: whole body

value: 7 days post irradiation


title: ATAC-Seq - Vero-D-EF1a-orf3a-2

value: EF1a-orf3a plasmid transfection, 48 hr post-transfection


title: 0 days post irradiation biol rep 3

value: 0 days post irradiation


title: ATAC-Seq - Vero-D-EF1a-M-2

value: EF1a-M plasmid transfection, 48 hr post-transfection


title: NC.D0_Plate1.C2

value: microglia


title: NC.D0_Plate1.C3


title: isi-unwounded, replicate 3

description:
isi-un3
isi1-2 mutant; unwounded

value: Unwounded


title: 3 days post irradiation biol rep 2

value: 3 days post irradiation


title: isi-wounded, replicate 1

description:
isi-w1
isi1-2 mutant; wounded leave 8


title: isi-unwounded, replicate 2

description:
isi-un2
isi1-2 mutant; unwounded


title: 5 days post irradiation biol rep 2

value: 5 days post irradiation


title: 1 days post irradiation biol rep 2

value: 1 days post irradiation


title: 0.5 days post irradiation biol rep 2

value: 0.5 days post irradiation


title: ATAC-Seq - Vero-D-EF1a-EGFP-1

value: EF1a-EGFP plasmid transfection, 48 hr post-transfection


title: NC.D0_Plate1.C1

value: retina

value: 16 weeks old

value: no treatment


title: ATAC-Seq - Vero-D-EF1a-orf10-1

value: EF1a-orf10 plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-D-EF1a-orf9c-1

value: EF1a-orf9c plasmid transfection, 48 hr post-transfection


title: NC.D0_Plate1.B5


title: 0 days post irradiation biol rep 2

value: SSP

value: whole body


title: Norm_vq110_rep3

city: Valencia

first: Jose

last: Leon

address: CPI Edificio 8E, Ingeniero Fausto Elio s/n

country: Spain

institute: IBMCP (CSIC-UPV)

data_processing:
SOAPnuke software Version v1.5.2 (Parameters -l 15 -q 0.2 -n 0.05) developed by BGI.
The following steps were performed: 1) Remove the reads containing the adaptor (adaptor pollution); 2) Remove reads whose N content is greater than 5%; and 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format.
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads.
GCF_000001735.4_TAIR10.1
Assembly: HISAT2 v2.0.4 (--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF)
Supplementary files format and content: Tab-delimited text files including FPKM, TPM and READ_COUNT values for each Sample were generate by using DESeq2.

source_name: whole seedlings

growth_protocol: Arabidopsis thaliana seedlings grown in MS medium supplemented with 1% sucrose under photoperiodic long-day conditions (16h ligh:8h darkness; 150 micromol photons m-2 s-1) and normoxic conditions (21% O2) for 14 days.

extract_protocol:
Total RNAs were extracted by the NucleoSpin Plant RNA kit (Macherey-Nagel) and the quality checked by Bioanalyzer with RIN > 8. 1 microgram of RNAs were used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using MGIEasy RNA Library Prep Kit V3.0 following manufacturer´s protocols.

treatment_protocol: At ZT=4 of day 15 seedlings were exposed to hypoxia (1% O2) or kept under normoxia (21% O2) for additional 4h under dim light (around 30 micromol photons m-2 s-1).

value: whole seedlings

value: mutant vq1vq10

tag: condition

value: Normoxia (21% oxygen)


title: NC.D0_Plate1.B4

value: microglia


title: ATAC-Seq - Vero-D-EF1a-orf9b-1

value: EF1a-orf9b plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-D-EF1a-N-2

value: EF1a-N plasmid transfection, 48 hr post-transfection


title: NC.D0_Plate1.B3


title: 7 days post irradiation biol rep 1

value: 7 days post irradiation


title: Norm_vq110_rep2


title: ATAC-Seq - Vero-D-EF1a-orf8-1

value: EF1a-orf8 plasmid transfection, 48 hr post-transfection


title: Norm_vq110_rep1


title: NC.D0_Plate1.B2


title: ATAC-Seq - Vero-D-EF1a-orf7b-1

value: EF1a-orf7b plasmid transfection, 48 hr post-transfection


title: isi-unwounded, replicate 1

description:
isi-un1
isi1-2 mutant; unwounded

value: isi1-2 mutant

value: 5 weeks

value: Unwounded

value: Leaf 13


title: NC.D0_Plate1.B1

value: retina

value: 16 weeks old

value: no treatment


title: ATAC-Seq - Vero-D-EF1a-orf7a-1

value: EF1a-orf7a plasmid transfection, 48 hr post-transfection


title: 5 days post irradiation biol rep 1

value: SSP

value: whole body

value: 5 days post irradiation


title: 1 days post irradiation biol rep 1

value: 1 days post irradiation


title: Norm_vq10_rep2

value: whole seedlings

value: mutant vq10

value: Normoxia (21% oxygen)


title: Norm_vq10_rep1


title: 0.5 days post irradiation biol rep 1

value: 0.5 days post irradiation


title: 0 days post irradiation biol rep 1

value: 0 days post irradiation


title: ATAC-Seq - Vero-D-EF1a-orf3b-1

value: EF1a-orf3b plasmid transfection, 48 hr post-transfection


title: Norm_vq1_rep3

value: mutant vq1


title: NC.D0_Plate1.A5

value: microglia


title: NC.D0_Plate1.A4


title: ATAC-Seq - Vero-D-EF1a-orf3a-1

value: EF1a-orf3a plasmid transfection, 48 hr post-transfection


title: Norm_vq1_rep2


title: NC.D0_Plate1.A3

value: retina


title: Norm_vq1_rep1


title: ATAC-Seq - Vero-D-EF1a-N-1

value: EF1a-N plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-D-EF1a-M-1

value: EF1a-M plasmid transfection, 48 hr post-transfection


title: NC.D0_Plate1.A2

value: 16 weeks old

value: no treatment


title: Norm_vq10_rep3


title: 3 days post irradiation biol rep 1

value: SSP

value: whole body

value: 3 days post irradiation


title: NC.D0_Plate1.A1


title: RNA-Seq - A549ACE2-Spike-2

value: Ancestral (WA1) spike expression, doxycycline induction, 48h


title: Norm_Col_rep3

value: whole seedlings

value: wt Col-0


title: NC.D0_Plate1.A6


title: RNA-Seq - A549ACE2-Spike-1


title: Norm_Col_rep2

value: Normoxia (21% oxygen)


title: No2.NC.D4_No2.Plate3.H6

value: 20-22 month old

value: nerve crush day 4

tag: strain background


title: Norm_Col_rep1


title: ATAC-Seq - Vero-D-EF1a-orf6-1

value: EF1a-orf6 plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-C-EF1a-nsp16-2

value: EF1a-nsp16 plasmid transfection, 48 hr post-transfection


title: Hypox_vq110_rep3

value: mutant vq1vq10

value: Hypoxia (1% oxygen, 4h)


title: RNA-Seq - A549ACE2-KO-Spike-1

source_name: A549ACE2 TP53ko

value: A549ACE2 TP53ko


title: No2.NC.D4_No2.Plate3.H4

value: microglia

value: retina


title: No2.NC.D4_No2.Plate3.H5


title: Hypox_vq110_rep2


title: Hypox_vq110_rep1


title: RNA-Seq - A549ACE2-KO-EGFP-2

value: EGFP expression, doxycycline induction, 48h


title: No2.NC.D4_No2.Plate3.H3


title: ATAC-Seq - Vero-D-EF1a-EV-1

value: EF1a-EV plasmid transfection, 48 hr post-transfection


title: RNA-Seq - A549ACE2-KO-EGFP-1


title: RNA-Seq - A549ACE2-KO-Delta-2

value: Delta (B.1.617.2) spike expression, doxycycline induction, 48h


title: No2.NC.D4_No2.Plate3.H1


title: RNA-Seq - A549ACE2-KO-Delta-1


title: RNA-Seq - A549ACE2-KO-Spike-2


title: ATAC-Seq - Vero-C-EF1a-E-2

value: EF1a-E plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-C-EF1a-nsp12-2

value: EF1a-nsp12 plasmid transfection, 48 hr post-transfection


title: Hypox_vq10_rep1

value: whole seedlings

value: mutant vq10


title: ATAC-Seq - Vero-C-EF1a-nsp11-2

value: EF1a-nsp11 plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate3.G5

value: 20-22 month old


title: No2.NC.D4_No2.Plate3.G6

value: nerve crush day 4


title: RNA-Seq - A549ACE2-EGFP-2


title: RNA-Seq - A549ACE2-EGFP-1


title: ATAC-Seq - Vero-C-EF1a-nsp10-2

value: EF1a-nsp10 plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-C-EF1a-nsp15-2

value: EF1a-nsp15 plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-C-EF1a-nsp9-2

value: EF1a-nsp9 plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-C-EF1a-nsp14-2

value: EF1a-nsp14 plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate3.G4


title: No2.NC.D4_No2.Plate3.H2


title: RNA-Seq - A549ACE2-Delta-2


title: Hypox_vq10_rep3

value: Hypoxia (1% oxygen, 4h)


title: ATAC-Seq - Vero-C-EF1a-nsp13-2

value: EF1a-nsp13 plasmid transfection, 48 hr post-transfection


title: Hypox_vq10_rep2


title: No2.NC.D4_No2.Plate3.G2

value: microglia

value: retina


title: RNA-Seq - A549ACE2-Delta-1


title: No2.NC.D4_No2.Plate3.G1


title: ATAC-Seq - Vero-C-EF1a-EV-1

value: EF1a-EV plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate3.F6


title: Hypox_vq1_rep3

value: mutant vq1


title: Hypox_Col_rep2

value: wt Col-0


title: Hypox_Col_rep3


title: miRNA-Seq - A549ACE2-Spike-2

data_processing:
Raw sequencing reads were aligned to mature microRNA human sequences from miRbase v22.1 using bowtie v1.2.2 using options “-n 0 -l 30 --norc --best --strata -m 1”. UMIs were extracted with fgbio v2.1.0 function “AnnotateBamWithUmis” and duplicates removed with picard v2.8.0 MarkDuplicates. Reads were determined by samtools v1.3.1.
Assembly: hg38
Supplementary files format and content: Mature microRNA read counts

extract_protocol:
Cells were lysed using Trizol reagent (Thermo Fisher) and RNA was extracted by phase separation. Total RNA was quantified by nanodrop (DeNovix DS-11) and TapeStation 4200 (RNA Screen Tape; Agilent Technologies, Inc) or 2100 Bioanalyzer (Total RNA Nano; Agilent Technologies, Inc).
A total of 100 ng total RNA was used for library preparation via the QIAseq miRNA Library Kit (#331502, Qiagen) according to manufacturer’s recommendations. Briefly, QIAseq miRNA 3' and 5' adapters were ligated to mature miRNAs. The ligated miRNAs were then reverse transcribed to cDNA using a reverse transcription (RT) primer with a Unique Molecular Index (UMI). Libraries underwent cleanup and amplification (16 PCR cycles) using a forward primer that has a unique index and the reverse primer has another unique index for dual indexing (QIAseq miRNA 96 Index Kit IL UDI, #331645, Qiagen). Successful library production, quality control, and quantification was performed using Tapestation (High Sensitivity D1000 ScreenTape). Libraries were pooled together and subjected to sequencing via a NovaSeq 6000.

value: Ancestral (WA1) spike expression, doxycycline induction, 48h


title: ATAC-Seq - Vero-C-EF1a-E-1

value: EF1a-E plasmid transfection, 48 hr post-transfection


title: Hypox_Col_rep1

value: whole seedlings


title: No2.NC.D4_No2.Plate3.F5


title: ATAC-Seq - Vero-C-EF1a-nsp15-1


title: miRNA-Seq - A549ACE2-KO-Spike-1

value: A549ACE2 TP53ko


title: sn_p2_smrt3_R12

description: 1 single nucleus

data_processing:
NextSeq 550 RTA software
data were processed with nf-core/rnaseq (https://github.com/nf-core/rnaseq)
deviation from default pipeline options (star_salmon): parameters for trimming samples 191-210: --clip_r1 19 --clip_r2 9 --three_prime_clip_r1 5 --three_prime_clip_r2 5
counts table was analysed with Deseq2 and p-Values calculated with Wald-test
Genome_build: Tair10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and transposon for every sample

molecule: nuclear RNA

source_name: seedling

growth_protocol: seedlings were grown on soil at standard growth conditions (16h light/8h dark) and shoot apices harvested 7 days after germination.

extract_protocol:
nuclei were extracted according to (DOI: 10.1007/978-1-0716-0179-2_7) and either 50 (bulk), 0 (neg control) or 1 single nucleus sorted into a single well.
For samples 1-190: Smart-seq2 single cell protocol (DOI: 10.1038/nmeth.2639). For samples 191-210: Smart-seq3 single cell protocol (according to Hagemann-Jensen et. al, https://doi.org/10.1038/s41587-020-0497-0).

tag: ecotype

tag: developmental age

value: 7 days after germination

value: stem cells


title: Hypox_vq1_rep2

tag: genotype


title: ATAC-Seq - Vero-C-EF1a-nsp8-2

tag: cell line

value: EF1a-nsp8 plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate3.F4

value: 20-22 month old

value: nerve crush day 4


title: ATAC-Seq - Vero-C-EF1a-nsp14-1

value: EF1a-nsp14 plasmid transfection, 48 hr post-transfection


title: miRNA-Seq - A549ACE2-KO-EGFP-2

value: EGFP expression, doxycycline induction, 48h


title: Hypox_vq1_rep1

value: Hypoxia (1% oxygen, 4h)


title: No2.NC.D4_No2.Plate3.F3

value: microglia


title: sn_p2_smrt3_R11

description: 1 single nucleus


title: sn_p2_smrt3_R10

description: 1 single nucleus


title: No2.NC.D4_No2.Plate3.G3

value: retina


title: ATAC-Seq - Vero-iDAPT-Alpha-TP-1

value: Alpha (B.1.1.7) spike expression, doxycycline induction, 48h


title: miRNA-Seq - A549ACE2-KO-EGFP-1


title: ATAC-Seq - Vero-C-EF1a-nsp13-1

value: EF1a-nsp13 plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate3.F2


title: miRNA-Seq - A549ACE2-Spike-1


title: ATAC-Seq - Vero-C-EF1a-nsp16-1

value: EF1a-nsp16 plasmid transfection, 48 hr post-transfection


title: sn_p2_smrt3_R9

description: 1 single nucleus


title: miRNA-Seq - A549ACE2-KO-Spike-2

value: Ancestral (WA1) spike expression, doxycycline induction, 48h


title: ATAC-Seq - Vero-C-EF1a-nsp12-1

value: EF1a-nsp12 plasmid transfection, 48 hr post-transfection


title: sn_p2_smrt3_R8

description: 1 single nucleus


title: miRNA-Seq - A549ACE2-KO-Delta-2

value: Delta (B.1.617.2) spike expression, doxycycline induction, 48h


title: miRNA-Seq - A549ACE2-KO-Delta-1

value: A549ACE2 TP53ko


title: No2.NC.D4_No2.Plate2.H6


title: No2.NC.D4_No2.Plate2.H5


title: ATAC-Seq - Vero-C-EF1a-nsp9-1

value: EF1a-nsp9 plasmid transfection, 48 hr post-transfection


title: miRNA-Seq - A549ACE2-EGFP-1


title: sn_p2_smrt3_R6

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: miRNA-Seq - A549ACE2-EGFP-2


title: No2.NC.D4_No2.Plate2.H4

value: 20-22 month old


title: miRNA-Seq - A549ACE2-Delta-2


title: No2.NC.D4_No2.Plate3.F1

value: nerve crush day 4


title: No2.NC.D4_No2.Plate2.H3


title: ATAC-Seq - Vero-C-EF1a-EGFP-1

value: EF1a-EGFP plasmid transfection, 48 hr post-transfection


title: sn_p2_smrt3_R4

description: 1 single nucleus


title: miRNA-Seq - A549ACE2-Delta-1


title: No2.NC.D4_No2.Plate2.H2


title: ATAC-Seq - Vero-C-EF1a-nsp8-1

value: EF1a-nsp8 plasmid transfection, 48 hr post-transfection


title: sn_p2_smrt3_R5

description: 1 single nucleus


title: ATAC-Seq - A549ACE2-KO-Delta-2


title: ATAC-Seq - Vero-C-EF1a-nsp10-1

value: EF1a-nsp10 plasmid transfection, 48 hr post-transfection


title: sn_p2_smrt3_R3

description: 1 single nucleus


title: ATAC-Seq - Vero-C-EF1a-nsp11-1

value: EF1a-nsp11 plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-B-CMV-nsp6-2

value: CMV-nsp6 plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate2.H1

value: microglia

value: retina


title: sn_p2_smrt3_R7

description: 1 single nucleus


title: sn_p2_smrt3_R2

description: 1 single nucleus


title: sn_p2_smrt3_R1

description: 1 single nucleus


title: No2.NC.D4_No2.Plate2.G6


title: ATAC-Seq - Vero-B-CMV-S-2

value: CMV-S plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - A549ACE2-KO-Spike-2

value: Ancestral (WA1) spike expression, doxycycline induction, 48h


title: ATAC-Seq - Vero-B-CMV-nsp3-2

value: CMV-nsp3 plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate2.G5


title: sn_p1_smrt3_R8

description: 1 single nucleus


title: ATAC-Seq - Vero-A-EF1a-nsp7-2

value: EF1a-nsp7 plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - A549ACE2-KO-EGFP-2

value: A549ACE2 TP53ko

value: EGFP expression, doxycycline induction, 48h


title: No2.NC.D4_No2.Plate2.G4


title: ATAC-Seq - A549ACE2-KO-Delta-1

value: Delta (B.1.617.2) spike expression, doxycycline induction, 48h


title: sn_p1_smrt3_R7

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: ATAC-Seq - A549ACE2-KO-Spike-1


title: ATAC-Seq - A549ACE2-KO-EGFP-1


title: sn_p1_smrt3_R6

description: 1 single nucleus


title: No2.NC.D4_No2.Plate2.G3

value: 20-22 month old

value: nerve crush day 4


title: No2.NC.D4_No2.Plate2.G2


title: sn_p1_smrt3_R5

description: 1 single nucleus


title: sn_p1_smrt3_R4

description: 1 single nucleus


title: ATAC-Seq - Vero-A-EF1a-nsp2-2

value: EF1a-nsp2 plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate2.G1


title: ATAC-Seq - Vero-A-EF1a-nsp4-2

value: EF1a-nsp4 plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate2.F6


title: ATAC-Seq - A549ACE2-Spike-2


title: ATAC-Seq - Vero-A-EF1a-nsp1-2

value: EF1a-nsp1 plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate2.F5


title: sn_p1_smrt3_R3

description: 1 single nucleus


title: ATAC-Seq - A549ACE2-Delta-1


title: No2.NC.D4_No2.Plate2.F4


title: ATAC-Seq - Vero-B-CMV-nsp6-1

value: CMV-nsp6 plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-B-CMV-nsp3-1


title: sn_p1_smrt3_R2

description: 1 single nucleus


title: ATAC-Seq - A549ACE2-EGFP-2


title: ATAC-Seq - Vero-B-CMV-S-1


title: sn_p1_smrt3_R1

description: 1 single nucleus


title: ATAC-Seq - A549ACE2-Spike-1


title: ATAC-Seq - A549ACE2-Delta-2


title: No2.NC.D4_No2.Plate2.F3

value: microglia


title: ATAC-Seq - Vero-B-CMV-EGFP-1

value: CMV-EGFP plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-B-CMV-EV-1

value: CMV-EV plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate2.F2

value: retina


title: sn_p2_smrt2_R93

description: 1 single nucleus


title: sn_p2_smrt2_R92

description: 1 single nucleus


title: B cell, unsorted, BCR

city: Suita

first: Daron

middle: M

last: Standley

state: Osaka

address: Yamadaoka 3-1

department: Genome Informatics

institute: Osaka University

description:
10x Genomics
scRNA-Seq (immune profiling)

data_processing:
Raw data were processed using Cell Ranger v6.0.0.
The outputs include gene expression and feature barcode matrix, as well as AIRR file for BCR VDJ sequences.
Demultiplexing (donor assignment) process of AIRR file was done using in-house python script.
Assembly: hg38
Supplementary files format and content: GEX: barcodes.tsv, features.tsv, matrix.mtx files.
Supplementary files format and content: FB: .h5 formatted files.
Supplementary files format and content: BCR: rearrangement.tsv files.

source_name: peripheral blood

extract_protocol:
Cryopreserved PBMCs from DTP-vaccinated donors were thawed quickly and resuspend in FACS buffer (2% FBS in PBS). Cells were stained by cell surface markers to obtain the antigen-experienced cell population (CD19+CD27+), Human Total Seq C Hashtags to retain the donor information, and one of the fluorescent-labeled toxins (DT, TT, PT) to obtain toxin-binding and non binding B cells. Sorting was done using BD Aria II Cell Sorter. Totally we have four groups of samples: DT-, TT-, PT-sorted B cells, and unsorted B cells, each of which are containing 4 donors origin.
Library construction was performed according to the manufacturer's protocol (Single cell immune profiling, 5' v2, 10X Genomics). Hashtag-labeled B cells were resuspended in the master mix and loaded onto the chip together with partitioning oil and gel beads to generate GEM. The poly-A RNA from cell lysate was retrotranscripted to cDNA in each GEM containing the Illumina R1 sequencing primer, UMI, and 10x barcode. Simultaneously in the same partition, 10x barcoded DNA from the cell surface protein Feature barcode (hashtag) were produced. The pooled barcoded cDNA and DNA was then cleaned up, amplified by PCR, and separated by size to generate V(D)J and 5' Gene expression libraries, and cell surface protein (hashtag) libraries. During the library construction, Illumina R2 sequencing primer and sample index were added and finally, the libraries were sequenced.

tag: donor

value: mixed samples, 4 donors

tag: disease state

value: healthy

value: peripheral blood

value: CD19+CD27+ B cells

value: DTP vaccination

tag: time

value: 7 days post vaccine

tag: sorting probe


title: ATAC-Seq - A549ACE2-EGFP-1

tag: enzyme

tag: treatment

value: EGFP expression, doxycycline induction, 48h


title: No2.NC.D4_No2.Plate2.F1

tag: tissue

tag: age

value: 20-22 month old


title: sn_p2_smrt2_R91

description: 1 single nucleus

value: 7 days after germination

tag: cell type

value: stem cells


title: ATAC-Seq - Vero-A-EF1a-nsp5-2

value: EF1a-nsp5 plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate1.H6

value: nerve crush day 2

tag: strain


title: B cell, unsorted, Feature Barcode


title: ATAC-Seq - Vero-A-EF1a-nsp5-1


title: sn_p2_smrt2_R90

description: 1 single nucleus


title: ATAC-Seq - Vero-A-EF1a-nsp4-1

value: EF1a-nsp4 plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-A-EF1a-nsp7-1

value: EF1a-nsp7 plasmid transfection, 48 hr post-transfection


title: ATAC-Seq - Vero-A-EF1a-nsp2-1

value: EF1a-nsp2 plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate1.H4

value: microglia


title: B cell, unsorted, Gene Expression


title: sn_p2_smrt2_R88

description: 1 single nucleus


title: No2.NC.D4_No2.Plate1.H3

value: retina


title: B cell, PT-sorted, BCR

value: mixed samples, 4 donors

value: PT


title: sn_p2_smrt2_R87

description: 1 single nucleus


title: No2.NC.D4_No2.Plate1.H5


title: B cell, PT-sorted, Feature Barcode

value: healthy

value: peripheral blood


title: ATAC-Seq - Vero-A-EF1a-EGFP-1

value: EF1a-EGFP plasmid transfection, 48 hr post-transfection


title: sn_p2_smrt2_R86

description: 1 single nucleus


title: No2.NC.D4_No2.Plate1.H1


title: sn_p2_smrt2_R85

description: 1 single nucleus


title: B cell, TT-sorted, BCR

value: CD19+CD27+ B cells

value: DTP vaccination

value: 7 days post vaccine

value: TT


title: ATAC-Seq - Vero-A-EF1a-EV-1

value: EF1a-EV plasmid transfection, 48 hr post-transfection


title: No2.NC.D4_No2.Plate1.G6

value: 20-22 month old


title: ATAC-Seq - Vero-HKU5-SARS-4

value: HKU5-SARS Infection, MOI 0.5, 48 hpi


title: sn_p2_smrt2_R84

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: No2.NC.D4_No2.Plate1.H2

value: nerve crush day 2


title: ATAC-Seq - Vero-A-EF1a-nsp1-1

value: EF1a-nsp1 plasmid transfection, 48 hr post-transfection


title: B cell, TT-sorted, Feature Barcode


title: B cell, TT-sorted, Gene Expression


title: No2.NC.D4_No2.Plate1.G4

value: microglia

value: retina


title: B cell, DT-sorted, BCR

value: mixed samples, 4 donors

value: DT


title: No2.NC.D4_No2.Plate1.G5


title: ATAC-Seq - Vero-HKU5-SARS-3


title: sn_p2_smrt2_R83

description: 1 single nucleus


title: sn_p2_smrt2_R82

description: 1 single nucleus


title: B cell, DT-sorted, Feature Barcode

value: healthy

value: peripheral blood


title: No2.NC.D4_No2.Plate1.G3


title: B cell, PT-sorted, Gene Expression

value: CD19+CD27+ B cells

value: PT


title: sn_p2_smrt2_R81

description: 1 single nucleus


title: B cell, DT-sorted, Gene Expression

value: DTP vaccination

value: 7 days post vaccine


title: ATAC-Seq - Vero-HKU5-SARS-1


title: No2.NC.D4_No2.Plate1.G2


title: ATAC-Seq - Vero-Mock-4

value: Mock Infection


title: sn_p2_smrt2_R80

description: 1 single nucleus


title: K-IL21-K-IL15_D

city: Philadelphia

first: Caimei

last: Zhang

state: PA

address: 3400 Civic Center Boulevard Atrium, Ground Floor

department: Center for Cellular Immunotherapies

institute: University of Pennsylvania

data_processing:
Quality control: Raw data raw reads of fastq format were firstly processed through fastp software. In this step, clean data clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome:Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: Excel file includes gene raw count for each sample
Supplementary files format and content: Excel file includes FPKM values for each sample

source_name: peripherial blood NK cells

growth_protocol: NK cells were cultured in SCGM supplemented with 10% human AB serum, 2 mmol/L Glutamax,100 U/mL IL-2 and 1% PenStrep.

extract_protocol:
RNA was extracted using QIAGEN RNeasy Mini Kit and following the manufacturer’s instructions
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification detection.

treatment_protocol: NK cells were stimulated with irradiated feeders on day0 and restimulated with same type of feeders or different type of feeders on day10

value: peripherial blood NK cells

value: primary NK cells

value: NK cells


title: K-IL21-K-IL15_C


title: sn_p2_smrt2_R79

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: No2.NC.D4_No2.Plate1.F6

value: 20-22 month old

value: nerve crush day 2


title: ATAC-Seq - Vero-Mock-3


title: ATAC-Seq - Vero-Mock-2


title: ATAC-Seq - Vero-HKU5-SARS-2

value: HKU5-SARS Infection, MOI 0.5, 48 hpi


title: sn_p2_smrt2_R78

description: 1 single nucleus


title: K-IL21-K-IL15_B


title: No2.NC.D4_No2.Plate1.F4

value: microglia

value: retina


title: sn_p2_smrt2_R77

description: 1 single nucleus


title: ATAC-Seq - Vero-MERS-4

value: MERS-CoV Infection, MOI 0.5, 48 hpi


title: No2.NC.D4_No2.Plate1.F3


title: ATAC-Seq - Vero-Mock-1


title: ATAC-Seq - Vero-MERS-3


title: K-IL15-K-IL21_C


title: sn_p2_smrt2_R74

description: 1 single nucleus


title: ATAC-Seq - Vero-MERS-2


title: sn_p2_smrt2_R76

description: 1 single nucleus


title: K-IL21-K-IL15_A


title: K-IL15-K-IL21_B


title: No2.NC.D4_No2.Plate1.F2


title: No2.NC.D4_No2.Plate1.F5


title: No2.NC.D4_No2.Plate1.F1


title: sn_p2_smrt2_R75

description: 1 single nucleus


title: sn_p2_smrt2_R73

description: 1 single nucleus


title: K-IL15-K-IL21_A


title: ATAC-Seq - Vero-MERS-1


title: sn_p2_smrt2_R89

description: 1 single nucleus


title: No2.NC.D4_No2.Plate1.G1


title: No2.NC.D2_No2.Plate3.E6


title: ATAC-Seq - Vero-SARS2-4

value: SARS-CoV-2 Infection, MOI 0.5, 48 hpi


title: K-IL15-IL21_D


title: K-IL15-K-IL21_D


title: No2.NC.D2_No2.Plate3.E5


title: sn_p2_smrt2_R71

description: 1 single nucleus


title: ATAC-Seq - Vero-SARS2-3


title: sn_p2_smrt2_R72

description: 1 single nucleus


title: K-IL15-IL21_C


title: No2.NC.D2_No2.Plate3.E4


title: ATAC-Seq - Vero-SARS2-1


title: sn_p2_smrt2_R69

description: 1 single nucleus


title: No2.NC.D2_No2.Plate3.E2


title: No2.NC.D2_No2.Plate3.E3


title: ATAC-Seq - Vero-SARS2-2


title: sn_p2_smrt2_R68

description: 1 single nucleus


title: No2.NC.D2_No2.Plate3.E1


title: sn_p2_smrt2_R70

description: 1 single nucleus


title: sn_p2_smrt2_R67

description: 1 single nucleus


title: K-IL15-IL21_A


title: K-IL21_D


title: K-IL21_C


title: K-IL15-IL21_B


title: sPAP_m3

city: Lodz

first: Przemysław

middle: Adam

last: Płociński

state: lodzkie

address: Lodowa 106

department: Mycobacterium Physiology and Genetics

country: Poland

institute: Institute of Medical Biology of the Polish Academy of Sciences

data_processing:
unzipping the .gz file with gunzip function with Ubuntu Linux command line
seqencing adapter removal with Cutadapt software with parameters set cutadapt -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -g TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -G AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -A TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15 && cutadapt -a TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -g GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -A GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT -G TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG -q 15
quality trimming was done with Sickle -pe script setting variable parameters as -t sanger -q 20 -l 20
mapping reads to the reference genome with BWA-mem software with -t 30 -k 20 settings
sorting and indexing of the alignemnt files with Samtools
samtools view -b -F 4 step was included whenever extraction of mappable reads was required
bazam -bam *.bam (-L bed.bed) -o *.fastq was then used to convert the data format to fastq, which could be serached with bbduk.sh -Xmx5g -literal ARGUMENT, whenever required
samtools view -h *.bam | samclip --ref H37Rv_v4.fasta --max 3 --invert | samtools sort > *.bam was used to calculate the softclipping statistics presented in the manuscript associated with this data submission
counting reads to features with HTSeq.count -t CDS -i Locus -m intersection-nonempty
count matrix was build in excel by merging the HTSeq.count output files
Assembly: NC_000962.3 (Mycobacterium tuberculosis, H37Rv_v4.fasta) or NC_008596.1 (Mycolicibacterium smegmatis, MC2_v4.fasta) were used for mapping.

organism: Mycobacterium tuberculosis H37Rv

source_name: strain carrying Cas9 plasmid for targeted PAP (Rv3907c) depletion grown in 7H9/10% OADC medium

growth_protocol: The Mycobacterium tuberculosis H37Rv wild-type strain and ∆rv3143 mutant were grown in 7H9 broth (Becton-Dickinson) supplemented with 10% OADC enrichment (Becton-Dickinson). For RNA sequencing, the Mtb wild-type and ∆rv3143 mutant were grown to mid-logarythmic phase of growth. Bacteria were cultured in triplicate. 100 ml of each culture was spun down and subjected directly to total RNA isolation.

extract_protocol:
RNA was isolated using TRIzol LS reagent (Invitrogen). Cells were lysed by bead beating with the MP FastPrep system (MP Biomedicals) using lysing matrix B. DNA contamination of the RNA samples was removed by DNase I turbo (Invitrogen) digestion according to the manufacturer’s protocol. The quantity and integrity of the DNase I-treated RNA was assessed using an Agilent 2100 BioAnalyzer according to the manufacturer's instructions (Agilent RNA 6000 Nano Kit).
1mg of crude isolated RNA was used for preparation of each small RNA libraries with TruSeq kit and detailed protocol provided by the manufacturer (Illumina). For total RNA-Seq, RNA samples were purified using AMPure XP magnetic beads (Becton Dickinson) with a 2.2:1 bead-to-RNA ratio. 2mgs of the purified RNA was used for total RNA library. The ribosomal RNA was removed with the riboPools Pan-Bacteria (siTools) according to the manufacturer’s protocol. The Illumina-compatible RNA/cDNA sequencing libraries were prepared with the use of KAPA Stranded RNA-Seq kit (Roche) according to the detailed instructions provided by the manufacturer. For polyA selected libraries, the total RNA was incubated with poly(dT) beads, than washed extensively before recovering the enriched polyA fraction for further processing with VAHTS mRNA-seq V3 Library Prep Kit for Illumina® (Vazyme).

treatment_protocol: No treatment was applied. Wild type and mutant strain grown under the same conditions are compared.

value: Cas9 mutant

value: anhydrotetracycline 100ng/ml

tag: growth phase

value: grown to mid-exponential phase


title: sPAP_m2


title: No2.NC.D2_No2.Plate3.D6


title: K-IL21_B


title: sn_p2_smrt2_R66

description: 1 single nucleus


title: No2.NC.D2_No2.Plate3.D5


title: sCas9_3

source_name: strain carrying an empty Cas9 plasmid (pLJR965, Rock et al.2017) grown in 7H9/10% OADC  medium

value: Cas9 control


title: sn_p2_smrt2_R65

description: 1 single nucleus


title: sn_p2_smrt2_R64

description: 1 single nucleus


title: K-IL21_A


title: K-IL15_D


title: No2.NC.D2_No2.Plate3.D4


title: sCas9_2


title: No2.NC.D2_No2.Plate3.D3


title: No2.NC.D2_No2.Plate3.D2


title: sCas9_1


title: PNPPAP3

description: This sample was used for polyadenylation rates estimation in comparison to the other samples in this study. Quantified gene expression not performed for this sample.

source_name: strain carrying Cas9 plasmid for simultaneous, targeted PAP (Rv3907c) and PNP (Rv2783c) depletion grown in 7H9/10% OADC medium


title: PNPPAP2


title: No2.NC.D2_No2.Plate3.D1


title: K-IL15_B


title: K-IL15_C


title: K-IL15_A


title: No2.NC.D2_No2.Plate2.E6


title: K-WT_D


title: sn_p2_smrt2_R60

description: 1 single nucleus


title: PNPPAP1


title: sn_p2_smrt2_R59

description: 1 single nucleus


title: sn_p2_smrt2_R62

description: 1 single nucleus


title: sPAP_m1


title: No2.NC.D2_No2.Plate2.E5


title: PAP_w3


title: K-WT_C


title: No2.NC.D2_No2.Plate2.E4


title: PAP_w2


title: sn_p2_smrt2_R58

description: 1 single nucleus


title: K-WT_B


title: No2.NC.D2_No2.Plate2.E3


title: PAP_w1


title: sn_p2_smrt2_R63

description: 1 single nucleus


title: K-WT_A


title: sn_p2_smrt2_R57

description: 1 single nucleus


title: PAP_m3


title: No2.NC.D2_No2.Plate2.E2


title: sn_p2_smrt2_R61

description: 1 single nucleus


title: Day0_D


title: sn_p2_smrt2_R56

description: 1 single nucleus


title: sn_p2_smrt2_R55

description: 1 single nucleus


title: Day0_C


title: No2.NC.D2_No2.Plate2.D6


title: No2.NC.D2_No2.Plate2.D5


title: sn_p2_smrt2_R54

description: 1 single nucleus


title: PAP_m1


title: Day0_B


title: PAP_m2


title: Day0_A


title: No2.NC.D2_No2.Plate2.D4


title: Cas9_3


title: Cas9_2


title: No2.NC.D2_No2.Plate2.D3


title: Cas9_1


title: HNRNPD_KO_nascent_rep2

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

description: nascent RNA

data_processing:
The Hisat2 and feature counts software were used to map clean reads to reference genome (hg19) and calculate the gene expression level which was normalized to FPKM.
the CIRI2 software (v 2.0.6) was utilized to predict the junction of circRNAs.
MACS2 was used to identify peaks in individual replicates (-q 0.001).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include reads of RNAs for each sample

growth_protocol: HEK293T cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was extracted with Trizol.
The rRNA was removed by Illumina Ribo-Zero Gold kit and surplus RNA was purified for end repair and 50-adaptor ligation. Then, reverse transcription was performed with random primers containing 3’ adaptor sequences. Finally, the cDNAs were purified and amplified with PCR reaction. The products with 300-500 length were purified and quantified. These libraries were utilized to 150 nt paired-end sequencing with an Illumina Nova seq 6000 system (Novogene, China).

value: Human Embryonic Kidney Cells

value: HNRNPD KO


title: No2.NC.D2_No2.Plate2.D2

data_processing:
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software. Trimmed reads were then mapped to the mouse GRCm38.p6 (mm10) genome with STAR software (version 2.7.2b). Reads on annotated genes were counted using featureCounts (version 1.6.1). FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.


title: No2.NC.D2_No2.Plate2.D1


title: HNRNPD_KO_input_rep2

description: nascent RNA


title: sn_p2_smrt2_R50

description: 1 single nucleus


title: sn_p2_smrt2_R52

description: 1 single nucleus


title: AP-750, replicate 3, scRNAseq

city: Shanghai

first: Li

last: Xiaoyun

state: other

address: china

institute: Gastroenteroloy

data_processing:
Raw reads were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/Celescope) v1.9.0 pipeline.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Fresh liver tissues were stored in sCelLiveTM Tissue Preservation Solution (Singleron Bio Co., Nanjing, China) pre-cooling on ice immediately once being collected. About 10 min later, the liver tissues were washed with HBSS three times and then digested with 2 ml sCelLiveTM Tissue Dissociation Solution (Singleron) via the Singleron PythoN™ Automated Tissue Dissociation System (Singleron) at 37 °C for 15 min. The solution was then centrifuged at 500 x g for 5 min and suspended in PBS. Finally, the suspensions were stained with trypan blue (Sigma, United States), and cellular viability was evaluated microscopically. NPC single-cell suspensions were prepared at a concentration of 1 × 105 cells/ml in PBS.
NPC single-cell suspensions were then loaded onto microfluidic devices, and scRNA-seq libraries were constructed using the GEXSCOPE® Single-Cell RNA Library Kit (Singleron Biotechnologies) according to the manufacturer’s instructions (Singleron GEXSCOPE®) protocol (Dura et al. 2019). The individual libraries were diluted to 4 nM and pooled for sequencing. These libraries were then sequenced on an Illumina HiSeq X with 150 bp paired-end reads.

value: liver NPCs cells

value: liver

tag: condition

value: AILI

value: 750 mg/kg APAP

value: 6-8 weeks old


title: AP-300, replicate 3, scRNAseq

value: 300 mg/kg APAP


title: HNRNPD_KO_nascent_rep1

description: nascent RNA


title: No2.NC.D2_No2.Plate2.E1

source_name: retina

extract_protocol:
Total RNA were directly extracted with lysis buffer inculding Rnase inhibitor from single cell sorted with FACS.
RNA sequence library preparation, sequencing, mapping, gene expression, and gene ontology (GO) enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). cDNA synthesis and amplification of RNA derived from lysed cell was sequentially conducted in a same PCR tube. After purification, amplified cDNA was validated and quantified. Following tagmentation of cDNA, adapter addition and PCR amplification were conducted using Nextera XT DNA Library Prep Kit (Illumina).

value: 20-22 month old

value: nerve crush day 2

tag: strain background


title: sn_p2_smrt2_R49

description: 1 single nucleus

tag: ecotype

value: 7 days after germination

value: stem cells


title: HNRNPD_KO_input_rep1

description: nascent RNA


title: sn_p2_smrt2_R51

description: 1 single nucleus

tag: developmental age


title: sn_p2_smrt2_R53

description: 1 single nucleus


title: No2.NC.D2_No2.Plate1.E6

value: microglia

value: retina

tag: genotype


title: con, replicate 3, scRNAseq

value: normal control

value: saline


title: sn_p2_smrt2_R48

description: 1 single nucleus


title: HNRNPD_WT_nascent_rep2

description: nascent RNA

tag: cell line

value: WT


title: No2.NC.D2_No2.Plate1.E4


title: sn_p2_smrt2_R46

description: 1 single nucleus


title: sn_p2_smrt2_R47

description: 1 single nucleus


title: No2.NC.D2_No2.Plate1.E5


title: FLAG-EED-K19R TSA 4h Input

city: Macau

first: Gang

last: Li

address: E12 Avenida da Universidade, Taipa, Macau

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

data_processing:
Illumina RTA software was used for basecalling and Illumina bcl2fastq 2.17 software was used for demultiplexing.
Sequencing reads were quality checked with FastQC v0.11.7.
Reads were trimmed with TrimGalore v0.6.0 to remove low quality ends, adaptor sequence (--stringency5) and reads shorter than 50 bps (for paired end reads) or 35 bps (for single end reads).
The pre-processed reads were aligned to the mm10 mouse reference genome using  Bowtie2 v2.3.4.1.
The aligned reads with mapQ > 10 were converted to bam format using Samtools v1.9. Duplicated reads were removed using Picard v2.18.5 - MarkDuplicates, keeping reads with mapQ > 10 that are not within the ENCODE DAC blacklist regions.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files were generated using Deeptools v3.0.2 with RPKM (reads per kilobase per million) normalization.

source_name: mouse embryonic stem cells

growth_protocol: Wildtype mESCs, EED knockout mutant mESCs, FLAG-EED wildtype and FLAG-EED K19R mutant knock-in mESCs were cultured on gelatin-coated dishes in high-glucose DMEM supplemented with 15% FBS, 1mM sodium pyruvate (Gibco), 1x GlutaMAX (Gibco), 1x nonessential amino acids (NEAA, Gibco), 40 μM β-mercaptoethanol (Acros Organics), 1000 U/ml Leukemia Inhibitory Factor (LIF) (EMD Millipore), 1% Penicillin/Streptomycin (Gibco), with or without 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021) at 37°C in a humidified atmosphere with 5% (v/v) CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645L).

treatment_protocol: Wildtype mESCs and EED knockout mutant mESCs were culture with LIF. FLAG-EED wildtype and FLAG-EED K19R mutant knock-in mESCs were cultured with LIF + 2i and treated with TSA (2 uM or 100 ng/l) for indicated times.

value: embryonic stem cells

value: FLAG-EED K19R mutant

value: culture with LIF + 2i, treated with TSA for 4h

tag: chip antibody


title: mESC FLAG Ctrl Input

value: wildtype

value: culture with LIF + 2i, untreated


title: No2.NC.D2_No2.Plate1.E2


title: FLAG-EED WT TSA 4h Input

value: FLAG-EED wildtype


title: sn_p2_smrt2_R44

description: 1 single nucleus


title: FLAG-EED WT 0h Input


title: HNRNPD_WT_input_rep1

description: nascent RNA

value: Human Embryonic Kidney Cells


title: HNRNPD_WT_input_rep2

description: nascent RNA


title: HNRNPD_KO_polyA_rep1

value: HNRNPD KO


title: HNRNPD_KO_polyA_rep2


title: sn_p2_smrt2_R43

description: 1 single nucleus


title: No2.NC.D2_No2.Plate1.E1

value: 20-22 month old


title: EED knockout mESCs Input

value: EED knockout mutant

value: culture with LIF


title: HNRNPD_WT_polyA_rep2


title: HNRNPD_WT_nascent_rep1

description: nascent RNA


title: Wildtype mESCs TSA 12h Input

value: culture with LIF, treated with TSA for 12h


title: No2.NC.D2_No2.Plate1.E3

value: microglia

value: nerve crush day 2


title: HNRNPD_WT_polyA_rep1


title: Wildtype mESCs TSA 2h Input

value: culture with LIF, treated with TSA for 2h


title: sn_p2_smrt2_R45

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: FLAG-EED-K19R 0h Input

value: embryonic stem cells


title: No2.NC.D2_No2.Plate1.D3

value: retina


title: sn_p2_smrt2_R39

description: 1 single nucleus


title: Wildtype mESCs Input


title: HNRNPD_circ_KO_rep1


title: No2.NC.D2_No2.Plate1.D2


title: No2.NC.D2_No2.Plate1.D6


title: sn_p2_smrt2_R38

description: 1 single nucleus


title: No2.NC.D2_No2.Plate1.D1


title: HNRNPD_circ_WT_rep2

value: WT


title: sn_p2_smrt2_R42

description: 1 single nucleus


title: HNRNPD_circ_WT_rep1


title: No2.NC.D2_No2.Plate1.D5


title: FLAG-EED-K19R TSA 4h H3K27me3

value: FLAG-EED K19R mutant

value: culture with LIF + 2i, treated with TSA for 4h

value: H3K27me3 (Abcam, ab6002)


title: sn_p2_smrt2_R41

description: 1 single nucleus


title: No2.NC.D2_No2.Plate1.D4


title: FLAG-EED-K19R 0h H3K27me3

value: FLAG-EED wildtype


title: No2.NC.D0_No2.Plate3.C5

value: no treatment


title: sn_p2_smrt2_R36

description: 1 single nucleus


title: sn_p2_smrt2_R40

description: 1 single nucleus


title: HBMEC cells, normal human RBCs, TNF treatment, 8hr, biol rep 3

first: Ying

last: Zheng

address: 1400 NE Campus Parkway

department: Bioengineering

institute: University of Washington

data_processing:
RNA-seq data were aligned to the hg38 human genome using TopHat and genes with > 4 rpm were kept for further analysis
Assembly: hg38
Supplementary files format and content: Tab-delimited text files

source_name: Human brain microvascular endothelial cells, primary human red blood cells, IT4Var19 Plasmodium falciparum-infected red blood cells

growth_protocol: 3D HBMEC vessels were cultured under perfusion in Lonza EGM-2MV

extract_protocol:
RNA was harvested using RNAeasy micro kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMART-Seq v4 ultra low input RNA kit (Takarabio) following manufacturer instructions

treatment_protocol: Vessels were treated with 10ng/mL TNF for 18 hours prior to blood perfusion. Vessels were perfused with either normal or infected red blood cells for 1 hour following TNF treatment or control

value: Brain endothelial cells, red blood cells

value: TNF


title: sn_p2_smrt2_R35

description: 1 single nucleus


title: FLAG-EED WT TSA 4h H3K27me3

value: culture with LIF + 2i, untreated


title: HNRNPD_circ_KO_rep2

value: Human Embryonic Kidney Cells

value: HNRNPD KO


title: FLAG-EED WT 0h H3K27me3


title: sn_p2_smrt2_R34

description: 1 single nucleus


title: HBMEC cells, P. falciparum-iRBCs, TNF treatment, 24hr, biol rep 3

value: P. falciparum iRBCs, TNF


title: mESC FLAG Ctrl

value: wildtype

value: ANTI-FLAG M2 Affinity Gel (A2220)


title: HBMEC cells, P. falciparum-iRBCs, no treatment, 24hr, biol rep 2

value: P. falciparum iRBCs


title: No2.NC.D0_No2.Plate3.C6

first: Kota

last: Sato

address: 1-1, Seiryo-machi, Aoba-ku

institute: Tohoku University

value: microglia

value: 20-22 month old


title: No2.NC.D0_No2.Plate3.C2

value: retina


title: No2.NC.D0_No2.Plate3.C3


title: FLAG-EED-K19R 0h FLAG-EED

value: embryonic stem cells

value: FLAG-EED K19R mutant


title: sn_p2_smrt2_R37

description: 1 single nucleus

value: 7 days after germination

value: stem cells


title: HBMEC cells, P. falciparum-iRBCs, no treatment, 8hr, biol rep 2


title: No2.NC.D0_No2.Plate3.C1

value: no treatment


title: FLAG-EED WT TSA 4h FLAG-EED

value: FLAG-EED wildtype

value: culture with LIF + 2i, treated with TSA for 4h


title: sn_p2_smrt2_R31

description: 1 single nucleus


title: HBMEC cells, normal human RBCs, no treatment, 24hr, biol rep 3

value: Brain endothelial cells, red blood cells


title: No2.NC.D0_No2.Plate3.B6


title: No2.NC.D0_No2.Plate3.B5


title: No2.NC.D0_No2.Plate3.C4


title: sn_p2_smrt2_R30

description: 1 single nucleus


title: HBMEC cells, P. falciparum-iRBCs, TNF treatment, 24hr, biol rep 2


title: sn_p2_smrt2_R29

description: 1 single nucleus


title: HBMEC cells, normal human RBCs, no treatment, 8hr, biol rep 3


title: FLAG-EED-K19R EB 10d rep1

data_processing:
Illumina RTA software was used for basecalling and Illumina bcl2fastq 2.17 software was used for demultiplexing.
Illumina Hiseq 2000 reads were quality checked with FastQC v0.11.7.
Reads were trimmed with TrimGalore v0.6.0 to remove low quality ends, adaptor sequence (--stringency5) and reads shorter than 50 bps (for paired end reads).
The pre-processed reads were aligned to the mm10 mouse reference genome using STAR v2.7.0c.
The raw count of genes was quantified using featureCounts v1.6.3 of Subread.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_genename_counts.txt: Tab-delimited text files include raw count values for each sample.

source_name: mouse embryoid bodies

growth_protocol: Wildtype mESCs, FLAG-EED wildtype and FLAG-EED K19R mutant knock-in mESCs were cultured on gelatin-coated dishes in high-glucose DMEM supplemented with 15% FBS, 1mM sodium pyruvate (Gibco), 1x GlutaMAX (Gibco), 1x nonessential amino acids (NEAA, Gibco), 40 μM β-mercaptoethanol (Acros Organics), 1000 U/ml Leukemia Inhibitory Factor (LIF) (EMD Millipore), 1% Penicillin/Streptomycin (Gibco), with or without 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021) at 37°C in a humidified atmosphere with 5% (v/v) CO2. Embryoid bodies (EBs) were cultured on low-attachment surface plates in differentiation medium and placed in a rotary shaking incubator set to 50 rpm at 37°C with 5% (v/v) CO2 and 85% humidity. in suspension for up to 10 days with medium changes every 2 days.

extract_protocol:
Cells were harvested at desired time points for total RNA isolation using RNeasy Mini kit (Qiagen).
RNA-seq library was prepared using the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina.

treatment_protocol: Wildtype mESCs were culture with LIF. FLAG-EED wildtype and FLAG-EED K19R mutant knock-in mESCs were cultured with LIF + 2i. EBs were cultured in differentiation medium without LIF and 2i.

value: embryoid bodies

tag: developmental stage

value: day 10

value: culture without LIF and 2i


title: sn_p2_smrt2_R33

description: 1 single nucleus


title: No2.NC.D0_No2.Plate3.B4


title: FLAG-EED WT 0h FLAG-EED

value: culture with LIF + 2i, untreated


title: HBMEC cells, P. falciparum-iRBCs, TNF treatment, 8hr, biol rep 3

tag: time

value: P. falciparum iRBCs, TNF


title: HBMEC cells, P. falciparum-iRBCs, TNF treatment, 8hr, biol rep 2


title: sn_p2_smrt2_R27

description: 1 single nucleus


title: FLAG-EED-K19R EB 6d rep2

value: day 6


title: FLAG-EED-K19R EB 10d rep2


title: sn_p2_smrt2_R28

description: 1 single nucleus


title: sn_p2_smrt2_R32

description: 1 single nucleus


title: FLAG-EED-K19R TSA 4h FLAG-EED

value: ANTI-FLAG M2 Affinity Gel (A2220)


title: No2.NC.D0_No2.Plate3.B2

value: microglia

value: 20-22 month old


title: FLAG-EED-K19R EB 6d rep1


title: HBMEC cells, P. falciparum-iRBCs, no treatment, 8hr, biol rep 1

value: P. falciparum iRBCs


title: sn_p2_smrt2_R26

description: 1 single nucleus


title: sn_p2_smrt2_R25

description: 1 single nucleus


title: FLAG-EED-K19R EB 2d rep2

value: FLAG-EED K19R mutant

value: day 2


title: No2.NC.D0_No2.Plate3.B1

value: retina


title: HBMEC cells, P. falciparum-iRBCs, no treatment, 24hr, biol rep 1

value: TNF


title: No2.NC.D0_No2.Plate3.A6

value: no treatment


title: FLAG-EED-K19R EB 2d rep1