title: Mouse ovary, PBS injected, 65 wks old 2

city: Seoul

first: Min-Hee

last: Kang

state: Seoul

address: 120 Neungdong-ro

department: Stem Cell and Regenerative Biotechnology

country: South Korea

institute: Konkuk University

data_processing:
Sequence reads were trimmed using Trimmomatic (Bolger et al., 2014) and the following criteria: first trimming: base quality < 3, window size = 4, and mean quality = 15; second trimming: min length = 36 bp
Trimmed reads were aligned to the UCSC mm10 database using HISAT2 (Kim et al., 2019) and quantified with StringTie (Pertea et al., 2015) using gene/transcript-based annotations from NCBI Annotation Release 108.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM and TPM values of each gene for each Sample

source_name: Ovary

extract_protocol:
Total RNA was extracted from ovarian tissue using TRIzol® Reagent (15596026, Thermo Fisher) and sequencing libraries were prepared according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Young (n=20, 8 weeks old) and old (n=40, 65 weeks old) BDF1 mice were utilized in this study. MIT-001 or PBS was intraperitoneally administered at a dose of 0.5 mg/kg for 7 days

value: Ovary

value: Wild type

value: PBS injected


title: BY4741_A

status: Public on Oct 12 2023

type: SRA

city: Illkirch-Graffenstaden

first: David

last: Moreno Fortuno

state: Bas Rhin

address: 1 Rue Laurent Fries

country: France

institute: INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE

description: BY4741 yeast cells

library_source: transcriptomic

data_processing:
adaptor sequences were trimmed from reads with Cutadapt (Version 3.7), setting a minimum read length of 20nt, as well as a quality cutoff of 20
reads were mapped to reference genome with RNA STAR (Version 2.7.8a)
read counts per gene were summarized with featureCounts (Version 2.0.1), indicating that the RNAseq library was stranded (reverse)
differential gene expression was calculated using limma (Version 3.48.0), using the limma-voom method, filtering lowly expressed genes (less than 0.5 CPM), contrasting sis2_Delta libraries vs BY4741 libraries
Assembly: Saccharomyces cerevisiae genome assembly R64 (sacCer3)
Supplementary files format and content: raw_counts_sis2_rnaseq.tabular: tabular file containing the raw counts corresponding to each gene in each of the libraries
Supplementary files format and content: limma-voom_sis2d-wt.tabular: tabular file containing the limma-voom output of the sis2-wt comparison, including logFC and adjusted pvalue for each gene

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast cells were grown in 15ml of Synthetic complete media with 2% glucose until mid-log phase

extract_protocol:
80 million cells were pelleted and total RNA was extracted with the rYeast total RNA kit (IBI), following the manufacturer instructions
stranded RNA-seq libraries were prepared with the KAPA mRNA HyperPrep Kit, following the manufacturer instructions

tag: cell type

value: yeast cells

tag: genotype

value: BY4741 wt

tag: treatment

value: Synthetic complete media 2% glucose


title: ATAC-Seq_Ebf1_E13-5_WT_12

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

country: USA

institute: New York University, NYU Langone Medical Center

library_source: genomic

data_processing:
Basecalls performed using CASAVA
RNA-Seq reads were mapped to mm10 using STAR guided by GTF and ChIP-Seq reads were mapped using bowtie2
Calculating insert size and standard deviation performed using Picard tools
RNA-Seq read counting performed using HT-seq
ATAC-Seq peak calling was performed using MACS2
Normalization and Deferential expression analyses performed using DEseq2
BAM to bedgraph performed using bedtools
bedgraph to bigwig performed using bedGraphToBigWig v4
Statistics and plotting performed in R v3.3.0
Assembly: mm10
Supplementary files format and content: BigWig (coverage for mapped reads)

molecule: genomic DNA

organism: Mus musculus

source_name: heart

extract_protocol:
RNAs were extracted from isolated cells using the RNeasy Mini kit (Qiagen).
Sequencing libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina).
Samples were sequenced 50 bp paired-ended at 10 million to 20 million reads per replicate on an Illumina HiSeq. 2500 instrument. Library preparation and sequencing were performed at New York University School of Medicine Genome Technology Center. All the reads were mapped to the mouse reference genome (mm10) using the STAR aligner (v2.5.0c)69. Alignments were guided by a Gene Transfer File (GTF, version GRCm38.74) and the mean read insert sizes and their standard deviations were calculated using Picard tools (v.1.126) (http://broadinstitute.github.io/picard/). The read count tables were generated using HTSeq (v0.6.0)70and normalized based on their library size factors using DESeq. 2 (v3.0)71 and differential expression analysis was performed. The Read Per Million (RPM) normalized BigWig files were generated using BEDTools (v2.17.0)72 and bedGraphToBigWig tool (v4), and downstream statistical analyses and generating plots were performed in R environment (v3.1.1) (http://www.r-project.org/).

tag: tissue

value: heart

value: cardiac

value: WT


title: 3_153965, PDAC xenografts, AsPC-1_SB3

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

institute: NCI

data_processing:
12 mRNA-Seq samples were pooled and sequenced on NovaSeq 6000 SP using Illumina Stranded mRNAseq ligation and paired-end sequencing. The samples have 133 to 164 million pass filter reads with more than 88% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

organism: Homo sapiens

source_name: PDAC cell line xenograft

extract_protocol:
RNA isolation was done using the RNeasy Plus Mini Kit (QIAGEN). Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NovaSeq 6000 SP machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: condition

value: SERPINB3-overexpressing transgene

tag: cell line


title: 2_153964, PDAC xenografts, AsPC-1_SB3


title: Mouse ovary, MIT-001 injected, 65 wks old 2

value: MIT-001 injected


title: AXGX4days

city: London

first: Probir

last: Chakravarty

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Library generation for 10x Genomics analysis were performed following the Chromium Single Cell 3′ Reagents Kits (10x Genomics) and sequenced on an Hiseq4000 or Novaseq (Illumina)
Raw reads were initially processed by the Cell Ranger v.3.0.2 pipeline, aligning to the mm10 transcriptome + eGFP sequence using STAR (v.2.5.1b)
All subsequent analyses were performed in R v.3.6.1  using the Seurat (v3) package
Assembly: mm10
Supplementary files format and content: Tab-separated barcodes ID's, features files and count files

source_name: Pituitary

extract_protocol:
The anterior lobe of freshly dissected pituitaries was minced and incubated for 15mn at 37ºC in 1mg/ml Papain (Sigma 10108014001), 10mg/ml DNAse I (Sigma 10104159001) and 10mg/ml Rock inhibitor (Abmole Bioscience M1817) in HBSS (Sigma H9394). pH was adjusted by addition of NaOH. The enzymatic solution was removed, and the cells were mechanically resuspended in HBSS supplemented with DNAse I and Rock inhibitor, as above. Cells were FACsorted for GFP using a large nozzle (100mm) and low pressure (20psi) for optimal cell survival.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Sox9iresGFP positive

value: Pituitary

tag: strain

tag: age

value: 7 to 10 w-old


title: Mouse ovary, PBS injected, 65 wks old 1


title: Mouse ovary, MIT-001 injected, 65 wks old 1


title: HLOs, Healthy iPSC 3, Control, day 32 [HAR96]

city: Cincinnati

first: Hasan Al

last: Reza

state: OH

address: 3333 Burnet Ave

department: Developmental Biology

institute: CCHMC

data_processing:
Samples were sequenced with 150bp pair-end sequencing at a depth of 20M reads per sample by Novogene. Inc.
Clean data were generated from the raw data that was filtered by data-processing steps, including removal of adapter sequences, reads with more than 10% N, and low-quality sequences (the percentage of low-quality bases of quality value ≤ 5 is greater than 50% in a read).
Trimmed sequence reads were mapped to Gencode Release 39 (GRCh38.p13) using Salmon 1.8.0 pipeline to obtain raw transcript counts.
Raw counts data was imported with Tximport and was converted to a DESeq2 dataset and normalized using DESeq2's variance stabilizing transformation to obtain normalized Log2 Counts-per-Million (CPM) values.
Assembly: GRCh38.p13/hg38
Supplementary files format and content: comma-separated values files include log2 vst normalized CPM values for each Sample.

source_name: Human Liver Organoids

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Over 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Inc.

value: Human Liver Organoids

value: Hepatocytes

value: wild type

tag: time

value: Day 32

value: Bilirubin 10 mg/L


title: AX4days

description: 10x Genomics


title: GX4days

description: 10x Genomics


title: ATAC-Seq_Ebf1_E13-5_KO_7


title: sis2_Delta_Β

description: sis2Δ yeast cells

value: BY4741 sis2_delta::kanMX


title: 1_153963, PDAC xenografts, AsPC-1_SB3


title: Mouse ovary, PBS injected, 8wks old 2

value: Ovary

value: Wild type

value: PBS injected


title: 5_153973, PDAC xenografts, AsPC-1_SB3


title: Unchallenged

description: 10x Genomics


title: Mouse ovary, PBS injected, 8wks old 1


title: ATAC-Seq_Ebf1_E13-5_KO_11

value: heart


title: HLOs, Healthy iPSC 2, Control, day 32 [HAR95]


title: HLOs, Healthy iPSC 1, Control, day 32 [HAR94]

data_processing:
Samples were sequenced with 150bp pair-end sequencing at a depth of 20M reads per sample by Novogene. Inc.
Clean data were generated from the raw data that was filtered by data-processing steps, including removal of adapter sequences, reads with more than 10% N, and low-quality sequences (the percentage of low-quality bases of quality value ≤ 5 is greater than 50% in a read).
Trimmed sequence reads were mapped to Gencode Release 39 (GRCh38.p13) using Salmon 1.8.0 pipeline to obtain raw transcript counts.
Raw counts data was imported with Tximport and was converted to a DESeq2 dataset and normalized using DESeq2's variance stabilizing transformation to obtain normalized Log2 Counts-per-Million (CPM) values.
Assembly: GRCh38.p13/hg38
Supplementary files format and content: comma-separated values files include log2 vst normalized CPM values for each Sample


title: HASMC,TGF-β,illumina, sample 4

city: shanghai

first: wu

last: hao

state: shanghai

address: No. 650 Xin Songjiang Road

department: Precision Research Center for Refractory Diseases, Institute for Clinical Research

country: China

institute: Shanghai General Hospital

data_processing:
Sequence reads were trimmed using trimmomatic
Trimmed sequence reads were mapped to GRCh38 using Hisat2
Transcript extraction and normalization were performed using SringTie
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: HASMC

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

extract_protocol:
miR-221 was transfected 24h after HASMC adherence and incubated for 48h
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Differentiation was induced by treatment of 2-day post HASMC cells with 10ug/ml TGF-β or 10ug/ml PDGF (Sigma),

value: HASMC

value: Human Aortic Smooth Muscle Cells


title: HASMC,TGF-β,illumina, sample 3

value: WT


title: HLOs, Healthy iPSC 3, Mife 1 uM, day 32 [HAR54]

value: Mifepristone 1 uM + Bilirubin 10 mg/L


title: HLOs, Healthy iPSC 3, Mife 1 uM, day 32 [HAR53]


title: HLOs, Healthy iPSC 1, Mife 1 uM, day 32 [HAR52]


title: RA, Volume overload, P21, RNA-seq, rep1

city: Shanghai

first: Yuqing

last: Hu

address: 1678 Dongfang Road, Pudong New District, Shanghai

institute: Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
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.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
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.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.We used clusterProfiler R package to test the
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to annotation for the Variablesite.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(3.2.5) software was used to analysis the AS event.
PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions.
WGCNA (Weighted correlation network analysis) was used to describe the gene association modes among different samples.
Assembly: GRCm38(mm10)
Supplementary files format and content: FPKM

source_name: Right atrium

extract_protocol:
Myocardium of RA was rapidly removed from executed rat and flash frozen in liquid nitrogen, RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Right atrium

value: volume overload


title: RA, sham-operated, P21, RNA-seq,  rep3

value: sham-operated


title: RA, Volume overload, P21, RNA-seq, rep2


title: ATAC-Seq_Ebf1_E13-5_KO_8

value: cardiac


title: Control THP-1 cells, LPS and ATP treated, biol rep 3

city: Maywood

first: Edward

middle: M

last: Campbell

state: IL

address: 2160 S 1st Ave

institute: Loyola University Chicago

data_processing:
Analysis was performed using R on the server and RStudio on the local computer. The genome (GRCh38.p12) was indexed using STAR. The quality of the files was checked using FastQC. The reads were aligned to the genome using STAR. The gene counts were determined using featureCounts. DESeq2 was used for the differential gene expression analysis.
Assembly: GRCh38.p12
Supplementary files format and content: .xlxs file with the counts for each sample (output of featureCounts)

growth_protocol: THP-1 cells were maintained in RPMI supplemented with 10% characterized fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using the Macherey-Nagel NucleoSpin RNA Plus kit. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for RNA-Seq using the NovaSeq special Oligo-dT mRNA directional PE100-S1 flowcell ~30M clusters/sample ~60M PE reads/sample.

treatment_protocol: THP-1 cells were differentiated with PMA (Sigma) for 48 hrs. The media was changed, and the cells rested for 72 hrs prior to treatment. Cells were treated with 100 ng/mL LPS (Sigma) for 4 hrs then 5 mM ATP (Sigma) for 30 min.

value: macrophage

value: CRISPR control

value: differentiated with PMA, 100 ng/mL LPS (4 hrs), 5 mM ATP (30 min)


title: RA, sham-operated, P21, RNA-seq, rep2


title: HASMC,PDGF,illumina, sample 4


title: HASMC,TGF-β,illumina, sample 2


title: HASMC,TGF-β,illumina, sample 1


title: HASMC,PDGF,illumina, sample 3


title: RA, sham-operated, P21, RNA-seq, rep1


title: VMP1 KO THP-1 cells, untreated, biol rep 3

value: VMP1 KO

value: differentiated with PMA


title: HASMC,PDGF,illumina, sample 2


title: VMP1 KO THP-1 cells, LPS and ATP treated, biol rep 3


title: ATAC-Seq_Ebf1_E13-5_KO_10


title: Control THP-1 cells, untreated, biol rep 3


title: HASMC,PDGF,illumina, sample 1


title: LEAP_TS-Blood_Pool8

city: Boston

first: Patrick

middle: T

last: Griffin

state: MA

address: 77 Avenue Louis Pasteur

department: Harvard Medical School, Dept. of Genetics

institute: Patrick Griffin

description:
bisulfite converted DNA
LEAP_TS-Blood_AllPools.tar.gz

data_processing:
https://github.com/patricktgriffin/TIME-Seq
Assembly: mm10,hg19
Supplementary files format and content: bismark.cov
Library strategy: TIME-Seq

source_name: Whole blood

value: Whole blood

value: various

tag: Sex

value: mixed


title: HASMC,NC mimic,illumina, sample 4

value: NC mimic,48h


title: VMP1 KO THP-1 cells, LPS and ATP treated, biol rep 2


title: RA, Volume overload, P21, RNA-seq, rep3


title: HASMC,NC mimic,illumina,sample 3

value: HASMC


title: HASMC,NC mimic,illumina, sample 2

value: Human Aortic Smooth Muscle Cells


title: Control THP-1 cells, untreated, biol rep 2


title: LEAP_TS-Blood_Pool3


title: LEAP_TS-Blood_Pool6


title: HASMC,miR-221 mimic,illumina, sample 4

value: WT

value: miR-221 mimic,48h


title: LEAP_TS-Blood_Pool2


title: HASMC,NC mimic,illumina, sample 1


title: VMP1 KO THP-1 cells, untreated, biol rep 1


title: HASMC,miR-221 mimic,illumina, sample 3


title: LEAP_TS-Blood_Pool18


title: VMP1 KO THP-1 cells, LPS and ATP treated, biol rep 1


title: LEAP_TS-Blood_Pool17


title: HASMC,miR-221 mimic,illumina, sample 2


title: HASMC,miR-221 mimic,illumina, sample 1


title: LEAP_TS-Blood_Pool7


title: LEAP_TS-Blood_Pool15


title: LEAP_TS-Blood_Pool9


title: AMnp_day14_rep2

city: Buffalo

first: Jian

last: Feng

state: NEW YORK

address: 955 Main St, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

data_processing:
Base calling was performed by bcl2fastq2 (v2.20.0).
Raw reads were trimmed by Cutadapt (v1.16) with command “-j 6 -u 3 -U 3 --output=out1.fq.gz --paired-output=out2.fq.gz --error-rate=0.1 --times=1 --overlap=3 --pair-filter=any --quality-cutoff=20”.
Trimmed reads were aligned to hg38 reference genome by HISAT2 (galaxy version 2.1.0) with default parameters.
Read counts were generated by featureCounts (subreads version 2.0.1) with annotated transcripts (RefSeq Release 109.20201120).
Assembly: hg38
Supplementary files format and content: count_matrix.tsv: Tab-delimited table with read counts for each gene and each sample.

source_name: Human foreskin fibroblasts

growth_protocol: Primary human fibroblasts (AG22056, Coriell Institute) were maintained in fibroblast medium consisting of high glucose Dulbecco’s Modified Eagle Medium (DMEM) (Gibco) supplemented with 10% heat inactivated fetal bovine serum (Gibco), 100 U/ml penicillin, 100 ug/ml streptomycin (Gibco), 0.1 mM non-essential amino acids (Gibco) and 2 mM L-Glutamine at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and purified by RNase-Free DNase Set (Qiagen).
RNA libraries were prepared using the TruSeq Stranded RNA Library Preparation Kit (Illumina) with ribosomal RNA removal beads.

treatment_protocol: The fibroblasts were seeded on a Matrigel (Corning)-coated 12-well plate (5×10^4 cells per well) and incubated at 37°C in 5% CO2 for 16 h. Next day, fibroblasts were infected with the indicated combinations of lentiviruses (MOI=10 for all viruses) with the presence of 8 µg/ml polybrene (Sigma). After 16 h, virus-containing medium was removed and cells were washed 3 times with DMEM/F12 medium (Gibco) to remove remaining serum, and cultured in DMEM/F12 for 24 h. The following day (induction day 0), the medium was replaced by neural induction medium (DMEM/F12, 1×N2 (Gibco), 1×B27 (Gibco), 0.1 mM NEAA, 0.5 uM dorsomorphin (Tocris), 2.5 µM SB431542 (Tocris), 1 µM PD0332991 (Tocris), 3 µM CHIR99021 (Tocris), 0.2 mM vitamin C (Sigma), 10 µM Y27632 (Tocris), 0.5 mM db-cAMP (ApexBio), 20 ng/ml NGF (PeproTech), 20 ng/ml GDNF (PeproTech), 20 ng/ml BDNF (PeproTech), 1 µg/ml doxycycline (Tocris)) and cells were maintained at 37°C in 5% CO2. The medium was changed every other day for the duration of the culture period.

value: Foreskin fibroblasts

value: transduced with ASCL1, miR124-9/9*, PTBP2 shRNA, p53 shRNA, rtTA through lentiviruses

value: induction day 14


title: AMnp_day14_rep3


title: root, WT_20

city: Xuzhou

first: Jiahao

last: Zhu

address: Shanghai Road 101

institute: Jiangsu Normal University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GT4SP_v3
Supplementary files format and content: tab-delimited text file includes FPKM and count values for each Sample

organism: Ipomoea batatas

source_name: root

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

value: root

value: 20 days


title: LEAP_TS-Blood_Pool14


title: Control THP-1 cells, LPS and ATP treated, biol rep 2

value: macrophage

value: CRISPR control


title: root, WT_4M

value: 4 months


title: root, WT_1M

value: 1 month


title: AMnp_day14_rep1


title: LEAP_TS-Blood_Pool4

value: Whole blood


title: LEAP_TS-Blood_Pool13

value: various


title: VMP1 KO THP-1 cells, untreated, biol rep 2

value: VMP1 KO

value: differentiated with PMA


title: AMnp_day7_rep3

value: induction day 7


title: Control THP-1 cells, LPS and ATP treated, biol rep 1

value: differentiated with PMA, 100 ng/mL LPS (4 hrs), 5 mM ATP (30 min)


title: LEAP_TS-Blood_Pool12

value: mixed


title: AMnp_day7_rep2


title: root, ov8_4M

value: MBP3 overexpression


title: root, ov8_1M


title: LEAP_TS-Blood_Pool16


title: Control THP-1 cells, untreated, biol rep 1


title: LEAP_TS-Blood_Pool10


title: AMnp_day3_rep3

value: Foreskin fibroblasts

value: induction day 3


title: root, ov3_20


title: LEAP_TS-Blood_Pool1


title: root, ov3_4M


title: TS-Clocks_CellCulture_Pool2

description:
bisulfite converted DNA
TS-Clocks_CellCulture.tar.gz

source_name: Cultured primary embryonic fibroblasts, primary adult ear firboblasts


title: root, ov3_1M


title: TS-Clocks_CellCulture_Pool1

value: Cultured primary embryonic fibroblasts, primary adult ear firboblasts


title: AMp_day14_rep3

value: transduced with ASCL1, miR124-9/9*, p53 shRNA, rtTA through lentiviruses

value: induction day 14


title: AMnp_day3_rep1

value: transduced with ASCL1, miR124-9/9*, PTBP2 shRNA, p53 shRNA, rtTA through lentiviruses


title: root, ov2_20

value: root

value: 20 days


title: AMnp_day3_rep2


title: root, ov2_4M

value: 4 months


title: 21-19-Liver-3

description:
bisulfite converted DNA
TS-LiverOnly_AllPools.tar.gz

source_name: Liver

value: Liver


title: 21-19-Liver-2

value: various


title: root, ov8_20


title: 21-19-Liver-1


title: LEAP_TS-Blood_Pool11

value: Whole blood


title: AMnp_day7_rep1


title: DHX9 knockdown, POLR2A-ChIP, rep2

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

institute: UC-Riverside

data_processing:
Raw reads were aligned to human hg38 reference genome using Bowtie2 (v2.4.5)
Genome coverage bigwig files for Integrative Genomics Viewer visualization were generated by deeptools (v3.5.1)48 bamCoverage using RPKM for the normalization
Peaks were generated by macs2 (v2.2.7.1) callpeak
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

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

extract_protocol:
the cells were crosslinked with 1% formaldehyde at room temperature for 10 min with gentle shaking, and quenched with 125 mM glycine for 10 min. After washing with ice-cold PBS buffer for three times, the cells were resuspended in cell lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.5% NP-40, protease inhibitors) at 4°C on a rotator for 20 min. After centrifugation at 3000 g for 3 min, the pellets were resuspended in RIPA buffer (50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, protease inhibitors) and rotated at 4°C for 20 min, followed by a brief sonication on a Qsonica Sonicator q125 (42% amplitude, 10s on/10s off, 80 s). After incubation for another 20 min, cell lysate was sonicated on a Covaris S220 Sonicator for 6 min with a peak incident power of 140 W, a duty cycle of 10.1% and 200 cycles per burst at 4°C. After centrifugation at 4°C for 10 min, 50 µL of supernatant was saved as “Input” sample, and the rest of supernatant was subjected to IP experiment.
The DNA-sequencing library was prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s instructions.

value: Human embryonic kidney

value: DHX9 knockdown

tag: chip antibody

value: POLR2A (Thermo, #MA1-26249)


title: AMp_day14_rep2


title: AMp_day7_rep2

value: induction day 7


title: AMp_day14_rep1


title: DHX9 knockdown, POLR2A-ChIP, rep1


title: TS-TissueClocks_Pool9

description:
bisulfite converted DNA
TS-TissueClocks.tar.gz

source_name: Ear Skin, Liver, Kidney, White fat

value: Ear Skin, Liver, Kidney, White fat

value: mixed


title: AMp_day7_rep1

value: Foreskin fibroblasts


title: TS-TissueClocks_Pool8


title: U2AF1 knockdown, POLR2A-ChIP, rep2

value: U2AF1 knockdown


title: U2AF1 knockdown, POLR2A-ChIP, rep1


title: TS-TissueClocks_Pool7


title: shCtrl, POLR2A-ChIP, rep2

value: wildtype


title: AMp_day3_rep2

value: transduced with ASCL1, miR124-9/9*, p53 shRNA, rtTA through lentiviruses

value: induction day 3


title: TS-TissueClocks_Pool6


title: AMp_day3_rep1


title: shCtrl, POLR2A-ChIP, rep1


title: DHX9 knockdown, Input


title: AMn_day14_rep3

value: transduced with ASCL1, miR124-9/9*, PTBP2 shRNA, rtTA through lentiviruses

value: induction day 14


title: TS-TissueClocks_Pool4


title: root, ov2_1M

value: root

value: MBP3 overexpression

value: 1 month


title: TS-TissueClocks_Pool5

value: various


title: AMp_day7_rep3


title: AMn_day14_rep2


title: U2AF1 knockdown, Input

value: Human embryonic kidney


title: TS-TissueClocks_Pool2


title: TS-WAT_Pool1

description:
bisulfite converted DNA
TS-Liver_Skin_WAT_AllPools.tar.gz

source_name: White fat

value: White fat


title: AMn_day14_rep1


title: TS-TissueClocks_Pool3


title: shCtrl HEK293T, Input


title: AMn_day7_rep3


title: TS-TissueClocks_Pool10


title: AMp_day3_rep3


title: AMn_day7_rep1


title: TS-TissueClocks_Pool1


title: TS-Skin_Pool2

source_name: Ear skin

value: Ear skin


title: AMn_day7_rep2

value: induction day 7


title: AMn_day3_rep3


title: TS-Skin_Pool1


title: AMn_day3_rep2


title: TS-Muscle-Pool4

description:
bisulfite converted DNA
TS-Muscle_AllPools.tar.gz

source_name: Gastrocnemius Muscle

value: Gastrocnemius Muscle


title: AMn_day3_rep1


title: T-ALL cell_Control_biological rep1 (ORM control)

type: RNA

city: Madrid

first: Javier

last: Redondo-Muñoz

address: C/ Ramiro de Maeztu 9

country: Spain

institute: Centro de Investigaciones Biológicas Margarita Salas - CSIC

description: Gene expression data from T-ALL cells cultured in suspension after 10 days 3D confinement

hyb_protocol: RNA was hybridized to Clariom™ S Human Array following manufacturer’s instructions in a GeneChip Hybridization Oven 645 at 45ºC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: The intensity cell files were then imported, normalized for background correction (used RMA for normalization) with Transcriptome Analysis Console (TAC)

label: Biotin

source_name: Control Jurkat cells

label_protocol: RNA was labeled using the GeneChip WT PLUS Reagent kit

growth_protocol: Jurkat cells were cultured in RPMI (supplemented with 10% FBS) at 37oC  and 5% CO2

extract_protocol: 10x106 cells were lysed using TRI reagent (Sigma) for 30 min. Then, chloroform was added, mixed and incubated for 30 min. After 15 min centrifugation at 13000 rpm, the soluble phase containing the RNA was collected and precipitated with isopropanol for 15 min on ice. The pellet obtained by 15 min 13000 rpm centrifugation at 4ºC, was washed with cold ethanol 80%, centrifugated at 8000 rpm for 5 min and allowed to dry. Total RNA was resuspended in RNAse-free H2O, and purity and concentration were determined by Nanodrop measurement.

treatment_protocol: Control cells are Jurkat cells cultured in normal conditions in suspension in RPMI supplememented with 10% FBS at 37ºC 5% CO2. Jurkat cells were allowed to migrate across 3 μm transwell inserts for 24h. One-round migration (ORM) cells were collected from the bottom chamber of Transwell inserts (Corning Costar, 6.5 mm diameter, 3 μm pore size) after 24h. Cells were lysed and mRNA was isolated and hybridized on Affymetrix microarrays to compare expression profiles. We used 2 replicates of each sample.

value: Jurkat


title: TS-Muscle-Pool3

value: mixed


title: TS-Muscle-Pool2


title: Anp_day14_rep2

value: Foreskin fibroblasts

value: transduced with ASCL1, PTBP2 shRNA, p53 shRNA, rtTA through lentiviruses


title: TS-Muscle-Pool1


title: T-ALL cell_Control_biological rep2 (ORM control)


title: T-ALL cell_MA_biological rep2

middle: Redondo

last: Muñoz

state: Madrid

address: C. Ramiro de Maeztu, 9

department: Molecular Biomedicine

institute: Centro de Investigaciones Biológicas Margarita Salas (CSIC)

description:
MA cells 2
Gene expression data from Migratory-altered cells through persistent confined conditions.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC).

data_processing: The intensity CEL files were then imported, normalized for background correction (used RMA for normalization) with Transcriptome Analysis Console (TAC).

source_name: MA Jurkat cells

label_protocol: RNA was labeled using the GeneChip WT PLUS Reagent kit.

growth_protocol: Jurkat cells were cultured in RPMI (supplemented with 10% FBS) at 37oC and 5% CO2.

extract_protocol: RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel) according to the manufacturer’s instructions.

treatment_protocol: Migratory-altered (MA) cells were generated as follows: 100 µL of medium without serum containing 3x10^5 Jurkat cells was added on the upper chamber of Transwell inserts (3 μm pore size), and 600 μL of medium with serum was added to the bottom chamber. After 24h, migrated cells were collected from the bottom chamber, counted and added again to the upper chamber of new inserts, under the same conditions. The same process was repeated 3 times. Then, migrated cells from the bottom chamber were collected, expanded, and maintained in culture in RPMI (supplemented with 10% FBS) at 37oC and 5% CO2.

value: Migratory-altered


title: Anp_day7_rep3


title: TS-Liver_Pool2

value: Liver


title: CS_RNA_root_rep1

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

data_processing:
For CAGE-seq, only the R1 read were kept to mapping. Cutadaptwas applied to trim 3’ adaptor and 9 bases at the 5’end, used SortMeRNA to remove the reads originating from chloroplast, mitochondria and rRNA. Clean reads were mapped to the IWGSC (version 1.0) with Bowtie2 Only unique mapped reads were used for analysis. The 5′ coordinate of R1 reads was considered the position of the transcription start sites.
For ChIP-seq, Bisulfite-seq and RNA-seq, reads were trimmed with the Trim Galore and cutadapt. For RNA-sequencing, clean reads were aligned with HISAT2. SortMeRNA was used to remove the reads originating from chloroplast, mitochondria and rRNA. The featureCount was used to determine the RNA-seq read density of the high-confidence genes in the IWGSC RefSeq genome assembly (version 1.1). For ChIP-seq data, clean reads were aligned with bwa program. The MACS2 was used to identify the peaks.
For Bisulfite-seq data, the clean reads were then aligned by the Bismark program. The extent of the cytosine methylation was determined with the bismark_methylation_extractor implemented in the Bismark program. Next, the methylation ratio of a cytosine was calculated as the number of mCs divided by the number of reads covering the position. Bases covered by fewer than three reads were considered low confidence positions whose methylation ratios were not recorded.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: CAGE-seq signal in each site were provided in bed file.

organism: Triticum aestivum

source_name: Triticum aestivum 12-days-old seedlings

growth_protocol: Common wheat (Triticum aestivum cultivar ‘Chinese Spring’) seeds were surface-sterilized via a 10-min incubation in 30% H2O2 and then thoroughly washed five times with distilled water. The seeds were germinated in water for 3 days at 22 °C. The germinated seeds with residual endosperm were transferred to soil (1:1:3 mixture of vermiculite: perlite: peat soil) or Hoagland solution and grown under 16 h light/ 8 h dark condition at 22 °C in greenhouse.

extract_protocol:
The seedlings (above-ground parts) in soil were harvested after 9-day growth. The root in Hoagland solution were harvested after 9-day growth. The spikelets at booting stage (Feeke 10) were harvested. The fresh immature embryos (14days post anthesis) were isolated and either frozen in liquid nitrogen
For CAGE-seq，total RNA was treated with RQ1 DNase to remove DNA. The total RNA was treated with T4 polynucleotide kinase subsequently digested with Terminator 5´-Phosphate-Dependent Exonuclease to enrich the capped mRNA. Next, reverse transcription was performed with RT primer harboring a 3'-adaptor sequence and randomized hexamer. Subsequently, the 5’adaptor harboring three additional rG at the 3’terminus was added to the RT reaction to allow template switching and tagging of the 5’ adaptor. The cDNAs were treated with Exonuclease I to digest the primers, purified and amplified with PCR primers. The libraries were applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

treatment_protocol: No treatment applied

value: 12-days-old seedlings

tag: cultivar

value: Chinses Spring

tag: age/tissue

value: 9-days root


title: CS_RNA_embryo_rep1

value: fresh immature embryos (14days post anthesis)


title: Anp_day14_rep1

value: induction day 14


title: Anp_day7_rep2


title: Anp_day7_rep1


title: MertkKO extraction socket biol rep 3

city: Ann Arbor

first: Joseph

last: Decker

state: Michigan

address: 1011 N University Avenue

department: Cariology, Restorative Sciences, and Endodontics

institute: University of Michigan

data_processing:
Reads were trimmed using Cutadapt (version 2.3)
Data quality was ensured using FastQC (version 0.11.8)
Fastq was used to screen for contamination
Reads were mapped using STAR (version 2.8.8a)
Assembly: GRCm39 (MertkKO data), CRCh38 (hMSC data)
Supplementary files format and content: tab-deliminted file including TPM values for each transcript

source_name: Tooth extraction socket

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen)
RNA libraries were generated using the SMART-Seq v4 PLUS kit per manufacturer protocols (Takara)

value: Tooth extraction socket

value: MertkKO (mouse)


title: TS-Liver_Pool1

value: various


title: JW1_spikelet_H3K9ac

data_processing:
The sequencing reads were trimmed with fastp (0.22.0).The clean reads were aligned with bwa program (version 0.7.17-r1188).Peaks were called using MACS v1.4.2 with "--nolambda --nomodel --gsize=1500000000" parameters.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: bed(peak)

source_name: spikelets at booting stage (Feeke 10)

extract_protocol:
Spikelets at booting stage (Feeke 10)were harvested and directly vacuum-infiltrated with a formaldehyde cross-linking solution for ChIP-seq. More than 10 ng of ChIP DNA extracted from each sample was used to prepare the sequencing samples.
Libraries were constructed and sequenced by Genenergy Biotechnology Co. Ltd. (Shanghai, China) and Novogene (Beijing, China). The libraries were sequenced with the HiSeq X Ten system (illumina, San Diego, California, USA) to produce 150-bp paired-end reads.

value: spikelets at booting stage (Feeke 10)

value: WT


title: MertkKO extraction socket biol rep 2


title: Anp_day14_rep3


title: T-ALL cell_control_biological rep1

description:
Control cells 1
Gene expression data from T-ALL cells control.

source_name: Jurkat cells control

value: Control


title: T-ALL cell_MA_biological rep1

description:
MA cells 1
Gene expression data from Migratory-altered cells through persistent confined conditions.

value: Jurkat


title: MertkKO extraction socket biol rep 1


title: Anp_day3_rep3

value: induction day 3


title: CS_root_H3K9ac_rep1

value: Millipore, Upstate, USA

tag: chip antibody manufacturer

value: Upstate

tag: chip antibody catalog #


title: Anp_day3_rep2

value: Foreskin fibroblasts

value: transduced with ASCL1, PTBP2 shRNA, p53 shRNA, rtTA through lentiviruses


title: T-ALL cell_control_biological rep2

description:
Control cells 2
Gene expression data from T-ALL cells control.


title: T-ALL cell_ORM_biological rep1

description: Gene expression data from T-ALL cells control

source_name: Jurkat cells upon one round migration through 3 μm pores


title: JW1_spikelet_H3K4me3


title: WT extraction socket biol rep 3

value: WT (C57BL/6j mouse)


title: CS_root_H3K4me3_rep1

value: 12-days-old seedlings

value: Chinses Spring

value: Abcam, Cambridge, England

value: Abcam


title: WT extraction socket biol rep 2

value: Tooth extraction socket


title: snRNAseq_LaFet2

first: Jaroslav

last: Bendl

state: New York

address: One Gustave L. Levy Place, Department of Genetics and Genomics Sciences, Box 1210

department: Genetics and Genomics Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing data alignment, filtering, barcode counting, peak calling and counting of both ATAC-seq and gene expression molecules were performed with cellranger-arc (v.1.0.0).
We processed the outputs of Cell Ranger ARC using Seurat v4.0 and Signac v1.1.0 to create a multi-omic Seurat object with paired gene expression and DNA accessibility profiles for each sample. We used MACS2 [PMID:24743991] as implemented in the function CallPeaks in Signac [PMID:34997233] to call peaks from the fragment files. We removed any peaks on nonstandard chromosomes overlapping annotated genomic blacklist regions fromor the hg38 genome [PMID:31249361]. We then quantified fragment counts for each peak, per cell, using the FeatureMatrix function in Signac. Per-cell quality control metrics for each modality were computed, including mitochondrial percentage, nucleosome signal and transcriptional start site (TSS) enrichment score. Next, we combined the individual Seurat objects for all the samples into one single object using the merge function in Seurat. We then performed quality control based on metrics for both modalities by retaining cells with total RNA-seq count > 200 and < 50,000, total ATAC-seq count > 200 and < 100,000, mitochondrial percentage < 5%, nucleosome signal < 3 and TSS enrichment score > 1. Genes or peaks which are detected in < 10 cells are removed. As a result, 45,549 out of 53,185 single cells are retained, with 5,887 RNA UMI counts and 18,066 unique ATAC-seq fragments (29.3% fragments overlapping peaks) on average.
Assembly: hg38
Supplementary files format and content: bigwigs_per_cell_type.gz
Supplementary files format and content: count_matrix.RDS.gz

source_name: Cortical plate

extract_protocol:
25mg of frozen postmortem human brain tissue was homogenized in cold lysis buffer (0.32M Sucrose, 5 mM CaCl2, 3 mM Magnesium acetate, 0.1 mM, EDTA, 10mM Tris-HCl, pH8, 1 mM DTT, 0.1% Triton X-100) and filtered through a 40 µm cell strainer. The flow-through was underlaid with sucrose solution (1.8 M Sucrose, 3 mM Magnesium acetate, 1 mM DTT, 10 mM Tris-HCl, pH8) and centrifuged at 107,000 g for 1 hour at 4°C. Pellets were resuspended in PBS supplemented with 0.5% bovine serum albumin (BSA). Prior to FANS, volumes were brought up to 250 µl with PBS and 7AAD (Invitrogen) was added according to manufacturer’s instructions. 7AAD positive nuclei were sorted into tubes pre-coated with 5% BSA using a FACSAria flow cytometer (BD Biosciences).
Nuclei were subjected to 2 washes in 200 µl wash buffer (10x Genomics), after which they were re-suspended in 30 µl nuclei buffer (10x Genomics) and quantified (Countess II, Life Technologies). 8000 nuclei from each sample were subjected to the Chromium Next GEM Single Cell Multiome ATAC-seq and Gene Expression protocol (10x Genomics), according to manufacturer’s instructions. Resulting libraries were quantified using the KAPA library quantification kit (KAPA Biosystems) and fragment sizes determined by Tapestation (Agilent). All libraries were sequenced at New York Genome Center (NYGC) using the Novaseq platform (Illumina).

value: Cortical plate

tag: donor id

value: 24 gestational weeks


title: T-ALL cell_ORM_biological rep2

description: Gene expression data from T-ALL cells cultured in 3D conditions for 1 hour


title: CS_embryo_H3K27me3_rep1

value: fresh immature embryos (14days post anthesis)


title: WT extraction socket biol rep 1


title: snRNAseq_LaFet1

value: 23 gestational weeks


title: snRNAseq_EaFet2

value: 19 gestational weeks


title: CS_embryo_H3K9ac_rep1


title: AXSham48hrs

description: 10x Genomics

source_name: Pituitary

value: Sox9iresGFP positive

value: Pituitary

value: 7 to 10 w-old


title: CS_embryo_H3K4me3_rep1


title: AX48hrs

description: 10x Genomics


title: cs_bisulfite_root

value: 9-days root


title: Ketamine-treated susceptible

city: Nanjing

first: Chaoli

last: Huang

state: Jiangsu

address: 300 Guangzhou Road

institute: he First Affiliated Hospital of Nanjing Medical University

data_processing:
Thirty-one bases from  read 1 were used to determine the spatial barcode and the unique molecular identifier, and 121 bases from read 2 were used to cover the genetic region.
Dimensionality reduction analysis and clustering of the quantitative results of ST were performed using t-distributed Stochastic Neighbor Embedding (t-SNE).
Differential expression analysis was carried out according to the pre-labeled anatomical areas on the brains.
The GO annotation enrichment analyses were performed using the Gene Ontology resource (http://geneontology.org).
Assembly: mm10
Supplementary files format and content: Excel files showing gene expression
Supplementary files format and content: PNG files showing clustering results
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

source_name: Brain

extract_protocol:
Mice were euthanized using CO2. Brain tissues were dissected out and embedded in Tissue-Tek (OCT) and snap-frozen using an isopentane–dry ice slurry. The OCT-embedded brains were cryosectioned sagittally to a thickness of 10 mm and placed onto spatially barcoded arrays on ST glass slides (10x Genomics).
Briefly, glass slides with tissue sections attached to spatially barcoded arrays were permeabilized by collagenase in HBSS-BSA buffer for 20 min and 0.1% pepsin in 0.1M HCl for 5 min at 37℃. Then reverse transcription was performed by adding the cDNA synthesis master mix at 42℃ overnight to get the cDNA attached on the array. Tissue on the array was then degraded by incubation with 2.5 mg/mL proteinase K in PDK buffer at 56℃ for 1 h with intermittent shaking at 300 rpm, which left the cDNA coupled to the arrayed oligonucleotides on the slide. Then the probe was collected by adding 70 μL of release mix to the array chambers. The release mix was composed of 100 U/mL USER enzyme, 1× first strand buffer, 0.5 mM dNTPs, and 0.19 μg/μL BSA. Incubation was performed at 37℃ for 2 h, and 65 μL of the released probe mixture was collected from each array chamber at the end of the incubation. Then the library of the released probes was prepared through second strand cDNA synthesis, in vitro transcription, adaptor ligation, second cDNA synthesis, qPCR quantification, and PCR amplification. Second strand cDNA synthesis was performed by adding 5 mL mixture to each sample. The mixture was composed of 2.7× First Strand Buffer, 3.7 U/μL DNA polymerase I, and 0.18 U/μL RNaseH and the reaction was incubated at 16℃ for 2 h. Then, 5 mL of T4 DNA polymerase were added to each sample and the samples were incubated at 16℃ for 20 min. In vitro transcription was performed by adding 5.6 μL mixture to each sample and incubating the samples at 37℃ for 14 h. The mixture was composed of 1× T7 Reaction Buffer, 7.5 mM of each NTP, 1× T7 Enzyme Mix, and 1 U/mL SUPERaseIN. Adaptor ligation was performed by adding 4.5 μL of the ligation mixture to each sample and incubating the samples at 25℃ for 1 h. The ligation mixture was obtained by incubating 8 μL of amplified RNA and 2.5 μL of ligation adapter. The second cDNA synthesis was set up by first incubating the samples at 65℃ for 5 min with 1.7 μM primer (5′-GTGACTGGAGTTCAGACGTGTGCTCTTCCGA-3′) and 1 μL dNTPs. Then, the samples were placed on ice and 8 μL of RT reaction mixture was added to each sample. The samples were incubated at 50℃ for 1 h. For second strand cDNA synthesis, in vitro transcription, adaptor ligation, and second cDNA synthesis, purification, and elution were performed after each experiment. Purification was performed using the Agencourt RNAClean XP beads following the manufacturer’s instructions, and elution was performed in 10 mL Milli-Q DNase/RNase-free water. qPCR quantification was performed in 10 μL final volume. The qPCR reaction mixture contained 2 μL of purified sample, 1× qPCR Mix, 0.5 μM PCR InPE1.0 primer (5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′), 0.01 μM PCR InPE2.0 primer (5′-GTGACTGGAGTTCA GACGTGTGCTCTTCCGATCT-3′), 0.5 μM PCR Index primer (5′-CAAGCAGA AGACGGCATACGAGATXXXXXXGTGACTGGAGTTC-3′), and 13 EVA green. The conditions were as follows: 98℃ for 3 min and 25 cycles of 98℃ for 20 s, 60℃ for 30 s, and 72℃ for 30 s. qPCR quantification was performed in a final volume of 25 μL with the above conditions plus a final extension at 72℃ for 5 min and the number of cycles identified by qPCR. The final libraries were purified by an automated MBS robot and eluted in 20 mL of Elution Buffer.

treatment_protocol: C02KL was administered with ketamine intraperitoneally (i.p.) at a dosage of 10 mg/kg. Other mice were administered with saline.

value: Brain

value: WT

value: Ketamine


title: snRNAseq_Adult2

source_name: Prefrontal cortex

value: Prefrontal cortex

value: 39 years


title: snRNAseq_Adult1

value: 20 years


title: Resilient

value: Saline


title: cs_bisulfite_spikelet_I

value: 12-days-old seedlings

value: Chinses Spring

value: spikelets at booting stage (Feeke 10)


title: Anp_day3_rep1

source_name: Human foreskin fibroblasts

value: Foreskin fibroblasts

value: transduced with ASCL1, PTBP2 shRNA, p53 shRNA, rtTA through lentiviruses

value: induction day 3


title: Susceptible


title: snRNAseq_Adol2

value: 14 years


title: CS_root_H3K27me3_rep1

value: Millipore, Upstate, USA

value: Upstate


title: snRNAseq_Adol1


title: Control


title: DEL52_OT1865

first: María José

last: Jiménez

address: C. de Melchor Fernández Almagro, 3

department: Structural Biology

institute: Spanish National Cancer Research Centre

description:
Hom Calr mutant
Purified RNA
Unstranded RNA-seq

data_processing:
RNA-seq processing:
Raw reads were analyzed with nextpresso v1.9.2.5 pipeline (DOI: 10.2174/1574893612666170810153850), as follows:
Sequencing quality and contamination were checked with FastQC v0.11.7 and FastQ Screen v0.13.0. FASTQs were downsampled to 35,000,000 reads using Seqtk and aligned outside the pipeline to the mouse reference genome (GRCm38) with STAR v2.7.3a (--outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard). Raw counts were obtained with HTSeq-count v0.6.1 (--stranded no --mode intersection-nonempty --minaqual 0 --type exon --idattr gene_id) using the mouse gene annotation from GENCODE vM24.
Transcript-level differential expression analysis was performed with Cufflinks v2.2.1 (-c 10 --library-type fr-unstranded --frag-bias-correct GRCm38.fa --no-effective-length-correction --dispersion-method pooled --max-bundle-frags 500000 --seed 123L --library-norm-method geometric) using a 0.05 FDR and removing background level and flat pattern genes.
Gene-level differential expression analysis was performed with DESeq2 v1.12.4 using a 0.05 FDR and removing background level and flat pattern genes. Genes were ranked according to the shrunken log2 Fold Change and GSEAPreranked v2.2.2 was used to perform gene set enrichment analysis for Hallmarks, Biocarta, Reactome and KEGG v7.0 signatures, setting 1000 gene set permutations, a classic enrichment statistic, a random seed of 123 and a min/max gene set size of 10/2,500 respectively.
Assembly: GRCm38
Supplementary files format and content: Tabulated text files with normalized counts obtained with DESeq2 (for genes) or with Cufflinks (for isoforms).

source_name: Sorted hematopoietic stem cells

growth_protocol: MxCre or Calr fl/fl MxCre mice, pI:pC induced, long-term hematopoietic stem cell sort 14 days after induction start: lineage negative, kit positive sca-1 positive, CD48 negative CD150 positive cells.

extract_protocol:
RNA was isolated from sorted cell pellets using PicoPure RNA isolation kits (Applied Biosystems, KIT0204).
Takara SMART-Seq v4 kit was used for cDNA synthesis, shearing was performed according to the Covaris Protocol and library preparation was done with Swift ACCEL-NGS™ 2S PLUS DNA kit.

treatment_protocol: No treatment.

value: CALR knockin crossed with MxCre expressing mice

value: Calr fl/fl (Calr del52/del52) MxCre

value: Sorted hematopoietic stem cells


title: SCC90-siDNp63 Repl.3

city: Strasbourg

first: Alain

last: Jung

address: 17 Rue Albert Calmette

institute: Institut de cancérologie Strasbourg Europe

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
kallisto v0.46.2 was used for quantification of rawdata with a prebuilt indice constructed from Ensembl reference transcriptome.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is an tsv file showing Ensembl gene id, abundance. and counts for SCC90 + siCTRL (BNWK 60, BNWK 61, BNWK 62) and SCC90 siDeltaNp63 (BNWK 63, BNWK 64, BNWK 65) replicates

source_name: SCC90 HPV+ OSCC cell line

growth_protocol: SCC90 cells were maintained at 37°C with 5% CO2 and 90% humidity in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal calf serum, 10nM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid and 1% non-essential amino acids.

extract_protocol:
Total RNA was harvested from pelleted cells using a standard TRIZol procedure (TRI Reagent® : TR 118 Molecular Research Center), according to the manufacturer’s instructions.
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: SCC90 cells were transfected with 10nM of DeltaNp63 siRNA (Eurogentec; sense strand: 5’-ACGAGGAGCCGTTCTAATC-3’; antisense strand: 5’-ACCTGGAAAACAATGCCCAGA-3’)  to 3E05 SCC90 cells using Lipofectamine RNAiMAX, according to the manufacturer's instructions. The Eurogentec SR-CL011-005 scrambled siRNA was used as a negative control. Total protein and RNA was extracted 72h post-transfection.

tag: sirna

value: anti-DeltaNp63 siRNA


title: Mx1_Cre6266

description:
Wildtype control
Purified RNA
Unstranded RNA-seq

value: Calr +/+ (Calr wildtype) MxCre

tag: cell type


title: Mx1_Cre6261

tag: genotype


title: snRNAseq_Child1

value: Prefrontal cortex

value: 4 years


title: snRNAseq_Inf2

value: 0 years


title: snRNAseq_EaFet1

value: Cortical plate

value: 18 gestational weeks


title: SCC90-siDNp63 Repl.1


title: cs_bisulfite_embryo

value: 12-days-old seedlings

value: Chinses Spring

value: fresh immature embryos (14days post anthesis)


title: DEL52_6246


title: SCC90-siCTRL Repl.1

value: scrambled siRNA


title: SCC90-siCTRL Repl.2


title: DEL52_6244


title: snATACseq_LaFet2

data_processing:
Raw sequencing data alignment, filtering, barcode counting, peak calling and counting of both ATAC-seq and gene expression molecules were performed with cellranger-arc (v.1.0.0).
We processed the outputs of Cell Ranger ARC using Seurat v4.0 and Signac v1.1.0 to create a multi-omic Seurat object with paired gene expression and DNA accessibility profiles for each sample. We used MACS2 [PMID:24743991] as implemented in the function CallPeaks in Signac [PMID:34997233] to call peaks from the fragment files. We removed any peaks on nonstandard chromosomes overlapping annotated genomic blacklist regions fromor the hg38 genome [PMID:31249361]. We then quantified fragment counts for each peak, per cell, using the FeatureMatrix function in Signac. Per-cell quality control metrics for each modality were computed, including mitochondrial percentage, nucleosome signal and transcriptional start site (TSS) enrichment score. Next, we combined the individual Seurat objects for all the samples into one single object using the merge function in Seurat. We then performed quality control based on metrics for both modalities by retaining cells with total RNA-seq count > 200 and < 50,000, total ATAC-seq count > 200 and < 100,000, mitochondrial percentage < 5%, nucleosome signal < 3 and TSS enrichment score > 1. Genes or peaks which are detected in < 10 cells are removed. As a result, 45,549 out of 53,185 single cells are retained, with 5,887 RNA UMI counts and 18,066 unique ATAC-seq fragments (29.3% fragments overlapping peaks) on average.
Assembly: hg38
Supplementary files format and content: bigwigs_per_cell_type.gz
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: peaks.gz

value: 24 gestational weeks


title: SCC90-siCTRL Repl.3


title: snRNAseq_Inf1


title: Mx1_Cre2


title: SCC90-siDNp63 Repl.2


title: snATACseq_LaFet1

value: 23 gestational weeks


title: snRNAseq_Child2

value: 6 years


title: snATACseq_EaFet2

value: 19 gestational weeks


title: Mx1_Cre1

value: CALR knockin crossed with MxCre expressing mice


title: DKO rep2 [in vivo]

city: Hangzhou

first: Wanqiang

last: Sheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Department of Immunology

institute: Zhejiang University School of Medicine

data_processing:
Raw reads in fastq format were first processed using Trimmomatic and the low-quality reads were removed to obtain the clean reads. Only clean reads passing the QC were used for subsequent analyses.
The clean reads were mapped to the mouse reference genome (GRCm38) using hisat2 (version 2.1.0). FPKM of each gene was calculated using Cufflinks (version 2.2.1). The read counts of each gene were obtained by HTSeq-count (version 0.11.2).
Differential expression analysis was performed using R package DESeq2 (version 1.22.2). Hierarchical cluster analysis of differentially expressed genes (DEGs) was performed to demonstrate the expression pattern of genes in different groups and samples. To be called DEGs, we required the log2FC > 1 and q value < 0.05. The reported statistical significances were corrected for multiple testing using the Benjamini-Hochberg procedure with a false discovery rate less than 0.05.
Assembly: GRCm38
Supplementary files format and content: Count table for each sample

source_name: B16/F10 tumor cells

growth_protocol: The newly thawed B16-GFP cells were cultured for two passages with addition of 1 μg/ml puromycin, followed by one more passage without puromycin, before implantation into immunocompetent mice.

extract_protocol:
Tumor masses were harvested from GFP-labeled B16/F10 tumor-bearing mice on day 14, and dissociated into single cells. Tumor cells from one individual tumor-carrying mouse as treated as a biological replicate. Tumor cells were incubated with 7-AAD Viability Staining Solution to exclude dead cells. The GFP+ cells were then sorted on a BD Aria. Approximately 150,000~250,000 sorted cells for each biological replicate were directly lysed in 1 ml TRIzol Reagent (Life Technologies, cat#15596018). After incubation for 3 mins, 0.2 ml chloroform was added and mixed by inverting the tubes several times. Samples were incubated for 2~3 mins and later centrifuged for 15 minutes at 15,000g at 4 °C. The upper aqueous phase containing the RNA was collected and mixed with equal volume of 70% ethanol, which was then loaded into a spin column from a RNA Clean ＆ Concentrator TM-5 Kit (ZYMO Research, R1013) and subjected to RNA isolation according to the instruction manual. The on-column DNase digestion was conducted to eliminate DNA contamination.
Total RNA was quantified by a NanoDrop 2000 spectrophotometer (Thermo Scientific) and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies) with RIN > 9.7. The poly(A)+ RNA was enriched and subjected to library construction using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, RS-122-2101) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Novaseq 6000 platform to generate 150 bp paired-end reads. Over 40 million raw reads for each sample were generated.

treatment_protocol: B16-GFP cells were implanted into immunocompetent mice via s.c. injection.

value: Implanted GFP-labeled B16/F10 tumor

value: LSD1/CPT1A DKO


title: Bchla-Null mutant, one hour after lights off (EN: early night), replicate 1

city: Neuchâtel

first: Diego

last: Gonzalez

address: Rue Emile-Argand

country: Switzerland

institute: Laboratory of Microbiology, University of Neuchâtel

data_processing:
trimming and filtering (fastP, 12bps trimmed at 5')
mapping on Porphyrobacter sp. ULC335 genome (bowtie2)
read counting (featureCounts, default)
Assembly: Porphyrobacter sp. ULC335 (GCA_025917005.1)
Supplementary files format and content: read counts per feature (Geneid, Chr, Start, End, Strand, Length, Counts)

organism: Porphyrobacter sp. ULC335

source_name: Cells

growth_protocol: BG11-por medium, batch growth in MC1000 multicultivator to stationary phase

extract_protocol:
RNeasy mini-kit columns (Qiagen)
Illumina Stranded Total RNA Prep with Ribo-Zero Plus

treatment_protocol: 12:12 dark/light cycles, 150µmol/s/m2

value: Cells

value: stationary phase

value: Bchla-Null mutant

tag: treatment

value: 12:12, dark/light, 150 micromol/s/m2


title: Bchla-Null mutant, one hour after lights off (EN: early night), replicate 3

tag: tissue


title: Bchla-Null mutant, one hour after lights off (EN: early night), replicate 2


title: snATACseq_EaFet1

city: New York City

value: Cortical plate


title: Bchla-Null mutant, one hour before lights off (LD: late day), replicate 3


title: snATACseq_Adult2

value: Prefrontal cortex

value: 39 years


title: DKO rep1 [in vivo]


title: Brg1-cKO_1

city: New York

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

data_processing:
Raw sequencing reads from mice were mapped to mm10 using TopHat (Trapnell, C. et al.)
Counts of reads mapping to genes were obtained using HTSseq-counts (Anders, S. et al.) software against Ensembl v75 (mm10) annotation
Differential expression was done using the DESeq2 (Love, M. I. et al.) package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file

source_name: Kidney

extract_protocol:
For each samples, we used 3000 cells for total RNA preparation in replicates using NucleoSpin RNA XS kit (TakaraBio). mRNA were purified from total RNA using magnetic beads (New England Biolabs)
Random priming strand-specific RNA-seq libraries were generated using with SMART-seq Stranded kit (TakaraBio) and single-end 75-bp sequencing was performed using Illumina HiSeq 2500 system.

tag: group


title: Brg1-cKO-2


title: Bchla-Null mutant, one hour before lights off (LD: late day), replicate 2


title: KO rep3 [in vivo]

value: LSD1 KO


title: Control_2

value: control


title: snATACseq_Adult1

value: 20 years


title: Bchla-Null mutant, one hour before lights off (LD: late day), replicate 1


title: KO rep2 [in vivo]


title: snATACseq_Adol2

value: 14 years


title: KO rep1 [in vivo]


title: snATACseq_Adol1


title: Bchla-Null mutant, one hour after lights on (ED: early day), replicate 3


title: Bchla-Null mutant, one hour after lights on (ED: early day), replicate 2


title: 24_Yuuki_24_S24

city: Bethesda

first: Stefan

last: Ambs

address: Building 37, Room 3050B

institute: NCI

data_processing:
16 mRNA-Seq samples were pooled and sequenced on NextSeq using Illumina Stranded mRNAseq ligation and paired-end sequencing. The samples have 22 to 29 million pass filter reads with more than 85% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

extract_protocol:
RNA isolation was done using TRIzol. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NextSeq machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Pancreatic cancer cell line

tag: condition

value: AsPC-1_SERPINB3 overexpression_4

tag: cell line

value: AsPC

value: SERPINB3 overexpression


title: Scr rep2 [in vivo]

tag: strain

value: Implanted GFP-labeled B16/F10 tumor

value: Scramble


title: snATACseq_Child2

tag: age

value: 6 years


title: Bchla-Null mutant, one hour after lights on (ED: early day), replicate 1

value: Cells

value: stationary phase


title: Scr rep1 [in vivo]


title: snATACseq_Child1

value: 4 years


title: 23_Yuuki_23_S23

value: AsPC-1_SERPINB3 overexpression_3


title: 22_Yuuki_22_S22

value: AsPC-1_SERPINB3 overexpression_2


title: 21_Yuuki_21_S21

value: AsPC-1_SERPINB3 overexpression_1


title: Bchla-Null mutant, one hour before lights on (LN: late night), replicate 2

value: Bchla-Null mutant

value: 12:12, dark/light, 150 micromol/s/m2


title: VSV rep2 [in vitro]

source_name: B16/F10 cells

growth_protocol: B16/F10 cells were cultured in DMEM growth medium supplemented with 10% heat-inactivated FBS and 1% penicillin/streptomycin in a 5% CO2 incubator at 37°C.

extract_protocol:
B16 cells from one individual well as a techical eplicate. Approximately 500,000 cells for each biological replicate were directly lysed in 0.5 ml TRIzol Reagent (TaKaRa, 9109). After incubation for 5 min, 100 μl chloroform was added and mixed by gentle inversion several times. Samples were incubated for 3 min at RT and then centrifuged for 15 mins at 12,000 g at 4 °C. The upper aqueous phase containing the RNA was collected and mixed with equal volume of freshly prepared 70% ethanol, which was then loaded into a spin column from a RNA Clean ＆ ConcentratorTM-5 Kit (ZYMO Research, R1013) and subjected to RNA isolation according to the manufacturer’s instructions.
Total RNA was quantified by a NanoDrop 2000 spectrophotometer (Thermo Scientific) and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies) with RIN > 9.7. The poly(A)+ RNA was enriched and subjected to library construction using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, RS-122-2101) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Novaseq 6000 platform to generate 150 bp paired-end reads. Over 40 million raw reads for each sample were generated.

treatment_protocol: B16/F10 cells were depleted of LSD1 by CRISPR/Cas9, or infected with VSV-GFP (MOI=1) or mock for 1 h in FBS-free DMEM and then put back in fresh complete medium for 12 h.

tag: source

value: in vitro culture

tag: cell line source

value: B16/F10 cells

tag: cell type source

value: melanoma cell line

value: WT; VSV-GFP infection


title: VSV rep1 [in vitro]


title: Bchla-Null mutant, one hour before lights on (LN: late night), replicate 3


title: snATACseq_Inf2

value: Prefrontal cortex

value: 0 years


title: KO rep2 [in vitro]

value: LSD1 KO


title: 20_Yuuki_20_S20

value: Pancreatic cancer cell line

value: AsPC

value: control


title: 19_Yuuki_19_S19


title: Bchla-Null mutant, one hour before lights on (LN: late night), replicate 1

value: Cells

value: stationary phase


title: Control_1


title: snATACseq_Inf1


title: Wild-type, one hour after lights off (EN: early night), replicate 3

value: wild-type


title: 18_Yuuki_18_S18


title: KO rep1 [in vitro]


title: Wild-type, one hour after lights off (EN: early night), replicate 2


title: Scr rep1 [in vitro]

value: WT; mock


title: Wild-type, one hour after lights off (EN: early night), replicate 1


title: HIF1A-AS1 overexpressed group-3

city: Wuhan

first: Wenying

last: Zhong

address: Shizi Street No.1

institute: Huazhong Agricultural University

data_processing:
Illumina PE150/SE50  software used for basecalling.
Compare the clean reads to the reference sequence useing Hisat2 software
Use Stringtie software to splice the reads into transcripts and quantify them
Quantitative expression levels of all detected and predicted samples
Supplementary files format and content: count and FPKM

source_name: vascular smooth muscle cells

growth_protocol: HA-VSMCs were purchased from the Shanghai Cell Bank of the Chinese Academy of Sciences (Shanghai, China). The cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco), which contained 10% fetal bovine serum (Gibco) in a 5% CO2 incubator at 37 °C. When the cell density was more than 80%, washing the cells twice by sterilized PBS. Subsequently, 0.25% trypsin was added to dissociate the cell-cell contacts. After centrifugation (1000 r/min, 5min), the cells were resuspended in complete medium with 10% fetal bovine serum for further use.

extract_protocol:
Total RNA was extracted from DCs using TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc.), accordance with the instructions of the kits used.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were transfected with empty vector and HIF1A-AS1 overexpressing vector, respectively. The cells were passaged at 1:10 with fresh growth medium 48 h after transfection, and then selected by adding selective medium in the next day. The expression levels of HAF1A-AS1 were assessed by RT-qPCR.

value: HIF1A-AS1 overexpressing cells

value: HA-VSMC

tag: vector


title: HIF1A-AS1 overexpressed group-2


title: 17_Yuuki_17_S17


title: Scr rep2 [in vitro]


title: 16_Yuuki_16_S16

source_name: Panc 10.05_Ctrl_1

value: Panc 10.05_SERPINB3 overexpression_4

value: SERPINB3 overexpression


title: nomal control-3

value: empty vector transduced cells


title: HIF1A-AS1 overexpressed group-1


title: 15_Yuuki_15_S15

value: Panc 10.05_SERPINB3 overexpression_3


title: nomal control-2


title: Wild-type, one hour before lights off (LD: late day), replicate 3

value: 12:12, dark/light, 150 micromol/s/m2


title: 17CS-infected Irg1-/- mouse

first: Sebastian

middle: A

last: Riquelme

address: 650W 168th Street Black Building 4th Floor Room 427

institute: Columbia University

description:
10x Genomics
AK8

data_processing: FASTQ file generation, alignment, filtering, barcode counting, and UMI counting were done using the 10X Cell Ranger software.

source_name: whole lung

extract_protocol:
16 hours after infection, mice were euthanized, their lungs were harvested, and single cell suspensions of the lungs were were placed in an Eppendorf tube containing an enzymatic digestion solution of collagenase I (2 mg/mL), dispase (20 mg/mL), elastase (1 mg/mL), and DNAse (1 uL/mL) in PBS. The lungs were minced within the tube and then incubated with shaking at 37C for 30 minutes. 4 volumes of PBS supplemented with 10% FBS was added to quench the digestion, and the digestion solution was strained over a 70-micron filter. The cell suspension was spun down at 4C and 1400 rpm for 7 min. Red blood cell lysis was performed using the Invitrogen RBC lysis buffer. The resulting cell pellet was resuspended in PBS supplemented with 0.04% BSA
10x Genomics droplet-based cell and molecule-specific barcoding

treatment_protocol: WT or Irg1-/- C57bl/6 mice (8-week old) were treated with PBS or infected either with WT PAO1 or a mix of the 17 host-adapted P. aeruginosa clinical isolates (106 total CFU per mouse in 50uL).

value: mixed

value: whole lung

value: Irg1-/- C57Bl/6NJ

value: 8 weeks old


title: 17CS-infected WT mouse

description:
10x Genomics
AK7

value: WT C57Bl/6NJ


title: PAO1-infected Irg1-/- mouse

description:
10x Genomics
AK6


title: 14_Yuuki_14_S14

value: Pancreatic cancer cell line

value: Panc 10.05_SERPINB3 overexpression_2


title: Wild-type, one hour before lights off (LD: late day), replicate 2

value: Cells

value: stationary phase


title: 12_Yuuki_12_S12

value: Panc 10.05_Ctrl_4

value: control


title: Wild-type, one hour before lights off (LD: late day), replicate 1

value: wild-type


title: nomal control-1

value: HA-VSMC


title: PBS-treated Irg1-/- mouse

description:
10x Genomics
AK2


title: 13_Yuuki_13_S13

value: Panc 10.05_SERPINB3 overexpression_1

value: SERPINB3 overexpression


title: 11_Yuuki_11_S11

value: Panc 10.05_Ctrl_3


title: Wild-type, one hour after lights on (ED: early day), replicate 2

value: 12:12, dark/light, 150 micromol/s/m2


title: PAO1-infected WT mouse

description:
10x Genomics
AK5

value: mixed


title: Mycelium, Treatment 2 (EG_2)

first: Zhou

last: Duanxu

state: zhejiang

address: wushu street NO.666

institute: Zhejiang Agriculture and Forest University

data_processing:
The data from high-throughput sequencing were analyzed using the OmicShare tools, a free online platform for data analysis (www.majorbio.com).
Supplementary files format and content: Expression analysis table include TPM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Graphilbum sp.

source_name: Fungal hyphae

growth_protocol: The strains were cultured on potato dextrose agar (PDA) medium at 28°C for 5 days.

extract_protocol:
The mycelium was divided and induced with about 300 PWNs (Bursaphelenchus xylophilus) for 24 h, respectively
The libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mycelium was collected and washed three times with 0.1 Mphosphate buffer saline (PBS) (pH 6.8-7.2).

value: Fungal hyphae


title: Mycelium, Treatment 1 (EG_1)


title: PBS-treated WT mouse

description:
10x Genomics
AK1

value: whole lung


title: Wild-type, one hour after lights on (ED: early day), replicate 1


title: 10_Yuuki_10_S10

value: Panc 10.05_Ctrl_2


title: Wild-type, one hour before lights on (LN: late night), replicate 3


title: Mycelium, Control 2 (CK_2)


title: goat_male_E125, replicate1, scRNAseq

city: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1
Assembly: ARS1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Capra hircus

source_name: testis

extract_protocol:
For the collection of the testicular germ cells and somatic cells, testes were dissected under a dissection microscope and transferred to a 15 mL tube digested with 1 mg/mL collagenase IV, 1 mg/mL hyaluronidase, 0.25% trypsin, and 1 mg/mL DNase I for 30 min at 37C. To prepare the single-cell suspension for 10x Genomics single-cell RNA-seq, the cell suspension was repeatedly pipetted after adding serum, filtered through a 40 mm membrane, and resuspended in 0.1% serum/PBS.
The cell suspension (1000 living cells per microliter determined by CountStar) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53C for 45 min, followed by 85C for 5 min, and hold at 4C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200. According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 30 Library and Gel Bead Kit V3.1 The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

value: testis

tag: Sex

value: male

tag: developmental stage


title: 9_Yuuki_9_S9

value: Pancreatic cancer cell line

value: Panc 10.05_Ctrl_1


title: Mycelium, Treatment 3 (EG_3)


title: Wild-type, one hour before lights on (LN: late night), replicate 2

value: Cells

value: stationary phase


title: Mycelium, Control 1 (CK_1)


title: Wild-type, one hour after lights on (ED: early day), replicate 3


title: goat_male_E105, replicate1, scRNAseq

description: 10x Genomics


title: Wild-type, one hour before lights on (LN: late night), replicate 1


title: goat_male_E85, replicate1, scRNAseq

description: 10x Genomics


title: Control Organoids

city: Toronto

first: Gordon

last: Keller

state: Ontario

address: 101 College St

department: Medicine

country: Canada

institute: McEwen Stem Cell Institute

data_processing:
Raw data of Illumina's base call files (Cell Ranger to process 10x Genomics data)
Bam files and read count matrix (QC by Cell Ranger)
Updated read count matrix and imputed it
Assembly: Genome_build: GRCH38
Supplementary files format and content: cloupe

source_name: human embyronic stem cell derived cells

extract_protocol:
10X Genomics Single Cell 3ʹ Reagent Kits v3 protocols
10X Genomics 3ʹ Gene Expression Library Construction (fragmentation Mix, purified cDNA for Library Construction, and adaptor ligation mix)

treatment_protocol: Cells were grown in 2g DMEM F12 prior to sequencing and dissociated with Collagenase Type II overnight at room temperature followed by a wash and dissociation into single cells with TrypLE for 5 mins at 37 degrees.

value: human embyronic stem cell derived cells

value: Cardiovascular


title: Cardiac Injury Organoids

value: Hypoxia, TGFB1, Isoproteronol


title: Mycelium, Control 3 (CK_3)


title: MDECs, negative mimic control#3

status: Public on Oct 11 2023

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

data_processing:
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: EquCab2
Supplementary_files_format_and_content: Normalized counts file is a comma-separated value matrix containing the DESeq2 normalized counts for each of the samples.

organism: Equus caballus

source_name: Horse mammary derived epithelial cells incubated with negative mimic control + DMBA

extract_protocol: Libraries were prepared according to the Illumina TruSeq stranded mRNA sample preparation kit.

value: mammary derived epithelial cells (MDECs)

value: negative mimic control + DMBA

value: control


title: Adult_rat, T cells,_NTG_Replicate 6

city: Montigny-le-Bretonneux

first: Frédéric

last: Crémazy

address: 2 avenue de la source de la Bièvre

institute: UVSQ/INSERM

data_processing:
Transcripts were aligned to the rat genome Rnr 6.0 using STAR version 2.7.1 then reads were counted using featureCount.
Differential analysis was performed with DESeq2 including batch effect.
Assembly: rn6
Supplementary files format and content: readcounts and DEG analysis

organism: Rattus norvegicus

source_name: Mesenteric Lymph Node

extract_protocol:
Total RNA was purified from mLN Tn sorted from 4 wk- (Monarch® Total RNA Miniprep Kit, NEB) or 3 mo-old rats (RNeasy micro kit, QIAGEN). Samples with RNA integrity number >7 were sequenced.
Libraries were prepared using NEBNext® Low Input RNA Library Prep Kit (3 mo-old) or NEBNext® rRNA Depletion Kit and NEBNext® Ultra II Directional RN Library Prep Kit (4 wk-old) and sequenced on an Illumina HiSeq 2000 (3 mo-old) or NextSeq 500/550 (4 wk-old), paired-end 75 bases.

value: Mesenteric Lymph Node

value: T cells

value: NTG


title: Premorbid rat, T cells, NTG, Replicate 2

source_name: Thymus

value: Thymus


title: Premorbid rat, T cells, HLA B27, Replicate 3

value: HLA B27


title: Premorbid rat, T cells, HLA B27, Replicate 2


title: Adult_rat, T cells,_NTG_Replicate 5


title: Adult_rat, T cells,_NTG_Replicate 4


title: Adult_rat, T cells,_HLA B27_Replicate 6


title: Premorbid rat, T cells, NTG, Replicate 5


title: Premorbid rat, T cells, HLA B27, Replicate 4


title: Premorbid rat, T cells, NTG, Replicate 1


title: Premorbid rat, T cells, NTG, Replicate 3


title: Premorbid rat, T cells, HLA B27, Replicate 1


title: Premorbid rat, T cells, HLA B27, Replicate 7


title: Premorbid rat, T cells, HLA B27, Replicate 5


title: Adult_rat, T cells,_NTG_Replicate 3


title: Premorbid rat, T cells, HLA B27, Replicate 6


title: Adult_rat, T cells,_NTG_Replicate 2


title: Premorbid rat, T cells, NTG, Replicate 4


title: MDECs, negative mimic control#2


title: Adult_rat, T cells,_HLA B27_Replicate 3


title: MDECs, miR-214 mimic #3

source_name: Horse mammary derived epithelial cells incubated with miR-214 mimic + DMBA

value: miR-214 mimic + DMBA

value: miR-214-3p overexpression


title: Adult_rat, T cells,_HLA B27_Replicate 7


title: Malignant [G4_2]

city: Bogotá

first: Andrés

last: Rincón-Riveros

address: Calle 1a #9-85

department: Grupo de investigación en biología del cáncer

country: Colombia

institute: Instituto Nacional de Cancerología

data_processing:
Quality control was performed with FastQC v0.11.9 to remove low-quality reads.
The 5' and 3' sequencing adapters were removed using the Trim Galore tool, which implements Cutadapt v2.8 (https://github.com/marcelm/cutadapt)
The reads were mapped against the reference genome (GRCh38.p13), and a count table was constructed with the identified small RNAs using the Spliced Transcripts Alignment to a Reference (STAR) software
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file include TPM and Raw values for each Sample

source_name: Plasma derived exosomes

extract_protocol:
sncRNA was isolated using miRneasy mini kit (Qiagen). 20 ng of sRNA was used for the construction of sequencing libraries.
Small RNAs were then extracted from the exosomes samples for further library construction using BGI UMI library preparation kits and protocols.
The sequencing libraries were sequenced using single-end 50bp sequencing to 20M reads of data on the DNBSEQTM technology platform.

value: Plasma derived exosomes

tag: disease

value: Diffuse gastric cancer

tag: tumor stage

value: Stage IV

value: Malignant

tag: molecule type

value: small-RNA


title: Malignant [G4_3]

tag: genotype


title: Adult_rat, T cells,_NTG_Replicate 1

tag: cell type


title: Adult_rat, T cells,_NTG, IgG, Replicate 2

data_processing:
Reads were trimmed with fastp and aligned to the rat genome Rnr_6.0 using Bowtie2
The peak calling was performed with MACS2, normalized on IgG signal
Assembly: rn6
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
mLN Tn (2-7 x 105 cells) were sorted from 4 wk- or 3 mo-old rats, fixed using 1% paraformaldehyde (Electron Microscopy Sciences) for 8 min. After cell nuclei lysis, chromatin was fragmented (Bioruptor PICO/Diagenode), immunoprecipitated overnight at 4°C using rabbit polyclonal Abs: IgG (Diagenode, 1µg), m/r anti-H3K4Me3 (Diagenode, 1µg), m/r anti-H3K27Ac Abs (Active Motif, 5µg), then tagmented using the ChIP-mentation Kit for Histones (Diagenode).
Libraries were prepared according to the ChIPmentation Kit guidelines (Diagenode)
ChIPmentation

tag: tissue

tag: antibody

value: IgG


title: Adult_rat, T cells,_NTG, H3K4me3, Replicate 3


title: Adult_rat, T cells,_NTG, IgG, Replicate 1


title: Adult_rat, T cells,_HLA B27_Replicate 4


title: Adult_rat, T cells,_HLA B27_Replicate 1


title: MDECs, miR-214 mimic #1

tag: treatment


title: Adult_rat, T cells,_NTG_Replicate 7


title: Malignant [G4_1]

value: Intestinal-type gastric cancer


title: Malignant [G4_4]


title: Adult_rat, T cells,_HLA B27_Replicate 2


title: Malignant [G4_5]


title: MDECs, miR-214 mimic #2

value: mammary derived epithelial cells (MDECs)


title: MDECs, negative mimic control#1

value: negative mimic control + DMBA


title: Malignant [G3_5]

value: Stage III


title: Adult_rat, T cells,_NTG, H3K4me3, Replicate 2

value: Mesenteric Lymph Node


title: Adult_rat, T cells,_NTG, H3K27ac, Replicate 1

value: T cells


title: Adult_rat, T cells,_NTG, H3K4me3, Replicate 1

value: NTG


title: Malignant [G3_1]


title: Adult_rat, T cells,_HLA B27_Replicate 5


title: Malignant [G3_3]


title: Adult_rat, T cells,_NTG, H3K27ac, Replicate 2


title: Malignant [G2_5]

value: Stage II


title: Malignant [G2_7]


title: Malignant [G3_4]


title: Adult_rat, T cells,_HLA B27, IgG, Replicate 1

value: HLA B27


title: Adult_rat, T cells,_HLA B27, H3K4me3, Replicate 3


title: Malignant [G3_2]


title: Adult_rat, T cells,_HLA B27, IgG, Replicate 3


title: Adult_rat, T cells,_HLA B27, IgG, Replicate 2


title: Malignant [G2_4]


title: Adult_rat, T cells,_NTG, H3K27ac, Replicate 3


title: Malignant [G2_3]


title: Malignant [G2_6]


title: Adult_rat, T cells,_HLA B27, H3K27ac, Replicate 1


title: Adult_rat, T cells,_HLA B27, H3K4me3, Replicate 2


title: Adult_rat, T cells,_HLA B27, H3K4me3, Replicate 1


title: Benign [C9]

value: Acute gastritis

value: Gastritis

value: Benign


title: Malignant [G2_2]

value: Plasma derived exosomes

value: Diffuse gastric cancer


title: Benign [C8]

value: Chronic gastritis


title: Adult_rat, T cells,_HLA B27, H3K27ac, Replicate 2


title: Adult_rat, T cells,_HLA B27, H3K27ac, Replicate 3


title: Malignant [G1_1]

value: Stage I

value: Malignant

value: small-RNA


title: Malignant [G1_3]


title: Malignant [G2_1]


title: C1

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_27

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

value: Control

value: serum


title: C3 / C4

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_29


title: PZ22 / PZ23 / PZ25 / PZ28

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_26

value: ZIKV


title: Benign [C10]


title: Adult_rat, T cells,_NTG, IgG, Replicate 3

value: Mesenteric Lymph Node

value: IgG


title: PZ10 / PZ20 / PZ21

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_25


title: Malignant [G1_2]

value: Intestinal-type gastric cancer


title: C2

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_28


title: Benign [C6]


title: PZ11 / PZ19 / PZ26

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_24


title: Benign [C5]


title: PZ14 / PZ15 / PZ24

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_23


title: UCSF segmental schwannomatosis #1 Tumor b

type: genomic

city: Stanford

first: David

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

hyb_protocol: bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting

data_processing: Methylation data were preprocessed using the minfi package (v.1.30.0) in R. The detection p-value for each sample was computed. Functional normalization with NOOB background correction and dye-bias normalization was performed.

label: Cy5 and Cy3

source_name: FFPE tumor tissue of schwannoma

label_protocol: standard Illumina protocol

growth_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients.  No ex vivo culture or xenografting was performed.

extract_protocol: Tumor tissue was selectively punched from formalin-fixed, paraffin-embedded tissue blocks using using disposable biopsy punches.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients at time of initial diagnosis before any radiation or chemotherapy had been administered.  No ex vivo culture or xenografting was performed.

tag: patient sex

value: Female

tag: disease state

value: schwannoma

value: Schwannoma nerve sheath tumor

tag: tumor location

value: Sciatic nerve

tag: oncogenic driver


title: Benign [C7]

value: Gastric changes after gastric bypass surgery

value: Benign lesion

value: Benign


title: UCSF segmental schwannomatosis #2 Tumor a

value: Spinal accessory nerve


title: Benign [C4]

value: Plasma derived exosomes

value: Chronic gastritis

value: Gastritis


title: Benign [C3]

value: small-RNA


title: PZ9 / PZ13 / PZ18

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_22

value: serum


title: PZ12- / PZ16 / PZ17

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_21

value: ZIKV


title: PZ27

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_20


title: Benign [C1]


title: Benign [C2]

value: Esophagitis


title: UCSF segmental schwannomatosis #1 Tumor a


title: PZ4 / PZ5

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_18


title: PD18

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_14


title: UCSF segmental schwannomatosis #1 Tumor d


title: PD17

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_13


title: PZ3 / PZ8

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_19


title: UCSF segmental schwannomatosis #1 Tumor c


title: Plasma EVs, NAFLD_HCC_6

city: Bangkok

first: Bootsakorn

last: Boonkaew

state: Bangkok

address: 1873 Rama IV

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

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: Non-hepatitis B-, non-hepatitis C-related hepatocellular carcinoma

tag: age

value: 65 years

value: Male

value: plasma

tag: sample type

value: EV


title: Plasma EVs, NAFLD_HCC_4

value: 60 years

tag: Sex


title: Plasma EVs, NAFLD_HCC_9

value: 67 years


title: Plasma EVs, NAFLD_HCC_8

value: Female


title: UCSF segmental schwannomatosis #2 Tumor b

value: schwannoma

value: Schwannoma nerve sheath tumor


title: PZ6 / PZ7

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_16


title: PD19

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_15

value: DENV


title: Plasma EVs, NAFLD_HCC_7

value: 61 years


title: PD15

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_11


title: PD16

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_12


title: Plasma EVs, NAFLD_HCC_5

value: 76 years


title: PD10 / PD11

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_07

value: DENV / DENV


title: PD9

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_06

value: serum


title: Plasma EVs, NAFLD_HCC_1

value: 63 years


title: Plasma EVs, NAFLD_6

value: Non-alcoholic fatty liver disease

value: 46 years


title: PD7 / PD8

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_05

value: DENV-2 / DENV


title: Plasma EVs, NAFLD_HCC_3

value: Non-hepatitis B-, non-hepatitis C-related hepatocellular carcinoma

value: 72 years


title: Plasma EVs, NAFLD_4

value: 58 years

value: plasma

value: EV


title: PD5 / PD6

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_04

value: DENV-3 / DENV-3


title: PZ1 / PZ2

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_17

value: ZIKV


title: Plasma EVs, NAFLD_2

value: 55 years

value: Male


title: PD3 / PD4

description:
Please refer to S1 Table in the manuscript for a comprehensive description of the patients' characteristics.
DZ_03

value: DENV-3 / DENV


title: Plasma EVs, NAFLD_1

value: 41 years

value: Female


title: Plasma EVs, NAFLD_HCC_2

value: 68 years