title: blood_HUNT_21

description:
HUNT_21
Specimen 21 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_127

status: Public on Dec 10 2024

type: RNA

city: Trondheim

first: Pål

last: Sætrom

address: Erling Skjalgsons gate 1

department: Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology, NTNU

description:
HUNT_127
Specimen 127 from the HUNT biobank, sampled on Tempus tubes

hyb_protocol: Biotin-labelled cRNA was hybridized to Illumina HumanHT-12 v4 Expression BeadChips (Illumina, Inc., San Diego, CA, USA) according to the manufacturer's protocol.

scan_protocol: Microarrays were scanned with the BeadArray Reader (Illumina).

data_processing:
Illumina BeadArray studio (Illumina) was used to handle Illumina data. Data analysis was performed using R (http://cran.r-project.org), together with tools from the Bioconductor project (lumi package). The recommended detection score cut off suggested by the lumi detectionCall function was used, leaving data from 30,715 of 47,323 probes to be used for further analyses. The 30,715 probes were log2-transformed and normalized using quantile–quantile normalization.  We corrected for differences in gene expression between the PAXgene and Tempus systems by using a separate set of control samples to measure latent expression differences between PAXgene and Tempus for each gene (ArrayExpress accession number: E-MTAB-5138; PMID: 28335817; doi: 10.1186/s13104-017-2455-6). These gene-specific expression differences were then subtracted from the gene expression values in samples isolated from PAXgene tubes.
R and the Bioconductor package lumi was used to normalize the data as follows:  Assume that the non-normalized expression data filtered for detected probes is stored as a LumiBatch object in the variable data, that the probe-specific logFC expression differences between PAXgene and Tempus are stored as a vector in the variable delta, and that the indexes of samples that should be batch corrected (i.e. PAXgene samples) are stored in the variable pax. The following steps in R would then normalize the data:
data.t <- lumiT(data, method=log2)
data.q <- lumiN(data.t, method=quantile)
data.n <- data.q
e.data <- exprs(data.n)
e.data[,pax] <- e.data[,pax] - delta
exprs(data.n) <- e.data
Matrix_non-normalized.txt includes the raw unfiltered and unnormalised data, as output from Illumina's GenomeStudio version 1.9.0.

molecule: total RNA

organism: Homo sapiens

source_name: peripheral whole blood

label_protocol: The Illumina TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX, USA) was used to amplify RNA for hybridization on Illumina BeadChips. Total RNA was used in the first strand cDNA synthesis by reverse transcription. Following the second strand cDNA synthesis and cDNA purification steps, in vitro transcription to synthesize cRNA was carried out for 12 h.

extract_protocol: Total content in the tubes (blood and preservative in either PAXgene or Tempus) was diluted with 1× PBS (1:1 vol of blood: 1× PBS). The tubes were subsequently vortexed for 30 s before centrifugation for 60 min (4500 rcf, 4 °C) using a swing out rotor. The supernatant was removed and the tubes were decanted upside down for 2 min to dry. Buffer 1 (350 μL) from the PAXgene kit was added and the pellet was dissolved by pipetting up and down. The samples were transferred to sterile 1.5 mL tubes (Eppendorf AG, Hamburg, Germany) before adding Buffer 2 (300 μL) and proteinase K (40 μL), both from the PAXgene kit. The samples were vortexed and incubated for 10 min at 55 °C using a shaker incubator (1200 rpm, Eppendorf thermomixer comfort, Eppendorf). After a quick spin down, the lysate was directly pipetted to a PAXgene spin column and centrifuged for 3 min (1500 rcf). The supernatant was transferred to a new tube and 100% ethanol (812 μL, 1.25 times the present volume) was added and mixed by turning the tube upside down. The lysate- and ethanol mix was transferred to filter from the mirVana kit (Life Technologies, Part Number AM1560), centrifuged for 15 s (9000 rcf) and the flow-through was discarded. Since the filter has a maximum volume of 700 μL, this process was repeated until all the mix was run through. Wash solution 1 (700 μL) from the mirVana kit (Life Technologies) was added and the samples were centrifuged for 15 s (9000 rcf). The flow-through was subsequently discarded before 500 μL Wash solution 2/3 (Life Technologies) was added. The samples were again centrifuged for 15 s (9000 rcf). The flow-through was discarded before treating with DNase1 (80 µL) (PreAnalytiX) for 15 min at room temperature. The filter was washed with a second round of Wash solution 2/3 (500 μL), and centrifuged for 15 s (9000 rcf). The filter was dried for one min by centrifuging (9000 rcf) before it was transferred to a new collection tube. To elute the RNA 50, μL pre-heated nuclease free water (Tempus kit, Applied Biosystems) was added followed by spinning for 30 s (9000 rcf). The elution step was repeated and the tubes were centrifuged for 2 min. The eluate was transferred to a new sterile 1.5 mL tube (Eppendorf AG) without disturbing the debris. Finally, the samples were incubated at 65 °C for 5 min before RNA yield and quality were measured.

treatment_protocol: Cancer samples: During diagnostic work-up under the suspicion of presence of lung cancer, venous blood was collected by phlebotomy with butterfly needle from 123 patients with their consent. Blood was collected into PAXgene tubes. All samples were inverted 10 times before being stored at -80°C. Prior to isolation of RNA, the tubes were thawed at room temperature for 16 h as recommended by the PAXgene protocol for enhanced yields.  Control samples, NOWAC cohort: A total of 63 samples from healthy women from the Norwegian Women and Cancer Cohort (NOWAC) was drawn on PAXgene tubes with their consent.  Control samples, HUNT cohort: A total of 118 samples from healthy volunteers, men and women, included in the HUNT study in 2008 was drawn on Tempus tubes.  All samples from the control cohorts arrived at our facility frozen and were stored at -80℃. Before RNA isolation, tubes were thawed in the dark for 16 h at room temperature.

tag: tissue

value: peripheral whole blood

tag: biobank

value: HUNT

tag: gender

value: Male

value: Young

value: smoker

tag: crp

tag: Stage

tag: histology

tag: block

tag: outlier

value: FALSE

tag: dataset

tag: status

value: control


title: blood_HUNT_12

description:
HUNT_12
Specimen 12 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_120

description:
HUNT_120
Specimen 120 from the HUNT biobank, sampled on Tempus tubes

value: Old


title: blood_HUNT_126

description:
HUNT_126
Specimen 126 from the HUNT biobank, sampled on Tempus tubes

value: Female

value: Test


title: blood_HUNT_128

description:
HUNT_128
Specimen 128 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_13

description:
HUNT_13
Specimen 13 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_139

description:
HUNT_139
Specimen 139 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_122

description:
HUNT_122
Specimen 122 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_114

description:
HUNT_114
Specimen 114 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_115

description:
HUNT_115
Specimen 115 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_113

description:
HUNT_113
Specimen 113 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_119

description:
HUNT_119
Specimen 119 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_118

description:
HUNT_118
Specimen 118 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_11

description:
HUNT_11
Specimen 11 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_134

description:
HUNT_134
Specimen 134 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_112

description:
HUNT_112
Specimen 112 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_108

description:
HUNT_108
Specimen 108 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_106

description:
HUNT_106
Specimen 106 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_110

description:
HUNT_110
Specimen 110 from the HUNT biobank, sampled on Tempus tubes


title: scRNASeq,Trp53_WT,Rep3

type: SRA

city: Toronto

first: Sajid

middle: A

last: Marhon

state: ON

address: 101 College Street

country: Canada

institute: Princess Margaret Cancer Centre

description:
10x Genomics
scRNASeq_Clustering_Trp53_KO_Trp53_WT.SEURAT_GlobalClustering_CellClusters.tsv.gz
scRNASeq_Clustering_Trp53_KO_Trp53_WT.SEURAT_UMAPPlot_Coordinates.tsv.gz
scRNASeq_T_Cell_Differential_Markers_Table.tsv.gz
scRNASeq_DGE_Treatment_Control_Metadata.SEURAT_DiffExprMarkers_Metadata_CellClass_AllDatasets_sct.tsv.gz
scRNASeq_Multi_CR_DGE_Metadata_SubClass_Comparisons.SEURAT_DiffExprMarkers_Metadata_SubClass1_sct.tsv.gz
scRNASeq_Multi_CR_DGE_Metadata_SubClass_Comparisons.SEURAT_DiffExprMarkers_Metadata_SubClass2_sct.tsv.gz
scRNASeq_Multi_CR_DGE_Metadata_SubClass_Comparisons.SEURAT_DiffExprMarkers_Metadata_SubClass3_sct.tsv.gz
scRNASeq_Multi_CR_DGE_Metadata_SubClass_Comparisons.SEURAT_DiffExprMarkers_Metadata_SubClass4_sct.tsv.gz
scRNASeq_Trp53_KO_Trp53_WT_Cell_Type_Prediction.tsv.gz

library_source: transcriptomic single cell

data_processing:
10X scRNAseq datasets were processed by cellranger pipeline using the command count to generate single cell feature counts for each library.  The feature matrices of the datasets were processed using Seurat package to perform QC and normalization of the multiple datasets.  Normalized datasets were merged and integrated to correct the batch effects.   Dimensional reduction and clustering of the integrated datasets was performed.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Mus musculus

source_name: Murine C57BL/6 ovarian surface epithelium

extract_protocol:
Ascites fluid was immediately transferred to 10ml EDTA-coated tubes that were centrifuged at 600xg for 10 minutes at 4°C in a swing bucket rotor centrifuge. Cleared ascites fluid was discarded, and cell pellet was resuspended in 5ml 1x ACK buffer (150mM NH4Cl, 10mM KHCO3, 0.1 mM Na2EDTA) to lyse red blood cells. Following 1 minute incubation, cells were centrifuged 350xg for 5 minutes at 4°C. Supernatant containing lysed red blood cells was discarded, and 1x ACK treatment followed by centrifugation was repeated once more. Remaining cells were washed with 1x PBS to remove ACK buffer.Cells were then washed on 0.2ml FACS buffer (2% FBS or 0.5% BSA in 1xPBS). To identify viable cells, cells were stained with LIVE/DEAD® Fixable Violet Dead Cell Dye (ThermoFisher Scientific, catalog No. L-34963). Extracellular surface markers (CD45) were subsequently stained at 4°C for 30 minutes directly in polypropylene tubes. Antibody dilutions were typically 1:100 in FACS buffer. Cells were centrifuged for 5 minutes at 300-400xg, and supernatant containing antibodies was discarded. Live cells were immediately subjected to FACS by the SickKids-UHN Flow Cytometry Facility. At least sorted 4000 cells / group were then immediately subjected to 10x Genomics library preparation by the Princess Margaret Cancer Genomics Centre for sequencing on an Illumina HiSeq2500.
At least 4000 sorted cells / group were subjected to 10x Genomics library preparation as per manufacturer's protocol by the Princess Margaret Cancer Genomics Centre for sequencing on an Illumina HiSeq2500.

treatment_protocol: Intraperitoneal injections of 5x10^6 ID8 cells in 0.2ml PBS were performed on 6-8 week C57BL/6 female mice. Upon animal protocol endpoint, ascites fluid was extracted with a 20 gauge needle fixed to a 10ml syringe with peritoneal cavity intact immediately following euthanization.

tag: cell line

tag: cell type

value: epithelial

tag: genotype

tag: treatment

value: immortalized, untreated

tag: time

value: Fresh necropsy


title: scRNASeq,Trp53_WT,Rep2

value: Murine C57BL/6 ovarian surface epithelium


title: scRNASeq,Trp53_WT,Rep1


title: blood_HUNT_107

description:
HUNT_107
Specimen 107 from the HUNT biobank, sampled on Tempus tubes


title: scRNASeq,Trp53_KO,Rep3


title: scRNASeq,Trp53_KO,Rep1


title: sgHcar1 MC38 cells 20 mM lactate RNA-seq.rep3

city: Shanghai

first: Jiacheng

last: He

address: 500 Dongchuan Road

country: China

institute: East China Normal University

library_source: transcriptomic

data_processing:
Quality control; Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome; We selected Hisat2 as the mapping tool; 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. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level; featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Murine colon adenocarcinoma cells

extract_protocol:
Cells were removed, 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: colon

value: 20 mM lactate for 24 hours


title: scRNASeq,Trp53_KO,Rep2


title: blood_HUNT_105

description:
HUNT_105
Specimen 105 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_103

description:
HUNT_103
Specimen 103 from the HUNT biobank, sampled on Tempus tubes


title: sgHcar1 MC38 cells 20 mM lactate RNA-seq.rep1


title: sgHcar1 MC38 cells 20 mM lactate RNA-seq.rep2


title: blood_HUNT_100

description:
HUNT_100
Specimen 100 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_101

description:
HUNT_101
Specimen 101 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_104

description:
HUNT_104
Specimen 104 from the HUNT biobank, sampled on Tempus tubes


title: blood_HUNT_10

description:
HUNT_10
Specimen 10 from the HUNT biobank, sampled on Tempus tubes


title: sgHcar1 MC38 cells control RNA-seq.rep1

value: PBS


title: blood_HUNT_1

description:
HUNT_1
Specimen 1 from the HUNT biobank, sampled on Tempus tubes

value: peripheral whole blood


title: sgHcar1 MC38 cells control RNA-seq.rep2


title: blood_HUNT_102

description:
HUNT_102
Specimen 102 from the HUNT biobank, sampled on Tempus tubes

value: HUNT


title: sgControl MC38 cells control RNA-seq.rep2


title: sgControl MC38 cells 20 mM lactate RNA-seq.rep3


title: sgControl MC38 cells 20 mM lactate RNA-seq.rep1


title: sgControl MC38 cells control RNA-seq.rep1


title: CBMC_154 [AD014]

type: genomic

city: Tucson

first: Donata

last: Vercelli

state: Arizona

address: 1657 E. Helen St.

country: USA

institute: University of Arizona

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation850 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Probes were removed if: detection P-value were > 0.01 in at least 75% of samples, previously identified as cross-reactive by Pidsley 2016, located on the sex chromosomes, or overlapped common SNPs (MAF > 0.05)
normalization steps: background subtract and controls normalization, SWAN algorithm, and quantile normalization
batch correction (ComBat), latent factor analysis (CorrConf), and adjustment for covariates
M-values, not batch corrected:
processed_matrix_Mvals_n155.csv
M-values, data adjusted for batch, latent factors and covariates:
normalized_matrix_adjBatch-LF-covars_n155.csv

label: Cy5 and Cy3

molecule: genomic DNA

source_name: CBMC

label_protocol: Standard Illumina Protocol

growth_protocol: CBMCs isolated from cord blood using ficoll gradient and fresh frozen for analysis

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

tag: tissue/cell type

value: CBMCs

tag: prenatal immune status

value: high, Q2-4


title: CBMC_153 [AD093]


title: CBMC_151 [AD094]


title: CBMC_152 [AD085]


title: CBMC_149 [AD078]


title: CBMC_150 [AD086]

value: low, Q1


title: CBMC_148 [AD070]


title: CBMC_146 [AD046]


title: CBMC_147 [AD054]


title: sgHcar1 MC38 cells control RNA-seq.rep3

tag: tissue


title: CBMC_145 [AD038]


title: CBMC_144 [AD061]


title: sgControl MC38 cells 20 mM lactate RNA-seq.rep2


title: CBMC_143 [AD053]


title: CBMC_140 [AD063]


title: CBMC_142 [AD045]


title: sgControl MC38 cells control RNA-seq.rep3


title: CBMC_141 [AD029]


title: CBMC_139 [AD055]


title: CBMC_133 [AD111]


title: CBMC_138 [AD015]


title: CBMC_134 [AD119]


title: CBMC_137 [AD007]


title: CBMC_135 [AD127]


title: CBMC_132 [AD103]


title: CBMC_131 [AD010]


title: CBMC_130 [AD089]


title: MV4-11, 24 h, JPX-0750 rep3

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

data_processing:
Initial quality check with FastQC (version 0.11.9).
Quality filtering and trimming with PRINSEQ-lite (version 0.20.4).
Alignment of the high quality reads against the human reference sequence (GRCh38) with STAR (version 2.4.2a).
Post-processing of the alignments with samtools (version 1.4).
Counts per gene were obtained with featureCounts (version 2.0.3).
Normalization and differential gene expression analysis was then done with DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited tsv file includes normalized counts per gene for each sample

growth_protocol: Cells were maintained in RPMI-1640 (Gibco) supplemented with 10% FBS (Biowest), 0.06 g/L penicillin/0.1 g/L streptomycin (Pen/Strep, VWR), and 2 mM L-glutamine (Life Technologies).

extract_protocol:
RNA extraction followed the standard protocol employing the RNeasy Mini Kit (QIAGEN).
RNA libraries for QuantSeq were prepared according to the manufacturer's protocol.

treatment_protocol: Cells were incubated for 24 h with compounds


title: MV4-11, 24 h, JPX-0750 rep1


title: CBMC_129 [AD073]


title: MV4-11, 24 h, JPX-0750 rep2


title: MV4-11, 24 h, JPX-0700 rep3


title: MV4-11, 24 h, JPX-0700 rep1


title: MV4-11, 24 h, DMSO control rep3

value: DMSO


title: CBMC_126 [AD174]


title: CBMC_127 [AD182]


title: CBMC_136 [AD151]


title: CBMC_125 [AD134]


title: CBMC_124 [AD192]


title: CBMC_123 [AD176]


title: Neutrophil, Control,7

city: Birmingham

first: Frances

last: Grudzinska

address: Edgbaston

department: Institute of Inflammation and Ageing

country: United Kingdom

institute: University of Birmingham

data_processing:
Public sever at usegalaxy.org
Sequence reads were trimmed using Cutadapt
Trimmed sequences were mapped to GRCh38/hg38 using RNA STAR
Read count and normalisation were performed using featureCounts
Differential expression was assessed using DESeq2
Assembly: hg38
Supplementary files format and content: tab delimited text file with normalised counts for each sample

source_name: Peripheral blood

extract_protocol:
RNA was isolated using RNAqueous-Micro Total RNA Isolation Kit according to manufacturer's instructions
RNA libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit according to manufacturer's instructions

value: Neutrophil

value: Peripheral blood

value: CONTROL


title: CBMC_122 [AD168]


title: MV4-11, 24 h, DMSO control rep1


title: CBMC_120 [AD220]


title: CBMC_121 [AD205]


title: CBMC_119 [AD204]


title: CBMC_155 [AD030]


title: Neutrophil, Control,6


title: Neutrophil, Control,5


title: Neutrophil, Control,3


title: Neutrophil, Control,4


title: CBMC_128 [AD065]


title: CBMC_118 [AD227]


title: MV4-11, 24 h, JPX-0700 rep2


title: Neutrophil, Control,2


title: CBMC_117 [AD059]


title: CBMC_116 [AD043]


title: CBMC_115 [AD003]


title: Neutrophil, Control,1


title: MV4-11, 24 h, DMSO control rep2


title: Neutrophil,CAP,7

value: CAP


title: Neutrophil,CAP,6


title: Neutrophil,CAP,5


title: Neutrophil,CAP,3


title: CBMC_114 [AD202]


title: Neutrophil,CAP,4


title: CBMC_111 [AD217]


title: CBMC_109 [AD104]


title: Neutrophil,CAP,1


title: CBMC_108 [AD175]


title: CBMC_107 [AD004]


title: CBMC_106 [AD083]


title: CBMC_113 [AD194]


title: CBMC_112 [AD233]


title: CBMC_104 [AD222]


title: CBMC_110 [AD112]


title: CBMC_102 [AD229]


title: CBMC_103 [AD198]


title: Neutrophil,CAP,2


title: ob/ob mouse fat_di-SQ treatment 42days_rep2

city: Ibaraki, Tsukuba

first: Yu

last: Cheng

address: Amakubo

country: Japan

institute: University of Tsukuba

description: Gene expression data from eWAT of ob/ob mouse, with 5µM di-SQ treatment for 42 days

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, mouse; Thermofisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (Thermofisher Scientific).

data_processing:
The raw image data was normalized following the SST-RMA method using the Transcriptome Analysis Console (TAC) software (ver. 4.0, Thermofisher Scientific) (Summarization: SST-RMA, Anova Method: eBays, DABG <0.05, Pos/Neg AUC Threshold: 0.7).
algorithm: RMA (SST-RMA, Transcriptome Analysis Console, version 4)

label: biotin

source_name: eWAT of ob/ob mouse with 5µM di-SQ treatment for 42 days

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol from 100 ng/ uL total RNA

growth_protocol: 6-week-old, male, C57BL/6J (wild type, n=6) and C57BL/6JHamSlc-ob/ob (ob/ob, n=24) mice (Japan SLC, Inc)

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: Squalene was purchased from Tokyo Chemical Industry Co., Ltd.,diethylene glycol oligomer squalene (5µM) were synthesized by National Institute of Advanced Industrial Science and Technology. Mice were housed in approved animal care facilities (21–22°C, constant humidity, reverse 12/12-hour light-dark cycle, with unrestricted access to water and chow food). After a one-week acclimatization period, ob/ob mice were treated with distill water (ob/ob group) or di-SQ (di-SQ group randomly by oral gavage daily morning for 42 days. A group of wild-type mice was added as a baseline for microarray experiment treated with distill water (wild type group) by oral gavage daily morning after a week acclimatization period.

value: eWAT from C57BL/6JHamSlc-ob/ob mice (Japan SLC, Inc)


title: ob/ob mouse fat_di-SQ treatment 42days_rep3


title: CBMC_99 [AD084]


title: CBMC_98 [AD076]


title: wild type mouse fat_No treatment_rep2

description: Gene expression data from eWAT of wild type mouse, with no treatment for 42 days

source_name: eWAT of wild type mouse with no treatment for 42 days

value: eWAT from C57BL/6J mice (Japan SLC, Inc)


title: CBMC_100 [AD092]


title: CBMC_96 [AD052]


title: CBMC_97 [AD068]


title: CBMC_105 [AD230]


title: CBMC_95 [AD044]


title: CBMC_94 [AD036]


title: CBMC_101 [AD221]


title: wild type mouse fat_No treatment_rep1


title: CBMC_92 [AD088]


title: wild type mouse fat_No treatment_rep3


title: CBMC_91 [AD080]


title: ob/ob mouse fat_No treatment_rep1

description: Gene expression data from eWAT of ob/ob mouse, with no treatment for 42 days

source_name: eWAT of ob/ob mouse with no treatment for 42 days


title: ob/ob mouse liver_di-SQ treatment 42days_rep1

description: Gene expression data from liver of ob/ob mouse, with 5µM di-SQ treatment for 42 days

source_name: liver of ob/ob mouse with 5µM di-SQ treatment for 42 days

value: liver from C57BL/6JHamSlc-ob/ob mice (Japan SLC, Inc)


title: CBMC_90 [AD064]


title: ob/ob mouse liver_di-SQ treatment 42days_rep2


title: CBMC_89 [AD056]


title: ob/ob mouse fat_No treatment_rep2


title: Treat3_1

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.27.4 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.3 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.36.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: hg38
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: SCVI 273

growth_protocol: SCVI 273 hiPSCs were cultured on Matrigel-coated general cell culture plates and maintained in E8 basal medium supplemented with E8 supplement (1X) (Life Technology). Daily medium changes and passages were conducted at 70-80% confluency. The differentiation of hiPSCs into cardiomyocytes was executed through the Wnt modulation protocol. For the differentiation of hiPSCs into CMs, on day 0, hiPSCs were subjected to the basal medium RPMI1640 supplemented with B27 (1X) without insulin (B27(INS-)), accompanied by the addition of 6~7 μM CHIR99021 for a duration of 2 days. On Day 2, medium was replaced with B27(INS-) without CHIR99021, and on Day 3 the canonical Wnt/β-Catenin pathway was inhibited through the administration of 2 μM C59 inhibitor to B27(INS-) medium. Subsequent maintenance of B27(INS-) was sustained from Day 5 until Day 7, followed by a transition to RPMI1640 supplemented with B27 supplement (1X) containing insulin (B27(INS+)) on Day 7. Metabolic selection was performed on Day 9, involving the deprivation of D-glucose in B27(INS+) supplemented RPMI1640 medium. HiPSC-CMs were trypsinized at Day 11 using 10X TrypLE at 37 °C for ~30 minutes, whereafter they were replated in replating medium (RPMI1640 supplemented with B27(INS+), 10% FBS, and 1:100 Revitacell (Thermo Fisher)). Hereafter, cells were exposed to downstream experimental conditions.

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 1µg of total RNA was used as input for VaZyme_VAHTS Universal Stranded mRNA-seq - V6 (Vazyme). Sequencing was performed on the NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

treatment_protocol: D12 hiPSC-CMs from the SCVI 273 line were cultured for 7 days under following conditions with RPMI1640 as base medium: B27 supplement (+insulin) (Sample name = WT), B26 supplement (-insulin) (Sample name = Treat 1), B26 supplement (-insulin) and 3μM CHIR99021 (Sample name = Treat 2), B27 supplement (+insulin) and  3μM CHIR99021 (Sample name = Treat 3). For each sample type, three independent biological replicates are collected.

value: SCVI 273

value: hiPSC-CMs

value: B27+ CHIR+


title: Treat2_2

value: B27- CHIR+


title: GD14.5, replicate 4, RNAseq

city: Jinan

first: ling

middle: feng

last: lai

state: Shandong

address: Number 6699, Qingdao road

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Tab-delimited text file includes FPKM values for each Sample.

source_name: pancreatic islet

extract_protocol:
Total RNAs were extracted from the pancreatic islets of virgin and GD14.5 female mouse by using the TRIzol Reagent (Cat# 15596026, Invitrogen).
The extracted RNA samples were enriched with eukaryotic mRNA using magnetic beads with Oligo (dT), followed by terminal repair, poly (A) addition, sequencing junction, and PCR amplification.

value: pancreatic islet

tag: time point

tag: Sex

value: female


title: Treat3_3


title: wild type mouse liver_No treatment_rep3

description: Gene expression data from liver of wild type mouse, with no treatment for 42 days

source_name: liver of wild type mouse with no treatment for 42 days

value: liver from C57BL/6J mice (Japan SLC, Inc)


title: wild type mouse liver_No treatment_rep1


title: ob/ob mouse fat_No treatment_rep3


title: Treat2_3


title: ob/ob mouse liver_No treatment_rep2

description: Gene expression data from liver of ob/ob mouse, with no treatment for 42 days

source_name: liver of ob/ob mouse with no treatment for 42 days


title: ob/ob mouse liver_No treatment_rep3


title: Treat3_2


title: wild type mouse liver_No treatment_rep2


title: ob/ob mouse liver_No treatment_rep1


title: CBMC_93 [AD096]

value: CBMCs

value: high, Q2-4


title: Treat2_1


title: GD14.5, replicate 3, RNAseq


title: ob/ob mouse liver_di-SQ treatment 42days_rep3


title: Treat1_3

value: B27- CHIR -


title: CBMC_86 [AD195]

value: low, Q1


title: Treat1_2


title: ob/ob mouse fat_di-SQ treatment 42days_rep1


title: GD14.5, replicate 2, RNAseq


title: CBMC_88 [AD040]


title: Treat1_1


title: CBMC_87 [AD203]


title: GD14.5, replicate 1, RNAseq


title: WT_2

value: B27+ CHIR-


title: CBMC_84 [AD218]


title: WT_1


title: CBMC_82 [AD232]


title: P17

city: New Haven

first: Andrew

last: Martins

state: Connecticut

address: 100 College Street Rm 1155

department: Immunobiology

institute: Yale School of Medicine

description:
bulk RNAseq from PBMCs of the samples run in CITEseq, used for SNP calling and demuxlet of the CITEseq data
demuxletResults.tar.gz

data_processing:
10x Genomics CellRanger
Data was analyzed using the Seurat R package. Please see manuscript for details and link to code.
Assembly: Hg19
Supplementary files format and content: R data objects: Seurat single cell objects; .csv files of demuxlet and VDJ results

molecule: polyA RNA

source_name: Blood

extract_protocol:
10x Genomics Chromium single cell
10x Genomics 5'

value: Blood

value: Peripheral blood mononuclear cells

tag: age in_years

tag: age

value: 45 years

tag: gender

value: F

tag: condition

value: ctrl


title: CBMC_83 [AD210]


title: P16

value: 5 days

value: M


title: P14

value: 6 years


title: Virgin, replicate 4, RNAseq

value: Virgin


title: P19

value: 23 years


title: P13

value: 5 years


title: CBMC_81 [AD224]


title: P15

description:
Not_included_in_citeseq
bulk RNAseq from PBMCs of the samples run in CITEseq, used for SNP calling and demuxlet of the CITEseq data
demuxletResults.tar.gz

value: 2 years


title: Virgin, replicate 2, RNAseq

value: pancreatic islet

value: female


title: Virgin, replicate 1, RNAseq


title: Virgin, replicate 3, RNAseq


title: CBMC_85 [AD234]

value: CBMCs

value: high, Q2-4


title: Virgin, replicate 5, RNAseq


title: P11

value: 43 years

value: Rag

tag: gene

tag: phenotype

value: CID-G/AI


title: CBMC_79 [AD074]


title: WT_3

value: SCVI 273

value: hiPSC-CMs

value: B27+ CHIR-


title: CBMC_80 [AD090]


title: P18

value: Blood

value: Peripheral blood mononuclear cells

value: 19 years

value: F

value: ctrl


title: CBMC_78 [AD066]


title: P09

value: OS


title: P08

value: 14 mon

value: M

value: SCID


title: SHsiSUV3

city: Guangzhou

first: Meng

last: Li

address: 651 East Dongfeng Road

department: Department of Pediatric Oncology

institute: Sun Yat-sen University Cancer Center

description: expression

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Assembly: hg38
Supplementary files format and content: row counts,tpm values and FPMK values of each sample

source_name: SK-N-SH

growth_protocol: SK-N-SH cell lines were maintained  in MEM supplemented with 10% FBS and 1% penicillin–streptomycin solution, cultured in a 5% CO2 and humidified incubator maintained at 37°C.

extract_protocol:
The total RNA from the cultured cells was extracted with the Trizol reagent (Life Technologies, USA),
The preparation for library construction was referred to protocals of (DNBSEQ) BGI-NGS-JK-RNA-001 A01.

treatment_protocol: SK-N-SH cells were treated with DMSO/chaetocin or transfected with siNC/siSUV39H1

value: SK-N-SH

value: neuroblastoma cell line


title: CBMC_77 [AD058]

value: CBMCs

value: high, Q2-4


title: CBMC_76 [AD050]


title: P12

value: 8 years

value: Rag

value: CID-G/AI


title: P06

value: AS


title: P07

value: Blood

value: 23 years


title: SHsiNC3

description: expression

value: WT

value: siNC


title: CBMC_75 [AD042]


title: P03

value: Peripheral blood mononuclear cells

value: 4 mon


title: P05

value: 8 mon


title: P01

value: 15 mon


title: SHsiSUV1

description: expression


title: CBMC_74 [AD034]


title: SHsiNC1

description: expression


title: P10

value: 9 mon

value: F

value: SCID


title: SHsiNC2

description: expression

value: SK-N-SH

value: neuroblastoma cell line


title: SH50nM3

description: expression

value: chaetocin


title: CBMC_72 [AD184]

value: CBMCs

value: high, Q2-4


title: CBMC_73 [AD190]


title: Set3 mRNA-seq of HEK293T cells with siSRSF3, Replicate1

city: Frederick

last: Gonatopoulos-Pournatzis

state: Maryland

address: 1050 Boyles Street

institute: National Cancer Institute

description: Set3 mRNA-seq: siSRSF3 treated HEK293T samples with siNT2 as control

data_processing:
The sequencing reads from FASTQ files were trimmed for adapters with the tool Cutadapt.
Differential splicing analysis was performed with VAST-TOOLS with default parameters, which uses Bowtie for alignment step to subsequently assess splicing phenotypes.
Assembly: human reference genome (hg38)
Supplementary files format and content: Excel file with separate sheets containing differential splicing analysis results for different samples

growth_protocol: Hek293T cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with high glucose and pyruvate (Gibco #11995073) supplemented with 10% heat-inactivated fetal bovine serum (HI-FBS) (Gibco #16140071) and 1% penicillin-streptomycin (Gibco #15140122). All cells were grown at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted from using the RNeasy Plus Mini Kit (Qiagen #74136).
The library was prepared using the Illumina® Stranded mRNA Prep kit
Next-generation sequencing was performed on an Illumina NovaSeq Xplus 10B platform (200 cycles kit).

treatment_protocol: HEK293T cells were treated with Aurora-A inhibitor (MLN8237) for 24 hours or depleted of endogenous splicing factors by transfecting siRNA (Dharmacon) using Lipofectamine RNAiMax for 48 hours, prior cell lysis for RNA extraction.

value: Human embryonic kidney

value: siRNA


title: Set3 mRNA-seq of HEK293T cells with siNT2, Replicate 2

description: Set3 mRNA-seq: siNT2 treated HEK293T samples as control for all Set3 test samples


title: Set3 mRNA-seq of HEK293T cells with siSRSF3, Replicate2


title: Set3 mRNA-seq of HEK293T cells with siRBM39, Replicate1

description: Set3 mRNA-seq: siRBM39 treated HEK293T samples with siNT2 as control


title: SHsiSUV2

description: expression


title: SH50nM2

description: expression


title: CBMC_71 [AD183]


title: Set2 mRNA-seq of HEK293T cells with siSRSF7, Replicate2

description: Set2 mRNA-seq: siSRSF7 treated HEK293T samples with siNT1 as control


title: Set3 mRNA-seq of HEK293T cells with siNT2, Replicate 1


title: P04

value: Blood

value: Rag

value: OS


title: SH50nM1

description: expression

value: WT


title: CBMC_70 [AD179]


title: P02

value: Peripheral blood mononuclear cells

value: 13 years

value: AS


title: Set2 mRNA-seq of HEK293T cells with siSRSF2, Replicate2

description: Set2 mRNA-seq: siSRSF2 treated HEK293T samples with siNT1 as control


title: SH0nM3

description: expression

value: DMSO


title: CBMC_69 [AD177]


title: Set3 mRNA-seq of HEK293T cells with siRBM39, Replicate2


title: Set2 mRNA-seq of HEK293T cells with siSRSF2, Replicate1


title: Set2 mRNA-seq of HEK293T cells with siSRSF1, Replicate2

description: Set2 mRNA-seq: siSRSF1 treated HEK293T samples with siNT1 as control


title: CBMC_68 [AD113]


title: Set2 mRNA-seq of HEK293T cells with siSF3B5, Replicate2

description: Set2 mRNA-seq: siSF3B5 treated HEK293T samples with siNT1 as control


title: Set2 mRNA-seq of HEK293T cells with siSRSF1, Replicate1


title: CBMC_67 [AD102]


title: SH0nM1

description: expression


title: SH0nM2

description: expression


title: Set2 mRNA-seq of HEK293T cells with siNT1, Replicate2

description: Set2 mRNA-seq: siNT1 treated HEK293T samples as control for all Set2 test samples


title: Set2 mRNA-seq of HEK293T cells with siSF3B5, Replicate1


title: CBMC_66 [AD100]


title: Set1 mRNA-seq of HEK293T cells with MLN8237, Replicate1

description: Set1 mRNA-seq: MLN8237 treated HEK293T samples with DMSO as control

value: Aurora-A inhibition


title: Set1 mRNA-seq of HEK293T cells with DMSO, Replicate2

description: Set1 mRNA-seq: DMSO  treated HEK293T samples as control for Set1 test samples

value: DMSO control


title: Mo(cIgG+IFN_beta)_rep3

city: SUZHOU

first: Xiao-Ming

last: Gao

state: JiangSu

address: No. 199, Ren'ai Road

department: Institute of Biology and Medical Sciences, School of Biology and Basic Medical Sciences

institute: Soochow University

description: Total RNA was polyA enriched, fragmented and converted into a library of Illumina-compatible sequencing templated with Illumina mRNA-seq sample preparation kit according to the manufacturer’s instructions. The cDNA library was size-fractionated in a 1% agarose gel. 200-250 bp fragments were isolated and amplified by PCR with Illumina primers PE1 and PE2 for 15 cycles. The integrity and quality of total RNA and size-selected libraries was evaluated with Bioanalyzer 2100 (Agilent Tech).

data_processing:
Raw data was filtered by SOAPnuke
Reads were mapped to human reference genome hg19 using BWA/Bowtie2 tool
Genes expression level is quantified by RSEM package.
The differentially expression was indentified by R package DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Raw_gene_counts_matrix.csv

source_name: Monocytes

growth_protocol: Freshly isolated CD14+ human blood monocytes were cultured for 24 hrs in RPMI medium in microtiter tissue culture plates pre-coated with IVIG (cIgG), or without (RPMI), at 37°C and 5% CO2.

treatment_protocol: Freshly fractionated monocytes from 3 unrelated healthy donors were cultured for 24 hrs in RPMI-10 medium for preparation of Mo(RPMI) and Mo(cIgG), then half of these cultures were washed and given a 12 hrs IFN-alpha/beta (10 ng/mL) stimulation, resulting in additional groups of Mo(RPMI+IFN-alpha/beta) and Mo(cIgG+IFN-alpha/beta), respectively.

tag: donor

value: donor_id: 3

value: Peripheral blood monuclear cells

tag: agent

value: stimulated with: precultured with IVIG(10 ng/ml) for 24h and IFN-beta for 12hr


title: Set2 mRNA-seq of HEK293T cells with siNT1, Replicate1

tag: cell line

tag: cell type


title: Mo(cIgG+IFN_beta)_rep2

extract_protocol: Total RNA was polyA enriched, fragmented and converted into a library of Illumina-compatible sequencing templated with Illumina mRNA-seq sample preparation kit according to the manufacturer’s instructions. The cDNA library was size-fractionated in a 1% agarose gel. 200-250 bp fragments were isolated and amplified by PCR with Illumina primers PE1 and PE2 for 15 cycles. The integrity and quality of total RNA and size-selected libraries was evaluated with Bioanalyzer 2100 (Agilent Tech).

value: donor_id: 2


title: Set1 mRNA-seq of HEK293T cells with DMSO, Replicate1

tag: treatment


title: CBMC_65 [AD097]

value: CBMCs

value: high, Q2-4


title: Set1 mRNA-seq of HEK293T cells with MLN8237, Replicate2

value: Human embryonic kidney


title: CBMC_64 [AD091]


title: cycling_TIG3T_CBX8_ChIPseq

city: Clayton

first: Evan

last: Healy

state: VIC

address: 23 Innovation Way, Building 77,, Monash University

country: Australia

institute: Monash University

description: Library name: cycling_TIG3T_CBX8_ChIPseq

library_source: genomic

data_processing:
ChIP-RX samples were aligned to the human hg38 and mouse mm10 genomes using bowtie2.
Files were sorted, duplicates removed and indexes using the SAMtools suite
Scale factors were calculated for ChIP-Rx samples and bigwigs (Rx- or RPKM-normalised) were generated using the bamCoverage tool (from the deepTools suite)
Peaks were called using macs2 with a cut-off q-value of 1x10-3 for Polycomb protein ChIPs and 1x10-9 for histone modification ChIPs. Average plots generated using deeptools computeMatrix and plotProfile.
RNA-seq data was aligned to the human genome (hg38) using hisat2. SAM files were then converted to BAM using the SAMtools suite of programs and bigwig files were generated using bamCoverage, as part of the deepTools suite.
Reads were quantified and annotated based on Ensembl 98 hg38 genome using featureCounts. DESeq2 R package was used to determine differential gene expression changes.
Quant-seq fastq files were trimmed and PolyA tails removed using the bbduk tool. Analysis was performed as described for RNA-seq and Volcano plots were generated from DESeq results using the EnhancedVolcano R package.
Assembly: hg38, mm10, dm6
Supplementary files format and content: bigWig files contain ChIP-RX RRPM (or RPKM) scaled librarys. Tab delimited .tsv file contains RNA-Seq raw read counts for Ensemble genenames output from featureCounts.

growth_protocol: TIG3 TERT-immortalised fibroblasts and IMR90 primary fibroblasts were cultuered in DMEM 4.5g/L Glucose with L-Glutamine and Sodium Pyruvate (Lonza) supplemented with 10% FBS (Gibco) and 1% Penicillin-Streptomycin (Gibco)

extract_protocol:
Cells were harvested from dishes using trypsin (Gibco), crosslinked with 1% formaldehyde and isolated nuclei were sonicated prior to incubating with the indicatd antibodies
Libraries were constructed using the NEB library preparation kit as per manufacturers protocol.

treatment_protocol:
To induce quiescence, fibroblasts were cultured in DMEM media (plus 1% Pen/Strep) without FBS for 96-120 hours. Cells were induced to re-enter the cell cycle by culturing cells in DMEM containing 20% FBS (plus 1% Pen/Strep) and harvested 24 hours later
For the treatment of asynchronous fibroblasts with A-395 or UNC6852, the compounds were added to cells in a serum-containing media.
For the treatment of quiescent fibroblasts with A-395 or UNC6852, the cells were cultured in a serum-free media for 48hours to induce quiescence. The compounds were added and cells were maintained in a serum-free media.

value: lung fibroblasts

value: cycling

tag: antibody


title: Set2 mRNA-seq of HEK293T cells with siSRSF7, Replicate1

value: siRNA


title: Mo(cIgG+IFN_alpha)_rep3

value: stimulated with: precultured with IVIG(10 ng/ml) for 24h and IFN-alpha for 12hr


title: CBMC_62 [AD133]

tag: tissue/cell type


title: Mo(cIgG+IFN_alpha)_rep2


title: quiescent_TIG3T_CBX8_ChIPseq

description: Library name: quiescent_TIG3T_CBX8_ChIPseq

value: quiescent


title: Mo(cIgG+IFN_alpha)_rep1

value: donor_id: 1


title: CBMC_61 [AD109]

tag: prenatal immune status

value: low, Q1


title: Co-culture HUVECs and iMSCs Donor 2

city: Aachen

first: Julian

last: Gonzalez-Rubio

address: Forckenbeckstraße 55

department: BioTex

institute: RWTH University Aachen

description: Library name: Sample 5

data_processing:
FASTQ files were generated using the bcl2fastq software (Illumina) and processed using Nextflow 23.10.0 with the nf-core/RNA-seq pipeline (Version 3.12). Lane-level reads were trimmed with Trim Galore 0.6.7 and aligned to the human genome (GRCh39) with STAR 2.7.9a. Gene-level and transcript-level quantification was performed by Salmon v1.10.1 (Patro et al. 2017) and all the posterior analysis was done using custom scripts in R version 4.3.2 with the DESeq2 v.1.32.0 framework. Gene Set Enrichment Analysis (GSEA) was performed using clusterProfiler version 4.6.2, employing hallmark gene sets from MSigDB. Pre-ranked gene lists, generated from differential gene expression analysis, were added to clusterProfiler to identify enriched biological pathways. Results were corrected for multiple testing, and FDR q-values below 0.05 were considered significant.
Assembly: GRCh39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Fibrin co-culture

growth_protocol: The fibrin gels were cultured with EGM MV2 media fro ten days.

extract_protocol:
First, 1 mL TRIzol (Invitrogen, Waltham, USA) was added to the samples and incubated for 5 minutes. The gels were pipetted up and down vigorously until completely dissociated in the TRIzol solution and were then frozen at -20 ºC. On the day of isolation, the samples were thawed, mixed with 0.2 mL of chloroform, and thoroughly shaken. This mixture was separated into two phases by centrifugation for 15 minutes at 12,000 g at 4ºC. The aqueous phase was removed and added to 0.5 mL isopropanol to precipitate the RNA. The mixture was incubated for 10 minutes at 4°C, followed by centrifugation at 12,000 g for 10 minutes at 4°C. A white, gel-like RNA pellet was formed at the bottom of the tube and the supernatant was carefully removed using a pipette. To further purify the RNA, the pellet was resuspended in 1 mL of 75% ethanol. The sample was briefly vortexed and then centrifuged at 7,500 g for 5 minutes at 4°C. The supernatant was discarded and the RNA pellet was air-dried for 10-15 minutes until no liquid was left which was then resuspended in RNase-free water.
The 3’mRNA-Seq libraries were generated using the QuantSeq 3’mRNA-Seq v2 Library Prep Kit FWD with UDIs (Lexogen, Vienna, Austria), following the protocol provided by the manufacturer.

tag: tissue

value: Fibrin co-culture

value: iMSCs + HUVECs


title: Co-culture HUVECs and iMSCs Donor 1

description: Library name: Sample 4


title: Co-culture HUVECs and BMSCs Donor 1

description: Library name: Sample 1

value: BMSCs + HUVECs


title: Co-culture HUVECs and BMSCs Donor 2

description: Library name: Sample 2


title: Co-culture HUVECs and BMSCs Donor 3

description: Library name: Sample 3


title: Mo(RPMI+IFN_beta)_rep3

value: donor_id: 3

value: stimulated with: IFN-beta for 12hr


title: Co-culture HUVECs and iMSCs Donor 3

description: Library name: Sample 6


title: CBMC_60 [AD049]


title: Mo(cIgG+IFN_beta)_rep1

value: Peripheral blood monuclear cells

value: stimulated with: precultured with IVIG(10 ng/ml) for 24h and IFN-beta for 12hr


title: Mo(RPMI+IFN_beta)_rep2

value: donor_id: 2


title: CBMC_63 [AD157]

value: CBMCs

value: high, Q2-4


title: PBMC, Acute Survivor, BSR231.44

city: Oxford

first: Andre

last: Goncalves

address: Old Road Campus, Roosevelt Dr, Headington

department: Department of Paediatrics

institute: University of Oxford

description: RNA from PBMCs was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany), quantified using Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific), and integrity checked in a 2200 TapeStation system using RNA ScreenTape (Agilent Technologies, Santa Clara, CA). The cDNA libraries were constructed using the QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina FWD (Lexogen GmbH, Austria), following the manufacturer's protocol. The concentration and the median size of the libraries were assessed by 2200 TapeStation with a DNA1000 ScreenTape (Agilent). The final pool of libraries was quantified by qPCR using the Kapa Sybr Green qPCR Kit (Roche Diagnostics, Mannheim, Germany) and subjected to a single-end sequencing (75 bp) in a NextSeq 500 Sequencing with NextSeq 500/550 High Output Kit v2.5 (Illumina, San Diego, CA). Raw single-end reads were preprocessed for quality control. Sequencing quality was assessed before and after adapter trimming using the program FastQC (Andrews 2010). The Trimmomatic software version 0.39 (Bolger, Lohse, and Usadel 2014) was used to remove adapters sequence trimming the 5, and 3 ends with a mean quality score below 25 (Phred+33) and discard reads shorter than 36 bp after trimming. We used the parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36. After preprocessing, the high-quality reads were mapped into the reference genome Homo sapiens (version GRCh38) with the bowtie2 program (version 2.2.5) (Langmead and Salzberg 2012). To quantify the gene abundance of the mapped reads in each sample, we used the featureCounts tool from the R/Bioconductor package Rsubread (Liao, Smyth, and Shi 2019) with the following parameters: GTF.featureType = gene, GTF.attrType = gene_id, isPairedEnd = FALSE, minOverlap = value 1, allowMultiOverlap = FALSE, countMultiMappingReads = FALSE. Normalization of the gene counts was performed with counts per million normalization (CPM) and quantile normalization, which accounts for differences in library size.

data_processing:
Raw single-end reads were preprocessed for quality control. Sequencing quality was assessed before and after adapter trimming using the program FastQC (Andrews 2010). The Trimmomatic software version 0.39 (Bolger, Lohse, and Usadel 2014) was used to remove adapters sequence trimming the 5, and 3 ends with a mean quality score below 25 (Phred+33) and discard reads shorter than 36 bp after trimming. We used the parameters LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36. After preprocessing, the high-quality reads were mapped into the reference genome Homo sapiens (version GRCh38) with the bowtie2 program (version 2.2.5) (Langmead and Salzberg 2012). To quantify the gene abundance of the mapped reads in each sample, we used the featureCounts tool from the R/Bioconductor package Rsubread (Liao, Smyth, and Shi 2019) with the following parameters: GTF.featureType = gene, GTF.attrType = gene_id, isPairedEnd = FALSE, minOverlap = value 1, allowMultiOverlap = FALSE, countMultiMappingReads = FALSE. Normalization of the gene counts was performed with counts per million normalization (CPM) and quantile normalization, which accounts for differences in library size.
Assembly: GRCh38

source_name: PBMC

value: PBMC


title: PBMC, Acute Non-survivor, BSR232.58

extract_protocol:
RNA from PBMCs was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany), quantified using Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific), and integrity checked in a 2200 TapeStation system using RNA ScreenTape (Agilent Technologies, Santa Clara, CA).
The cDNA libraries were constructed using the QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina FWD (Lexogen GmbH, Austria), following the manufacturer's protocol. The concentration and the median size of the libraries were assessed by 2200 TapeStation with a DNA1000 ScreenTape (Agilent). The final pool of libraries was quantified by qPCR using the Kapa Sybr Green qPCR Kit (Roche Diagnostics, Mannheim, Germany) and subjected to a single-end sequencing (75 bp) in a NextSeq 500 Sequencing with NextSeq 500/550 High Output Kit v2.5 (Illumina, San Diego, CA).


title: CBMC_58 [AD001]


title: CBMC_59 [AD041]


title: PBMC, Acute Survivor, BSR230.42


title: Mo(RPMI+IFN_beta)_rep1


title: PBMC, Control, BSR233.28

value: Control


title: PBMC, Control, BSR234.29


title: Mo(RPMI+IFN_alpha)_rep3

value: stimulated with: IFN-alpha for 12hr


title: CBMC_57 [AD216]


title: PBMC, Acute Survivor, BSR236.43


title: PBMC, Acute Survivor, BSR235.52


title: Mo(RPMI+IFN_alpha)_rep2


title: PBMC, Control, BSR237.26


title: CBMC_56 [AD208]


title: Mo(RPMI+IFN_alpha)_rep1


title: PBMC, Acute Survivor, BSR240.17


title: CBMC_55 [AD200]


title: PBMC, Acute Non-survivor, BSR244.10


title: PBMC, Control, BSR242.65


title: CBMC_53 [AD223]


title: PBMC, Acute Non-survivor, BSR241.59


title: Mo(RPMI)_rep2

value: stimulated with: none


title: PBMC, Acute Survivor, BSR245.46


title: PBMC, Control, BSR246.24


title: CBMC_54 [AD231]


title: PBMC, Acute Non-survivor, BSR248.60


title: Mo(RPMI)_rep1


title: PBMC, Control, BSR247.66


title: CBMC_52 [AD207]


title: PBMC, Acute Non-survivor, BSR250.2


title: CBMC_51 [AD118]


title: PBMC, Acute Non-survivor, BSR251.16


title: CBMC_50 [AD110]


title: PBMC, Acute Survivor, BSR252.1


title: CBMC_49 [AD145]


title: PBMC, Acute Non-survivor, BSR239.12


title: T89I, loaded 0 hours +GSK205, sample4

city: Saint Louis

first: Farshid

last: Guilak

state: MO

address: 660 S Euclid Ave, Campus Box 8233

department: Dept of Orthopedics

institute: Washington University in St. Louis

description: Library name: 4d10_205_0hr_d

data_processing:
RNA-seq reads were  aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 4.0.3-8 software.
Assembly: GRCh38.101
Supplementary files format and content: .txt file contains raw gene counts for each sample

source_name: Tissue-engineered cartilage

extract_protocol:
Total RNA was isolated using the Qiagen Total RNA Purification Plus Kit (Norgen Biotek, 48400) followed by a DNAse clean-up (Norgen 25720)
Library preparation was performed with 1 to 3ug of total RNA. Ribosomal RNA was removed by a hybridization method using Ribo-ZERO kits (Illumina-EpiCentre). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

value: Tissue-engineered cartilage

value: hiPSC

tag: genotype

value: Loaded, 0 hours + GSK205


title: T89I, loaded 0 hours +GSK205, sample3

description: Library name: 4d10_205_0hr_c


title: T89I, loaded 0 hours +GSK205, sample2

description: Library name: 4d10_205_0hr_b


title: PBMC, Acute Non-survivor, BSR254.62


title: PBMC, Acute Survivor, BSR253.19


title: Mo(RPMI)_rep3


title: T89I, loaded 0 hours +GSK205, sample1

description: Library name: 4d10_205_0hr_a


title: PBMC, Acute Survivor, BSR255.6


title: PBMC, Acute Survivor, BSR256.57


title: CBMC_48 [AD143]


title: PBMC, Control, BSR257.22


title: PBMC, Acute Non-survivor, BSR258.15


title: PBMC, Acute Non-survivor, BSR259.20


title: CBMC_47 [AD124]

value: low, Q1


title: T89I, loaded 24 hours +GSK205, sample4

description: Library name: 4d10_205_24hr_d

value: Loaded, 24 hours + GSK205


title: PBMC, Acute Survivor, BSR260.45


title: T89I, loaded 24 hours +GSK205, sample2

description: Library name: 4d10_205_24hr_b


title: CBMC_46 [AD123]


title: T89I, loaded 24 hours +GSK205, sample3

description: Library name: 4d10_205_24hr_c


title: PBMC, Acute Non-survivor, BSR262.56


title: PBMC, Acute Survivor, BSR261.3


title: T89I, loaded 24 hours +GSK205, sample1

description: Library name: 4d10_205_24hr_a


title: T89I, free-swelling +GSK205, sample4

description: Library name: 4d10_205_fs_d

value: Free-swelling + GSK205


title: PBMC, Control, BSR249.25


title: CBMC_45 [AD120]


title: PBMC, Control, BSR263.23


title: CBMC_44 [AD167]


title: PBMC, Acute Non-survivor, BSR265.4


title: T89I, free-swelling +GSK205, sample3

description: Library name: 4d10_205_fs_c


title: PBMC, Control, BSR266.64


title: PBMC, Acute Survivor, BSR268.8


title: PBMC, Control, BSR269.27


title: CBMC_42 [AD158]


title: PBMC, Acute Survivor, BSR270.7


title: T89I, free-swelling +GSK205, sample2

description: Library name: 4d10_205_fs_b


title: PBMC, Acute Survivor, BSR264.50


title: CBMC_41 [AD152]


title: PBMC, Acute Non-survivor, BSR272.11


title: CBMC_43 [AD164]


title: PBMC, Acute Survivor, BSR273.34


title: PBMC, Control, BSR275.33


title: T89I, loaded 0 hours, sample3

description: Library name: 4d10_veh_0hr_c

value: Loaded, 0 hours


title: T89I, loaded 0 hours, sample4

description: Library name: 4d10_veh_0hr_d


title: PBMC, Control, BSR276.21


title: PBMC, Acute Non-survivor, BSR277.9


title: CBMC_38 [AD031]


title: T89I, loaded 0 hours, sample2

description: Library name: 4d10_veh_0hr_b


title: PBMC, Acute Non-survivor, BSR278.51


title: PBMC, Acute Non-survivor, BSR279.61


title: PBMC, Acute Survivor, BSR280.13


title: CBMC_37 [AD026]


title: CBMC_36 [AD025]


title: T89I, loaded 0 hours, sample1

description: Library name: 4d10_veh_0hr_a


title: PBMC, Control, BSR281.32


title: CBMC_35 [AD024]


title: T89I, loaded 24 hours, sample4

description: Library name: 4d10_veh_24hr_d

value: Loaded, 24 hours


title: PBMC, Acute Non-survivor, BSR283.54


title: PBMC, Acute Non-survivor, BSR282.18


title: T89I, loaded 24 hours, sample3

description: Library name: 4d10_veh_24hr_c


title: CBMC_34 [AD079]


title: PBMC, Acute Survivor, BSR284.48


title: CBMC_40 [AD148]


title: PBMC, Acute Non-survivor, BSR274.55


title: PBMC, Acute Survivor, BSR285.47


title: T89I, free-swelling +GSK205, sample1

description: Library name: 4d10_205_fs_a


title: CBMC_39 [AD146]


title: T89I, loaded 24 hours, sample2

description: Library name: 4d10_veh_24hr_b


title: PBMC, Acute Non-survivor, BSR286.53


title: CBMC_33 [AD077]


title: PBMC, Acute Non-survivor, BSR287.49


title: T89I, loaded 24 hours, sample1

description: Library name: 4d10_veh_24hr_a


title: AS_A395_R3_144h_Quantseq

description: quantseqcounts.tsv

data_processing:
ChIP-RX samples were aligned to the human hg38 and mouse mm10 genomes using bowtie2.
Files were sorted, duplicates removed and indexes using the SAMtools suite
Scale factors were calculated for ChIP-Rx samples and bigwigs (Rx- or RPKM-normalised) were generated using the bamCoverage tool (from the deepTools suite)
Peaks were called using macs2 with a cut-off q-value of 1x10-3 for Polycomb protein ChIPs and 1x10-9 for histone modification ChIPs. Average plots generated using deeptools computeMatrix and plotProfile.
RNA-seq data was aligned to the human genome (hg38) using hisat2. SAM files were then converted to BAM using the SAMtools suite of programs and bigwig files were generated using bamCoverage, as part of the deepTools suite.
Reads were quantified and annotated based on Ensembl 98 hg38 genome using featureCounts. DESeq2 R package was used to determine differential gene expression changes.
Quant-seq fastq files were trimmed and PolyA tails removed using the bbduk tool. Analysis was performed as described for RNA-seq and Volcano plots were generated from DESeq results using the EnhancedVolcano R package.
Assembly: hg38 & mm10
Supplementary files format and content: bigWig files contain ChIP-RX RRPM (or RPKM) scaled librarys. Tab delimited .tsv file contains RNA-Seq or Quant-seq raw read counts for Ensemble genenames/geneids output from featureCounts.

source_name: TIG3 TERT-immortalised fibroblasts

value: Asynchronous TIG3 TERT-immortalised fibroblasts treated with A-395 for 144 hours

value: lung fibroblasts

tag: chip antibody


title: AS_A395_R2_144h_Quantseq

description: quantseqcounts.tsv


title: T89I, free-swelling, sample4

description: Library name: 4d10_veh_fs_d

value: Free-swelling


title: CBMC_32 [AD075]

source_name: CBMC

value: CBMCs


title: CBMC_31 [AD071]

value: high, Q2-4


title: AS_A395_R1_144h_Quantseq

description: quantseqcounts.tsv


title: AS_DMSO_R3_144h_Quantseq

description: quantseqcounts.tsv

value: Asynchronous TIG3 TERT-immortalised fibroblasts treated with DMSO for 144 hours


title: T89I, free-swelling, sample3

description: Library name: 4d10_veh_fs_c


title: AS_DMSO_R1_144h_Quantseq

description: quantseqcounts.tsv


title: T89I, free-swelling, sample2

description: Library name: 4d10_veh_fs_b


title: CBMC_29 [AD051]


title: CBMC_30 [AD067]


title: AS_DMSO_R2_144h_Quantseq

description: quantseqcounts.tsv


title: quiescent_A395_R2_144h_Quantseq

description: quantseqcounts.tsv

value: quiescent TIG3 TERT-immortalised fibroblasts treated with A395 for 144 hours


title: T89I, free-swelling, sample1

description: Library name: 4d10_veh_fs_a


title: quiescent_A395_R3_144h_Quantseq

description: quantseqcounts.tsv


title: CBMC_27 [AD016]


title: V620I, loaded 0 hours +GSK205, sample4

description: Library name: 2a8_205_0hr_d


title: quiescent_DMSO_R3_144h_Quantseq

description: quantseqcounts.tsv

value: quiescent TIG3 TERT-immortalised fibroblasts treated with DMSO for 144 hours


title: CBMC_28 [AD018]


title: V620I, loaded 0 hours +GSK205, sample3

description: Library name: 2a8_205_0hr_c


title: quiescent_A395_R1_144h_Quantseq

description: quantseqcounts.tsv


title: quiescent_DMSO_R2_144h_Quantseq

description: quantseqcounts.tsv


title: quiescent_DMSO_R1_144h_Quantseq

description: quantseqcounts.tsv


title: quiescent_Rep2_RNAseq

description: rnaseqcounts.tsv

value: quiescent TIG3 TERT-immortalised fibroblasts


title: CBMC_25 [AD008]


title: quiescent_Rep1_RNAseq

description: rnaseqcounts.tsv


title: V620I, loaded 0 hours +GSK205, sample1

description: Library name: 2a8_205_0hr_a

value: Tissue-engineered cartilage


title: quiescent_IMR90_INPUT

source_name: IMR90 primary fibroblasts

value: quiescent IMR90 fibroblasts


title: cycling_IMR90_INPUT

value: cycling IMR90 fibroblasts


title: CBMC_24 [AD186]


title: V620I, loaded 24 hours +GSK205, sample4

description: Library name: 2a8_205_24hr_d

value: hiPSC


title: CBMC_23 [AD178]

value: low, Q1


title: CBMC_22 [AD170]


title: cycling_IMR90_H3K27me3_ChIPseq


title: PBMC, Acute Survivor, BSR271.5

value: PBMC


title: quiescent_IMR90_H3K27me1_ChIPseq


title: V620I, loaded 24 hours +GSK205, sample1

description: Library name: 2a8_205_24hr_a

value: Loaded, 24 hours + GSK205


title: CBMC_21 [AD154]


title: cycling_Rep2_RNAseq

description: rnaseqcounts.tsv

value: cycling TIG3 TERT-immortalised fibroblasts


title: CBMC_20 [AD138]


title: quiescent_IMR90_H3K27me2_ChIPseq


title: quiescent_TIG3T_INPUT


title: cycling_Rep1_RNAseq

description: rnaseqcounts.tsv


title: quiescent_IMR90_H3K27me3_ChIPseq


title: V620I, loaded 0 hours +GSK205, sample2

description: Library name: 2a8_205_0hr_b

value: Loaded, 0 hours + GSK205


title: V620I, free-swelling +GSK205, sample4

description: Library name: 2a8_205_fs_d

value: Free-swelling + GSK205


title: V620I, free-swelling +GSK205, sample3

description: Library name: 2a8_205_fs_c


title: cycling_TIG3T_INPUT

value: lung fibroblasts


title: cycling_IMR90_H3K27me2_ChIPseq


title: CBMC_19 [AD116]

value: CBMCs


title: quiescent_UNC6852_TIG3T_H3K27me3_ChIPRx

description: Mus musculus spike-in

value: quiescent TIG3 TERT-immortalised fibroblasts treated with UNC6852 for 72 hours


title: quiescent_DMSO_TIG3T_H3K27me3_ChIPRx

description: Mus musculus spike-in

value: quiescent TIG3 TERT-immortalised fibroblasts treated with DMSO for 72 hours


title: V620I, free-swelling +GSK205, sample2

description: Library name: 2a8_205_fs_b


title: CBMC_26 [AD009]

value: high, Q2-4


title: quiescent_UNC6852_TIG3T_CBX7_ChIPRx

description: Mus musculus spike-in


title: cycling_IMR90_H3K27me1_ChIPseq


title: V620I, loaded 24 hours +GSK205, sample3

description: Library name: 2a8_205_24hr_c


title: quiescent_UNC6852_TIG3T_EED_ChIPRx

description: Mus musculus spike-in

value: EED


title: CBMC_18 [AD187]


title: V620I, free-swelling +GSK205, sample1

description: Library name: 2a8_205_fs_a


title: quiescent_DMSO_TIG3T_EED_ChIPRx

description: Mus musculus spike-in


title: cycling_TIG3T_H2AK119ub1_ChIPRx

description: Mus musculus spike-in


title: V620I, loaded 0 hours, sample4

description: Library name: 2a8_veh_0hr_d

value: Loaded, 0 hours


title: CBMC_15 [AD114]


title: V620I, loaded 0 hours, sample3

description: Library name: 2a8_veh_0hr_c

value: Tissue-engineered cartilage


title: cycling_TIG3T_CBX7_ChIPRx

description: Mus musculus spike-in


title: CBMC_14 [AD106]


title: cycling_TIG3T_EED_ChIPRx

description: Mus musculus spike-in


title: quiescent_TIG3T_H2AK119ub1_ChIPRx

description: Mus musculus spike-in

value: quiescent TIG3 TERT-immortalised fibroblasts


title: V620I, loaded 0 hours, sample2

description: Library name: 2a8_veh_0hr_b


title: cycling_TIG3T_PHC1_ChIPRx

description: Mus musculus spike-in


title: V620I, loaded 0 hours, sample1

description: Library name: 2a8_veh_0hr_a


title: quiescent_TIG3T_PHC1_ChIPRx

description: Mus musculus spike-in


title: CBMC_13 [AD185]


title: cycling_TIG3T_EZH2_ChIPRx

description: Mus musculus spike-in


title: quiescent_TIG3T_EED_ChIPRx

description: Mus musculus spike-in


title: V620I, loaded 24 hours, sample3

description: Library name: 2a8_veh_24hr_c

value: Loaded, 24 hours


title: V620I, loaded 24 hours, sample4

description: Library name: 2a8_veh_24hr_d

value: hiPSC


title: CBMC_11 [AD161]


title: CBMC_17 [AD171]

value: low, Q1


title: quiescent_TIG3T_EZH2_ChIPRx

description: Mus musculus spike-in


title: Cigarette smoke, Mouse lung, Day28, MWCNT, replicate 3

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression at day 28 post-instillation in 80 µg/mouse MWCNT-exposed mouse lung, with cigarette smoke exposure.

hyb_protocol: Each labeled cRNA probe was used separately for hybridization to a 4×44 K Whole Mouse Genome Microarray (G2519F#26655; Agilent Technologies) at 65 °C for 17 h.

scan_protocol: Hybridized microarray slides were washed according to the manufacturer’s instructions and scanned with a DNA Microarray Scanner (Agilent, G2505C) at 5 μm resolution.

data_processing:
The scanned images were analyzed numerically using Agilent Feature Extraction Software, version 12.0.3.1.
log2 average normalized signal intensity

label_protocol: Cyanine-3-labeled cRNA was prepared from RNA using a Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer’s instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop 2000 spectrophotometer.

growth_protocol: The mice were housed in polycarbonate cages under controlled environmental conditions (temperature: 20–26 °C, humidity: 30–70%) with ad libitum access to a chow diet. After a one-week acclimatization period, 90 nine-week-old female C57BL/6JJcl mice were divided into two groups: a mainstream cigarette smoke (CS) exposure group for chronic obstructive pulmonary disease (COPD) modeling and a no-smoke control (NSC) group.

extract_protocol: Blood-perfused rat right lungs (n = 4 per group per time point) were homogenized using QIAzol lysis reagent with a Tissue Ruptor (Qiagen, Tokyo, Japan). Total RNA from the homogenates was extracted using the RNeasy Midi kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: The COPD model mice were exposed to mainstream cigarette smoke generated from commercial cigarettes using a Tobacco Smoke Inhalation Experimental Apparatus. The smoke concentration was maintained at 5%, with exposure sessions lasting 60 minutes per day, 5 days per week, for 13 weeks. NSC mice were housed under the same conditions but without smoke exposure.  After 13 weeks, nine mice from each group (NSC and COPD model) underwent necropsy, while the remaining 36 mice received intratracheal instillation with either CNFs or MWCNTs, or their respective vehicle solutions (V1, V2). Mice were anesthetized with isoflurane and received a single intratracheal instillation of 40 µL of test solution (80 µg/mouse) using a feeding needle.  Lungs were excised from animals at Day 0 and Day 28 post-instillation for microarray analysis to assess the transcriptional impact of CNFs and MWCNTs.

value: Mouse lung

tag: treatment 1

value: Cigarette smoke

tag: treatment 2

value: MWCNT

tag: time


title: quiescent_TIG3T_EZH1_ChIPRx

description: Mus musculus spike-in

data_processing:
ChIP-RX samples were aligned to the human hg38 and mouse mm10 genomes using bowtie2.
Files were sorted, duplicuates removed and indexes using the SAMtools suite
Assembly: hg38 & mm10


title: quiescent_DMSO_TIG3T_CBX7_ChIPRx

description: Mus musculus spike-in


title: CBMC_16 [AD163]

data_processing:
Probes were removed if: detection P-value were > 0.01 in at least 75% of samples, previously identified as cross-reactive by Pidsley 2016, located on the sex chromosomes, or overlapped common SNPs (MAF > 0.05)
normalization steps: background subtract and controls normalization, SWAN algorithm, and quantile normalization
batch correction (ComBat), latent factor analysis (CorrConf), and adjustment for covariates
M-values, not batch corrected:
processed_matrix_Mvals_n155.csv
M-values, data adjusted for batch, latent factors and covariates:
normalized_matrix_adjBatch-LF-covars_n155.csv


title: V620I, loaded 24 hours, sample1

description: Library name: 2a8_veh_24hr_a


title: Cigarette smoke, Mouse lung, Day28, MWCNT, replicate 2


title: V620I, loaded 24 hours, sample2

description: Library name: 2a8_veh_24hr_b


title: cycling_TIG3T_EZH1_ChIPRx

description: Mus musculus spike-in

value: cycling TIG3 TERT-immortalised fibroblasts


title: CBMC_8 [AD188]


title: Cigarette smoke, Mouse lung, Day28, Control for MWCNT, replicate 3

description: Gene expression at day 28 post-instillation in mouse lung as a control for MWCNT, with cigarette smoke exposure.

value: Vehicle control for MWCNT


title: V620I, free-swelling, sample3

description: Library name: 2a8_veh_fs_c

value: Free-swelling


title: Cigarette smoke, Mouse lung, Day28, Control for MWCNT, replicate 1


title: quiescent_TIG3T_CBX7_ChIPRx

description: Mus musculus spike-in

value: lung fibroblasts


title: Cigarette smoke, Mouse lung, Day28, Control for MWCNT, replicate 4


title: CBMC_9 [AD129]

value: CBMCs


title: CBMC_12 [AD169]


title: CBMC_6 [AD172]


title: V620I, free-swelling, sample4

description: Library name: 2a8_veh_fs_d


title: Cigarette smoke, Mouse lung, Day28, CNF, replicate 4

description: Gene expression at day 28 post-instillation in 80 µg/mouse CNF-exposed mouse lung, with cigarette smoke exposure.

value: CNF


title: Cigarette smoke, Mouse lung, Day28, MWCNT, replicate 1


title: Cigarette smoke, Mouse lung, Day28, Control for MWCNT, replicate 2


title: CBMC_7 [AD180]


title: Cigarette smoke, Mouse lung, Day28, CNF, replicate 3


title: Cigarette smoke, Mouse lung, Day28, CNF, replicate 2


title: V620I, free-swelling, sample2

description: Library name: 2a8_veh_fs_b


title: Cigarette smoke, Mouse lung, Day28, MWCNT, replicate 4


title: CBMC_10 [AD137]

value: high, Q2-4


title: Cigarette smoke, Mouse lung, Day28, Control for CNF, replicate 3

description: Gene expression at day 28 post-instillation in mouse lung as a control for CNF, with cigarette smoke exposure.

value: Vehicle control for CNF


title: Cigarette smoke, Mouse lung, Day28, Control for CNF, replicate 4


title: CBMC_4 [AD140]


title: Wildtype, loaded 0 hours +GSK205, sample4

description: Library name: bjff_205_0hr_d

value: Wildtype

value: Loaded, 0 hours + GSK205


title: CBMC_3 [AD155]


title: Cigarette smoke, Mouse lung, Day28, Control for CNF, replicate 2


title: Wildtype, loaded 0 hours +GSK205, sample3

description: Library name: bjff_205_0hr_c

value: Tissue-engineered cartilage


title: CBMC_5 [AD156]


title: No smoke control, Mouse lung, Day28, MWCNT, replicate 4

description: Gene expression at day 28 post-instillation in 80 µg/mouse MWCNT-exposed mouse lung, without smoke exposure.

value: No smoke


title: Wildtype, loaded 0 hours +GSK205, sample1

description: Library name: bjff_205_0hr_a

value: hiPSC


title: CBMC_1 [AD099]

value: low, Q1


title: Cigarette smoke, Mouse lung, Day28, CNF, replicate 1

value: Mouse lung


title: No smoke control, Mouse lung, Day28, Control for MWCNT, replicate 4

description: Gene expression at day 28 post-instillation in mouse lung as a control for MWCNT, without smoke exposure.


title: V620I, free-swelling, sample1

description: Library name: 2a8_veh_fs_a


title: Wildtype, loaded 24 hours +GSK205, sample3

description: Library name: bjff_205_24hr_c

value: Loaded, 24 hours + GSK205


title: CBMC_2 [AD107]


title: No smoke control, Mouse lung, Day28, MWCNT, replicate 2

value: MWCNT


title: No smoke control, Mouse lung, Day28, MWCNT, replicate 1


title: No smoke control, Mouse lung, Day28, MWCNT, replicate 3


title: Wildtype, loaded 24 hours +GSK205, sample4

description: Library name: bjff_205_24hr_d


title: No smoke control, Mouse lung, Day28, Control for MWCNT, replicate 2


title: Cigarette smoke, Mouse lung, Day28, Control for CNF, replicate 1

value: Cigarette smoke


title: Vcor BAA-450 wild-type RNA, replicate 3

city: Bloomington

first: Julia

last: van Kessel

state: IN

address: 1001 E 3rd Street, Biology Building

department: Biology

institute: Indiana University

data_processing:
The raw RNA-seq reads were cleaned using Trimmomatic version 0.38 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases. Reads shorter than 20 bases post-trimming were excluded. (parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20)
The cleaned reads were aligned to the corresponding genome reference (Vibrio coralliilyticus ATCC BAA-450 reference from the assembly GCF_000176135.1_ASM17613v1 for BAA-450 reads and Vibrio coralliilyticus OCN008 reference from the assembly GCF_011212705.1_ASM1121270v1 for OCN008 reads) using bowtie2 version 2.4.2 (Langmead et al. 2012).
Individual gene expression was quantified by counting the number reads mapping to each of the annotated genes using featureCounts tool of subread package (version 2.0.0) (Liao et al. 2014). Those reads that mapped to antisense strand, or mapped to multiple regions on the genome or those reads that overlapped with multiple genes were excluded. (parameters: -s 2 -p -B -C)
Assembly: Vibrio coralliilyticus ATCC BAA-450 reference from the assembly GCF_000176135.1_ASM17613v1 for BAA-450 reads and Vibrio coralliilyticus OCN008 reference from the assembly GCF_011212705.1_ASM1121270v1 for OCN008 reads
Supplementary files format and content: Tab deliminted text files containing counts of reads overlapping with coding regions of the genes.

organism: Vibrio coralliilyticus

source_name: Bacterial

growth_protocol: All Vcor samples grew in sterile LB marine (LM) medium (Lysogeny broth supplemented with 10 g NaCl L-1 and dissolved in purified water) in a shaking incubator (275 RPM) at 30°C. Samples were backdiluted 1:1,000 and grown to an OD600=1.5, which corresponds to high cell density in Vibrio. Once grown, cells pellets were collected, freezed in liquid nitrogen, and stored in a -80°C freezer until RNA extraction.

extract_protocol: Thawed pellets resuspended in TRIZOL (Invitrogen; 5 min. incubation) and chloroform (5 min. incubation) then pelleted at 4°C.Trasfered upper aqueous phase to new tube and mixed with isopropanol (incubated 10 min.). Centrifuged (max speed; supernatant discarded) and resuspended pellet in EtOH (75%). Centrifuged (supernatant discarded) and pellet resuspended in RNA-free water then incubated 15 min. at 56°C. Samples DNase treated (Ambion DNase-free kit protocol, included DNaseI inactivation step) and cleaned via QIAGEN RNeasy kit. Extracted RNA stored in -80°C freezer.

treatment_protocol: Samples originate from two sets Vibrio coralliilyticus strains, OCN008 and BAA-450, and two genotypes, wild-type (reference sample) and VcpR-null. Each sample set (i.e. OCN008 wild-type, OCN008::ΔvcpR, BAA-450 wild-type, BAA-450::ΔvcpR) received the same treatment.

tag: cell line/strain

value: wild-type

tag: condition

value: Bacterial


title: Wildtype, loaded 0 hours +GSK205, sample2

description: Library name: bjff_205_0hr_b


title: No smoke control, Mouse lung, Day28, CNF, replicate 2

description: Gene expression at day 28 post-instillation in 80 µg/mouse CNF-exposed mouse lung, without smoke exposure.


title: No smoke control, Mouse lung, Day28, Control for MWCNT, replicate 1

value: Vehicle control for MWCNT


title: Wildtype, loaded 24 hours +GSK205, sample1

description: Library name: bjff_205_24hr_a


title: Vcor BAA-450 wild-type RNA, replicate 2


title: Wildtype, loaded 24 hours +GSK205, sample2

description: Library name: bjff_205_24hr_b


title: Vcor BAA-450 ΔvcpR RNA, replicate 2

value: delta-vcpR


title: No smoke control, Mouse lung, Day28, Control for MWCNT, replicate 3


title: No smoke control, Mouse lung, Day28, CNF, replicate 4

value: CNF


title: No smoke control, Mouse lung, Day28, Control for CNF, replicate 3

description: Gene expression at day 28 post-instillation in mouse lung as a control for CNF, without smoke exposure.


title: No smoke control, Mouse lung, Day28, Control for CNF, replicate 1


title: Vcor BAA-450 wild-type RNA, replicate 1


title: No smoke control, Mouse lung, Day28, CNF, replicate 3


title: Cigarette smoke, Mouse lung, Day00, Day0 control, replicate 3

description: Gene expression in mouse lung tissue at day 0 post-instillation, with cigarette smoke exposure but no additional treatment.

value: No treatment


title: Cigarette smoke, Mouse lung, Day00, Day0 control, replicate 2


title: Wildtype, free-swelling +GSK205, sample1

description: Library name: bjff_205_fs_a

value: Free-swelling + GSK205


title: Cigarette smoke, Mouse lung, Day00, Day0 control, replicate 1


title: No smoke control, Mouse lung, Day00, Day0 control, replicate 4

description: Gene expression in mouse lung tissue at day 0 post-instillation, without smoke exposure or treatment.


title: Vcor OCN008 wild-type RNA, replicate 2


title: No smoke control, Mouse lung, Day28, CNF, replicate 1


title: Vcor OCN008 wild-type RNA, replicate 1


title: Wildtype, free-swelling +GSK205, sample4

description: Library name: bjff_205_fs_d

value: Wildtype


title: Wildtype, free-swelling +GSK205, sample3

description: Library name: bjff_205_fs_c


title: No smoke control, Mouse lung, Day28, Control for CNF, replicate 2

value: Vehicle control for CNF


title: Vcor BAA-450 ΔvcpR RNA, replicate 1


title: Wildtype, loaded 0 hours, sample2

description: Library name: bjff_veh_0hr_b

value: Tissue-engineered cartilage

value: Loaded, 0 hours


title: Vcor OCN008 ΔvcpR RNA, replicate 2


title: Wildtype, free-swelling +GSK205, sample2

description: Library name: bjff_205_fs_b

value: hiPSC


title: Vcor OCN008 wild-type RNA, replicate 3


title: Wildtype, loaded 0 hours, sample4

description: Library name: bjff_veh_0hr_d


title: Wildtype, loaded 0 hours, sample1

description: Library name: bjff_veh_0hr_a


title: No smoke control, Mouse lung, Day00, Day0 control, replicate 3

value: No smoke


title: No smoke control, Mouse lung, Day28, Control for CNF, replicate 4

value: Mouse lung


title: Vcor BAA-450 ΔvcpR RNA, replicate 3


title: No smoke control, Mouse lung, Day00, Day0 control, replicate 2


title: Wildtype, loaded 0 hours, sample3

description: Library name: bjff_veh_0hr_c


title: Vcor OCN008 ΔvcpR RNA, replicate 3


title: chimeric_human_filtered_oligodendroglia_MET_3

city: Edinburgh

first: Nadine

last: Bestard-Cuche

address: 5 Little France Drive

institute: University of Edinburgh

description: 10X Genomics

data_processing:
The alignment to the reference genome, demultiplexing, barcoded processing, gene counting and cell calling were made using the Cell Ranger software (v5.0.0).
Assembly: GRCh38 2020-A, mm10, GRCh38-and-mm10-2020-A concatenation
Supplementary files format and content: CellRanger output (h5 format)
Supplementary files format and content: metadata in CSV files, with for each cell (on the rows) the following information (columns): nCount_originalexp nFeature_originalexp Barcode Project Treatment animalID Chemistry sum detected subsets_mt_sum subsets_mt_detected subsets_mt_percent total outlier subsets_mt_percent.1 sizeFactor scDblFinder.sample scDblFinder.class scDblFinder.score scDblFinder.weighted scDblFinder.cxds_score SampleID Sample chip S.Score G2M.Score Phase paper_annot

source_name: transplanted cells

extract_protocol:
To harvest cells for single-cell RNAseq the monolayer oligodendrocytes were incubated in accutase solution for 5min at 37°C. Cells were collected into centrifuges 400×g for 5 min. The pellet was resuspended in Oligo Base medium for counting. The cell suspension was placed on ice when possible. The cortical brain organoids were dissociated using the Worthington Papain dissociation system, with extended sphere incubation in papain/DNase to 45min. Ten organoids were pulled together per sample. Cells from chimeric animal tissue were collected as previously described in (Neumann et al., 2019), with noted variations. In brief, animals were perfused using ice-cold HBSS+/+ (14025092, Thermo Fisher Scientific) and a brain matrix was used to excise the cc into HBSS-/- (12549069, Thermo Fisher Scientific) supplemented with 0.4 Units of RNase inhibitors (N808011, Life Technologies), where the tissue was mechanically dissociated with a scalpel. From this point onwards, 0.2 Units of RNase inhibitors were used at each step. The tissue was washed twice with HBSS-/-, centrifuged for 5min at 1,500rpm, resuspended in 0.62 units Research Grade Liberase DH (LIBDH-RO, Roche) and incubated for 40min at 37°C with gentle rocking. 2ml of MEM (12492013, Thermo Fisher Scientific) containing 0.5% BSA, 500 Units bovine pancreas DNase (DN25, Sigma-Aldrich) & 0.5ml FBS were added, and the tissue was mechanically triturated with a P1000 pipette and strained through a 70μm mesh. Tubes containing tissue were filled to full volume with MEM containing 0.5% BSA, centrifuged for 10min at 1,500rpm and resuspended into 0.2% BSA. Two cc were pulled together per sample. Live cells were sorted with LSRFortessa analyser (BIO-RAD) at the FACS facility at the Centre for Regenerative Medicine by Fiona Rossi and mixed human and mouse cells were centrifuged and resuspended in 100μl of 0.2% BSA.
Cell suspensions were processed by the Chromium Controller (10X Genomics) and barcoded libraries constructed using the Chromium Next GEM Single Cell 3’ v3.1 kit (PN-1000121) following manufacturer’s instructions. Samples were sequenced with Illumina NovaSeq6000.

value: transplanted cells

value: metformin


title: HepG2 25-HC addback rep10

city: Oakland

first: Marisa

last: Medina

state: CA

address: 5700 Martin Luther King Jr. Way

department: Pediatrics

institute: UCSF

data_processing:
Aligned using 2-pass alignment with STAR
Duplicate sequence fragments removed using Picard MarkDuplicates
Quantification of annotated genes using FeatureCounts
Library size adjustment, variance stabilization, and differential expression analysis in DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Raw gene counts; Library size adjusted and variance stabilized gene expression levels

source_name: HepG2 cells

growth_protocol: The HepG2 cell line was maintained under standard conditions and grown in Eagle’s minimum essential medium supplemented with 10% fetal bovine serum prior to experiment initiation.

extract_protocol:
RNA was extracted using the Qiagen RNAeasy mini-kit with QIAshredders.
Illumina polyA-selected, strand-specific (dUTP second strand marking protocol), paired-end library preparation

treatment_protocol: Some cell aliquots were maintained in FBS-containing media for 24 or 48 hours, while others were exposed to simvastatin in FBS or lipoprotein deficient serum (LPDS) containing media for 24 or 48 hours. Finally, after 24 hr statin+LPDS, LDL-cholesterol or 25-hydroxycholesterol was added to the media for an additional 24 hours.

tag: treatments

value: 10% LPDS + 2 µM simvastatin followed by 1 µg/ml 25-hydroxycholesterol addback

tag: duration

value: 24 hr + 24 hr addback


title: HepG2 24 hr FBS rep10

value: 10% FBS

value: 24 hr


title: Wildtype, loaded 24 hours, sample3

description: Library name: bjff_veh_24hr_c

value: Loaded, 24 hours


title: HepG2 LDL-C addback rep10

value: 10% LPDS + 2 µM simvastatin followed by 50 µg/ml LDL-cholesterol addback


title: chimeric_human_filtered_oligodendroglia_MET_2

description: 10X Genomics


title: HepG2 LDL-C addback rep9


title: HepG2 48 hr LPDS+statin rep10

value: 10% LPDS + 2 µM simvastatin

value: 48 hr


title: chimeric_human_filtered_oligodendroglia_MET_1

description: 10X Genomics


title: Vcor OCN008 ΔvcpR RNA, replicate 1

value: delta-vcpR

value: Bacterial


title: Cigarette smoke, Mouse lung, Day00, Day0 control, replicate 4

value: Cigarette smoke

value: No treatment


title: HepG2 48 hr LPDS+statin rep9


title: HepG2 48 hr FBS rep10


title: Wildtype, loaded 24 hours, sample4

description: Library name: bjff_veh_24hr_d

value: Tissue-engineered cartilage

value: hiPSC

value: Wildtype


title: HepG2 24 hr LPDS+statin rep10


title: chimeric_human_filtered_oligodendroglia_CTRL_2

description: 10X Genomics

value: transplanted cells

value: vehicle (ddH2O)


title: Wildtype, free-swelling, sample3

description: Library name: bjff_veh_fs_c

value: Free-swelling


title: HepG2 24 hr FBS rep9


title: chimeric_human_filtered_oligodendroglia_CTRL_1

description: 10X Genomics


title: Wildtype, loaded 24 hours, sample2

description: Library name: bjff_veh_24hr_b


title: Wildtype, loaded 24 hours, sample1

description: Library name: bjff_veh_24hr_a


title: HepG2 25-HC addback rep8

value: 10% LPDS + 2 µM simvastatin followed by 1 µg/ml 25-hydroxycholesterol addback

value: 24 hr + 24 hr addback


title: HepG2 24 hr FBS+statin rep9

value: 10% FBS + 2 µM simvastatin

value: 24 hr


title: No smoke control, Mouse lung, Day00, Day0 control, replicate 1

value: Mouse lung

value: No smoke


title: HepG2 48 hr FBS rep9

value: 10% FBS

value: 48 hr


title: Wildtype, free-swelling, sample4

description: Library name: bjff_veh_fs_d


title: HepG2 24 hr LPDS+statin rep9

value: 10% LPDS + 2 µM simvastatin


title: HepG2 LDL-C addback rep8

value: 10% LPDS + 2 µM simvastatin followed by 50 µg/ml LDL-cholesterol addback


title: HepG2 48 hr LPDS+statin rep8


title: HepG2 24 hr FBS+statin rep8


title: HepG2 48 hr FBS rep8


title: Wildtype, free-swelling, sample1

description: Library name: bjff_veh_fs_a


title: HepG2 25-HC addback rep9


title: HepG2 24 hr LPDS+statin rep8


title: cortical_organoid_oligodendroglia_2

description: 10X Genomics

source_name: organoid

value: organoid


title: cortical_organoid_oligodendroglia_4

description: 10X Genomics


title: Wildtype, free-swelling, sample2

description: Library name: bjff_veh_fs_b

value: Tissue-engineered cartilage


title: HepG2 24 hr FBS+statin rep7


title: cortical_organoid_oligodendroglia_3

description: 10X Genomics


title: 44C_4

city: Kunming

first: Jingming

last: Xie

state: Yunnan

address: 374# Dianmian Road

department: Orthopedics

institute: The Second Affiliated Hospital of Kunming Medical University

data_processing:
Quality control  Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome  Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Novel transcripts prediction The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: cell line

growth_protocol: ATDC5 cells inoculated in a medium consisting of 90% high sugar DMEM and 10% FBS, and incubated at 37°C in 95% air and 5% CO2.

extract_protocol:
Total RNA from ATDC5 cells treated with different temperatures (37°C, 40°C or 44°C) was extracted using the TRIzol™ Plus RNA Purification Kit.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: ATDC5 in the three groups was subjected to temperatures of 37C, 40C and 44C for 10 min, respectively.

value: cell line

value: Cartilage progenitor cells

value: WT

value: Treatment at 44C for 10 min


title: cortical_organoid_oligodendroglia_1

description: 10X Genomics


title: HepG2 24 hr FBS rep8


title: 44C_3


title: HepG2 25-HC addback rep7


title: HepG2 LDL-C addback rep7


title: monolayer_oligodendroglia_3

description: 10X Genomics

source_name: in vitro

value: in vitro


title: 44C_2


title: HepG2 48 hr LPDS+statin rep7


title: monolayer_oligodendroglia_2

description: 10X Genomics


title: HepG2 48 hr FBS rep7


title: HepG2 24 hr LPDS+statin rep7


title: HepG2 24 hr FBS rep7


title: monolayer_oligodendroglia_1

description: 10X Genomics


title: 40C_4

value: Treatment at 40C for 10 min


title: HepG2 24 hr FBS+statin rep6


title: HepG2 25-HC addback rep6

value: 10% LPDS + 2 µM simvastatin followed by 1 µg/ml 25-hydroxycholesterol addback

value: 24 hr + 24 hr addback


title: HepG2 LDL-C addback rep6


title: 44C_1


title: 40C_3


title: HepG2 48 hr LPDS+statin rep6


title: HepG2 24 hr LPDS+statin rep6

value: 24 hr


title: 40C_2


title: HepG2 48 hr FBS rep6


title: OMM2.3, erianin-treatment, IP, rep2

city: Shanghai

first: Sipeng

last: Zuo

state: Shanghai

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
HISAT2 software (v2.0.4)
Assembly: Hg 38
Supplementary files format and content: Excel files including complete raw counts, differentially expressed genes, and differentially methylated mRNA

source_name: uveal melanoma

extract_protocol:
For RNA-seq, The integrity of total RNA was assessed using a 2100 Bioanalyzer from Agilent Technologies, while the concentration was determined using a Qubit 2.0 fluorometer with the Qubit RNA assay kit from Invitrogen. For meRIP-seq, RNA was randomly fragmented and incubated overnight with protein A/G beads conjugated to m5C antibodies.
For RNA-seq, sequencing libraries were prepared utilizing the Illumina TruSeq RNA Sample Prep Kit (Illumina, USA), and high-throughput sequencing was performed on an Illumina HiSeq 3000 platform (Illumina, USA).  For meRIP-seq, the captured RNA was eluted and extracted using TRIzol reagent. Library construction was performed for both input samples and m5C IP samples. The libraries were assessed using an Agilent 2100 Bioanalyzer (Agilent, USA) and sequenced on a NovaSeq 6000 platform (Illumina, USA). Following quality control and removal of low-quality reads, the clean reads from all libraries were aligned to the reference genome (HG19) using HISAT2 software (v2.0.4).
RNA-seq and merip-m5C-seq

value: uveal melanoma

value: cancer cell

value: Erianin

tag: group

value: IP


title: 40C_1

tag: cell line


title: OMM2.3, control, IP, rep2

tag: cell type

value: Normal


title: HepG2 24 hr FBS+statin rep5

value: 10% FBS + 2 µM simvastatin


title: 37C_4

tag: treatment

value: Treatment at 37C for 10 min


title: HepG2 LDL-C addback rep5

value: 10% LPDS + 2 µM simvastatin followed by 50 µg/ml LDL-cholesterol addback


title: HepG2 24 hr FBS rep6

value: 10% FBS


title: OMM2.3, control, Input, rep2

value: Input


title: 37C_3

value: cell line

value: Cartilage progenitor cells

value: WT


title: HepG2 48 hr LPDS+statin rep5

value: 10% LPDS + 2 µM simvastatin

value: 48 hr


title: HepG2 25-HC addback rep5

value: 10% LPDS + 2 µM simvastatin followed by 1 µg/ml 25-hydroxycholesterol addback

value: 24 hr + 24 hr addback


title: OMM2.3, erianin-treatment, Input, rep1

value: uveal melanoma


title: OMM2.3, erianin-treatment, IP, rep1

value: cancer cell


title: HepG2 48 hr FBS rep5


title: OMM2.3, erianin-treatment, Input, rep2

value: Erianin


title: HepG2 24 hr FBS rep5

value: 24 hr


title: HepG2 24 hr LPDS+statin rep5


title: OMM2.3, control, Input, rep1

value: Normal


title: HepG2 24 hr FBS+statin rep4

value: 10% FBS + 2 µM simvastatin


title: HepG2 25-HC addback rep4


title: 37C_1

value: Treatment at 37C for 10 min


title: HepG2 LDL-C addback rep4

value: 10% LPDS + 2 µM simvastatin followed by 50 µg/ml LDL-cholesterol addback


title: OMM2.3, control, IP, rep1

value: IP


title: HepG2 48 hr LPDS+statin rep4


title: lysine

city: Tianjin, China

first: Tang

last: Qiang

address: 22 Qixiangtai Road, Heping District 300070, Tianjin, China

institute: Tianjin medical university

data_processing:
Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).
The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.
Reads were processed using the Cell Ranger 4.0 pipeline with default and recommended parameters.
Gene-Barcode matrices were generated for each sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts.
This output was then imported into the Seurat (v3.2.0) R toolkit for quality control and downstream analysis of our single-cell RNAseq data.
Assembly: GRCh38
Supplementary files format and content: raw-count

source_name: mesenteric lymphatic node

extract_protocol:
All the remaining procedures of single cell including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mesenteric lymphatic node

value: immune cell

tag: strain

value: 100mg/kg lysine daily after 2 days of  DSS treatment


title: tcr08

description:
Mixed Pool of samples
T cell receptor amplicons from 10x 5' kit
VDJresults.tar.gz

library_source: other

data_processing:
*library strategy: CITE-seq
10x Genomics CellRanger
Data was analyzed using the Seurat R package. Please see manuscript for details and link to code.
Assembly: Hg19
Supplementary files format and content: R data objects: Seurat single cell objects; .csv files of demuxlet and VDJ results

molecule: other

source_name: Blood

value: Blood

value: Peripheral blood mononuclear cells


title: HepG2 25-HC addback rep3