title: S_100213


title: DVS192 RNA-seq

status: Public on Mar 14 2022

type: SRA

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
DVS192_S11_L002_R1_001

library_source: transcriptomic

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

organism: Homo sapiens

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

tag: flowcell

tag: Sex

value: Female

tag: age

tag: plateletfunctionscore

tag: logscaledsalicylatelevel


title: S_100212

type: RNA

city: New York

first: Erik

middle: Roy

last: Rasmussen

state: NY

address: 430 East 29th Street

institute: Eli Lilly

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Data was normalized using SCAN (SCAN.UPC package from Bioconductor).
Probe group file: Decipher-v1.r1.pgf
Meta-probeset file: Decipher-v1.r1.mps
Background probe file: Decipher-v1.r1.antigenomic.bgp
CEL layout file: Decipher-v1.r1.clf
Quality Control Content file: Decipher-v1.r1.qcc

label: biotin

molecule: total RNA

source_name: FFPE bladder cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications.

growth_protocol: Not Applicable

extract_protocol: NOT PROVIDED

treatment_protocol: Not Applicable

tag: treatment

value: LY3009806 + Docetaxel

tag: primary site

value: Bladder


title: S_100210

value: Placebo + Docetaxel


title: S_100232


title: RNA16

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

data_processing:
alignment and gene count by STAR (version 2.5.2b)
gene annotation used GENCODE version 25 (Ensembl 85)
differential expression analysis carried out in R (3.3.3) using Bioconductor package DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-deliminated data matrix of normalized gene counts

organism: Mus musculus

source_name: BPDCN primary samples

growth_protocol: After being quickly thawed in a 37ºC water bath, cryopreserved primary BPDCN cells were resuspended in 10 mL of MEM, Alpha 1X (Corning) supplemented with 20% FBS (Invitrogen), and centrifuged at 300 g for 5 minutes.  Cells were resuspended in mixture of 10 mL of MEM, Alpha 1X containing 20% FBS, 0.1 mg/ml heparin, 10 units/mL DNase (Thermo Scientific), and 10mM MgSO4 (Sigma). Cells were incubated for 15 minutes in 37ºC incubator in the above mixture and centrifuged at 300 g for 5 minutes. After centrifugation, BPDCN cells were resuspended in the injection medium (serum-free RPMI 1640 medium) at a concentration of 2×106 BPDCN cells/100 µL. Cells were kept on ice until injection into immunodeficient NSG or NSGS mice (purchased from Jackson lab) via the tail vein (100 µL/mouse).

extract_protocol:
RNA was isolated using Qiagen RNeasy Kit and used for RT-PCR or RNA Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Peripheral blood

tag: strain

value: NSG-S

value: spleen

value: UCART123  1M group relapse

tag: cell population

value: from CD123- cells


title: S_100209

value: Non-Bladder


title: S_100211


title: DVS190 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS190_S9_L002_R1_001

value: 325 mg Aspirin


title: DVS191 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS191_S10_L002_R1_001

value: 81 mg Aspirin


title: S_100220


title: S_100208


title: RNA13

value: UCART123  1M group


title: S_100206


title: DVS176 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS176_S21_L003_R1_001


title: A549 cells transduced with shLITATS1-2 (Replicate #2) [sample_11]

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

data_processing:
RNA-Seq files were processed using the opensource BIOWDL RNAseq pipeline v4.0.0 (https://zenodo.org/record/3975552#.YiBgxIzMKV4) developed at the LUMC.
This pipeline performs FASTQ preprocessing (including quality control, quality trimming, and adapter clipping), RNA-Seq alignment, read quantification, and optionally transcript assembly.
FastQC was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.10) with default settings.
RNA-Seq reads’ alignment was performed using STAR (v2.7.5a) on GRCh38 human reference genome.
The gene read quantification was performed using HTSeq-count (v0.12.4) with setting “–stranded=no”. The gene annotation used for quantification was Ensembl version 99.
Assembly: GRCh38
Supplementary files format and content: raw read count in TSV format

source_name: human lung adenocarcinoma cell line

growth_protocol: A549 cells were purchased from American Type Culture Collection (ATCC) and cultured in Dulbecco’s modified Eagle medium (DMEM; Thermo Fisher Scientific; 41965062) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific; 16000044) and 100 U/mL penicillin/streptomycin (Thermo Fisher Scientific; 15140163).

extract_protocol:
RNA was extracted by a NucleoSpin RNA kit (Macherey Nagel; Cat. Nr.: 740955) according to the manufacturer's instructions.
Library preparation and sequencing were performed by Beijing Genomics Institute (BGI) in China using the DNBSEQ platform.

treatment_protocol: Cells were transduced with lentiviral expressing constructs overnight. After two days culture, 1 ng/mL puromycin was added to the medium for selecting stable cells. After another 3 days culture, cells were ready for RNA isolation.

tag: cell line/type

value: A549 cells (human lung adenocarcinoma cell line)

value: Transduced with expressing construct for shLITATS1-2


title: RNA12

value: UCART123 1M group

value: from CD123+ cells


title: S_100237


title: DVS175 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS175_S29_L004_R1_001

value: Pass

value: Female


title: A549 cells transduced with shLITATS1-2 (Replicate #3) [sample_12]


title: S_100203

value: LY3009806 + Docetaxel

value: Bladder


title: RNA10

value: Peripheral blood


title: DVS177 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS177_S1_L001_R1_001


title: DVS189 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS189_S8_L002_R1_001


title: RNA7

value: NSG-S


title: S_100201


title: S_100204


title: RNA9

value: spleen

value: UCART123 3M group


title: DVS149 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS149_S7_L002_R1_001


title: RNA5

value: UCART123 10M group

value: from CD123- cells


title: A549 cells transduced with shLITATS1-2 (Replicate #1) [sample_10]


title: RNA8


title: S_100202

value: Placebo + Docetaxel


title: S_100199


title: A549 cells transduced with shLITATS1-1 (Replicate #3) [sample_9]

value: Transduced with expressing construct for shLITATS1-1


title: RNA6

value: Untreated


title: DVS133 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS133_S26_L004_R1_001

value: 180 mg Ticagrelor


title: S_100205

value: Non-Bladder


title: A549 cells transduced with shLITATS1-1 (Replicate #1) [sample_7]

value: A549 cells (human lung adenocarcinoma cell line)


title: A549 cells transduced with shLITATS1-1 (Replicate #2) [sample_8]


title: S_100200


title: DVS132 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS132_S25_L004_R1_001


title: RNA3


title: A549 cells transduced with shNT (Replicate #3) [sample_6]

value: Transduced with expressing construct for a non-targeting shRNA


title: RNA4

value: UCART123  1M group relapse


title: A549 cells transduced with shNT (Replicate #2) [sample_5]


title: RNA1

value: from CD123+ cells


title: DVS131 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS131_S24_L004_R1_001

value: Pass

value: 325 mg Aspirin

value: Female


title: S_100198

value: LY3009806 + Docetaxel

value: Bladder


title: A549 cells transduced with shNT (Replicate #1) [sample_4]


title: RNA2

value: Peripheral blood

value: NSG-S

value: spleen


title: DVS174 RNA-seq

value: Fail


title: Patient 76-P.41554.txt_miRNA

city: Tokyo

first: Sophia

last: Subat

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

country: Japan

institute: Japanese Foundation for Cancer Research

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).

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

source_name: lung adenocarcinoma

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

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

value: lung adenocarcinoma

tag: alk rearrangement status

value: positive


title: DVS.99 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-99_S13_L002_R1_001


title: S_100196

value: Placebo + Docetaxel


title: Patient 75-P.40310.txt_miRNA


title: DVS129 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS129_S22_L003_R1_001


title: Patient 73-P.39630.txt_miRNA


title: mfn1-/-mfn2-/-, 10 weeks old, rep 1

city: Dallas

first: Prashant

last: Mishra

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Data was processed using the BICF RNASeq Analysis Workflow (ssh://git@git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq.git) provided by the UTSouthwestern Bioinformatics Core Facility.
Reads were trimmed (trimgalore), and aligned to the reference genome using HiSAT2.
Readcounts were calculated using featureCounts.
Differential expression analysis was performed using DeSeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text files including logCPM counts for each sample.

source_name: tibialis anterior muscle

growth_protocol: Animals were maintained on standard chow diet, ad libitum, under a standard 12 hr light-dark cycle.

extract_protocol:
Skeletal muscle was dissected, frozen in liquid nitrogen, and homogenized. Total RNA was purified using the Rneasy Fibrous Tissue Mini Kit (Qiagen 74704).
The RNA-seq library was prepared using SMARTer® Stranded Total RNA Sample Prep Kit (Takara Bio) following the manufacturer’s protocol

treatment_protocol: None.

value: Tibialis anterior muscle

tag: genotype

value: 10 weeks


title: mfn1-/-mfn2-/-, 10 weeks old, rep 2


title: mfn1-/-mfn2-/-, 8 weeks old, rep 4

value: 8 weeks


title: S_100195


title: DVS.98 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-98_S12_L002_R1_001

value: 81 mg Aspirin


title: S_100197


title: S_100191


title: Patient 74-P.39736.txt_miRNA


title: S_100192


title: S_100194

value: Non-Bladder


title: mfn1-/-mfn2-/-, 8 weeks old, rep 3


title: Patient 72-P.39415.txt_miRNA


title: S_100188


title: DVS.97 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-97_S11_L002_R1_001

value: Pass


title: DVS130 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS130_S23_L004_R1_001


title: mfn1-/-mfn2-/-, 8 weeks old, rep 1


title: Patient 71-P.38143.txt_miRNA


title: mfn1-/-mfn2-/-, 6 weeks old, rep 3

value: 6 weeks


title: Patient 68-P.35799.txt_miRNA


title: DVS.89 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-89_S8_L001_R1_001

value: Male


title: S_100185


title: DVS123 RNA-seq


title: mfn1-/-mfn2-/-, 6 weeks old, rep 2


title: Patient 70-P.36885.txt_miRNA


title: DVS.90 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-90_S9_L002_R1_001


title: DVS.88 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-88_S7_L001_R1_001

value: 325 mg Aspirin


title: S_100184

value: LY3009806 + Docetaxel

value: Bladder


title: mfn1-/-mfn2-/-, 6 weeks old, rep 4


title: Patient 67-P.35648.txt_miRNA


title: mfn1-/-mfn2-/-, 6 weeks old, rep 1


title: S_100186


title: DVS.8R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-8R_CAGATC_L001_R1_CAT


title: S_100187


title: Patient 66-P.33560.txt_miRNA


title: Patient 69-P.36567.txt_miRNA


title: mfn1-/-mfn2-/-, 8 weeks old, rep 2


title: S_100189


title: DVS.91 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-91_S10_L002_R1_001

value: 180 mg Ticagrelor


title: mfn1-/-mfn2-/-, 4 weeks old, rep 3

value: 4 weeks


title: DVS.87 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-87_S6_L001_R1_001


title: S_100183


title: S_100180


title: mfn1-/-mfn2-/-, 4 weeks old, rep 2


title: S_100182


title: Patient 65-P.32659.txt_miRNA


title: Patient 63-P.27265.txt_miRNA


title: DVS.86 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-86_S5_L001_R1_001


title: Patient 62-P.26813.txt_miRNA


title: S_100179


title: mfn1-/-mfn2-/-, 4 weeks old, rep 4


title: S_100181


title: wild-type, 10 weeks old, rep 1

value: wild-type


title: Patient 61-P.26422.txt_miRNA

value: lung adenocarcinoma


title: Patient 64-P.27998.txt_miRNA

value: positive


title: Patient 60-P.26020.txt_miRNA


title: DVS.85 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-85_S4_L001_R1_001


title: wild-type, 8 weeks old, rep 3


title: DVS.84 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-84_S3_L001_R1_001


title: mfn1-/-mfn2-/-, 4 weeks old, rep 1


title: Patient 58-P.22231.txt_miRNA


title: S_100174


title: wild-type, 10 weeks old, rep 2


title: wild-type, 8 weeks old, rep 1


title: DVS.39R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-39R_GTGAAA_L006_R1_CAT


title: DVS.32R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-32R_GATCAG_L005_R1_CAT


title: S_100173

value: Placebo + Docetaxel


title: DVS.82 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-82_S1_L001_R1_001


title: wild-type, 6 weeks old, rep 4

value: Tibialis anterior muscle


title: S_100178


title: S_100176


title: S_100171


title: DVS.7R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-7R_TGACCA_L001_R1_CAT


title: wild-type, 6 weeks old, rep 3


title: wild-type, 8 weeks old, rep 2


title: DVS.29R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-29R_AGTTCC_L004_R1_CAT


title: Patient 59-P.24461.txt_miRNA

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


title: wild-type, 8 weeks old, rep 4


title: DVS.31R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-31R_TTAGGC_L005_R1_CAT


title: DVS.45R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-45R_AGTCAA_L007_R1_CAT


title: Patient 53-P.12552.txt_miRNA


title: DVS.27R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-27R_TGACCA_L004_R1_CAT

value: Female


title: S_100168


title: S_100175


title: Patient 52-P.12215.txt_miRNA


title: wild-type, 6 weeks old, rep 1


title: S_100167


title: DVS.26R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-26R_CGATGT_L004_R1_CAT


title: Patient 57-P.20653.txt_miRNA


title: DVS.83 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-83_S2_L001_R1_001


title: S_100166


title: S_100177


title: Patient 55-P.12872.txt_miRNA


title: S_100165


title: S_100169


title: DVS.24R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-24R_GGCTAC_L008_R1_CAT


title: S_100172


title: wild-type, 4 weeks old, rep 2


title: DVS.229 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-229_S16_L002_R1_001


title: Patient 56-P.19854.txt_miRNA


title: Patient 49-P.9968.txt_miRNA


title: Patient 54-P.12727.txt_miRNA


title: DVS.30R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-30R_CCGTCC_L004_R1_CAT


title: DVS.228 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-228_S15_L002_R1_001


title: wild-type, 6 weeks old, rep 2


title: DVS.25R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-25R_AGTCAA_L008_R1_CAT


title: wild-type, 4 weeks old, rep 3


title: S_100162


title: S_100163


title: S_100164


title: Patient 48-P.9034.txt_miRNA


title: S_100161


title: wild-type, 4 weeks old, rep 1


title: wild-type, 4 weeks old, rep 4


title: Macrophages-FOXO3-KO3

city: New Orleans

first: Suzana

last: Savkovic

state: LA

address: 1324 Tulane Ave

department: Pathology

institute: Tulane Univeristy

data_processing:
Paired-end were aligned to mm10 transcriptome using STAR(v.2.6.1d).  Abundance levels were calculated using Kallisto(v.0.46.0) and differential expression testing performed using DESeq2.
Abundance levels (read counts) were collated for each sample across all conditions
Genome_build: mm10
Supplementary_files_format_and_content: text files of read counts

source_name: Intraperitoneal macrophage

growth_protocol: Mice were housed in microisolator cages under pathogen free conditions and had free access to standard chow diet and water.

extract_protocol:
Total RNA from harvested macrophages was isolated using the miRNeasy kit (Zymo Research, Irvibe,CA) following the manufacturer’s instructions.
paired-end sequencing of 76bp reads on Illumina NextSeq

value: FOXO3 KO

value: Intraperitoneal macrophage

value: 6-8 weeks old


title: DVS.226 RNA-seq

value: Fail

value: 81 mg Aspirin


title: Patient 47-P.8993.txt_miRNA


title: Patient 51-P.10172.txt_miRNA


title: DVS.227 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-227_S14_L002_R1_001

value: Pass


title: Patient 46-P.8398.txt_miRNA


title: Macrophages-FOXO3-KO2


title: Patient 50-P.10027.txt_miRNA


title: Macrophages-WT3

value: WT


title: DVS.225 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-225_S12_L002_R1_001


title: DVS.224 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-224_S34_L005_R1_001

value: Male


title: Patient 45-P.7378.txt_miRNA


title: Patient 44-P.6445.txt_miRNA


title: Macrophages-WT2


title: Patient 43-P.4808.txt_miRNA


title: S_100160

value: LY3009806 + Docetaxel

value: Non-Bladder


title: Macrophages-WT1


title: S_100158


title: Macrophages-FOXO3-KO1


title: S_100156

value: Bladder


title: DVS.222R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-222R_S11_L002_R1_001

value: 180 mg Ticagrelor


title: S_100157


title: Patient 41-P.2374.txt_miRNA

value: lung adenocarcinoma


title: Patient 42-P.4180.txt_miRNA

value: positive


title: 86A9

city: Vancouver

first: Fabio

last: Rossi

state: BC

address: 2222 Health Sciences Mall

department: School of Biomedical Engineering

country: Canada

institute: University of British Columbia

description: Sorted on CD45+ NK1/Ly6G/CD3e- CD11bing SiglecF+

data_processing:
Illumina base call files were de-multiplexed by bcl2fastq2 (v. 2.20) on Basespace. Adaptor sequences were trimmed and low-quality reads (< 35 base pairs) were discarded. Additionally, Bowtie was used to remove read pairs that aligned against abundant sequences. Demultiplexed read sequences were then aligned to the mm10 genome reference using STAR aligner. The number of aligned reads to each annotated gene was tallied with RnaReadCounter to generate read-count matrices for all samples, which were used as inputs for downstream analyses. Bowtie, STAR, and RnaReadCounter are tools built under RNA-Seq Alignment (v 1.1.1).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample

extract_protocol:
Muscle were digested, single cell suspension stained and eosinophils were sorted as follow: CD45+ NK1/Ly6G/CD3e- CD11bing SiglecF+, diretly into RNAzol
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on the Illumina NextSeq 500 with Paired End 42bp × 42bp reads.

tag: ttissue

value: Muscle 3 days post ntx

tag: cell type

value: Eosinophil


title: DVS.220 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-220_S9_L002_R1_001

value: 325 mg Aspirin

value: Female


title: DVS.218 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-218_S7_L001_R1_001


title: Patient 39-P.2001.txt_miRNA

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


title: Patient 40-P.2075.txt_miRNA


title: DVS.219 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-219_S8_L001_R1_001


title: 81E3


title: 82C6


title: 87A3


title: S_100154

value: Placebo + Docetaxel


title: DVS.217 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-217_S6_L001_R1_001


title: DVS.221 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-221_S10_L002_R1_001


title: Patient 38-P.833.txt_miRNA


title: S_100151


title: DVS.216 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-216_S5_L001_R1_001


title: Patient 37-P.351.txt_miRNA


title: DVS.215 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-215_S4_L001_R1_001


title: 86A8


title: S_100153


title: S_100150


title: Patient 36-P.231.txt_miRNA


title: DVS.214 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-214_S3_L001_R1_001


title: 82C7


title: 81E2


title: TSCclone-shP150_late2cell_RNAseq_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.
tpm_embryo_gene_counts_matrix.tsv

data_processing:
Adaptor sequences were excluded using Trime Galora!. RNA-seq reads were aligned to mouse genome (mm10) using HISAT2 command (version 2.1.0) with default parameters (Kim et al., 2015). The expression levels were quantified to transcripts per million (TPM) using StringTie command (version 2.1.1) (Liao et al., 2014; Pertea et al., 2015) .
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

source_name: Late 2-cell embryo

growth_protocol: MII oocytes were collected from adult B6D2F1 female mice via superovulation and enucleated in HEPES-buffered KSOM medium containing 7.5 g/ml cytochalasin B (Calbiochem # 250233) using a Piezo-driven micromanipulator (Primetech # PMM-150FU). The donor nuclei of TSCs were injected into the enucleated oocytes using a Piezo-driven micromanipulator. After 1 hour incubation in KSOM, reconstructed SCNT oocytes were activated by incubating in Ca-free KSOM containing 3 mM strontium chloride, 5 g/ml cytochalasin B, and 50 nM Trichostatin A (TSA) for 1 hour, and further cultured in KSOM with 5 µg/ml cytochalasin B and 50 nM TSA for 4 hours. Some SCNT embryos were injected with 10 pl of 1500 ng/ml mouse Kdm4d mRNA at 5–6 hours post activation (hpa) using a Piezo-driven micromanipulator. The embryos were cultured with KSOM containing 50 nM TSA for an additional 3–5 hours (i.e., 8–10 hpa), followed by further culture in KSOM.

extract_protocol: SMART-Seq v4 PLUS Kit (TAKARA #R400752) was used to construct RNA-seq libraries from late 2 cell embryos. We picked up 5 embryos per reaction and subjected to construction of libraries according to manufactures instructions. Next-seq was used for sequencing with 75 bp single-end mode.

value: hybrid C57BL/6 / DBA2

value: Late 2-cell embryo


title: Patient 34-N.6400.txt_miRNA

value: negative


title: S_100149


title: Patient 35-N.10385.txt_miRNA


title: S_100147


title: TSCclone-shP150_late2cell_RNAseq_rep1

description:
Biological replicate 1 of 2.
tpm_embryo_gene_counts_matrix.tsv


title: S_100148


title: Patient 33-N.3947.txt_miRNA


title: TSCclone-shCont_late2cell_RNAseq_rep3

description:
Biological replicate 3 of 3.
tpm_embryo_gene_counts_matrix.tsv


title: DVS.212 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-212_S1_L001_R1_001

value: Pass


title: DVS.211 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-211_S63_L008_R1_001


title: S_100146


title: DVS.210 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-210_S62_L008_R1_001


title: Patient 32-N.3767.txt_miRNA


title: Patient 31-N.3479.txt_miRNA


title: TSCclone-shCont_late2cell_RNAseq_rep1

description:
Biological replicate 1 of 3.
tpm_embryo_gene_counts_matrix.tsv


title: TSCclone-Kdm4d_late2cell_RNAseq_rep3


title: TSCclone-shCont_late2cell_RNAseq_rep2

description:
Biological replicate 2 of 3.
tpm_embryo_gene_counts_matrix.tsv


title: non-ST-elevation MI (NSTEMI) 3

city: Salamanca

first: Luis

middle: Miguel

last: Rincon

state: Salamanca

address: Paseo de San Vicente 58-182

department: Cardiology

country: Spain

institute: Hospital Universitario de Salamanca

description: Test

data_processing: Array data was normalized using the average of the expression of all miRNAs exhibiting CT equal to or less than 34.Data was analyzed using GenEx v.6 software

label: SYBR Green

source_name: Serum

label_protocol: PCR assays were performed using miRCURY LNA Universal RT microRNA PCR, 4x Human panel I+II in 384well PCR plates (type R), one reaction each of 752 human microRNAs plus control assays. For use with Roche LightCycler 480 instruments, following manufacturer´s indications  (Exiqon 203616).  miRCURY LNA™ Universal RT microRNA PCR, Polyadenylation and cDNA synthesis kit II (Exiqon) was used for cDNA synthesis. 4ul of RNA was used as template for RT in a final volume of 20 μL. An external RNA (cell-miR-39) was added and further amplified as a control of cDNA synthesis efficiency. Quantitative real-time PCR were performed (Light Cycler 480, Roche. PCR initial heat activation 2 min 95°C; step cycling: Denaturation 10s 95°C, Combined annealing/extension 60 s 56°C .Number of cycles 45. Melting curve analysis 60–95°C

extract_protocol: Isolation of total RNA enriched in miRNAs was performed using the miRCURY  RNA Isolation kit-Biofluids (Exiqon, 300112) and 200ul of serum

tag: sample type

value: individual sample


title: Patient 30-N.3323.txt_miRNA


title: DVS.209 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-209_S61_L008_R1_001

value: 81 mg Aspirin

value: Male


title: Patient 29-N.3236.txt_miRNA


title: non-ST-elevation MI (NSTEMI) 1

description: Test


title: DVS.208 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-208_S60_L008_R1_001


title: ST-segment elevation MI (STEMI) 3

description: Test


title: Patient 28-N.3221.txt_miRNA

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


title: DVS.207 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-207_S59_L008_R1_001


title: DVS.206 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-206_S58_L008_R1_001


title: Patient 27-N.3081.txt_miRNA


title: TSCclone_late2cell_RNAseq_rep3


title: ST-segment elevation MI (STEMI) 1

description: Test


title: non-ST-elevation MI (NSTEMI) 2

description: Test


title: DVS.205 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-205_S57_L008_R1_001


title: Patient 26-N.2993.txt_miRNA


title: TSCclone_late2cell_RNAseq_rep2


title: Patient 25-N.2784.txt_miRNA


title: DVS.204 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-204_S56_L008_R1_001


title: Healthy pool 1

description: Control

value: pool of five patients


title: ST-segment elevation MI (STEMI) 2

description: Test


title: Patient 24-N.2766.txt_miRNA


title: TSCclone_late2cell_RNAseq_rep1


title: DVS.213 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-213_S2_L001_R1_001


title: DVS.203 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-203_S55_L007_R1_001


title: High density layer 2 TraDIS replicate B

city: Clayton

first: Thomas

middle: R

last: Smallman

state: Victoria

address: 19 Innovation walk

department: Microbiology

country: Australia

institute: Monash University

library_source: genomic

data_processing:
Raw fastq files were trimmed for Illumina and TraDIS adapter sequences using Trimmomatic v0.38 (http://www.usadellab.org/cms/?page=trimmomatic)
All trimmed read files were analysed using Bio-TraDIS v1.4.1 (https://github.com/sanger-pathogens/Bio-Tradis 10.1093/bioinformatics/btw022), bactera_tradis script was used to align trimmed reads that contained a correct Himar1 transposon tag to the Pasteurella multocida VP161 reference genome to identify transposon insertion sites, tradis_gene_insert_sites was used to generate gene-wise unique and total Himar1 insertions counts
The tradis_essentiality.R script from Bio-TraDIS v1.4.1 was used to identify genes essential for growth in rich media by comparing normalized unique Himar1 insertion sites across the entire genome
Genes important for capsule production were identified using modified TraDIS scripts (https://github.com/francesca-short/tradis_scripts https://doi.org/10.1128/mBio.01863-18), the Tradis_comparison_positive_selection.R script was used to identify genes that had a log2 fold change increase > 2 for Himar1 insertions in the HD2 TraDIS libraries compared to the LD2 TraDIS libraries, with a q-value < 0.001 and an insertion index > 0.8.
Genome_build: Pasteurella multocida strain VP161 (NZ_CP048792.1)
Supplementary_files_format_and_content: unique Himar1 and total Himar1 insertions per gene, text file, comma separated

molecule: genomic DNA

organism: Pasteurella multocida

source_name: Bacterial cells

growth_protocol: Growth to OD600 0.5 in heart infusion broth

extract_protocol:
HiYield genomic DNA MiniKit (RBC bioscience)
Modified TraDIS library preparation protocol based on 10.1093/bioinformatics/btw022
Illumina MiSeq v2, 150 bp single end

treatment_protocol:
separation twice through a 10%-40%-80% Percoll gradient
As above

value: AL3145 Himar1 mutants recovered from high density layer 2

tag: library

value: TraDIS library


title: High density layer 2 TraDIS replicate C


title: IVF_late2cell_RNAseq_rep3


title: TSCclone-Kdm4d_late2cell_RNAseq_rep2


title: High density layer 2 TraDIS replicate A


title: IVF_late2cell_RNAseq_rep2


title: TSCclone-Kdm4d_late2cell_RNAseq_rep1


title: Low density layer 2 TraDIS replicate C

value: AL3145 Himar1 mutants recovered from low density layer 2


title: DVS.201 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-201_S53_L007_R1_001

tag: flowcell


title: Patient 23-N.2745.txt_miRNA

value: lung adenocarcinoma


title: IVF_late2cell_RNAseq_rep1


title: DVS.202 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-202_S54_L007_R1_001

value: 180 mg Ticagrelor

tag: Sex


title: Low density layer 2 TraDIS replicate B


title: DVS.200 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-200_S52_L007_R1_001

tag: age


title: Low density layer 2 TraDIS replicate A


title: Patient 21-N.2532.txt_miRNA


title: DVS.1R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-1R_ATCACG_L008_R1_CAT

tag: plateletfunctionscore


title: Rich media TraDIS replicate B2

treatment_protocol:
none
As above

value: AL3145 Himar1 mutants recovered following growth in rich media


title: DVS.19R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-19R_GTGAAA_L003_R1_CAT

tag: logscaledsalicylatelevel


title: Patient 20-N.2326.txt_miRNA


title: Rich media TraDIS replicate B1


title: DVS.198 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-198_S50_L007_R1_001


title: Patient 19-N.2317.txt_miRNA


title: DVS.199 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-199_S51_L007_R1_001

value: 325 mg Aspirin


title: Patient 18-N.2245.txt_miRNA


title: Rich media TraDIS replicate A2


title: Patient 17-N.2231.txt_miRNA


title: Rich media TraDIS replicate A1


title: Patient 22-N.2697.txt_miRNA


title: Healthy pool 2

description: Control


title: Patient 16-N.2145.txt_miRNA


title: DVS.197 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-197_S49_L007_R1_001

value: Female


title: brain endothelial cell_NgBR-siRNA_rep3

city: Mineola

first: Qing

middle: Robert

last: Miao

address: 101 Mineola Blvd

department: Foundations of Medicine

institute: NYU Long Island School of Medicine

data_processing:
Sequencing reads were processed through the MAPR-Seq
Differential expression analysis completed with edgeR
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Human brain microvascular endothelial cells were purcashed from Cell Systems (ACBRI376) and kept in complete growth mediuem from Cell Systems (4Z0-500).

extract_protocol:
RNA were isolated using Qiagen Rneasy Mini kit (74106).
Libraries were prepared according to manufacturer’s protocols (TruSeq stranded mRNA, Illumina, San Diego, CA, USA)

treatment_protocol: Cells were transfected with siRNA for 48 hours

value: human brain microvascular endothelial cells

tag: treatment

value: NgBR siRNA


title: DVS.196 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-196_S48_L007_R1_001


title: DVS.195 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-195_S47_L006_R1_001


title: L2AKOLDL

city: Bronx

first: Julio

last: Madrigal-Matute

state: New York

address: 1300 Morris Park Ave, C504

department: Developmental and Molecular Biology

institute: Albert Einstein College of Medicine

hyb_protocol: Hybridized to Agilent Mouse 8x60K.

scan_protocol: standard Agilent protocol

data_processing: Data were processed using the oligo package and normalized using Robust Multiarray Average (RMA) method. Gene set was filtered to remove genes without Entrez or GO annotation (21912 genes out of 55682) and genes with an IQR > 0.5.

source_name: VSMCs

label_protocol: Cy3-labeled RNA (0.6 μg) from each condition were hybridized to Agilent Mouse 8x60K.

growth_protocol: Aortic vascular smooth muscle cells (VSMC) were isolated from 5 aortas of wild-type (WT) and LAMP-2AKO (L2AKO). Briefly, adhering fat and connective tissue were removed by blunt dissection from the thoracic aorta. Vessels were opened longitudinally and preincubated in DMEM (Whitaker) containing 1 mg/mL collagenase (type II, 290 U/mg), penicillin (100 U/mL), streptomycin (100 lg/mL), and glutamine (2 mmol/L) (Sigma) for 15 to 20 minutes at 37°C in 95% air/5% CO2. Then aortas were minced into 1-mm pieces, incubated for an additional 1.5 to 2 hours, and rinsed twice with PBS to remove the cells, which were counted and seeded at a concentration of 104 cells/cm2 in plastic culture flashes (Costar) in DMEM with 10% FBS. Cells were harvested for passaging at 2- to 3-day intervals and used between the 12 and 16 passages.

extract_protocol: VSMCs were harvested using Trizol reagent. Rnaeasy plus mini kit was used to isolate RNA. 1 ug of total RNA for the microarray.

treatment_protocol: VSMCs were grown to confluence in growth medium and then for experimental analysis, cells were incubated for 24h in DMEM media plus 5% LPDS with or without with or without LDL (150 μg/ml LDL-cholesterol) plus 0.1 U/ml of bovine lipoprotein lipase

value: VSMCs

tag: passage

tag: genotype/variation


title: Patient 14-N.1547_miRNA

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

tag: tissue

value: negative


title: brain endothelial cell_NgBR-siRNA_rep1


title: WTCtrl

tag: strain

value: wild type

value: control


title: L2AKOCtrl


title: Patient 13-N.1515_miRNA


title: brain endothelial cell_Control siRNA_rep2

value: control siRNA


title: Patient S54

city: Heidelberg

first: Jan

last: Budczies

address: Im Neuenheimer Feld 224

department: Institute Of Pathology

country: Germany

institute: Heidelberg University Hospital

hyb_protocol: Probes and target transcripts were hybridized at 65°C for 18 hours according to the manufacturer's recommendations.

scan_protocol: The samples were scanned at maximum resolution on the nCounter Digital Analyzer.

data_processing: Sample normalization of the gene expression data was performed by fitting a linear model to negative and positive controls and subsequent housekeeping gene normalization. For the latter, the 20 panel genes with the lowest coefficient of variation and an expression level of at least 100 in the TCGA lung ADC dataset were used as housekeepers (AKT1, API5, DNAJC14, EIF2B4, ELA, ERCC3, GLUD1, HDAC3, HMGB1, IFNAR1, MLH1, OAZ1, PUM1, RIPK1, SF3A1, STAT3, TBC1D10B, TLK2, TMUB2, and UBB).

source_name: colorectal cancer tissue

label_protocol: standard protocol

extract_protocol: 5 µm FFPE tissue sections of normal colorectal mucosa or carcinoma samples from Lynch syndrome individuals were deparaffinized and microdissected manually. Tumor areas with at least 80% tumor cell content were selected. Then, samples were digested with Proteinase K overnight. Nucleic acids were extracted with the automated system Promega Maxwell 16 LEV RNA FFPE Purification Kit (Promega, Madison, WI), treated with DNaseI at room temperature for 15 min (TURBO DNA-free ™ Kit, Thermo Fisher Scientific, Waltham, Massachusetts, USA) and used for RNA-based library preparation. The RNA concentration was measured fluorimetrically using the QuBit 2.0 RNA high sensitivity kit (ThermoFisher Scientific, Waltham, MA) with a minimum of 1 ng/ml set as quality threshold.

tag: group

value: carcinoma (Lynch syndrome)


title: DVS.194 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-194_S46_L006_R1_001

value: Pass


title: WTLDL

value: LDL (150 μg/ml LDL-cholesterol) plus 0.1 U/ml of bovine lipoprotein lipase


title: DVS.193 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-193_S45_L006_R1_001


title: Patient 12-N.1434_miRNA

tag: alk rearrangement status


title: brain endothelial cell_NgBR-siRNA_rep2


title: DVS.188 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-188_S44_L006_R1_001


title: Patient S53


title: GP124TTAC1

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

institute: Japanese Foundation Cancer Research

data_processing:
Fastq files were generated by CASAVA-1.8.2 from Illumina Hiseq output.
Fastq files were mapped to hg19 reference genome by bowtie2 to generate bam files.
Expression level is quantified by RSEM-1.3.0.
Genome_build: hg19
Supplementary_files_format_and_content: Rsem.genes.results file has columns named TPM and FPKM. Each columns represent Transcripts Per Million mapped reads and Fragments Per Kilobase of transcript and Million mapped reads for each gene.

source_name: juvenile gastric cancer tissue

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.
cDNA library was prepared with Ilumina TruSeq Stranded mRNA Library Preparation Kit

tag: disease

value: gastric cancer


title: Patient 15-N.1939.txt_miRNA


title: Patient 11-N.1354_miRNA


title: Patient S52


title: DVS.187 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-187_S43_L006_R1_001


title: Patient S55


title: brain endothelial cell_Control-siRNA_rep3


title: GP115TTAC1


title: Patient 9-N.795_miRNA


title: DVS.186 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-186_S42_L006_R1_001

value: 81 mg Aspirin


title: Patient S51


title: GP113TTAC1


title: Patient S50


title: brain endothelial cell_Control-siRNA_rep1


title: Patient 8-N.584_miRNA

value: lung adenocarcinoma


title: DVS.185 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-185_S41_L006_R1_001


title: Patient S49


title: DVS.183 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-183_S39_L005_R1_001

value: 180 mg Ticagrelor


title: Patient 7-N.557_miRNA


title: S_100155

value: Placebo + Docetaxel

tag: primary site

value: Bladder


title: 1Z174TTAC1


title: Patient S48


title: mRNA_PDX_rep5

source_name: mRNA from Patient Derived Xenograft sample

value: xenograft tumor


title: DVS.184R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-184R_S40_L006_R1_001

value: Female


title: Patient S47


title: DVS.182 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-182_S38_L005_R1_001


title: Patient 5-N.464_miRNA


title: mRNA_PDX_rep4


title: Patient 6-N.492_miRNA


title: Patient S45

source_name: colorectal mucosa tissue

value: mucosa (Lynch syndrome tumor patient)


title: DVS.181 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-181_S37_L005_R1_001


title: mRNA_PDX_rep3


title: Patient 4-N.321_miRNA


title: Patient S36


title: mRNA_PDX_rep2


title: DVS.180 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-180_S36_L005_R1_001

value: 325 mg Aspirin


title: Patient 3-N.215_miRNA

value: negative


title: DVS.17R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-17R_GCCAAT_L003_R1_CAT

value: Male


title: Patient S35


title: Patient 2-N.174_miRNA


title: Patient S34


title: Patient S46


title: DVS.179 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-179_S35_L005_R1_001


title: Patient 1-N.165_miRNA


title: Shear Input Rep2

city: PHILADELPHIA

first: Arndt

last: Siekmann

state: Pennsylvania

address: 421 Curie Boulevard, 1114 Biomedical Research Building II/III

department: Perelman School of Medicine

institute: UNIVERSITY OF PENNSYLVANIA

data_processing:
Sequencing reads were aligned to hg19 (human) or danRer10 (zebrafish) genomes
RNA-Seq. Data was mapped using TopHat2 v2.1.1. and differential gene expression analysis between flow-treated samples and static controls was performed using DESeq2. Read counts were obtained with HTSeq
ChIP-Seq. Sequencing reads from ChIP and input samples were mapped with Bowtie 2 v2.3.5. and Samtools v1.9.was used to edit the alignments. Reads were downsampled to equivalent read depth. Peak calling was performed with Genrich (https://github.com/jsh58/Genrich) applying the following parameters: genrich -v -e Y,MT -E blacklist.bed -t Sample1ChIP.bam, Sample2ChIP.bam -c Sample1Input.bam, Sample2Input.bam -o Sample.narrowPeak -k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50and peaks with FDR < 0.05 were used for further analysis.
ATAC-Seq. Sequencing reads were mapped with Bowtie2, downsampled to equivalent read depth and peak calling was performed with Genrich in ATAC-Seq mode using the following parameters: genrich -j -v -y -r -e Y,MT -E blacklist.bed -t Sample1.bam, Sample2.bam -o Sample.narrowPeak -k Sample.bedGraphish. Differential peak analysis was performed with DiffBind 50 and peaks with FDR < 0.05 were used for further analysis.
ChIP-Seq and ATAC-Seq tracks were produced with deepTools bamCoverage and normalized to sequencing depth
Assembly: hg19
Assembly: danRer10

source_name: Human umbilical vein endothelial cells

growth_protocol:
HUVEC were seeded on 6-cm BTF glass plates coated with cross-linked gelatin and cultured to confluence (approximately 105 cells/cm2) in EC growth medium.
Zebrafish were grown and crossed under standard conditions

extract_protocol:
RNA for RNA-Seq was extracted with RNeasy Micro Kit (Qiagen). Cells were cross-linked with formaldehyde (final concentration 1 %) for 5 min, sonicated and the cromatin was used for H3K27ac ChIP. For ATAC HUVEC were first frozen in the medium containing 10 % DMSO and used for OMNI-ATAC after thawing. For zebrafish RNA-Seq 300 embryos per condition were collected in ice cold 10 % DMSO and kept at -80°C for 2 min. Afterwards, embryos were washed twice with 1x Hanks’Balanced Salt Solution (HBSS, Gibco, # 14185-052)and deyolked with calcium-free Ringer’s solution. Embryos were then dissociated with trypsin-EDTA (0.5 %) and collagenase type IV (50 mg/ml). The reaction was stopped by addition of FCS (5 %) andcells were collected by centrifugation at 350 g for 5 min at 4°C and washed twice with 1x HBSS followed by centrifugation. After a final wash, cells were resuspended in 1x HBSS, passed through a 40 m nylon filter to obtain a single cell suspension, which was subjected to fluorescence-activated cell sorting (FACS). EGFP positive ECs were collected in RLT buffer (RNeasy Micro kit, Qiagen).
RNA Seq libraries were prepared using TruSeq Stranded Total RNA Sample Prep with RiboZero depletion. ChIP-Seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina). ATAC-Seq libraries were prepared using the protocol by Buenorosto et al (Buenorosto, Nat Met, 2013)

treatment_protocol:
The maximum flow of 18 dyn/cm2 was achieved by computer-controlled cone rotation in culture medium containing 3% polyvinylpyrrolidone (PVP) within ten minutes (ramp function) and then kept constant for the required time. The experiments were perfomed in in a BioTechFlow system (BTF system; MOS Technologies) at 37°C and under constant CO2 perfusion. Static controls were incubated in a cell culture incubator.
48 hpf Tg(kdrl:H2B-EGFP)mu122 zebrafish embryos were dechorionated at 48 hours post fertilization (hpf) using pronase and treated for 4 h with nifedipine (12.5 nM, Biomol, # Cay11106) and tricaine (1.3 mM, Sigma-Aldrich, # A5040) to stop the heart beat or with a corresponding amount of DMSO as a control.

value: Shear stress (18 dyn/cm2 for 6 h)

tag: chip antibody


title: DVS.169R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-169R_S31_L004_R1_001


title: DVS.16R RNA-seq

value: Fail


title: GP108TTAC1


title: Shear Input Rep1


title: Patient S31

value: mucosa (Lynch syndrome healthy carrier)


title: DVS.170R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-170R_S32_L004_R1_001

value: Pass


title: Patient S28


title: Control ChIP-Seq Rep1

value: Untreated

value: H3K27ac (Abcam, #ab4729)


title: Patient S27


title: Patient S33


title: Control Input Rep2


title: DVS.165 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-165_S29_L004_R1_001


title: Merb 8 h rep2

city: Madrid

first: Felipe

last: Cortés Ledesma

state: Madrid

address: Melchor Fernández Almagro 3

department: Molecular Oncology

institute: CNIO

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v1.2.0 with parameter -m 1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample and were computed using custom R scripts that made use of the Bioconductor library GenomicAlignments and GenomicFeatures. bigWig files were generated using bamCoverage function from deepTools v2.4.1 with parameters --binSize 50 –normalizeUsingRPKM. Refs: Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan M, Carey V (2013). “Software for Computing and Annotating Genomic Ranges.” PLoS Computational Biology, 9. doi: 10.1371/journal.pcbi.1003118, http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003118. deepTools2: A next Generation Web Server for Deep-Sequencing Data Analysis. Nucleic Acids Research (2016). doi:10.1093/nar/gkw257.

source_name: retinal pigment epithelium

growth_protocol: RPE-1 cells were serum starved by 48h incubation in Dubelcco’s Modified Eagle’s Medium (DMEM) F-12 (Sigma) supplemented with penicillin, streptomycin and 0.1% Fetal Bovine Serum (FBS) (Sigma) at 37ºC in 5% CO2

extract_protocol:
Total RNA was isolated with the RNeasy kit from Qiagen following instructions from the manufacturer
cDNA libraries were prepared with TruSeq Stranded mRNA (lllumina) using 150ng of total RNA

treatment_protocol: RPE-1 cells were treated with merbarone (200μM) for 240 or 480 minutes.

tag: cell line

value: hTERT RPE-1

tag: genotype

value: wild type


title: Control Input Rep1


title: DVS.166 RNA-seq

first: Deepak

last: Voora

address: 101 Science Dr

institute: Duke

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-166_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

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.

value: 180 mg Ticagrelor

tag: flowcell


title: Patient S30


title: Patient S25


title: Patient S24


title: Merb 4 h rep1


title: DVS.163 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-163_S27_L004_R1_001

value: 81 mg Aspirin

tag: Sex


title: Merb 8 h rep1


title: H9 primed 7d EZH2i

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Raw scRNA-seq FASTQ files for EZH2i d2, d4, untreated naïve cells, and EZH2i d7 and untreated primed cells, were aligned to the human GRCh38 reference genome using Cell Ranger version 6.1.1 with default settings for the ‘cellranger multi’ pipeline (10X Genomics). Reads from EZH2i d7 naïve were aligned on the same reference with the default setting for the “cellranger count” pipeline (10X Genomics). High-quality cells from the EZH2i-related dataset were required to have 1000< nGene < 6000 and percent.mito less than 0.15. After quality control and exclusion of mitochondrial genes, we focused on genes with one or more counts in at least five cells (assessed for each dataset separately).  We then calculated the log-normalized counts using the deconvolution strategy implemented by the computeSumFactors function in R scran package  followed by rescaled normalization using the multiBatchNorm function in the R batchelor package so that the size factors were comparable across batches. log-normalized expression after rescaling was then used for the human dataset integration and differentially expressed gene detection.
Genome_build: hg38
Supplementary_files_format_and_content: results from cellranger

source_name: EZH2i-treated primed cells at Day7

growth_protocol: Primed H9 (Wicell; WA09) p28(11) were thawed using Nutristem hESC XF medium (Biological Industries; 05-100-1A) and were cultured on tissue culture plates (Sarstedt; 83.3922) pre-coated with 10% LN521 (Biolamina; LN521-02). Passaging was done when confluency reached 70-80%. naïve H9 p28(8) naïve p7 that had been previously converted to the naïve stem cell state using naïveCultTM induction media (Stemcell Technologies; 05580) were thawed onto high-density mouse (ICR) inactivated embryonic fibroblasts (MEFs, Gibco; A24903) plates using naïveCult expansion media (Stemcell Technologies; 05590) supplemented with 10µM ROCKi (Merck; Y-27632). Passaging was done every four to five days with media supplemented with 10µM ROCKi.  All hESCs were cultured at 37°C, 5% O2 and 5% CO2.

extract_protocol: Samples EZH2i d2, d4 and untreated control naïve as well as EZH2i d7 and untreated control primed cells were multiplexed following the manufacturer’s protocol. In brief, cells were dissociated, treated with mouse feeder removal beads (naïve cells), counted and resuspended in Cell Multiplexing Oligo. After oligo incubation, cells were washed for a total of three times using PBS-/- containing 1% BSA (Sigma Aldrich; A7284) and counted using the NucleoCounter® NC-200™ automated cell counter. At this point, cells were pooled accordingly: EZH2i d2, d4 and WT naïve cells, and EZH2i d7 and WT primed cells, respectively, and each pool was counted once more.The EZH2i d7 naïve cell sample was collected following the dissociation protocol outlined above. Again, mouse feeder removal beads were used to reduce the amount of MEFs going through into the final cell product. naïve cells were counted and diluted to 1 x 10^6 cells/ml.

treatment_protocol: For the EZH2i treatment, primed and naïve cells were grown in respective media, supplemented with 10µM EZSolution™ EPZ-6438 (BioVision; 2428-5) for seven days, with daily media changes. All cells were passage on d3-4 counting from the start of treatment. For sample collection, primed and naïve H9 were dissociated using TrypLE Select (Gibco; 12563011). Primed cells were washed once with phosphate buffered saline (PBS; Sigma D8537) and counted using Moxi Z mini automated cell counter (Orflo; MXZ001). Harvested naïve cells were centrifuged at 300 x g for 4 min, resuspended in fresh naïveCult expansion media and  kept on ice. Mouse feeder removal microbeads (Milteny Biotech; 130-095-531) were used according to the manufacturer’s protocol to reduce the amount of MEFs in the naïve cell samples.

tag: cell type

value: primed H9 hESCs


title: Merb 4 h rep2


title: DVS.162 RNA-seq

city: Durham

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-162_S26_L004_R1_001

tag: age

tag: plateletfunctionscore


title: Shear RNA-Seq Rep1

tag: treatment


title: mRNA_PDX_rep1

value: xenograft tumor


title: DVS.171R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-171R_S33_L005_R1_001

tag: logscaledsalicylatelevel


title: DVS.164 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-164_S28_L004_R1_001

value: Female


title: DVS.160 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-160_S25_L004_R1_001


title: Shear RNA-Seq Rep2


title: Control RNA-Seq Rep2


title: H9 primed untreated

source_name: Untreated primed cells

value: untreated


title: H9 naïve 7d EZH2i

source_name: EZH2i-treated naïve cells at day 7

value: naive H9 hESCs


title: Shear ChIP-Seq Rep1


title: Patient S32


title: Control RNA-Seq Rep1


title: Patient S15


title: Patient S17


title: Patient S22

value: mucosa (Lynch syndrome tumor patient)


title: DVS.159 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-159_S24_L003_R1_001


title: Patient 10-N.866_miRNA

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

source_name: lung adenocarcinoma

value: lung adenocarcinoma

value: negative


title: Patient S16


title: Patient S23


title: DVS.156 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-156_S21_L003_R1_001


title: H9 naïve 2d EZH2i

source_name: EZH2i-treated naïve cells at day 2


title: DVS.157 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-157_S22_L003_R1_001

value: 325 mg Aspirin


title: H9 naïve 4d EZH2i

source_name: EZH2i-treated naïve cells at day 4


title: H9 naïve untreated

source_name: Untreated naïve cells


title: Patient S13


title: Patient S14


title: DVS.155 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-155_S20_L003_R1_001

value: Male


title: DVS.154 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-154_S19_L003_R1_001

value: Pass


title: TSC_ATACseq_rep2

description:
Biological replicate 2 of 2.
TSC_ATACseq.bw

data_processing:
Adaptor sequences and low-quality reads were excluded using Trimmomatic (version 0.36) (Bolger et al., 2014). Reads were aligned to the mouse genome (mm10) using bowtie2 command (version 1.2.2) with “-N 1 --maxins 2000” option. PCR duplicates and mitochondrial reads were removed by samtools command.
Signal tracks for each sample were generated using deeptools (version 3.4.3) bamCoveraeg command with default parameters and were normalized to 1 million reads (RPKM).
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: Libraries for ATAC-seq were prepared according to previous studies (Corces et al., 2017). Collected cells were washed and subjected to tagmentation by Tn5 transposase from the Illumina Nextera DNA Library Preparation Kit (Illumina #15032354) for 30 min at 37 °C. Transposed DNA was purified by QIAGEN MinElute PCR Purification Kit (Qiagen #28204) and amplified by PCR using published primers (Buenrostro et al., 2015).

value: TSC


title: Control ChIP-Seq Rep2

value: Untreated

value: H3K27ac (Abcam, #ab4729)


title: ARID1AE22, RNA-seq

city: Grand Rapids

first: Ronald

middle: L

last: Chandler

state: Michigan

address: 400 Monroe Ave NW

institute: Michigan State University

description: RNA library from 12Z-ESR1 cells after ARID1A siRNA control and estradiol treatment

data_processing:
Raw reads were trimmed with cutadapt and Trim Galore! followed by quality control analysis via FastQC.
Trimmed reads were aligned GRCh38.p12 genome assembly, indexed to GENCODE (v28) GFF3 annotation via STAR aligner with flag ‘--quantMode GeneCounts’ for feature counting.
STAR sample gene counts were concatenated for Stranded-Reverse (libtype), corresponding to column 4 of STAR output ReadsPerGene.out.tab file.
Low count genes were filtered prior to DESeq2 count normalization (at least 1 count per sample on average) and subsequent differential-expression analysis comparisons within flow cells (i.e. respective wild-type samples were used). Calculated differential-expression probabilities were corrected for multiple testing by independent hypothesis weighting (IHW) for downstream analysis.
Genome_build: GRCh38.p12 indexed to GENCODE (v28) GFF3 annotation
Supplementary_files_format_and_content: Comma-separated values (CSV) and tab-separated values (TSV) tabular text files including gene counts (STAR output) and non-thresholded DESeq2 differential-expression analysis.

growth_protocol: 12Z cells were grown in phenol red-free DMEM/F12 + 10% FBS, 1% L-glutamine. 24 hours post transfection, cells were switched to media containing 10% charcoal-stripped FBS. During E2 treatment, cells were grown under serum-starved conditions of 0.5% charcoal-stripped FBS.

extract_protocol:
72 hours after siRNA transfection, RNA was prepared using the Quick-RNA Miniprep Kit (Zymo Research).
RNA-seq libraries were prepared using the KAPA mRNA HyperPrep mRNA-seq Kit from 500 ng of total RNA material.

treatment_protocol: Cells were transfected with siRNAs using Lipofectamine RNAiMax reagent. 48 hours after siRNA transfection, cells were treated with estradiol or vehicle.

value: endometriotic epithelial cells

value: ARID1A knockdown

value: 10 nM estradiol


title: ARID1AE23, RNA-seq


title: TSC_ATACseq_rep1

description:
Biological replicate 1 of 2.
TSC_ATACseq.bw


title: DVS.158 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-158_S23_L003_R1_001

value: 81 mg Aspirin


title: Patient S02


title: DVS.153 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-153_S18_L003_R1_001


title: ARID1AE21, RNA-seq


title: ESC_ATACseq_rep2

description:
Biological replicate 2 of 2.
ESC_ATACseq.bw

source_name: Embryonic stem cell

value: ESC


title: DVS.152 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-152_S17_L003_R1_001


title: ARID1Avehicle2, RNA-seq

description: RNA library from 12Z-ESR1 cells after ARID1A siRNA control and vehicle treatment

value: Vehicle


title: DVS.151 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-151_S16_L002_R1_001


title: ARID1Avehicle1, RNA-seq


title: Patient 77-P.42477.txt_mRNA

description:
ALK+42477
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.

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: alk rearrangement  status

value: positive


title: DVS.148 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-148_S15_L002_R1_001

value: 180 mg Ticagrelor

value: Female


title: M w 0S 4

first: Elizabeth

last: Rideout

address: 2350 Health Sciences Mall

department: Cellular and Physiological Sciences

institute: The University of British Columbia

data_processing:
Sequencing was performed using on a NextSeq 500 sequencer.
Sequence quality was assessed using FastQC on Illumina BaseSpace
Reads were aligned to Drosophila melanogaster genome (UCSC dm3) using STAR aligner with default settings
For differential expression analysis, fragments per kilobase of transcript per million mapped reads were calculated using the DESeq2 normalization method
Log fold changes and significance for differential expression were determined and a significance threshold of 0.05 was selected for adjusted p values determined with Bonferroni correction
Assembly: UCSC dm3
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Drosophila melanogaster

source_name: w1118 Male

extract_protocol:
10 108hr (AEL) male and female larvae were removed from Drosophila diet (1S or 0S) and flash frozen on dry ice. RNA was isolated using Trizol reagent. Quality control of  samples was performed using the Agilent 2100 Bioanalyzer to confirm sample quality.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: male

tag: tissue

value: Whole larva

tag: developmental stage

value: 108 AEL

tag: diet


title: NONtgE23, RNA-seq

description: RNA library from 12Z-ESR1 cells after non-targeting siRNA control and estradiol treatment

value: Control


title: DVS.147R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-147R_S14_L002_R1_001

value: Pass


title: NONtgE22, RNA-seq


title: Patient 74-P.39736.txt_mRNA

first: Sophia

last: Subat

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

institute: Japanese Foundation for Cancer Research

description:
ALK+39736
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

value: lung adenocarcinoma


title: Patient 71-P.38143.txt_mRNA

description:
ALK+38143
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 72-P.39415.txt_mRNA

description:
ALK+39415
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: M w 0S 2

tag: strain


title: Patient 76-P.41554.txt_mRNA

description:
ALK+41554
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 70-P.36885.txt_mRNA

description:
ALK+36885
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: M w 0S 3


title: DVS.146 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-146_S13_L002_R1_001

value: 325 mg Aspirin


title: DVS.145 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-145_S12_L002_R1_001


title: Patient 73-P.39630.txt_mRNA

description:
ALK+39630
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: ARID1Avehicle3, RNA-seq


title: Patient 75-P.40310.txt_mRNA

description:
ALK+40310
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: M w 0S 1


title: DVS.144 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-144_S11_L002_R1_001


title: ESC_ATACseq_rep1

description:
Biological replicate 1 of 2.
ESC_ATACseq.bw


title: M w 1S 4


title: NONtgE21, RNA-seq


title: NONtgVehicle2, RNA-seq

description: RNA library from 12Z-ESR1 cells after non-targeting siRNA control and vehicle treatment

source_name: NONtgVehicle


title: NONtgVehicle3, RNA-seq


title: M w 1S 3


title: Patient 66-P.33560.txt_mRNA

description:
ALK+33560
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 67-P.35648.txt_mRNA

description:
ALK+35648
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DVS.143 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-143_S10_L002_R1_001


title: Patient 65-P.32659.txt_mRNA

description:
ALK+32659
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DVS.142 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-142_S9_L002_R1_001


title: M w 1S 2


title: NONtgVehicle1, RNA-seq


title: Patient 69-P.36567.txt_mRNA

description:
ALK+36567
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 64-P.27998.txt_mRNA

description:
ALK+27998
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: miRNA-Seq BT20 siADAR#2

city: Boston

first: Allison

middle: R.

last: Baker

state: MA

address: 3 Blackfan Circle

institute: Harvard University

description: small RNA

data_processing:
Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Adapter sequences, other contaminant sequences were trimmed from reads using Atropos
poly(A+) seq was aligned to GRCh38 using hisat2, smRNA seq was aligned to miRBasev21 using seqbuster
For poly(A+) seq, gene counts were generated by featureCounts and TPM measurements generated using Salmon
For smRNA seq, normalized expression values were generated with bcbioSmallRna
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with log2 raw gene counts for every gene and every sample

growth_protocol: BT20 cells were grown in DMEM/F12 media with 10% FBS and penicillin/streptomycin.

extract_protocol:
Total RNA was isolated using the mirVana miRNA Isolation Kit
Library preparation was performed using the KAPA mRNA HyperPrep kit for poly(A+) RNA-seq and the Bioo Scientific NextFlex Small RNA-Seq kit with 4N adapters for small RNA-seq.

treatment_protocol: Cells were reverse transfected for 72hr with 5nM Silencer Select siRNAs from ThermoFisher (siControl (Silencer Select Negative Control #1 4390843), siADAR1 #1 (s1007), siADAR1 #2 (119581)). All siRNAs were transfected using Lipofectamine RNAimax (Thermo Fisher).

value: ADAR1 #2 siRNA


title: F w 0S 4

source_name: w1118 Female

value: female


title: Patient 68-P.35799.txt_mRNA

description:
ALK+35799
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: F w 0S 3


title: miRNA-Seq BT20 siControl

description: small RNA

value: Control siRNA


title: DVS.140 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-140_S7_L001_R1_001


title: miRNA-Seq BT20 siADAR#1

description: small RNA

value: ADAR1 #1 siRNA


title: Patient 62-P.26813.txt_mRNA

description:
ALK+26813
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: F w 0S 2


title: DVS.139 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-139_S6_L001_R1_001


title: RNA-Seq BT20 siADAR#2

description: poly(A+) RNA


title: F w 0S 1


title: DVS.137 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-137_S4_L001_R1_001


title: RNA-Seq BT20 siADAR#1

description: poly(A+) RNA


title: DVS.138 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-138_S5_L001_R1_001


title: Patient 63-P.27265.txt_mRNA

description:
ALK+27265
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 61-P.26422.txt_mRNA

description:
ALK+26422
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 60-P.26020.txt_mRNA

description:
ALK+26020
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: RNA-Seq BT20 siControl

description: poly(A+) RNA


title: M w 1S 1


title: F w 1S 2


title: DVS.135 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-135_S2_L001_R1_001

value: 81 mg Aspirin


title: F w 1S 3


title: WM3734_shJ_72h_c

city: Essen

first: Alexander

last: Roesch

address: Hufelandstrasse 55

department: Department of Dermatology

institute: University hospital Essen

data_processing:
Read quality was assessed using fastQC and the reads were mapped against the hg38 reference genome using STAR version 2.7.
Quantification on gene-level was performed during the alignment, using the "--quantmode GeneCounts" option in STAR.
Gene counts were then normalized using the size-factor normalization in the bioconductor package DESeq2 version 1.28.
Genome_build: hg38

source_name: melanoma cells

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit according to the manufacturer’s protocol (Qiagen Venlo, Netherlands).
Barcoded stranded mRNA-seq RNA libraries were generated using the NEB Ultra II stranded RNA library prep kit.

tag: melanoma cells

value: induced with 500 ng/ml doxycycline for 72 h

tag: treatment duration

tag: growth medium


title: DVS.134 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-134_S1_L001_R1_001


title: DVS.136 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-136_S3_L001_R1_001


title: DVS.141 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-141_S8_L001_R1_001


title: WM3734_shJ_72h_d


title: Patient 58-P.22231.txt_mRNA

city: Tokyo

description:
ALK+22231
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 59-P.24461.txt_mRNA

description:
ALK+24461
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: F w 1S 1


title: F w 1S 4


title: WM3734_shJ_72h_b


title: Patient 57-P.20653.txt_mRNA

description:
ALK+20653
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: WM3734_scr_72h_d


title: DVS.126 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-126_S37_L005_R1_001


title: WM3734_scr_72h_c


title: WM3734_scr_72h_b


title: High-fat diet+Minocycline PVN rep 3

city: Hershey

first: Anirban

last: Paul

state: PA

address: 500 University Drive

department: Neural and Behavioral Sciences

institute: Penn State College of Medicine

description:
HFDMIN-03
Bulk RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were aligned using HISAT2.
Mapped reads were assigned to genomic features using featureCounts (Liao et al., 2014).
Differential expression was calculated using edgeR (McCarthy et al., 2012; Robinson et al., 2009).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Raw_gene_counts_matrix.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: Brain

extract_protocol:
Control, HFD, and HFD+Mino mice (n=3/group) underwent the same diet exposure as the mice in the above groups but did not undergo metabolic testing. At the end of study, mean body mass was not different between these mice and their respective groups in the other cohorts described above. PVN tissue punches were then utilized for RNAseq. Approximately 30-60 mg of tissue sample was transferred to a safe-lock microcentrifuge tube (Eppendorf). A mass of stainless-steel beads (Next Advance, cat# SSB14B) equal to the mass of the tissue was added to the tube. Two volumes of TRI Reagent® (Zymo Research) were added to the tube and samples were immediately mixed in a bead mill homogenizer (Bullet Blender, Next Advance) for 1 min at a speed of ten. Samples were visually inspected to confirm desired homogenization and then incubated at 37°C for 5 min. The TRI Reagent® was added up to 0.6 ml, and samples were mixed in the Bullet Blender for 1 min. Total RNA was extracted using Direct-zol™ RNA Miniprep Kit (Zymo Research). Optical density values of extracted RNA were measured using NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RNA integration number (RIN) was measured using BioAnalyzer (Agilent Technologies) RNA 6000 Nano Kit.
The cDNA libraries were prepared using the SMARTer Ultra Low Input RNA Kit for Sequencing – v4 (TAKARA Bio) and Nextera XT DNA Library Prep Kit (Illumina) as per manufacturer's instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and then denatured using the Illumina protocol. The denatured libraries were loaded onto an S1 flow cell on an Illumina NovaSeq 6000 (Illumina) and run for 2X50 cycles according to the manufacturer's instructions. De-multiplexed sequencing reads were generated using Illumina bcl2fastq (released version 2.18.0.12) allowing no mismatches in the index read.

value: Paraventricular nucleus

value: post natal day 35

value: wild type

value: High-fat diet

value: Minocycline


title: Patient 56-P.19854.txt_mRNA

description:
ALK+19854
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

value: positive


title: DVS.125 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-125_S36_L005_R1_001

value: Female


title: High-fat diet+Minocycline PVN rep 2

description:
HFDMIN-02
Bulk RNA-seq


title: CSM152_Cpd1_48h_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.
Genome_build: hg38

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.

value: melanoma cells

tag: cell line

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: DVS.124 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-124_S35_L005_R1_001

value: Pass


title: DVS.128 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-128_S39_L005_R1_001

value: 180 mg Ticagrelor


title: Patient 55-P.12872.txt_mRNA

description:
ALK+12872
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

value: lung adenocarcinoma


title: High-fat diet+Minocycline PVN rep 1

description:
HFDMIN-01
Bulk RNA-seq

tag: genotype


title: CSM152_Cpd1_48h_rep2


title: Patient 54-P.12727.txt_mRNA

description:
ALK+12727
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DVS.121R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-121R_S34_L005_R1_001

tag: flowcell


title: DVS.127 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-127_S38_L005_R1_001

tag: Sex


title: Patient 52-P.12215.txt_mRNA

description:
ALK+12215
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Patient 53-P.12552.txt_mRNA

description:
ALK+12552
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: CSM152_Cpd1_48h_rep1

tag: cell type


title: WM3734_sh_KDM5B_62

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed with Illumina GenomeStudio Gene Expression Module using defaults.

source_name: WM3734 melanoma cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol:
grown in Tu2%, Knockdown of KMD5B via sh62
Tu2% media

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: shRNA

value: Knockdown of KMD5B


title: High-fat diet PVN rep 3

description:
HFD-05
Bulk RNA-seq

tag: age


title: Patient 50-P.10027.txt_mRNA

description:
ALK+10027
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: CSM152_DMSO_48h_rep3

tag: treatment

value: 48h treatment with DMSO


title: DVS.120R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-120R_S33_L005_R1_001

tag: plateletfunctionscore

tag: logscaledsalicylatelevel


title: WM3734_sh_scramble

description: SCR

growth_protocol:
grown in Tu2%, control cell line with scramble sh.
Tu2% media

value: scramble sh.


title: Patient 51-P.10172.txt_mRNA

description:
ALK+10172
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

tag: tissue

tag: alk rearrangement  status


title: High-fat diet PVN rep 2

description:
HFD-04
Bulk RNA-seq

tag: diet


title: Patient 49-P.9968.txt_mRNA

description:
ALK+9968
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: DVS.118R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-118R_S32_L004_R1_001

value: 81 mg Aspirin


title: High-fat diet PVN rep 1

description:
HFD-03
Bulk RNA-seq

tag: strain


title: DVS.117R RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-117R_S31_L004_R1_001


title: CSM152_DMSO_48h_rep2


title: CSM152_DMSO_48h_rep1


title: Chow PVN rep 3

description:
CTRL-03
Bulk RNA-seq

value: Chow


title: DVS.116 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-116_S19_L003_R1_001


title: Patient 48-P.9034.txt_mRNA

description:
ALK+9034
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Chow PVN rep 2

description:
CTRL-02
Bulk RNA-seq

value: Paraventricular nucleus


title: CSM152_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)

value: RPMI medium with 10% FBS


title: Patient 47-P.8993.txt_mRNA

description:
ALK+8993
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: Chow PVN rep 1

description:
CTRL-01
Bulk RNA-seq

value: post natal day 35

value: wild type


title: CSM152_Cpd1_24h_rep1


title: DVS.114 RNA-seq

description:
processed data file:
QCed_counts.txt
Log2_normalized_expression.txt
Voom_weights.txt
DVS-114_S29_L004_R1_001

value: Male


title: CSM152_Cpd1_24h_rep2


title: Patient 46-P.8398.txt_mRNA

description:
ALK+8398
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0

value: positive


title: KO_naive_2

city: Paris

first: Paul

last: Gueguen

address: 26 rue D'Ulm

department: Inserm U932

country: France

institute: Institut Curie

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)

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


title: Patient 45-P.7378.txt_mRNA

description:
ALK+7378
One glass slide formatted with eight high-definition 60K arrays. Based on miRBase Release 19.0


title: KO_naive_1