title: D9_Low_CD8_S14_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

data_processing:
Samples were demultiplexed using Illumina bcl2fastqsoftware (v1.2.4) and aligned to the Human (GRCh38) genome with STAR (v2.6.1).
Sequencing data quality was assessed with FastQC software and Illumina adapter sequences, polyA tails, and short reads (less than 20 bases) were trimmed using Cutadapt (v1.18).
Gene expression was quantified with quant3p (github.com/ctlab/quant3p). Downstream analyses were performed in R.
Genome_build: hg38
Supplementary_files_format_and_content: RawData_RNAseq_HL.csv: Comma-separated text files include raw counts from quant3p.

extract_protocol:
RNA-seq was performed following MARS-seq protocol adapted for bulk RNA-seq with minor modifications. Briefly, 7000 to 10000 cells were sorted in 100µl of Lysis/Binding Buffer (Ambion), vortexed and stored at -80ºC until further processing. Poly-A RNA was reverse-transcribed using poly-dT oligos carrying a 7 nt-index. Pooled samples were subjected to linear amplification by IVT. Resulting aRNA was fragmented and dephosphorylated. Ligation of partial Illumina adaptor sequences was followed by a second reverse-transcription reaction. Full Illumina adaptor sequences were added during final library amplification. RNA-seq libraries quantification was done with Qubit 3.0 Fluorometer (Life Technologies) and size profiles were examined using Agilent’s 4200 TapeStation System. Libraries were sequenced in an Illumina NextSeq 500 at a sequence depth of 10 million reads per sample.
MARS-seq (Illumina)

value: D9_Low_CD8 CAR T cells


title: C1

status: Public on Oct 05 2022

type: SRA

city: Linfen

first: lin

middle: jin

last: feng

state: Shanxi

address: gongyuan 1 street

department: College of Life Sciences

country: China

institute: Shanxi Normal University

library_source: transcriptomic

data_processing:
Clean data were obtained by removing reads containing adapters, calls marked as N, and low-quality reads from the raw data.
The high-quality reads were mapped to the Arabidopsis TAIR10 genome using Hisat2 v2.0.5.
The expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced for each gene was calculated based on the length of the gene and read count mapped to the gene.
Assembly: Arabidopsis TAIR10 genome
Supplementary files format and content: Alignment information from reads to reference sequences.
Supplementary files format and content: gene_fpkm.txt: Tab-delimited text file includes FPKM values.
Supplementary files format and content: TreatmentvsControl_deg_all.txt: Tab-delimited text file

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen) from the treatment group and the control group seedlings.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: seedlings

tag: genotype

value: WT

tag: treatment

value: MS Medium

tag: time

value: 6 h


title: pre-treatment monolayer, d20, rep2

city: Toronto

first: Neal

middle: I

last: Callaghan

state: Ontario

address: 661 University Ave

department: Institute of Biomedical Engineering

country: Canada

institute: University of Toronto

description:
d20_2
monolayer_counts.xlsx

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic.
Trimmed sequence reads were mapped to GR.Ch38 using Salmon in mapping-based mode with default settings.
Gene-level read counts were obtained from Salmon output files using Tximeta.
Assembly: GR.Ch38
Supplementary files format and content: Excel files containing raw read counts for each sample

organism: Homo sapiens

source_name: PGPC-17 induced pluripotent stem cells

extract_protocol:
Total RNA was extracted from iPSC-CM monolayers using the Qiagen RNeasy Micro kit. Total RNA was extracted from Biowire II tissues using the PicoPure™ kit (Thermo-Fisher).
For iPSC-CM monolayer samples, RNA libraries for RNA-seq were prepared using the Stranded Total RNA Prep kit (Illumina Inc, USA). For Biowire samples, RNA libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian kit (Takara Bio Inc., Japan).

tag: cell line

value: PGPC-17 induced pluripotent stem cells

tag: cell type

value: cardiomyocyte

tag: media

value: Control

tag: culture format

value: Monolayer


title: sc5_D18_BCMA_d0 [scRNA-seq]

city: PAMPLONA

first: Juan R

last: Rodriguez-Madoz

address: AV PIO XII 53

country: Spain

institute: CIMA

data_processing:
The raw scRNA-seq data were demultiplexed, aligned to the Human (GRCh38) reference and the feature-barcode matrix was quantified using Cell Ranger (v3.0.1) from 10X Genomics. Further computational analysis was performed using Seurat (v3.1.5). Cells were subjected to QC filters based on the number of detected genes, number of UMIs and proportion of UMIs mapped to mitochondrial and ribosomal genes per cell. The thresholds filters for each variable were selected based on their distribution within each of the single cell libraries and visual inspection of quality control scatter plots. Genes detected in fewer than three cells and cells where fewer than 150 genes had nonzero counts were filtered out and excluded from subsequent analysis. Low-quality cells where more than 10% and more than 40% mitochondrial or ribosomal content respectively, were also discarded. In addition, cells with more than the 97.5th percentile of detected genes per sample, were discarded to remove likely doublet or multiplet captures.
Each dataset was subjected to normalization, identification of highly variable genes and removal of unwanted sources of variation using Seurat (v3.1.5). Integration of all the dataset was based on Seurat’s canonical correlation analysis. Different resolution parameters for unsupervised clustering were examined to determine the optimal number of clusters. For this study, the first 40 PCs and 3000 highly variable genes identified by Seurat were used for sample integration and unsupervised clustering analysis with the resolution set to 0.8, yielding a total of 23 cell clusters. Non-linear dimensional reduction was performed using t-distributed stochastic neighbour embedding (t-SNE) and UMAP.
TCR V(D)J sequence assembly, paired clonotype calling, TCR diversity and clonality analysis. TCR reconstruction and paired TCR clonotype analysis was performed using Cell Ranger v3.0.2 for V(D)J sequence assembly. The CDR3 motif was located, and the productivity was determined for each single cell. The clonotype landscape was then assessed, and the clonal fraction of each identified clonotype was calculated. The TCR clonotype diversity matrix was calculated using the tcR R package. TCR clonality was defined as 1-Peilou’s evenness and was calculated on productive rearrangements as previously described. Clonality values approaching 0 indicate a very even distribution of clone frequencies, whereas values approaching 1 indicate an increasingly.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every cell recovered as per Cell Ranger (v3.0.1). barcodes.tsv (10X Genomics Chromium Raw Gene BC Cellular Barcodes), features.tsv (10X Genomics Chromium Raw Gene BC Cellular Genes), matrix.mtx (10X Genomics Chromium Raw Gene BC Cellular Matrix) files.
Supplementary_files_format_and_content: *VDJ.csv: Comma-separated text files.

molecule: polyA RNA

source_name: Donor cells

growth_protocol: PBMCs were isolated from peripheral blood of healthy donors using Ficoll-PaqueTM Plus (GE Healthcare) and then CD4+ and CD8+ cells were isolated using CD4 and CD8 MicroBeads (Miltenyi Biotec) in the AutoMACS Pro Separator (Miltenyi Biotec). Isolated T cells were cultured at a concentration of 1×10^6 cells/ml in RPMI 1640 culture medium (Lonza) supplemented with 3% human serum (Sigma), 1% penicillin/streptomycin (Gibco) and 625 IU/ml of human IL-7 and 85 IU/ml of human IL-15 (Miltenyi Biotec), and activated with 10 µl/ml T cell TransAct (Miltenyi Biotec).

extract_protocol:
FACS-sorted CAR T cells (BFP+ cells) from three independent donors were interrogated using the 10X Chromium platform for simultaneous transcriptome and TCR profiling, with 28,117 cells (range, 7,416-10,5093 cells/donor) passing our quality control (QC) thresholds and taken into subsequent analysis. These cells were sequenced to an average depth of 42,296 reads/cell, yielding an average of 2,541 genes/cell.
scRNA-seq was performed using the Chromium Single Cell 5′ Reagent Kit (10X Genomics) according to the manufacturer’s instructions. Briefly, CAR T cells were sorted in 100µl 1X PBS, 0.04% BSA and their concentration and viability were determined using Nexcelom’s Cellometer K2 Fluorescent Cell Counter. Cell concentration was adjusted to 700 to 1200 cells/µl to maximize the likelihood of achieving the desired cell recovery target. Then single-cell suspension was mixed with RT Master Mix and loaded together with barcoded single-cell 5′ gel beads and partitioning oil into separate single cell A Chips to generate Gel Beads in Emulsion (GEMs) using Chromium Controller. Thus, individual cells were lysed and the polyadenylated RNA was reverse-transcribed and barcoded inside each GEM. Barcoded complementary DNA (cDNA) was recovered through post GEM-RT cleanup and PCR-amplified. cDNA was quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and its profile examined using High Sensitivity D5000 ScreenTape Assay (Agilent Technologies). Fifty nanograms of double-stranded cDNA were used for 5′ Gene Expression library construction. cDNA was fragmented, end-repaired, A-tailed and ligated to an adaptor. A final PCR-amplification with barcoded primers was performed for sample indexing.
Single-cell TCR repertoire sequencing. TCRTCR α/β sequencing was performed with 10X Genomics Single Cell V(D)J Immune Profiling Solution (10× Genomics). Briefly, full-length V, D and J gene segments were amplified from barcoded cDNA using a Chromium Single Cell V(D)J Enrichment Kit (human T cells) by means of two sequential PCRs with primers targeting the adaptor and the gene constant region. Enriched cDNA was quantified as described above and 50 ng were further used for library construction as described above. After quality control and quantification, Single Cell V(D)J enriched libraries were pooled and sequenced in an Illumina’s HiSeq X (Read1: 150 cycles; Read2: 150 cycles, i7 index: 8 cycles) at an average depth of 5000 reads per cell.

treatment_protocol: After 48h, T cells were infected with the CAR lentiviral vector at MOI 2 and 10 µl/ml of LentiBoost (Sirion Biotech), to enhance viral infection. CAR T cells were expanded in RPMI 1640 culture medium (Lonza) supplemented with 3% human serum (Sigma), 1% penicillin/streptomycin (Gibco) and 625 IU/ml of human IL-7 and 85 IU/ml of human IL-15 (Miltenyi Biotec). CAR T cells were counted, and the concentration was adjusted to 1×10^6 cells/ml every two days until day 13-14 of the production.

tag: diagnosis

value: Healthy

value: Blood

value: BFP+ CAR T cells


title: T47D_WT_clone1_mimic_miR_331_3p

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

country: USA

institute: University of Utah

data_processing:
Reads were aligned to the human genome using HISAT2.
Sam files were then converted to bam files and sorted via Samtools.
Read counts for each gene were determined from alignments to hg19 UCSC knownGene gene models using featuresCounts from the SubRead package.
Normalization and differential expression analysis were performed using DeSeq2.
Assembly: hg19
Supplementary files format and content: Raw gene counts in a text file

growth_protocol: Cells were cultured in RPMI1640 Media (ThermoFisher Scientific) supplemented with 10% FBS (Sigma-Aldrich) and 1% penicillin-streptomycin (ThermoFisher Scientific).

extract_protocol:
24 hours post-transfection, cells were collected, washed with PBS, then treated with RLT Plus lysis buffer supplemented with 1% BME. RNA was extracted using a Quick-RNA RNA Miniprep kit (Zymo Research).
Poly-A selected RNA-seq libraries were generated using a KAPA Stranded mRNA-Seq kit (KAPA Biosystems) and 500ng RNA per sample as starting material.

treatment_protocol: T-47D cells were grown in 100mm plates in hormone-deprived media for four days then plated into 12-well plates at approximately 50% confluence and allowed to adhere for 24 hours. Cells were then transfected with a miRNA mimic or inhibitor for a given miRNA or with a mimic or inhibitor negative control at a 10nM final concentration.

value: mammary gland ductal carcinoma

tag: esr1 genotype

value: hsa-miR-331-3p mimic


title: D9_Low_CD4_S13_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D9_Low_CD4 CAR T cells


title: T47D_WT_clone2_mimic_miR_301b_3p

value: hsa-mir-301b-3p mimic


title: T47D_WT_clone1_mimic_miR_301b_3p


title: RNA-Seq pLT-WSTF-OIS-3

city: Boston

first: Zhixun

last: Dou

state: MA

address: 185 Cambridge Street, CPZN 4-234

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of hg19 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.
Assembly: hg19

source_name: Primary human diploid fibroblasts IMR90 cells

extract_protocol: none provided by the submitter

tag: cells

tag: conditions

value: HRasV12-induced senescence

tag: overexpressed gene

value: WSTF


title: D9_High_CD8_S18_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D9_High_CD8 CAR T cells


title: RNA-Seq pLT-WSTF-OIS-2


title: RNA-Seq pLT-WSTF-OIS-1


title: T47D_D538G_clone2_mimic_neg_ctrl

value: mimic negative control


title: D8a_Low_CD8_S8_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D8a_Low_CD8 CAR T cells


title: RNA-Seq pLT-OIS-3

value: Vector


title: T47D_D538G_clone1_mimic_neg_ctrl


title: D8a_Low_CD4_S7_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D8a_Low_CD4 CAR T cells


title: Liver_CLP+ADSCs4_5

city: Chengdu

first: Tao

last: Wang

state: Sichuan

address: No.1, Keyuan 4 Rd

department: Regenerative Medicine Research Center

institute: Sichuan University West China Hospital

description:
L-A4-5
Liver_gene_FPKM.txt

data_processing:
RNA sequencing was carried out with the PE150 sequencing pattern via the Illumina NovaSeq 6000 (Illumina, USA) platform.
The raw reads were filtered using Cutadapt software to remove low-quality and undetermined bases.
After obtaining the clean reads, HISAT2 software (version 2.0.4) was used to map to the reference genome.
Differential gene expression analysis was conducted using the R package edgeR
Differentially expressed genes (DEGs) were selected as those with a false discovery rate (FDR) adjusted p value <0.05 and a log2-fold change (log2FC) >1 or <-1.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

organism: Mus musculus

source_name: Liver

extract_protocol:
Total RNA was extracted from PBMCs samples using TRIzol reagent (Thermo Fisher, USA) according to the manufacturers instructions.
The concentration of RNA was determined by Gene Quant pro 1000 (Thermo Fisher, USA). Total RNA quality was assessed via RNA integrity number (RIN) using a Bioanalyzer 2100 (Agilent, USA). Then, cDNA libraries were constructed, and the final average insert size was 300±50 bp.

treatment_protocol: Different doses of ADSCs (1×107, 2×107 or 4×107 cells/kg, resuspended in 0.2 mL of 1% albumin solution) or vehicle (1% albumin) were administered intravenously at 6 h after CLP surgery via the tail vein.

value: Liver

tag: strain background

value: allogeneic ADSCs at 4×107 cells/kg


title: RNA-Seq pLT-OIS-2


title: T47D_D538G_clone2_mimic_miR_181c_5p

value: hsa-miR-181c-5p mimic


title: D8a_High_CD8_S12_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: Healthy

value: D8a_High_CD8 CAR T cells


title: D9_High_CD4_S17_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: Blood

value: D9_High_CD4 CAR T cells


title: RNA-Seq pLT-OIS-1


title: T47D_D538G_clone1_mimic_miR_181c_5p

value: mammary gland ductal carcinoma


title: D8a_High_CD4_S11_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D8a_High_CD4 CAR T cells


title: extrahepatic cholangiocarcinoma cell line TFK-1

type: genomic

city: Wuhan

first: Fei

last: Xiong

state: Hubei

address: Jiefang Road No.1095

institute: Huazhong University of Science and Technology

description: extrahepatic cholangiocarcinoma vs normal bile duct

hyb_protocol: The hybridization was performed by Hybridization Kit 40 (NimbleGen, Cat. # KIT002-2). 6 ug input sample and 6 ug MeDIP sample were resuspended, mixed with Hybridization Solution Master Mix and placed the tube in the Hybridization System sample block (pre-heated to 42°C). Then hybridizations and washes were completed by Hybridization System (NimbleGen, Cat. # 00895/00896) according to the instructions.

scan_protocol: The Cy3 and Cy5 signals were scanned by GenePix 4000B. Wavelength (532 nm = Cy3, 635 nm = Cy5). The image for the 532nm and 635nm wavelengths. Signal data was extracted by GenePix Pro6.0 and exported to separated Pair. files.

data_processing: Two types of signal values could be compared using the MEDME algorithm and the comparison results that are >2 folds or <0.5 fold are deemed as differential methylation. Differential methylation was evaluated by relative methylation (RMS) which means the methylation level of the probes at the same amount of CpG islands.

molecule: genomic DNA

source_name: Extrahepatic cholangiocarcinoma, input DNA

label_protocol: 1 ug of input sample and MeDIP sample were labeled by Cy3 and Cy5 dye-labeled random primer respectively (TriLink Biotechnologies, Cat. # N46-0001-50, N46-0002-50).

growth_protocol: TFK-1 was maintained in RPMI-1640 with 10% FBS. Normal bile duct sample was obtained from a cholangiocarcinoma patient.

extract_protocol: The extraction was performed by DNeasy Blood & Tissue Kit (QIAGEN, Catalog no. 69504). Cut the sample into small pieces, and place in a 1.5 ml microcentrifuge tube, followed by proteinase K treatment, RNase A treatment, phenol/chloroform extraction and ethanol precipitation according to the instruction. The Genomic DNA was then collected by DNeasy Mini spins and eluted by AE buffer, followed by MeDIP-ChIP with Anti-5-methyl cytidine antibody (1ug/ul) (Diagenode).

value: Extrahepatic cholangiocarcinoma

tag: fraction

value: Input DNA

source_name: Extrahepatic cholangiocarcinoma, IP DNA

value: IP DNA


title: Normal bile duct

source_name: Normal bile duct, input DNA

value: Normal bile duct

source_name: Normal bile duct, IP DNA


title: RNA-Seq pLT-WSTF-3

value: Proliferating

value: WSTF


title: Liver_CLP+ADSCs4_4

description:
L-A4-4
Liver_gene_FPKM.txt


title: T47D_D538G_clone2_mimic_miR_301b_3p

value: hsa-mir-301b-3p mimic


title: Liver_CLP+ADSCs4_3

description:
L-A4-3
Liver_gene_FPKM.txt


title: Liver_CLP+ADSCs4_2

description:
L-A4-2
Liver_gene_FPKM.txt


title: D7_Low_CD8_S2_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D7_Low_CD8 CAR T cells


title: T47D_WT_clone2_mimic_miR_331_3p

value: WT

value: hsa-miR-331-3p mimic


title: RNA-Seq pLT-WSTF-2


title: T47D_D538G_clone1_mimic_miR_301b_3p


title: D7_Low_CD4_S1_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D7_Low_CD4 CAR T cells


title: RNA-Seq pLT-WSTF-1


title: T47D_Y537S_clone2_inhibitor_neg_ctrl

value: inhibitor negative control


title: M4BeS2: LNM cell line_in mouse_rep2

city: Evry

first: Jorg

last: Tost

address: 2 rue Gaston Cremieux

country: France

institute: CEA-Institut de Genomique, Centre National de Genotypage

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Infinium Human Methylation 450 K bead arrays (Illumina Inc., San Diego, CA). Processing was done according to the manufacturer’s protocol using an automated pipeline.  of bisulfite-treated DNA was analyzed using the Infinium  Human Methylation 450 K bead arrays spanning approximately  over 480,000 CpG sites/sample (Illumina Inc., San  Diego, CA). Processing was done according to the manufacturer’s  protocol using an automated pipeline, and the  arrays were scanned on an Illumina iScan platform (Illumina  Inc., San Diego, CA) established at the Life & Brain  Center (Bonn, Germany)

data_processing: Subset quantile normalization, revised version of Touleimat & tost, Epigenomics 2012

label: Cy3, Cy5

source_name: Cultured cell line

label_protocol: Standard Illumina Protocol

growth_protocol: grown in DMEM (Invitrogen, France) supplemented with 10% fetal bovine serum (Sigma, France), 2 mM glutamine, 100 UI/mL penicillin-streptomycin and 1.25 µg/mL fungizone (both from Invitrogen) in 5% CO2 atmosphere. Numerations of viable cells were performed using an Automated Cell Viability Analyzer (Beckman Coulter Vi-Cell). All cell lines were stored in ampoules in liquid azote after receipt, kept under twenty passages and Cell lines were tested for mycoplasma contamination using the MycoAlertTM Mycoplasma Detection Kit (Lonza, Switzerland).

extract_protocol: Genomic DNA from cell lines was isolated using DNeasy Tissue kit (Qiagen, France).

value: melanoma


title: M4BeS2-1: LNM cell line_in mouse_rep1

scan_protocol: the arrays were scanned on an Illumina iScan platform


title: Liver_CLP+ADSCs2_4

description:
L-A2-4
Liver_gene_FPKM.txt

value: Liver

value: allogeneic ADSCs at 2×107 cells/kg


title: D7_High_CD8_S6_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: Healthy

value: Blood

value: D7_High_CD8 CAR T cells


title: Liver_CLP+ADSCs4_1

description:
L-A4-1
Liver_gene_FPKM.txt

value: allogeneic ADSCs at 4×107 cells/kg


title: M4BeS2-3: LNM cell line_in mouse_rep3


title: D7_High_CD4_S5_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D7_High_CD4 CAR T cells


title: T47D_Y537S_clone1_inhibitor_neg_ctrl

value: mammary gland ductal carcinoma


title: Liver_CLP+ADSCs2_3

description:
L-A2-3
Liver_gene_FPKM.txt


title: M4Be-1: LNM cell line_rep1


title: WM266-2: meta cut cell line_rep2


title: TW12-3: LNM cell line_in rat_rep3


title: M4Be-3: LNM cell line_rep3


title: TW12-1: LNM cell line_in rat_rep1


title: RNA-Seq pLT-2

value: Proliferating

value: Vector


title: D18_Low_CD8_d0_S26_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D18_Low_CD8_d0 CAR T cells


title: TW12-2: LNM cell line_in rat_rep2


title: T47D_Y537S_clone2_inhibitor_let_7f

value: hsa-let-7f inhibitor


title: C2

value: seedlings

value: WT

value: MS Medium

value: 6 h


title: ATAC-Seq WSTF-OIS-D7-r3

library_source: genomic

data_processing:
Mapping was performed with BWA aligner (PMID:23104886) using hg19 reference genome.
Assembly: hg19

value: HRasV12-induced senescence

value: WSTF


title: RNA-Seq pLT-1


title: T47D_Y537S_clone1_inhibitor_let_7f


title: D18_High_CD8_d0_S30_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D18_High_CD8_d0 CAR T cells


title: Liver_CLP+ADSCs1_5

description:
L-A1-5
Liver_gene_FPKM.txt

value: Liver

value: allogeneic ADSCs at 1×107 cells/kg


title: D18_Low_CD4_d0_S25_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: Healthy

value: Blood

value: D18_Low_CD4_d0 CAR T cells


title: ATAC-Seq WSTF-OIS-D7-r2


title: T47D_Y537S_clone1_mimic_neg_ctrl

value: mammary gland ductal carcinoma

value: mimic negative control


title: WM115-1: primary cell line_rep1

value: melanoma


title: WM266-1: meta cut cell line_rep1


title: D18_High_CD4_d0_S29_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D18_High_CD4_d0 CAR T cells


title: Liver_CLP+ADSCs1_4

description:
L-A1-4
Liver_gene_FPKM.txt


title: T47D_Y537S_clone2_mimic_neg_ctrl


title: D14_Low_CD8_d0_S14_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D14_Low_CD8_d0 CAR T cells


title: Liver_CLP+ADSCs1_3

description:
L-A1-3
Liver_gene_FPKM.txt


title: T47D_Y537S_clone2_mimic_miR_331_3p

value: hsa-miR-331-3p mimic


title: ATAC-Seq WSTF-OIS-D7-r1


title: ATAC-Seq pLT-OIS-D7-r3

value: Vector


title: WM115-2: primary cell line_rep2


title: T47D_Y537S_clone1_mimic_miR_331_3p


title: ATAC-Seq pLT-OIS-D7-r2


title: D14_Low_CD4_d0_S13_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D14_Low_CD4_d0 CAR T cells


title: M4Be-2: LNM cell line_rep2


title: WM266-3: meta cut cell line_rep3


title: T47D_Y537S_clone2_mimic_miR_301b_3p

value: hsa-mir-301b-3p mimic


title: WM115-3: primary cell line_rep3


title: D14_High_CD8_d0_S18_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D14_High_CD8_d0 CAR T cells


title: Liver_CLP+ADSCs1_1

description:
L-A1-1
Liver_gene_FPKM.txt


title: ATAC-Seq pLT-OIS-D7-r1

value: HRasV12-induced senescence


title: Liver_CLP+ADSCs1_2

description:
L-A1-2
Liver_gene_FPKM.txt


title: T47D_Y537S_clone1_mimic_miR_301b_3p


title: D14_High_CD4_d0_S17_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D14_High_CD4_d0 CAR T cells


title: Liver_CLP+Vehicle_4

description:
L-C4
Liver_gene_FPKM.txt

value: Liver

value: Vehicle


title: D10_Low_CD8_d0_S2_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: Healthy

value: D10_Low_CD8_d0 CAR T cells


title: ATAC-Seq pLT-WSTF-3

value: Proliferating

value: WSTF


title: GCTB2_scRNA

city: Guangzhou

first: Meiling

last: Yang

address: No. 106, Zhongshan Road,Yuexiu District

institute: Guangdong Provincial People’s Hospital（Guangdong Academy of Medical Sciences）

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw data were processed using Cell Ranger (v3.0.2) to align reads, generate feature-barcode matrices, and perform gene expression analysis. We used the mkfastq pipelines to make fastq files and used the cell count pipelines for alignment (with reference genome Hg19), filtering, barcode counting, and UMI counting.
Assembly: Hg19
Supplementary files format and content: Matrix table with raw UMI counts for every gene and every single cell in the specific patients

source_name: giant cell tumor of bone

extract_protocol:
Fresh tumor tissues were surgically removed from GCTB patients and minced into 2-4 mm pieces. The pieces were transferred to the tube with digestive enzyme from Tumor Dissociation Kit (Cat# 130-095-929, Miltenyi Biotec) and incubated at 37 ℃ for 30 min on a shaker. After digestion, 2% FBS was added to neutralize enzyme lysate, and the tissues were filtered through a 70 μm filter. Subsequently, the samples were centrifuged at 350 × g for 5 min and the supernatants were discarded. To remove red blood cells, the cell pellets were suspended in red blood cell lysis buffer (Beyotime) for 30 s. The solution was then centrifuged at 350 × g for 5 min and resuspended in Dulbecco’s phosphate-buffered saline (DPBS; Thermo Fisher). The samples were stained with trypan blue (Solarbio) and the cellular viability was evaluated. Finally, single cells were encapsulated into emulsion droplets using the Chromium Controller (10× Genomics).
The scRNA-seq libraries were constructed using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit (10x Genomics)

value: giant cell tumor of bone

value: denosumab


title: Liver_CLP+Vehicle_3

description:
L-C3
Liver_gene_FPKM.txt


title: ATAC-Seq pLT-WSTF-2


title: D10_Low_CD4_d0_S1_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: Blood

value: D10_Low_CD4_d0 CAR T cells


title: GCTB1_scRNA

description: 10x Genomics

value: naive


title: Liver_CLP+Vehicle_2

description:
L-C2
Liver_gene_FPKM.txt


title: ATAC-Seq pLT-WSTF-1


title: D10_High_CD8_d0_S6_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D10_High_CD8_d0 CAR T cells


title: ATAC-Seq pLT-3

value: Vector


title: Liver_CLP+Vehicle_1

description:
L-C1
Liver_gene_FPKM.txt


title: D10_High_CD4_d0_S5_R1_001 [RNA-seq]

description: Poly-A mRNA sequencing

value: D10_High_CD4_d0 CAR T cells


title: PBMCs_CLP+ADSCs4_5

description:
P-A4-5
PBMCs_gene_FPKM.txt

source_name: PBMCs

value: PBMCs

value: allogeneic ADSCs at 4×107 cells/kg


title: RNA-Seq pLT-3


title: PEDS0009, sgETV6, H3K4me3

first: Kenneth

middle: N

last: Ross

address: 450 Brookline Ave., Room LC6115

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
The raw Illumina sequencer output was converted to FASTQ format using the program bcl2fastq (v2.17).
Sequencing read quality was examined using FastQC (http://www.bioinformatics.babraham.ac.uk) (v0.11.9).
Trimming of low-quality reads and clipping of sequencing adapters was done using the program Trimmomatic (v0.36) and all reads shorter than 40bp after trimming were dropped. After Trimmomatic, an extra adapter trimming step was run using kseq from CUT&RUN Tools 2.0 (Yu, et al. Bioinformatics, 2022 https://github.com/fl-yu/CUT-RUNTools-2.0/blob/master/docs/INSTALL.md).
Reads were aligned to the human genome (hg19) using Bowtie2 (v2.3.5) using the ‘—very_sensitive’ preset collection of parameters and the ‘—dovetail’ flag.
Bam to Sam file conversion was done with SamTools (v1.9) and duplicate reads were removed using Picard-tools (v2.19.0) (http://picard.sourceforge.net).
CUT&RUN peaks were called using MACS2 (v2.1.4) with the command callpeak with the minimum False Discovery Rates (FDR) set to q < 0.01.
CUT&RUN samples also included E. coli spike-in for sample normalization so samples were also aligned to the Escherichia coli (Escherichia_coli_K_12_DH10B NCBI 2008-03-17) genome using the same pipeline.
BigWig files were created from bam files using the program bamCoverage in the python deeptools software suite (v3.3.0) with a default read extension length of 180.  Deduplicated read counts were normalized to the E. coli spike-in control levels using picard DownsampleSam before running bamCoverage.
Assembly: hg19
Supplementary files format and content: BigWig files (*.bw) have read coverage after read counts have been normalized to spike-in levels
Supplementary files format and content: peak files (*.narrowPeak) are tab delimited files with the genome coordinates, peak names, scores, and log p-values for the peaks from the combined replicates
Library strategy: CUT&RUN

source_name: Newly derived Ewing sarcoma cell line

growth_protocol: Low-passage, newly derived Ewing sarcoma cell line PEDS0009 (CCLF_PEDS_0009_T) was obtained from the Cancer Cell Line Factory (Broad Institute, Cambridge, MA) and was derived as previously described (Guenther et al., Clinical Cancer Research 2019).   PEDS0009 was cultured in RPMI-1640 supplemented with 10% FBS and 1% pen-strep.

extract_protocol:
CUT & RUN (Cleavage Under Targets & Release Using Nuclease) was performed as previously described105-107 with slight modifications. Briefly, 500,000 cells per condition were bound to activated ConA Beads (EpiCypher 21-1401). Next, the ConA bead-cell mixture was resuspended in a cold antibody buffer and FLI-1-(ab133485; 1mcg per sample) antibody or 0.5 mcg H3K4me3 (EpiCyper 13-0041) as positive and 0.5 mcg  IgG (EpiCypher 13-0042) as negative control were  per sample added over night. Next, pAG-MNase (EpiCypher 15-1016) was added to each reaction to allow binding to the antibody-labeled chromatin. E.coli Spike-in DNA (EpiCypher 18-1401) was added following MNase activation. Subsequently, targeted chromatin was digested and released by the addition of CaCl2. The fragmented chromatin was purified using the CUTANA DNA Purification Kit (EpiCypher 14-0050.
Quantification, library preparation and sequencing was performed by the genomics core at DFCI.  DNA libraries were pooled and sequenced (2 x 150 bp paired end) on the Illumina NovaSeq 6000 platform.

treatment_protocol: PEDS0009 cells were transduced with lentivirally-packaged CRISPR/Cas9 constructs and sgRNA sequences for ETV6 and controls.  sgRNA sequences used to target ETV6 were taken from the Broad Institute AVANA CRISPR/Cas9 screen and are available for download at the DepMap Portal (https://depmap.org).  The sgETV6-1 forward sequence was 5’-GCAGCCAATTTACTGGAGCA-3’. The sgETV6-2 forward sequence was 5’-GCAGGGATGACGTAGCCCAG-3’. The sgETV6-3 forward sequence was 5’-GTGTGTGTATAGAGTTTCCA-3’. The sgETV6-4 forward sequence was 5’-GTTATGGTGCACATTATCCA-3’. For  control sgRNA, sgChr2.2 was used as a cutting control and targets a gene desert on Chromosome 2, 5’-GGTGTGCGTATGAAGCAGTG-3’. For ligation into the LentiCRISPRv2 plasmid, additional bases were added. 5’-CACCG-3’ was added to the beginning of the forward sequence. 5’-AAAC-3’ and 5’-C-3’ were added at the beginning and end of the reverse sequence, respectively.

value: Newly derived Ewing sarcoma cell line

tag: modification type

value: CRISPR

tag: modification

value: 5.5 days

tag: chip antibody

value: H3K4me3 (EpiCyper 13-0041)


title: PEDS0009, sgChr2, H3K4me3

tag: tissue


title: ATAC-Seq pLT-2


title: Liver_CLP+ADSCs2_2

description:
L-A2-2
Liver_gene_FPKM.txt

value: Liver

tag: treatment

value: allogeneic ADSCs at 2×107 cells/kg


title: PBMCs_CLP+ADSCs4_4

description:
P-A4-4
PBMCs_gene_FPKM.txt


title: ATAC-Seq pLT-1

value: Proliferating


title: PEDS0009, sgETV6, IgG

tag: time

value: IgG (EpiCypher 13-0042, 0.5mcg)


title: PBMCs_CLP+ADSCs4_3

description:
P-A4-3
PBMCs_gene_FPKM.txt


title: PEDS0009, sgETV6, FLI1

tag: cell line

value: FLI1 (ab133485; 1mcg per sample)


title: FLAG-NR2E1-input

city: Shanghai

first: Haibin

last: Tian

address: 1239 Siping Road

institute: Tongji University

data_processing:
Bowtie (version 0.12.8) was then used to map the clean reads to the human hg19 reference genome.
The binding peaks were identified by MACS (version 1.4.2)
Genome_build: hg19
Supplementary_files_format_and_content: annotated_tss_genetic peaks

extract_protocol:
The cells were collected by scraping and were lysed with lysate buffer, the nuclear pellet was digested by micrococcal nuclease. Immunoprecipitation was performed on the lysate with 2μg of anti-FLAG antibody
The DNA fragments were then sequenced using the Illumina HiSeq X-ten platform.

tag: cell type

value: iRPE


title: PEDS0009, sgChr2, IgG


title: PBMCs_CLP+ADSCs4_2

description:
P-A4-2
PBMCs_gene_FPKM.txt


title: PBMCs_CLP+ADSCs4_1

description:
P-A4-1
PBMCs_gene_FPKM.txt


title: PEDS0009, sgChr2, FLI1


title: PBMCs_CLP+ADSCs2_4

description:
P-A2-4
PBMCs_gene_FPKM.txt


title: PBMCs_CLP+ADSCs2_3

description:
P-A2-3
PBMCs_gene_FPKM.txt


title: FLAG-CRX-input

source_name: FLAG-CRX-input


title: FLAG-NR2E1-2


title: PBMCs_CLP+ADSCs2_2

description:
P-A2-2
PBMCs_gene_FPKM.txt


title: IP, ETV6, B

city: Paris

first: Javiera

last: Villar

address: 25 rue d'Ulm

institute: Institut Curie

data_processing:
Quality of sequencing data was assessed using FastQC.
Reads were aligned to the genome using BWA-Mem.
Peak calling was performed with MACS2 using default parameters for each donor and corresponding input.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: blood

extract_protocol:
Chromatin immunoprecipitation was performed from 80 millions monocytes as starting material, using the ChIP-IT High Sensitivity kit (Active Motif) following manufacturer’s instructions. Monocytes were homogenized using a 7 mL Dounce glass homogenizer (Clinisciences). Sonication was performed using a Bioruptor Pico instrument (Diagenode) using 20 cycles (30 seconds on and 30 seconds off). Chromatin was immunoprecipitated using antibodies against ETV3 (ref A303-737A, polyclonal, Bethyl) or ETV6 (clone R1092.1.1A9, CDI Laboratories Inc).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIPSeq Library Prep Kit (Illumina). 4-6 ng of DNA was used for each sample. Sequencing was performed in 1 sequencing unit of NovaSeq 6000 (Illumina) (100-nt593 length reads, paired end).

treatment_protocol: Monocytes from 2 individual donors were cultured for 3 days in the presence of 100 ng/mL M-CSF, 5 ng/mL IL-4 and 20 ng/mL TNF-α.

tag: individual

value: donorB

value: blood

value: Monocytes

value: ETV6 (CDI Laboratories Inc, clone R1092.1.1A9)


title: PBMCs_CLP+ADSCs2_1

description:
P-A2-1
PBMCs_gene_FPKM.txt


title: FLAG-MITF-A-2

source_name: FLAG-MITF-A


title: FLAG-MITF-A-1


title: PBMCs_CLP+ADSCs1_4

description:
P-A1-4
PBMCs_gene_FPKM.txt

value: allogeneic ADSCs at 1×107 cells/kg


title: Input, B


title: FLAG-CRX-2

source_name: FLAG-CRX


title: Input, A

value: donorA


title: PBMCs_CLP+ADSCs1_3

description:
P-A1-3
PBMCs_gene_FPKM.txt

value: PBMCs


title: IP, ETV3, A


title: FLAG-CRX-1


title: FLAG-MITF-A-input

source_name: FLAG-MITF-A-input


title: Monocytes, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where HTO sequences were concatenated and treated as Custom library with default settings (v3.1) and aligning to the hg38 genome.
Assembly: hg38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: Blood

extract_protocol:
Peripheral Blood Mononuclear Cells (PBMC) were prepared by centrifugation on a Ficoll gradient (Lymphoprep, StemCell). Blood CD14+ monocytes were isolated from healthy donors’ PBMC by positive selection using magnetic beads (Miltenyi). Monocytes were 95%–98% CD14+CD16- as assessed by flow cytometry.
Library was prepared using Chromium Single Cell 3ʹ v3.1 protocol (10x Genomics).

value: Blood

value: Blood CD14+ monocytes

tag: library type

value: HTO

tag: antibodies/tags

value: Anti CD298 + Anti β2M :Donor1--/TotalSeq-A0251 ; Donor2--/TotalSeq-A0252

tag: individuals

value: Donor1 (same as DonorA) and Donor2 (same as DonorB)


title: Monocytes, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: FLAG-C-MYC-2

source_name: FLAG-C-MYC


title: PBMCs_CLP+ADSCs1_2

description:
P-A1-2
PBMCs_gene_FPKM.txt


title: IP, ETV6, A


title: PBMCs_CLP+ADSCs1_1

description:
P-A1-1
PBMCs_gene_FPKM.txt


title: IP, ETV3, B


title: FLAG-C-MYC-input

source_name: FLAG-C-MYC-input


title: FLAG-C-MYC-1


title: PBMCs_CLP+Vehicle_4

description:
P-C4
PBMCs_gene_FPKM.txt

value: Vehicle


title: FLAG-NR2E1-1


title: PBMCs_CLP+Vehicle_3

description:
P-C3
PBMCs_gene_FPKM.txt


title: human ciliary body, sample 1, scRNAseq

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

description:
BD
S1

data_processing:
Quality control and preprocessing of the FASTQ sequencing data was performed using the fastp preprocessor tool with the default parameters. The UMI-Tools method that models the errors in the UMI sequence was used to improve quantification accuracy. Thereafter, the UMI-based clean read data were mapped to the human genome (Ensemble version 91), and a gene expression matrix (UMI counts per gene per cell) was obtained
Assembly: human genome (Ensemble version 91)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: S1 (sample 1 from pair #1)

extract_protocol:
The ciliary body tissues from each pair of the eyes were incubated in PBS containing 0.04% BSA, 1.2 U/ml dispase and 50 U/ml penicillin-streptomycin for 15 min. Thereafter, trypsin, hyaluronidase, kynurenic acid, MgCl2 and CaCl2 with appropriate conc. were added in the digestion buffer, followed by another 15-min incubation of the mixture at 37 °C for 15min. Tissue digest was terminated, followed by the pipetting, mincing, filtering, spining and rinsing steps to yield single cell suspension. A BD Rhapsody analysis system was used to prepare single cell whole transcriptome according to the manufacture’s instruction.
Single cell transcriptomic sequencing libraries were prepared by following a series of PCR steps including random priming and extension (RPE), RPE PCR and whole-transcriptome amplification (WTA) index PCR according to the manufacture’s instruction.
Normalized libraries were sequenced on NovaSeq Illumina with a 150 bp paired-end run.

value: human ciliary body (HCB)

value: S1 (sample 1 from pair #1)


title: PBMCs_CLP+ADSCs1_5

description:
P-A1-5
PBMCs_gene_FPKM.txt


title: R590_C

city: Sydney

first: Ling

last: Zhu

state: New South Wales

address: Save Sight Institute, Level 2, South Block, Sydney Eye Hospital, 8 Macquarie St

country: Australia

institute: the University of Sydney

description: From donor 04

data_processing:
Real-Time Analysis (RTA) software (RTA3.4.4) used for basecalling.
Remove reads with adaptor contamination. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read
STAR software (v2.6.1d) is used to accomplish the mapping.
FeatureCounts (v1.5.0-p3) was used to count the read numbers mapped of each gene.
Assembly: Genome Reference Consortium Human Build 38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: human retina explant

growth_protocol: the human retina tissues were cultured in Neurobasal-A medium  (gibco, 10596) supplemented with 10%FBS and 1% penicillin-streptomycin (Thermo Fisher Scientific, NSW, Australia) supplemented with 1% FBS, 2% B‐27 (Thermo Fisher Scientific), 1% N‐2 (Thermo Fisher Scientific), 1% Glutamax (Gibco, Thermo Fisher, NSW, Australia) and 1% penicillin-streptomycin (Sigma‐Aldrich)

extract_protocol:
STAR software (v2.6.1d) is used to accomplish the mapping.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the human retina tissues were treated with either 8 μM ERK1/2 inhibitor or same concentration DMSO for 24h

value: human retina explant

value: DMSO


title: R590_PD

description: From donor 04

value: ERK1/2 inhibitor


title: PBMCs_CLP+Vehicle_2

description:
P-C2
PBMCs_gene_FPKM.txt


title: PBMCs_CLP+Vehicle_1

description:
P-C1
PBMCs_gene_FPKM.txt


title: R230_C

description: From donor 03


title: R230_PD

description: From donor 03


title: R169_C

description: From donor 02


title: human ciliary body, sample 3, scRNAseq

description:
BD
S3

source_name: S3 (sample 3 from pair #3)

value: S3 (sample 3 from pair #3)


title: Down syndrome CPC S2

city: Pune

first: Nishant

last: Singhal

state: Maharashtra

address: Ganeskhind Road

country: India

institute: National Centre for Cell Science

data_processing:
Raw dat was aligned to the transcriptome derived from UCSC genome assembly hg19, using STAR with default parameters.
Read counts for each transcript were measured using feature Counts
Differentilly expressed genes were determined using DESeq2 and a cut-off of 0.05 on adjusted p-valus (corrected for multipple hypotheses testing) was used fro creating lists and heatmaps.

source_name: Down syndrome human iPSCs

extract_protocol:
Down syndrome and isogenic normal human iPSCs were differentiated for 24 days in vitro. Subconfluent DIV24 cells were harvested in Trizol lysis buffer (Qiagen RNAeasy). Total RNA  was collected using the RNAeasy reagent (Qiagen) following the manufacturer’s instructions.
mRNA-seq libraries were prepared from 1 ug of total RNA using the Illumina mRNA-seq Sample Preparation kit following the manufacturer’s instructions

value: cortical progenitor cells (CPCs)

value: in vitro differentiated cells


title: Isogenic Normal CPC S1

source_name: Isogenic Normal human iPSCs


title: Isogenic Normal CPC S3


title: Isogenic Normal CPC S2


title: Down syndrome CPC S3


title: KO2

city: 北京市

first: Zhongyan

last: Wu

address: 学院路38号北京大学医学部

institute: PKUISB

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie.
FPKM values were calculated.
Assembly: mm10
Supplementary files format and content: gene_fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.

source_name: Brain (cerebral cortex)

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

value: Brain (cerebral cortex)

tag: genotype

value: Fam69c KO

tag: age

value: 12 months


title: KO1

address: 学院路38号北京大学医学部


title: human ciliary body, sample 2, scRNAseq

description:
BD
S2

source_name: S2 (sample 2 from pair #2)

value: S2 (sample 2 from pair #2)


title: KO3

address: 学院路38号北京大学医学部


title: Down syndrome CPC S1


title: D1258_C

description: From donor 01


title: R169_PD

description: From donor 02


title: WT3

address: 学院路38号北京大学医学部

value: WT


title: WT2

address: 学院路38号北京大学医学部


title: RP-2

city: Lanzhou

first: Chen

last: Lv

address: No.1 Yingmen Village

institute: Gansu Agricultural University

data_processing:
Unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: ftp://ftp.ensembl.org/pub/release-96/fasta/bos_taurus/dna/
Supplementary files format and content: txt,expression profiles

organism: Bos taurus

source_name: caudal vein blood

extract_protocol:
Total RNA from the NC and RP groups was isolated and purified using TRIzol reagentt (Thermo Fisher Scientific, Waltham, MA, USA).
Approximately 5 µg of total RNA were used to prepare six small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

tag: breed

value: Holstein

value: caudal vein blood

tag: developmental stage

value: postpartum


title: RP-1

tag: status

value: fetal membranes retained


title: WT1

address: 学院路38号北京大学医学部


title: NC-3

value: control


title: RP-3


title: PR patient, after anti-PD-1 treatment

city: Jinan

first: Xihan

last: Liu

state: Shandong

address: Wenhuaxi Road #44

institute: Shandong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: .txt files include RPKM values for each Sample

source_name: Peripheral blood

extract_protocol:
Peripheral blood RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral blood

value: after anti-PD-1 treatment


title: NC-2


title: D1258_PD

description: From donor 01

value: human retina explant


title: SHAM-NaCL-3

city: Albuquerque

first: Michela

last: Dell'Orco

state: NM

address: 1 University of New Mexico, MSC08 4740

institute: University of New Mexico

data_processing:
Raw sequencing data generated from Illumina NovaSeq 6000 that pass the Illumina chastity filter are used for following analysis. Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned to reference genome. Based on alignment statistical analysis (mapping ratio, rRNA/mtRNA content, fragment sequence bias), we determine whether the results can be used for subsequent data analysis. If so, the expression profiling, differentially expressed genes and differentially expressed transcripts are calculated. The novel genes and transcripts are also predicted. Principal Component Analysis (PCA), Correlation Analysis, Hierarchical Clustering, Gene Ontology (GO), Pathway Analysis, scatter plots and volcano plots are performed for the differentially expressed genes in R or Python environment for statistical computing and graphics.
The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM in group ≥ 0.5.
Assembly: GRCm38
Supplementary files format and content: *.xlsx: Excel files include FPKM values.

source_name: cortex

extract_protocol:
Brains were removed and the cortexes were dissected, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Total RNA is enriched by oligo (dT) magnetic beads (rRNA removed); 2. RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific. The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method. To sequence the libraries on the Illumina NovaSeq 6000 instrument, the barcoded libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified in situ, and subsequently sequenced for 150 cycles for both ends on Illumina NovaSeq 6000 instrument. The completed libraries were qualified on Agilent 2100 Bioanalyzer for concentration, fragment size distribution between 400 ∼ 600 bp, and adapter dimer contamination. The amount was determined by absolute quantification qPCR method. The barcoded libraries were mixed in equal amounts and used for sequencing on the instrument.

value: cortex

tag: strain

value: 7-8 weeks

tag: Sex

value: female

tag: diagnosis

value: healthy

value: NaCl


title: SHAM-NaCL-2

tag: tissue


title: PD patient3, after anti-PD-1 treatment

tag: treatment


title: Liver_CLP+ADSCs2_1

description:
L-A2-1
Liver_gene_FPKM.txt

source_name: Liver

value: Liver

tag: strain background

value: allogeneic ADSCs at 2×107 cells/kg


title: A673 ETV6 dTAG cells - 72 hour dTAGV-1 treated - ATAC-seq - replicate 3

data_processing:
The raw Illumina sequencer output was converted to FASTQ format using the program bcl2fastq (v2.17).
Sequencing read quality was examined using FastQC (http://www.bioinformatics.babraham.ac.uk) (v0.11.9).
Trimming of low-quality reads and clipping of sequencing adapters was done using the program Trimmomatic (v0.36) and all reads shorter than 40bp after trimming were dropped.
Reads were aligned to the human genome (hg19) using Bowtie2 (v2.3.5) using the ‘—very_sensitive’ preset collection of parameters.
After alignment, samtools (v1.9)was used to remove mitochondrial reads (ChrM).
Bam to Sam file conversion was done with SamTools (v1.9) and duplicate reads were removed using Picard-tools (v2.19.0) (http://picard.sourceforge.net).
ATAC-seq peaks were called using MACS2 (v2.1.4) with the command callpeak and the minimum False Discovery Rates (FDR) set to q < 0.01
BigWig files were created from deduplicated bam files from picard tools using the program bamCoverage in the python deeptools software suite (v3.3.0) with a default read extension length of 180.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks files (*.xls) are tab deimited files with peak locations and strengths and were generated by MACS2. BigWig (*.bw) files were produced using deeptools (v3.3.0) bamCoverage.

source_name: A673 Ewing sarcoma cell line

growth_protocol: A673 Ewing sarcoma parental cells were co-transduced with the following lentivirally packaged constructs. Four sgRNAs targeting exon-intron junctions of the endogenous ETV6 gene were cloned,  into a version of the LentiCRISPRv2 plasmid backbone conferring blasticidin resistance (Addgene 83480). The sgRNA sequences used were (1) sgETV6-endo-1, 5’-TCCTGCTCAGTGTAGCATTA-3’, (2) sgETV6-endo-2, 5’-GAACACTCACGCAGGTGCGC-3’, (3) sgETV6-endo-3, 5’-TCCAGACTCTCACCTGAATG-3’, and (4) sgETV6-endo-4, 5’-AGTTCATAGAGCACATCACC-3’. A codon-optimized gblock encoding coding sequences of ETV6 was cloned into the pLEX_305 vector backbone (Addgene 91798) to C-terminally tag the ETV6 protein with the FKBP12F36V protein domain and a HA epitope tag. Ewing sarcoma cells were spin-infected. Cells were incubated for 24 hours, after which viral media was replaced by media containing 1 µg/ml puromycin and 5 µg/ml blasticidin (Life Technologies, #A1113903) and supplemented with 40% FBS for 48-72 hours. Non-infected control cells were treated with puromycin or blasticidin to confirm selection. Cells were cultured in Dulbecco’s Modified Eagle’s Media supplemented with 15% FBS and 1% penicillin streptomycin glutamine, as well as 0.5 µg/ml puromycin and 2.5 µg/ml blasticidin to maintain selection. Cells were split at a ratio of 1:5 every other day.

extract_protocol:
ATAC-seq was performed using a publicly available protocol (https://www.med.upenn.edu/kaestnerlab/assets/user-content/documents/ATAC-seq%20Protocol%20(Omni)%20-%20Kaestner%20Lab.pdf). 100,000 cells from each sample were washed in PBS and resuspended in 1.5 ml reaction tubes in 50 µl Lysis Buffer (48.5 µl Resuspension Buffer, 0.5 µl 10% NP-40, 0.5 µl 10% Tween-20, 0.5 µl 1% Digitonin; Resuspension Buffer was comprised of 10 mM 1M Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2). The lysis reaction was incubated for 3 minutes on ice. To each sample, 1 ml of Wash Buffer (990 µl Resuspension Buffer, 10 µl 10% Tween-20) was added and tubes were inverted a few times. Cells were pelleted by centrifugation at 500xg for 10 minutes at 4°C. The supernatant was discarded such that intact nuclei in the pellet were isolated. The nuclei were resuspended in 50 µl Transposition Reaction Mix, comprised of 25 µl 2X Tagment DNA Buffer and 2.5 µl Tagment DNA Enzyme 1 (Illumina Inc., # 20034197), 16.5 µl PBS, 0.5 µl 10% Tween-20, 0.5 µl 1% Digitonin, and 5 µl H2O. Samples were incubated at 37°C for 30 minutes on a thermomixer at 1,000rpm. Following incubation, DNA from each sample was extracted using a reaction cleanup kit (Qiagen, # 28204) and DNA was eluted using 10 µl Elution Buffer. DNA was PCR-amplified for 5 cycles. 5 µl from each partially amplified library was used to perform qPCR to determine the required number of additional PCR cycles, calculated as the number of cycles needed to reach 1/3 of the maximum R in each qPCR reaction. Samples were amplified an additional 3 or 4 PCR cycles.
Libraries were purified using a double-sided Agencourt AMPure XP bead purification (Beckman Coulter, # A63880), first at 0.5X the reaction volume, conserving the supernatant, and then at 1.3X the reaction volume. Purified libraries were eluted in 20 µl H2O. The molarity of each library was estimated by measuring the DNA concentration using the Qubit dsDNA Broad Range Assay kit (Thermo Fisher Scientific, # Q32850) and by analyzing the distribution of DNA fragment sizes using the Tapestation D5000 dsDNA assay (Agilent; ScreenTape, # 5067-5588; Ladder, # 5067-5590; Reagents, # 5067-5589). Each library was diluted to 4 nanomolar and libraries were pooled in equal volumes. Libraries were sequenced in 37-basepair paired-end fashion for 75 cycles, aiming for >60 million reads per sample, on the Illumina NextSeq 500 instrument.

treatment_protocol: The dTAGV-1 molecule was generously provided by the Gray Laboratory (Dana-Farber Cancer Institute, Boston, MA) and used at a stock concentration of 10 millimolar suspended in DMSO. A673 ETV6-dTAG cells were seeded at 1 million cells per 15 cm dish for the 72-hour time point.  Following seeding, cells were allowed to adhere for 24 hours prior to treatment. Existing media was aspirated and DMSO or dTAGV-1-containing media was added. For all experiments, dTAGV-1 was used at a final concentration of 1 micromolar. Equivalent volumes of DMSO were used as control.

tag: cell line

tag: modification type

value: dTAG

tag: modification

value: ETV6 dTAG

tag: time

value: 72 hours


title: NC-1

value: Holstein

value: caudal vein blood


title: PD patient1, after anti-PD-1 treatment


title: PD patient2, after anti-PD-1 treatment


title: SHAM-NaCL-1

value: WT


title: SD-KCL-3-RIGHT

value: KCL


title: PD patient3, before anti-PD-1 treatment

value: Peripheral blood

value: at baseline


title: SD-KCL-1-RIGHT


title: A673 ETV6 dTAG cells - 72 hour dTAGV-1 treated - ATAC-seq - replicate 2


title: A673 ETV6 dTAG cells - 72 hour DMSO treated - ATAC-seq - replicate 3

value: DMSO


title: PR patient, before anti-PD-1 treatment


title: SD-KCL-2-RIGHT

value: cortex


title: A673 ETV6 dTAG cells - 72 hour dTAGV-1 treated - ATAC-seq - replicate 1


title: PEDS0009, sgETV6, Rb, rep2

data_processing:
Quality control on raw sequencing reads were performed using FastQC (http://www.bioinformatics.babraham.ac.uk) (v0.11.4).
Adapter sequences and/or low-quality reads were trimmed using trim_galore (http://www.bioinformatics.babraham.ac.uk) (0.4.4_dev).
Reads were aligned to human (hg19) and spike-in Escherichia coli (Escherichia_coli_K_12_DH10B NCBI 2008-03-17) genomes using Bowtie2 (v2.3.4.3)12,13 with the following options ’--no-unal --no-mixed --no-discordant --dovetail --phred33 -q -I 10 -X 700’. ‘--very-sensitive’ option was added when aligning to spike-in genome.
SamTools (v1.9) was used to convert sam to bam with ‘-bq 10’ option.
Counts of mapped reads were spike-in normalized by calculating a scale factor using the “median ratio method” from DESeq2. Spike-in normalization in conjunction with median ratio method provide a robust normalization method to appropriately account for global changes of ETV6 occupancies.
Peaks in each biological replicate were called using MACS2 (v 2.2.7.1) with the spike-in normalization. All duplicate reads were kept in the analysis.
Assembly: hg19
Supplementary files format and content: BigWig files (*.bw) have read coverage after read counts have been normalized to spike-in levels
Supplementary files format and content: BigWig files (*_comb.bw) have read coverage for the combined replicate 1 and 2 data (after read counts have been normalized to spike-in levels)
Supplementary files format and content: peak file (peaks_all_sgCh2_ETV6.narrowPeak) is a tab delimited file with the genome coordinates, peak names, scores, and log p-values for all the peaks from the combined replicates
Supplementary files format and content: peak file (peaks_sgCh2_ETV6_fdr05_idr01_meanT80_FC8.narrowPeak) is a tab delimited file with the genome coordinates, peak names, scores, and log p-values for the peaks from the combined replicates after the peaks have been filtered (to ensure high quality peaks that are most likely to represent biological signals) for False Discovery Rate (FDR) <0.05, IDR<0.01, mean normalized counts of ETV6 > 80, and log2 Fold-Change >8
Library strategy: CUT&Tag

source_name: Newly derived Ewing sarcoma cell line

extract_protocol:
CUT&Tag (Cleavage Under Targets and Tagmentation) was performed as described (Kaya-Okur, et al., Nature Cummunications, 2019) with slight modifications by the Lessnick Laboratory (Nationwide Children’s Hospital, Columbus, OH). 250,000 cells per CUT&Tag condition were bound to BioMag® Plus Concanavalin A-coated magnetic beads (Bangs Laboratories, BP531) and incubated with primary antibodies (ETV6 rabbit, Bethyl A303-674, 1:50; ETV6 mouse, Sigma WH0002120M1, 1:50; Rabbit anti-mouse, Abcam, ab46540, 1:50) overnight at 4 °C and secondary antibodies (guinea pig anti-rabbit IgG, Antibodies-Online ABIN101961, 1:100; Rabbit anti-mouse, Abcam ab46540, 1:100) for 1 hour at room temperature. Adapter-loaded Protein A-Tn5 fusion protein was added at a dilution of 1:250 and incubated for 1 hour at room temperature. To activate the Tn5, tagmentation buffer containing MgCl2 was added and samples were incubated for 1 hour at 37°C. Reactions were stopped by addition of EDTA and DNA was solubilized with SDS and Proteinase K for 1 hour at 50°C. Total DNA was purified using Phenol/Chloroform extraction followed by Ethanol precipitation.
CUT&Tag libraries were prepared with NEBNext HiFi 2x PCR Master Mix (NEB M0541S) and indexed primers10 using a combined Annealing/Extension step at 63°C for 10 seconds and 15 cycles followed by a 1.1X post-amplification AMPure XP (Beckman Coulter, A63880) bead cleanup. The fragment size distributions and concentrations of the final libraries were determined using the High Sensitivity D1000 Screen tape assay (Agilent, 5067-5584 and 5067-5585) on the Agilent 2200 TapeStation System. Libraries were pooled and sequenced (2 x 150 bp paired end) on the Illumina HiSeq4000 platform (Nationwide Children’s Hospital Institute for Genomic Medicine). Two independent replicates of each CUT&Tag sample were prepared.

value: Newly derived Ewing sarcoma cell line

value: CRISPR

value: 5.5 days

tag: chip antibody

value: Rabbit anti-mouse, Abcam, ab46540


title: PD patient2, before anti-PD-1 treatment


title: hiPSC line: control 1

city: London

first: Sonia

last: Gandhi

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38, release 89
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hiPSC made from fibroblasts

extract_protocol:
3 control mDA neuron samples were washed with PBS once, and then incubated with Accutase (GibcoTM) for 5 minutes to obtain a single cell suspension. The samples were then diluted 1/3 before usage. The quality and concentration of each single-cell suspension was measured using Trypan blue and the Eve automatic cell counter. Each sample presented a concentration between a 1200-1700 cell/µl and viability ranged between 55-68%, samples with a viability above 57% were used for sequencing.
Approximately 10000 cells were loaded for each sample into a separate channel of a Chromium Chip G for use in the 10X Chromium Controller (cat: PN-1000120). The cells were partitioned into nanoliter scale Gel Beads in emulsions (GEMs) and lysed using the 10x Genomics Single Cell 3′ Chip V3.1 GEM, Library and Gel Bead Kit (cat: PN-1000121). cDNA synthesis and library construction were performed as per the manufacturer’s instructions. The RNA was reversed transcribed and amplified using 12 cycles of PCR. Libraries were prepared from 10µl of the cDNA and 13 cycles of amplification. Each library was prepared using Single Index Kit T Set A (cat: PN-1000213) and sequenced on the HiSeq4000 system (Illumina) using 100 bp paired-end run at a depth of 65-100 million reads. Libraries were generated in independent runs for the different samples.

value: hiPSC made from fibroblasts

tag: cell type

value: midbrain dopaminergic neuron

value: healthy control - Male

value: No treatment - Basal


title: SD-KCL-3-LEFT

tag: genotype

value: 7-8 weeks

value: female

value: healthy


title: hiPSC line: control 3

description: 10x Genomics

value: healthy control - Female


title: PEDS0009, sgETV6, Rb, rep1


title: PD patient1, before anti-PD-1 treatment


title: A673 ETV6 dTAG cells - 72 hour DMSO treated - ATAC-seq - replicate 2

value: dTAG

value: ETV6 dTAG

value: 72 hours


title: PEDS0009, sgETV6, ETV6, rep2

value: ETV6 (Sigma WH0002120M1)


title: EW8 ETV6 dTAG cells - 24 hour dTAGV-1 treated  - HA-tag ChIP-seq

data_processing:
The raw Illumina sequencer output was converted to FASTQ format using the program bcl2fastq (v2.17).
Sequencing read quality was examined using FastQC (http://www.bioinformatics.babraham.ac.uk) (v0.11.9).
Trimming of low-quality reads and clipping of sequencing adapters was done using the program Trimmomatic (v0.36) and all reads shorter than 40bp after trimming were dropped.
Reads were aligned to the human genome (hg19) using Bowtie2 (v2.3.5) using the ‘—very_sensitive’ preset collection of parameters.
Bam to Sam file conversion was done with SamTools (v1.9) and duplicate reads were removed using Picard-tools (v2.19.0) (http://picard.sourceforge.net).
ChIP-seq peaks were called using MACS2 (v2.1.4) with the command callpeak with the ChIP-seq treatment and control bam files and minimum False Discovery Rates (FDR) set to q < 0.01
BigWig files were created from bam files using the program bamCoverage in the python deeptools software suite (v3.3.0) with a default read extension length of 180. For parental cell line samples and untreated ETV6 dTAG samples, bamCoverage was run on the deduplicated bam files from picard tools.  For the DMSO and dTAGV-1 treated ETV6 dTAG samples, deduplicated read counts were adjusted to normalize to the fly spike-in control levels using picard DownsampleSam before running bamCoverage.
Genome_build: hg19
Supplementary_files_format_and_content: *.xls files are tab delimited text files with ChIP-seq peaks data from MACS2; *.bw files are read coverage files in bigWig format from bamCoverage

source_name: EW8 Ewing sarcoma cell line

growth_protocol: All cell lines were genotyped by short tandem repeat analysis and Mycoplasma tested. Additionally, whole exome sequencing and RNA-sequencing were previously performed to validate cell line identity. A673 and EW8 Ewing sarcoma cells were grown in Dulbecco’s Modified Eagle’s Media (DMEM) (Thermo Fisher Scientific, # MT10013CM), supplemented with 10% Fetal Bovine Serum (Sigma-Aldrich, #F2442) and 1% Penicillin-Streptomycin (Life Technologies, #15140163). For dTAG cell lines, A673 and EW8 Ewing sarcoma parental cells were co-transduced with the following lentivirally packaged constructs. Four sgRNAs targeting exon-intron junctions of the endogenous ETV6 gene were cloned into a version of the LentiCRISPRv2 plasmid backbone conferring blasticidin resistance (Addgene 83480). The sgRNA sequences used were (1) sgETV6-endo-1, 5’-TCCTGCTCAGTGTAGCATTA-3’, (2) sgETV6-endo-2, 5’-GAACACTCACGCAGGTGCGC-3’, (3) sgETV6-endo-3, 5’-TCCAGACTCTCACCTGAATG-3’, and (4) sgETV6-endo-4, 5’-AGTTCATAGAGCACATCACC-3’. A codon-optimized gblock encoding coding sequences of ETV6 was cloned into the pLEX_305 vector backbone (Addgene 91798) to C-terminally tag the ETV6 protein with the FKBP12F36V protein domain and a HA epitope tag. Cells were incubated for 24 hours, after which viral media was replaced by media containing 1 µg/ml puromycin and 5 µg/ml blasticidin (Life Technologies, #A1113903) and supplemented with 40% FBS for 48-72 hours. Non-infected control cells were treated with puromycin or blasticidin to confirm selection. Cells were cultured in Dulbecco’s Modified Eagle’s Media supplemented with 15% FBS and 1% penicillin streptomycin glutamine, as well as 0.5 µg/ml puromycin and 2.5 µg/ml blasticidin to maintain selection. Cells were split at a ratio of 1:5 every other day.

extract_protocol:
Prior to immunoprecipitation (IP), antibodies targeting proteins of interest were conjugated to magnetic beads as follows. For each IP, 100 µl of magnetic Protein A Dynabeads (Thermo Fisher Scientific, 10002D) were washed three times in 1 ml BSA blocking solution (0.5% w/v sterile-filtered Bovine Serum Albumin in H2O) and resuspended in 250 µl of the solution. Beads were then rotated overnight at 4ºC with antibody, using 5 µg of antibody to detect H3K27ac (Abcam, # 4729) or 10 µg of antibody to detect TFs (anti-HA, Abcam, # ab9110; anti-FLI1, Abcam, ab15289). For comparative studies (i.e., comparing the relative binding of EWS/FLI), 2 µg of spike-in antibody recognizing a Drosophila-specific histone variant was added (Active Motif, # 61686). The following morning, the antibody-conjugated beads were washed four times in 1 ml BSA blocking solution and then resuspended in 100 µl of the solution and stored at 4ºC until use. To prepare sheared chromatin, Ewing sarcoma cells (20 million cells per ChIP reaction) were collected in a 1.5 ml reaction tube and washed twice in 1 ml PBS. Cells were then crosslinked by resuspension in 1 ml PBS containing 1% methanol-free formaldehyde (Thermo Fisher Scientific, # 28906) and rotated for 10 minutes at room temperature at 12 RPM. The fixation reaction was quenched by adding 100 µl of 1.25M glycine (Sigma Aldrich, # G7126) and 100 µl 1M Tris-HCl pH 8.0 (Thermo Fisher Scientific, # 15568025). Cell pellets were washed twice with 1 ml PBS at room temperature and resuspended in 1 ml of SDS Lysis Buffer (0.5% SDS, 5 mM EDTA, 50 mM Tris-HCl pH 8.0) supplemented with protease inhibitor cocktail (Thermo Fisher Scientific, # PI78429) and incubated at room temperature for 2 minutes with gentle agitation. Lysates were centrifuged at 15,000xg for 10 minutes at 4°C. The supernatant was discarded and the transparent nuclear pellet was re-suspended in 950 µl of ChIP IP Buffer (2 parts SDS Lysis Buffer and 1 part Triton Dilution Buffer, which was composed of 100 mM Tris-HCl pH 8.0, 100mM NaCl, 5mM EDTA, 0.2% NaN3, and 5% Triton X-100) supplemented with protease inhibitor cocktail and transferred to a milliTUBE (Covaris Inc, # 520130) for shearing of chromatin. Sonication was performed on an E220 Focus Ultra Sonicator (Covaris) using the settings 5% duty cycle, 140W peak power, 200 cycles per burst, at 4°C, at 30 minutes per milliTUBE. Following sonication, sheared chromatin was transferred to a 1.5 ml reaction tube and centrifuged at 15,000xg for 10 minutes at 4°C to pellet debris. The supernatant, constituting cleared sheared chromatin, was transferred to a new reaction tube. To prepare the ChIP DNA Input sample, 5 µl of sheared chromatin was transferred to a PCR strip-tube and mixed with 40 µl de-crosslinking buffer (100 mM NaHCO3 and 1% SDS buffer), 1 µl RNAse A (Thermo Fisher Scientific, # 12091021), and 1 µl Proteinase K (Thermo Fisher Scientific, # AM2546). The tube was incubated for 2 hours at 65°C in a thermal cycler to de-crosslink DNA-protein covalent bonds. DNA was then isolated using Agencourt AMPure XP bead-based purification at a 1.2X ratio (Beckman Coulter, # A63881), eluted in 50 µl H2O, and stored at -20ºC. The remaining sheared chromatin was divided or pooled according to the target of interest; at least 5 million cells were used for immunoprecipitation of histone marks and 40 million cells for transcription factors (TFs). Each IP reaction was brought up to a total volume of at least 1 ml with ChIP IP buffer in a 1.5 ml tube. Pooled reactions were conducted in 2 ml or 5 ml reaction tubes. 50 ng of Drosophila spike-in chromatin was added for each H3K27ac ChIP reaction, while 20 ng of spike-in chromatin was added for each TF ChIP reaction. The 100 µl conjugated bead-antibody solution was then added to the sheared chromatin. IP reactions were rotated overnight at 4°C. The following day, ChIP reactions were washed twice in 1 ml low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), then twice in 1 ml high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), then twice in 1 ml lithium chloride buffer (0.25 M LiCl, 1% IGEPAL-CH 630, 1% sodium deoxycholate, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), and then once in 700 µl Tris-EDTA buffer (Sigma Aldrich, # 93283). All washes were performed on ice using buffers that had been stored at 4ºC. Chromatin was eluted from beads using 100 µl fresh ChIP Elution Buffer (1% SDS, 0.1M NaHCO3) and rotated at room temperature for 15 minutes. Eluate was transferred to PCR tubes and mixed with 8 µl 2.5M NaCl, 1 µl RNAse A, and 1 µl Proteinase K. Samples were de-crosslinked for 12-16 hours at 65°C on a thermal cycler. ChIP DNA was extracted from the de-crosslinked samples using AMPure XP beads at a 1.2X ratio and eluted in 20 µl of H2O. DNA from input and ChIP samples were quantified using a Qubit fluorometer (Thermo Fisher) and the Qubit dsDNA high sensitivity assay (# Q32851).
ChIP-seq libraries were prepared using the SMARTer ThruPLEX DNA-Seq kit (Takara Bio, # R400674). H3K27ac ChIP-seq samples were amplified 4 PCR cycles. TF ChIP-Seq samples were amplified 10 PCR cycles. Samples were single-indexed (Takara Bio, # R400695). The concentration of DNA in each library was measured by Qubit and the average of DNA fragment sizes was measured by Tapestation. The approximate molarity of each library was calculated. Each library was diluted to a concentration of 4 nanomolar and equal volumes of each library were pooled. The approximate molarity of the pool was then determined by Qubit and Tapestation and adjusted for sequencing according to Illumina standards. Libraries were sequenced, in 37-basepair paired-end fashion for 75 cycles (Illumina Inc, # 20024906), at a depth of roughly 30 million reads per sample, on the Illumina NextSeq 500 instrument.

treatment_protocol: The dTAGV-1 molecule was generously provided by the Gray Laboratory (Dana-Farber Cancer Institute, Boston, MA) and used at a stock concentration of 10 millimolar suspended in DMSO. For ChIP-seq experiments, A673 ETV6-dTAG cells were seeded at 5 million cells per 15 cm dish for the 6-hour time point and 1 million cells per 15 cm dish for the 72-hour time point. EW8 ETV6-dTAG cells were seeded at 7.7 million cells per 15 cm dish for the 6-hour time point and at 1 million cells per 15 cm dish for the 72-hour time point. Following seeding, cells were allowed to adhere for 24 hours prior to treatment. Existing media was aspirated and DMSO or dTAGV-1-containing media was added. For all experiments, dTAGV-1 was used at a final concentration of 1 micromolar. Equivalent volumes of DMSO were used as control.

tag: chip anti-body

value: HA (Abcam, # ab9110)

value: 24 hours


title: Participant 13, stimulated cells

city: Oxford

first: Ricardo

middle: C.

last: Ferreira

address: Wellcome Trust Centre For Human Genetics, Roosevelt Drive

department: Wellcome Trust Centre for Human Genetics

institute: University of Oxford

description: polyA RNA and surface protein

data_processing:
See https://doi.org/10.1101/2022.04.05.22273167
Assembly: GRCh37.EBVB95-8wt.ERCC
Supplementary files format and content: Tab-delimited text file including unique molecule identifier (UMI) counts for each cell
Supplementary files format and content: Tab-delimited text file including metadata for each cell

source_name: CD4+ Tregs, CD4+ Teffs, CD8+ T cells, CD56br NK, CD56dim NK

extract_protocol: Single-cell capture and cDNA library preparation was performed using the BD Rhapsody Express Single-cell analysis system (BD Biosciences), according to the manufacturer’s instructions.

tag: disease state

tag: subject

value: Participant 13

value: PMA + ionomycin, 90 min


title: PEDS0009, sgChr2, Rb, rep2

value: Newly derived Ewing sarcoma cell line

value: CRISPR

value: 5.5 days

value: Rabbit anti-mouse, Abcam, ab46540


title: SHAM-F-3

value: cortex

value: Thy1-ChR2-YFP heterozygous

tag: age

value: sham


title: Participant 13, unstimulated cells

description: polyA RNA and surface protein

value: CD4+ Tregs, CD4+ Teffs, CD8+ T cells, CD56br NK, CD56dim NK


title: Participant 12, stimulated cells

description: polyA RNA and surface protein

value: Participant 12


title: hiPSC line: control 4

description: 10x Genomics

value: hiPSC made from fibroblasts

value: midbrain dopaminergic neuron

value: healthy control - Male

value: No treatment - Basal


title: PEDS0009, sgChr2, Rb, rep1


title: SHAM-F-2

tag: strain

value: 7-8 weeks

value: female

value: healthy


title: EW8 ETV6 dTAG cells - 72 hour DMSO treated  - input DNA reference

value: dTAG

value: ETV6 dTAG

value: 72 hours

value: DMSO


title: PEDS0009, sgChr2, ETV6, rep2

description:
sgCh2_ETV6_scaled_comb.bw
peaks_all_sgCh2_ETV6.narrowPeak
peaks_sgCh2_ETV6_fdr05_idr01_meanT80_FC8.narrowPeak

value: Newly derived Ewing sarcoma cell line

value: CRISPR

value: 5.5 days

value: ETV6 (Sigma WH0002120M1)


title: EW8 ETV6 dTAG cells - 72 hour dTAGV-1 treated  - input DNA reference


title: SD-F-3-Right

value: cortex

value: Thy1-ChR2-YFP heterozygous

tag: Sex

value: optogenetic stimulation


title: SD-KCL-2-LEFT

value: WT

tag: diagnosis

value: KCL


title: PEDS0009, sgChr2, ETV6, rep1

tag: tissue


title: SHAM-F-1

tag: treatment

value: sham


title: A673 ETV6 dTAG cells - 72 hour DMSO treated - ATAC-seq - replicate 1


title: Participant 12, unstimulated cells

description: polyA RNA and surface protein

value: Participant 12

value: CD4+ Tregs, CD4+ Teffs, CD8+ T cells, CD56br NK, CD56dim NK


title: Participant 11, stimulated cells

description: polyA RNA and surface protein

value: Participant 11

value: PMA + ionomycin, 90 min


title: EW8 ETV6 dTAG cells - 72 hour dTAGV-1 treated  - FLI1 ChIP-seq - replicate 2

value: FLI1 (Abcam, ab15289)

value: dTAG

value: ETV6 dTAG


title: EW8 ETV6 dTAG cells - 72 hour dTAGV-1 treated  - FLI1 ChIP-seq - replicate 1

value: 72 hours


title: A673 ETV6 dTAG cells - 24 hour dTAGV-1 treated - CUT&Tag input DNA control anti-body replicate 2

data_processing:
Quality control on raw sequencing reads were performed using FastQC (http://www.bioinformatics.babraham.ac.uk) (v0.11.4).
Adapter sequences and/or low-quality reads were trimmed using trim_galore (http://www.bioinformatics.babraham.ac.uk) (0.4.4_dev).
Reads were aligned to human (hg19) and spike-in Escherichia coli (Escherichia_coli_K_12_DH10B NCBI 2008-03-17) genomes using Bowtie2 (v2.3.4.3)12,13 with the following options ’--no-unal --no-mixed --no-discordant --dovetail --phred33 -q -I 10 -X 700’. ‘--very-sensitive’ option was added when aligning to spike-in genome.
SamTools (v1.9)14 was used to convert sam to bam with ‘-bq 10’ option.
Counts of mapped reads were spike-in normalized by calculating a scale factor using the “median ratio method” from DESeq2. Spike-in normalization in conjunction with median ratio method provide a robust normalization method to appropriately account for global changes of ETV6 occupancies.
Peaks in each biological replicate were called using MACS2 (v 2.2.7.1) with the spike-in normalization. All duplicate reads were kept in the analysis.
To ensure reproducibility and consistency of peaks called across multiple biological replicates, we calculated Irreproducibility Discovery Rate (IDR) and combined the replicates with Rabbit anti-mouse as controls using DiffBind (v2.14.0) and DESEq2 (v1.26.0). To ensure high quality peaks that are most likely to represent biological signals, the final peak lists were generated with following thresholds: IDR < 0.005, False Discovery Rate (FDR) < 0.05, log2 Fold-Change > 3 and mean normalized counts of ETV6 > 80 (Bethyl antibody) and > 300 (Sigma antibody).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files (*.bw) have read coverage for the combined replicate 1 and 2 data (in the case of ETV6 dTAG samples read counts have been normalized to spike-in levels); peak files (*.narrowPeak) are tab delimited files with the genome coordinates, peak names, scores, and log p-values for the peaks from the combined replicates

value: Rabbit anti-mouse, Abcam, ab46540

value: 24 hours


title: EW8 ETV6 dTAG cells - 24 hour DMSO treated  - HA-tag ChIP-seq

value: HA (Abcam, # ab9110)

value: DMSO


title: EW8 ETV6 dTAG cells - 72 hour DMSO treated  - FLI1 ChIP-seq - replicate 2


title: SD-KCL-1-LEFT

value: cortex

value: 7-8 weeks

value: female

value: healthy


title: Participant 11, unstimulated cells

description: polyA RNA and surface protein


title: EW8 ETV6 dTAG cells - 72 hour DMSO treated  - FLI1 ChIP-seq - replicate 1


title: PEDS0009, sgETV6, ETV6, rep1

value: Newly derived Ewing sarcoma cell line

value: CRISPR

value: 5.5 days

value: ETV6 (Sigma WH0002120M1)


title: Participant 10, stimulated cells

description: polyA RNA and surface protein

value: Participant 10

value: CD4+ Tregs, CD4+ Teffs, CD8+ T cells, CD56br NK, CD56dim NK

value: PMA + ionomycin, 90 min


title: SD-F-1-Right

value: Thy1-ChR2-YFP heterozygous

value: optogenetic stimulation


title: A673 ETV6 dTAG cells - 24 hour dTAGV-1 treated - CUT&Tag input DNA control replicate 1

value: Rabbit anti-mouse, Abcam, ab46540

value: dTAG

value: ETV6 dTAG


title: Participant 10, unstimulated cells

description: polyA RNA and surface protein


title: A673 ETV6 dTAG cells - 72 hour dTAGV-1 treated  - input DNA reference

value: 72 hours


title: SD-F-3-Left

value: cortex


title: A673 ETV6 dTAG cells - 24 hour DMSO treated - CUT&Tag input DNA control replicate 2

value: 24 hours

value: DMSO


title: Participant 9, stimulated cells

description: polyA RNA and surface protein

value: Participant 9


title: SD-F-2-Right

value: 7-8 weeks

value: female

value: healthy


title: A673 ETV6 dTAG cells - 72 hour DMSO treated  - input DNA reference


title: MLE-12 cells, pCI-neo [PCI-Neo-82]

first: Dongting

last: yao

state: Shanghai

address: 徐汇区广元路145号科研楼4楼

institute: nternational Peace Maternity and Child Health Hospital of China Welfare Institution, School of Medicine

data_processing:
Sequence reads were trimmed for low-quality sequence using Seqtk
Trimmed sequence reads were mapped to GRCm38 using Hisat2（version:2.0.4）
Read count extraction and normalization were performed using Stringtie（version:1.3.0）
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: MLE-12 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using MagBeads Total RNA Extraction Kit（Cat#T02-096)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

value: Murine lung epithelial

value: Control


title: A673 ETV6 dTAG cells - 72 hour dTAGV-1 treated  - FLI1 ChIP-seq - replicate 2

value: FLI1 (Abcam, ab15289)


title: SD-F-2-Left


title: A673 ETV6 dTAG cells - 72 hour DMSO treated  - FLI1 ChIP-seq - replicate 2


title: Participant 8, stimulated cells

description: polyA RNA and surface protein

value: Participant 8

value: CD4+ Tregs, CD4+ Teffs, CD8+ T cells, CD56br NK, CD56dim NK

value: PMA + ionomycin, 90 min


title: A673 ETV6 dTAG cells - 72 hour dTAGV-1 treated  - FLI1 ChIP-seq - replicate 1


title: Participant 9, unstimulated cells

description: polyA RNA and surface protein


title: A673 ETV6 dTAG cells - 24 hour DMSO treated - ETV6 HA-tag CUT&Tag with CST anti-body replicate 2

description:
peaks_ETV6_dTAG_DMSO_HA_CST_fdr05_idr005_meanT700_FC8.narrowPeak
ETV6-dTAG_DMSO_HA-CST_comb_spike.bw

value: HA-Tag (CST (C29F4) Rabbit mAb #3724)


title: MLE-12 cells, pCI-neo [PCI-Neo-86-2]

address: 徐汇区广元路145号科研楼4楼


title: SD-F-1-Left

value: Thy1-ChR2-YFP heterozygous

value: optogenetic stimulation


title: A673 ETV6 dTAG cells - 24 hour DMSO treated - CUT&Tag input DNA control replicate 1

value: Rabbit anti-mouse, Abcam, ab46540

value: dTAG

value: ETV6 dTAG


title: MLE-12 cells, pCI-neo [PCI-Neo-86]

address: 徐汇区广元路145号科研楼4楼


title: A673 ETV6 dTAG cells - 24 hour dTAGV-1 treated - ETV6 HA-tag CUT&Tag with CST anti-body replicate 2

description:
peaks_ETV6_dTAG_BNN_HA_CST_fdr05_idr005_meanT700_FC8.narrowPeak
ETV6-dTAG_BNN_HA-CST_comb_spike.bw

value: 24 hours


title: A673 ETV6 dTAG cells - 24 hour dTAGV-1 treated - ETV6 HA-tag CUT&Tag with CST anti-body replicate 1


title: Participant 8, unstimulated cells

description: polyA RNA and surface protein


title: Participant 7, stimulated cells

description: polyA RNA and surface protein

value: Participant 7


title: MLE-12 cells, pCI-neo-Serpine1  [PAI-PCI-82-guobiaoda]

address: 徐汇区广元路145号科研楼4楼

value: Serpine1 overexpression


title: EW8 ETV6 dTAG cells - 6 hour dTAGV-1 treated  - input DNA reference

value: 6 hours


title: A673 ETV6 dTAG cells - 24 hour dTAGV-1 treated - ETV6 HA-tag CUT&Tag with Abcam anti-body replicate 2

description:
peaks_ETV6_dTAG_BNN_HA_ab_fdr05_idr005_meanT700_FC8.narrowPeak
ETV6-dTAG_BNN_HA-ab_comb_spike.bw

value: HA-Tag (Abcam, # ab9110)


title: Participant 7, unstimulated cells

description: polyA RNA and surface protein


title: A673 ETV6 dTAG cells - 72 hour DMSO treated  - FLI1 ChIP-seq - replicate 1

value: 72 hours

value: DMSO


title: Participant 6, stimulated cells

description: polyA RNA and surface protein

value: Participant 6


title: EW8 ETV6 dTAG cells - 6 hour DMSO treated  - input DNA reference


title: MLE-12 cells, pCI-neo-Serpine1  [PAI-PCI-86-2]

address: 徐汇区广元路145号科研楼4楼

value: Murine lung epithelial


title: Participant 6, unstimulated cells

description: polyA RNA and surface protein

value: CD4+ Tregs, CD4+ Teffs, CD8+ T cells, CD56br NK, CD56dim NK


title: A673 ETV6 dTAG cells - 24 hour dTAGV-1 treated - ETV6 HA-tag CUT&Tag with Abcam anti-body replicate 1


title: MLE-12 cells, pCI-neo-Serpine1  [PAI-PCI-86]

address: 徐汇区广元路145号科研楼4楼


title: EW8 ETV6 dTAG cells - 6 hour dTAGV-1 treated  - H3K27ac ChIP-seq - replicate 2


title: A673 ETV6 dTAG cells - 24 hour DMSO treated - ETV6 HA-tag CUT&Tag with Abcam anti-body replicate 2

description:
peaks_ETV6_dTAG_DMSO_HA_ab_fdr05_idr005_meanT700_FC8.narrowPeak
ETV6-dTAG_DMSO_HA-ab_comb_spike.bw


title: EW8 ETV6 dTAG cells - 6 hour dTAGV-1 treated  - H3K27ac ChIP-seq - replicate 1


title: Participant 5, stimulated cells

description: polyA RNA and surface protein

value: Participant 5

value: PMA + ionomycin, 90 min


title: A673 ETV6 dTAG cells - 24 hour DMSO treated - ETV6 HA-tag CUT&Tag with CST anti-body replicate 1

value: HA-Tag (CST (C29F4) Rabbit mAb #3724)


title: Participant 4, unstimulated cells

description: polyA RNA and surface protein

value: Participant 4


title: Participant 5, unstimulated cells

description: polyA RNA and surface protein


title: offspring Lung tissue, NS-5

address: 徐汇区广元路145号科研楼4楼

source_name: Lung

value: Lung

tag: developmental stage

value: intraperitoneal injection of NS


title: EW8 ETV6 dTAG cells - 6 hour DMSO treated  - H3K27ac ChIP-seq - replicate 1

tag: cell line

value: dTAG

value: ETV6 dTAG


title: EW8 ETV6 dTAG cells - 6 hour DMSO treated  - H3K27ac ChIP-seq - replicate 2

tag: modification type


title: offspring Lung tissue, NS-4

address: 徐汇区广元路145号科研楼4楼


title: offspring Lung tissue, NS-1

address: 徐汇区广元路145号科研楼4楼


title: A673 ETV6 dTAG cells - 24 hour DMSO treated - ETV6 HA-tag CUT&Tag with Abcam anti-body replicate 1

tag: modification

value: 24 hours


title: offspring Lung tissue, NS-3

address: 徐汇区广元路145号科研楼4楼


title: Participant 4, stimulated cells

description: polyA RNA and surface protein


title: Parental A673 cell line - CUT&Tag input DNA control replicate 1

value: Rabbit anti-mouse, Abcam, ab46540

tag: time


title: Participant 3, unstimulated cells

description: polyA RNA and surface protein

value: Participant 3


title: offspring Lung tissue, NS-2

address: 徐汇区广元路145号科研楼4楼


title: Participant 3, stimulated cells

description: polyA RNA and surface protein


title: EW8 ETV6 dTAG cells - 6 hour dTAGV-1 treated  - FLI1 ChIP-seq - replicate 2

value: FLI1 (Abcam, ab15289)

value: 6 hours


title: Parental A673 cell line - ETV6 CUT&Tag with Sigma anti-body replicate 2

description:
peaks_A673_ETV6_S_fdr05_idr005_meanT300_FC8.narrowPeak
A673-ETV6-S_comb_spike.bw

value: ETV6 (Sigma WH0002120M1)


title: Parental A673 cell line - CUT&Tag input DNA control replicate 2


title: Parental A673 cell line - ETV6 CUT&Tag with Sigma anti-body replicate 1


title: EW8 ETV6 dTAG cells - 6 hour DMSO treated  - FLI1 ChIP-seq - replicate 2

value: DMSO


title: EW8 ETV6 dTAG cells - 6 hour dTAGV-1 treated  - FLI1 ChIP-seq - replicate 1


title: Participant 2, stimulated cells

description: polyA RNA and surface protein

value: Participant 2


title: Parental A673 cell line - ETV6 CUT&Tag with Bethyl anti-body replicate 2

description:
peaks_A673_ETV6_B_fdr05_idr005_meanT200_FC8.narrowPeak
A673-ETV6-B_comb_spike.bw

value: ETV6 (Bethyl A303-674)


title: EW8 ETV6 dTAG cells - 6 hour DMSO treated  - FLI1 ChIP-seq - replicate 1


title: offspring Lung tissue, LPS-4

address: 徐汇区广元路145号科研楼4楼

value: intraperitoneal injection of LPS


title: Parental A673 cell line - ETV6 CUT&Tag with Bethyl anti-body replicate 1


title: Participant 2, unstimulated cells

description: polyA RNA and surface protein

value: CD4+ Tregs, CD4+ Teffs, CD8+ T cells, CD56br NK, CD56dim NK


title: offspring Lung tissue, LPS-3

address: 徐汇区广元路145号科研楼4楼


title: A673 ETV6 dTAG cells - 6 hour dTAGV-1 treated  - input DNA reference - replicate 2


title: Participant 1, stimulated cells

description: polyA RNA and surface protein

value: Participant 1

value: PMA + ionomycin, 90 min


title: offspring Lung tissue, LPS-2

address: 徐汇区广元路145号科研楼4楼

value: Lung


title: Participant 1, unstimulated cells

description: polyA RNA and surface protein


title: offspring Lung tissue, LPS-1

address: 徐汇区广元路145号科研楼4楼


title: H3Q5ser-HeLa-3_S4_L001

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Paired end reads from 3 replicates each for H3K9me3 and H3Q5ser modifications in HeLa cell line (with a single input sample) were processed by trimming the adapter sequences using Trim Galore.
Trimmed reads were further aligned to the hg38 Ensembl v90 human reference genome using HISATv2.2.1.
Peak calling was performed using MACS software to obtain sites of H3K9me3 and H3Q5ser histone modifications.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file

source_name: HeLa

extract_protocol:
Adherent HeLa S3 cells were crosslinked with 1% formaldehyde for 10 minutes, and the reaction was stopped with 0.125 M glycine for 10 minutes. Chromatin was sheared by sonication (Covaris S220) to 200-800 bp in ChIP lysis buffer (50 mM Hepes, pH 7.4, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 0.5 mM PMSF). 5-10 ug of sonicated chromatin were incubated with H3K9me3 antibody (Active Motif, #39161) and H3Q5ser antibody (Millipore Sigma, #ABE1791) at 4°C for 4 h, then incubated with washed Protein A/G Dynabeads (Invitrogen, #10001D) at 4°C for 2 h. The beads were washed once with ChIP Lysis Buffer, High Salt Buffer (50 mM Tris, pH 7.4, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate), LiCl Buffer (20 mM Tris, pH 7.4, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and TE Buffer (10 mM Tris PH8.0, 1 mM EDTA) in sequence. The beads were resuspended with Elution Buffer (50 mM Tris, pH 8.0, 10 mM EDTA, 1% SDS) and incubated at 65°C for overnight. The crosslink-reversed ChIP product was then treated using RNase A and Proteinase K. The final sample was extracted using QIAquick PCR Purification Kit (Qiagen).
ChIP-seq library is prepared using a SWIFT Accel-NGS® 2S DNA Library Kit

tag: chip antibody

value: H3Q5ser (Millipore Sigma, #ABE1791)

value: HeLa


title: RARα TG, 10nM RA (input)

city: Ann Arbor

first: Chang

last: Kim

address: 109 Zina Pitcher

institute: University of Michigan

data_processing:
Reads were quality trimmed and Illumina adapter sequences were removed.
Alignment of reads to the GRCm38 mm10 Ensembl mouse genome was performed with Bowtie.
ChIP-seq coverage plots in bigWig files were created with bins of 100bp and normalized to reads per million.
Differences in H3k27ac enriched signal by subtracting normalized input with bigwigCompare.
Peaks were called uing MACS2
Assembly: mm10
Supplementary files format and content: bigWig files containing H3K27ac signal - input signal

source_name: CD4 T cells

growth_protocol: Naïve CD4 T cells (>95% pure) were cultured in cRPMI (w/charcoal-stripped FBS) and activated with anti-CD3 and anti-CD28 in the presence of mIL-6 (20 ng/mL), mIL-1β (10 ng/mL), mIL-21 (10 ng/mL), mIL-23 (10 ng/mL), mTNFα (5 ng/mL), hTGFβ-1 (5 ng/mL), anti-IFNγ (10 μg/mL), and anti-IL-4 (10 μg/mL) for 16h.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Samples were Mnase treated for 6 minutes and sonicated to achieve desired chromatin banding of 150-900bp. IP was performed overnight with clone D5E4 for H3k27ac using the magnetic SimpleChIP kit (Cell Signaling)
Indexed libraries were generated using the ThruPLEX DNA-seq kit (Takara; Mountain View, CA) with 13 cycles of amplification
ChIPseq. 1 x 50 bp sequencing was performed on a NovaSeq 6000 (Illumina; San Diego, CA).

treatment_protocol: Cells were cultured with or without RA at 10nM for the 16h of culture.

tag: cell type

value: CD4 T cells

tag: culture conditions

value: 16h w/ 10nM RA

value: RAR{alpha} TG


title: A673 ETV6 dTAG cells - 6 hour DMSO treated  - input DNA reference - replicate 2

city: Boston

tag: chip anti-body

value: dTAG

value: ETV6 dTAG


title: A673 ETV6 dTAG cells - 6 hour dTAGV-1 treated  - H3K27ac ChIP-seq - replicate 1

description: A673_ETV6-dTAG_dTAGV-1_06hr_H3K27ac_rep1

value: 6 hours


title: A673 ETV6 dTAG cells - 6 hour dTAGV-1 treated  - H3K27ac ChIP-seq - replicate 2

description: A673_ETV6-dTAG_dTAGV-1_06hr_H3K27ac_rep2


title: RARα TG, 0nM RA (input)

value: 16h w/o RA

tag: genotype


title: offspring Lung tissue, LPS-5

address: 徐汇区广元路145号科研楼4楼


title: RARα TG, 10nM RA (H3k27ac)


title: A673 ETV6 dTAG cells - 6 hour DMSO treated  - input DNA reference - replicate 1

value: DMSO


title: Input-HeLa_S1_L001

value: none (input)


title: H3K9me3-HeLa-3_S7_L001

value: H3K9me3 (Active Motif, #39161)


title: LIVE_ATAC, Rep2

first: M Joaquina

last: Delas

department: Briscoe Lab

data_processing:
Data was processed using the nf-core atacseq pipeline (https://nf-co.re/atacseq) with the following options: --genome mm10  -r 1.2.0
Counts across the library consensus peak were used as input for DESeq2 to generate the consensus_peaks.mLb.vsd.csv file
Assembly: mm10
Supplementary files format and content: Counts across the library consensus peak were used as input for DESeq2 to generate the consensus_peaks.mLb.vsd.csv file

growth_protocol: Mouse ES cell lines were maintained in ES cell medium with 1000 U/ml LIF (Chemicon, Int ESG1107) on mitotically inactive primary mouse embryo fibroblasts (feeders) in ES cell medium (Dulbecco’s Modified Eagle Medium (DMEM) Knock Out (Gibco, Cat No. 10829-018) complemented with 10% Foetal Bovine Serum, Penicillin/Streptomycin (Gibco, Cat No. 15140122), 2mM L-Glutamine (Gibco, Cat No. 25030024), 2mM Non-essential amino acids (Gibco, Cat No. 11140-035), and 0.1 mM 2-mercaptoethanol (Gibco, Cat. No. 21985-023)). For spinal cord neural differentiation, ES cells were dissociated using 0.05% trypsin-EDTA (Gibco, Cat No. 25300054) and then plated onto 0.1% gelatinised (Gibco) tissue culture plates for three successive periods of 15 mins to remove feeders. Differentiations were carried out in N2B27 media (Advanced DMEM - F12 (Gibco, Cat No. 21331-020) and Neurobasal medium (Gibco, Cat No. A35829-01) (1:1), supplemented with 1xN2 (Gibco), 1xB27 (Gibco), 2 mM L-glutamine (Gibco, Cat No. 25030024), 40 μg/ml BSA (Sigma), and 0.1 mM 2-mercaptoethanol (Gibco, Cat. No. 21985-023)) with the indicated additives. Cells were plated onto 6-well plates (Corning, Cat. No. 353046) precoated in Matrigel (Corning, Cat. No. 356231) diluted 1/50 and 1/100 in Advanced DMEM - F12 (Gibco, Cat No. 21331-020) at a density of 20,000 cells per 35mm well in 1.5 ml. The media was supplemented on the different days as follows: Day 0 to Day 2, 10ng/ml bFGF (R&D, Cat No. 100-18B) and 5 μM LGK (Cayman Chemical Company, Cat. No. 1.800.364.9897); Day2 to Day 3 for 20 h, 10ng/ml bFGF (R&D, Cat No. 100-18B), 5 μM CHIR99021 (Axon Medchem, Cat. No. 1386), 10 μM SB-431542 (Tocris, Cat. No. S0400), and 2μM  DMH1 (Adooq Bioscience, Cat. No. A12820); from Day 3 to D5, 100 nM RA (Sigma, Cat No. R2625) and 100 nM SAG (Merck, Cat. No. 566660-5mg).

extract_protocol:
Trasposition was performed as previously described with 50,000 cells.
Transposed DNA was first amplified as described in Corces et al (2017) and Ma et al (2020)

value: NPs


title: H3Q5ser-HeLa-2_S3_L001