title: CART_Mock_2_day8_scATAC-seq

city: Paris

first: Sebastian

last: Amigorena

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description:
10X Genomics
Metadata_Seurat_Object_CD4_Tcells_scATACseq.tsv
Metadata_Seurat_Object_CD8_Tcells_scATACseq.tsv

library_source: genomic single cell

data_processing:
Single-cell ATAC peaks were analyzed using Cell Ranger ATAC (v1.2.0) to perform quality control, sample de-multiplexing, read filtering and alignment, barcode counting, detection of accessible chromatin peaks, cell calling and count matrix generation.
Sequencing reads were aligned to the human genome using GRCh38 reference data files (v1.2.0) with default parameters. Downstream analyses were performed using Seurat (v4.1.0) (63) and Signac (v1.6.0).
Annotations from EnsDb.Hsapiens.v86 package (v2.99.0) were used to associate peak genomic coordinates to genes.
Prior to the merging of all samples (3 mock samples and 3 gSUV samples), a set of common unified peaks was created using Signac and the R package GenomicRanges (v1.42.0).
Peaks smaller than 20 bp and longer than 10 kb were filtered out. Only barcodes considered as true cells by Cell Ranger were kept for the analysis.
For each sample, a Fragment object was created and peaks were quantified to obtain matrices of peaks per cell using respectively CreateFragmentObject and FeatureMatrix functions from Signac.
Combining both fragment data and matrices, Seurat objects were created using CreateChromatinAssay and CreateSeuratObject functions. A unique Seurat object was then created merging all objects previously obtained.
Only cells with more than 2000 counts and 2000 unique different peaks were kept for the downstream analysis.
Peaks were normalized using term frequency-inverse document frequency (TF-IDF) normalization to correct for differences in cellular sequencing depth and differences across peaks.
Assembly: GRCh38
Supplementary files format and content: CellRanger output from filtered_peak_bc_matrix  directory (barcodes, peaks, matrix), fragments  files and singlecell.csv file
Supplementary files format and content: Annotated metadata from processed single cell Seurat object for CD4 and CD8 cells separately

source_name: CAR-T cells

growth_protocol: CAR T cell production: To produce CAR T cells to inject to the mice, total CD3+ T cells (heterologous populations of naïve, memory, and effector cells) purified from peripheral blood mononuclear cells (PBMCs) were isolated from anonymous healthy donor leukapheresis ring (provided by EFS-Etablissement Francais du Sang) by density gradient centrifugation using Lymphoprep. T cells were plated at a concentration 106 cells /ml (5 x 105 cells in 24 well plate) using X-VIVO 15 media supplemented with 5% human serum (Sigma Aldrich) and 0.5 µM β–mercaptoethanol (referred to as complete X-VIVO), and stimulated with Dynabeads human T-Activator CD3/CD28 in a ratio of 1 bead per cell.  CAR transduction was achieved by lentiviral particles obtained from Flash Therapeutics and CARs were under the control of EF1a promoter. T cells were transduced approximately 24 hours after activation at a multiplicity of infection of 5. Viral vectors were added in 500 µl of complete X-VIVO with a final concentration of 4 µg/mL of Polybrene. After 16-18 hours the supernatant was almost completely discarded, and cell suspension was completed to a final volume of 2 mL with complete X-VIVO containing 100 IU/ml of rhIL-2. The following day, cells were subjected to CRISPR-Cas9 nucleofection (to invalidate SUV39H1): cells were harvested and activation beads were removed with magnets. crRNA targeting SUV39H1 and tracrRNA were first annealed at equimolar concentration to form the duplex at 95°C for 5 min. RNPs were then formed by combining precomplexed duplex (crRNA:tracrRNA) with Hifi Cas9 Nuclease V3 at a molar ratio of 3:1 and incubating them 10 min at room temperature. Nucleofection was done with P3 Primary Cell 4D-Nuleofector® X kit S adding between 1 to 2 x 106 cells with 10 µg of Cas9 in 5 µl of RNP and 20 µl of nucleofection solution. After electroporation using the EO-115 program (4D-Nucleofector Core Unit, Lonza), 200 µl of complete X-VIVO 15 with 500 IU/ml rhIL-2 was added to each reaction and cells were cultured at 32°C. After 16 h, cells were diluted in complete X-VIVO 15 with 500 IU/ml rhIL-2 at a concentration of 106 cells/ml. Cells were collected after 72 h (D0) to check CAR expression, KO efficiency and phenotyping for injections into tumor-bearing mice.

extract_protocol:
T cell isolation from mouse lungs: Lungs were cut in small pieces and digested with Liberase TL (0.15 mg/mL) and DNAse (1 mg/mL) at 37°C for 30 minutes. With the plunger end of a syringe, digested lung tissue were mashed through a 70 μm cell strainer to obtain single cell suspensions. Then, mononuclear cells were enriched using a density gradient medium (Lymphoprep, STEMCELL technologies) and centrifugation for 30 min at 400 x g, room temperature. Murine cells were removed using Mouse Cell Depletion kit and human T cells were sorted using the Sony SH800S sorter before  single cell ATAC sequencing protocol. Three biological replicates were used, from T cells independently isolated from eight mice per condition: (Three pooled mice for mock_1 and mock_2, and two pooled mice for mock_3; three pooled mice for SUV39H1KO_1 and SUV39H1KO_2, and two pooled mice for SUV39H1KO_3).
Single-cell ATAC-sequencing: T cell nuclei were isolated following the 10x Genomics Demonstrated Protocol for Single Cell ATAC Sequencing for low cell input (CG000169 Rev D). Briefly, 4x104 sorted T cells were washed in PBS/0.04% BSA, pelleted at 300 x g for 5 min at 4°C, resuspended in 50 µl of freshly prepared lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40 Substitute, 0.01% Digitonin, and 1% BSA) and incubated on ice for 4 min. 50 µl of wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA) were added to the lysates, which were then centrifuged at 500 x g for 5 min at 4°C and resuspended in 50 µl of chilled diluted Nuclei Buffer. The nuclei were finally pelleted again at 500 × g for 5 min at 4°C and resuspended in 7 µl of diluted Nuclei Buffer (10× Genomics Part Number 2000153). After visual inspection in a phase-contrast microscope, nuclei concentration was assessed with a Countess II FL Automated Cell Counter before proceeding immediately to processing for single cell ATAC sequencing using 10× Chromium, 10× Genomics library preparation and the Chromium Single Cell ATAC Reagent Kits User Guide (CG000168 Rev D).

treatment_protocol: Mouse tumor model and CAR T cell treatment: Metastatic lung xenografts were established via the intravenous injection of 1x106 A549-CD19-Luciferase cells into NSG female mice. Twenty-one days after the injection of the tumor cells mice were treated with 0.9x106 41BBz-CAR T cells (mock or SUV39H1 knock-out), injected via lateral tail vein. Eight days after CAR T cell infusion eight mice per condition were sacrificed and lungs were dissected.

tag: day

tag: genotype

value: MOCK

value: CAR-T cells


title: CART_Suv39h1KO_1_day8_scATAC-seq

status: Public on Oct 30 2023

type: SRA

molecule: genomic DNA

organism: Homo sapiens

value: gSUV

tag: cell type


title: CART_Mock_3_day8_scATAC-seq


title: CART_Suv39h1KO_3_day8_scATAC-seq


title: CART_Suv39h1KO_2_day8_scATAC-seq


title: CART_Mock_1_day8_scATAC-seq


title: CART_Suv39h1KO_N2_day28

description:
10x Genomics
Metadata_Seurat_Object_CD4_Tcells_scRNA_seq.tsv
Metadata_Seurat_Object_CD8_Tcells_scRNA_seq.tsv
D28_Suv39h1KO_N2

library_source: transcriptomic single cell

data_processing:
Single-cell expression was analyzed using the Cell Ranger Single Cell Software Suite (v3.1.0) to perform quality control, sample demultiplexing, barcode processing, and single-cell 3′ gene counting.
Sequencing reads were aligned to the GRCh38 transcriptome using the Cell Ranger suite with default parameters.
Downstream analyses were performed using Seurat (v4.1.0) (63) and miQC algorithm (64).
Based on inspection of the UMI distribution over mitochondrial content
After filtering  a total of 55337 single cells were analyzed.  any cell with more than 9% of mitochondrial UMI counts was discarded.
Assembly: GRCh38
Supplementary files format and content: CellRanger output from filtered_feature_bc_matrix directory (barcodes, features, matrix)
Supplementary files format and content: Annotated metadata from processed single cell Seurat object for CD4 and CD8 cells separately

molecule: polyA RNA

extract_protocol:
T cell isolation from mouse lungs: Lungs were cut in small pieces and digested with Liberase TL (0.15 mg/mL) and DNAse (1 mg/mL) at 37oC for 30 minutes. With the plunger end of a syringe, digested lung tissue were mashed through a 70 μm cell strainer to obtain single cell suspensions. Then, mononuclear cells were enriched using a density gradient medium (Lymphoprep, STEMCELL technologies) and centrifugation for 30 min at 400 x g, room temperature. Murine cells were removed using Mouse Cell Depletion kit and human T cells were sorted using the Sony SH800S sorter before  single cell sequencing protocol.
Chromium 10X Single-Cell 3' mRNA sequencing: From each mouse (three mock and three SUV39H1KO), 10000 cells were loaded on a 10x Chromium Controller (10X Genomics) according to manufacturer’s instructions, based on the 10x GEMCode proprietary technology. The Chromium Single Cell 3´ v3 Reagent kit (10X Genomics) was used to generate the cDNA and prepare the libraries, according to the manufacturer’s protocol. Briefly, cells were encapsulated into droplets with gel beads coated with primers containing 10X cell barcodes, unique molecular identifiers (UMI), and a poly(dT) sequence. After Gel Bead-in-Emulsion reverse transcription (GEM-RT) reaction and clean-up, cDNA was amplified using a GeneAmp PCR System 9700 with 96-Well Gold Sample Block Module (Applied Biosystems) (98°C for 3 min; 11×cycles: 98°C for 15 s, 63°C for 20 s and 72°C for 1 min; held at 4°C). Amplified cDNA product was cleaned up with the SPRI select Reagent Kit (Beckman Coulter). Library quantification and quality assessment was performed using Qubit fluorometric assay (Invitrogen) with dsDNA HS (High Sensitivity) Assay Kit and Bioanalyzer Agilent 2100, using a High Sensitivity DNA chip. The libraries were sequenced with the NovaSeq system (Illumina).

treatment_protocol: Mouse tumor model and CAR T cell treatment: Metastatic lung xenografts were established via the intravenous injection of 1x106 A549-CD19-Luciferase cells into NSG female mice. Twenty-one days after the injection of the tumor cells mice were treated with 0.9x106 41BBz-CAR T cells (mock or SUV39H1 knock-out), injected via lateral tail vein. Eight and twenty-eight days after CAR T cell infusion three mice per condition and timepoint were sacrificed and lungs were dissected.


title: CART_Suv39h1KO_N3_day28

description:
10x Genomics
Metadata_Seurat_Object_CD4_Tcells_scRNA_seq.tsv
Metadata_Seurat_Object_CD8_Tcells_scRNA_seq.tsv
D28_Suv39h1KO_N3


title: CART_Suv39h1KO_N1_day28

description:
10x Genomics
Metadata_Seurat_Object_CD4_Tcells_scRNA_seq.tsv
Metadata_Seurat_Object_CD8_Tcells_scRNA_seq.tsv
D28_Suv39h1KO_N1


title: CART_Suv39h1KO_N1_day8

description:
10x Genomics
Metadata_Seurat_Object_CD4_Tcells_scRNA_seq.tsv
Metadata_Seurat_Object_CD8_Tcells_scRNA_seq.tsv
D8_Suv39h1KO_N1

value: Mock


title: CART_Mock_N1_day28

description:
10x Genomics
Metadata_Seurat_Object_CD4_Tcells_scRNA_seq.tsv
Metadata_Seurat_Object_CD8_Tcells_scRNA_seq.tsv
D28_Mock_N1


title: CART_Mock_N2_day8

description:
10x Genomics
Metadata_Seurat_Object_CD4_Tcells_scRNA_seq.tsv
Metadata_Seurat_Object_CD8_Tcells_scRNA_seq.tsv
D8_Mock_N2


title: CART_Mock_N3_day28

description:
10x Genomics
Metadata_Seurat_Object_CD4_Tcells_scRNA_seq.tsv
Metadata_Seurat_Object_CD8_Tcells_scRNA_seq.tsv
D28_Mock_N3


title: CART_Suv39h1KO_N2_day8

description:
10x Genomics
Metadata_Seurat_Object_CD4_Tcells_scRNA_seq.tsv
Metadata_Seurat_Object_CD8_Tcells_scRNA_seq.tsv
D8_Suv39h1KO_N2


title: CART_Mock_N2_day28

description:
10x Genomics
Metadata_Seurat_Object_CD4_Tcells_scRNA_seq.tsv
Metadata_Seurat_Object_CD8_Tcells_scRNA_seq.tsv
D28_Mock_N2


title: CART_Suv39h1KO_N3_day8

description:
10x Genomics
Metadata_Seurat_Object_CD4_Tcells_scRNA_seq.tsv
Metadata_Seurat_Object_CD8_Tcells_scRNA_seq.tsv
D8_Suv39h1KO_N3


title: CART_Mock_N1_day8

description:
10x Genomics
Metadata_Seurat_Object_CD4_Tcells_scRNA_seq.tsv
Metadata_Seurat_Object_CD8_Tcells_scRNA_seq.tsv
D8_Mock_N1


title: MCF7 ChIP input rep 2

city: Grand Forks

first: Sergei

last: Nechaev

state: North Dakota

address: Columbia Hall Room 1733c, 501 North Columbia Road Stop 9061

department: Biomedical Sciences

country: USA

institute: University of North Dakota

library_source: genomic

data_processing:
Raw files were adapter-trimmed with trimmomatic and aligned to hg19 genome using hisat2. For HSF1 ChIP-seq, raw fastq files were randomly subset to 40M read pairs prior to alignment. After removing PCR duplicates with MarkDuplicates (Picard),  peaks were called using MACS2 with FDR cutoff 0.01 and then merged between replicates. Read coverage was calculated using bamCoverage and read counts were normalized to sequencing depth. Signal was calculated using multibigwigsummary.
Assembly: hg19
Supplementary files format and content: bw - bigwig files.
Supplementary files format and content: narrowPeak - peaks called for each replicate

growth_protocol: All cells were purchased from the American Type Culture Collection and used within the first 15 passages. Cells were grown in 15 cm dishes as before {Samarakkody et al., 2015, #72840} and growth media was replaced with fresh media 24 hours before treatments {Mahat and Lis, 2017, #290391; Vihervaara et al., 2017, #282616}.

extract_protocol:
Approximately 2x107 cells were crosslinked with 1% ethanol-free formaldehyde (Thermo) in serum-free DMEM/F12 media at 25C for 10min, quenched with 125mM Glycine, and lysed in buffer (1% Sodium-Dodecyl Sulfate (SDS), 50mM Tris (pH=8), 10mM EDTA, 1X PMSF and protease inhibitor cocktail) followed by disruption in the Covaris S2 sonicator for 6 minutes (with peak power = 140, Duty factor = 5, Cycles/burst = 200). Protein A and Protein G Dynabeads (Invitrogen) premixed at 1:1 ratio were used for pre-clearing for 1 hour at 4C. One percent of each precleared sample was taken as input, with at least two inputs taken for each sample and averaged for ChIP percent input calculation. Samples were incubated with 5g of primary antibodies in 2 ml of dilution buffer (1% Triton-X, 2mM EDTA, 20mM Tris pH=8.0, 150mM NaCl, 1X Phenylmethylsulfonyl fluoride (PMSF) and cOmplete protease inhibitor cocktail (Sigma)) with slow rotation overnight at 4C followed by washing
DNA library was prepared from validated ChIP material using NEBNext Ultra II DNA library kit (New England Biolabs) protocol without size selection. Final PCR amplification of cDNA templates was done using TruSeq Illumina Small RNA PCR primers, 250 M dNTP mix, 1x HF buffer, 1M Betaine, 1xEvagreen dye (Biotium) and Phusion DNA polymerase.

treatment_protocol: Heat-Shock treatment was started by placing a dish onto a heated water surface for 1 minute to raise the temperature quickly and continued in a 42°C 5% CO2 incubator for the remaining time. Arsenic treatment was performed by the addition of 500 mM Sodium meta-arsenite (Sigma) at the ambient 37°C with 5% CO2 {Khalil et al., 2006, #243125}.

tag: cell line

value: mammary gland, adenocarcinoma

tag: antibody

value: input

tag: treatment

value: Heat shock


title: MCF7 HS HSF1  rep 3

value: HSF1 (Enzo # ADI-SPA-901-D)

value: Untreated


title: CRD vs LT017T-C

status: Public on Oct 31 2023

type: genomic

city: Daejeon

first: Tae Jeong

last: Oh

address: 44-6 10-ro Yuseong-gu

country: South Korea

institute: Genomictree, Inc.

description: methylation profiling in LT017T sample

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, microarrays were washed 1 minute at room temperature with CGH/ChIP-on-chip Wash Buffer 1 (Agilent) and 1 minute with 37°C CGH/ChIP-on-chip Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.3.2.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: CRD

label_protocol: The enriched DNA fragments was amplified using WGA2 kit (Sigma). 4 µg of amplified enriched DNA was labeled using Bioprime kit as following manufacturer's instructions

extract_protocol:
Fresh-frozen primary tumors and paired tumor-adjacent normal tissues of lung cancer patients
Genomic DNA extracted using Qiaquick DNA mini kit following manufacturer's instructions
0.5ug genomic DNA was fragmented with sonication. The fragmented DNA was incubated with MBD2bt protein, and then the enriched methylated DNA fragments was purified using Magnetic bead.

tag: reference

value: pooled DNA of 13 adjacent normal samples

tag: test

value: enriched methylated DNA of primary lung tumor tissue

tag: Sex

value: male

tag: age

tag: Stage

value: I


title: MCF7 NHS HSF1  rep 3

value: Arsenic


title: MCF7 ChIP input rep 1


title: CART_Mock_N3_day8

description:
10x Genomics
Metadata_Seurat_Object_CD4_Tcells_scRNA_seq.tsv
Metadata_Seurat_Object_CD8_Tcells_scRNA_seq.tsv
D8_Mock_N3


title: skmls2

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

library_source: transcriptomic

data_processing:
HISAT2 software was used to accomplish the mapping.
Mapping information from all samples was combined and placed as input into the regular StringTie assembler. The outputs were provided as GTF files.
FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) was used to estimate gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.
The input data for differential gene expression analysis is read counts from gene expression level analysis. The differential gene expression analysis contains three steps: 1) Read counts Normalization; 2) Model dependent p-value estimation; 3) FDR value estimation based on multiple hypothesis testing.
Assembly: ensembl_homo_sapiens_grch38_p12_gca_000001405_27
Supplementary files format and content: tab-delimited texts files includes raw counts for each sample

molecule: total RNA

source_name: skin

growth_protocol: A375, SKMel28 cell lines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmorsphere with 5% CO2 at 37°C

extract_protocol:
RNA was harvested using the NucleoSpin RNA kit (Macherey-Nagel, France) according to the manufacturer’s recommendations. 2µg of Total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using mRNA library preparation (poly A enrichment) throught the NovaSeq PE150 Sequencing Platform & Strategy

treatment_protocol: A375-R, and SKMel28-R resistant cells were maintained in 1 μmol.L-1 vemurafenib

tag: tissue

value: skin

value: skml

value: sensible


title: skmls3


title: skmlr3

value: restistant


title: skmlr2


title: skmls1


title: skmlr1


title: CRD vs LT011T-C

description: methylation profiling in LT011T sample


title: a375r1


title: a375s1


title: a375s2


title: a375r2


title: a375s3


title: a375r3


title: FOXF1_KO_Atria_d9.5_R3 [184707]

city: Vienna

first: Clara

last: Schmidt

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology GmbH

description:
184707
featurecounts.vst.gene_FOXF1KO.tsv

data_processing:
Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref = polyA.fa.gz,truseq.fa.gz k = 13 ktrim = r useshortkmers = t mink = 5 qtrim = r trimq = 10 min length = 20). Reads mapping to abundant sequences included in the iGenomes NCBI GRCh38 references were removed using bowtie2 v2.3.4.1 alignment. The remaining reads were analyzed using genome and gene annotation for the GRCh38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c, and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1). Differential gene expression analysis on raw counts, and principal component analysis on variance stabilized, transformed count data were performed using DESeq2 v1.18.1.
Assembly: GRCh38
Supplementary files format and content: featurecounts.count.gene.tsv: Tab-delimited text files with per gene read counts.

source_name: cardiac

growth_protocol: hPSCs (WTC line) are seeded in a 24-well plate (TPP, #92024) at 30-40k cells per well in E8 + ROCKi (5?M Y-27632, Tocris #1254). All differentiation media are based on CDM. 24 hours after seeding in the 24-well plate, the cells are induced with mesoderm induction media. Mesoderm induction media is made up of CDM containing FGF2 (30 ng/ml, Cambridge University), LY294002 (5 ?M, Tocris, #1130), Activin A (specific concentrations for different cardioid subtype, Cambridge University), BMP4 (10 ng/ml, R&D Systems RD-314-BP-050), and CHIR99021 (specific concentrations for different cardioid subtypes, see below, R&D Systems RD-4423/50). After 36-40 hours, cells are dissociated with TrypleE (Gibco, #12605010) and seeded in a Corning ultra-low attachment 96 well plate (Corning, #7007) at 15-20k cells/well in Cardiac Mesoderm Patterning Media One made up of CDM containing ROCKi and for all protocols besides the LV cardioids 1 ?g/ml of insulin (Roche, #11376497001) plus specific factors depending on cardioid subtype (see below). After seeding, the cells are spun down in a centrifuge for 4 mins at 200g. At day 2.5, the cells are fed with Cardiac Mesoderm Patterning Media One. For the next two days, the medium is changed to Cardiac Mesoderm Patterning Media Two, made up of CDM containing specific factors depending on the cardioid subtype (see below) and exchanged daily. For the subsequent two days, media is exchanged every day with Cardiomyocyte Differentiation Media CDM medium

extract_protocol:
RNA was isolated using an in-house RNA bead isolation kit semi-automated using KingFisher devices (KingFisher Duo Prime).
Using the QuantSeq 30 mRNA-Seq Library Prep Kit FWD (Lexogen GmbH, #015), the bulk RNA-seq library was generated according to the manufacturerÆs instructions. After the preparation of the library, samples were checked for an adequate size distribution with a fragment analyzer.Then the RNA-seq library was submitted to the Vienna Biocenter Core Facilities (VBCF) Next-Generation-Sequencing (NGS) facility for sequencing.

value: cardiac

value: WTC

value: Cardiomyocytes


title: 224105_OFT_d9p5_TNI

description:
10x Genomics Flex
seurat_object.rds
barcodes.tsv.gz
genes.tsv.gz
matrix.mtx.gz
meta.tsv

data_processing:
ScRNAseq reads were processed with cellranger v7.1.0 (10X Genomics), using the prebuild 10X GRCh38-2020-A
Further processing of the scRNAseq data was performed in R software v4.2.2 with Seurat v4.3.0.
Cells were retained if their mitochondrial content was below 7% and the gene number metric was above an adaptive, sample-specific thresholds (>2 median absolute deviation for log-transformed number of expressed genes).
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)
Supplementary files format and content: RDS object

growth_protocol:
hPSCs (WTC line) are seeded in a 24-well plate (TPP, #92024) at 30-40k cells per well in E8 + ROCKi (5μM Y-27632, Tocris #1254). All differentiation media are based on CDM. 24 hours after seeding in the 24-well plate, the cells are induced with mesoderm induction media.
Mesoderm Induction Media for WTC lines
For LV (FHF-derived) cardioid differentiations, Activin is used at 5 ng/mL and CHIR99021 at 3 μM. For RV (aSHF-derived), atria (pSHF-derived), and OFT differentiations Activin is used at 50 ng/mL and CHIR99021 at 4 μM. For AVC differentiation, Activin is used at 10 ng/mL and CHIR99021 at 2 μM.
Cardiac Mesoderm Patterning Media 1 (day 1.5 – 3.5)
LV (FHF-derived): BMP4 (10ng/ml), FGF2 (8 ng/ml), insulin (10 μg/ml), C59 (2 μM, Tocris, #5148/10) and retinoic acid (50 nM, Sigma Aldrich, #R2625) (Hofbauer et al., 2021b). RV (aSHF-derived): The TGF-beta inhibitor SB 431542 (10 μM, Tocris, #1614/10) C59 (2 μM), OFT (aSHF-derived): SB 431542 (10 μM) and XAV-939 (5μM).
Atria (pSHF-derived): SB 431542 (10 μM), XAV-939 (5μM) and retinoic acid (500 nM). AVC (pSHF-derived): SB 431542 (10 μM), XAV-939 (5μM), retinoic acid (500nM) and BMP4 (10ng/ml).
Cardiac Mesoderm Patterning Media 2 (day 3.5 – 5.5)
LV: BMP4 (10ng/ml), FGF2 (8 ng/ml), insulin (10 μg/ml), C59 (2 μM) and retinoic acid (50 nM)) (Hofbauer et al., 2021b).
RV: either C59 (2 μM), BMP4 (10ng/ml), FGF2 (8 ng/ml), insulin
(10 μg/ml), and retinoic acid (500nM).
OFT: XAV-939 (5μM), BMP4 (10ng/ml), FGF2 (8 ng/ml) and insulin (10 μg/ml).
Atria and AVC: XAV-939 (5μM), BMP4 (10ng/ml), FGF2 (8 ng/ml), insulin (10 μg/ml), and retinoic acid (500nM).
Cardiac Mesoderm Patterning Media 2 (day 5.5-d7.5)
All protocols: BMP4 (10ng/ml), FGF2 (8 ng/ml) and insulin
(10 μg/ml)
Atria Specification (d7.5-d9.5)
Retinoic acid (500nM, Sigma Aldrich, #R2625), FGF2 (15ng/mL, Cambridge University), LDN-193189 (200nM, Stemgent, #04-0074) and LY-411575 (3μM, MedChemExpess, #HY-50752)

extract_protocol:
Cardioids were submitted to the VBCF NGS facility for fixation and library preparation using 10x Genomics Chromium Single Cell Gene Expression Flex.
NovaSeq S4 PE150 XP

tag: cell subtype

value: OFT


title: 224105_LV_d7p5_TNI

value: LV


title: 224106_RV_d9p5_TNT2

value: RV


title: 224106_OFT_d9p5_TNT2


title: 224105_RV_d9p5_TNI


title: 224106_LV_d7p5_TNT2


title: 224106_AVC_d9p5_TNT2

value: AVC


title: 224107_AVC_d9p5_TNI


title: FOXF1_KO_Atria_d9.5_R2 [184697]

description:
184697
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_KO_RV_d9.5_R3 [184705]

description:
184705
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_WT_RV_d9.5_R3 [184704]

description:
184704
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_KO_Atria_d3.5_R2 [184702]

description:
184702
featurecounts.vst.gene_FOXF1KO.tsv

value: cardiac progenitors


title: FOXF1_WT_FHF_d9.5_R3 [184703]

description:
184703
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_KO_RV_d9.5_R2 [184695]

description:
184695
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_WT_Atria_d9.5_R2 [184696]

description:
184696
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_WT_FHF_d3.5_R2 [184698]

description:
184698
featurecounts.vst.gene_FOXF1KO.tsv


title: 224105_Atria_d9p5_TNI

value: Atria


title: FOXF1_WT_Atria_d3.5_R2 [184701]

description:
184701
featurecounts.vst.gene_FOXF1KO.tsv


title: CRD vs LT011NT-C

description: methylation profiling in LT011NT sample

value: pooled DNA of 13 adjacent normal samples

value: enriched methylated DNA of adjacent normal tissue


title: FOXF1_WT_Atria_d9.5_R3 [184706]

description:
184706
featurecounts.vst.gene_FOXF1KO.tsv


title: CRD vs LT005NT-C

description: methylation profiling in LT005NT sample

value: male

value: I


title: CRD vs LT005T-C

description: methylation profiling in LT005T sample

value: enriched methylated DNA of primary lung tumor tissue


title: FOXF1_WT_RV_d9.5_R2 [184694]

description:
184694
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_KO_FHF_d9.5_R2 [184693]

description:
184693
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_WT_RV_d9.5_R1 [184682]

description:
184682
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_WT_FHF_d3.5_R1 [184686]

description:
184686
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_KO_Atria_d3.5_R1 [184691]

description:
184691
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_WT_FHF_d9.5_R2 [184692]

description:
184692
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_KO_RV_d9.5_R1 [184683]

description:
184683
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_KO_RV_d3.5_R2 [184689]

description:
184689
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_WT_Atria_d9.5_R1 [184684]

description:
184684
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_KO_Atria_d9.5_R1 [184685]

description:
184685
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_KO_FHF_d9.5_R1 [184681]

description:
184681
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_KO_FHF_d3.5_R1 [184687]

description:
184687
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_WT_RV_d3.5_R2 [184688]

description:
184688
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_WT_Atria_d3.5_R1 [184690]

description:
184690
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_WT_FHF_d9.5_R1 [184680]

description:
184680
featurecounts.vst.gene_FOXF1KO.tsv


title: FOXF1_KO_RV_d3.5_R1 [184677]

description:
184677
featurecounts.vst.gene_FOXF1KO.tsv


title: TBX5_KO_AVC_d9.5_R3 [220949]

description:
220949
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_AVC_d3.5_R2 [220896]

description:
220896
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_AVC_d3.5_R1 [220889]

description:
220889
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_AVC_d9.5_R2 [220875]

description:
220875
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_AVC_d9.5_R1 [220951]

description:
220951
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_Atria_d3.5_R1 [220874]

description:
220874
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_Atria_d9.5_R2 [220940]

description:
220940
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_Atria_d3.5_R3 [220901]

description:
220901
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_Atria_d9.5_R1 [220920]

description:
220920
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_AVC_d9.5_R1 [220921]

description:
220921
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_Atria_d3.5_R2 [220886]

description:
220886
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_AVC_d3.5_R2 [220897]

description:
220897
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_AVC_d9.5_R2 [220941]

description:
220941
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_AVC_d3.5_R1 [220888]

description:
220888
featurecounts.vst.geneTBX5KO.tsv


title: FOXF1_WT_RV_d3.5_R1 [184676]

description:
184676
featurecounts.vst.gene_FOXF1KO.tsv


title: TBX5_KO_Atria_d9.5_R3 [220947]

description:
220947
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_LV_d9.5_R2 [220950]

description:
220950
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_LV_d9.5_R1 [220918]

description:
220918
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_RV_d9.5_R3 [220945]

description:
220945
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_RV_d3.5_R1 [220881]

description:
220881
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_LV_d3.5_R1 [220872]

description:
220872
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_RV_d9.5_R1 [220919]

description:
220919
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_RV_d3.5_R2 [220898]

description:
220898
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_LV_d3.5_R2 [220878]

description:
220878
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_RV_d9.5_R2 [220939]

description:
220939
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_Atria_d9.5_R1 [220946]

description:
220946
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_LV_d3.5_R3 [220893]

description:
220893
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_LV_d9.5_R2 [220938]

description:
220938
featurecounts.vst.geneTBX5KO.tsv


title: ISL1_KO_Atria_d9.5 [181266]

description:
181266
featurecounts.vst.gene_ISL1KO.tsv


title: TBX5_WT_LV_d3.5_R1 [220877]

description:
220877
featurecounts.vst.geneTBX5KO.tsv


title: ISL1_KO_FHF_d9.5 [181267]

description:
181267
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_Atria_d9.5 [181298]

description:
181298
featurecounts.vst.gene_ISL1KO.tsv


title: TBX5_WT_LV_d3.5_R2 [220892]

description:
220892
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_LV_d9.5_R1 [220942]

description:
220942
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_LV_d9.5_R3 [220943]

description:
220943
featurecounts.vst.geneTBX5KO.tsv


title: ISL1_KO_FHF_d9.5 [181283]

description:
181283
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_FHF_d9.5 [181299]

description:
181299
featurecounts.vst.gene_ISL1KO.tsv


title: TBX5_WT_Atria_d9.5_R2 [220953]

description:
220953
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_RV_d9.5_R1 [220944]

description:
220944
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_Atria_d3.5_R2 [220899]

description:
220899
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_Atria_d3.5_R1 [220885]

description:
220885
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_WT_RV_d9.5_R2 [220952]

description:
220952
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_RV_d3.5_R2 [220882]

description:
220882
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_RV_d3.5_R3 [220900]

description:
220900
featurecounts.vst.geneTBX5KO.tsv


title: TBX5_KO_RV_d3.5_R1 [220873]

description:
220873
featurecounts.vst.geneTBX5KO.tsv


title: ISL1_KO_Atria_d9.5 [181282]

description:
181282
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_FHF_d9.5 [181263]

description:
181263
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_Atria_d3.5 [181274]

description:
181274
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_RV_d9.5 [181264]

description:
181264
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_RV_d9.5 [181260]

description:
181260
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_FHF_d3.5 [181275]

description:
181275
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_Atria_d9.5 [181262]

description:
181262
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_FHF_d9.5 [181295]

description:
181295
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_OFT_d9.5 [181293]

description:
181293
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_FHF_d3.5 [181291]

description:
181291
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_Atria_d3.5 [181290]

description:
181290
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_Atria_d3.5 [181258]

description:
181258
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_RV_d9.5 [181276]

description:
181276
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_FHF_d9.5 [181279]

description:
181279
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_OFT_d9.5 [181281]

description:
181281
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_OFT_d9.5 [181265]

description:
181265
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_Atria_d9.5 [181294]

description:
181294
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_Atria_d9.5 [181278]

description:
181278
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_OFT_d9.5 [181297]

description:
181297
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_OFT_d3.5 [181289]

description:
181289
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_RV_d9.5 [181280]

description:
181280
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_OFT_d9.5 [181277]

description:
181277
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_RV_d9.5 [181292]

description:
181292
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_FHF_d3.5 [181259]

description:
181259
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_RV_d9.5 [181296]

description:
181296
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_RV_d3.5 [181288]

description:
181288
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_RV_d3.5 [181256]

description:
181256
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_OFT_d3.5 [181273]

description:
181273
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_OFT_d3.5 [181257]

description:
181257
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_FHF_d3.5 [181287]

description:
181287
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_KO_RV_d3.5 [181272]

description:
181272
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_FHF_d3.5 [181271]

description:
181271
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_Atria_d3.5 [181286]

description:
181286
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_RV_d3.5 [181284]

description:
181284
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_OFT_d3.5 [181253]

description:
181253
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_Atria_d3.5 [181254]

description:
181254
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_OFT_d3.5 [181285]

description:
181285
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_RV_d3.5 [181268]

description:
181268
featurecounts.vst.gene_ISL1KO.tsv


title: WT-siCon-Input

city: Chicago

first: Benjamin

middle: J

last: Weidemann

state: IL

address: 303 E. Superior St.

department: Medicine

institute: NORTHWESTERN UNIVERSITY

data_processing:
Alignment using bowtie2 (ChIP), ENCODE Pipeline (ATAC), Cellranger mkfastq and count (snATAC), STAR (RNA)
Quantification and annotation using HOMER (ChIP, ATAC), Cellranger count (snATAC), RSEM (RNA)
Differential analysis, QC, and visualization using R v4.1.0 (DESeq2, ChIPpeakAnno, Seurat, Signac, ggplot2, rtracklayer)
Rhythmic analysis of synchronized human ATAC-seq data (eJTK_Cycle)
Assembly: mm10
Supplementary files format and content: bigWig files (*.bw.gz)
Supplementary files format and content: HiCPro validPair files (*.validPairs)
Supplementary files format and content: Homer peak files (*peaks.txt)

organism: Mus musculus

growth_protocol: DMEM + 15% FBS (cells), RPMI + 10% FBS or human AB serum (islets)

extract_protocol:
Omni-ATAC protocol for bulk ATAC-seq, 10X Protocol for snATAC-seq, DirectZol MicroPrep (Zymo) for RNA, AQuA HiChIP for HiChIP
10X Protocol for snATAC-seq. NEBNext Ultra II for RNA, ChIP, and HiChIP-seq. Nextera (Tn5) for ATAC-Seq

treatment_protocol: Cells synchronized using 1 hour 10 micromolar forskolin pulse

value: beta cell

value: WT

value: control siRNA


title: WT-siPDX1-SIN3A-1

value: Pdx1 siRNA

value: SIN3A (Cell Signaling #8056S)


title: AGSHP-3.Input

city: Jinan

first: Mingjie

last: Chang

state: Shandong

address: WenHua XiLu

country: China

institute: Shandong University

data_processing:
Adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), clean reads of input libraries were aligned to reference genome by STAR software, circRNAs were identified by DCC software.
After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software.
Differentially methylated sites were identified by diffReps, peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and chosen by home-made scripts.
Assembly: HG19
Library strategy: MeRIP-seq

source_name: Stomach

growth_protocol: AGS cells were cultured using F12K + 12% FBS,  the culture conditions were 37°C, 5% CO2.

extract_protocol:
RNA was extracted using trizol reagent
Total RNA was subjected to immunoprecipitation with the GenSeq® m6A-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA)

treatment_protocol: Experimental group: AGS cells were infected with Hp26695 at MOI=100 for 12h; Control group: AGS cells were treated with equal volume PBS for 12h.

value: Stomach

value: AGS

value: Gastric cancer cell line


title: AGSHP-2.IP

value: AGS cells were infected with Hp26695 at MOI=100 for 12h


title: ISL1_WT_FHF_d3.5 [181255]

description:
181255
featurecounts.vst.gene_ISL1KO.tsv

value: cardiac

value: WTC


title: AGSHP-3.IP


title: ISL1_WT_RV_d3.5 [181252]

description:
181252
featurecounts.vst.gene_ISL1KO.tsv

value: cardiac progenitors


title: WT-siCon-SIN3A-2


title: WT-siPDX1-Input


title: AGSHP-1.Input


title: WT-siCon-SIN3A-1


title: BKO-Control-Input


title: AGS+PBS-3.IP

value: AGS cells were treated with equal volume PBS for 12h


title: AGS+PBS-2.IP


title: BKO-IL1B-Input


title: AGSHP-2.Input


title: WT-siPDX1-SIN3A-2


title: ISL1_WT_OFT_d3.5 [181269]

description:
181269
featurecounts.vst.gene_ISL1KO.tsv


title: ISL1_WT_Atria_d3.5 [181270]

description:
181270
featurecounts.vst.gene_ISL1KO.tsv


title: BKO-IL1B-PDX1-3


title: AGSHP-1.IP


title: AGS+PBS-2.Input


title: WT-Control-Input


title: AGS+PBS-3.Input


title: AGS+PBS-1.IP


title: BKO-IL1B-PDX1-2


title: WT-IL1B-Input


title: ST3_BMP7-replicate 1, scRNAseq

city: Miami

first: Juan

last: Domínguez-Bendala

state: FL

address: 1450 NW 10th Ave

department: Diabetes Research Institute

institute: University of Miami Miller School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Human reference, GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Seuratobject in RDS file format

source_name: Pancreas

extract_protocol:
Pancreatic slices are washed 3x with dPBS transferred into 15ml of prewarmed (37C) Dissociation solution- Triple-E. 10 minutes incubation at 37C follows. Brief vortex 5seconds bursts repeated 10x and additional 2min. incubation. The vortex step is repeated one more time.  Dissociated slices are immediately washed in 20ml of wash medium and spun down at 1500 RPM. Washing is repeated and cells are put through 40-micron strainer. The single cells are now washed one time with dPBS at 4 C resuspended in 1ml dPBS and 10 µl of single cell suspension is taken to control  number and viability with Trypan blue. After additional spin, the pellet is resuspended in 200 µl of ice cold dPBS. 800 µl of ice cold methanol is added dropwise with constant stirring to prevent clumping during fixation. Fixed cells are kept in-20C for 24 hrs and later in -80C.  Single cell suspension is taken to control  number and viability with Trypan blue .After additional spin, the pellet is resuspended in 200 µl of ice cold dPBS. 800 µl of ice cold methanol is added dropwise with constant stirring to prevent clumping during fixation. Fixed cells are kept in-20C for 24 hrs and later in -80C. Slices are washed 3x with dPBS transferred into 15ml of prewarmed (37C) Dissociation solution- Triple-E. 10 minutes incubation at 37C follows. Brief vortex 5 seconds bursts repeated 10x and additional 2min. incubation. The vortex step is repeated one more time.  Dissociated slices are immediately washed in 20ml of wash medium and spun down at 1500 RPM. Washing is repeated and cells are put through 40-micron strainer. The single cells are now washed one time with dPBS at 4 C resuspended in 1ml dPBS and 10 µl of single cell suspension is taken to control  number and viability with Trypan blue. After additional spin, the pellet is resuspended in 200 µl of ice cold dPBS. 800 µl of ice cold methanol is added dropwise with constant stirring to prevent clumping during fixation. Fixed cells are kept in-200C for 24 hrs and later in -80 C.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Pancreas

value: All Pancreas cell types

value: NO TREATMENT after removal of BMP-7


title: ST2_CONTROL-replicate 3, scRNAseq

description: 10x Genomics

value: NO TREATMENT


title: ST3_CONTROL-replicate 2, scRNAseq

description: 10x Genomics


title: ST2_CONTROL-replicate 2, scRNAseq

description: 10x Genomics


title: ST3_BMP7-replicate 3, scRNAseq

description: 10x Genomics


title: ST3_CONTROL-replicate 3, scRNAseq

description: 10x Genomics


title: ST3_CONTROL-replicate 1, scRNAseq

description: 10x Genomics


title: ST3_BMP7-replicate 2, scRNAseq

description: 10x Genomics


title: ST2_CONTROL-replicate 1, scRNAseq

description: 10x Genomics


title: ST2_BMP7-replicate 3, scRNAseq

description: 10x Genomics

value: 100 ng/ml of BMP-7 TREATMENT


title: AGS+PBS-1.Input


title: ST2_BMP7-replicate 2, scRNAseq

description: 10x Genomics


title: ST2_BMP7-replicate 1, scRNAseq

description: 10x Genomics


title: BKO-IL1B-p65-3

value: beta cell


title: WT-IL1B-PDX1-3

value: WT


title: BKO-Control-p65-3


title: BKO-IL1B-p65-1


title: WT-IL1B-p65-2


title: BKO-IL1B-p65-2


title: WT-IL1B-p65-3


title: Ascites_IG_14

city: Turku

first: Maija

last: Hollmén

address: Tykistökatu 6A 4th floor

country: Finland

institute: University of Turku

data_processing:
Demultiplexing, read alignment and quality control were performed using Cell Ranger package v5.0.1 (Batch 1) and v6.1.1 (Batch 2) [ https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger ].
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files (barcodes and features) and matrix files (UMI counts).

source_name: Ovarian cancer patient ascites cells

growth_protocol: Ovarian cancer ascites cells were obtained from ovarian cancer patient ascites fluid by centrifugation and red blood cell lysis. The cells were thawed and cultured ex vivo in IMDM + 10% FCS + 1% glut + penn.strep.

extract_protocol:
After the 48h antibody treatments, ascites cells were washed twice with 0.04% BSA-PBS, filtered through 70 μm nylon nets and resulting cell suspensions subjected to single-cell RNA-sequencing.
Single-cell partitioning and library preparation were done according to manufacturer's instructions using Chromium Next GEM Single Cell 3' GEM Library & Gel Bead Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit (10X Genomics). For batch 1, single indexes were used (protocol CG000204) and for batch 2, dual indexes were used (protocol CG000315).

treatment_protocol: Ex vivo cultured cells (500 000) were treated with 10 μg bexmarilimab (FP-1305; clone CP12, Abzena) or its isotype control IgG4 (human irrelevant IgG4 (S241P, L248E], Abzena) for 48h.

tag: disease state

value: Ovarian cancer

value: ascites cells

tag: scrnaseq batch


title: BKO-Control-PDX1-2


title: WT-IL1B-PDX1-2


title: BKO-Control-PDX1-1


title: Ascites_BEX_12

value: Bexmarilimab


title: WT-IL1B-p65-1


title: BKO-Control-p65-2


title: BKO-IL1B-PDX1-1


title: BKO-Control-PDX1-3


title: Ascites_IG_11


title: Ascites_BEX_14


title: WT-Control-PDX1-2


title: WT-Control-PDX1-3


title: BKO-Control-p65-1


title: Ascites_BEX_10


title: WT-Control-p65-3


title: Ascites_IG_12


title: Ascites_IG_10


title: WT-IL1B-PDX1-1


title: WT-Control-p65-2


title: Ascites_BEX_9


title: WT-Control-p65-1


title: Ascites_IG_9


title: Ascites_BEX_8


title: Ascites_BEX_11


title: Ascites_IG_8


title: MCF7 PRO-seq HS rep2

description: nascent RNA

data_processing:
Illumina small RNA TruSeq adapters were trimmed and reads shorter than 15 bp were discarded. Trimmed reads were used to remove ribosomal RNAs and remaining reads were aligned to hg19 using hisat2. Individual samples were normalized using 3’-ends of long genes where the elongating Pol II could not have reached within the timing of treatment. Differentially expressed genes were defined using DeSeq2 (p adj<0.05). Bigwig files were generated using bamcoverage using offset 1 option to detect 3'-ends of RNAs separately for each strand, with bin size 1
Assembly: hg19
Supplementary files format and content: bigwig fop forward and reverse strand for each sample
Library strategy: PRO-seq

extract_protocol:
Precision Run-On sequencing (PRO-seq) was performed as previously described {Mahat et al., 2016}. Briefly, nuclei were extracted from ~2x107 cells and run-on reactions were carried on at 37°C for 3 minutes using 3ml of each 11-biotin-labelled ribonucleotide stocks (Perkin Elmer).
Libraries were prepared as described in Mahat et al., 2016 using custom Illumina small RNA compatible linkers, alkaline degradation, enzymatic treatments and streptavidin selection of nascent RNA on magnetic beads according to the cited protocol.

value: mammary gland, adenocarcinoma

value: Heat shock


title: MCF7 PRO-seq As rep2

description: nascent RNA

value: Arsenic


title: Ascites_BEX_1


title: Ascites_IG_1


title: MCF7 PRO-seq NHS rep2

description: nascent RNA

value: Untreated


title: WT-Control-PDX1-1


title: MCF7 PRO-seq As rep1

description: nascent RNA


title: K562 PRO-seq As

description: nascent RNA

value: bone marrow, myelogenous leukemia


title: K562 PRO-seq HS

description: nascent RNA


title: MCF7 PRO-seq HS rep1

description: nascent RNA


title: K562 PRO-seq NHS

description: nascent RNA


title: Transposon junction gDNA MSPA55 rep 2

city: Odense M

first: Magnus

middle: Zimmermann

last: Østergaard

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: MSPA55 rep 2

data_processing:
Adapter removal with Cutadapt
Reference alignment with Bowtie 2
Deduplication with Samtools
Read count quantitation with Seqmonk
Statistical analysis with EdgeR
Assembly: NC_002516
Supplementary files format and content: .xlsx spreadsheet of Seqmonk probe report containing per-probe corrected read counts and fold changes and p-value (calculated with EdgeR) between phage-infected samples and control. Tabs contain probes passing statistical test for each condition.

organism: Pseudomonas aeruginosa

source_name: Bacterium

extract_protocol:
Dneasy Blood & Tissue kit
Illumina library prep
Transposase-based adapter ligation and targeted PCR enrichment

value: Bacterium


title: Transposon junction gDNA Fyn8-2 rep 3

description: Fyn8-2 rep 3


title: Transposon junction gDNA control rep 1

description: Control rep 1


title: Transposon junction gDNA Fyn8-2 rep 2

description: Fyn8-2 rep 2


title: Transposon junction gDNA Fyn8-2 rep 1

description: Fyn8-2 rep 1


title: Transposon junction gDNA MSPA55 rep 3

description: MSPA55 rep 3


title: Transposon junction gDNA MSPA56 rep 3

description: MSPA56 rep 3


title: Transposon junction gDNA Fyn8-1 rep 3

description: Fyn8-1 rep 3


title: Transposon junction gDNA Fyn8-1 rep 2

description: Fyn8-1 rep 2


title: Transposon junction gDNA MSPA56 rep 1

description: MSPA56 rep 1


title: Transposon junction gDNA MSPA56 rep 2

description: MSPA56 rep 2


title: Transposon junction gDNA control rep 2

description: Control rep 2


title: Transposon junction gDNA control rep 3

description: Control rep 3


title: Transposon junction gDNA Fyn8-1 rep 1

description: Fyn8-1 rep 1


title: Transposon junction gDNA MSPA55 rep 1

description: MSPA55 rep 1


title: MCF7 PRO-seq NHS rep1

description: nascent RNA


title: YDJ8374 min glc+rad rep 2

city: Stanford

first: Christopher

middle: M

last: Jakobson

state: CA

address: 318 Campus Dr, Clark Center W350

department: Chemical and Systems Biology

institute: Stanford University School of Medicine

description:
8374_+_2
tpmSummary.csv

data_processing:
Raw reads were trimmed of adaptors and filtered for quality by BGI.
Transcriptomic reads were pseudo-aligned to the genome using Kallisto.
Kallisto was used to generate transcripts per million (TPM) estimates.
Allele-specific expression was estimated using custom code in MATLAB based on Kallisto pseudo-alignments.
Assembly: Saccharomyces cerevisiae R64.1
Supplementary files format and content: radAseData.csv contains allele-specific expression data for the F0 heterozygous diploid YJM5924 with and with radicicol treatment.
Supplementary files format and content: tpmSummary.csv contains TPM estimates for the homozygous parental diploids with and with radicicol treatment.

organism: Saccharomyces cerevisiae

source_name: yeast cell

extract_protocol:
Total RNA was extracted from snap-frozen yeast cells and subjected to polyA selection.
Libraries were constructed using the DNBSEQ Eukaryotic Strand-specific mRNA library protocol.

value: yeast cell

tag: ploidy

value: RM11 homozygous diploid

value: minimal glucose + 10µM radicicol


title: YDJ8374 min glc-rad rep 2

description:
8374_-_2
tpmSummary.csv

value: minimal glucose no radicicol


title: YDJ8374 min glc+rad rep 3

description:
8374_+_3
tpmSummary.csv


title: pluri_WTC_R1 [176198]

source_name: pluripotency

growth_protocol:
hPSCs (WTC line) are seeded in a 24-well plate (TPP, #92024) at 30-40k cells per well in E8 + ROCKi (5μM Y-27632, Tocris #1254). All differentiation media are based on CDM. 24 hours after seeding in the 24-well plate, the cells are induced with mesoderm induction media. Mesoderm induction media is made up of CDM containing FGF2 (30 ng/ml, Cambridge University), LY294002 (5 μM, Tocris, #1130), Activin A (specific concentrations for different cardioid subtype, Cambridge University), BMP4 (10 ng/ml, R&D Systems RD-314-BP-050), and CHIR99021 (specific concentrations for different cardioid subtypes, see below, R&D Systems RD-4423/50). After 36-40 hours, cells are dissociated with TrypleE (Gibco, #12605010) and seeded in a Corning ultra-low attachment 96 well plate (Corning, #7007) at 15-20k cells/well in Cardiac Mesoderm Patterning Media One made up of CDM containing ROCKi and for all protocols besides the LV cardioids 1 μg/ml of insulin (Roche, #11376497001) plus specific factors depending on cardioid subtype (see below). After seeding, the cells are spun down in a centrifuge for 4 mins at 200g. At day 2.5, the cells are fed with Cardiac Mesoderm Patterning Media One. For the next two days, the medium is changed to Cardiac Mesoderm Patterning Media Two, made up of CDM containing specific factors depending on the cardioid subtype (see below) and exchanged daily. For the subsequent two days, media is exchanged every day with Cardiomyocyte Differentiation Media CDM medium  containing BMP4 (10ng/ml), FGF2 (8 ng/ml), and insulin (10 μg/ml)). This medium was termed Cardiomyocyte Specification Media (Hofbauer et al., 2021b). For the subsequent days of culture, media is exchanged every other day with CDM containing insulin (10 μg/ml).
*******************************************************
Specific media composition of cardioid subtypes:
*******************************************************
(1) Mesoderm Induction Media for WTC lines (day 0 – 1.5)
For LV (FHF-derived) cardioid differentiations, Activin is used at 5 ng/mL and CHIR99021 at 3 μM.
For RV (aSHF-derived), atria (pSHF-derived), and OFT differentiations Activin is used at 50 ng/mL and CHIR99021 at 4 μM. For AVC differentiation, Activin is used at 10 ng/mL and CHIR99021 at 2 μM.
---
(2) Cardiac Mesoderm Patterning Media 1 (day 1.5 – 3.5)
LV (FHF-derived): BMP4 (10ng/ml), FGF2 (8 ng/ml), insulin (10 μg/ml), C59 (2 μM, Tocris, #5148/10) and retinoic acid (50 nM, Sigma Aldrich, #R2625) (Hofbauer et al., 2021b).
RV (aSHF-derived): The TGF-beta inhibitor SB 431542 (10 μM, Tocris, #1614/10) and either C59 (2 μM) or XAV-939 (5 μM, SelleckChem, # S1180) (Figures 1-4).
OFT (aSHF-derived): SB 431542 (10 μM) and XAV-939 (5μM).
Atria (pSHF-derived): SB 431542 (10 μM), XAV-939 (5μM) and retinoic acid (500 nM).
AVC (pSHF-derived): SB 431542 (10 μM), XAV-939 (5μM), retinoic acid (500nM) and BMP4 (10ng/ml).
---
(3) Cardiac Mesoderm Patterning Media 2 (day 3.5 – 5.5)
LV: BMP4 (10ng/ml), FGF2 (8 ng/ml), insulin (10 μg/ml), C59 (2 μM) and retinoic acid (50 nM)) (Hofbauer etal., 2021b).
RV: either C59 (2 μM)(Figures 5-7) or XAV-939 (Figures 1-4) (5μM), BMP4 (10ng/ml), FGF2 (8 ng/ml), insulin (10 μg/ml), and retinoic acid (500nM).
OFT: XAV-939 (5μM), BMP4 (10ng/ml), FGF2 (8 ng/ml) and insulin (10 μg/ml).
Atria and AVC: XAV-939 (5μM), BMP4 (10ng/ml), FGF2 (8 ng/ml), insulin (10 μg/ml), and retinoic acid (500 nM).

extract_protocol:
RNA was isolated using an in-house RNA bead isolation kit semi-automated using KingFisher devices (KingFisher Duo Prime).
Using the QuantSeq 30 mRNA-Seq Library Prep Kit FWD (Lexogen GmbH, #015), the bulk RNA-seq library was generated according to the manufacturer’s instructions. After the preparation of the library, samples were checked for an adequate size distribution with a fragment analyzer.Then the RNA-seq library was submitted to the Vienna Biocenter Core Facilities (VBCF) Next-Generation-Sequencing (NGS) facility for sequencing.

value: pluripotency

value: WTC

value: pluripotent stem cells


title: LV_d14_R3 [176336]

value: cardiac

value: Cardiomyocytes


title: LV_d14_R2 [176335]


title: YDJ8374 min glc-rad rep 1

description:
8374_-_1
tpmSummary.csv


title: pluri_WTC_R2 [176199]


title: LV_d14_R1 [176180]


title: pluri_WTC_R3 [176200]


title: YDJ8374 min glc-rad rep 3

description:
8374_-_3
tpmSummary.csv


title: YDJ8374 min glc+rad rep 1

description:
8374_+_1
tpmSummary.csv


title: RV_d14_R2 [176178]


title: OFT_d14_R3 [176176]


title: RV_d14_R1 [176333]


title: RV_d14_R3 [176334]


title: YDJ8370 min glc+rad rep 3

description:
8370_+_3
tpmSummary.csv

value: YJM975 homozygous diploid


title: WT mouse #8

city: Groningen

first: Marieke

middle: C.

last: Bolling

address: Hanzeplein 1

department: Department of Dermatology

country: Netherlands

institute: University of Groningen, University Medical Centre Groningen

data_processing:
Alignment against mm39 using STAR 2-pass version 2.7.9a
Duplicate marking using GATK version 4.2.4.0
Read counting per exon aggregated by gene on GENCODE vM30 using featureCounts (subread version 2.0.3)
Expression count filtering and TMM normalization using edgeR version 3.36.0
Assembly: mm39, GENCODE vM30
Supplementary files format and content: featureCounts output, tab-delimited txt, raw counts
Supplementary files format and content: featureCounts output, tab-delimited txt, TMM normalized counts (log transformed)

source_name: healthy WT skin

extract_protocol:
RNA from posdered snap-frozen tissue was isolated in TRIzol (Sigma) using TissueLyser (Quiagen)
QuantSeq 3' mRNA kit (Lexogen) was used to prepare cDNA sequence libraries

value: healthy WT skin

value: WT


title: KO mouse #4

source_name: healthy looking KO skin

value: healthy looking KO skin

value: KO


title: YDJ8370 min glc+rad rep 2

description:
8370_+_2
tpmSummary.csv


title: WT mouse #5


title: WT mouse #7


title: YDJ8370 min glc+rad rep 1

description:
8370_+_1
tpmSummary.csv


title: WT mouse #6


title: KO mouse #3


title: sgKLF5-B

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

data_processing:
Data were quantified as transcripts per million (TPM) using kallisto
Assembly: GRCh38
Supplementary files format and content: Excel file includes TPM values for each sample

extract_protocol:
RNAs were extracted from cells in triplicate using a Direct-zol RNA Miniprep Plus kit (R2071, Zymo Research, Irvine, CA)
Poly-A RNA libraries for RNA-seq were prepared by Nex-Gen Core at The University of Texas Medical Branch

treatment_protocol: 1M cells were cultured for 24hrs in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% heated-inactivated fetal bovine serum (FBS; #S11150, R&D System, Minneapolis, MN) and 100μg/ml of Normocin (ant-nr-1, InvivoGen, San Diego, CA) prior to RNA isolation and stranded RNAseq.

value: Lung cancer cell line

tag: replicate

value: B


title: YDJ8370 min glc-rad rep 3

description:
8370_-_3
tpmSummary.csv


title: sgDAZAP2-A

value: A


title: sgKLF5-C

value: C


title: sgDAZAP2-C


title: sgDAZAP2-B


title: KO mouse #2


title: OFT_d14_R2 [176332]


title: AVC_d14_R3 [176330]


title: sgNC-B

value: sgNC


title: sgVTA1-A


title: sgNC-C


title: sgVTA1-B


title: sgNC-A


title: sgVTA1-C


title: sgKLF5-A


title: OFT_d14_R1 [176331]


title: Mouse dermal fibroblasts cultured as monolayers

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Fastq files were generated from raw sequencer output using the mkfastq command of cellranger 7.0.0
Cell-containing droplets were identified and quantified using the count command of cellranger 7.0.0
Assembly: mm10
Supplementary files format and content: HDF5 format files containing filtered feature-barcode matrices generated by 10X Cellranger (v7.0.0)

source_name: Ear and Tail

growth_protocol: For monalayre, cells were plated on cell culture plate and maintained with DMEM/F-12 supplemented with mouse EGF, mbFGF and mIGF-1 (all 20 ng/ml). For the spheroid culture, cells were plated at 100-300 cells per well in ULA 96 well round-bottom plates (Corning® Costar® Ultra-Low Attachment Multiple Well Plate, Cat#7007) in 200 µl DMEM/F-12 supplemented with mouse or human EGF, mbFGF and mIGF-1 (all 20 ng/ml) plus 10 µM ROCKi. Cells were maintained in 5% CO2, 21% O2 and 74% N2 at 37oC for 7 days. Half of the culture medium was removed and replaced every other day.

extract_protocol:
Between 70,000-100,000 mouse adherence-cultured fibroblasts (monolayer) and dissociated spheroid cells (single cells) were freshly prepared and their gene expression profile analyzed using single-cell 3' RNA-sequencing
Sequencing libraries were prepared using the Single Cell 3' Reagent Kits V3.1 (10x Genomics, Pleasanton, CA, USA) with the 10X Chromium controller, and sequenced on NextSeq 500

value: Ear and Tail

value: Primary cells

value: Dermal Fibroblast

value: Wild type

value: cultured as monolayers


title: Mouse dermal fibroblasts cultured as spheroids

value: cultured as spheroids


title: anti-PD1_3 YUMM 2.1

city: New York

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

description: CD45+ sorted cells from the tumor with anti-PD1 antibody treatment, Replicate 3

data_processing:
We first assessed the quality of paired-end reads with FASTQC (v0.11.8).
we filtered reads with BBDUK from BBTOOLS (v37.53) to remove adapters, known artefacts, and quality trimmed (PHRED quality score <10).
Reads that became too short after trimming (N<60 bp) were discarded. Singleton reads (i.e., reads whose mate has been discarded) were not retained.
We estimated the transcript-level quantification of cleaned RNA-seq data using SALMON (v1.0.0) by a quasi-mapping on Mus musculus GRCm38 (39).
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: SALMON - format - .sf.txt - TMM and read counts

source_name: Skin tumor

extract_protocol:
Total RNA was extracted and amplified from CD45+ sorted samples using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara). The RNA Integrity Number of each sample was determined using the 2100 Bioanalyzer instrument (Agilent Technologies). Samples were selected with stringent criteria based on RNA Integrity Number of 7.0 or greater, and a minimum of 500 ng of total RNA. Total RNA was subjected to ribosomal RNA depletion and further used as input for library construction by the Nextera XT DNA Library Preparation Kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: We injected immunocompetent C57BL/6J mice with YUMM2.1 cells subcutaneously to generate allografts, followed by treatment with IgG control, anti-B7-H3, or anti-PD1 once the tumors reached 20-50 mm3.

value: YUMM 2.1

tag: strain

value: CD45+ sorted cells


title: WAP-MYC hepsin wt and ko tumor cells transplanted into FVBN mouse mammary  fat pad

city: Helsinki

first: Topi

last: Tervonen

address: Haartmaninkatu 8

institute: University of Helsinki

description: Sequencing was done using a strategy where 3'-UTRs were sequenced from mRNA fragments. In the process, all samples are pooled into a single library, where each sample is labeled with unique sample barcodes. After  alignment each sample is demultiplexed using drop-seq tools and these 12bp long barcodes.

data_processing:
Sequencing with 75 cycles produced 21 bp Read 1 (bases 1-12 sample barcode, bases 13-20 UMI) and 62 bp Read 2 (sequence derived from the mRNA).
Raw sequence data was inspected using FastQC and multiQC to ensure the quality of sequencing results (Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc; Ewels P. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016).  Subsequently, reads were filtered to remove low quality reads and reads shorter than 20 bp using Trimmomatic (Bolgeret al. Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics. 2014).
Reads passing the filter were then processed further using Drop-seq tools and the pipeline originally suggested in Drop-seq paper (v. 2.3.0,Macoskoet al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell. 2015). In brief, the raw, filtered read libraries were converted to sorted BAM files using Picard tools (http://broadinstitute.github.io/picard). This was followed by tagging reads with sample specific barcodes and unique molecular identifiers (UMIs). Tagged reads were then trimmed for 5’ adapters and 3’ poly A tails. Alignment ready reads were converted from BAM formatted files to fastq files that were used as an input for STAR aligner (Dobin A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013).
Alignments were done using data from GENCODE Release M25 human genome (GRCm38.p6) and comprehensive gene annotation files (Frankish A. et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 2019) with default STAR settings. Following the alignment, the uniquely aligned reads were sorted and merged with previous unaligned tagged BAM file to regain barcodes and UMI’s lost during the alignment step. Next, annotation tags are added to aligned and barcode tagged BAM files to complete the alignment process. Finally, Drop-seq tools are used to detect and correct systematic synthesis errors present in sample barcode sequences. Digital expression matrices are then created by counting the total number of unique UMI sequences (UMI sequences that differ only by a single base are merged together) for each transcript.
DESeq2 was then used to identify differentially expressed genes (Love MI. et al. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 2014).
Assembly: GENCODE Release M25 Mouse genome (GRCm38.p6) and comprehensive gene annotation files.
Supplementary files format and content: Raw gene expression matrix (MS excel format) from drop-seq Digital Gene Expression (DGE) outputs.
Supplementary files format and content: List of samples and sample specific barcodes used for pooling (MS xlsx format).

source_name: mammary tumor

extract_protocol:
RNA was extracted from tumors using Precellys hard-tissue beads and TRIzol. RNA was then DNase treated and purified using RNeasy Mini Kit from Qiagen.
Custom library construction protocol.
3' RNA-Seq (Drop-seq-like)

value: mammary tumor

value: cells isolated from WAP-MYC mouse mammary tumor

value: primary cell


title: YDJ8370 min glc-rad rep 1

description:
8370_-_1
tpmSummary.csv

value: yeast cell

value: YJM975 homozygous diploid

value: minimal glucose no radicicol


title: YDJ5924 SD-CSM+rad rep 2

description:
x5924_SD_2A_refCounts_1
radAseData.csv

value: F0 heterozygous diploid

value: SD-CSM + 10µM radicicol


title: YDJ8370 min glc-rad rep 2

description:
8370_-_2
tpmSummary.csv


title: YDJ5924 SD-CSM+rad rep 1

description:
x5924_SD_1A_refCounts_1
radAseData.csv


title: YDJ5924 SD-CSM-rad rep 3

description:
x5924_SD_3A_refCounts
radAseData.csv

value: SD-CSM no radicicol


title: YDJ5924 SD-CSM+rad rep 3

description:
x5924_SD_3A_refCounts_1
radAseData.csv


title: YDJ5924 SD-CSM-rad rep 2

description:
x5924_SD_2A_refCounts
radAseData.csv


title: YDJ5924 SD-CSM-rad rep 1

description:
x5924_SD_1A_refCounts
radAseData.csv


title: MYC-OFF HCC mouse, rep3

first: Dean

last: Felsher

address: 269 Campus Drive

institute: Stanford University

data_processing:
kallisto (version 0.46.2) was used to pseudoalign reads with the following options specified in "kallisto quant": --single -l 200 -s 20
Assembly: mm10
Supplementary files format and content: Estimated counts and TPMs

source_name: hepatocellular carcinoma

extract_protocol:
Tissue was harvested and flash frozen on dry ice. RNA was extracted using QIAGEN RNeasy kit.
RNA-Seq libraries were constructed via the BGISEQ-500 library construction protocol

value: hepatocellular carcinoma

tag: genotype

value: LAP-tTA/tetO-MYC

value: doxycycline (MYC off)


title: S16-P4-F66 ,grade4,SDD3,RNAseq

city: Guangzhou

first: Jianru

last: Wang

state: Guangdong

address: No. 58, Zhongshan road II, Guangzhou 510080, People’s Republic of China

institute: Sun Yat-sen University First Affiliated Hospital

description:
bulk RNA-seq
FPKM.txt

data_processing:
scRNA-seq: The feature-barcode matrices were obtained by aligning reads to the human genome (GRCh38) using Cell Ranger v6.1.1
bulk RNA-seq: Hisat2 2.1.0 mapping to reference genome
bulk RNA-seq: count counting
Assembly: GRCh38
Supplementary files format and content: scRNA-seq: Tab-separated values files and matrix files
Supplementary files format and content: bulk RNA-seq: TXT file contain FPKM for each sample

source_name: nucleus pulposus tissue

extract_protocol:
scRNA-seq: cut the outer layer of AF , then the inner layer of AF), and then  start to achieve NP. After that we washed the NP tissues with 0.9% normal saline three times. And transport it in ice-cold preservation solution.
bulk RNA-seq: Total RNA was extracted from NP tissue, and treated with the GeneRead™ rRNA Depletion kit (Qiagen) to remove ribosomal RNA
scRNA-seq: Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, scRNA-seq data analysis was performed by NovelBio Bio-Pharm Technology Co.,Ltd. with NovelBrain Cloud Analysis Platform. We applied fastp with default parameter filtering of the adaptor sequence to remove the low-quality reads and obtain the clean data. Then the feature-barcode matrices were obtained by aligning reads to the human genome (GRCh38 Ensemble: version 104) using CellRanger v6.1.1. We performed the down sample analysis of samples sequenced according to the mapped barcoded reads per cell of each sample and finally created the aggregated matrix. Cells containing over 200 expressed genes and a mitochondrial UMI rate below 20% passed the cell quality filtering and mitochondrial genes were removed from the expression table.
bulk RNA-seq: a VAHTS Stranded RNA-seq Library preparation kit for Illumina (Vazyme) was used to construct strand-specific libraries

value: nucleus pulposus tissue

tag: cell type

value: nucleus pulposus cells(NPCs)

tag: grade

tag: status

value: SDD


title: LV_d9.5_R1 [176165]

value: cardiac

tag: cell line

value: WTC

value: Cardiomyocytes


title: AVC_d14_R1 [176171]


title: LV_d9.5_R3 [176167]


title: Atria_d14_R1 [176168]


title: AVC_d14_R2 [176172]


title: Atria_d14_R3 [176170]


title: IgG_Control_3 YUMM 2.1

description: CD45+ sorted cells from the tumor with IgG control treatment, Replicate 3

value: YUMM 2.1

tag: treatment

value: Isotype control

value: CD45+ sorted cells


title: RV_d9.5_R3 [176164]


title: IgG Control 2

description: IgG control treatment to bulk tumor, Replicate 2

data_processing:
We first assessed the quality of paired-end reads with FASTQC (v0.11.8).
we filtered reads with BBDUK from BBTOOLS (v37.53) to remove adapters, known artefacts, and quality trimmed (PHRED quality score <10).
Reads that became too short after trimming (N<60 bp) were discarded. Singleton reads (i.e., reads whose mate has been discarded) were not retained.
We estimated the transcript-level quantification of cleaned RNA-seq data using SALMON (v1.0.0) by a quasi-mapping on Mus musculus GRCm38 (39).
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: SALMON - format - .sf - TMM and read counts

extract_protocol:
Total RNA was extracted from samples using the RNeasy Protect Mini Kit (Qiagen). The RNA Integrity Number of each sample was determined using the 2100 Bioanalyzer instrument (Agilent Technologies). Samples were selected with stringent criteria based on RNA Integrity Number of 7.0 or greater, and a minimum of 500 ng of total RNA. Total RNA was subjected to ribosomal RNA depletion and further used as input for library construction by the Illumina TruSeq Standard Total RNA library Pre Gold kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: We injected immunocompetent C57BL/6J mice with YUMMER1.7 cells subcutaneously to generate allografts, followed by treatment with IgG control, anti-B7-H3 or anti-PD1 once the tumors reached 20-50 mm3.

value: Skin tumor


title: anti-PD1_2 YUMM 2.1

description: CD45+ sorted cells from the tumor with anti-PD1 antibody treatment, Replicate 2


title: anti-PD1 2

description: anti-PD1 antibody treatment to bulk tumor, Replicate 2


title: anti-B7-H3_2 YUMM 2.1

description: CD45+ sorted cells from the tumor with anti-B7-H3 antibody treatment, Replicate 2


title: anti-PD1 1

description: anti-PD1 antibody treatment to bulk tumor, Replicate 1


title: anti-PD1_1 YUMM 2.1

description: CD45+ sorted cells from the tumor with anti-PD1 antibody treatment, Replicate 1


title: anti-B7-H3 2

description: anti-B7-H3 antibody treatment to bulk tumor, Replicate 2


title: IgG_Control_1 YUMM 2.1

description: CD45+ sorted cells from the tumor with IgG control treatment, Replicate 1


title: anti-B7-H3 3

description: anti-B7-H3 antibody treatment to bulk tumor, Replicate 3


title: IgG Control 1

description: IgG control treatment to bulk tumor, Replicate 1


title: LV_d9.5_R2 [176166]

data_processing:
Reads were preprocessed using umi2index (Lexogen) to add the UMI sequence to the read identifier, and trimmed using BBDuk v38.06 (ref = polyA.fa.gz,truseq.fa.gz k = 13 ktrim = r useshortkmers = t mink = 5 qtrim = r trimq = 10 min length = 20). Reads mapping to abundant sequences included in the iGenomes NCBI GRCh38 references were removed using bowtie2 v2.3.4.1 alignment. The remaining reads were analyzed using genome and gene annotation for the GRCh38 assembly obtained from Homo sapiens Ensembl release 94. Reads were aligned to the genome using star v2.6.0c, and reads in genes were counted with featureCounts (subread v1.6.2) using strand-specific read counting (-s 1). Differential gene expression analysis on raw counts, and principal component analysis on variance stabilized, transformed count data were performed using DESeq2 v1.18.1.
Assembly: GRCh38
Supplementary files format and content: featurecounts.count.gene.tsv: Tab-delimited text files with per gene read counts.


title: Atria_d14_R2 [176329]


title: anti-B7-H3 1

description: anti-B7-H3 antibody treatment to bulk tumor, Replicate 1


title: IgG_Control_2 YUMM 2.1

description: CD45+ sorted cells from the tumor with IgG control treatment, Replicate 2


title: anti-B7-H3_1 YUMM 2.1

description: CD45+ sorted cells from the tumor with anti-B7-H3 antibody treatment, Replicate 1


title: anti-PD1 3

description: anti-PD1 antibody treatment to bulk tumor, Replicate 3


title: anti-B7-H3_3 YUMM 2.1

description: CD45+ sorted cells from the tumor with anti-B7-H3 antibody treatment, Replicate 3


title: MYC-OFF HCC mouse, rep2


title: IgG Control 3

description: IgG control treatment to bulk tumor, Replicate 3


title: anti-B7H3 + anti-PD1_3

treatment_protocol: We injected immunocompetent C57BL/6J mice with Yumm2.1 cells subcutaneously to generate allografts, followed by treatment with IgG control, anti-B7-H3, anti-PD1, or both (anti-B7-H3 plus anti-PD1) once the tumors reached 20-50 mm3.

value: anti-B7H3 + anti-PD1


title: MYC-ON HCC mouse, rep6


title: S15-P4-M65, grade 4,SDD2,RNAseq

description:
bulk RNA-seq
FPKM.txt

value: grade 4


title: S14-P3-M50, grade 3,SDD1,RNAseq

description:
bulk RNA-seq
FPKM.txt

value: grade 3


title: RV_d9.5_R2 [176163]


title: MYC-OFF HCC mouse, rep1


title: S12-P2-F58, grade 2,MDD2,RNAseq

description:
bulk RNA-seq
FPKM.txt

value: grade 2

value: MDD


title: anti-B7H3 + anti-PD1_2


title: S11-P2-M50, grade 2, MDD1,RNAseq

description:
bulk RNA-seq
FPKM.txt


title: AVC_d9.5_R3 [176158]


title: OFT_d9.5_R1 [176328]


title: AsPC1-MSK1-A10 replicate 3

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

data_processing:
The base calling was performed using RTA 1.18.64.0
Reads were aligned to mm10 genome index and GRCH38 annotations using tophat version 2.1.0 with parameters -T -G mm10.gtf
Aligned read counts are estimated from alignment file and GRCH38 gtf using Htseq-count version 0.6.0.
Genome_build: GRCH38
Supplementary_files_format_and_content: Raw read counts in .txt format

growth_protocol: AsPC1 cells stably expressing two individual shRNAs against MSK1 were grown in RPMI medium with 10% Fetal bovine serum and Penicilline and Streptomycin at 37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C. Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries. The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: AsPC1 cells that expressed shRNA targeting MSK1 (#1,#2) were used for preparing the total RNA and to perfrom RNA Seq.

value: MSK1 A10 (shRNA#2)


title: MYC-ON HCC mouse, rep3

value: hepatocellular carcinoma

value: LAP-tTA/tetO-MYC


title: RV_d9.5_R1 [176162]


title: MYC-ON HCC mouse, rep5


title: OFT_d9.5_R3 [176161]


title: OFT_d9.5_R2 [176160]


title: S13-P2-M52, grade 2,MDD3,RNAseq

description:
bulk RNA-seq
FPKM.txt

value: nucleus pulposus tissue

value: nucleus pulposus cells(NPCs)


title: MYC-ON HCC mouse, rep2


title: AsPC1-MSK1-A10 replicate 2


title: AVC_d9.5_R2 [176157]

value: cardiac


title: AsPC1-MSK1-A10 replicate 1


title: MYC-ON HCC mouse, rep4


title: FVB/N mouse, liver tissue, rep1

source_name: liver

value: liver

value: FVB/N


title: anti-PD1_1

value: YUMM 2.1


title: anti-B7H3_3


title: anti-PD1_3


title: anti-B7H3 + anti-PD1_1


title: anti-B7H3_1


title: anti-B7H3_2


title: anti-PD1_2


title: MYC-ON HCC mouse, rep1


title: FVB/N mouse, liver tissue, rep2


title: IgG_Control_3

value: Isotype control


title: IgG_Control_2


title: IgG_Control_1


title: Huh7_CCL5_stimulation_rep3

city: Tianjin

first: Yafei

address: No.94 Weijin Road, Nankai District

department: School of Medicine

institute: Nankai University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp(parameter;default)
Clean reads were mapped to  human GRCh38 genome using by Hisat2（v2.2.0）
The expression level of genes were calculated by StringTie （v2.1.2） and normalized to FPKM (Fragments per kilo base of transcript per million mapped reads.
DEseq2（1.26.0） was used to detect DEGs (Different expressed genes), and DEGs with fold change > 2 or <-2 and  adjusted P value <= 0.001 were considered to be significantly different expressed genes.
GO enrichment analysis and KEGG enrichment analysis were performed using clusterProfiler, a function of R.  The significant levels of terms and pathways were corrected by Q value with a rigorous threshold  (Q value < 0.05)
Assembly: human GRCh38 genome
Supplementary files format and content: counts
Supplementary files format and content: FPKM

growth_protocol: Huh7 cells were cultured in Dulbecco's Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), without the presence of antibiotics. The cells were maintained in a humidified incubator at a temperature of 37 ℃ with 5% CO2.

extract_protocol:
24 hours after different stimulation, huh7 cells were washed with PBS and lysed with TRIzol for RNA extraction to perfom RNA sequencing.
The RNA samples were processed for RNA-seq library construction using the VAHTS Universal V6 RNA-seq Library Prep Kit for MGI® (Vazyme, NRM604-01).

treatment_protocol: After the cells attached to the bottom, 100ng/ml of CCL5 or an equivalent amount of ddH2O was added to the plates.

value: hepatoma cell

value: WT

value: 100ng/ml CCL5


title: Huh7_CCL5_stimulation_rep1


title: Huh7_Control_rep3


title: Huh7_CCL5_stimulation_rep2


title: PANC1-MSK1-A10 replicate 3

growth_protocol: PANC1 cells stably expressing two individual shRNAs against MSK1 were grown in DMEM medium with 10% Fetal bovine serum and Penicilline and Streptomycin at 37 C under 5% CO2 condition.

treatment_protocol: PANC1 cells that expressed shRNA targeting MSK1 (#1,#2) were used for preparing the total RNA and to perfrom RNA Seq.


title: PANC1-MSK1-A10 replicate 2


title: AsPC1-MSK1-A9 replicate 3

value: MSK1 A9 (shRNA#1)


title: AsPC1-NS replicate 2

value: non silencing shRNA (TRC)


title: Huh7_Control_rep2


title: AsPC1-NS replicate 3


title: LV_d7.5_R2 [176151]

value: WTC

value: Cardiomyocytes


title: AsPC1-MSK1-A9 replicate 2


title: Atria_d9.5_R1 [176153]


title: RV_d7.5_R3 [176149]


title: LV_d7.5_R3 [176152]


title: AsPC1-NS replicate 1


title: RV_d7.5_R2 [176148]


title: Atria_d9.5_R3 [176155]


title: Huh7_Control_rep1


title: AVC_d9.5_R1 [176156]


title: LV_d7.5_R1 [176150]


title: Atria_d9.5_R2 [176327]


title: Primary osteosarcoma, treatment-naïve, ATAC

city: Auburn

first: Bruce

middle: F

last: Smith

address: 1265 HC Morgan Dr

department: Pathobiology

institute: Auburn University College of Veterinary Medicine

description:
10x Genomics
Same tumor as GSM5974063 in GEO dataset GSE199489

data_processing:
Cell Ranger (v7.1.0) was used to demultiplex, process barcodes, and align and count reads
Analysis was accomplished using the Cell Ranger ARC Count (v2.0.2) pipeline and the output was loaded into Seurat (v4.3.0) for further processing.
R processing scripts using Seurat available at https://github.com/rln0005/OSA_snMultiomeSeq
Assembly: canFam6 (Dog_10K_Boxer_Tasha) (GCF_000002285.5)
Supplementary files format and content: filtered_feature_bc_matrix.h5: Filtered feature barcode matrix stored as a CSC sparse matrix in hdf5 format. The rows consist of all the gene and peak features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells. (CellRanger Output)
Supplementary files format and content: atac_fragments.tsv.gz: Count and barcode information for every ATAC fragment observed in the experiment in TSV format. (CellRanger Output)
Supplementary files format and content: gex_molecule_info.h5: Count and barcode information for every GEX molecule observed in the experiment in hdf5 format. (CellRanger Output)

organism: Canis lupus familiaris

source_name: Osteosarcoma

extract_protocol:
Nuclei were isolated from 42 mg flash frozen OSA tissue by following the Nuclei Isolation kit protocol from 10x Genomics (Pleasanton CA, USA, CG000505 Rev A) with minor ad-justments to enhance homogenization while retaining nuclear morphology. The Lysis Buffer provided with the kit was diluted with phosphate buffered saline (PBS) to 0.5 strength and the sample was briefly homogenized (1-2 sec) using a bladed homogenizer on ice, followed by a 5-minute incubation on ice. The nuclei isolation protocol from 10x Genomics was then followed according to the manufacturer’s directions
Libraries were prepared according to the Chromium Next GEM single-cell multiome ATAC + gene expression user guide (10x Genomics, Pleasanton, CA, USA, CG000338 Rev F).

value: Osteosarcoma

tag: disease

value: Male

tag: breed

value: Doberman Pinscher

tag: tissue source

value: Distal radius

tag: clinical description

value: 7 YO at time of amputation, no evidence of macrometastatic lung disease


title: Primary osteosarcoma, treatment-naïve, GEX

molecule: nuclear RNA

tag: tissue

tag: Sex


title: AsPC1-MSK1-A9 replicate 1


title: Human MSC deposited in mouse lung_2

first: Yuanchen

last: Ma

state: State

address: No74,Zhongshan Road2, Yuexiu District,Guangzhou,Guangdong China

institute: SYSU

data_processing:
Sequencing reads were trimmed for adaptor sequence/low quality sequence using trim_galore version 0.6.2(parameter -q 20 --length 25 -e 0.1)
Trimmed sequence reads were mapped to GRCh38/hg38 using hisat2 version 2.1.0
Read count extraction were performed using HTSeq version 0.11.2 (parameter -a 10 -t exon)
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: Bone marrow

extract_protocol:
MSC samples from five different donors were used for the genome-wide RNA-seq analysis. TRI Reagent (TR118, Molecular Research Center, Inc.) was used to extract total RNA according to the manufacturer’s protocol.
RNA samples with an RNA integrity number > 8 were used to prepare libraries, and paired-end sequencing was performed by CapitalBio Technology (China) following a standard protocol.

value: Bone marrow

value: cultured mesenchymal stromal cell

value: mesenchymal stem cells


title: Human MSC deposited in mouse lung_3


title: PANC1-MSK1-A10 replicate 1

value: MSK1 A10 (shRNA#2)


title: RV_d7.5_R1 [176147]

first: Clara

last: Schmidt

address: Dr. Bohr-Gasse 3

institute: IMBA - Institute of Molecular Biotechnology GmbH

source_name: cardiac

value: cardiac


title: OFT_d7.5_R3 [176146]


title: PANC1-NS replicate 1


title: PANC1-MSK1-A9 replicate 3


title: RNA-Seq of siYZ-TNFa-3

city: Hiroshima-city

first: Hiroki

last: Yoshii

state: Hiroshima-ken

address: 1-2-3 Kasumi Minami-ku

country: Japan

institute: Hiroshima University

data_processing:
The construction and sequencing of the cDNA library were carried out by the Beijing Genomics Institute using the DNBSEQ platform.
The sequence data was filtered using SOAPnuke 1.5.2, and the clean reads were mapped to the reference genome using HISAT2 2.0.4.
After performing alignment using Bowtie2 2.2.5, the expression levels of individual genes were quantified using RSEM 1.2.8. Differential expression analysis was conducted using DESeq2 1.16.1 with parameters of fold change ≥2 and adjusted P value <0.05.
Assembly: GRCh38
Supplementary files format and content: Counts matrix showing gene-level counts for each sample

source_name: bone marrow

growth_protocol: MSCs were cultured in DMEM (Sigma-Aldrich, Osaka, Japan) supplemented with 10% fetal bovine serum (FBS; Hyclone, Logan, UT), 100 U/mL penicillin (Sigma-Aldrich), and 100 mg/ml streptomycin (Sigma-Aldrich).

extract_protocol:
Total RNA from cultured MSCs was isolated using RNA-iso (Takara, Otsu, Japan) and quantified by spectrometry at 260 and 280 nm.
1) mRNA enrichment and purification:  Oligo dT Selection (mRNA enrichment): Use oligo dT beads to enrich mRNA with poly A tail.  2) RNA fragment and reverse transcription  Fragment the RNA and first-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP.  3) End repair, add A and adaptor ligation  The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments;  4) PCR amplification  Prior to PCR amplification, the dUTP-marked strand is selectively degraded by Uracil-DNA-Glycosylase(UDG). The remaining strand is amplified to generate a cDNA library suitable for sequencing. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer;  5) Single strand separation and cyclization  Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase;  6) DNA nanoball synthesis  7) Sequencing on DNBSEQ (DNBSEQ Technology) platform

treatment_protocol: The siRNAs for human YAP, TAZ or negative control siRNA were chemically synthesized by FASMAC (FASMAC, Kanagawa, Japan). MSCs were seeded in 24-well plastic culture plates and maintained for 48 hr. Then, siRNAs (10 pmol/ml) were transfected into the cells by using Lipofectamine RNAi-MAX (Invitrogen, Carlsbad, CA). After 48 hr cultivation, MSCs were stimulated with or without 10 ng/ml TNF-a for 24 hr.

value: bone marrow

value: primary mscs

value: TNF-α


title: PANC1-MSK1-A9 replicate 2

value: MSK1 A9 (shRNA#1)


title: PANC1-NS replicate 2

value: non silencing shRNA (TRC)


title: PANC1-MSK1-A9 replicate 1


title: PANC1-NS replicate 3


title: RNA-Seq of siYZ-NS-2


title: RNA-Seq of siYZ-NS-1


title: Human MSC deposited in mouse lung_1


title: Human  MSC_2


title: Human  MSC_1


title: RNA-Seq of siYZ-TNFa-2


title: AVC_d7.5_R1 [176325]

city: Vienna

value: WTC


title: RNA-Seq of siYZ-TNFa-1


title: RNA-Seq of sicontrol-TNFa-3


title: Atria_d7.5_R3 [176140]

value: Cardiomyocytes


title: RNA-Seq of siYZ-NS-3


title: Human  MSC_3


title: AVC_d7.5_R3 [176143]


title: OFT_d7.5_R2 [176145]


title: K562 HS HSF1 rep 2

city: Grand Forks

first: Sergei

last: Nechaev

address: Columbia Hall Room 1733c, 501 North Columbia Road Stop 9061

institute: University of North Dakota

data_processing:
Raw files were adapter-trimmed with trimmomatic and aligned to hg19 genome using hisat2. For HSF1 ChIP-seq, raw fastq files were randomly subset to 40M read pairs prior to alignment. After removing PCR duplicates with MarkDuplicates (Picard),   peaks were called using MACS2 with FDR cutoff 0.01 and then merged between replicates . Read coverage was calculated using bamCoverage and read counts were normalized to sequencing depth. Signal was calculated using multibigwigsummary.
Assembly: hg19
Supplementary files format and content: bw - bigwig files.
Supplementary files format and content: narrowPeak - peaks called for each replicate

extract_protocol:
Approximately 2x107 cells were crosslinked with 1% ethanol-free formaldehyde (Thermo) in serum-free DMEM/F12 media at 25C for 10min, quenched with 125mM Glycine, and lysed in buffer (1% Sodium-Dodecyl Sulfate (SDS), 50mM Tris (pH=8), 10mM EDTA, 1X PMSF and protease inhibitor cocktail) followed by disruption in the Covaris S2 sonicator for 6 minutes (with peak power = 140, Duty factor = 5, Cycles/burst = 200). Protein A and Protein G Dynabeads (Invitrogen) premixed at 1:1 ratio were used for pre-clearing for 1 hour at 4C. One percent of each precleared sample was taken as input, with at least two inputs taken for each sample and averaged for ChIP percent input calculation. Samples were incubated with 5g of primary antibodies in 2 ml of dilution buffer (1% Triton-X, 2mM EDTA, 20mM Tris pH=8.0, 150mM NaCl, 1X Phenylmethylsulfonyl fluoride (PMSF) and cOmplete protease inhibitor cocktail (Sigma)) with slow rotation overnight at 4C followed by washing
DNA library was prepared from validated ChIP material using NEBNext Ultra II DNA library kit (New England Biolabs) protocol without size selection. Final PCR amplification of cDNA templates was done using TruSeq Illumina Small RNA PCR primers, 250 M dNTP mix, 1x HF buffer, 1M Betaine, 1xEvagreen dye (Biotium) and Phusion DNA polymerase.

value: bone marrow, myelogenous leukemia

tag: chip antibody

value: HSF1 (Enzo # ADI-SPA-901-D)

value: Heat shock


title: AVC_d7.5_R2 [176326]


title: OFT_d7.5_R1 [176144]


title: K562 As HSF1 rep 2

value: Arsenic


title: K562 NHS HSF1  rep 2

value: Untreated


title: RNA-Seq of sicontrol-TNFa-1


title: RNA-Seq of sicontrol-NS-3


title: RNA-Seq of sicontrol-NS-2


title: RNA-Seq of sicontrol-NS-1


title: CTX2

first: HUI

last: CHEN

address: Guangzhou Huangpu Road

department: medicine

institute: Jinan University School of Medicine

data_processing:
The clean reads were mapped to the reference genome using HISAT2 . After that, Ericscript (v0.5.5)  and rMATS (V3.2.5)  were used to detect fusion genes and differential splicing genes (DSGs), respectively
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: COV434 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells)
The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).

treatment_protocol: Use 4HC at a concentration of 15 μM to act on COV434 cells for 24 hours

value: granulosa cells

value: CTX

value: CTX-Induced


title: CTX3


title: CTX1


title: RNA-Seq of sicontrol-TNFa-2

value: mesenchymal stem cells


title: Control3A

value: WT


title: Control2A


title: MCF7 NHS HSF1  rep 1

value: mammary gland, adenocarcinoma


title: OFT_d5.5_R3 [176131]

value: cardiac

value: cardiac progenitors


title: Atria_d7.5_R2 [176139]


title: LV_d5.5_R3 [176137]


title: LV_d5.5_R1 [176135]


title: RV_d5.5_R1 [176132]


title: RV_d5.5_R2 [176324]


title: MCF7 As HSF1 rep 1


title: MCF7 As HSF1 rep 2


title: MCF7 HS HSF1 rep 2


title: MCF7 NHS HSF1  rep 2


title: MCF7 HS HSF1 rep 1


title: Atria_d7.5_R1 [176138]


title: K562 HS HSF1 rep 1


title: LV_d5.5_R2 [176136]


title: K562 NHS HSF1  rep 1


title: K562 As HSF1 rep 1


title: RV_d5.5_R3 [176134]


title: PANC1 non silencing shRNA replicate 3A

description:
Sample_PDAC3_003
non silcencing shRNA  (TRC)

data_processing:
Bases were called using RTA 1.18.64.0
reads were mapped with the STAR aligner (version STAR_2.5.2b) to the GRCH38 genome using overhang of 100 with the following options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM SortedByCoordinate
reads counts were obtained for each gene (gencode.v25.primary_assembly.annotation.gtf) using the R (v3.3.1) bioconductor GenomicAlignments (v1.10.1)
DESeq2(v1.14.1) was used to call differential expressed genes directly from read counts.
Genome_build: GRCH38
Supplementary_files_format_and_content: The read counts per gene are contained in an R binary file (counts.Rdata).  The 'counts' object of type “RangedSummarizedExperiment” contains the read counts. counts.csv is text printout of count data from counts.Rdata

source_name: non silencing shRNA  (TRC)

growth_protocol: PANC1 cell lines were grown in DMEM medium with 10% Fetal bovine serum and Penicillin and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: PANC1 cells that expressed shRNA targeting HOXC6 (#1,#2) or shRNA targeting KLF7 (#1,#2) or Non-specific (NS) were used for preparing the total RNA and to perfrom gene expression array.

tag: shRNA

value: non-specific


title: PANC1 HOXC6 B2 (shRNA#2) replicate 2

description:
Sample_PDAC8_008
HOXC6 B2 (shRNA#2)

source_name: HOXC6 B2 (shRNA#2)


title: PANC1 non silencing shRNA replicate 2A

description:
Sample_PDAC2_002
non silcencing shRNA  (TRC)


title: PANC1 non silencing shRNA replicate 1A

description:
Sample_PDAC1_001
non silcencing shRNA  (TRC)


title: PANC1 HOXC6 B2 (shRNA#2) replicate 3

description:
Sample_PDAC9_009
HOXC6 B2 (shRNA#2)


title: PANC1 HOXC6 A12 (shRNA#1) replicate 2

description:
Sample_PDAC5_005
HOXC6 A12 (shRNA#1)

source_name: HOXC6 A12 (shRNA#1)


title: PANC1 HOXC6 A12 (shRNA#1) replicate 3

description:
Sample_PDAC6_006
HOXC6 A12 (shRNA#1)


title: PANC1 HOXC6 A12 (shRNA#1) replicate 1

description:
Sample_PDAC4_004
HOXC6 A12 (shRNA#1)