title: PD14

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_10

value: serum


title: Plasma EVs, Healthy_8

status: Public on Oct 11 2023

type: RNA

city: Bangkok

first: Bootsakorn

last: Boonkaew

state: Bangkok

address: 1873 Rama IV

department: Biochemistry

country: Thailand

institute: Chulalongkorn University

hyb_protocol: miRNAs were hybridized to capture and reporter probes at 65°C for 18 hours, followed by purification based on a two-step magnetic bead method.

scan_protocol: Digital images are captured and quantification by nCounter Prep Station and Digital Analyzer.

data_processing: Digital images are processed and the barcode counts are shown in a comma separated value (CSV) by the nSolver 4.0 software to obtain the count of individual miRNA. The miRNA data were analyzed by normalization to the top 100 miRNA counts in each sample.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Plasma extracellular vesicles

label_protocol: Three µL of the concentrated miRNAs were applied to human NanoString nCounter miRNA expression assay (NanoString Technologies, WA, USA) using the nCounter Human miRNA Panel v3 for detection of 800 miRNAs according to the manufacturer’s instructions. To capture miRNAs, a color-coded probe pair consisting of a reporter probe with a signal on its 5' end and a capture probe with a biotin on its 3' end. was used.

extract_protocol: Extracellular vesicles (EVs) from plasma of patients and healthy controls were isolated using ExoQuick™ Exosome Isolation Kit (SBI, System Biosciences, CA, USA) according to the manufacturer’s protocol. miRNA from EVs was extracted using miRNeasy Serum/Plasma Kit (Qiagen, Hilden, Germany), To concentrate isolated miRNAs, 320 µL of RNase-free water was added to the miRNA, loaded onto an Amicon Ultra YM-3 filter (Merck Millipore, NJ, USA), and centrifuged at 14,000 x g at 25 ºC for 90 min.

tag: disease status

value: Healthy

tag: age

value: 64 years

tag: Sex

value: Female

tag: tissue

value: plasma

tag: sample type

value: EV


title: PD1

type: protein

city: San Lorenzo

first: Victor

middle: Hugo

last: Aquino

state: Central

address: Dr. Cecilio Báez c / Dr. Gaspar Villamayor

department: Research Institute for Health Sciences

country: Paraguay

institute: National University of Asuncion

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_01

hyb_protocol: The peptide microarray slide was incubated for 15 min at room temperature in standard buffer (PBS, pH 7.4, 0.05% Tween 20), then, in blocking buffer (PBS, pH 7.4, 0.05% Tween 20, 1% BSA) with shaking (140 rpm) for 60 min at room temperature and in staining buffer (standard buffer with 10% blocking buffer) with shaking (140 rpm) for 15 min at room for temperature for equilibration. The sub-arrays were incubated with individual or a pool of up to four (equal volumes) serum samples (1:80 dilution in staining buffer, pH 7.4) overnight at 4°C. The arrays were washed 3x1 min at 140 rpm with the standard buffer, followed by incubation with the secondary antibody (Goat anti-Human IgG Fc Creoss-Adsorbed Secondary Antibody - DyLigt 650, Invitrogen, USA, diluted 1:5000 in a staining buffer) for 30 min with shaking (140 rpm) at room temperature, in the dark. The arrays were washed 3x1 min in the standard buffer with shaking (140 rpm). Then, the slide was dipped two times into the dipping buffer (1 mM Tris, pH 7.4) and dried carefully in a stream of air.

scan_protocol: The array images were obtained with the Axon GenePix 4000B scanner (Molecular Devices, USA) or InnoScan 710 (Innopsys, France), using a 635-nm laser and a 10-μm resolution.

data_processing: Each spot median fluorescence intensity, with local background subtraction, was computed with the GenePix Pro 7 Molecular Devices, USA, or Mapix, Innopsys, France, software. Fluorescence intensity values <1 were converted to 0. Then, fluorescence intensity values were normalized against the negative controls (HA peptides). This normalization was done by dividing the fluorescence intensity value of each spot by the mean fluorescence intensity of the negative control spots. Normalized fluorescence intensity values <1 were converted to 1. The normalized data were log2-transformed to reduce variability. The final fluorescence intensity value for each peptide was the mean of the fluorescence intensity value of the duplicated peptide spots.

molecule: protein

source_name: Serum

label_protocol: The secondary antibody was the Goat anti-Human IgG Fc Cross-Adsorbed antibody conjugated to the DyLigt 650 (Invitrogen, USA).

extract_protocol: Blood samples were collected via venipuncture, and the resulting sera were separated and stored at -80°C.

tag: infecting virus


title: Plasma EVs, Healthy_7

value: 44 years

value: Male


title: PD13

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_09


title: DynamicDCF2 (AL_DCF)

type: SRA

city: Shiga

first: RODI

middle: KADO

last: ABDALKADER

address: 1-1-1 Noji-Higashi, Kusatsu

country: Japan

institute: Ritsumeikan University

library_source: transcriptomic

data_processing:
Analyze the quality control of the sequenced raw reads. Overall reads’ quality, total bases, total reads, GC (%) and basic statistics are calculated (FastQC v0.11.7)
In order to reduce biases in analysis, artifacts such as low quality reads, adaptor sequence, contaminant DNA, or PCR duplicates are removed.
Trimmed reads are mapped to reference genome with HISAT2, splice-aware aligner (Trimmomatic 0.38, HISAT2 version 2.1.0, Bowtie2 2.3.5.1).
Transcript is assembled by StringTie with aligned reads. This process provides information of known transcripts, novel transcripts, and alternative splicing transcripts.
Expression profiles are represented as read count and normalization values which are calculated based on transcript length and depth of coverage (StringTie version 2.1.3b).
Assembly: GRCh38
Supplementary files format and content: Normalization values are provided as FPKM (Fragments Per Kilobase of transcript per Million Mapped reads) / RPKM (Reads Per Kilobase of transcript per Million mapped reads) and TPM(Transcripts Per Kilobase Million)

source_name: HCE-T

growth_protocol: HCE-T cells were grown in a culture medium of DMEM/F12 supplemented with 5% fetal bovine serum, 5 μg/mL insulin, 10 ng/mL human epithelial growth factor, and 0.5% dimethyl sulfoxide. The cells were passaged at a ratio of 1:4 using trypsin-EDTA solution. For the construction of the corneal epithelial barrier in the microfluidic device, the cell suspension was introduced into the upper channel of the device through a cell inlet with a cross-sectional area of 0.23 cm2, at a density of 1x106 cells per mL. The microfluidic device was placed in a humidified incubator at 37°C and5% CO2 for 7 days, with the medium in each chamber was changed every 24 h

extract_protocol:
Total RNA was extracted from differentiated primary myoblasts using the RNeasy mini kit (QIAGEN).
RNA-seq library construction (TruSeq stranded mRNA LT Sample Prep Kit)

treatment_protocol: Prior to the initiation of the AL stimulus, microfluidic channels were filled with fresh culture medium. For drug treatment with DCF, DCF was added to the upper channels at a final concentration of 50 μM, with a volume of 15 μL in the channel and 20 μL in the reservoir. The upper channels were exposed to the AL flow.

tag: cell line

value: HCE-T

tag: cell type

value: Human corneal epithelial cell line

tag: derived tissue

value: Corneal epithelium

tag: treatement

value: DynamicDCF2 (AL_DCF)


title: Dynamic1 (AL)

value: Dynamic1 (AL)


title: Ctrl2 (ST)

value: Ctrl2 (ST)


title: Plasma EVs, Healthy_5

value: 40 years


title: Plasma EVs, Healthy_9

value: 62 years


title: Ctrl1 (ST)

value: Ctrl1 (ST)


title: Plasma EVs, NAFLD_8

value: Non-alcoholic fatty liver disease

value: 51 years


title: Plasma EVs, Healthy_4

value: Healthy


title: PD12

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_08

value: serum


title: Plasma EVs, NAFLD_7

value: 60 years

value: Female

value: plasma


title: Plasma EVs, Healthy_2

value: 53 years

value: Male

value: EV


title: Plasma EVs, Healthy_3

value: 57 years


title: Plasma EVs, NAFLD_5

value: 56 years


title: NGG, Donor3, ABE, CD25-high

city: San Francisco

first: Carl

last: Ward

address: 1650 Owens Street

department: Gladstone-UCSF Institute of Genomic Immunology

country: USA

institute: Gladstone Institutes

description:
199_5A_CD25_hi
BE022_NGG_IFNG_CD25.count.txt

library_source: genomic

data_processing:
MAGeCK count, for details see publication
Library strategy: CRISPR screen

molecule: genomic DNA

source_name: T cells

extract_protocol:
for details see publication
see publication

tag: cell subtype

value: T cells


title: NGG, Donor2, ABE, CD25-low

description:
196_4A_CD25_lo
BE022_NGG_IFNG_CD25.count.txt


title: Plasma EVs, NAFLD_9


title: Plasma EVs, NAFLD_3

value: 58 years


title: StaticDCF2 (ST_DCF)

value: HCE-T

value: Human corneal epithelial cell line

value: Corneal epithelium

value: StaticDCF2 (ST_DCF)


title: StaticDCF1 (ST_DCF)

value: StaticDCF1 (ST_DCF)


title: NGG, Donor2, ABE, CD25-high

description:
195_4A_CD25_hi
BE022_NGG_IFNG_CD25.count.txt


title: DynamicDCF1 (AL_DCF)

value: DynamicDCF1 (AL_DCF)


title: PD2

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_02

value: serum


title: NGG, Donor1, CBE, CD25-low

description:
194_3C_CD25_lo
BE022_NGG_IFNG_CD25.count.txt


title: Dynamic2 (AL)

value: Dynamic2 (AL)


title: Plasma EVs, Healthy_6

value: Healthy

value: Female


title: DSP-1001660009069-G-G01

city: Cleveland

first: Peter

last: Bazeley

state: OH

address: 9500 Euclid Avenue

department: Lerner Research Institute

institute: Cleveland Clinic

hyb_protocol: Slides were then hybridized with human whole transcriptome overnight (nanoString, #GMX-RNA-NGS-HuWTA-4) at 37°C.

scan_protocol: Slides were washed twice then loaded into the GeoMx for imaging. Once the samples were imaged, and regions of interest (ROIs) were selected, and any segmentation made.  During collection, each capture area (whole ROI or segmented areas) was exposed to UV light that cleaved the linker and released the barcoded oligos for capture by microfluidics.  The released barcodes were collected in 96-well plates and were used in the NGS readout library preparation procedure protocol. The resulted libraries were sequenced by the Illumina NextSeq 6000 platform using reversed, 2 x 27 base paired reads. The resulting GeoMx DSP data was then coupled to next generation sequencing (NGS) readout.

data_processing: Nanostring DSP quantification DCC files were analyzed with R version 4.1.3 [42]. R packages GeoMxWorkflows [43], GeomxTools [44], and NanoStringNCTools [45] were used to perform data normalization and quality control. Default values were used unless otherwise indicated. DCC counts and the PKC file (Whole Transcriptome Atlas, https://nanostring.com/wp-content/uploads/Hs_R_NGS_WTA_v1.0.pkc_.zip) were imported and. Ssegments identified as containing primarily ECM were excluded. All 0 counts were imputed to a value of 1. pseudocount of 1 to all counts was added. Candidate segment filter criteria were 1000 minimum reads, 80% trimming, 80% stitching, 80% alignment, 50% sequencing saturation, 10 reads as a minimum negative control count, 1000 reads as a maximum observed in NCT wells, and an area of 5000. Geometric means for negative and endogenous control probes were calculated. One segment was removed due to low negative and endogenous probe geometric means, which also had a sequencing saturation under 30%. A global (across all segments) probe filter criteria was applied of a minimum probe ratio of 0.1 (geometric mean of a given probe’s counts across all segments, divided by geometric mean of all probes for the corresponding gene target across all segments) and if found to be an outlier via Grubb’s test in at least 20% of segments. Additionally, probes were filtered for a given segment if found to be an outlier according to Grubb’s test in that segment. Probe counts were aggregated to gene counts. A limit of quantification (LOQ) per segment was calculated as the product of the negative probes’ geometric mean and the square of negative probes’ standard deviation for each segment, or a value of 2, whichever was larger. Segments with less than 1% of genes above the LOQ were considered for exclusion. Genes were excluded if having a LOQ across segments < 1%, leaving 11,799 genes for downstream analysis. 75th percentile (Q3) normalization was applied to the gene counts, which were then log2-transformed.

source_name: breast

label_protocol: The next morning slides underwent stringent washes and were prepared for morphology marker staining. Slides were treated with blocking buffer for 30 minutes at room temperature in a humidified chamber, then co-incubated with fluorescently labeled visualization markers; PanCK (pan-cytokeratin [CK], (Novus, Clone: AE1+AE3, Cat#: NBP2-34528), and with SYTO 13 (Thermo Fisher, Cat#S7575) for nuclei detection for 1 hour at room temperature in a humidified chamber.

extract_protocol: Serially sectioned FFPE sections (5 μm) of specimens were prepared to generate consecutive sections that were processed for H&E and RNA hybridization. After drying overnight, the slides were baked at 42°C for 3.0 hours and again baked at 60°C for 3.0 hours just prior to deparaffinization. RNA assay slides were deparaffinized and subjected to antigen retrieval (Tris-EDTA, pH9.0; 15 minutes;>99°C), and enzymatic exposure of RNA targets (0.5µg/ml Proteinase K; 15 minutes; 37°C).

tag: patient

tag: tissue segment

value: epithelium

tag: genotype

tag: scan batch


title: NGG, Donor3, CBE, IFNg-low

description:
062_5C_IFNG_lo
BE022_NGG_IFNG_CD25.count.txt

value: CBE,IFNg-low


title: NGG, Donor3, CBE, IFNg-high

description:
061_5C_IFNG_hi
BE022_NGG_IFNG_CD25.count.txt

value: CBE,IFNg-high


title: NGG, Donor3, CBE, CD25-low

description:
202_5C_CD25_lo
BE022_NGG_IFNG_CD25.count.txt


title: DSP-1001660009069-G-F09


title: DSP-1001660009069-G-F10

value: stroma


title: NGG, Donor3, ABE, CD25-low

description:
200_5A_CD25_lo
BE022_NGG_IFNG_CD25.count.txt


title: DSP-1001660009069-G-F06


title: DSP-1001660009069-G-F07


title: DSP-1001660009069-G-G04


title: DSP-1001660009069-G-G02


title: DSP-1001660009069-G-G03


title: NGG, Donor3, CBE, CD25-high

description:
201_5C_CD25_hi
BE022_NGG_IFNG_CD25.count.txt


title: DSP-1001660009069-G-F03


title: DSP-1001660009069-G-F12


title: DSP-1001660009069-G-F02


title: NGG, Donor1, ABE, CD25-low

description:
192_3A_CD25_lo
BE022_NGG_IFNG_CD25.count.txt


title: NGG, Donor2, CBE, TNFa-high

description:
BE022_053_CBE_Donor4_TNFa-high
BE022_NGG_TNFa.count.txt

value: CBE,TNFa-high


title: NGG, Donor1, ABE, CD25-high

description:
191_3A_CD25_hi
BE022_NGG_IFNG_CD25.count.txt

value: T cells


title: Plasma EVs, Healthy_1

value: 60 years

value: plasma

value: EV


title: NGG, Donor3, ABE, TNFa-high

description:
BE022_059_ABE_Donor5_TNFa-high
BE022_NGG_TNFa.count.txt

value: ABE,TNFa-high


title: NGG, Donor3, CBE, TNFa-low

description:
BE022_066_CBE_Donor5_TNFa-low
BE022_NGG_TNFa.count.txt

value: CBE,TNFa-low


title: NGG, Donor1, CBE, CD25-high

description:
193_3C_CD25_hi
BE022_NGG_IFNG_CD25.count.txt


title: DSP-1001660009069-G-F11


title: DSP-1001660009069-G-F08


title: NGG, Donor2, ABE, TNFa-low

description:
BE022_048_ABE_Donor4_TNFa-low
BE022_NGG_TNFa.count.txt

value: ABE,TNFa-low


title: NGG, Donor2, CBE, TNFa-low

description:
BE022_054_CBE_Donor4_TNFa-low
BE022_NGG_TNFa.count.txt


title: NGG, Donor3, ABE, TNFa-low

description:
BE022_060_ABE_Donor5_TNFa-low
BE022_NGG_TNFa.count.txt


title: NGG, Donor2, CBE, IFNg-low

description:
050_4C_IFNG_lo
BE022_NGG_IFNG_CD25.count.txt


title: NGG, Donor3, CBE, TNFa-high

description:
BE022_065_CBE_Donor5_TNFa-high
BE022_NGG_TNFa.count.txt


title: DSP-1001660009069-G-F04


title: NGG, Donor2, ABE, IFNg-high

description:
043_4A_IFNG_hi
BE022_NGG_IFNG_CD25.count.txt

value: ABE,IFNg-high


title: NGG, Donor2, ABE, IFNg-low

description:
044_4A_IFNG_lo
BE022_NGG_IFNG_CD25.count.txt

value: ABE,IFNg-low


title: DSP-1001660009069-G-F01


title: NGG, Donor1, CBE, TNFa-low

description:
BE022_042_CBE_Donor3_TNFa-low
BE022_NGG_TNFa.count.txt


title: DSP-1001660009069-G-F05


title: NGG, Donor1, CBE, TNFa-high

description:
BE022_041_CBE_Donor3_TNFa-high
BE022_NGG_TNFa.count.txt


title: NGG, Donor1, CBE, IFNg-low

description:
038_3C_IFNG_lo
BE022_NGG_IFNG_CD25.count.txt


title: DSP-1001660009069-G-E11


title: NGG, Donor2, ABE, TNFa-high

description:
BE022_047_ABE_Donor4_TNFa-high
BE022_NGG_TNFa.count.txt


title: NGG, Donor2, CBE, IFNg-high

description:
049_4C_IFNG_hi
BE022_NGG_IFNG_CD25.count.txt


title: NGG, Donor1, CBE, IFNg-high

description:
037_3C_IFNG_hi
BE022_NGG_IFNG_CD25.count.txt


title: DSP-1001660009069-G-E09


title: NGG, Donor1, ABE, TNFa-low

description:
BE022_036_ABE_Donor3_TNFa-low
BE022_NGG_TNFa.count.txt


title: DSP-1001660009069-G-E10


title: NGG, Donor1, ABE, TNFa-high

description:
BE022_035_ABE_Donor3_TNFa-high
BE022_NGG_TNFa.count.txt


title: NGG, Donor1, ABE, IFNg-low

description:
032_3A_IFNG_lo
BE022_NGG_IFNG_CD25.count.txt


title: DSP-1001660009069-G-E12


title: DSP-1001660009069-G-E07


title: DSP-1001660009069-G-E06


title: DSP-1001660009069-G-E05


title: DSP-1001660009069-G-E03

value: WT


title: DSP-1001660009069-G-E04


title: DSP-1001660009069-G-E08


title: NGG, Donor1, ABE, IFNg-high

description:
031_3A_IFNG_hi
BE022_NGG_IFNG_CD25.count.txt


title: DSP-1001660009069-G-E01


title: NGG, Donor3, CBE, PD1-low

description:
030_5C_PD1-low
BE022_NGG_PD1.txt


title: DSP-1001660009069-G-E02


title: NGG, Donor3, ABE, PD1-low

description:
026_5A_PD1-low
BE022_NGG_PD1.txt


title: NGG, Donor3, CBE, PD1-high

description:
029_5C_PD1-high
BE022_NGG_PD1.txt


title: NGG, Donor3, ABE, PD1-high

description:
025_5A_PD1-high
BE022_NGG_PD1.txt


title: DSP-1001660009069-G-D12


title: NGG, Donor2, CBE, PD1-low

description:
022_4C_PD1-low
BE022_NGG_PD1.txt


title: DSP-1001660009069-G-D11


title: NGG, Donor2, ABE, PD1-low

description:
018_4A_PD1-low
BE022_NGG_PD1.txt


title: NGG, Donor2, CBE, PD1-high

description:
021_4C_PD1-high
BE022_NGG_PD1.txt


title: NGG, Donor2, ABE, PD1-high

description:
017_4A_PD1-high
BE022_NGG_PD1.txt


title: DSP-1001660009069-G-D08


title: DSP-1001660009069-G-D09


title: DSP-1001660009069-G-D06


title: NGG, Donor1, CBE, PD1-low

description:
014_3C_PD1-low
BE022_NGG_PD1.txt


title: NGG, Donor1, ABE, PD1-high

description:
009_3A_PD1-high
BE022_NGG_PD1.txt


title: NGG, Donor1, ABE, PD1-low

description:
010_3A_PD1-low
BE022_NGG_PD1.txt


title: NGG, Donor1, CBE, PD1-high

description:
013_3C_PD1-high
BE022_NGG_PD1.txt


title: NG, Donor 2, CD8, TNFa, Low

description:
020_D3_CD8_TNFa_low
BE026_NG_TNFa.count.txt

value: CD8,TNFa, Low


title: DSP-1001660009069-G-D10


title: DSP-1001660009069-G-D05


title: NG, Donor 2, CD4, TNFa, High

description:
017_D3_CD4_TNFa_high
BE026_NG_TNFa.count.txt

value: CD4,TNFa, High


title: NG, Donor 2, CD4, TNFa, Low

description:
018_D3_CD4_TNFa_low
BE026_NG_TNFa.count.txt

value: CD4,TNFa, Low


title: NG, Donor 2, CD8, TNFa, High

description:
019_D3_CD8_TNFa_high
BE026_NG_TNFa.count.txt

value: CD8,TNFa, High


title: DSP-1001660009069-G-D02


title: DSP-1001660009069-G-D01

value: epithelium


title: DSP-1001660009069-G-C11


title: DSP-1001660009069-G-C10

value: stroma


title: DSP-1001660009069-G-D03


title: DSP-1001660009069-G-C08


title: DSP-1001660009069-G-C09


title: DSP-1001660009069-G-D04


title: DSP-1001660009069-G-C07


title: NG, Donor 1, CD8, TNFa, High

description:
015_D1_CD8_TNFa_high
BE026_NG_TNFa.count.txt


title: DSP-1001660009069-G-C06


title: NG, Donor 1, CD4, TNFa, Low

description:
014_D1_CD4_TNFa_low
BE026_NG_TNFa.count.txt


title: DSP-1001660009069-G-C12


title: DSP-1001660009069-G-C05


title: C33A cells, infected with Ad4-HPV16E7, rep 3

city: Dalian

first: Yunting

last: Shao

address: No.2 Linggong Road, Ganjingzi District

country: China

institute: School of Biomedical Engineering, Dalian University of Technology

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: disease

value: cervical cancer

value: human cervical cancer cells

tag: treatment


title: DSP-1001660009069-G-C04


title: DSP-1001660009069-G-D07


title: C33A cells, infected with Ad4, rep 2


title: C33A cells, infected with Ad4, rep 1

value: cervicalcancer


title: DSP-1001660009069-G-C03


title: DSP-1001660009069-G-C02


title: DSP-1001660009069-G-C01


title: DSP-1001660009069-G-B12


title: C33A cells, Control, rep 3

value: Control


title: DSP-1001660009069-G-B10


title: DSP-1001660009069-G-B11


title: C33A cells, Control, rep 2


title: NG, Donor 1, CD8, TNFa, Low

description:
016_D1_CD8_TNFa_low
BE026_NG_TNFa.count.txt

value: T cells


title: C33A cells, Control, rep 1


title: C33A cells, infected with Ad4-HPV16E7, rep 2


title: DSP-1001660009069-G-B08


title: DSP-1001660009069-G-B04


title: C33A cells, infected with Ad4-HPV16E7, rep 1


title: DSP-1001660009069-G-B06


title: DSP-1001660009069-G-B02


title: DSP-1001660009069-G-B01


title: DSP-1001660009069-G-A11


title: DSP-1001660009069-G-B05


title: DSP-1001660009069-G-A06


title: DSP-1001660009069-G-B09


title: DSP-1001660009069-G-A09


title: DSP-1001660009069-G-A05


title: DSP-1001660009069-G-A02


title: DSP-1001660009069-G-B07


title: DSP-1001660007412-B-D01


title: DSP-1001660009069-G-B03


title: DSP-1001660009069-G-A03


title: DSP-1001660007412-B-C11


title: C33A cells, infected with Ad4, rep 3


title: DSP-1001660007412-B-C09


title: DSP-1001660009069-G-A08


title: DSP-1001660007412-B-C10


title: sample111

city: Changsha

first: Sha

last: Wang

address: 87 Xiangya Road

institute: Xiangya Hospital

description: Gene expression data from retinoblastoma

hyb_protocol: Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix, corresponding to the U133plus 2.0 arrays

scan_protocol: Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.

data_processing: Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: HGU133Plus2_Hs_ENTREZG

source_name: retinoblastoma

label_protocol: 100ng of total RNA were amplified to produced biotinylated complementary RNAs, as recommended by Affymetrix.

growth_protocol: Immediately following enucleation, a needle was inserted through the anterior chamber of the eye to extract a tumor sample by aspiration. The tumor specimen was placed in RPMI medium on ice, cells were re-suspended, counted and separated into two tubes (for DNA and RNA preparation). The tubes were then centrifuged to remove all media and snap frozen for later extraction.

extract_protocol: Tumor RNA was extracted using Qiazol (Qiagen, Shanghai, China) according to the manufacturer instructions and purified using miRNeasy Mini kit (Qiagen).

value: retinoblastoma

tag: rb1 mutation

value: no

tag: growth

value: endophytic

tag: chroid

value: extended


title: sample114

tag: tissue


title: sample110


title: DSP-1001660009069-G-A10


title: DSP-1001660007412-B-C12


title: sample112

value: exophytic

value: minimal


title: sample109

value: mixed


title: sample108

value: yes


title: sample113


title: sample106


title: DSP-1001660007412-B-C05


title: sample107


title: sample103


title: DSP-1001660007412-B-C07


title: DSP-1001660007412-B-C06


title: DSP-1001660007412-B-C08


title: sample104


title: sample102


title: DSP-1001660007412-B-C04


title: sample100


title: sample101


title: sample105


title: sample99


title: sample96


title: DSP-1001660007412-B-C02


title: DSP-1001660007412-B-C01


title: DSP-1001660007412-B-B11


title: sample97


title: sample93


title: DSP-1001660007412-B-B12


title: sample95


title: sample94


title: NG, Donor 1, CD4, TNFa, High

description:
013_D1_CD4_TNFa_high
BE026_NG_TNFa.count.txt

value: CD4,TNFa, High


title: sample90


title: sample91


title: sample89


title: DSP-1001660007412-B-C03


title: sample98


title: SNU719 RNAseq rep2

city: Philadelphia

first: Italo

last: Tempera

address: 3601 Spruce Street

institute: The Wistar Institute

data_processing:
RNA-seq data was aligned using bowtie2 against hg19 version of the Human genome.
All unaligned reads were then aligned against NC_007605.1 version of EBV genome
RSEM v1.2.12 software was used to estimate raw read counts and RPKM for Human and EBV genes
Assembly: hg19, NC_007605.1
Supplementary files format and content: Tab-delimited text file includes raw read counts for each replicate

organism:
Homo sapiens
human gammaherpesvirus 4

growth_protocol: SNU719 cell line was cultured in RPMI 1640 supplemented with Fetal Bovine Serum at a concentration of 10% and supplemented with 1% penicillin-streptomycin in a humidified incubator containing 5% CO2 at 37 ̊C

extract_protocol:
Total RNA from SNU719 cell line was isolated from 2x106 cells using a Direct-zol RNA Kit (Zymo Research, cat. No. R2050) according to the manufacturer’s protocol.
Libraries were prepared using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen) to generate Illumina-compatible sequencing libraries according to the manufacturer’s instructions

value: WT

value: Gastric tubular adenocarcinoma

tag: infection

value: Human gammaherpesvirus 4


title: SNU719 RNAseq rep1


title: DSP-1001660007412-B-B09

value: stroma


title: DSP-1001660007412-B-B08

value: epithelium


title: sample92


title: DSP-1001660007412-B-B07


title: sample87


title: SNU719 RNAseq rep3


title: SNU719 H3K27ac HiChIP rep2

data_processing:
Illumina HiSeq 2500 paired-end sequencing
Sequenced reads were aligned to the EBV genome assembly (Genbank: NC_007605.1) using HiC-Pro v2.10.0 pipeline
hichipper software was used to perform restriction site bias modeling and interaction identification.
diffloop R package was used to estimate significance of differential contact based on raw count matrix files. Only significantly changed associations (FDR<1%) were kept
EBV-EBV interactions were visualized using UCSC Genome Browser, EBV-Human interactions were plotted as circos graph using the circlize package (version 0.4.12) of R (version 4.0.5)
Assembly: hg19, NC_007605.1
Supplementary files format and content: mango files listing all interactions with the respective p-value
Supplementary files format and content: bedpe files listing all interchromosomal interactions with respective read counts
Library strategy: HiChIP

growth_protocol: YCCEL1 and SNU719 cell lines were cultured in RPMI 1640 supplemented with Fetal Bovine Serum at a concentration of 10% and supplemented with 1% penicillin-streptomycin in a humidified incubator containing 5% CO2 at 37 ̊C

extract_protocol:
25 million cells were fixed with 1% formaldehyde for 10 min and then quenched with 0.125 M glycine for 5 min at RT. Ligation products were immunoprecipitated with 25 µg H3K27ac (Active Motif 39133). 5 μL of Streptavidin C-1 beads were used for biotin pull-down.
After the last wash with Tween Wash Buffer bead-bound DNA was used to prepare libraries with Ultralow Library Systems V2 (Tecan Genomics, part no. 0344NB-32) as per manufacturer’s protocol

tag: chip antibody

value: H3K27ac (Active Motif 39133)


title: sample88


title: reverse_rep3

city: Utrecht

first: Jurian

last: Schuijers

address: Universiteitsweg 100

department: Center for Molecular Medicine

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Read QC (FastQC)
Sequence trimming (TrimGalore)
rRNA removal (SortMeRNA)
Mapping and read-group annotation (STAR)
Alignment-QC (RSeQC, Preseq)
PCR duplicate detection (Sambamba MarkDup)
Gene-expression/biotype quantification ( featureCounts)
Gene-expression normalization ( edgeR, DESeq2)
Transcript quantification (Salmon)
Variant calling (GATK4)
QC report (MultiQC, CustomQC)
Assembly: Human - GRCh38
Supplementary files format and content: Tab delimited matrix with DeSeq2 feature counts

molecule: polyA RNA

source_name: Colon

growth_protocol: HCT116 cells were cultured under standard conditions in DMEM media with 10% FCS

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy mini spin columns
Libraries were constructed using the TruSeq RNA stranded polyA kit according to manufacturers instructions

treatment_protocol: Cells were stimulated with 1ug/ul Doxycycline 48 prior to RNA extraction

value: Colon

tag: cell line

value: Colorectal cancer

value: reverse

value: +dox


title: DSP-1001660007412-B-B04


title: sample84

value: retinoblastoma


title: YCCEL1 H3K27ac HiChIP rep1

tag: cell type

value: Gastric adenocarcinoma


title: DSP-1001660007412-B-B05


title: reverse_rep2


title: DSP-1001660007412-B-B06


title: sample85


title: sample83


title: SNU719 H3K27ac HiChIP rep1


title: DSP-1001660007412-B-B03


title: sample82


title: reverse_rep1


title: DSP-1001660007412-B-B02


title: YCCEL1 H3K27ac HiChIP rep2


title: scramble_rep2

value: scramble


title: DSP-1001660007412-B-B01


title: DSP-1001660007412-B-A12


title: DSP-1001660007412-B-A10


title: CR3_rep3


title: sample86


title: sample79

value: endophytic


title: DSP-1001660007412-B-A11


title: sample76

value: mixed

value: minimal


title: sample78

value: yes


title: DSP-1001660007412-B-A08

value: WT


title: scramble_rep3


title: mCherry_control_rep3

value: mCherry


title: sample81


title: DSP-1001660007412-B-A09


title: sample77


title: scramble_rep1


title: mCherry_control_rep2


title: sample73

value: exophytic


title: sample80


title: DSP-1001660007412-B-A05


title: DSP-1001660007412-B-A07


title: mCherry_control_rep1


title: CR3_rep2


title: sample72

value: extended


title: CR3_rep1


title: sample75


title: DSP-1001660007412-B-A06

value: stroma


title: DSP-1001660007412-B-A04


title: DSP-1001660007412-B-A03

value: epithelium


title: sample71


title: sample70

value: no


title: DSP-1001660006157-C-D03


title: sample69


title: sample68


title: WTmock_5

city: Essen

first: Bettina

last: Budeus

address: Virchowstrasse 173

department: Institute for Cell Biology

country: Germany

institute: University Hospital Essen

hyb_protocol: Following fragmentation, cRNA was hybridized on Clariom_S_Mouse Arrays with the Affymetrix GeneChip Hybridization, Wash and Stain kit, according to manufacturer's instructions.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 and GeneChip Command Console 7 software.

data_processing: Data were normalized according to vsn and imported into Gene Spring GX 7.3.1 and filtered according to a minimum amount of 4 present calls (according to GC-RMA normalization and flagging by MAS5) within at least one condition (cell type) and raw signal above 50. Remaining probe sets were exported, processed with ComBat software to compell batch effects and reimported into Gene Spring for further analysis.

organism: Mus musculus

label_protocol: Two rounded in vitro transcription protocol with Ambion MessageAmpII kit and MessageAmp Biotin Enhanced-Kit according to manufacturer's instructions.

extract_protocol: RNeasy Micro Kit (Qiagen, Düsseldorf, Germany) according to the manufacturer's instructions

value: lung

tag: celltype

value: macrophage

value: WT-mock

value: mock infected


title: DSP-1001660007412-B-A02


title: WTmock_4


title: sample67

value: retinoblastoma


title: DSP-1001660006157-C-C12


title: sample66


title: DSP-1001660006157-C-D02


title: WTmock_2


title: sample65


title: DSP-1001660006157-C-C11


title: WTmock_1


title: sample64


title: DSP-1001660006157-C-C08


title: DSP-1001660006157-C-D01


title: DSP-1001660006157-C-C10


title: sample63


title: WT_Sp_12

source_name: wildtype

value: infected with Streptococcus pneumoniae


title: sample62


title: WT_Sp_13


title: DSP-1001660006157-C-C09


title: WT_Sp_14


title: DSP-1001660006157-C-C07


title: PZ5

description:
New born with microcephaly, born to a Mather with Zika
DZ_64

tag: virus

value: ZIKV

value: ND

tag: collection date

tag: onset of symptoms

value: UK

tag: age

tag: sex

value: M

tag: igg-denv

tag: igm-denv

tag: igg-zikv

tag: igm-zikv

tag: city

value: São Joaquim da Barra, SP

tag: country

value: Brazil


title: WT_Sp_11

tag: tissue

tag: genotype

value: WT

tag: treatment


title: WTmock_3


title: PZ28

description:
Blood donor
DZ_63

value: N

value: P

value: Sao Carlos


title: DSP-1001660006157-C-C06

tag: patient

tag: tissue segment

value: epithelium

tag: scan batch


title: PZ25

description:
Blood donor
DZ_62

tag: virus


title: sample57

tag: rb1 mutation

value: no

tag: growth

value: exophytic

tag: chroid

value: extended


title: PZ23

description:
Blood donor
DZ_61

tag: collection date

tag: onset of symptoms

tag: age

tag: sex


title: DSP-1001660006157-C-C05

value: stroma


title: sample58

value: retinoblastoma

value: endophytic


title: DSP-1001660006157-C-C02


title: DSP-1001660006157-C-C01


title: DSP-1001660006157-C-C04


title: PZ21

description:
Blood donor
DZ_59

value: ZIKV

tag: igg-denv

tag: igm-denv

tag: igg-zikv

tag: igm-zikv


title: sample59

tag: tissue


title: sample60


title: PZ22

description:
Blood donor
DZ_60

value: ND

tag: city

tag: country


title: sample61


title: DSP-1001660006157-C-B12

tag: patient

tag: tissue segment

tag: genotype


title: PZ10

description:
Blood donor
DZ_57

tag: virus

value: UK


title: sample56

tag: rb1 mutation

tag: growth

value: mixed


title: PZ20

description:
Blood donor
DZ_58

tag: collection date

value: M


title: DSP-1001660006157-C-B11

tag: scan batch


title: sample55

tag: chroid


title: sample54

value: minimal


title: DSP-1001660006157-C-B10


title: 1411-AB-2

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

description: Control

library_source: transcriptomic single cell

data_processing: none provided

source_name: Whole Blood

growth_protocol: Cells were not grown or cultured.

extract_protocol:
Whole blood was collected on the day of enrollment and buffy coats transferred to a separate 50 mL conical. For red blood cell lysis, 20 mL of 0.2% NaCl was added. After a 45-60 second incubation, 30 mL of 1.8% NaCl was added. Cells were washed in PBS and then resuspended in PBS at a concentration of 10^6 cells/mL for library preparation. All centrifugations were performed at room temperature.
scRNA-seq libraries were prepared by the University of Michigan Advanced Genomics Core using the Chromium single cell 3′ library and gel bead kit v3 (10x Genomics) according to the manufacturer's protocol.

treatment_protocol: Cells were not treated.

value: Whole Blood


title: sample53

value: yes


title: WT_Sp_15

value: lung

tag: celltype

value: macrophage

value: WT

tag: treatment

value: infected with Streptococcus pneumoniae


title: DSP-1001660006157-C-B09

value: epithelium


title: sample52

value: exophytic


title: 1411-AB-1

description: Covid


title: PZ19

description:
Blood donor
DZ_55

tag: onset of symptoms

tag: age

tag: sex

tag: igg-denv

value: N

tag: igm-denv

value: P

value: Sao Carlos

value: Brazil


title: 1396-AB-2

description: Control

tag: tissue


title: 1373-AB-1

description: Covid


title: 1354-AB-1

description: Covid


title: 2595-SY-1

description: Covid


title: sample51

value: retinoblastoma


title: 2548-SY-1

description: Covid


title: DSP-1001660006157-C-B08

tag: patient

value: stroma


title: PZ27

description:
Blood donor
DZ_56

value: ZIKV

value: ND

value: UK

tag: igg-zikv

tag: igm-zikv

tag: city

tag: country


title: 2589-SY-1

description: Covid

value: Whole Blood


title: PZ14

description:
Blood donor
DZ_51

tag: virus

value: M


title: PZ24

description:
Blood donor
DZ_52

tag: collection date


title: PZ26

description:
Blood donor
DZ_54

value: F


title: sample50

tag: rb1 mutation

value: yes

tag: growth


title: sample49

value: no

tag: chroid

value: extended


title: DSP-1001660006157-C-B05

tag: tissue segment

value: epithelium

tag: genotype

tag: scan batch


title: sample48

value: endophytic


title: DSP-1001660006157-C-B07


title: sample46

value: mixed


title: DSP-1001660006157-C-B06


title: sample47


title: DSP-1001660006157-C-B04


title: DSP-1001660006157-C-B03


title: PZ15

description:
Blood donor
DZ_50

tag: onset of symptoms

tag: age

tag: sex

value: N

value: P


title: 2539-SY-2

description: Covid

tag: tissue


title: DSP-1001660006157-C-B02

tag: patient

value: WT


title: sample45

value: retinoblastoma


title: PZ11

description:
Blood donor
DZ_53

tag: igg-denv

tag: igm-denv

tag: igg-zikv

value: Sao Carlos

value: Brazil


title: PZ9

description:
Blood donor
DZ_49

value: ZIKV

value: ND

tag: igm-zikv

tag: city

tag: country


title: 2524-SY-1

description: Covid

value: Whole Blood


title: PZ18

description:
Blood donor
DZ_48

tag: virus

tag: collection date

value: UK

value: M


title: DSP-1001660006157-C-B01


title: sample44

tag: rb1 mutation

tag: growth

value: exophytic

tag: chroid

value: deep


title: 2508-SY-1

description: Covid


title: PZ13

description:
Blood donor
DZ_47


title: sample43

value: no

value: minimal


title: PZ17

description:
Blood donor
DZ_46


title: 2433-SY-1

description: Covid


title: 2381-SY-2

description: Covid


title: DSP-1001660006157-C-A12

tag: tissue segment

value: stroma

tag: genotype

tag: scan batch


title: PZ12

description:
Blood donor
DZ_45

tag: onset of symptoms

tag: age

tag: sex

value: F


title: sample42

tag: tissue

value: endophytic


title: PZ16

description:
Blood donor
DZ_44

tag: igg-denv

value: N

tag: igm-denv

value: P


title: DSP-1001660006157-C-A11

tag: patient

value: epithelium

value: WT


title: 2381-SY-1

description: Covid


title: 2344-SY-1

description: Covid


title: sample41

value: retinoblastoma


title: 2316-SY-2

description: Covid


title: PD47

tag: igg-zikv

tag: igm-zikv

tag: city

value: San lorenzo

value: Paraguay


title: PD48

tag: virus

value: ZIKV

value: ND

tag: collection date

value: Bebedouro, SP

tag: country

value: Brazil


title: DSP-1001660006157-C-A10


title: sample40

tag: rb1 mutation

tag: growth

value: exophytic

tag: chroid

value: deep


title: DSP-1001660006157-C-A08

tag: tissue segment

tag: genotype

tag: scan batch


title: DSP-1001660006157-C-A09


title: DSP-1001660006157-C-A07


title: sample39

value: no


title: sample74


title: sample38


title: PD46

tag: onset of symptoms

tag: age

tag: sex

value: M

value: UK


title: DSP-1001660006157-C-A06

value: stroma


title: 2304-SY-3

description: Covid

tag: tissue

value: Whole Blood


title: sample36

value: endophytic

value: minimal


title: sample37


title: PD45

value: P

value: F

tag: igg-denv

tag: igm-denv

value: San Lorenzo


title: 2304-SY-2

description: Covid


title: 2272-SY-1

description: Covid


title: PD44

value: DENV

tag: igg-zikv

tag: igm-zikv

value: Fernando de la Mora

value: Paraguay


title: Donor6A

city: New York

first: Vilas

last: Menon

state: NY

department: Neurology

institute: Columbia University Medical Center

data_processing:
fastq files were run through 10x Genomics Cellranger v3.0.2
output bam files from cellranger were processed using BAMboozle for anonymization
Assembly: hg38
Supplementary files format and content: Counts tables for all barcodes in standard hdf5 output from Cellranger

source_name: Lumbar spinal cord

extract_protocol:
Nuclei were isolated from frozen human tissue using a triton-based protocol, as described in the publication. (Yadav, Matson, et al. 2022)
10x Genomics Chromium 3' v3 chemistry

value: Lumbar spinal cord


title: DSP-1001660006157-C-A05

tag: patient

value: epithelium

value: WT


title: sample35

value: retinoblastoma


title: PD43

tag: virus

value: ND

tag: collection date

tag: city

value: Villa Ygatimi


title: DSP-1001660006157-C-A02


title: PD42

value: N

value: Asuncion

tag: country


title: 2316-SY-1

description: Covid

value: Whole Blood


title: sample33

tag: rb1 mutation

tag: growth

value: exophytic

tag: chroid

value: extended


title: BCR_p22122-s002_RLk17_wk-10-53-55-63-74-90_Capture2

city: Atlanta

first: rohini

last: mopuri

state: GA

address: 954 Gatewood Rd NE

institute: Emory National Primate Research Center

data_processing:
Demultiplexing, barcode processing, gene and HTO counting was done with Cellranger6.0.1 into a single set of files for each capture. VDJ was done using cellranger v3.1.0.
Assembly: Mmul10,ensembl100
Supplementary files format and content: Tab separated values and matrix files
Library strategy: BCR-seq

organism: Macaca mulatta

source_name: Blood

extract_protocol:
CD14-, CD3-, CD20+, IgG+, and gp120-His double positive antigen specific, IgG+ circulating B cells from PBMC cryopreserved at weeks 10, 26, 55, 63, and 90 (necropsy). A cell hashing antibody that was unique for each animal was included in the phenotyping panel, so that sorted cells could be pooled for 10X Genomics sequencing and later deconvoluted by hashtag barcode. The following hashtags were used at : TotalSeq-C anti-human Hashtag 1, TotalSeq-C anti-human Hashtag 2 , TotalSeq-C anti-human Hashtag 3, TotalSeq-C anti-human Hashtag 4 , TotalSeq-C anti-human Hashtag 5 , TotalSeq-C anti-human HLA-DR , TotalSeq-C anti-human CD20, TotalSeq-C anti-human CD22 , TotalSeq-C anti-human HLA A/B/C , TotalSeq-C anti-human CD40.
Following reverse transcription, the cDNA was prepared to create gene expression libraries, BCR VDJ libraries and feature barcode libraries.

value: Blood

tag: cell type

value: Antigen Specific B lymphocytes

tag: condition

tag: library type

value: VDJ (BCR seq)


title: BCR_p22122-s003_RVn17-wk26_15C172-wk63-necropsy_ROa17-wk74

value: mixed sample(Week26 for RVn17 - R66M trimer , Week63 and Week90 for 15C172 - Z1800M trimer , Week74 for ROa17 - Z1800M gp120)


title: PD41

value: P

tag: onset of symptoms

tag: age

tag: sex

value: F

value: Itaugua


title: BCR_p22122-s001_RLk17_wk-10-53-55-63-74-90_Capture1

tag: tissue


title: BCR_p22066-s003_RTm17-RVn17-RFj17-RTe17-wk10

value: mixed sample(Week10 for RTm17,RVn17,RFj17,RTe17)


title: PD40

value: DENV

tag: igg-denv

tag: igm-denv

tag: igg-zikv

value: Fernando de la Mora

value: Paraguay


title: PD39

tag: virus

value: ND

tag: igm-zikv

value: Fernando de la mora


title: 2158-SY-2

description: Covid


title: 2227-SY-1

description: Covid


title: BCR_p22066-s001_RPh17-RVe17-RVn17-RVh17-necropsy_RPh17-15C172-wk63

value: mixed sample(Week 90 for RPh17,RVe17,RVn17,RVh17 ; Week63 Lymph node for RPh17,15C172)


title: 2145-SY-2

description: Covid

value: Whole Blood


title: PD38

tag: collection date

value: N

tag: city

value: San lorenzo


title: sample34

value: retinoblastoma

tag: rb1 mutation

value: no

value: endophytic


title: BCR_p21165-s021_RPh17-RVe17-RTm17-RVn17-necropsy

value: Blood

value: Antigen Specific B lymphocytes

value: mixed sample(Week90 for RPh17,RVe17,RTm17,RVn17 - R66M trimer)

value: VDJ (BCR seq)


title: sample30

tag: growth

value: extended


title: BCR_p21165-s020_RTe17-RLf17-RLl17-RWb17-necropsy

value: mixed sample(Week90 for RTe17,RLf17,RLl17,RWb17 - R66M gp120 , R66M trimer)


title: 2129-SY-1

description: Covid


title: sample29

value: mixed

tag: chroid


title: sample32


title: 2124-SY-3

description: Covid


title: sample28

value: exophytic


title: PD37

value: P

value: ND

value: M

value: Mariano Roque Alonso

tag: country

value: Paraguay


title: 2158-SY-3

description: Covid

value: Whole Blood


title: sample31

value: retinoblastoma


title: sample27

value: no


title: BCR_p21165-s018_650-15C172-RFj17-RSb17-necropsy

tag: cell type

tag: condition

value: mixed sample(Week90 for 6SO,15C172,RFj17,RSb17- Z1800M gp120,Z1800M trimer)


title: BCR_p21165-s019_RYf17-MA277-RVh17-RGi17-necropsy

value: Blood

value: mixed sample(Week90 for RYf17,MA277,RVh17,RGi17 - Z1800M trimer , R66M gp120)

tag: library type


title: 2124-SY-2

description: Covid


title: PD35

tag: onset of symptoms

value: UK

tag: age

value: F

value: Ribeirao Preto

value: Brazil


title: PD36

tag: sex


title: PD34

tag: igg-denv


title: sample26

tag: tissue


title: BCR_p21165-s017_RRb17-RPz16-RLk17-ROa17-necropsy

value: Antigen Specific B lymphocytes

value: mixed sample(Week90 for RRb17,RPz16,RLk17,ROa17 - Z1800M gp120)

value: VDJ (BCR seq)


title: 2078-SY-2

description: Covid


title: PD33

value: P

value: ND

tag: igm-denv

value: N

tag: igg-zikv


title: sample25

value: exophytic


title: BCR_p21165-s015_RTm17-RVn17-wk55-wk63

value: mixed sample(Week55 and Week63 for RTm17,RVn17 -R66M trimer)


title: 2055-SY-2

description: Covid

value: Whole Blood


title: sample23

value: retinoblastoma

value: no

value: endophytic


title: 2055-SY-1

description: Covid


title: BCR_p21165-s013_RPh17-RVe17-wk55-wk63

value: Blood

value: mixed sample(Week55 and Week63 for RPh17,RVe17 -R66M trimer)


title: PD32

tag: virus

value: UK

value: F

tag: igm-zikv


title: PD31

tag: collection date

value: M

tag: city

value: Ribeirao Preto

value: Brazil


title: 2103-SY-2

description: Covid


title: BCR_p21165-s012_RLl17-RWb17-wk10-wk26

value: Antigen Specific B lymphocytes

value: mixed sample(Week10 and Week26 for  RWb17, RLl17 -R66M trimer, R66M gp120)

value: VDJ (BCR seq)


title: 2027-SY-2

description: Covid


title: 2003-SY-1

description: Covid


title: PD30

value: P

value: ND

value: N


title: sample22

tag: rb1 mutation

tag: growth

value: exophytic

value: minimal


title: PD29

tag: country


title: 1987-SY-2

description: Covid

value: Whole Blood


title: PD9

value: DENV


title: BCR_p21165-s011_RLl17-RWb17-wk55-wk63

value: Blood

tag: cell type

value: mixed sample(Week55 and Week63 for RWb17, RLl17 -R66M trimer, R66M gp120)


title: BCR_p21165-s010_RTe17-RLf17-wk10-wk26

tag: condition

value: mixed sample(Week10 and Week26 for  RTe17, RLf17 - R66M gp120)


title: sample24

value: retinoblastoma

value: no

value: endophytic

tag: chroid


title: 2241-SY-1

description: Covid


title: sample19


title: BCR_p21165-s009_RTe17-RLf17-wk55-wk63

value: mixed sample(Week55 and Week63 for RTe17, RLf17 - R66M gp120)

tag: library type


title: 1906-AB-1

description: Covid


title: 1963-SY-1

description: Covid


title: sample18


title: BCR_p21165-s014_RPh17-RVe17-wk10-wk26

value: Antigen Specific B lymphocytes

value: mixed sample(Week10 and Week26 for  RPh17,RVe17 -R66M trimer)


title: PD11

tag: onset of symptoms

tag: age

value: F

value: Ribeirao Preto

value: Brazil


title: PD2

value: P

value: ND

tag: sex

tag: igg-denv


title: BCR_p21165-s007_RVh17-RGi17-wk55-wk63

tag: tissue

value: mixed sample(Week55 and Week63 for RVh17, RGi17 - R66M gp120)

value: VDJ (BCR seq)


title: 1826-AB-1

description: Covid

value: Whole Blood


title: PD6

tag: igm-denv

tag: igg-zikv


title: sample16


title: BCR_p21165-s006_6S0-MA277-wk10-wk26

value: Blood

value: mixed sample(Week10 and Week26 for 6S0,MA277 - Z1800M gp120 , Z1800M trimer)


title: PD5

tag: virus

value: M

tag: igm-zikv


title: sample21

value: retinoblastoma

value: yes

value: exophytic


title: 1819-AB-1

description: Covid


title: sample15

value: no


title: 1682-AB-2

description: Control


title: sample14

value: extended


title: BCR_p21165-s004_RSb17-RYf17-MA277-wk55-wk63-capture1

value: Antigen Specific B lymphocytes

value: mixed sample(Week55 and Week63 for RSb17,RYf17,MA277 - Z1800M trimer)


title: HepG2 cells, shcircEPB41(2)#2, rep2

city: HEFEI

first: Yang

last: Yang

state: ANHUI

address: NO. 96, JinZhai Road

institute: University of Science and Technology of China

data_processing:
RNA sequencing reads were mapped to human genome (hg19) using STAR (version 2.5), only uniquely mapped reads (with MAPQ>10) with <5nt/100nt mismatches and properly paired reads were used.
For gene expression analysis, the number of read in the coding sequence (CDS) region of protein-coding genes and exonic region of non-coding genes were counted and analysed using DESeq2 (Bioconductor)
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Liver

tag: cell line

tag: genotype

value: circEPB41(2) knockdown

tag: treatment


title: BCR_p21165-s003_RSb17-RYf17-wk10-wk26

value: mixed sample(Week10 and Week26 for RSb17,RYf17 - Z1800M trimer)


title: sample17

tag: rb1 mutation

tag: growth


title: BCR_p21165-s008_RVh17-RGi17-wk10-wk26

tag: cell type

tag: condition

value: mixed sample(Week10 and Week26 for RVh17, RGi17 - R66M gp120)


title: PD8

value: DENV

value: P

value: ND

tag: collection date

value: F

tag: city

value: Ribeirao Preto

tag: country

value: Brazil


title: BCR_p21165-s002_15C172-RFj17-wk10-wk26

value: Blood

value: mixed sample(Week10 and Week26 for 15C172,RFj17 - Z1800M trimer)

tag: library type

value: VDJ (BCR seq)


title: PD26

tag: onset of symptoms

tag: age

tag: sex

tag: igg-denv


title: HepG2 cells, shcircEPB41(2)#2, rep1

tag: tissue


title: PD25

tag: virus

value: M

tag: igm-denv

tag: igg-zikv

tag: igm-zikv


title: 1801-SY-1

description: Covid

value: Whole Blood


title: sample13

value: retinoblastoma

tag: rb1 mutation

value: mixed

tag: chroid


title: sample11

value: no

tag: growth


title: sample12

value: yes


title: BCR_p21165-s001_RRb17-RPz16-15C172-RFj15-wk55

tag: cell type

value: Antigen Specific B lymphocytes

tag: condition

value: mixed sample(Week55 for RRb17,RPz16 - Z1800M gp120 ; 15c172,RFj17 - Z1800M trimer)


title: HepG2 cells, shcircEPB41(2)#1, rep1

value: Liver

tag: cell line

tag: genotype

value: circEPB41(2) knockdown

tag: treatment


title: PD28

value: P

value: ND

tag: collection date

tag: onset of symptoms

value: UK

value: N

tag: city

tag: country


title: sample10

tag: tissue

value: endophytic

value: minimal


title: BCR_p21165-s005_RSb17-RYf17-MA277-wk55-wk63-capture2

value: Blood

value: mixed sample(Week55 and Week63 for RSb17,RYf17,MA277 - Z1800M trimer)

tag: library type

value: VDJ (BCR seq)


title: BCR_p21096-s004_RRb17-wk10-wk26-RPz16-wk10-wk26

value: mixed sample(Week10 and Week26 for RRb17,RPz17 - Z1800M gp120)


title: HepG2 cells, shControl, rep2

value: WT

value: shControl


title: PD27

tag: virus

tag: age

tag: sex

value: F

tag: igg-denv

tag: igm-denv

value: Ribeirao Preto

value: Brazil


title: PD4

value: DENV

value: M

tag: igg-zikv

tag: igm-zikv


title: sample9

value: retinoblastoma

tag: rb1 mutation

value: no

tag: growth

tag: chroid

value: deep


title: PD24

value: P

value: ND


title: HepG2 cells, shControl, rep1

value: Liver

tag: cell line

tag: genotype

tag: treatment


title: HepG2 cells, shcircEPB41(2)#1, rep2

value: circEPB41(2) knockdown


title: PD15

tag: collection date

tag: onset of symptoms

tag: city


title: BCR_p21096-s002_RLK17-wk63

tag: tissue

value: Blood

tag: cell type

value: Antigen Specific B lymphocytes

tag: condition

value: sample(Week63 RLk17 - Z1800M gp120)

tag: library type


title: sample8

value: yes

value: mixed

value: extended


title: HTO_p22122-s003_RVn17-wk26_15C172-wk63-necropsy_ROa17-wk74

library_source: other

data_processing:
Demultiplexing, barcode processing, gene and HTO counting was done with Cellranger6.0.1 into a single set of files for each capture. VDJ was done using cellranger v3.1.0.
Assembly: Mmul10,ensembl100
Supplementary files format and content: Tab separated values and matrix files
Library strategy: CITE-seq

molecule: other

value: mixed sample(Week26 for RVn17 - R66M trimer , Week63 and Week90 for 15C172 - Z1800M trimer , Week74 for ROa17 - Z1800M gp120)

value: HTO

tag: hto

value: RVn17_wk26 :Hashtag 1, 15C172_wk63 :Hashtag 2 , 15C172_wk90 :Hashtag 3 , ROa17_wk74 :Hashtag 4


title: PD22

tag: virus

value: DENV

tag: age

tag: sex

value: M

tag: igg-denv

tag: igm-denv

value: Ribeirao Preto

tag: country

value: Brazil


title: BCR_p21065_s001_RRb17-RPz16-15C172-RFj17

value: mixed sample(Week63 for RRb17,RPz16 - Z1800M gp120 ; 15C172,RFj17- Z1800M trimer)

value: VDJ (BCR seq)


title: PD14

value: P

value: ND

value: F

tag: igg-zikv

tag: igm-zikv


title: PD23


title: BCR_p21096-s001_ROa17-wk63-wk55-RLK17-wk55

value: Blood

value: Antigen Specific B lymphocytes

value: mixed sample(Week63 for ROa17, Week55 for ROa17,RLk17 - Z1800M gp120)


title: HTO_p22122-s001_RLk17_wk-10-53-55-63-74-90_Capture1

value: RLk17_wk10:Hashtag 1,RLk17_wk53:Hashtag 2,RLk17_wk55:Hashtag 3,RLk17_wk63:Hashtag 4 , RLk17_wk74 :Hashtag 5 , RLk17_wk90 :HLA-DR


title: BCR_p21096-s003_ROa17-wk10-wk26-RLk17-wk10-wk26

value: mixed sample(Week10 and Week26 for RLk17,ROa17 - Z1800M gp120)


title: sample4

value: retinoblastoma

tag: rb1 mutation

value: no

tag: growth

value: exophytic

tag: chroid

value: extended


title: PD12

tag: collection date

tag: onset of symptoms

tag: city


title: PD13

value: M


title: HTO_p22066-s003_RTm17-RVn17-RFj17-RTe17-wk10

tag: tissue

tag: cell type

tag: condition

value: mixed sample(Week10 for RTm17,RVn17,RFj17,RTe17)

value: HTO

value: RTm17 _wk10:Hashtag 3,RVn17_wk10:Hashtag 4,RFj17_wk10:Hashtag 5,RTe17_wk10:HLA-DR


title: PD21

tag: virus

value: Ribeirao Preto

value: Brazil


title: sample6


title: sample5

value: endophytic

value: deep


title: HTO_p22066-s001_RPh17-RVe17-RVn17-RVh17-necropsy_RPh17-15C172-wk63

value: Blood

value: mixed sample(Week 90 for RPh17,RVe17,RVn17,RVh17 ; Week63 Lymph node for RPh17,15C172)

tag: library type

tag: hto

value: RPh17_wknecropsy:Hashtag 1,RVe17_wknecropsy:Hashtag 2,RVn17_wknecropsy:Hashtag 3,RVh17_wknecropsy:Hashtag 4, RPh17_LN_wk63 :Hashtag 5, 15C172_LN_wk63 :HLA-DR


title: sample3

value: yes


title: sample7

value: mixed

value: minimal


title: PD20

value: DENV

value: P

value: ND

tag: age

tag: sex

tag: igg-denv


title: HTO_p22122-s002_RLk17_wk-10-53-55-63-74-90_Capture2

value: Antigen Specific B lymphocytes

value: RLk17_wk10:Hashtag 1,RLk17_wk53:Hashtag 2,RLk17_wk55:Hashtag 3,RLk17_wk63:Hashtag 4 , RLk17_wk74 :Hashtag 5 , RLk17_wk90 :HLA-DR


title: sample2

value: retinoblastoma


title: HTO_p21165-s020_RTe17-RLf17-RLl17-RWb17-necropsy

value: mixed sample(Week90 for RTe17,RLf17,RLl17,RWb17 - R66M gp120 , R66M trimer)

value: HTO


title: C2

description:
Control
DZ_02

value: Control

value: N

value: F

tag: igm-denv

tag: igg-zikv

value: Ribeirao Preto

tag: country

value: Brazil


title: HTO_p21165-s019_RYf17-MA277-RVh17-RGi17-necropsy

value: Blood

value: mixed sample(Week90 for RYf17,MA277,RVh17,RGi17 - Z1800M trimer , R66M gp120)

value: RYf17_wknecropsy:Hashtag 1,MA277_wknecropsy:Hashtag 2,RVh17_wknecropsy:Hashtag 4,RGi17_wknecropsy:Hashtag 5


title: HTO_p21165-s018_650-15C172-RFj17-RSb17-necropsy

value: mixed sample(Week90 for 6SO,15C172,RFj17,RSb17- Z1800M gp120,Z1800M trimer)

value: 6S0_wknecropsy:HLA-ABC,15C172_wknecropsy:Hashtag 1,RFj17_wknecropsy:Hashtag 4,RSb17_wknecropsy:Hashtag 5


title: CHM13_tc_3

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

data_processing:
Illumina Real Time Analysis version RTA 2.4.11 and bcl2fastq2 v2.20 were run to demultiplex reads and generate FASTQ files.
ChIP-seq data was aligned to human genome references hg38 and CHM13v1 using bwa with the following parameters: bwa mem -k 50 -c 1000000. Secondary and supplementary alignments were excluded using samtools to filter out reads with SAM FLAG 2308.
Read coverage was calculated and normalized to Reads Per Million from BAM files using the GenomicRanges library in R. RPM coverage for replicate samples was averaged to create an average RPM bigWig track.
Peaks were called using macs2 with the following parameters: -g 2.9e9 -q 0.01 --nomodel. Reference peak sets for each factor were created using the reduce function from GenomicRanges in R to create a single collection of candidate loci, and then discarding any loci not observed in at least 2 replicates.
Assembly: hg38, CHM13v1
Supplementary files format and content: Reference peaks for each factor in each cell line, from data aligned to either hg38 or CHM13v1 as indicated.
Supplementary files format and content: RPM coverage of averaged replicates in bigWig format for each factor in each cell line from data aligned to either hg38 or CHM13v1 as indicated.

source_name: cell line

growth_protocol: RPE-1 cells were cultured in 150 mm dishes (Corning) up to 80% confluence in 20 ml of culture medium.

extract_protocol:
To fix cells, 16% methanol-free formaldehyde solution (Pierce) was added directly to the culture medium to a final concentration of 1% and incubated at room temperature for 10 min with gentle agitation. Formaldehyde was quenched with glycine (final =125 mM) for 5 min at room temperature. Cells were washed 3 times in 1x ice-cold phosphate buffered saline (PBS) containing 1mM PMSF, 1x protease inhibitory cocktail (PIC) (Roche) and harvested by using a cell lifter, spun down at 2000 rpm for 15 min (RPE-1)/1200 rpm for 8 min (CHM13) at 40C. Pellet was washed in 2 ml Buffer A2 (15 mM HEPES, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS, 0.5% N-lauroylsarcosine, 1mM DTT, 1 mM PMSF, 1x PIC, spun at 2,000/1800 rpm for 5/8 min at 40C (RPE-1 and CHM13 respectively). For RPE-1 cells, 8 x 10e6 cells were re-suspended in 1.8 mL Buffer A2 and distributed in 6 nos. 1.5 mL Bioruptor® tubes. Cells were sonicated using Bioruptor bath sonicator for 2 rounds of 7 cycles (1 cycle: 30" ON, 30" OFF) at 40C with 1 min of incubation on ice followed by vortexing between each round. 1 x 10e7 CHM13 cells, were resuspended in 1 mL of buffer A2 and aliquoted into 1.5 mL tubes (Covaris®). Cells were sonicated for 8 min (Power: 140, Duty factor: 6, 200 bursts/cycle) on Covaris S220 ultrasonicator. Sonicated chromatin was pooled and spun at 14,000 rpm for 15 min, 40C and the pellet was discarded. All steps from here on were performed in Low protein binding microcentrifuge tubes (Thermo Scientific, 90410). Bead preparation and antibody binding: 30-50 µL of DynabeadsTM Protein G (Invitrogen, 10003D) were used per ChIP. Beads for each ChIP were distributed in 1.5 mL tubes, washed twice in 1x PBS and once 0.5% bovine serum albumin (BSA)-1x PBS. For antibody binding, each tube of beads was resuspended in 800 µL of 0.5% BSA-1x PBS and incubated with 5 µg of each antibody for 3 h at 40C on a nutator at low speed. Antibody bound beads were washed once in 0.5% BSA-1x PBS. Pre-clearing: DynabeadsTM Protein G beads were prepared as before and 10 µL of blocked beads were used to pre-clear ~100 µg of chromatin for 3 h at 40C. 10% of pre-cleared chromatin was removed as Input and flash frozen in liquid nitrogen. Chromatin immunoprecipitation: ~75-100 µg of pre-cleared chromatin (amounts varied across replicates but constant for each antigen in a single experiment) was added to antibody-bead conjugates, volume was made up to 800 µL with Buffer A2 and incubated overnight at 40C on a nutator at low speed. The following day, beads were collected using DynamagTM (Invitrogen) and supernatant was discarded. Beads were washed 3 times in low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100), 3 times in high salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100) and once in LiCl buffer (20 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Triton X-100, 0.1% NP-40, 0.5% sodium deoxycholate). Washes were 10 min each at 40C. Chromatin elution and de-crosslinking: 100 µL elution buffer (EB) (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) and 100 µL TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA) were added to beads in each tube and incubated at 650C for 15 min. Supernatant was collected and the step was repeated once more. Input volume was made up to 400 µL with 1:1 EB:TE and treated similarly. NaCl (final = 210 mM) and 20 µg (2 µL) Proteinase K (Invitrogen) were added to each tube of eluted chromatin overnight at 650C on a thermomixer at 600 rpm. 10 µg of RNaseA (Invitrogen) to each tube and incubated at 370C for 1h. DNA purification: DNA was extracted with equal volume of phenol:chloroform:isoamyl alcohol (25:24:1) and the aqueous layer was transferred to new tube containing NaCl (final = 200 mM) and 2 µL GlycoBlueTM (ThermoFisher Scientific, AM9515). 750 µL of ice-cold 100% ethanol was added, and tubes were incubated at -800C for 1 h, centrifuged at 14,000 rpm for 30 min at 40C, DNA pellet was washed once with 70% ethanol and air-dried. Finally, DNA pellets were re-suspended in ultrapure distilled water (Invitrogen).
Libraries were prepared using the KAPA HTP Library Prep Kit for Illumina (Roche, KK8234) and Bioo Scientific NEXTflex DNA barcodes (Perkin Elmer, NOVA-514104). The resulting libraries were purified using the Agencourt AMPure XP system (Beckman Coulter, A63882) then quantified using a Bioanalyzer HS DNA kit (Agilent Technologies, 5067-4626) and a Qubit fluorometer (Life Technologies) with Qubit dsDNA HS assay kit (Invitrogen, Q32851). Post amplification size selection (275-700 bp) was performed on all libraries using a PippinHT (Sage Science) using 1.5% cassette (HTC1510). Libraries were pooled, requantified, and sequenced as 150 bp paired reads on a mid-output flow cell using the Illumina NextSeq 500 instrument.

value: cell line

tag: cell line

value: hydatidiform mole

tag: replicate


title: C1

description:
Control
DZ_01

value: ND

tag: collection date

tag: igm-zikv


title: CHM13_tc_2


title: HTO_p21165-s017_RRb17-RPz16-RLk17-ROa17-necropsy

value: Antigen Specific B lymphocytes

value: mixed sample(Week90 for RRb17,RPz16,RLk17,ROa17 - Z1800M gp120)

value: RRb17_wknecropsy:Hashtag 1,RPz16_wknecropsy:Hashtag 2,RLk17_wknecropsy:Hashtag 3,ROa17_wknecropsy:Hashtag 4


title: CHM13_tc_1


title: mir163-biol rep 1

city: Taichung City

first: Jeng-Shane

last: Lin

state: Taiwan (R.O.C.)

address: Room 516, Life Science Building,145 Xingda Rd., South Dist.

country: Taiwan

institute: National Chung Hsing University

data_processing:
Raw sequences were obtained from the Illumina bcl2fastq v2.17.1.14 and expected to generate 6 G per sample.
Trimmomatics was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using TopHat/Cufflinks for gene expression estimation.
For differential expression analysis, CummeRbund was employed to perform statistical analyses of gene expression profiles.
The reference genome and gene annotations were retrieved from Ensembl database.
Assembly: TAIR10
Supplementary files format and content: WT-163 file includes FPKM values

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis thaliana (Col-0) was grown in a controlled environment at 22°C under 16 h light/8 h dark with cool fluorescent light at 100 μmolm-2 s-1.

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual.
Library construction of all samples were used by NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: The 7-day-old seedlings were used.

value: seedlings

tag: ecotype

tag: genotype

value: mir163 mutant

tag: treatment

value: 7-day-old seedlings without treatment


title: HuH7_KO1

city: Bunkyo-ku

first: Shu

last: Shimada

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

institute: Tokyo Medical and Dental University

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) were performed following the manufacturer's instruction by using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000.

data_processing: The data were normalized by robust multichip analysis (RMA) using affy package in R/Bioconductor.

source_name: KDM6B knockout human hepatocellular carcinoma cell line HuH7

label_protocol: Amplified RNA was prepared by using 3' IVT Express Kit (Affymetrix).

growth_protocol: Human hepatocellular carcinoma cell line HuH7 was purchased from the American Type Culture Collection, and then grown in RPMI 1640 medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in a humidified incubator at 37°C with 5% CO2. After transfection of the gRNA Cloning Vector (#41824, Addgene) targeting KDM6B (5'- CACAGCGCCCTTCGATACGG -3') and the hCas9 Vector (#41815, Addgene) into HuH7 and selection by G418, several KDM6B knockout subclones were obtained by limiting dilution.

extract_protocol: Total RNA was extracted from cells by using RNeasy Protect Mini Kit (QIAGEN). Contaminating DNA was removed by digestion with RNase-Free DNase Set (QIAGEN). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).

tag: cell line background

tag: cell type

value: KDM6B knockout


title: WT-biol rep 3

tag: tissue

value: WT


title: sample1

value: retinoblastoma

tag: rb1 mutation

value: yes

tag: growth

value: exophytic

tag: chroid


title: HTO_p21165-s015_RTm17-RVn17-wk55-wk63

value: Blood

tag: condition

value: mixed sample(Week55 and Week63 for RTm17,RVn17 -R66M trimer)

tag: library type

value: HTO

tag: hto

value: RTm17_wk55:Hashtag 3,RTm17_wk63:Hashtag 4,RVn17_wk55:Hashtag 5,RVn17_wk63:HLA-DR


title: WT-biol rep 2


title: HuH7_WT2

source_name: KDM6B wild-type human hepatocellular carcinoma cell line HuH7

value: KDM6B wild-type


title: HuH7_KO2

value: human hepatocellular carcinoma cell line


title: HTO_p21165-s014_RPh17-RVe17-wk10-wk26

value: Antigen Specific B lymphocytes

value: mixed sample(Week10 and Week26 for  RPh17,RVe17 -R66M trimer)

value: RPh17_wk10:Hashtag 1,RPh17_wk26:Hashtag 2,RVe17_wk10:Hashtag 3,RVe17_wk26:HAL-DR


title: C5

description:
Control
DZ_03

data_processing: Each spot median fluorescence intensity, with local background subtraction, was computed with the GenePix Pro 7 Molecular Devices, USA, or Mapix, Innopsys, France, software. Fluorescence intensity values <1 were converted to 0. Then, fluorescence intensity values were normalized against the negative controls (HA peptides). This normalization was done by dividing the fluorescence intensity value of each spot by the mean fluorescence intensity of the negative control spots. Normalized fluorescence intensity values <1 were converted to 1. The normalized data were log2-transformed to reduce variability. The final fluorescence intensity value for each peptide was the mean of the fluorescence intensity value of the duplicated peptide spots.

extract_protocol: Blood samples were collected via venipuncture, and the resulting sera were separated and stored at -80°C.

tag: virus

value: Control

value: N

value: ND

tag: onset of symptoms

tag: age

tag: sex

value: F

tag: igg-denv

tag: igm-denv

tag: igg-zikv

tag: city

value: Ribeirao Preto

tag: country

value: Brazil


title: WT-biol rep 1

value: seedlings

tag: ecotype

tag: genotype

value: WT

tag: treatment

value: 7-day-old seedlings without treatment


title: HTO_p21165-s013_RPh17-RVe17-wk55-wk63

tag: tissue

value: Blood

tag: cell type

value: mixed sample(Week55 and Week63 for RPh17,RVe17 -R66M trimer)


title: CHM13_Rad21_ip_2

value: cell line

tag: cell line

value: hydatidiform mole

tag: replicate

tag: chip antibody

value: Abcam, ab992


title: mir163-biol rep 3

value: mir163 mutant


title: CHM13_Rad21_ip_1


title: HTO_p21165-s012_RLl17-RWb17-wk10-wk26

value: Antigen Specific B lymphocytes

tag: condition

value: mixed sample(Week10 and Week26 for  RWb17, RLl17 -R66M trimer, R66M gp120)

tag: library type

value: HTO

tag: hto

value: RLl17_wk10:Hashtag 1,RLl17_wk26:Hashtag 2,RWb17 _wk10:Hashtag 4,RWb17 _wk26:HLA-DR


title: MoS2_NIR_2

city: chongqing

first: ke

last: li

address: shazheng street 174

institute: chongqing university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Rattus norvegicus

source_name: Mouse breast cancer cells

growth_protocol: 10% FBS, 1% penicillin/streptomycin, high glucose DMEM

extract_protocol:
About 10e6 4T1 cells were isolated from different group and the mRNA library constructed using QIAseq FX Single Cell RNA Library Kit (QIAGEN) according to the manufacturer’s instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cell cultured with medium, MoS2 and MoS2+NIR

tag: cell states

value: photothermal therapy

tag: intervention


title: MoS2_NIR_3


title: CHM13_SA2_ip_3

value: Bethyl, A302-580A


title: HTO_p21165-s011_RLl17-RWb17-wk55-wk63

value: mixed sample(Week55 and Week63 for RWb17, RLl17 -R66M trimer, R66M gp120)

value: RLl17_wk55:hashtag 1,RLl17_wk63:hashtag 4,RWb17 _wk55:HLA-DR,RWb17 _wk63:CD22


title: CHM13_SA2_ip_2


title: CHM13_Rad21_ip_3


title: CHM13_SA2_ip_1


title: CHM13_SA1_ip_3

value: Bethyl, A302-579A


title: HuH7_WT1

tag: cell line background

value: human hepatocellular carcinoma cell line

value: KDM6B wild-type


title: CHM13_SA1_ip_2


title: MoS2_1

value: Normal culture condition


title: MoS2_2


title: HTO_p21165-s008_RVh17-RGi17-wk10-wk26

value: Blood

value: mixed sample(Week10 and Week26 for RVh17, RGi17 - R66M gp120)

value: RVh17_wk10:Hashtag 1,RVh17_wk26:Hashtag 2,RGi17_wk10:Hashtag 4,RGi17_wk26:Hashtag 5


title: CHM13_SA1_ip_1

value: cell line

value: hydatidiform mole


title: HTO_p21165-s007_RVh17-RGi17-wk55-wk63

value: Antigen Specific B lymphocytes

value: mixed sample(Week55 and Week63 for RVh17, RGi17 - R66M gp120)

value: RVh17_wk55:Hashtag 1,RVh17_wk63:Hashtag 2,RGi17_wk55:Hashtag 4,RGi17_wk63:Hashtag 5


title: Control_3

value: Control


title: HTO_p21165-s006_6S0-MA277-wk10-wk26

value: mixed sample(Week10 and Week26 for 6S0,MA277 - Z1800M gp120 , Z1800M trimer)

value: HTO


title: RPE-1_tc_2

value: human retinal pigment epithelial


title: HTO_p21165-s005_RSb17-RYf17-MA277-wk55-wk63-capture2

value: mixed sample(Week55 and Week63 for RSb17,RYf17,MA277 - Z1800M trimer)

value: RSb17 _wk55:Hashtag 4,RSb17 _wk63:Hashtag 5,RYf17_wk55:HLA-ABC,RYf17_wk63:CD40


title: Control_2


title: HTO_p21165-s021_RPh17-RVe17-RTm17-RVn17-necropsy

value: mixed sample(Week90 for RPh17,RVe17,RTm17,RVn17 - R66M trimer)

value: RPh17_wknecropsy:Hashtag 3,RVe17_wknecropsy:Hashtag 4,RTm17_wknecropsy:Hashtag 5,RVn17_wknecropsy:HLA-DR


title: Control_1

value: Normal culture condition


title: RPE-1_tc_1


title: HTO_p21165-s003_RSb17-RYf17-wk10-wk26

value: Blood

value: mixed sample(Week10 and Week26 for RSb17,RYf17 - Z1800M trimer)


title: HTO_p21165-s010_RTe17-RLf17-wk10-wk26

value: mixed sample(Week10 and Week26 for  RTe17, RLf17 - R66M gp120)


title: MoS2_3


title: HTO_p21165-s009_RTe17-RLf17-wk55-wk63

value: mixed sample(Week55 and Week63 for RTe17, RLf17 - R66M gp120)

value: RTe17_wk55:Hashtag 1,RTe17_wk63:Hashtag 2,RLf17_wk55:Hashtag 4,RLf17_wk63:Hashtag 5


title: RPE-1_Rad21_ip_2

value: cell line

value: Abcam, ab154769


title: RPE-1_Rad21_ip_1


title: HTO_p21165-s002_15C172-RFj17-wk10-wk26

value: Antigen Specific B lymphocytes

value: mixed sample(Week10 and Week26 for 15C172,RFj17 - Z1800M trimer)

value: 15C172_wk10:Hashtag 3,15C172_wk26:Hashtag 4,RFj17_wk10:Hashtag 2,RFJ17_wk26:HLA-DR


title: RPE-1_SA2_ip_2

value: Bethyl, A302-580A


title: RPE-1_SA2_ip_1

value: human retinal pigment epithelial


title: HTO_p21165-s001_RRb17-RPz16-15C172-RFj15-wk55

value: mixed sample(Week55 for RRb17,RPz16 - Z1800M gp120 ; 15c172,RFj17 - Z1800M trimer)

value: HTO

value: RRb17_wk55:Hashtag 3,RPz16_wk55:Hashtag 4,15C172_wk55:Hashtag 5,RFj17_wk55:HLA-DR


title: HTO_p21096-s004_RRb17-wk10-wk26-RPz16-wk10-wk26

value: mixed sample(Week10 and Week26 for RRb17,RPz17 - Z1800M gp120)

value: RRb17_wk10:Hashtag 1,RRb17_wk26:Hashtag 2,RPz16_wk10:Hashtag 3,RPz16_wk26:HLA-DR


title: RPE-1_SA1_ip_1

value: Bethyl, A302-579A


title: HTO_p21096-s003_ROa17-wk10-wk26-RLk17-wk10-wk26

value: Blood

value: mixed sample(Week10 and Week26 for RLk17,ROa17 - Z1800M gp120)

value: RLk17_wk10:Hashtag 3,RLk17_wk26:HLA-DR,ROa17_wk10:Hashtag 1,ROa17_wk26:Hashtag 2


title: RPE-1_SA1_ip_2


title: HTO_p21096-s001_ROa17-wk63-wk55-RLK17-wk55

value: mixed sample(Week63 for ROa17, Week55 for ROa17,RLk17 - Z1800M gp120)

value: RLk17_wk55:Hashtag 3,ROa17_wk55:Hashtag 1,ROa17_wk63:Hashtag 2


title: HepG2 cells, shcircEPB41(2)

data_processing:
Basecalling were performed using Illumina Casava1.7 software.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie2 (v2.3.1) Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Peak visualizations were prepared using Deeptools. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Sonicator (Diagenode).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Liver

value: circEPB41(2) knockdown

value: H3K9ac (Abclonal, A7255)


title: HTO_p21165-s004_RSb17-RYf17-MA277-wk55-wk63-capture1

value: Antigen Specific B lymphocytes

value: mixed sample(Week55 and Week63 for RSb17,RYf17,MA277 - Z1800M trimer)

value: RSb17 _wk55:Hashtag 4,RSb17 _wk63:Hashtag 5,RYf17_wk55:HLA-ABC,RYf17_wk63:CD40


title: HepG2 cells, shControl

value: control


title: Control [WT3_S56]

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

data_processing:
Data analysis was performed using Partek flow software. The raw sequencing files were aligned to mouse genome (mm10) using STAR aligner v 2.7.3a.
Annotation database - RefSeq transcripts 93
DESeq2 was used for identifying differentially expressed mRNAs (Fold change >=1.5 andp-value < 0.05).
Assembly: mm10
Supplementary files format and content: File format- xlsx; Raw counts
Supplementary files format and content: File format-xlsx; log CPM counts

source_name: Pancreatic islet

growth_protocol: Mice with β cell specific deletion of SERCA2 (βS2KO), generated by crossing Atp2a2tm1.1Iemr (MGI:4415164) with Ins1tm1.1(cre)Thor mice (MGI:5614359).    All mice we used were C57BL/6J background or backcrossed with C57BL/6J for at least 10 generations. Mice were maintained in a standard light-dark cycle with regular access to a chow diet and water ad libitum. Mice were maintained under protocols approved by the Indiana University Institutional Animal Care and Use Committee

extract_protocol:
Mouse islets were isolated by collagenase digestion. The islets were hand-picked, and allowed to recover overnight in regular RPMI supplemented with 10% FBS, 100U/ml penicillin, and 100μg/ml. RNA was harvested using Qiagen RNAeasy micro kit was used to obtain RNA and the RNA integrity was calciulated using Bio analyzer.
KAPA mRNA Hyperprep kit (KK8581); cDNA library preparation includes mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KK8581. Each resulting indexed library was quantified and its quality assessed by Qubit and Agilent Bioanalyzer, and multiple libraries pooled in equal molarity. The pooled libraries were then denatured, and neutralized, before loading to Illumina HiSeq 4000 sequencer at 300pM final concentration for 100b paired-end sequencing (Illumina, Inc.). Approximately 30M reads per library was generated.

value: Mouse pancreatic islet

value: Control

tag: Sex

value: Male

tag: age

value: 24 weeks

tag: strain background


title: HTO_p21065_s001_RRb17-RPz16-15C172-RFj17

value: mixed sample(Week63 for RRb17,RPz16 - Z1800M gp120 ; 15C172,RFj17- Z1800M trimer)

value: HTO

value: RRb17_wk63:Hashtag 3,RPz16_wk63:Hashtag 4,15C172_wk63:Hahtag 5,RFj17_wk63:HLA-DR


title: Fibroblast, CWG-cPIP, rep3

city: Honjo, Chuo-ku, Kumamoto

first: Kazuya

last: Matsuo

department: IMEG

institute: Kumamoto University

data_processing:
Local Run Manager was used for demultiplexing and FASTQ file generation after base calling.
The adapter sequence and low-quality ends were trimmed using Trim Galore! version 0.6.6.
The remaining reads were aligned to the mouse genome (UCSC mm10) and gene expression was counted using RSEM version 1.3.3 with STAR version 2.7.9a.
Gene expression for each sample was analyzed with DESeq2 version 1.36.0 and expressed as normalized counts calibrated by expression levels of spike-in controls in regularized logarithm.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized log2 values for each sample

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
After mixing with ERCC RNA spike-in cnotrols, RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

value: fibroblast

value: wild type

value: CWG-cPIP


title: Fibroblast, CWG-cPIP, rep2


title: Control [WT2_S55]


title: Fibroblast, CWG-cPIP, rep1


title: Control [WT1_S54]


title: Tcam-2 wild type_3

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

data_processing:
Alignment of raw sequencing reads to reference genome using hisat 2.0.5
Counting of reads per gene using featureCounts version 1.6.5
Normalization of counts using DESeq2
Assembly: GRCh38
Supplementary files format and content: Text file with counts of reads per gene for all samples
Supplementary files format and content: Text file with normalized expression values for all samples

source_name: testis

extract_protocol:
The cell samples were lysed in 350 µl of RLT buffer with β-mercaptoethanol and RNA, DNA and protein were extracted according to the manufacturer’s protocol AllPrep DNA/RNA/Protein Mini Kit (Qiagen, Hilden, Germany). The RNA samples were additionally purified according to the manufacturer’s protocol of Turbo DNA-free Kit (Thermo Fisher Scientific, MT, USA).
Sequencing libraries of cell samples were prepared using the the TruSeq Stranded Total RNA with Ribo-Zero Human (Illumina) and sequenced on an Illumina NovaSeq6000  platform
Paired end 150bp sequencing

value: testis

value: testicular seminoma cell line

value: WT

value: no modification


title: Tcam-2 wild type_2


title: GEX_p22122-s002_RLk17_wk-10-53-55-63-74-90_Capture2

description: Processed data for this sample is available on GSM7813040.

data_processing:
Demultiplexing, barcode processing, gene and HTO counting was done with Cellranger6.0.1 into a single set of files for each capture. VDJ was done using cellranger v3.1.0.
Assembly: Mmul10,ensembl100
Supplementary files format and content: Tab separated values and matrix files

value: Blood

value: Antigen Specific B lymphocytes

value: mRNA


title: Fibroblast, vehicle, rep3

value: vehicle


title: Microglia_control_P70_rep1

city: Fukuoka City

first: Ban-yu

last: Saitoh

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku,

department: Department of Neurology

institute: Kyushu University Graduate School of Medicine

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay mouse array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

source_name: Microglia isolated from whole brain, control, P70, replicate1

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: strain

value: Whole brain

tag: gender

value: control


title: Microglia_OVA_P70_rep1

source_name: Microglia isolated from whole brain, OVA, P70, replicate1

value: Male

tag: treatment

value: OVA


title: GEX_p22122-s003_RVn17-wk26_15C172-wk63-necropsy_ROa17-wk74

tag: tissue

value: mixed sample(Week26 for RVn17 - R66M trimer , Week63 and Week90 for 15C172 - Z1800M trimer , Week74 for ROa17 - Z1800M gp120)


title: GEX_p22122-s001_RLk17_wk-10-53-55-63-74-90_Capture1

description: Processed data files contain data from GSM7813040 and GSM7813041.

tag: cell type


title: Microglia_control_P30_rep1

source_name: Microglia isolated from whole brain, control, P30, replicate1


title: SERCA2 Knock out [KO2_S58]

value: Mouse pancreatic islet

tag: genotype

value: SERCA2 Knock out

value: 24 weeks


title: Microglia_OVA_P30_rep1

source_name: Microglia isolated from whole brain, OVA, P30, replicate1


title: Fibroblast, vehicle, rep1

tag: cell line

value: fibroblast

value: wild type


title: Tcam-2 negative control with non-specific sgRNAs for human genome_3

value: testis

value: testicular seminoma cell line

value: negative control

value: sgRNAs non-specific for human genome


title: SERCA2 Knock out [KO1_S57]


title: GEX_p22066-s003_RTm17-RVn17-RFj17-RTe17-wk10

value: Blood

value: Antigen Specific B lymphocytes

value: mixed sample(Week10 for RTm17,RVn17,RFj17,RTe17)


title: Striatum, CWG-cPIP, rep3

data_processing:
Local Run Manager was used for demultiplexing and FASTQ file generation after base calling.
The adapter sequence and low-quality ends were trimmed using Trim Galore! version 0.6.6.
The remaining reads were aligned to the mouse genome (UCSC mm10) and gene expression was counted using RSEM version 1.3.3 with STAR version 2.7.9a.
Gene expression for each sample was analyzed with DESeq2 version 1.36.0 and expressed as normalized counts in regularized logarithm.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized log2 values for each sample

source_name: Brain striatum

value: Brain striatum

tag: developmental stage

value: CWG-cPIP


title: Tcam-2 negative control with non-specific sgRNAs for human genome_2


title: Tcam-2 negative control with non-specific sgRNAs for human genome_1


title: Striatum, CWG-cPIP, rep2


title: GEX_p21165-s021_RPh17-RVe17-RTm17-RVn17-necropsy

tag: condition

value: mixed sample(Week90 for RPh17,RVe17,RTm17,RVn17 - R66M trimer)

value: mRNA


title: GEX_p22066-s001_RPh17-RVe17-RVn17-RVh17-necropsy_RPh17-15C172-wk63

value: mixed sample(Week 90 for RPh17,RVe17,RVn17,RVh17 ; Week63 Lymph node for RPh17,15C172)

tag: library type


title: Rosa26-WT (Control)

city: San Diego

first: Dong-Er

last: Zhang

state: California

address: 3855 Health Sciences Dr

department: Pathology

institute: UCSD

data_processing:
Sequencing was performed on an Illumina HiSeq4000.
10X Genomics Cell Ranger software package was used for data processing. The mkfastq command was used for demultiplexing from Illumina bcl files. The count command was used for alignment, filtering, and barcode and UMI counting in both sample sets. Read 1 is cell barcode and UMI. Read 2 is biological information.
Feature, barcode, and matrix files were generated as processed output from Cell Ranger pipeline.
Downstream data processing was performed in Seurat V3
Genome_build: mm10
Supplementary_files_format_and_content: Feature (.tsv), barcode (.tsv), and matrix files (.mtx) for Rosa26-AE9a and Rosa26-WT samples. Processed Cell Ranger outputs for downstream analysis in secondary single-cell analysis suite such as Seurat or Scanpy

source_name: bone marrow

growth_protocol:
In this study, we generated a germline transmitted Rosa26 AML11-ETO 9a knock-in mouse model by introducing a construct in between exons 1 and 2 of the Rosa26 locus. HA-tagged AE9a-GFP is preceded by a  floxed Neo resistance and stop codon cassette.
Mice were crossed with Vav-iCre expressing mice for hematopoietic specific recombination (R26-AE9a). Vav-iCre expressing mice were used as a control (R26-WT).

extract_protocol:
Bone marrow was isolated from 12-week-old R26-AE9a and R26-WT mice. LK cells were enriched using a lineage-depletion kit (MACS #130-090-858) and cKit enrichment kit (MACS #130-091-224).
Single-cell suspensions were converted to barcoded libraries using the 10X Genomics Chromium Single Cell 3’ GEM, Library & Gel bead Kit V3 and tagged using the Chromium i7 Multiplex Kit. Libraries were sequenced using Illumina Next Generation Sequencing systems (HiSeq4000).
10X Genomics single-cell RNA sequencing

tag: cell surface markers

value: Lin-cKit+

value: 12 weeks

value: bone marrow

value: control


title: SERCA2 Knock out [KO3_S59]

value: Mouse pancreatic islet

value: SERCA2 Knock out

value: Male

value: 24 weeks


title: GEX_p21165-s020_RTe17-RLf17-RLl17-RWb17-necropsy

value: mixed sample(Week90 for RTe17,RLf17,RLl17,RWb17 - R66M gp120 , R66M trimer)


title: Striatum, CWG-cPIP, rep1

value: wild type


title: Tcam-2 with activated ESX1 gene by CRISPRa system using specific sgRNAs for ESX1 sequence_3

value: testis

value: testicular seminoma cell line

value: ESX1 gene activation

value: sgRNAs specific for ESX1 gene


title: sample20

city: Changsha

first: Sha

last: Wang

institute: Xiangya Hospital

data_processing: Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: HGU133Plus2_Hs_ENTREZG

source_name: retinoblastoma

extract_protocol: Tumor RNA was extracted using Qiazol (Qiagen, Shanghai, China) according to the manufacturer instructions and purified using miRNeasy Mini kit (Qiagen).

value: retinoblastoma

tag: rb1 mutation

tag: growth

value: endophytic

tag: chroid


title: Fibroblast, vehicle, rep2

value: fibroblast

value: vehicle


title: GEX_p21165-s019_RYf17-MA277-RVh17-RGi17-necropsy

value: Blood

value: Antigen Specific B lymphocytes

value: mixed sample(Week90 for RYf17,MA277,RVh17,RGi17 - Z1800M trimer , R66M gp120)

value: mRNA


title: Rosa26-AE9a

value: Lin-cKit+

value: 12 weeks

value: bone marrow


title: Striatum, vehicle, rep3

value: Brain striatum


title: Tcam-2 wild type_1

value: WT

value: no modification


title: Tcam-2 with activated ESX1 gene by CRISPRa system using specific sgRNAs for ESX1 sequence_1

value: testis

value: testicular seminoma cell line


title: Striatum, vehicle, rep1

value: wild type


title: Striatum, vehicle, rep2


title: Tcam-2 with activated ESX1 gene by CRISPRa system using specific sgRNAs for ESX1 sequence_2

value: ESX1 gene activation

value: sgRNAs specific for ESX1 gene


title: mTOR_shFoxA1_R1881

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

data_processing:
ChIP-seq reads were first trimmed for adapter sequences and low-quality score bases using Trimmomatic v0.36. The resulting reads were mapped to the human reference genome (hg38) using BWA-MEM v0.7.12 in paired-end mode at default parameters. Only reads that had a unique alignment (mapping quality > 20) were retained and PCR duplicates were removed using Picard tools v2.0.1.
Peaks (summit +/- 150 bp) were called using MACS2 software suite v2.1.1.20160309at an FDR < 0.05 using sequenced libraries of respective input DNA as control. Peaks in mitochondrial chromosome and scaffold regions were removed.
Peak annotations, intersections, and bed files were performed using HOMER v4.11.1 and binding intensity heatmaps were generated using deepTools v3.5.0.
Assembly: hg38
Supplementary files format and content: Bedgraph and bigwig for ChIP samples and input as well as ChIP peak text files corrected using respective input controls

source_name: LNCaP

growth_protocol: LNCaP cells with either shFoxA1-mediated knockdown or shEV (empty vector) control were first androgen deprived by culturing them in RPMI medium containing 2% charcoal-stripped serum (CSS) for 48h. Then, cells were treated with vehicle (EtOH, 0.1% final) or 10nM R1881 (Steraloids, Cat#E3164-000) in freshly added CSS medium for another 24h.

extract_protocol:
Lysates were clarified from sonicated nuclei and cross-linked protein-DNA complexes were isolated with an mTOR-specific antibody, de-crosslinked and purified using a QIAquick PCR purification kit (Qiagen, Cat#28106).
Libraries were prepared at Novogene Bioinformatics Technology Co., Ltd using the NEBNext Ultra II DNA Library Prep kit according to manufacturer's recommendations and sequenced as paired-end 150bp reads on an Illumina NovaSeq 6000 sequencer.

value: LNCaP

value: Human prostate cancer

tag: chip antibody

value: mTOR (Abcam, ab32028)

value: shFoxA1 + 24h 10nM R1881 treatment


title: GEX_p21165-s018_650-15C172-RFj17-RSb17-necropsy

source_name: Blood

value: Blood

value: Antigen Specific B lymphocytes

value: mixed sample(Week90 for 6SO,15C172,RFj17,RSb17- Z1800M gp120,Z1800M trimer)


title: Hippocampus, CWG-cPIP, rep3

source_name: Brain hippocampus

value: Brain hippocampus

value: CWG-cPIP


title: GEX_p21165-s015_RTm17-RVn17-wk55-wk63

value: mixed sample(Week55 and Week63 for RTm17,RVn17 -R66M trimer)

value: mRNA


title: GEX_p21165-s017_RRb17-RPz16-RLk17-ROa17-necropsy

value: mixed sample(Week90 for RRb17,RPz16,RLk17,ROa17 - Z1800M gp120)


title: 52 V A  [JR12]

city: East Lansing

first: G. Andres

last: Contreras

address: 736 Wilson Road Room D202, Michigan State University

department: Large Animal Clinical Sciences

institute: Michigan State University

data_processing:
Data quality control was performed with FastQC v.0.11
After data filtering, clean reads were mapped to the rattus_norvegicus_rnor_6_0_gca_000001895_4 reference genome using HISAT 2.1.0
The mapped reads of each sample were assembled by StringTie (v1.3.3b)
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: ensembl_rattus_norvegicus_rnor_6_0_gca_000001895_4
Supplementary files format and content: tab delimited .txt file

source_name: Thoracic Aorta Perivascular Fat

growth_protocol: APVAT was separated from the aorta then minced and digested (using Liberase TL). Cells were expanded and used for adipogenesis experiments

extract_protocol:
RNA was extracted using the Maxwell®RSC simplyRNA cells kit (AS1390, Promega, Madison, WI)
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or 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. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification

treatment_protocol: Cells were induced with a standard adipogenic cocktail (insulin, IBMX, PPARg agonist, corticoid)

value: Thoracic Aorta Perivascular Fat

value: Stromal Vascular Fraction Derived Preadipocytes

value: Ventral Adipocyte


title: GEX_p21165-s014_RPh17-RVe17-wk10-wk26

value: mixed sample(Week10 and Week26 for  RPh17,RVe17 -R66M trimer)


title: GEX_p21165-s013_RPh17-RVe17-wk55-wk63

value: mixed sample(Week55 and Week63 for RPh17,RVe17 -R66M trimer)


title: Hippocampus, CWG-cPIP, rep2

value: wild type


title: Hippocampus, CWG-cPIP, rep1


title: mTOR_shEV_R1881

value: LNCaP

value: Human prostate cancer

value: shEV (empty vector) control + 24h 10nM R1881 treatment


title: 52 V P  [JR10]

value: Ventral Preadipocyte


title: mTOR_shFoxA1_EtOH

value: mTOR (Abcam, ab32028)

value: shFoxA1 + 24h EtOH (0.1% final) treatment


title: 52 D A  [JR11]

value: Lateral Adipocyte


title: miR-139-5p transfected cell

city: Kagoshima

first: Yuya

last: Tomioka

institute: Kagoshima University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded

source_name: miR-139-5p transfected cell

label_protocol: For cRNA amplification and labeling, Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) were used following the manufacter’s instructions.

growth_protocol: Normal cell culture medium RPMI 1640

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA transfection using Lipofectamin RNAiMAX

value: lung adenocarcinoma


title: mTOR_shEV_EtOH

value: shEV (empty vector) control + 24h EtOH (0.1% final) treatment


title: 52D P  [JR9]

value: Lateral Preadipocyte


title: GEX_p21165-s012_RLl17-RWb17-wk10-wk26

extract_protocol:
CD14-, CD3-, CD20+, IgG+, and gp120-His double positive antigen specific, IgG+ circulating B cells from PBMC cryopreserved at weeks 10, 26, 55, 63, and 90 (necropsy). A cell hashing antibody that was unique for each animal was included in the phenotyping panel, so that sorted cells could be pooled for 10X Genomics sequencing and later deconvoluted by hashtag barcode. The following hashtags were used at : TotalSeq-C anti-human Hashtag 1, TotalSeq-C anti-human Hashtag 2 , TotalSeq-C anti-human Hashtag 3, TotalSeq-C anti-human Hashtag 4 , TotalSeq-C anti-human Hashtag 5 , TotalSeq-C anti-human HLA-DR , TotalSeq-C anti-human CD20, TotalSeq-C anti-human CD22 , TotalSeq-C anti-human HLA A/B/C , TotalSeq-C anti-human CD40.
Following reverse transcription, the cDNA was prepared to create gene expression libraries, BCR VDJ libraries and feature barcode libraries.

value: Blood

value: Antigen Specific B lymphocytes

value: mixed sample(Week10 and Week26 for  RWb17, RLl17 -R66M trimer, R66M gp120)

value: mRNA


title: miR-139-3p transfected cell

source_name: miR-139-3p transfected cell


title: 62V A   [JR8]

value: Thoracic Aorta Perivascular Fat

value: Stromal Vascular Fraction Derived Preadipocytes

value: Ventral Adipocyte


title: Hippocampus, vehicle, rep3

value: Brain hippocampus

value: wild type

value: vehicle


title: input_shFoxA1_R1881

value: LNCaP

value: Human prostate cancer

value: shFoxA1 + 24h 10nM R1881 treatment


title: GEX_p21165-s011_RLl17-RWb17-wk55-wk63

value: mixed sample(Week55 and Week63 for RWb17, RLl17 -R66M trimer, R66M gp120)


title: Hippocampus, vehicle, rep2


title: 62D A  [JR7]

value: Lateral Adipocyte


title: Hippocampus, vehicle, rep1


title: input_shEV_R1881

value: shEV (empty vector) control + 24h 10nM R1881 treatment