title: CSM152_DMSO_24h_rep3

value: melanoma cells

value: 24h treatment with DMSO


title: CSM152_DMSO_24h_rep2

status: Public on Mar 14 2022

type: SRA

city: Essen

first: Alexander

last: Roesch

address: Hufelandstrasse 55

department: Department of Dermatology

country: Germany

institute: University hospital Essen

library_source: transcriptomic

data_processing:
The run was basecalled and demultiplexed using Illumina bcl2fastq2, version 2.20.0.42
Alignment was done using BWA mem, version 0.7.17. with default parameters.
statistical gene set analysis was performed to determine differential expression at both gene and transcript levels.
Genome_build: hg38

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit according to the manufacturer’s protocol (Qiagen Venlo, Netherlands).
Barcoded stranded mRNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Preparation v2 Kit (Illumina, San Diego, CA, USA) implemented on the liquid handling robot Beckman FXP2.

tag: cell type

tag: cell line

tag: treatment

tag: growth medium

value: RPMI medium with 10% FBS


title: Patient 44-P.6445.txt_mRNA

type: RNA

city: Tokyo

first: Sophia

last: Subat

address: 3-8-31 Ariake, Koto-ward,

country: Japan

institute: Japanese Foundation for Cancer Research

description:
ALK+6445
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

hyb_protocol: The cDNA was hybridized to the SurePrint G3 Human Gene Expression 8×60K Microarray (Design ID 028004, Agilent Technologies).

scan_protocol: After the hybridization, scanning of the arrays was carried out with the Agilent Micro Scanner System (G2565CA, Agilent Technologies)..

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.

source_name: lung adenocarcinoma

label_protocol: Total RNA was reverse transcribed into cDNA and labeled using the Low Input Quick Amp Labeling Kit (5190-2305, Agilent Technologies) following the manufacturer’s instructions.

extract_protocol: Total RNAs were extracted using miRNeasy Mini Kit and RNase-free (Qiagen, Hilden, Germany) according to the manufacturer’s instructions

tag: tissue

value: lung adenocarcinoma

tag: alk rearrangement  status

value: positive


title: CSM152_DMSO_24h_rep1


title: WT_naive_1

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

country: France

institute: Institut Curie

library_source: genomic

data_processing:
ATAC-Seq sequencing reads were aligned to  the mouse reference genome mm10 using BWAMEM (bwa-0.7.15, opt -k 19 -T 30 -M). Only  properly paired uniquely mapped reads were kept for further analysis (samtools -f 0x2 -q 30).  Peaks were called using MACS2 v2.1.2 with default parameters and a 5% FDR threshold.
Assembly: mm10
Supplementary files format and content: Peak calling files (.bed)

molecule: genomic DNA

organism: Mus musculus

source_name: CD8+ T cell

extract_protocol: Chromatin profiling was performed by ATAC-seq as described in Buenrostro et al. In brief,  50,000 cells per sample were washed in cold PBS and lysed. Transposition reaction was  performed at 37°C for 30 minutes and DNA was purified with MinElute PCR purification kit  (Qiagen). Transposed DNA was amplified for 5 cycles and additional PCR cycles were  evaluated by real time PCR.

value: CD8+ T cell

tag: genotype

value: WT


title: CSM152_Cpd1_12h_rep3

value: 12h treatment with Cpd1 (2-phenoxyethyl 4-(2-fluorophenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, PubChem name BAS00915510)


title: DVS.115 RNA-seq

city: Durham

first: Deepak

last: Voora

state: NC

address: 101 Science Dr

country: USA

institute: Duke

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-115_S30_L004_R1_001

data_processing:
DEEPAK: base calling
raw single-end sequencing reads were first trimmed to remove adapter sequences and low-quality bases using a sliding window approach with Trimmomatic v0.32 (SE, ILLUMINACLIP:adapters.fasta:2:20:7:1:true, LEADING:5, TRAILING:5, SLIDINGWINDOW:4:10, MINLEN:21).
Sequence reads were aligned with Bowtie2 v2.1.0 ( --local, -U) against a custom ribosomal RNA (rRNA) database created by searching the NCBI non-redundant nucleotide database (NR) for Homo Sapiens ribosomal rRNA sequences. Unmapped reads which did not align to the rRNA database were then aligned with TopHat2 v2.0.9 to the hg19 transcriptome (Ensemble v74).
Expression quantification was done using Cuffquant v2.2.0 and Cuffnorm v2.2.0 (cuffquant -u -b)
Cuffnorm counts were denomralized using cuffnorm reported scale factors, outlier samples identified and removed, lowley expressed genes removed
TMM normalization and then voom normalization of the Qced counts. R code: # Normalization steps  dge <- DGEList(counts=QCed_counts, samples = Metadata)  dge <- calcNormFactors(dge, method = "TMM")  design = model.matrix(~0+treatment_drug + sex.x + Qubitconc.ng.ul + Order_Flowcell, data = dge$samples)  v <- voom(dge, design)  cor <- duplicateCorrelation(v , design, block=dge$samples$StudyID)  print(cor$consensus.correlation)  # repeat both voom and correlation estimate, per gordan smyth https://support.bioconductor.org/p/59700/  v2 <- voom(dge, design, plot=TRUE,correlation=cor$consensus.correlation)  #v2$E is log2 normalized expresion, v2$weights are the gene-sample weights used in duplicate correlation and lmFit results  cor <- duplicateCorrelation(v2 , design, block=dge$samples$StudyID)    # Analysis steps    cor <- duplicateCorrelation(v2 , design, block=dge$samples$StudyID)  fit <- lmFit(v2 , design, block=dge$samples$StudyID, correlation = cor$consensus.correlation)  fit <- eBayes(fit)    contrastM = makeContrasts("LowDoseVsNone" = treatment_drug1-treatment_drug0,      "HighDoseVsNone" = treatment_drug2-treatment_drug0,      "TicagrelorVsNone"=treatment_drug3-treatment_drug0,      "AspirinVsNone" = .5*(treatment_drug1 + treatment_drug2) - treatment_drug0,      "ASAvsTicagrelorResponse" = .5*(treatment_drug1 + treatment_drug2) - treatment_drug3,      "ASAHighvsLow" = treatment_drug2-treatment_drug1,  levels = design  )    fit2 = contrasts.fit(fit, contrastM)  fit2 <- eBayes(fit2)
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: tab-delimited plain text file with denormalized cuffnorm gene counts for all samples and genes passing QC
Supplementary_files_format_and_content: tab-delimited text file with the numeric matrix of normalized expression values on the log2 scale. Obtained from the "$E" argument of the limma::voom object. To be used with file "voom_weights.txt" when testing in limma::lmFit
Supplementary_files_format_and_content: tab-delimited text file with numeric matrix of inverse variance weights from voom. Obtained from the "$weights" argument of the limma::voom object. To be used with file "Voom_normalized_expression.txt" when using limma::lmFit

molecule: polyA RNA

source_name: mRNA extracted from purified platelets

extract_protocol:
Platelet RNA samples from the same participant were batched together at every stage from platelet RNA extraction through sequencing in order to minimize introducing technical artifacts between visits.RNA Isolation from purified platelets using a phenol-chloroform method.  Platelet lysates thawed on wet ice. Molecular grade Chloroform [200ul m, EMD #CZ1057-6] was added to each 1 ml sample, shaken vigorously by hand for 15 seconds, and allowed to rest for 3 minutes at ambient temperature before centrifugation at 12,000 x g for 10 minutes at 4 degrees. The upper aqueous phase, 500ul 100% isopropanol [Sigma #19516], and 1ul glycogen [Invitrogen #10814-010], were mixed and incubated at ambient temperature for 10 minutes and centrifuged [12,000 x g for 10 minutes at 4 degrees]. After removing the supernatant, the pellet was resuspended with 1ml 75% ethanol [Sigma E-7023], pelleted [8000 x g for 8 minutes at 4 degrees], and eluted in 20ul molecular grade nuclease-free water.   DNase treatment was with 2ul (10% volume) 10X DNase Buffer, and 1ul DNase [Invitrogen DNA-free kit #AM1907] for 25 minutes at 37 degrees C. The purified RNA was then precipitated by adding 11.5ul 5M ammonium acetate [USB Ultrapure# 75901], 103.5ul 100% isopropanol and 1ul glycogen at -20 degrees overnight.
Samples with sufficient quantity and quality RNA went on to poly(A) mRNA capture and construction of stranded mRNA-seq libraries from total RNA was achieved using the commercially available KAPA Stranded mRNA-Seq Kit (catalog #KK8421). The manufacturer’s protocol was followed. In brief, mRNA transcripts were first captured from 100ng-200ng of total RNA using magnetic oligo-dT beads. Captured mRNA transcripts were then fragmented using heat and magnesium and reverse transcribed to produce dscDNA. Illumina sequencing adapters were then ligated to the dscDNA fragments and amplified to produce the final RNA-seq library. Libraries were indexed using molecular indexes allowing for multiple libraries to be pooled and sequenced on the same sequencing lane on a HiSeq 4000 Illumina sequencing platform.  Each lane consisted of 8-10 samples and yielded about 43 million single-end 50bp sequences per sample.

treatment_protocol: Participants were exposed to either no drug, 81mg/day aspirin, 325mg/day aspirin, or 90mg twice a day ticagrelor

value: Pass

value: 180 mg Ticagrelor

tag: flowcell

tag: Sex

value: Male

tag: age

tag: plateletfunctionscore

tag: logscaledsalicylatelevel


title: KO2


title: Patient 42-P.4180.txt_mRNA

description:
ALK+4180
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 41-P.2374.txt_mRNA

description:
ALK+2374
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DVS.109 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-109_S24_L003_R1_001

value: Female


title: DVS.108 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-108_S23_L003_R1_001

value: 325 mg Aspirin


title: CSM152_Cpd1_12h_rep2


title: Patient 40-P.2075.txt_mRNA

description:
ALK+2075
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: KO1


title: CSM152_Cpd1_12h_rep1


title: Patient 43-P.4808.txt_mRNA

description:
ALK+4808
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DVS.113 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-113_S28_L004_R1_001


title: DVS.106 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-106_S21_L003_R1_001


title: DVS.111 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-111_S26_L004_R1_001


title: WT_treated_PD1_2


title: WT_naive_2


title: Patient 39-P.2001.txt_mRNA

description:
ALK+2001
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 38-P.833.txt_mRNA

description:
ALK+833
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DVS.112 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-112_S27_L004_R1_001

value: 81 mg Aspirin


title: CSM152_DMSO_12h_rep3

value: 12h treatment with DMSO


title: KO_treated_PD1_2


title: DVS.107 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-107_S22_L003_R1_001


title: WT_2


title: Patient 36-P.231.txt_mRNA

description:
ALK+231
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DVS.110 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-110_S25_L004_R1_001


title: Patient 37-P.351.txt_mRNA

description:
ALK+351
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DVS.104 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-104_S18_L003_R1_001


title: CSM152_DMSO_12h_rep1


title: CSM152_DMSO_12h_rep2


title: Patient 35-N.10385.txt_mRNA

description:
ALK-10385
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

value: negative


title: KO_treated_PD1_1


title: WM3734_Cpd1_48h_rep3

value: 48h treatment with Cpd1 (2-phenoxyethyl 4-(2-fluorophenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, PubChem name BAS00915510)


title: WT_treated_PD1_1


title: WT_1


title: DVS.105 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-105_S20_L003_R1_001


title: 98

city: Boston

first: Camron

middle: D

last: Bryant

state: Massachusetts

address: 72 E Concord St

department: Pharmacology

institute: Boston University School of Medicine

data_processing:
We used the R/Bioconductor package “scruff” to conduct demultiplexing, read alignment, read counting, quality checking and data visualization (Wang et al., 2019).
Reads were trimmed for quality using Trimmomatic (Bolger et al., 2014).
Trimmed reads were then aligned to the mm10 mouse reference genome (Ensembl) to generate BAM files for alignment using STAR (Dobin et al., 2013)
For differential gene analysis in the spinal cord, the featureCounts read summarization program was used to count reads mapping to the “exon” feature in a GTF file obtained from Ensembl (GRCm38).
Assembly: GRCm38
Supplementary files format and content: Raw counts from featureCounts.

source_name: Left Lateral Lobe of Liver

extract_protocol:
RNA was extracted in RNAlater-preserved tissue using Trizol (Qiagen), ethanol precipitation, filtering columns (Qiagen), DNAse digestion (Qiagen), and elution with RNAse and nucleotide free water (Yazdani et al., 2015) and diluted to 100 ng/ul.
RNA library preparation (poly-A selection) and RNA-seq was conducted at the University of Chicago Genomics Facility on an Illumina NovaSEQ6000 using a NovaSEQ SP-100 bp flowcell/reagent cassette. ~30M clusters/sample, 60M PE reads/sample.

value: Left Lateral Lobe of Liver

tag: strain

value: BALB/cByJ

value: Saline

tag: rna extraction cohort


title: DVS.103 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-103_S17_L003_R1_001


title: Patient 33-N.3947.txt_mRNA

description:
ALK-3947
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

value: lung adenocarcinoma


title: WM3734_Cpd1_48h_rep2

value: melanoma cells


title: WM3734_Cpd1_48h_rep1


title: DVS.102R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-102R_S16_L002_R1_001


title: 96

value: Oxycodone


title: Patient 34-N.6400.txt_mRNA

description:
ALK-6400
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 31-N.3479.txt_mRNA

description:
ALK-3479
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: 95


title: Patient 32-N.3767.txt_mRNA

description:
ALK-3767
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: WM3734_DMSO_48h_rep3

value: 48h treatment with DMSO


title: DV.S9 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S9_AGTTCC_L001_R1_CAT


title: DVS.100 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-100_S14_L002_R1_001


title: WM3734_DMSO_48h_rep1


title: DVS.101R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-101R_S15_L002_R1_001


title: Patient 30-N.3323.txt_mRNA

description:
ALK-3323
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DV.S81 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S81_CTTGTA_L003_R1_CAT


title: WM3734_Cpd1_24h_rep3

value: 24h treatment with Cpd1 (2-phenoxyethyl 4-(2-fluorophenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, PubChem name BAS00915510)


title: 92


title: DV.S80 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S80_GTTTCG_L006_R1_CAT

value: Pass


title: DV.S79 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S79_GTGAAA_L006_R1_CAT


title: WM3734_Cpd1_24h_rep2


title: WM3734_Cpd1_24h_rep1


title: Patient 27-N.3081.txt_mRNA

description:
ALK-3081
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 28-N.3221.txt_mRNA

description:
ALK-3221
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: 89


title: WM3734_DMSO_48h_rep2


title: 87


title: Patient 25-N.2784.txt_mRNA

description:
ALK-2784
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: WM3734_DMSO_24h_rep3

value: 24h treatment with DMSO


title: DV.S77 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S77_GCCAAT_L006_R1_CAT

value: Male


title: WM3734_DMSO_24h_rep2


title: 84

value: Female


title: Patient 29-N.3236.txt_mRNA

description:
ALK-3236
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: WM3734_DMSO_24h_rep1


title: 94


title: DV.S76 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S76_ACAGTG_L006_R1_CAT


title: DV.S75 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S75_ATTCCT_L005_R1_CAT


title: 91


title: WM3734_Cpd1_12h_rep3

value: 12h treatment with Cpd1 (2-phenoxyethyl 4-(2-fluorophenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, PubChem name BAS00915510)


title: 83


title: 82


title: Patient 23-N.2745.txt_mRNA

description:
ALK-2745
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DV.S74 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S74_CGTACG_L005_R1_CAT

value: 81 mg Aspirin


title: Patient 24-N.2766.txt_mRNA

description:
ALK-2766
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: WM3734_Cpd1_12h_rep2


title: DV.S73 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S73_ATGTCA_L005_R1_CAT

value: 325 mg Aspirin


title: 81


title: Patient 21-N.2532.txt_mRNA

description:
ALK-2532
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

value: negative


title: Patient 22-N.2697.txt_mRNA

description:
ALK-2697
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 26-N.2993.txt_mRNA

description:
ALK-2993
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: WM3734_DMSO_12h_rep3

value: 12h treatment with DMSO


title: DV.S78 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S78_CTTGTA_L006_R1_CAT


title: DV.S72 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S72_GATCAG_L005_R1_CAT


title: 79

value: Left Lateral Lobe of Liver


title: 800

value: BALB/cByJ


title: WM3734_Cpd1_12h_rep1


title: Patient 20-N.2326.txt_mRNA

description:
ALK-2326
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: WM3734_DMSO_12h_rep2


title: 78

value: Saline


title: DV.S6R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S6R_CGATGT_L001_R1_CAT


title: DV.S71 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S71_TTAGGC_L005_R1_CAT

value: 180 mg Ticagrelor


title: WM3734_DMSO_12h_rep1

value: melanoma cells


title: DV.S70 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S70_CCGTCC_L004_R1_CAT


title: 77


title: 75

value: BALB/cJ


title: WM3734_Tet3G-KDM5B_10Dox_72h_rep3

data_processing:
The run was basecalled and demultiplexed using Illumina bcl2fastq2, version 2.20.0.42
Alignment was done using BWA mem, version 0.7.17. with default parameters.
statistical gene set analysis was performed to determine differential expression at both gene and transcript levels.
Quantification was done using the Partek Flow (E/M) and then normalized using total counts + 0.001 (to remove missing values).
Genome_build: hg19

source_name: melanoma cells

value: cells induced with 10 ng/ml Dox for 72h

tag: treatment duration


title: DV.S69 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S69_AGTTCC_L004_R1_CAT


title: WM3734_Tet3G-KDM5B_10Dox_72h_rep2


title: 73

value: Oxycodone


title: WM3734_Tet3G-KDM5B_10Dox_72h_rep1


title: DV.S68 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S68_CAGATC_L004_R1_CAT

value: Pass


title: DV.S67 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S67_TGACCA_L004_R1_CAT


title: 71


title: WM3734_Tet3G-KDM5B_0Dox_72h_rep3

value: non-induced cells (0 ng/ml Dox for 72h)


title: Patient 19-N.2317.txt_mRNA

description:
ALK-2317
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

value: lung adenocarcinoma


title: Patient 16-N.2145.txt_mRNA

description:
ALK-2145
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 15-N.1939.txt_mRNA

description:
ALK-1939
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 18-N.2245.txt_mRNA

description:
ALK-2245
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 14-N.1547_mRNA

description:
ALK-1547
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 17-N.2231.txt_mRNA

description:
ALK-2231
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: 70

value: Male


title: WM3734_Tet3G-KDM5B_0Dox_72h_rep2


title: DV.S66 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S66_CGATGT_L004_R1_CAT

value: Female


title: Patient 12-N.1434_mRNA

description:
ALK-1434
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 13-N.1515_mRNA

description:
ALK-1515
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DV.S65 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S65_AGTCAA_L003_R1_CAT

value: 81 mg Aspirin


title: 68


title: WM3734_Tet3G-KDM5B_0Dox_72h_rep1


title: DV.S64R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S64R_GGCTAC_L003_R1_CAT


title: WM3734_Tet3G-KDM5B_10Dox_48h_rep3

value: cells induced with 10 ng/ml Dox for 48h


title: DV.S63 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S63_TAGCTT_L003_R1_CAT


title: 66


title: DV.S62 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S62_ACTTGA_L003_R1_CAT


title: 63


title: WM3734_Tet3G-KDM5B_10Dox_48h_rep1


title: Patient 9-N.795_mRNA

description:
ALK-795
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

value: negative


title: Patient 11-N.1354_mRNA

description:
ALK-1354
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 10-N.866_mRNA

description:
ALK-866
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: WM3734_Tet3G-KDM5B_0Dox_48h_rep3

value: non-induced cells (0 ng/ml Dox for 48h)


title: 62

value: Left Lateral Lobe of Liver


title: Patient 8-N.584_mRNA

description:
ALK-584
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: 69


title: Patient 7-N.557_mRNA

description:
ALK-557
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DV.S60 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S60_GTTTCG_L002_R1_CAT

value: 325 mg Aspirin


title: DV.S59R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S59R_GTGAAA_L002_R1_CAT


title: 59


title: WM3734_Tet3G-KDM5B_0Dox_48h_rep1


title: DV.S55 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S55_ATTCCT_L001_R1_CAT


title: WM3734_Tet3G-KDM5B_10Dox_24h_rep3

value: cells induced with 10 ng/ml Dox for 24h


title: 65


title: Patient 6-N.492_mRNA

description:
ALK-492
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 5-N.464_mRNA

description:
ALK-464
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 4-N.321_mRNA

description:
ALK-321
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DV.S61R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S61R_ATCACG_L003_R1_CAT


title: 60


title: WM3734_Tet3G-KDM5B_10Dox_24h_rep2


title: DV.S53 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S53_ATGTCA_L001_R1_CAT


title: 57

value: Saline


title: WM3734_Tet3G-KDM5B_10Dox_48h_rep2

value: melanoma cells


title: Patient 3-N.215_mRNA

description:
ALK-215
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: 54

value: BALB/cJ


title: WM3734_Tet3G-KDM5B_10Dox_24h_rep1


title: WM3734_Tet3G-KDM5B_0Dox_48h_rep2


title: DV.S52 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S52_GATCAG_L001_R1_CAT


title: 53


title: Patient 2-N.174_mRNA

description:
ALK-174
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 1-N.165_mRNA

description:
ALK-165
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 77-P.42477.txt_miRNA

description: One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

hyb_protocol: The labeled cRNAs were then hybridized to the Unrestricted Human miRNA 8×60K Microarray, release 19.0 (Design ID 046064, Agilent Technologies), which covers 2,042 human miRNAs.

scan_protocol: After the hybridization, the arrays were washed and scanned with a high resolution using the Agilent Microarray Scanner System (G2565CA, Agilent Technologies).

label_protocol: input RNA was used to generate Cyanine-3-pCp labeled cRNA using the miRNA Complete Labeling Reagent and Hyb Kit (5190-0456, Agilent Technologies) according to the manufacturer’s instructions

tag: alk rearrangement status

value: positive


title: WM3734_Tet3G-KDM5B_0Dox_24h_rep3

value: non-induced cells (0 ng/ml Dox for 24h)


title: 7dpi_3

city: palmerston north

first: Carl

last: Mesarich

state: Manawatu-Wanganui

address: Tennent Drive

country: New Zealand

institute: Massey University

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S7V4

data_processing:
Sequence reads (raw data) was filtered to remove reads containg adapters, reads containin N>10% and reads containing low quality (Qscore<-5) base which is over 50% of the total base.
Reads were mapped to masked V. inaequalis MNH120 genome using Hisat2 v2.2.1.
Reads mapping to fungal genome were filtered using SAMtools v.1.12 (samtools view -b -F 4)
Reads were counted using featureCounts (featureCounts -a ../ViAnnotation/ViAnnotation.gff -o ./ViCounts2 -p -B -C -T 4 -t exon -g gene_id ../HISAT2/*.mapped.bam)
Counts were normalized using DESeq2 package v1.32.0
Assembly: V. inaequalis MNH120 genome  (https://mycocosm.jgi.doe.gov/Venin1/Venin1.info.html),  masked using mappability mask (http://lh3lh3.users.sourceforge.net/download/seqbility-20091110.tar.bz2). Gene annotation used in this RNA-seq analysis can be found in the DOI:10.5281/zenodo.6233646.
Supplementary files format and content: Raw gene counts of RNA-seq reads .csv format
Supplementary files format and content: DESeq2 normalized count reads .csv format

organism:
Malus domestica
Venturia inaequalis

source_name: Infected apple leaf

growth_protocol: V. inaequalis in culture grown at 20°C for 7 days (16 hour light period/day) under white fluorescent lights.

extract_protocol:
Total RNA was extracted using a Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA), and DNA removed following treatment with DNase I (InvitrogenTM, Thermo Fisher Scientific, MA, USA) according to the manufacturers’ instructions. RNA concentration and purity was quantified using a Nanodrop, ND-1000 Spectrophotometer (NanoDrop Technologies, Rockland, DE). RNA integrity was assessed on the Agilent 2100 Bioanalyser (Agilent Technologies, Waldbronn, Germany) using an Agilent RNA 6000 Nano Kit in conjunction with the Agilent 2100 Bioanalyzer software according to the manufacturer’s instructions. RNA samples with an RNA Integrity Number (RIN) value of 3.5 or more, were used for sequencing.
Library preparation based on Illumina standards:After quality control, mRNA from eukaryotic organisms was enriched using oligo(dT) beads. mRNA was fragmented randomly by addings fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom and secon-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA was completed through size selection and PCR enrichment.

tag: v.inaequalis strain

value: Detached apple leaf


title: DV.S51R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S51R_TTAGGC_L001_R1_CAT

value: Pass


title: WM3734_Tet3G-KDM5B_0Dox_24h_rep2


title: 58


title: WM3734_Tet3G-KDM5B_0Dox_24h_rep1


title: 7dpi_4

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S7V5


title: DV.S5 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S5_AGTCAA_L008_R1_CAT

value: 180 mg Ticagrelor


title: gastrocnemius of old exercise 1

city: Seoul

first: Summin

last: Lee

state: Gwanak-gu

address: 1, gwanak-ro

country: South Korea

institute: Seoul National university

data_processing:
We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Mus musculus (mm10) using HISAT v2.1.0(1).
HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes). These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform)/ a graph FM index (GFM) as Bowtie2. Because of its use of these efficient data structures and algorithms, HISAT generates spliced alignments several times faster than Bowtie and BWA widely used. . The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from the UCSC table browser (http://genome.uscs.edu).
Transcript assembly and abundance estimation using StringTie(2, 3). After alignment, StringTie v1.3.4d was used to assemble aligned reads into transcripts and to estimate their abundance. It provides the relative abundance estimates as FPKM values (Fragments Per Kilobase of exon per Million fragments mapped) of transcript and gene expressed in each sample. Also transcript assembly of known transcripts, novel transcripts, and alternative splicing transcripts was processed by StringTie v1.3.4d.
For variant calling of RNA-Seq data, trimmed reads were aligned to Mus musculus (mm10) with STAR(4) and then variant calling is performed by SAMTOOLS and BCFTOOLS with mapped reads.
Variant filtering for each sample was performed based on RMS mapping quality (Q ≥ 20) and read depth (d ≥ 100) in the varFilter module of vcftools(5).
Novel or known fusion genes of RNA-Seq data were detected by Defuse 0.8.1(6).

source_name: gastrocnemius of old exercise

extract_protocol:
Total RNAwas extracted from mice skeletal muscles using a total RNA  extraction kit (Ribozol, Amresco) following manufacture’s manual.
RNA libraries were prepared for sequencing using standard affymetrix protocol

treatment_protocol: Before 4 weeks of treadmill exercise were performed, adaptation  exercise was previously performed, mice were familiarized  with the treadmill for 15 min/session at a 0 m/min for 3 min, 5m/  min for 2 min and 8 m/min for 10 min and 6° incline once a day for  3 days prior to the experimental day. In 4 weeks of treadmill exercise,  mice allocated to perform treadmill running were subject to  6° incline and for warm up, 2 min speed of 0 m/min, speed of 5m/  min, 8 m/min, 10 m/min for 1 min each, and then 12 m/min for  30 min at first week, 2 m/min were increased every weeks, and cool  down at 5 m/min for 2 min for 1 session (37 min). 2 session/day  were performed. Between the session, there were at least 1 h break  time was given.

tag: gender

value: male

tag: intervention

value: 4 weeks of treadmill exercise


title: CSM152_Cpd1_rep2

tag: cell line

tag: treatment

value: 72h treatment with Cpd1 (2-phenoxyethyl 4-(2-fluorophenyl)-2,7,7-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate, PubChem name BAS00915510)

value: RPMI medium with 10% FBS


title: DV.S50R RNA-seq

value: Fail

value: 81 mg Aspirin

value: Female


title: 5dpi_4

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S5V4

tag: tissue


title: DV.S48R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S48R_CAGATC_L008_R1_CAT

value: Male


title: gastrocnemius of old exercise 2


title: DV.S47R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S47R_TGACCA_L008_R1_CAT


title: 7dpi_2

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S7V3


title: 5dpi_3

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S5V3


title: gastrocnemius of old exercise 3


title: CSM152_Cpd1_rep3

tag: growth medium


title: CSM152_DMSO_rep3

value: 72h treatment with DMSO


title: CSM152_DMSO_rep2


title: 7dpi_1

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S7V2


title: 5dpi_1

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S5V1


title: DV.S49R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S49R_AGTTCC_L008_R1_CAT


title: gastrocnemius of young exercise 2

source_name: gastrocnemius of young exercise


title: gastrocnemius of young exercise 1


title: CSM152_Cpd1_rep1


title: gastrocnemius of old control 4

source_name: gastrocnemius of old control

value: control


title: 3dpi_3

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S3V3


title: gastrocnemius of old control 5


title: gastrocnemius of young control 3

source_name: gastrocnemius of young control


title: DV.S41R RNA-seq

value: 325 mg Aspirin


title: gastrocnemius of old control 3


title: 5dpi_2

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S5V2


title: 3dpi_2

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S3V2


title: DV.S44R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S44R_GGCTAC_L007_R1_CAT


title: gastrocnemius of young control 2


title: 3dpi_1

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S3V1


title: WM3734_DMSO_rep3

value: melanoma cells


title: 3dpi_4

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S3V5


title: CSM152_DMSO_rep1


title: WM3734_Cpd1_rep3


title: WM3734_Cpd1_rep1


title: DV.S4 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S4_GGCTAC_L008_R1_CAT


title: DV.S40R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S40R_GTTTCG_L006_R1_CAT


title: DV.S43 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S43_TAGCTT_L007_R1_CAT


title: gastrocnemius of young exercise 4


title: gastrocnemius of young control 1


title: DV.S46R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S46R_CGATGT_L008_R1_CAT


title: 2dpi_4

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S2V5


title: soleus of old exercise 3

source_name: soleus of old exercise


title: WM3734_DMSO_rep2


title: WM3734_Cpd1_rep2


title: DV.S42R RNA-seq


title: DV.S38 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S38_CTTGTA_L006_R1_CAT


title: WM3734_DMSO_rep1


title: 2dpi_2

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S2V2


title: DV.S37R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S37R_GCCAAT_L006_R1_CAT


title: soleus of old exercise 1


title: DV.S36 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S36_ACAGTG_L006_R1_CAT


title: 2dpi_1

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S2V1


title: soleus of old control 5

source_name: soleus of old control


title: DV.S35R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S35R_ATTCCT_L005_R1_CAT


title: 24hpi_4

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S24V5


title: DV.S34 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S34_CGTACG_L005_R1_CAT


title: soleus of old control 3


title: ASI1-RIP2

city: Shanghai

first: chunxiang

last: chen

state: Shanghai

address: 300 fenglin road, xuhui district, Shanghai

country: China

institute: Shanghai Center for Plant Stress Biology

data_processing:
Raw RIP-seq reads were trimmed and filtered by sickle(version 1.33) using parameters -l 50 -q 20.
Then clean reads were mapped to the A. thaliana genome defined by GTF file which transformed from Araport11_GFF3_genes_transposons.201606.gff, using STAR_2.6.0c(5) with the parameter “–quantMode Transcrip-tomeSAM”.
Estimated read counts per transcript were obtained by Salmon(version 0.10.2) and summarized into estimated read counts per gene by tximport. Mitochondrial  and chloroplast genes were excluded from the analysis.
Transcripts enriched in the RIP samples relative to the RNA-seq samples were detected by edgeR as described in the tximport vignette .Genes with a log2foldchange ≥ 1 were considered putative RIP targets.
Genome_build: Araport11_GFF3_genes_transposons.201606.gff
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: 14 d seedlings

growth_protocol: grown at 22 ˚C on half Murashige and Skoog (MS) medium with 1% sucrose with a 16 h light/8 h dark photoperiod.

extract_protocol: antibody：(Anti-Flag, Sigma , F1804)；RIP assay was performed according to published protocol (Rowley et al., 2013, Methods)

treatment_protocol: 2 weeks old seedlings were crosslinked with 0.5% formaldehyde

tag: ecotype

tag: genotype/variation

value: whole seedlings


title: 24hpi_3

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S24V4


title: ASI1-RIP-input


title: DV.S33 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S33_ATGTCA_L005_R1_CAT

tag: flowcell

tag: Sex


title: soleus of young exercise 4

source_name: soleus of young exercise

tag: age


title: 2dpi_3

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S2V3


title: soleus of young exercise 2


title: ASI1-RIP1


title: 24hpi_2

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S24V3


title: 24hpi_1

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S24V1


title: WT-RIP-input

value: WT


title: Human placenta FFPE RNA repeat 1

city: Houston

first: Ruojia

last: Wu

address: 6500 Main St

institute: Rice University

description: RNA gene expression analyzed using TAC software

hyb_protocol: RNA was sent out for commercial microarrary service; RNA samples were sent to BioCenter at UT southwestern Medical District for standard RNA Affymetrix HTA2.0 Array

data_processing: Data processing was performed using TAC software by UT southwestern Medical District

label: biotin

source_name: healthy placenta tissue

extract_protocol: RNA was extracted from commercial human placenta FFPE tissue (purchased from BioChain Inc) using RNeasy FFPE Kit (Qiagen)

value: Placenta


title: DV.S28 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S28_CAGATC_L004_R1_CAT

value: Pass

tag: plateletfunctionscore

tag: logscaledsalicylatelevel


title: DV.S23 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S23_TAGCTT_L008_R1_CAT


title: 12hpi_3

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S12V4

value: Detached apple leaf


title: Human placenta FFPE RNA repeat 2

scan_protocol: RNA was sent out for commercial microarrary service; RNA samples were sent to BioCenter at UT southwestern Medical District for standard RNA Affymetrix HTA2.0 Array


title: DV.S3 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S3_TAGCTT_L008_R1_CAT


title: soleus of young exercise 1

value: male


title: WT-RIP1


title: 12hpi_4

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S12V5


title: soleus of old exercise 2

value: 4 weeks of treadmill exercise


title: soleus of young control 2

source_name: soleus of young control


title: soleus of young control 3


title: DV.S22 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S22_ACTTGA_L008_R1_CAT


title: DV.S15 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S15_ATTCCT_L002_R1_CAT

value: 180 mg Ticagrelor


title: DV.S54 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S54_CGTACG_L001_R1_CAT


title: EDM2_ChIP_input

description: ChIP-Seq

data_processing:
Raw paired-end reads were cleaned by Trim-galore (version 0.4.4_dev ) with default parameters. Then clean reads were mapped to the A. thaliana genome (TAIR10) by Bowtie2 (version 2.3.4.1) with default parameters ; mapped reads with only one read of a pair mapped, low mapping quality (MAPQ < 30) and all duplicates were identified and removed by SAMtools (version 1.3).
Enriched peaks were identified by SICER(version 1.1) with cut-off pvalue 1e−3, window size 200, gap size 600.
The normalized coverage files (bigWig) were generated by genomecov  from deeptools (version 3.0.1) and bedGraphToBigwig from kentUtils-master.
Genome_build: tair10
Supplementary_files_format_and_content: bigWig file contains the genomic position information of ASI1 for ASI1 sample and EDM2 for EDM2 sample (normalized by reads per million (RPM)).

extract_protocol: antibody：(Anti-Flag, Sigma , F1804)；ChIP assay was performed according to published protocol (Saleh et al., 2008 Nat Protocols)

treatment_protocol: 2 weeks old seedlings were crosslinked with 1 % formaldehyde

tag: antibody


title: WT_ChIP_F1(EDM2)

description: ChIP-Seq

value: WT, EDM2

value: Anti-Flag, Sigma , F1804


title: soleus of old control 4


title: DV.S20R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S20R_GTTTCG_L003_R1_CAT


title: DV.S21 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S21_ATCACG_L008_R1_CAT


title: WT R2

city: Atlanta

first: Rae

last: Hunter

state: Georgia

address: 1760 Haygood Drive NE

department: Pediatrics

institute: Emory University

hyb_protocol: standard protcol

scan_protocol: standard protcol

data_processing:
Data was uploaded in nSolver 4.0 Analysis Software. RCC files were imported using the RCC Import Wizard. Default setting for "Background Subtraction/ Thresholding were used.
For Normalization Parameters: Positive Control Normalization was selected. Codeset Content Normalization (housekeeping genes) were also selected and any housekeeping genes with an Avg Count value that is less than 100 were removed from the Normalization Codes list. Values of the genes in the Codeset Content list were normalized by the geometric mean of the Normalization Codes values (for each sample).
Fold changes were determined by building ratios, portioning samples by treatment groups. False discovery rate was selected (to generate adjusted p-values).
Experimental Wizard was used to select for Build Ratio data to generate any comparisons of the data and obtain raw data including QC values and also normalized data.

label: Oglionucleotide probe

source_name: T-cells, leukemia, rIL-12 treatment

label_protocol: Nanostring codeset: Immune Exhaustion Panel: Aubsequent protocols using RNA were carried out by Emory Integrated Genomics Core

growth_protocol: Bone marrow was harvested  from mice at day 7 and T-cells were isolated for Nanonstring analysis

extract_protocol: 9 cells samples extracted using miRNeasy micro kit, eluted in 14 ul nuclease free water

treatment_protocol: Mice were either untreated or treated with rIL-12 after initial engraftment of leukemia

tag: mouse group

value: leukemia

value: rIL-12 treatment

value: bone marrow

tag: cell type

value: T-cells


title: WT_ChIP_F2(EDM2)

description: ChIP-Seq


title: WT_ChIP_input(EDM2)

description: ChIP-Seq


title: EDM2_ChIP_F2

description: ChIP-Seq


title: 12hpi_1

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S12V2

tag: v.inaequalis strain


title: WT R3


title: EDM2_ChIP_F1

description: ChIP-Seq


title: DV.S2 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S2_ACTTGA_L008_R1_CAT

value: 81 mg Aspirin

value: Male


title: positive controls P0-NPC-2

city: changsha

first: dan

last: zhu

address: hunan

institute: Hunan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain

extract_protocol:
Total RNA was isolated from mouse astrocytes (negative control), mouse brain-derived NPCs (positive controls), and A-iSCs using Trizol. A total amount of 3 μg RNA per sample was collected for sequencing. Sequencing libraries were generated using NEBNext® UltraTM RNA library prep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: brain

value: positive controls


title: positive controls P0-NPC-1


title: positive controls P0-NPC-3


title: positive controls P56-NPC-3


title: WT_ChIP_input(ASI1)

description: ChIP-Seq

value: WT, ASl1

value: whole seedlings


title: WT B3

source_name: T-cells, leukemia, no treatment

value: No treatment


title: WT R1


title: positive controls P56-NPC-2


title: DV.S14 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S14_CGTACG_L002_R1_CAT

source_name: mRNA extracted from purified platelets

value: Pass


title: DV.S13 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S13_ATGTCA_L002_R1_CAT

value: 325 mg Aspirin


title: 12hpi_2

description:
Detached leafs of 4-6 week apple seedlings were infected with 5uL droplets of conidial suspension (1 x 105 ml) covering the entire leaf surface.
S12V3

value: Detached apple leaf


title: WT B2


title: DV.S12 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S12_GATCAG_L002_R1_CAT


title: soleus of young control 1

tag: gender

value: male

tag: intervention

value: control


title: WT-RIP2

value: WT


title: WT_ChIP_F2(ASI1)

description: ChIP-Seq

value: Anti-Flag, Sigma , F1804


title: DV.S11 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S11_TTAGGC_L002_R1_CAT


title: WT B1

value: leukemia

tag: treatment


title: WT_ChIP_F1(ASI1)

description: ChIP-Seq

tag: tissue


title: 5 day incubation A-iSCs-2

value: 5 day incubation


title: ASI1_ChIP_input

description: ChIP-Seq


title: positive controls P56-NPC-1


title: DV.S10 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DV-S10_CCGTCC_L001_R1_CAT

value: 180 mg Ticagrelor


title: 5 day incubation A-iSCs-3


title: WT N3

source_name: T-cells, no leukemia, no treatment

value: no leukemia

value: bone marrow

value: T-cells


title: 5 day incubation A-iSCs-1

value: brain


title: 0 day incubation, negative control AST-3

value: 0 day incubation, negative control


title: ASI1_ChIP_F1

description: ChIP-Seq

value: whole seedlings


title: WT N2

value: No treatment


title: 0 day incubation, negative control AST-1


title: 3D printed YPAC-16

city: Pohang

first: Yebin

last: Kim

state: Gyeongsangbukdo

address: Handongro 558

institute: Handong Global University

data_processing:
Raw data quality control through FastQC
Read mapping through Tophat
Reads were counted through HTSeq (v. 1.99.2)with the following parameters:  htseq-count -s no -m intersection-nonempty -f bam
Differential gene expression analysis by using Deseq2 package (v. 1.24.0)
A regularized log transformed FPKM value of ACTB was subtracted from regularized log transformed FPKM values of the other genes to calculate fold change value.
Assembly: hg38
Supplementary files format and content: Matrix table with the rlog transformated values for every samples and genes (Ensembl ID) with a sum of Deseq count value greater than 10 for each sample, txt file

source_name: Patient drived pancreatic cancer cells

growth_protocol: 2D- and 3D-cultured pancreatic cancer cells were plated in 96-well plates at a density of 3x103 cells per well in F- media.  (DMEM: F12 nutrient mix = 3:1; insulin, 5ug/ml; amphotericin B, 250ng/ml; gentamicin, 10ug/ml; cholera toxin, 0.1nM; EGF, 0.125ng/ml; hydrocortisone, 25ng/ml; ROCK inhibitor Y-27632, 10μM; adenine, 24ug/ml). All cells were grown for 6 day at 37°C incubator in a 5% CO2 atmosphere.

extract_protocol:
RNA was isolated using the MiniBEST Universal RNA Extraction kit (TAKARA, 9767A) according to the manufacturer’s instructions. RNA Extraction kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nontreatment

value: pancreatic cancer cells

tag: disease state

value: patient derived PDAC

tag: culture method

value: 3D printed


title: 3D printed YPAC-05


title: msc_cardio_bio2_IP

city: Milan

first: Francesco

last: Blasi

address: Via Adamello 16

country: Italy

institute: IFOM

description: ChIP-seq analysis on untreated growing mesenchymal stromal cells derived from heart. Immunoprecipitation was performed using  anti-PREP1  antibody (SCBT). Replicate 2.

data_processing:
Reads were aligned to the hg19 genome using bowtie2 v.2.2.9 with default parameters.
Duplicate reads were removed using Samtools rmdup v1.9.
Peaks were called using MACS version 2.1.1.20160309 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: biopsy2_MSC from heart

growth_protocol: Cardiac mesenchymal stromal cells were obtained from the right ventricular free wall of cadaveric donors within 24 hours of death (accidental death, healthy subjects) by collagenase solution (collagenase NB4 mix in IMDM medium to obtain a final solution with a concentration of 3 mg/mL) treatment. The tissue was incubated for 1.5 h at 37 °C under continuous rotating agitation and centrifuged at 400 x g for 10 min at RT. Then the supernatant was removed and the pellet resuspended and propagated in 1 mL of TMES medium (Iscove's Modified Dulbecco's Medium (IMDM), supplemented with 20% Fetal Bovine Serum (FBS), 10 ng/mL basic fibroblast growth factor, 10,000 U/mL Penicillin, 10,000 µg/mL Streptomycin, and 0.02 M L-Glutamine).

extract_protocol:
CHIP followed by de-crosslinking and purification with Qiaquick PCR Purification kit (Qiagen)
TruSeq ChIP Sample Prep Kit, Illumina

treatment_protocol: no treatment

value: Heart

value: Heart derived mesenchymal stromal cells

value: PREP1(Santa Cruz Biotechnology, sc6245)


title: WT N1


title: msc_cardio_bio2_input


title: 3D printed YPAC-30


title: msc_cardio_bio1_input

description: ChIP-seq analysis on untreated growing mesenchymal stromal cells derived from heart. Immunoprecipitation was performed using  anti-PREP1  antibody (SCBT). Replicate 1.

source_name: biopsy1_MSC from heart


title: HepG2 cells_transfection Flag-VP35_48 hours_rep2

city: beijing

first: Lin

last: Zhu

address: Taiping 27 road

institute: Academy of military medical sciences AMS PLA

description: Gene expression after 48hr in HepG2 cells transfected with ebola virus VP35 protein

hyb_protocol: Labeled controls and test samples labeled with Cy3-dCTP were dissolved in 80 μL hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95°C for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42°C and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42°C for 5 min, and 0.2× SSC for 5 min at room temperature).(Agilent), then dried immediately by brief centrifugation.

scan_protocol: The chips were scanned with a GeneChip Scanner G2565CA (Agilent).

data_processing: The scanned images were analyzed with Agilent Feature Extraction (v10.7) and GeneSpring software V13 (Agilent).

source_name: HepG2 cells, transfected Flag-VP35, 48 hours,

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Dye incorporation and cRNA yield were checked with the NanoDrop ND-8000 Spectrophotometer.

extract_protocol: Forty-eight hours later, total RNA was extracted using the RNeasy mini kit (QIAgen, USA) according to the manufacturer’s protocol.

treatment_protocol: HepG2 cells were transfected with the plasmids Flag-VP35 or Flag-vector.

value: liver

value: HepG2 cells

value: transfected Flag-VP35


title: HepG2 cells_transfection Flag-Vector_48 hours_rep2

description: Gene expression after 48hr in HepG2 cells transfected with Flag-vector

source_name: HepG2 cells, transfected Flag-Vector, 48 hours,

value: transfected Flag-Vector


title: scTCR-seq mouse 234

first: Elliot

last: Akama-Garren

state: MA

address: 200 Longwood Ave

institute: Harvard Medical School

description: VDJ enriched

data_processing:
Library strategy: TCR-Seq
Cellranger (v5.0.0) was used to generate count and vdj matrices by aligning to the GRCm38 (mm10) reference genome
Gene expression matrices were read using Seurat (v4.0.0) and filtered for cells with at least 200 genes detected and genes in at least 3 cells
Cells were further filtered for 200-3000 genes detected, more than 1000 reads detected, less than 5% mitochondrial RNA content, less than 25% ribosomal R content, S phase score less than 0.15, and G2/M phase score less than 0.15
Samples were merged, normalized, and integrated by condition in Seurat (v4.0.0)
BCRs were filtered for cell barcodes with productive heavy and light chain sequences
TCRs were filtered for cell barcodes with productive alpha and beta chain sequences
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with normalized gene counts for every gene (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with feature and sample-level metadata (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with BCR and sample-level metadata (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with TCR and sample-level metadata (columns) for each cell barcode (rows)

source_name: Spleen

extract_protocol:
CD45 cells were enriched using MACS and captured in droplets according to 10X Genomics protocols.
Gene expression or VDJ libraries were prepared following reverse transcription according to 10X Genomics protocols.

tag: chimera condition

value: WT

value: M


title: 3D printed YPAC-25


title: HepG2 cells_transfection Flag-VP35_48 hours_rep3


title: HepG2 cells_transfection Flag-Vector_48 hours_rep3


title: msc_cardio_bio1_IP


title: T17

data_processing:
sample de-multiplexing and alignment was performed using Cell Ranger Single Cell Software Suite (v2.0.1)
Assembly: mm10 (using refdata-cellranger-mm10-1.2.0)
Supplementary files format and content: Processed files are raw count UMI matrices which are given by Cellranger pipeline and integrated Seurat-v3 object

source_name: CD8+ T cell

extract_protocol: RNA from was extracted according to the Single Cell 3' Reagent kits.

value: untreated

tag: genotype

value: Suv39h1 KO

value: CD8+ T cell


title: 2D cultured YPAC-16

value: 2D cultured


title: T15


title: ASI1_ChIP_F2

description: ChIP-Seq

tag: ecotype

tag: genotype/variation

value: whole seedlings

value: Anti-Flag, Sigma , F1804


title: scTCR-seq mouse 233

description: VDJ enriched

tag: Sex


title: HepG2 cells_transfection Flag-Vector_48 hours_rep1


title: scTCR-seq mouse 232

description: VDJ enriched


title: 2D cultured YPAC-05

value: pancreatic cancer cells

value: patient derived PDAC


title: T12


title: HepG2 cells_transfection Flag-VP35_48 hours_rep1


title: 348_re-analyzed

city: Dublin

first: William

middle: P.

last: Martin

state: - Select State/Province -

address: Diabetes Complications Research Centre, Conway Institute, University College Dublin

country: Ireland

institute: University College Dublin

description: re-analysis of GSM4443553

data_processing:
Quality control of reads performed with fastqc.
Quality filtering of reads performed with trim_galore.
Alignment towards rn5 rat reference genome using STAR.
Quantification of aligned reads using featureCounts (Subread package).
Differential expression analysis using DESeq2.
Genome_build: rn5 rat reference genome
Supplementary_files_format_and_content: featureCounts tab delimited text files providing raw counts of aligned reads for each rat renal cortical sample.

organism: Rattus norvegicus

source_name: Renal cortex

extract_protocol:
RNA extraction from renal cortex was performed using an RNeasy Mini Kit (Qiagen). RNA was isolated according to manufacturer’s instructions. Renal cortical samples were preserved on dry ice prior to lysis steps. RNA samples were stored at -80 degrees Celsius until RNA-sequencing. RNA integrity was checked using a Bioananalyser system prior to sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols. Library preparation kit: TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold.

value: Zucker Diabetic Sprague Dawley

tag: age

value: 37 weeks

value: Renal cortex

tag: experimental group

value: SHAM


title: 0 day incubation, negative control AST-2

value: brain

value: 0 day incubation, negative control


title: 3D printed YPAC-02

value: 3D printed


title: scBCR-seq mouse 235

description: VDJ enriched

data_processing:
Library strategy: BCR-Seq
Cellranger (v5.0.0) was used to generate count and vdj matrices by aligning to the GRCm38 (mm10) reference genome
Gene expression matrices were read using Seurat (v4.0.0) and filtered for cells with at least 200 genes detected and genes in at least 3 cells
Cells were further filtered for 200-3000 genes detected, more than 1000 reads detected, less than 5% mitochondrial RNA content, less than 25% ribosomal R content, S phase score less than 0.15, and G2/M phase score less than 0.15
Samples were merged, normalized, and integrated by condition in Seurat (v4.0.0)
BCRs were filtered for cell barcodes with productive heavy and light chain sequences
TCRs were filtered for cell barcodes with productive alpha and beta chain sequences
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with normalized gene counts for every gene (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with feature and sample-level metadata (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with BCR and sample-level metadata (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with TCR and sample-level metadata (columns) for each cell barcode (rows)


title: scBCR-seq mouse 234

description: VDJ enriched

value: WT


title: 340_re-analyzed

description: re-analysis of GSM4443551


title: T10


title: 2D cultured YPAC-02


title: scTCR-seq mouse 235

description: VDJ enriched

value: M


title: 2D cultured YPAC-30


title: T9

value: untreated


title: 3D printed YPAC-26


title: scBCR-seq mouse 233

description: VDJ enriched


title: 2D cultured YPAC-26


title: T8

value: Suv39h1 KO


title: 334_re-analyzed

description: re-analysis of GSM4443550


title: 2D cultured YPAC-25


title: scBCR-seq mouse 232

description: VDJ enriched


title: 333_re-analyzed

description: re-analysis of GSM4443549


title: T5

value: CD8+ T cell


title: T4


title: scRNA-seq mouse 234

description: total RNA

data_processing:
Cellranger (v5.0.0) was used to generate count and vdj matrices by aligning to the GRCm38 (mm10) reference genome
Gene expression matrices were read using Seurat (v4.0.0) and filtered for cells with at least 200 genes detected and genes in at least 3 cells
Cells were further filtered for 200-3000 genes detected, more than 1000 reads detected, less than 5% mitochondrial RNA content, less than 25% ribosomal R content, S phase score less than 0.15, and G2/M phase score less than 0.15
Samples were merged, normalized, and integrated by condition in Seurat (v4.0.0)
BCRs were filtered for cell barcodes with productive heavy and light chain sequences
TCRs were filtered for cell barcodes with productive alpha and beta chain sequences
Genome_build: mm10
Supplementary_files_format_and_content: Matrix with normalized gene counts for every gene (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with feature and sample-level metadata (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with BCR and sample-level metadata (columns) for each cell barcode (rows)
Supplementary_files_format_and_content: Matrix with TCR and sample-level metadata (columns) for each cell barcode (rows)


title: 317_re-analyzed

description: re-analysis of GSM4443547


title: 321_re-analyzed

description: re-analysis of GSM4443548


title: scRNA-seq mouse 235

description: total RNA


title: M2MOCK48h_B

city: Chicago

first: Joyce

middle: huanhuan

last: Chen

state: IL

address: 5801 S Ellis Ave, Chicago

department: Pritzker School of Molecular Engineering

institute: Uchicago

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
After trimming the adaptors with cutadapt (version1.18),RNA reads were aligned and mapped to the GRCh38 human reference genome plus SARS-CoV-2 genome(NC_045512.2) by STAR (Version2.5.2) , and transcriptome reconstruction was performed by Cufflinks (Version 2.1.1)
The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: H1 ESC-derived M2 macrophages

growth_protocol: H1 human ES cells were maintained in a medium of DMEM/F12, 20% knockout serum replacement, 0.1 mM β-mercaptoethanol and 20 ng/ml bFGF. Human ES cells were differentiated to mesoderm, hematopoietic progenitor cells, monocytes and macrophages using growth factor and small molecule cocktails inclduing inclduing BMP, CHIR, FGF2,VEGF,SB431542,IL3,M-CSF,etc.

extract_protocol:
Total RNA was isolated using Direct-zol RNA Miniprep kit. Following RNA isolation, total RNA integrity was checked using a 2100 Bioanalyzer. RNA concentrations were measured using the NanoDrop system.
Preparation of RNA sample library and RNA-seq were performed by the Genomics Core Laboratory at Weill Cornell Medicine. Messenger RNA was prepared using TruSeq Stranded mRNA Sample Library Preparation kit (Illumina), according to the manufacturer’s instructions.

treatment_protocol: For macrophage polarization, monocytes from differentiating day13-15 were treated with 10ng/ml IFNγ+100ng/ml LPS to genarate M1 macrophages, 20ng/ml IL4 to generate M2 macrophages,respectively. To assay SARS-CoV-2 infection on macrophages, live SARS-CoV-2 was added at MOI=0.1 for 24hrs or 48hrs.

tag: treatment time


title: CNC rep 3

city: Baltimore

first: Tyler

middle: J

last: Creamer

state: Maryland

address: 733 N Broadway

department: Genetic Medicine

institute: Johns Hopkins University

data_processing:
Transcripts were aligned to the mouse genome (mm10) using RSEM (v1.2.25; rsem-calculate-expression). RSEM used bowtie2 as the aligner and then calculated and normalized gene and isoform expression level estimates (TPM).
Genome_build: mm10
Supplementary_files_format_and_content: Bulk RNA-Seq_sorted_gene_TPMmatrix.csv

source_name: sorted murine aortic cells of CNC lineage

extract_protocol:
Mice bearing a conditional CAG-Sun1/sfGFP (The Jackson Lab, 021039) tracer allele with either a Mef2cSHF (gifted by the K.R. Chien lab at the Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA) or Wnt1-Cre2 (The Jackson Laboratory, 003829) allele were sacrificed at 8 weeks of age. The aortic root and ascending aorta were dissected and cleaned with PBS. Minced tissue was transferred to ice-cold HBSS (Thermo Fisher Scientific, 14175095) containing 0.2 u/µL RNase inhibitor (Applied Biosystems, N8080119) and 5% D-trehalose (Quality Biosciences, A611-K480-95) and then digested with 1 mg/mL collagenase II(Worthington-Biochem, LS004176), 100ul elastase (MilliporeSigma, E1250), and 0.2mg/mL DNase I (Zymo Research, E1009) in a 37°C rotating water bath for 30 minutes with periodic agitation. After further trituration through a 21G needle, the digestion was stopped by addition of 10% Fetal Bovine Serum (FBS) (Corning Cellgro, 35-011-CV). Cells were pelleted by centrifugation, resuspended in the previously mentioned HBSS solution and passed through a 40 µm filter-cap tube. Cells were sorted using a DakoCytomation MoFlo at the Bloomberg Flow Cytometry and Immunology Core. Viability was determined by propidium iodide stain and GFP+ cells were sorted into a tube containing TriZol (ThermoFisher Scientific, 15596026). After separation by chloroform and addition of cold 70% ethanol, RNA was extracted using the PicoPure RNA Isolation Kit (ThermoFisher Scientific, KIT0204).
Total bulk RNA was normalized according to sorted cell number, reverse transcribed and amplified according to the SmartSeq2 protocol used for single-cell sequencing (Picelli, et al. Nat. Protoc. 2014). The amplified cDNA was fragmented and barcoded using the Nextera XT DNA Library Preparation Kit (Illumina) and the resulting libraries were pooled.

tag: lineage

value: CNC

tag: cell type

value: cardiac neural crest-derived cells


title: C181

data_processing:
Cellranger software (V6 from 10x Genomics) was used to process, align (mm10), and aggregate (--normalize=none) the raw data
The scRNA-seq data were filtered using the R package Seurat v4 according to the following settings: >600 genes detected per cell but <6000, >2000 total molecules detected per cell but <50000, and <25% mitochondrial genes per cell. For clustering and cell-type specific analysis, the data were normalized using SCTransform, this function employs a negative binomial regression to normalize UMI count data. As samples were collected in several batches, the data were integrated using reciprocal PCA in Seurat (uses FindIntegrationAnchors function with k.anchors set to 20 and IntegrateData function). The data were then subjected to principal component analysis (RunPCA), uniform manifold approximation and projection (RunUMAP), and the FindNeighbors and FindClusters functions in Seurat. Clusters were visualized using the DimPlot function. For differential expression analysis, the raw data (RNA assay) were normalized and scaled using the NormalizeData (log transformation) and ScaleData functions. Cluster defining markers and differentially expressed genes between genotypes were found using the FindMarkers function.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger output containing the filtered feature matrices, cloupe file, and web summary for each individual sample.

source_name: murine aortic cells

extract_protocol:
The aorta was perfused with 5mls of PBS injected through the left ventricle of the heart. The thoracic aorta from the aortic root to the arch (sinus of Valsalva to the branchpoint of the left subclavian artery) was collected and cut into small pieces and placed into a room temperature in 500 ul of solution A (HBSS (Thermo Fisher Scientific, 14175095), 50% D-Trehalose (Quality Biosciences, A611-K480-95), RNase inhibitor [20u/ul] (Applied Biosystems, N8080119)). 1ul/ml of room temperature DyeCycle Violet (DCV) (ThermoFisher, V35003) was added to stain double stranded DNA. After all aortic samples were collected, the tissue enzymatically digested by adding 500ul of solution B (Collagenase II [315U/mg] (Worthington-Biochem, LS004176), Elastase (MilliporeSigma, E1250), Dnase I [2620U/mg] (Zymo Research, E1009) in a thermomixer set to 800 rpm for 30 minutes or 1 hour at 37oC. After incubation, each sample was gently pushed through a 3ml syringe with a 21G needle 8 times to further disrupt the tissue. 100ul of 100% FBS (Corning, 35-010-CV) was added to each sample tube to inhibit the enzymes. The tubes were spun down at 800xg for 3.5 minutes at room temperature. The supernatant was discarded, and cells were resuspended in 500ul of solution A and 1ul/ml of DCV. The cell suspension was carefully pipetted through a 40um filter cap tube. Propidium iodide (PI) (ThermoFisher Scientific, P1304MP) was added to each sample and cells were sorted by flow cytometry to produce a single cell suspension of DCV+, PI- cells. 20ul of 1% BSA in HBSS was used as catch buffer.
10x Genomics 3' single index chemistry for single cell RNA sequencing as per manufacturer's protocol.
10x Genomics Chromium 3’ v3 chemistry, sequenced on an Illumina NovaSeq

tag: strain

tag: weeks post-deletion

tag: tacer

tag: digest time

tag: batch


title: M2MOCK48h_A

tag: treatment


title: 315_re-analyzed

description: re-analysis of GSM4443546

tag: tissue


title: scRNA-seq mouse 233

description: total RNA

tag: chimera condition


title: M1MOCK48h_B

source_name: H1 ESC-derived M1 macrophages

tag: genotype


title: 343_re-analyzed

description: re-analysis of GSM4443552


title: M1MOCK48h_A


title: CNC rep 1


title: C208


title: scRNA-seq mouse 232

description: total RNA


title: 311_re-analyzed

description: re-analysis of GSM4443545


title: CNC rep 2


title: M0MOCK48h_A

source_name: H1 ESC-derived M0 macrophages


title: 355_re-analyzed

description: re-analysis of GSM4443542

value: Sprague Dawley


title: 357_re-analyzed

description: re-analysis of GSM4443544


title: M0MOCK48h_B


title: C187


title: 354_re-analyzed

description: re-analysis of GSM4443541


title: 356_re-analyzed

description: re-analysis of GSM4443543


title: C232


title: Wild Type Asynchronous Replicate 1 HiC

city: Amsterdam

first: Angela

last: Sedeno Cacciatore

state: Noord-Holland

address: Plesmanlaan 121

department: Gene regulation

country: Netherlands

institute: Netherlands Cancer Institute

description: Wild Type Asynchronous Replicate 1

data_processing:
Raw sequence data was mapped and processed using HiC-Pro v2.9 (Servant et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions).

growth_protocol: HAP1 cells (Carette et al., 2011) were cultured in Iscove’s modified Dulbecco’s medium (Invitrogen), supplemented with 10% FCS (Clontech), 1% UltraGlutamin (Lonza) and 1% penicillin-streptomycin (Invitrogen).

extract_protocol:
Hi-C libraries were prepared as previously described (Rao et al., 2014). The protocol was adapted slightly for G1 analyses. An asynchronous pool of cells was first crosslinked using 2% formaldehyde. Then the 10% smallest cells were sorted based on Forward Scatter and Side Scatter. 5 million cells were collected for Hi-C analysis and then processed according to protocol following crosslinking.
Pulled-down DNA was end-repaired and an A-overhang was added. Sequencing adapters were ligated to the DNA samples to create sequencing libraries.

treatment_protocol: CRISPRs targeting ESCO1 (5’-CATGAGTACAAGGTCATCAA-3’ and 5’-AGCTTAACCGGAGATCACAA-3’), HDAC8 (5’-CAGTGGGCAGTCGCTGGTCC-3’ and 5’-CGGGACTATAGATATAAACC-3’), PDS5A (5’-GTGGCGTCGTGAGTGCCGACGGG-3’ and 5’-GGAAGATCGCTTACCCTCCG-3’), and PDS5B (5’-TCTGATATTTCCTTGACCCC-3’) were cloned into px330 (Addgene plasmid #42230). ∆WAPL cells were generated before (Haarhuis et al., 2017), and used as a parental cell line to generate double knockout cells for WAPL and ESCO1. Either blasticidine or puromycin resistance cassettes were used, as described previously (Blomen et al., 2015). Knockout cell lines were confirmed by PCR genotyping and Western Blotting Analysis.

tag: cell line

value: Wild Type


title: SHF rep 2

source_name: sorted murine aortic cells of SHF lineage

value: SHF

value: secondary heart field-derived cells


title: ∆HDAC8 Asynchronous Replicate 1 HiC

description: ∆HDAC8 Asynchronous Replicate 1


title: shP150_TSC_H3p3_rep2

city: Tsukuba

first: Masashi

last: Hada

state: Ibaraki

address: Koyadai 3-1-1

department: Bioresource Research Center

institute: RIKEN

description:
Biological replicate 2 of 2.
shP150_H3p3.bw

data_processing:
Adaptor sequences and low-quality reads were excluded using Trimmomatic (version 0.36) (Bolger et al., 2014). ChIP-seq reads were aligned to the mouse genome (mm10) or human genome (hg38) using bowtie command (version 1.2.2) with “-n 2 -M 1 --best --strata” option (Langmead et al., 2009). PCR duplicates were removed by samtools rmdup command. Signal tracks for each sample were generated using deeptools (version 3.4.3) bamCompare or bamCoveraeg command with default parameters and were normalized to 1 million reads (RPKM). Signals were visualized by the Integrative Genomics Viewer (version 2.5.3) (Robinson et al., 2011b).
To identify broad domain, we first divided the genome into 100-kb consecutive bins and calculated normalized signal to 10 million reads using parse2wig command (version 3.7.0) with “-n GR -f BAM -of 3 -np 10000000 -showzero” options [ref: nakato]. Sex chromosomes were removed for further analysis. Bines with no value in input sample and less than 300 in ChIP sample were removed, then the ChIP signals were divided by the input signals using corresponding bines. Regions in which ChIP/input ration is over 2.0 (H3K9me3) or 1.5 (H3.1/H3.2) was classified as a domain.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Trophoblast stem cell

growth_protocol: ESC and TSC lines were established from blastocysts generated by IVF. IVF was undertaken using oocytes from C57BL/6NCrSlc female mice and spermatozoa from DBA/2 male mice or JF1/Ms male mice. For establishment of ESCs, developing blastocysts were dropped onto Acidic Tyrode (Millipore #MR-004-D) to remove zona pellucida, then transferred to ESC medium containing KnockOut DMEM (Gibco # 10829018), 15% KnockOut serum replacement (KSR, Thermo #10828028), MEM Non-Essential Amino Acids Solution (Gibco #1140050), GlutaMAX supplement (Gibco #35050061), 100 µM 2-mercaptoethanol (2-ME, Sigma-Aldrich #M-7522), ESGRO Recombinant Mouse LIF Protein (Millipore #ESG1107), 1 µM PD0325901 (Stem gent #04-0006), and 1 µM CHIR99021 (Stem gent #04-0004). These blastocysts were putted onto layers of primary mouse embryonic fibroblasts treated with mitomycin-C (MMC-MEFs). After several passages, cell lines with typical ESC colonies were picked up and used for further analysis. In the case of TSCs, developing blastocysts were directory transferred to TSC medium containing the same amount of neurobasal medium (Gibco #21103049) and Dulbecco’s modified Eagle’s medium/F12 (Ham’s) (1:1) (Gibco #11320033), N2 supplement (Gibco #17502048), B27 supplement (Gibco #17504044), GlutaMAX supplement, 150 µM 2-ME, 1 µg/ml heparin (Sigma #H3149), 0.05% bovine serum albumin (Millipore #12657), 1% KSR, 50 ng/ml recombinant mouse basic FGF (Wako #062-05181), 20 ng/ml recombinant human activin A (R&D systems #338-AC), 10 µM XAV939 (Calbiochem #575545), and 5 µM Y27632 (Wako #036-24023) onto MMC-MEFs (Hirose et al., 2018; Ohinata and Tsukiyama, 2014). After several passages, cell lines with typical TSC colonies were used for further experiment.  Established ESC and TSC lines were adapted for feeder-free conditions. Briefly, ESCs were placed onto gelatin coated dish with ESC medium in which PD0325901 and CHIR99021 were removed and 1 µM GSK-3 Inhibitor IX (Millipore #361550) was added. TSCs were placed onto the dishes coated with 15 mg/ml human plasma fibronectin (Millipore #FC010) with TSC medium (Hirose et al., 2018; Ohinata and Tsukiyama, 2014). Medium was replaced every day and cells were passaged every 2 days

extract_protocol:
ChIP were performed as described previously (Harada et al., 2012). Briefly, 1x107 ESCs or TSCs were collected by trypsinization, and fixed using truChIP Chromatin Shearing Kits (Covaris #520154). Totally 2x107 cells were suspended with 2 ml of ChIP buffer (10 mM Tris-HCL pH8.0, 200 mM KCL, 1 mM CaCL2, 0.5%NP40, protease inhibitor cocktail) and incubated on ice for 5 min. Cells were sonicated using Handy Sonic (Tomy Seiko #UR-20P) with 5 sec sonication (intensity 7) and 15 sec interval for three times, then incubated with micrococcal nuclease (NEB #M0247) for 25 min at 37℃. Reaction was stopped by EDTA, then lysates were centrifuged by 15,000 rpm for 15 min at 4°C. Aliquot of supernatants were kept for input. Antibodies were pre-bounded to Dynabeads Protein G or Protein A (Invitrogen #10001D and #10004D) for at least 2 hours at 4°C with rotation. Supernatants were incubated with beads complexes at 4°C with rotation, then the immunocomplexes were washed by using ChIP buffer for 2 times, wash buffer (10 mM Tris-HCL pH8.0, 500 mM KCL, 1 mM CaCL2, 0.5%NP40, protease inhibitor cocktail) for 2 times, and TE buffer for one time. These complexes were eluted by elution buffer (10 mM Tris-HCl, 1% SDS, 5 mM EDTA and 300 mM NaCl) at 65°C for 30 min. Crosslinking was reversed by incubation at 65°C for 6 h, after which RNAs and proteins were degraded by adding RNase (Ambion #AM2286) at 37°C for 30 min and Proteinase K (Zymo Research #D3001-2) at 55°C for 2 hours, respectively. ChIPed-DNAs were purified using QIAquick PCR purification kits (Qiagen #28106).
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645) according to manufactures instructions. Single-end 65 bp sequencing was performed on a Hiseq 2500.

treatment_protocol: To establish stable TSC lines which express shRNA for LacZ and P150 by DOX dependent manner, 10 µg/ml blasticidin S (Fujifilm #026-18711) was added at next day after lentiviral infection, then cells were cultured for at least 1 week. To start knockdown, 2 µg/ml DOX was added in culture medium for two days.

value: hybrid C57BL/6 / JF1

tag: antibody


title: T2

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

institute: Institut Curie


title: 353_re-analyzed

description: re-analysis of GSM4443540

value: 37 weeks

value: Renal cortex


title: ∆PDS5B G1 Replicate 1 HiC

description: ∆PDS5B G1 Replicate 1


title: C231


title: 347

data_processing:
Quality control of reads performed with fastqc.
Quality filtering of reads performed with trim_galore.
Alignment towards rn5 rat reference genome using STAR.
Quantification of aligned reads using featureCounts (Subread package).
Differential expression analysis using DESeq2.
Genome_build: rn5 (Rnor_5.0) rat reference genome
Supplementary_files_format_and_content: *_featureCounts.txt: Tab-delimited text files providing raw counts of aligned reads for each rat renal cortical sample.

extract_protocol:
RNA extraction from renal cortex was performed using an RNeasy Mini Kit (Qiagen). RNA was isolated according to manufacturer’s instructions. Renal cortical samples were preserved on dry ice prior to lysis steps. RNA samples were stored at -80 degrees Celsius until RNA-sequencing. RNA integrity was checked using a Bioanalyser system prior to sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols. Library preparation kit: TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold.

value: Zucker Diabetic Sprague Dawley

value: Medical bypass


title: Hi-C H9 replicate D

city: Cleveland

first: Shanshan

last: Zhang

state: OH

address: 10900 Euclid Avenue

department: Department of Genome and Genetics

institute: Case Western Reserve University

description: There are 10 replicates for H9 HiC raw data. "H9.cool" is the processed file for combining the 10 replicates.

data_processing:
The paired-end Hi-C reads were mapped to human genome hg19 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
For Hi-C, we focus on cis-interactions and therefore only kept Hi-C paired-end reads which both ends are mapped to the same chromosome. Out of all the intra-chromosome paired-end reads, we also discard the reads with both ends mapped to the same HindIII fragments. Since cut-and-ligation events are expected to generate reads within 500bp upstream of HindIII cutting sites due to the size selection (“+” strand reads should be within 500bp upstream of a HindIII site, and “-“ strand reads should be within 500bp downstream a HindIII site), we only keep reads pairs with both ends satisfying this criteria.
We next split all these reads into three classes based on their strand orientations (“same-strand”, “inward”, or “outward”), and generated the resulting lists of fragment pairs (with Hi-C read counts) from each class of reads.
There are total ~840k fragments in human genome. They are assembled into ~335k anchors after short fragments (<5kb) are merged into neighboring anchors. For every anchor, we first count Hi-C reads from the anchor to every fragment within 2Mb range.
We estimated a background frequency between any two fragments based on the average reads count of all fragment pairs that have similar lengths, similar gap distance, GC content, and visibility. The fragment-to-fragment data can be then converted to anchor-to-anchor data by adding the read counts and background frequencies together based on the assignment of fragments to anchors. P values of the enrichment of Hi-C reads over the background frequency can be calculated using a negative binomial model. The statistical method has been described in previous publication (Jin, F. et al. Nature 2013, 503:290-294)
Genome_build: hg19
Supplementary_files_format_and_content: For each Hi-C, the fragment-to-fragment frequency are provided in the txt file.

growth_protocol: H9 cells were cultured on the hESC-qualified Matrigel (Corning, #354277) coated plates in mTeSR1 medium (StemCell Technologies, #05850).

extract_protocol:
For Hi-C, nuclei were extraced after fixing using a cell lysis buffer.
All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit.

value: embryonic stem cells

value: no treat

tag: protocol

value: Hi-C

tag: restriction enzyme

value: HindIII


title: 341

tag: age

tag: experimental group


title: C132


title: 352_re-analyzed

description: re-analysis of GSM4443539


title: C129


title: C131


title: shP150_TSC_H3p12_rep1

description:
Biological replicate 1 of 2.
shP150_H3p12.bw


title: C128


title: Hi-C H9 replicate C


title: shP150_TSC_H3p3_rep1

description:
Biological replicate 1 of 2.
shP150_H3p3.bw


title: 329


title: shP150_TSC_H3p12_rep2

description:
Biological replicate 2 of 2.
shP150_H3p12.bw


title: shP150_TSC_H3K9me3_rep2

description:
Biological replicate 2 of 2.
shP150_H3K9me3.bw


title: Hi-C H9 replicate B


title: W323


title: Hi-C H9 replicate A


title: SHF rep 1

tag: lineage


title: SHF rep 3

tag: cell type


title: shP150_TSC_input_rep2

description:
Biological replicate 2 of 2.
none

tag: strain

value: input


title: V783

tag: weeks post-deletion


title: 328


title: shP150_TSC_H3K9me3_rep1

description:
Biological replicate 1 of 2.
shP150_H3K9me3.bw


title: 316


title: V786

tag: tacer


title: Hi-C H9 replicate 4


title: shP150_TSC_input_rep1

description:
Biological replicate 1 of 2.
none


title: Hi-C H9 replicate 3


title: Hi-C H9 replicate E


title: gastric cancer cells AGS_exosome_rep3

city: Fuzhou

first: Sheng

state: Fujian

address: 20 Cha Zhong Lu

department: Department of Pathology

institute: The First Affiliated Hospital of Fujian Medical University

description: non-coding RNA

data_processing:
remove adapter, poly Ns, reads samller than 17 nts with fastqc
using miRDeep2, we align clean reads against sequences in miRBase22 library to predict known miRNA expression.
The expression levels were normalized to RPM (Reads per Million), that is number of reads mapping to miRNA/ number of reads in Clean data)×1000000
Differential expressed miRNAs were calculated using edgeR, and filtered using |log2(Fold Change)| >= 1 and p-value < 0.05
Assembly: miRBase22(reads were blasted directly against library)
Supplementary files format and content: comma seprated values; expressions of human miRNAs in RPM
Supplementary files format and content: comma seprated values; expressions of EBV miRNAs in RPM

source_name: gastric epithelial cells

growth_protocol: SNU-719 (EBV positive gastric cancer cell line) and AGS (EBV negative gastric cancer cell line) were cultured in RPMI-1640 and F12, respectively. 5% fetal bovine serum without exosomes and penicillin and streptomycin (100U/ mL) were added into the culture medium before use. When the cells grow vigorously (with a degree of fusion up to about 70%), the supernatant is collected.

extract_protocol:
Total RNA was extracted from cells and exosomes using the high pure RNA extraction kit (TRIzol) in accordance with the manufaxturer’s protocol. The OD260 and OD280 values and ratios of 1μL extracted samples were determined by ultraviolet spectrophotometer to determine the concentration and purity of extracted samples.
Approximately 1 μg of total RNA from each sample was used to prepare the miRNA sequencing library. The strips between 17 and 32 nt were cut by polyacrylamide gel electmphoresis（PAGE) and the products were recycled. T4 RNA ligase (Epicenter, San Diego, CA, USA) was used to connect the isolated small RNA to the 3' end and then the isolated small RNA to the 5 'end using the same method. The sRNA connected by the connector was used as the template for RT-PCR, and the single-stranded cDNA template was amplified into double-stranded cDNA, and then PCR amplification was conducted. Then the gel was cut and the target fragment library was recycled. The constructed library was used to detect quality and yield using Agilent 2100 Bioanalyzer and ABI StepOnePlus Real Time PCR System. The library with qualified quality test was sequenced.

treatment_protocol: No special treatment other than growth protocol described above was conducted.

tag: ebv status

value: negative

value: Stomach

value: untreated

value: AGS

tag: rna population

value: exosome


title: V932

tag: digest time

tag: batch


title: V930


title: shCont_TSC_H3p3_rep2

description:
Biological replicate 2 of 2.
shControl_H3p3.bw


title: gastric cancer cells AGS_exosome_rep2

description: non-coding RNA

tag: tissue

tag: treatment


title: Hi-C H9 replicate 2

tag: cell line


title: Hi-C H9 replicate 1


title: W318

tag: genotype


title: shCont_TSC_H3p3_rep1

description:
Biological replicate 1 of 2.
shControl_H3p3.bw

tag: antibody


title: gastric cancer cells AGS_exosome_rep1

description: non-coding RNA


title: shCont_TSC_H3p12_rep2

description:
Biological replicate 2 of 2.
shControl_H3p12.bw


title: V785


title: hESC_lung_M2

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2)
Cellranger mkfastq was used for sample demultiplexing and fastq generation.
Cellranger count was used to align reads to either the 10X pre-built human reference genome (GRCh38 v3.0.0) for hESC_lung_ctrl, M1 and M2
Genome_build: 10X pre-built human reference genome (GRCh38 v3.0.0) for hESC_lung_ctrl, M1 and M2
Supplementary_files_format_and_content: matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: Lung cells and M2 macrophages co-culture

growth_protocol: The hESC line-RUES2 or H1 was cultured on irradiated mouse embryonic fibroblasts (Global Stem) at a density of 20,000- 25,000 cells/cm2 in a medium of DMEM/F12, 20% knockout serum replacement (Life Technologies), 0.1 mM β-mercaptoethanol (Sigma Aldrich) and 20 ng/ml bFGF (R&D Systems), and medium was changed daily. hESC cultures were maintained in an undifferentiated state at 37 °C in a 5% CO2/air environment until stem cells reached about 90% confluence.

extract_protocol:
Single-cell suspensions were generated by dissociating the cultured RUES2 cells with 0.05% Trypsin/0.02% EDTA for 10-15 min, followed with passing through 40µM strainer.
Single-cell capture, reverse transcription, cell lysis, and library preparation was performed using the Single Cell 3' version 2 kit and chip according to the manufacturer’s protocol (10x Genomics)

treatment_protocol: hESC differentiation into endoderm was performed in serum-free differentiation (SFD) medium of IMDM/F12 (3:1) (Life Technologies) supplemented with N2 (Life Technologies), B27 (Life Technologies), 50 μg/ml  ascorbic acid, 2 mM Glutamax, 0.4 μM monothioglycerol, 0.05% BSA at 37 °C in a 5% CO2/5% O2/95% N2 environment. hESCs were treated with Accutase (Stemcell Technologies)  and plated onto low attachment 6-well plates (Corning Incorporated), resuspended in endoderm induction medium containing 10 μM Y-27632, 0.5 ng/ml human BMP-4, 2.5 ng/ml human bFGF, 100 ng/ml human Activin A, for 72-76 hours dependent on the formation rates of endoderm cells. On day 3, the endoderm bodies were dissociated into single cells using 0.05% Trypsin/0.02% EDTA and plated onto fibronectin-coated, 24-well tissue culture plates (~100,000–150,000 cells/well). For induction of anterior foregut endoderm (AFE), the endoderm cells were cultured in SFD medium supplemented with 1.5 μM Dorsomorphin dihydrochloride (R&D Systems) and 10 μM SB431542 (R&D Systems) for 48 h, and then switched to 24 h of 10 μM SB431542 and 1 μM IWP2 (R&D Systems) treatment. For induction of early stage lung progenitor cells (day 6–15), the resulting anterior foregut endoderm was treated with 3 μM CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human FGF-7, 10 ng/ml human BMP-4 and 50-60nM all-trans retinoic acid (ATRA), in SFD medium for 8–10 d. The day 10-15 cultures were maintained in a 5% CO2/air environment. On days 15 and 16, the lung progenitor cells were replated after one minute trypsinization onto fibronectin-coated plates, in the presence of SFD containing 3 μM CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human FGF7, in a 5% CO2/air environment. For differentiation of mature lung cells (day 25 to 55), cultures were re-plated after brief trypsinization onto 3.3% Matrigel-coated 24-well plates in SFD media containing maturation components containing 3 μM CHIR99021, 10 ng/ml human FGF-10; 10 ng/ml human FGF-7, and DCI (50 nM Dexamethasone, 0.1 mM 8-bromo-cAMP (Sigma Aldrich) and 0.1 mM IBMX (3,7-dihydro-1-methyl-3-(2-methylpropyl)-1H-purine-2,6-dione) (Sigma Aldrich)). For macrophages polarization, 100ng/mL LPS and 10ng/mL IFNγ were added for M1 macrophage induction, or 20 ng/m IL-4 was added for M2 macrophage supplemented with 50 ng/mL M-CSF, respectively.

value: RUES2 and H1 human embryonic stem cell

tag: cell types

value: hESC-derived lung cells and M2 macrophages

tag: protocol

value: co-culture


title: gastric cancer cells AGS_cell_rep3

description: non-coding RNA

value: whole cell


title: 325

tag: age

value: 37 weeks

value: Renal cortex

tag: experimental group


title: shCont_TSC_H3K9me3_rep2

description:
Biological replicate 2 of 2.
shControl_H3K9me3.bw

value: hybrid C57BL/6 / JF1


title: Hi-C H9 replicate 5

tag: cell type

value: embryonic stem cells

tag: restriction enzyme