title: GBM_3D_Control_002

city: New York

first: Caghan

last: Kizil

institute: Columbia University Irving Medical Center

description:
Library name: GBM_3D_Control_002
RNA-sequencing
L106307_Track-149161

data_processing:
Fastq files were used as input to be aligned to human genome, using gsnap and ensembl version 105.
Assembly: hg38
Supplementary files format and content: Tab separated counts for each gene.

source_name: brain

growth_protocol: Glioblastoma (GBM) is a devastating brain tumor with limited therapeutic success, largely due to the inability to pre-test patient-specific responses to treatment in a reliable and timely manner with diagnostic and analytical methods as current tests fail to provide actionable insights within the critical timeframes necessary for clinical decision-making. To address this gap, we developed a high-throughput 3D culture system utilizing matrix metalloproteinase-responsive starPEG-sulfated glycosaminoglycan hydrogels. This platform enables encapsulation of patient-derived GBM cells, recreating physiologically relevant microenvironments in 384-well plates for rapid, automated drug testing on primary tumor cells from patients. Transcriptomic analyses revealed that 3D cultures significantly resemble primary and recurrent GBM transcriptomic profiles, particularly in pathways critical for tumor growth, invasion, and therapeutic resistance, such as hypoxia, immune modulation, and extracellular matrix regulation. The platform’s versatility extends to drug screening, where single and combinatorial chemotherapeutic treatments elicited robust and reproducible cytoskeletal and transcriptomic responses. Notably, the system effectively characterized synergistic interactions between 5-fluorouracil and carmustine, highlighting its potential for optimizing combinatorial therapies. Our 3D model surpasses traditional 2D cultures in representing tumor-specific molecular programs, offering an invaluable tool for translational research. By delivering reliable, individualized data on therapeutic efficacy within a clinically relevant timeframe, this model holds transformative potential for personalized medicine, enabling optimized, patient-specific treatment strategies for GBM. Its scalability and compatibility with high-throughput workflows position this system as a critical innovation in GBM research, advancing the paradigm of personalized medicine in neuro-oncology.

extract_protocol:
Total RNA was extracted from the 3D encapsulated cells using the Norgen`s Total RNA purification kit, [Norgen Biotek Corporation], following the manufacturer’s protocol.
Complete cDNA was synthesized with SmartScribe reverse transcriptase using a universally tailed poly-dT primer and template switching oligo. Purified cDNA was amplified with Advantage 2 DNA Polymerase. After ultrasonic shearing of the amplified cDNA (Covaris S2) Illumina fragment library was prepared using NEBnext chemistries (New England Biolabs).

value: brain

value: Patient-derived Glioblastoma

value: Glioblastoma (3D)


title: GBM_3D_5-FU/U_001

status: Public on Jan 21 2026

type: SRA

state: NY

country: USA

description:
Library name: GBM_3D_5-FU/U_001
RNA-sequencing
L106306_Track-149160

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type


title: NP, EG, NR, rep2

city: Pontedera

first: Giada Graziana

last: Genchi

address: Viale Rinaldo Piaggio 34

country: Italy

institute: Istituto Italiano di Tecnologia

description:
Library name: Sample17
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.

data_processing:
Analysis of RNA sequencing data was performed with a custom in-house written Nextflow Pipeline developed by Omiqa Bioinformatics. This pipeline includes the following steps.
FastQ Quality Control with FastQC (v.0.11.9)
Alignment with STAR to the hg38 reference genome provided by Gencode (v2.7.11b)
Reading Counting with featureCounts (v2.18.0) by setting multi-mapping read counts to true and strandness to reversed, based on an initial quality control step
MultiQC report generation using FastQC, Star and Feature count data (v.1.10.1)
Differential Gene Expression Analysis with DESeq2 (v1.44.0)
Gene Ontology Analysis with clusterProfiler (v4.12.0)
Volcano Plot Generation with EnhancedVolcano (v1.22.0)
Heatmap Generation with pheatmap (v1.0.12)
Assembly: hg38
Supplementary files format and content: data.rds: alignment summary and read counts per gene for all samples
Supplementary files format and content: dds.rds: DEseq dds object
Supplementary files format and content: res.dge.filtered.rds: results of differential gene expression analysis

growth_protocol: SH-SY5Y neuroblastoma cells were maintained in HEPES-buffered proliferative medium within bioreactors under passive thermal conditioning during upload to the International Space Station (ISS). Once on board the ISS, bioreactors were equally distributed between static and dynamic slots of the Kubik incubator, implying exposure to real microgravity with cosmic radiation and simulated Earth gravity with cosmic radiation, respectively. The experiment started when cells were administered with HEPES-buffered differentiative medium (either added or not with nanoparticles at a final concentration of 20 µg/ml) and they were incubated at +37°C. At 48 h from start of incubation in Kubik, the medium was refreshed (either added or not with nanoparticles). At 96 h from start of incubation in Kubik, the cell cultures were rinsed with saline solution, fixed and cold stowed at -80°C. On Earth, cell cultures were exposed to the same thermal profile registered during spaceflight, and they were equally distributed between static and dynamic conditions, implying exposure to Earth gravity without cosmic radiation and simulated microgravity (by rotation on random positioning machine) without cosmic radiation.

extract_protocol:
Total RNA extraction and purification was conducted with MirVana PARIS kit (Ambion) by following the manufacturer’s instructions.
A quantity of 300 ng of total RNA underwent Poly(A) mRNA enrichment with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #7490). RNA library was built by using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7760/E7765).

treatment_protocol: SH-SY5Y were allowed to proliferate in DMEM-F12 medium supplemented with 15 mM HEPES, 10% FBS and 100 U/mL penicillin - 100 μg/mL streptomycin. Differentiation was induced by administration of DMEM-F12 medium supplemented with 15 mM HEPES, 2% FBS, 10 µM retinoic acid, 100 U/mL penicillin - 100 μg/mL streptomycin, and either added or not with 20 µg/ml polydopamine nanoparticles.

value: Neuroblastoma Cell

tag: genotype

value: WT

tag: treatment

value: with nanoparticles, with Earth gravity, without cosmic radiation


title: NNP, EG, NR, rep2

description:
Library name: Sample10
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.

value: without nanoparticles, with Earth gravity, without cosmic radiation


title: GBM_3D_5-FU/U and Carmustine_003

description:
Library name: GBM_3D_5-FU/U and Carmustine_003
RNA-sequencing
L106310_Track-149164


title: MDA-MB-231, DMSO, replicate 2 [RNA-seq]

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

description: Library name: MDA-MB-231 DMSO replicate2 [RNA-seq]

data_processing:
Reads were mapped to the genome (Ensembl GRCh38 release108) using STAR-v2.7.2b with ENCODE option.
RSEM-v1.3.1 was used to calculate read counts and normalization.
Assembly: hg38
Supplementary files format and content: tab separated RSEM results
Supplementary files format and content: bigWig

molecule: polyA RNA

source_name: Breast

growth_protocol: Cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was extracted from cells using Trizol reagent (Invitrogen, 15596026) according to manufacturer’s guide line.
The mRNA-seq libraries were made using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S) and the mRNA Magnetic Isolation Module (NEB, E7490S) following the manufacturer’s instructions.

treatment_protocol: For knockdown experiment, cells at approximately 70-80% confluency were transduced with the lentivirus for 24 h and selected with puromycin (2 μg/ml) for 72 h. For the drug treatment, cells were exposed to DMSO or GSK126 (Tocris Bioscience) for 72 h.

value: Breast

value: Immortalized Breast Cancer

value: DMSO


title: NNP, EG, NR, rep3

description:
Library name: Sample15
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.


title: NP, MG, CR, rep2

description:
Library name: Sample6
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.

value: with nanoparticles, with real microgravity, with cosmic radiation


title: MDA-MB-231, shEZH2, replicate 2 [RNA-seq]

description: Library name: MDA-MB-231 shEZH2 replicate 2 [RNA-seq]


title: MDA-MB-231, shSUZ12 [ATAC-seq]

description: Library name: MDA-MB-231 shSUZ12 [ATAC-seq]

library_source: genomic

data_processing:
All reads were aligned to hg38 / GRCh38 using Bowtie2 with parameters: ‘-k 4 – end-to–end’.
ATAC-seq reads were shifted by +4 bp for the positive strand and -5 bp for the negative strand before peak calling.
Assembly: hg38
Supplementary files format and content: bigWig, NarrowPeak

molecule: genomic DNA

extract_protocol:
50,000 cells were washed with PBS and lysed with lysis buffer (10 mM Tris–HCl pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1% NP-40, 0.01% Triton X-100 and 0.1% Tween-20) for 10min on ice. Isolated nucleus was incubated at 55°C for 1 h with 2x TD buffer [20 mM Tris–HCl pH 7.6, 10 mM MgCl2 and 20% dimethylformamide] and 2.5 μl of transposase.
The transposed DNA was purified using the DNA Clean & Concentrator-5 Kit (Zymo Research, D4003) and then amplified using the NEBNext High-Fidelity 2x PCR Master Mix (NEB, M0541S) for 7 cycles.

treatment_protocol: For knockdown experiment, cells at approximately 70-80% confluency were transduced with the lentivirus for 24 h and selected with puromycin (2 μg/ml) for 72 h.


title: MDA-MB-231, shEZH2, replicate 1 [ATAC-seq]

description: Library name: MDA-MB-231 shEZH2 replicate 1 [ATAC-seq]


title: MDA-MB-231, shE2F1, replicate 1 [ATAC-seq]

description: Library name: MDA-MB-231 shE2F1 replicate 1 [ATAC-seq]


title: NP, MG, CR, rep1

description:
Library name: Sample4
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.


title: MDA-MB-231, GSK126 [ATAC-seq]

description: Library name: MDA-MB-231 GSK126 [ATAC-seq]


title: MDA-MB-231, DMSO [ATAC-seq]

description: Library name: MDA-MB-231 DMSO [ATAC-seq]


title: NNP, MG, CR, rep2

description:
Library name: Sample2
CR: cosmic radiation, EG: Earth gravity, MG: real microgravity, NP: nanoparticles, NNP: no nanoparticles,  NR: no cosmic radiation, SEG: simulated Earth gravity, SMG: simulated microgravity.

value: without nanoparticles, with real microgravity, with cosmic radiation


title: MDA-MB-231, Control shRNA, replicate 2 [RNA-seq]

description: Library name: MDA-MB-231 Control shRNA replicate 2 [RNA-seq]

value: Control shRNA


title: GBM_3D_Control_001

description:
Library name: GBM_3D_Control_001
RNA-sequencing
L106305_Track-149159


title: Patients-Late_group_ATAC-seq#5

first: Hang-Rae

last: Kim

address: 81, Irowon-ro, Gangnam-gu

department: Samsung Precision Genome Mediciine Institute

institute: Samsung Medical Center

description:
Library name: L5
Omni-ATAC

data_processing:
The hg19 reference genome assembly was used for alignment of sequencing data in this study. ATAC-seq samples with paired-end reads were aligned using Bowtie2 (v2.0) software with the default parameter set and the “-X 2000” option. Following alignment, reads were converted to BED format using the “bamToBed” function in BEDtools. The resulting BED files were corrected for Tn5 insertion bias by offsetting coordinates by +4 bp for the positive strand and −5 bp for the negative strand to account for the 9 bp duplication introduced during Tn5 transposition.
Genome browser tracks were generated for each sample using MACS3 software with the “callpeak --bdg” option. The resulting bedGraph files were converted to bigWig format using the “bedGraphToBigWig” function in KentUtils. To ensure consistency across samples, genome browser tracks were normalized by applying a normalization factor calculated from 20 control peaks, as described previously (Shin et al., 2021).
Assembly: hg19
Supplementary files format and content: Normalized bigWig

source_name: Peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from heparinized peripheral blood using a Ficoll–Histopaque gradient (1.077 g/mL; GE Healthcare Life Sciences, Piscataway, NJ, USA). After isolation, cells were resuspended in a freezing medium containing 50% fetal bovine serum (FBS), 10% dimethyl sulfoxide (DMSO), and 40% RPMI-1640 (Invitrogen, Carlsbad, CA, USA) and stored in liquid nitrogen until use. For CD8+ T-cell purification, cryopreserved PBMCs were thawed and labeled with fluorescently conjugated antibodies specific to CD8. Cells were subsequently sorted using the FACSAria III cell sorter (BD Biosciences, San Jose, CA, USA). The purity of sorted populations was verified to exceed 95%.
ATAC-seq library was constructed using viable sorted CD8+ T cells (50,000 cells per reaction). Cells were washed with 1× cold Dulbecco’s phosphate-buffered saline (DPBS) at 4°C and pelleted by centrifugation at 500 × g for 5 min at 4°C. The pellet was resuspended in 50 μL of cold lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) and incubated on ice for 3 min. Following lysis, 1 mL of wash buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) was added. Nuclei were isolated by centrifugation at 500 × g for 10 min at 4°C and resuspended in the transposase reaction mix (25 μL 2× TD buffer, 16.5 μL 1× cold DPBS, 2.5 μL Tn5 transposase [Illumina], 0.5 μL 0.1% Tween-20 [Roche], 0.5 μL 0.01% Digitonin [Promega], and 5 μL nuclease-free water). The reaction was incubated at 37°C for 45 min on a thermomixer set at 1,000 rpm. Post-transposition, DNA was purified using a Qiagen PCR cleanup kit. Library amplification was performed with indexing primers from the Nextera kit (Illumina, San Diego, CA, USA). The optimal number of PCR cycles for each sample was determined via qPCR to avoid over-amplification. Final libraries were quantified using a Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and verified with the KAPA Library Quantification Kit (Roche Applied Science, Basel, Switzerland). Indexed libraries were pooled and sequenced on an Illumina NextSeq6000 platform using a paired-end 150 bp read strategy.

value: Peripheral blood

value: CD8+ T cell

tag: disease state

value: Late


title: GBM_3D_Control_003

description:
Library name: GBM_3D_Control_003
RNA-sequencing
L106309_Track-149163


title: GBM_3D_Carmustine_002

description:
Library name: GBM_3D_Carmustine_002
RNA-sequencing
L106308_Track-149162


title: MDA-MB-231, shE2F1, replicate 1 [RNA-seq]

description: Library name: MDA-MB-231 shE2F1 replicate 1 [RNA-seq]


title: MDA-MB-231, GSK126, replicate 2 [RNA-seq]

description: Library name: MDA-MB-231 GSK126 replicate2 [RNA-seq]

value: GSK126, 1μM


title: Patients-Late_group_ATAC-seq#3

description:
Library name: L3
Omni-ATAC


title: MDA-MB-231, shE2F1, replicate 2 [RNA-seq]

description: Library name: MDA-MB-231 shE2F1 replicate 2 [RNA-seq]


title: Patients-Late_group_ATAC-seq#6

description:
Library name: L6
Omni-ATAC


title: Patients-Late_group_ATAC-seq#4

description:
Library name: L4
Omni-ATAC


title: MDA-MB-231, Control shRNA, replicate 1 [RNA-seq]

description: Library name: MDA-MB-231 Control shRNA replicate 1 [RNA-seq]


title: MDA-MB-231, shEZH2, replicate 2 [ATAC-seq]

description: Library name: MDA-MB-231 shEZH2 replicate 2 [ATAC-seq]


title: Patients-Late_group_ATAC-seq#2

description:
Library name: L2
Omni-ATAC


title: MDA-MB-231, Control shRNA, replicate 2 [ATAC-seq]

description: Library name: MDA-MB-231 Control shRNA replicate 2 [ATAC-seq]


title: MDA-MB-231, shE2F1, replicate 2 [ATAC-seq]

description: Library name: MDA-MB-231 shE2F1 replicate 2 [ATAC-seq]


title: Patients-Early_group_ATAC-seq#7

description:
Library name: E7
Omni-ATAC

value: Early


title: Patients-Early_group_ATAC-seq#9

description:
Library name: E9
Omni-ATAC


title: Patients-Early_group_ATAC-seq#8

description:
Library name: E8
Omni-ATAC


title: MDA-MB-231, Control shRNA, replicate 1 [ATAC-seq]

description: Library name: MDA-MB-231 Control shRNA replicate 1 [ATAC-seq]


title: Patients-Early_group_ATAC-seq#6

description:
Library name: E6
Omni-ATAC


title: MDA-MB-231, shEZH2, replicate 1 [RNA-seq]

description: Library name: MDA-MB-231 shEZH2 replicate 1 [RNA-seq]


title: Patients-Late_group_ATAC-seq#1

description:
Library name: L1
Omni-ATAC


title: Patients-Early_group_ATAC-seq#2

description:
Library name: E2
Omni-ATAC


title: Patients-Early_group_ATAC-seq#10

description:
Library name: E10
Omni-ATAC


title: Patients-Early_group_ATAC-seq#11

description:
Library name: E11
Omni-ATAC


title: Patients-Early_group_ATAC-seq#5

description:
Library name: E5
Omni-ATAC


title: Patients-Early_group_ATAC-seq#3

description:
Library name: E3
Omni-ATAC


title: Patients-Early_group_ATAC-seq#1

description:
Library name: E1
Omni-ATAC


title: Healthy_group#6

description:
Library name: Second_H6
10x genomics

library_source: transcriptomic single cell

data_processing:
All cell barcodes and gene expression levels were compiled in a table format using Cell Ranger-6.1.1 (10x Genomics, Pleasanton, CA, USA).
Before analyzing the data, we ensured quality control of the cells across donors, sorting them by batch. For the first batch, we chosen cells with nFeature_RNA counts between 500 and 3,000, and nCount_RNA counts between 1,000 and 7,500. For the second batch, cells were selected based on criteria included nFeature_RNA counts ranging from 1,000 to 3,000, and nCount_RNA counts from 2,500 to 10,000. We normalized the gene expression data for each batch using the scTransform method and integrated the batches through reciprocal principal component analysis (rPCA) using 3,000 variable protein-coding genes, except immunoglobulin and T cell receptor genes. Following this, we performed PCA and Uniform Manifold Approximation and Projection (UMAP) to reduce the high-dimensional data and calculate cell distances using options ‘dims= 1:20’ through the RunPCA, RunUMAP, and FindNeighbors functions in Seurat R-package. Clusters were identified using the Louvain method with the FindClusters in Seurat R-package. For PBMC subset analysis, cells were reprocessed using the subset functions, followed by a sequential application of RunPCA, RunUMAP, FindNeighbors, and FindClusters functions in Seurat R-package.
Assembly: Human hg38
Supplementary files format and content: Cell Ranger software output files including Tab-Separated values files and matrix files(barcodes.tsv, features.tsv, matrix.mtx)

extract_protocol:
The biopsy proven IgAN patients older than 20 years who donated kidney tissue, blood and urine samples to the SNUH human biobank from 2006 to 2019 were included. Healthy subjects with eGFR ≥ 60 mL/min/1.73 m2 were selected as healthy controls. For the analysis of scRNA-seq, 17 patients were selected and the patients were divided into late- and early-stage according to the eGFR value, measured at the time of sample of peripheral blood. Blood samples were collected from a cohort of 26 donors consisting of 17 IgAN patients and 9 volunteer healthy donors and peripheral blood mononuclear cells (PBMCs) were purified using a Ficoll–Histopaque gradient (1.077 g/mL; GE Healthcare Life Sciences, Piscataway, NJ, USA). The samples were stored in liquid nitrogen until analysis, preserved in a freezing medium containing 50% fetal bovine serum. Live PBMCs were subsequently isolated using BD FACSAria™ III (BD Biosciences, Franklin Lakes, NJ, USA).
Among the 26 subjects, 8 scRNA-Seq libraries were prepared using Chromium Next GEM Single Cell 5' Reagent Kits v1.1 (10x Genomics, Pleasanton, CA, USA) (refer to first batch), while the remaining 18 were processed using Chromium Next GEM Single Cell 5’ Reagent Kits v2.0 (10x Genomics, Pleasanton, CA, USA) (refer to second batch).

value: Healthy

tag: batch

value: Second


title: Patients-Early_group#9

description:
Library name: Second_E9
10x genomics


title: Patients-Early_group#10

description:
Library name: Second_E10
10x genomics


title: M. extorquens AM1, Am03, RNA-seq, methanol 2.5%, replicate 2

city: Ulsan

first: Donghyuk

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

institute: UNIST

description:
Library name: ME_AM1_Am03_2_M_25
Column names in processed data files: Am03_Me2.5_2

library_source: other

data_processing:
Raw RNA-seq reads were first evaluated for quality using FastQC v0.12.1. Adapter trimming and quality filtering were performed using Trimmomatic v0.32 with the following parameters: -phred33 LEADING:3 TRAILING:3 CROP:40 MINLEN:40. To remove residual rRNA reads, computational rRNA removal was carried out using the STAR aligner v2.7.10b by first generating an index of rRNA sequences (--runMode genomeGenerate, --genomeSAindexNbases 14) and aligning reads with parameters: --outFilterMismatchNmax 3, --outFilterMultimapNmax 10, --outSAMprimaryFlag AllBestScore, --alignIntronMax 1, --outReadsUnmapped Fastx. Non-rRNA reads were then mapped to each strain’s reference genome (generated via breseq v0.36.1) using STAR with genome-specific indices (--sjdbOverhang 39) and default alignment parameters. The resulting BAM files were sorted using SAMtools v1.19.2, and read counts per gene were obtained using the ‘summarizeOverlaps’ function in R (GenomicAlignments package). Differential expression analysis was performed with DESeq2 v1.36, using a model that incorporated interaction terms to evaluate both strain and methanol concentration effects (design = ~ strains_group * methanol). Normalization was conducted using DESeq2’s size factor estimation. Genes with adjusted p-value < 0.05 and |log₂FoldChange| > 1 were considered significantly differentially expressed.
Assembly: GCF_000022685.1
Supplementary files format and content: Tab-delimited text file containing DESeq2 normalized gene-level counts for all samples.
Supplementary files format and content: Tab-delimited text file including TPM (Transcripts Per Million) values for all genes across all samples, used for relative expression comparison.
Supplementary files format and content: Tab-delimited text file containing differential expression results based on interaction terms between strain and methanol concentration. Includes log2 fold change, p-value, and adjusted p-value for each gene.

molecule: other

organism: Methylorubrum extorquens

source_name: bacterial culture

growth_protocol: Cells were grown in minimal medium with 0.5% or 2.5% methanol as the sole carbon source at 30°C with shaking.

extract_protocol:
The cell culture was treated with the RNAprotect reagent (Qiagen).
RNA libraries were prepared using KAPA RNA Hyper Prep kit for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a Qubit 4.0 (Thermo Scientific Inc., Wilmington, DE, USA).

tag: strain

value: bacterial culture

value: adapted strain (Am03)


title: Patients-Early_group_ATAC-seq#4

description:
Library name: E4
Omni-ATAC


title: M. extorquens AM1, Am05, RNA-seq, methanol 2.5%, replicate 1

description:
Library name: ME_AM1_Am05_1_M_25
Column names in processed data files: Am05_Me2.5_1

value: adapted strain (Am05)


title: Healthy_group#8

description:
Library name: Second_H8
10x genomics


title: M. extorquens AM1, Am05, RNA-seq, methanol 2.5%, replicate 2

description:
Library name: ME_AM1_Am05_2_M_25
Column names in processed data files: Am05_Me2.5_2


title: Healthy_group#9

description:
Library name: Second_H9
10x genomics


title: M. extorquens AM1, Am04, RNA-seq, methanol 2.5%, replicate 2

description:
Library name: ME_AM1_Am04_2_M_25
Column names in processed data files: Am04_Me2.5_2

value: adapted strain (Am04)


title: Patients-Early_group#5

description:
Library name: Second_E5
10x genomics


title: Patients-Early_group#6

description:
Library name: Second_E6
10x genomics


title: Healthy_group#5

description:
Library name: Second_H5
10x genomics


title: Healthy_group#3

description:
Library name: First_H3
10x genomics

value: First


title: Patients-Early_group#11

description:
Library name: Second_E11
10x genomics


title: Healthy_group#1

description:
Library name: First_H1
10x genomics


title: Healthy_group#7

description:
Library name: Second_H7
10x genomics


title: Healthy_group#2

description:
Library name: First_H2
10x genomics


title: Patients-Early_group#4

description:
Library name: Second_E4
10x genomics


title: Healthy_group#4

description:
Library name: First_H4
10x genomics


title: Patients-Early_group#3

description:
Library name: Second_E3
10x genomics


title: M. extorquens AM1, Am02, RNA-seq, methanol 2.5%, replicate 2

description:
Library name: ME_AM1_Am02_2_M_25
Column names in processed data files: Am02_Me2.5_2

value: adapted strain (Am02)


title: Patients-Early_group#8

description:
Library name: Second_E8
10x genomics


title: M. extorquens AM1, Am04, RNA-seq, methanol 2.5%, replicate 1

description:
Library name: ME_AM1_Am04_1_M_25
Column names in processed data files: Am04_Me2.5_1


title: M. extorquens AM1, Am02, RNA-seq, methanol 2.5%, replicate 1

description:
Library name: ME_AM1_Am02_1_M_25
Column names in processed data files: Am02_Me2.5_1


title: M. extorquens AM1, Am03, RNA-seq, methanol 2.5%, replicate 1

description:
Library name: ME_AM1_Am03_1_M_25
Column names in processed data files: Am03_Me2.5_1


title: Patients-Early_group#1

description:
Library name: First_E1
10x genomics


title: M. extorquens AM1, Am01, RNA-seq, methanol 2.5%, replicate 1

description:
Library name: ME_AM1_Am01_1_M_25
Column names in processed data files: Am01_Me2.5_1

value: adapted strain (Am01)


title: M. extorquens AM1, wt, RNA-seq, methanol 0.5%, replicate 2

description:
Library name: ME_AM1_wt_2_M_05
Column names in processed data files: WT_Me0.5_2

value: wild-type


title: M. extorquens AM1, wt, RNA-seq, methanol 0.5%, replicate 1

description:
Library name: ME_AM1_wt_1_M_05
Column names in processed data files: WT_Me0.5_1


title: Patients-Early_group#7

description:
Library name: Second_E7
10x genomics


title: Control experiment (replicate 1), Drosophila neural stem cells expressing Dam fused to RpII215

city: Portugal

first: Catarina

middle: CF

last: Homem

address: Rua Campo Mártires da Pátria, 130

country: Portugal

institute: CEDOC - NMS

description: Library name: neuroblast_Dam PolII_replicate 1

data_processing:
Targeted DamID results were analysed using the pipeline described by Marshal and Brand, 2015 (damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets).
Assembly: Dm6
Supplementary files format and content: Processed Targeted DamID data is included as bedgraph files with scores representing log2 Dam-RNA Pol II/Dam-only.

organism: Drosophila melanogaster

source_name: larval brain

growth_protocol: Drosophila melanogaster were grown under standard conditions at either 18, 25 and 29 degrees Celsius.

extract_protocol: Adaptors were ligated to DpnI-digested DNA followed by DpnII digestion, PCR amplification, sonication, and adaptors removal. Libraries were generated by Novogene, according to their how protocol. Sequencing was performed using Illumina NovaSeq 6000 by Novogene.

treatment_protocol: Flies were moved from 18 to 29 degrees Celsius for 24 hours prior to brain dissection, allowing for the expression of Dam-fusion protein.

value: larval brain

value: neural stem cells


title: Patients-Late_group#6

description:
Library name: Second_L6
10x genomics

value: Peripheral blood


title: Control experiment (replicate 2), Drosophila neural stem cells expressing Dam fused to RpII215

description: Library name: neuroblast_DamPol II_replicate 2


title: Patients-Late_group#4

description:
Library name: Second_L4
10x genomics


title: Control experiment (replicate 1), Drosophila neural stem cells expressing free-Dam protein

description: Library name: neuroblast_Dam_replicate 1


title: M. extorquens AM1, Am05, RNA-seq, methanol 0.5%, replicate 2

description:
Library name: ME_AM1_Am05_2_M_05
Column names in processed data files: Am05_Me0.5_2


title: M. extorquens AM1, Am01, RNA-seq, methanol 2.5%, replicate 2

description:
Library name: ME_AM1_Am01_2_M_25
Column names in processed data files: Am01_Me2.5_2


title: Patients-Early_group#2

description:
Library name: First_E2
10x genomics


title: Patients-Late_group#5

description:
Library name: Second_L5
10x genomics


title: M. extorquens AM1, Am04, RNA-seq, methanol 0.5%, replicate 1

description:
Library name: ME_AM1_Am04_1_M_05
Column names in processed data files: Am04_Me0.5_1


title: M. extorquens AM1, Am04, RNA-seq, methanol 0.5%, replicate 2

description:
Library name: ME_AM1_Am04_2_M_05
Column names in processed data files: Am04_Me0.5_2


title: M. extorquens AM1, Am05, RNA-seq, methanol 0.5%, replicate 1

description:
Library name: ME_AM1_Am05_1_M_05
Column names in processed data files: Am05_Me0.5_1


title: ZYY112 B16-OVA tumor cDC1s; day 21

type: RNA

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

description: B16-OVA tumor cDC1s; day 21

hyb_protocol: Labeled cDNA was included in a hybridization mix that was incubated on the Clariom S mouse array for 16 hours at 45◦c while rotating at 60 rpm.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

organism: Mus musculus

source_name: Intraumoral cDC1s  from B16-OVA tumor-bearing mice at 21 days after tumor inoculation

label_protocol: High-quality RNA was processed using Thermo Fisher (Affymetrix) Whole Transcript (WT) Plus assay kit

growth_protocol: Intratumoral cDC1s were sorted from B16-OVA tumor-bearing mice, followed by microarray analysis

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.


title: VCaP, polished, full-length

city: Chicago

first: Rendong

last: Yang

state: IL

address: 420 E Superior St

department: Urology

institute: Northwestern University

data_processing:
The library was sequenced on the Sequel platform. PacBio reads were processed through the IsoSeq3(v3.1.0) pipeline and the PacBio Isoseq transcripts were mapped using minimap2. Unique transcripts isoforms and their abuandance were obtained by collapse_isoforms_by_sam.py and get_abundance_post_collapse.py from Cupcake ToFU.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts of full-length reads for each Sample
Library strategy: Iso-seq

source_name: VCaP

extract_protocol: Total RNA  of 6 cell lines were extracted  using Promega ReliaPrep RNA Cell system(Z6011). 3' Race was done using 5'/3' RACE Kit, 2nd Generation (Roche). One microgram of total RNA was used for reverse transcription step with olig-anchor primer 5’-GACCACGCGTATCGATGTCGACTTTTTTTTTTTTTTTTV-3’ according to the manufacturer's instructions. One microliter  of the RT product was used for the subsequent PCR reaction using IGF1-AS1 exon1 specific forward primer (5'-ACTATGTTTCAGCGGCTGGT-3') and the PCR anchor reverse primer in the kit(5’-GACCACGCGTATCGATGTCGAC-3’). The PCR product was cleaned using a PCR cleaning kit(Qiagen) and submitted for PacBio sequencing.

value: VCaP

value: epithelial cell

value: WT


title: Control experiment (replicate 2), Drosophila neural stem cells expressing free-Dam protein

description: Library name: neuroblast_Dam_replicate 2


title: ZYY110 B16-OVA tumor cDC1s; day 21

description: B16-OVA tumor cDC1s; day 21

value: Intraumoral cDC1s  from B16-OVA tumor-bearing mice at 21 days after tumor inoculation


title: M. extorquens AM1, Am03, RNA-seq, methanol 0.5%, replicate 2

description:
Library name: ME_AM1_Am03_2_M_05
Column names in processed data files: Am03_Me0.5_2


title: hgcOPT_s5

first: Yong

last: Cheng

department: Hematology

institute: St. Jude Children's Reserach Hospital

description: Library name: hgcOPT_s5-captureC

data_processing:
HicPro (2.11.1) was used to map reads to their LV-inserted customized genome
Interactions were called using ChiCMaxima_Caller.r with a combinations of -w (window_size 10, 20, 30, 50) and -s (loess_span 0.01 and 0.05) parameters. Interactions were then filtered with (1) read pairs >=5; (2) interaction distance between 2.5kb and 500kb. (3) keep top 25% interactions based on enrichment score.
Assembly: hg19
Supplementary files format and content: bedpe
Library strategy: Capture Hi-C

source_name: Jurkat

growth_protocol: RPMI, 10%FBS, 1x Anti-anti. Cells were cultured at 37C at 5% CO2

extract_protocol:
Cultured cells were cross-linked in 2% formaldehyde for 10 min at room temperature with rotation. After quenching, chromatin was digested  using DpnII, then religated using T4 ligase, and sonicated using a E220 Focused-ultrasonicator (Covaris).
capure was performed using KAPA HyperCapture Kit (Roche)

value: Jurkat

value: CTCF-LV clone


title: Patients-Late_group#2

description:
Library name: First_L2
10x genomics

value: Late


title: Patients-Late_group#3

description:
Library name: Second_L3
10x genomics

value: Second


title: H727, polished, full-length


title: Patients-Late_group#1

description:
Library name: First_L1
10x genomics


title: M. extorquens AM1, Am03, RNA-seq, methanol 0.5%, replicate 1

description:
Library name: ME_AM1_Am03_1_M_05
Column names in processed data files: Am03_Me0.5_1

value: bacterial culture

value: adapted strain (Am03)


title: dCTCF_sc4

description: Library name: dCTCF_sc4-captureC

value: dCTCF-LV clone


title: ZYY103 B16-OVA tumor cDC1s; day 7

description: B16-OVA tumor cDC1s; day 7

source_name: Intraumoral cDC1s  from B16-OVA tumor-bearing mice at 7 days after tumor inoculation


title: dCTCF_sc3

description: Library name: dCTCF_sc3-captureC


title: ZYY102 B16-OVA tumor cDC1s; day 7

description: B16-OVA tumor cDC1s; day 7

value: Intraumoral cDC1s  from B16-OVA tumor-bearing mice at 7 days after tumor inoculation


title: hgcOPT_s22

description: Library name: hgcOPT_s22-captureC


title: ZYY101 B16-OVA tumor cDC1s; day 7

description: B16-OVA tumor cDC1s; day 7


title: M. extorquens AM1, Am02, RNA-seq, methanol 0.5%, replicate 1

description:
Library name: ME_AM1_Am02_1_M_05
Column names in processed data files: Am02_Me0.5_1

value: adapted strain (Am02)


title: ZYY104 B16-OVA tumor cDC1s; day 7

description: B16-OVA tumor cDC1s; day 7


title: ZYY109 B16-OVA tumor cDC1s; day 21

description: B16-OVA tumor cDC1s; day 21


title: M. extorquens AM1, Am02, RNA-seq, methanol 0.5%, replicate 2

description:
Library name: ME_AM1_Am02_2_M_05
Column names in processed data files: Am02_Me0.5_2


title: M. extorquens AM1, Am01, RNA-seq, methanol 0.5%, replicate 1

description:
Library name: ME_AM1_Am01_1_M_05
Column names in processed data files: Am01_Me0.5_1

value: adapted strain (Am01)


title: 20copy

description: Library name: 20copy-captureC


title: cDC1_TMRM_high_2

source_name: Splenic TMRM/MGhi cDC1 from naïve WT mice

growth_protocol: Splenic TMRM/MGhi or TMRM/MGlo cDC1, or TMRM/MGhi or TMRM/MGlo+DN cDC2 were sorted from WT mice and followed by microarray analysis


title: M. extorquens AM1, Am01, RNA-seq, methanol 0.5%, replicate 2

description:
Library name: ME_AM1_Am01_2_M_05
Column names in processed data files: Am01_Me0.5_2


title: cDC1_TMRM_high_3


title: dCTCF_sc13

description: Library name: dCTCF_sc13-captureC


title: 2659996_Jurkat_atac_rep_2

description: Library name: Jurkat_atac_rep_2

data_processing:
Adapter sequences were trimmed by skewer. BWA mem mapping to hg19
Duplicated reads were removed using samtools. Bw files were generated using  --normalizeUsing RPGC
Assembly: hg19
Supplementary files format and content: bigwiggle

extract_protocol:
DNAs were cleaned up with Zymo DNA Clean and Concentration kit.
PCR amplification using 2x NEBNext Master mix

treatment_protocol: cells were permeobilized and incubated with Tn5 for 30mins.


title: cDC1_TMRM_low_4

source_name: Splenic TMRM/MGlo cDC1 from naïve WT mice


title: 2659995_Jurkat_atac_rep_1

description: Library name: Jurkat_atac_rep_1


title: MDA-MB-231, GSK126, replicate 1 [RNA-seq]

description: Library name: MDA-MB-231 GSK126 replicate 1 [RNA-seq]

value: Breast

value: Immortalized Breast Cancer

value: GSK126, 1μM


title: cDC1_TMRM_low_2


title: ZYY111 B16-OVA tumor cDC1s; day 21

description: B16-OVA tumor cDC1s; day 21


title: cDC1_TMRM_high_1


title: 2659993_dCTCF_s13_atac_rep_1

description: Library name: dCTCF_s13_atac_rep_1

value: Stably expressing dCTCF_LV


title: cDC1_TMRM_low_3


title: MDA-MB-231, DMSO, replicate 1 [RNA-seq]

description: Library name: MDA-MB-231 DMSO replicate 1 [RNA-seq]

value: DMSO


title: cDC1_TMRM_low_1


title: 2659994_dCTCF_s13_atac_rep_2

description: Library name: dCTCF_s13_atac_rep_2


title: MDA-MB-231 GSK126 rep1 [RNA-seq]

value: GSK126, 1uM


title: Splenic_cDC1_KO_3

source_name: Splenic cDC1 sorted from CD11c-Cre; OPA1 flox mice bearning B16-OVA tumor

growth_protocol: Intratumoral cDC1/2 or splenic cDC1/2 were sorted from WT or CD11c-Cre; OPA1 flox mice bearing B16-OVA tumor, followed by microarray analysis


title: Splenic_cDC1_KO_2


title: Splenic_cDC1_KO_4


title: MDA-MB-231 DMSO rep1 [RNA-seq]


title: ESI017, APS-LM, 48hr, rep2

city: Cincinnati

first: Aryeh

last: Warmflash

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

description:
Library name: day2_10_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.APS.LM..48hr.

data_processing:
Raw reads (fastq.gz) were quantified using Salmon v1.10.2 in quasi-mapping mode with sequence-specific and GC bias correction enabled.
A precomputed transcriptome index based on the GCA_000001405.15 GRCh38_no_alt_analysis_set reference (hg38 alias) was used, generated using the selective-alignment method (salmon_sa_index:default).
Transcript-level quantification files (quant.sf) were imported into R v4.4.2 using the tximport package and summarized to gene-level counts.
Sample metadata were incorporated to retain experimental condition information, and a combined gene-level count matrix was generated for downstream analysis.
Assembly: GRCh38 (GCA_000001405.15 no_alt_analysis_set, hg38 alias)
Supplementary files format and content: Tab-delimited text files and CSV tables.

growth_protocol: Human pluripotent stem cells (ESI-017) were cultured in mTeSR PLUS medium (STEMCELL Technologies) on Matrigel-coated dishes (Corning, 1:200 in PBS) at 37 °C and 5 % CO₂. Cells were passaged using dispase (1:5 in DMEM/F12) and routinely tested mycoplasma-negative.

extract_protocol:
Cells were dissociated with Accutase, pelleted at 1000 rpm for 4 min, and lysed in Lysis Solution. Pellets were snap-frozen in liquid nitrogen and stored at −80 °C until processing. Total RNA was extracted using the RNAqueous-Micro Total RNA Isolation Kit (Invitrogen) according to the manufacturer’s protocol and stored at −20 °C until library preparation.
RNA libraries for RNA-seq were prepared using the Illumina poly(A)-selected stranded mRNA workflow (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB) following the manufacturer’s protocol. Sequencing was performed as paired-end 2 × 75 bp reads on an Illumina NextSeq 2000 platform by Novogene Corporation Inc.

treatment_protocol:
ESI017 were induced toward primitive-streak-like lineages following Loh et al. 2014 and 2016 protocols.
Day 1 treatments:
• Definitive endoderm DE(a): 100 ng/mL Activin A + 2 µM CHIR99021 in E6.
• Anterior primitive streak (APS): 30 ng/mL Activin A + 20 ng/mL bFGF + 4 µM CHIR99021.
• Mid primitive streak (MPS): 30 ng/mL Activin A + 20 ng/mL bFGF + 40 ng/mL BMP4 + 6 µM CHIR99021.
• Posterior primitive streak (PPS): 20 ng/mL bFGF + 40 ng/mL BMP4 + 6 µM CHIR99021.
Day 2 differentiations:
DE(a) → DE(b): 100 ng/mL Activin A + 250 nM LDN-193189.
APS → PM: 1 µM A-8301 + 20 ng/mL bFGF + 250 nM LDN-193189.
MPS → LM: 1 µM A-8301 + 30 ng/mL BMP4 + 4 µM IWP2.
After 48 h, cells were harvested for RNA extraction.

value: human pluripotent stem cells

value: wild type

value: APS for day1, LM for day2


title: 2659990_dCTCF_s3_atac_rep_2

description: Library name: dCTCF_s3_atac_rep_2

value: Jurkat


title: Splenic_cDC1_KO_1


title: MDA-MB-231 WT E2F1 [ChIP-seq]

data_processing:
Sequencing quality was assessed using FastQC v0.11.5. Illumina adapters were trimmed using cutadapt (v4.5; -e 0.2).
Reads were mapped to the human genome (ensGene_108.GRCh38) using Bowtie2 (v2.5.2; -X2000 --end-to-end). Reads were mapped to a single best-matching location. Reads marked as unmapped, unpaired mates, not primary alignment, reads failing platform quality checks, and PCR duplicates were removed using Picard and Samtools.
Reads in blacklist regions were excluded, and remaining peaks were called using MACS2 (v2.2.9.1; -q 0.01 --broad-cutoff 0.1 with the broad option for histone peaks). Aligned reads were converted to read coverage using the UCSCtoolkit.
Assembly: hg38
Supplementary files format and content: bigWig, NarrowPeak (E2F1 ChIP-seq), BroadPeak (H3K27me3 ChIP-seq)

extract_protocol:
Cells were harvested and washed by ice-cold PBS. Briefly, chromatins were digested by sonication. The digested chromatins were pre-cleared in RIPA buffer [20 mM Tris-HCl pH 8.0, 50 mM NaCl, 2 mM EDTA, 0.01% sodium dodecyl sulfate (SDS), 0.5% sodium deoxycholate and 1% NP-40], supplemented with a protease inhibitor cocktail and 1 mM PMSF for 2 h at 4°C with rotation using with rabbit IgG (Santa Cruz, sc-2027) or mouse IgG (Santa Cruz, sc-2025) on Dynabeads Protein G. The pre-cleared chromatins were incubated with antibodies on beads overnight at 4°C with rotation. The chromatins pulled down on beads were reverse-crosslinked overnight at 65°C in proteinase K (20 mg/ml) and 10% SDS followed by treatment with RNase A for 30 min at room temperature.
The DNA was purified by phenol/chloroform extraction. ChIP-seq libraries were prepared using the ACCEL-NGS 2S PLUS DNA LIBRARY Kit (Swift Bioscience, 28096) following the manufacturer’s instructions.

treatment_protocol: ChIP-seq for E2F1 or H3K27me3 were conducted in MDA-MB-231 cell lines. For knockdown experiment, cells at approximately 70-80% confluency were transduced with the lentivirus for 24 h and selected with puromycin (2 μg/ml) for 72 h. For the drug treatment, cells were exposed to DMSO or GSK126 (Tocris Bioscience) for 72 h.

tag: chip antibody

value: E2F1 (Santa cruz, sc-251)

value: Untreated


title: ESI017, PPS-LM, 48hr, rep2

description:
Library name: day2_12_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.PPS.LM..48hr.

value: PPS for day1, LM for day2


title: ESI017, DE(a)-LM, 48hr, rep2

description:
Library name: day2_9_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.DE.a..LM..48hr.

value: DE(a) for day1, LM for day2


title: ESI017, MPS-LM, 48hr, rep2

description:
Library name: day2_11_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.MPS.LM..48hr.

value: MPS for day1, LM for day2


title: Splenic_cDC1_WT_3

source_name: Splenic cDC1 sorted from WT mice bearning B16-OVA tumor


title: ESI017, mTeSR PLUS Control, 48hr, rep2

description:
Library name: mT_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts..Ctrl

value: mTeSR PLUS for 2 days


title: 2659988_hgcOPT_s22_atac_rep_2

description: Library name: hgcOPT_s22_atac_rep_2

value: Stably expressing CTCF_LV


title: 2659992_dCTCF_s4_atac_rep_2

description: Library name: dCTCF_s4_atac_rep_2


title: 2659989_dCTCF_s3_atac_rep_1

description: Library name: dCTCF_s3_atac_rep_1


title: ESI017, MPS-PM, 48hr, rep2

description:
Library name: day2_7_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.MPS.PM..48hr.

value: MPS for day1, PM for day2


title: 2659991_dCTCF_s4_atac_rep_1

description: Library name: dCTCF_s4_atac_rep_1


title: Splenic_cDC1_WT_2


title: ESI017, PPS-PM, 48hr, rep2

description:
Library name: day2_8_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.PPS.PM..48hr.

value: PPS for day1, PM for day2


title: VEH4

city: Chongqing

first: Zhiyu

last: Ling

address: No.288, Tianwen Avenue

country: China

institute: Chongqin medical university

description: Library name: VEH4

data_processing:
The data generated from Illumina/BGI platform were used forbioinformatics analysis. All of the analyses were performed using an in-housepipeline from Shanghai Applied Protein Technology. The major software andparameters are as follows: a.Quality control; b.Mapping; c.Quantification of gene expression level; d.Differential expression analysis; e.Enrichment analysis; f.Transcription factor analysis; g.PPI analysis; h.AS analysis.
Assembly: mm9
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted from the heart using TRIzol® Reagentaccording the manufacturer’s instructions (Magen). RNA samples weredetected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determinedby an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Onlyqualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib PrepKit (ABclonal, China) following the manufacturer’s instructions. The mRNAwas purified from 1 μg total RNA using oligo (dT) magnetic beads followed byfragmentation carried out using divalent cations at elevated temperatures inABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strandcDNAs were synthesized with random hexamer primers and ReverseTranscriptase (RNase H) using mRNA fragments as templates, followed bysecond-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, anddNTPs. The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligated cDNA wereused for PCR amplification. PCR products were purified (AMPure XP system)and library quality was assessed on an Agilent Bioanalyzer 4150 system.Finally, sequencing was performed with an Illumina Novaseq 6000 /MGISEQ-T7 instrument.

value: heart

value: WT

value: LPS+Vehicle


title: cDC1_TMRM_high_4


title: Splenic_cDC1_WT_1


title: ESI017, PPS-DE(b), 48hr, rep2

description:
Library name: day2_4_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.PPS.DE.b...48hr.

value: PPS for day1, DE(b) for day2


title: ESI017, DE(a)-PM, 48hr, rep2

description:
Library name: day2_5_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.DE.a..PM..48hr.

value: human pluripotent stem cells

value: DE(a) for day1, PM for day2


title: VEH3

description: Library name: VEH3


title: ESI017, APS-PM, 48hr, rep2

description:
Library name: day2_6_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.APS.PM..48hr.

value: wild type

value: APS for day1, PM for day2


title: 2659986_hgcOPT_s5_atac_rep_2

description: Library name: hgcOPT_s5_atac_rep_2

value: Jurkat


title: VEH2

description: Library name: VEH2


title: 2659987_hgcOPT_s22_atac_rep_1

description: Library name: hgcOPT_s22_atac_rep_1


title: VEH5

description: Library name: VEH5


title: 2659985_hgcOPT_s5_atac_rep_1

description: Library name: hgcOPT_s5_atac_rep_1


title: ESI017, APS-DE(b), 48hr, rep2

description:
Library name: day2_2_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.APS.DE.b...48hr.

value: APS for day1, DE(b) for day2


title: ESI017, DE(a)-DE(b), 48hr, rep2

description:
Library name: day2_1_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.DE.a..DE.b...48hr.

value: DE(a) for day1, DE(b) for day2


title: ART5

description: Library name: ART5

value: LPS+ART


title: 2659984_hgcOPT_s4_atac_rep_2

description: Library name: hgcOPT_s4_atac_rep_2


title: ESI017, MPS, 24hr, rep2

description:
Library name: day1_3_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.MPS..24hr.

value: MPS for day1


title: 2659983_hgcOPT_s4_atac_rep_1

description: Library name: hgcOPT_s4_atac_rep_1


title: MDA-MB-231 WT Input [ChIP-seq]

value: Breast

value: Immortalized Breast Cancer

value: Untreated


title: 2659982_20copy_atac_rep_2

description: Library name: 20copy_atac_rep_2

value: Stably expressing CTCF_LV


title: ESI017, mTeSR PLUS Control, 48hr, rep1

description:
Library name: mT
RNASeq1ExpressionMat.csv
column name: counts..Ctrl

value: mTeSR PLUS for 2 days


title: ESI017, APS, 24hr, rep2

description:
Library name: day1_2_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.APS..24hr.

value: APS for day1


title: ESI017, DE(a), 24hr, rep2

description:
Library name: day1_1_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.DE.a...24hr.

value: DE(a) for day1


title: ESI017, MPS-LM, 48hr, rep1

description:
Library name: day2_11
RNASeq1ExpressionMat.csv
column name: counts.MPS.LM..48hr.

value: MPS for day1, LM for day2


title: ESI017, MPS-DE(b), 48hr, rep2

description:
Library name: day2_3_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.MPS.DE.b...48hr.

value: human pluripotent stem cells

value: MPS for day1, DE(b) for day2


title: ART3

description: Library name: ART3

value: heart

value: WT


title: 2659981_20copy_atac_rep_1

description: Library name: 20copy_atac_rep_1

value: Jurkat


title: ESI017, APS-LM, 48hr, rep1

description:
Library name: day2_10
RNASeq1ExpressionMat.csv
column name: counts.APS.LM..48hr.

value: wild type

value: APS for day1, LM for day2


title: ART2

description: Library name: ART2

value: LPS+ART


title: ESI017, PPS-LM, 48hr, rep1

description:
Library name: day2_12
RNASeq1ExpressionMat.csv
column name: counts.PPS.LM..48hr.

value: PPS for day1, LM for day2


title: EA.HY926, LPS+lactate stimulation after ENO1 knockdown with siRNA, rep2

city: Shanghai

first: Xie

middle: xue

last: ru

address: wanyuan road 399

department: Institutes of Biomedical Sciences

institute: Fudan university

data_processing:
Libraries at a final concentration of 10 pM were clustered onto a single read flow cell by cBot and sequenced to 150 bp using an Illumina NovaSeq 6000 instrument (Illumina).
Assembly: Human NCBI genome build 36
Supplementary files format and content: tab-delimited text file included raw counts for each sample

growth_protocol: EA.HY926 cells were cultured in DMEM medium with 10% fetal bovine serum and 1% PS,and maintained in humidified cell incubators in 5% CO2 at 37 °C.

extract_protocol:
Total RNA in cells was extracted using Trizol Reagent,1000ng RNA was used for construction of sequencing libralies.
The TruSeq RNA Sample Preparation Kit (Illumina) was used for library preparation

treatment_protocol: LPS 16h, lactate 3h

value: Endothelial cell

value: ENO1 knockdown

value: EA.HY926, LPS+lactate stimulation after ENO1 knockdown with siRNA , rep2


title: ESI017, PPS, 24hr, rep2

description:
Library name: day1_4_rep
RNASeq1ExpressionMat_repeat.csv
column name: counts.PPS..24hr.

value: PPS for day1


title: scRNA-seq of thioglycollate-elicited peritoneal cells from LysM-S1pr1 KO mice

city: Boston

first: Yueh-Chien

last: Lin

state: Massachusetts

address: 1 Blackfan Circle, Karp Research Building, 12F

department: Vascular Biology Program

institute: Boston Children's Hospital

description:
Library name: KO_Cre_plus
Single-cell RNA sequencing of thioglycollate-elicited peritoneal cells. Downstream analyses focused on neutrophil populations identified based on canonical marker expression.

data_processing:
Raw sequencing data were processed using Cell Ranger for sample demultiplexing, barcode assignment, and UMI counting.
Filtered gene–barcode UMI count matrices were generated for each sample.
Downstream analyses were performed using Seurat.
Assembly: mm10
Supplementary files format and content: Processed data include filtered gene–barcode UMI count matrices in Matrix Market format (matrix.mtx.gz) with accompanying barcode and feature annotation files.
Supplementary files format and content: Additional processed files include cell-level metadata and downstream analysis outputs.

source_name: Peritoneal cavity

growth_protocol: Mice were housed under specific pathogen–free conditions with ad libitum access to food and water.

extract_protocol:
Peritoneal cells were harvested by lavage, filtered to generate single-cell suspensions, and processed for single-cell RNA sequencing.
Single-cell libraries were prepared using the 10x Genomics Chromium platform according to the manufacturer’s instructions.

treatment_protocol: Mice received intraperitoneal injection of thioglycollate broth to elicit inflammatory peritoneal cells prior to sample collection.

value: Peritoneal cavity

value: LysM-S1pr1 knockout

value: Thioglycollate elicitation, 10 h


title: EA.HY926, LPS+lactate stimulation after ENO1 knockdown with siRNA, rep3


title: ESI017, APS-PM, 48hr, rep1

description:
Library name: day2_6
RNASeq1ExpressionMat.csv
column name: counts.APS.PM..48hr.

value: APS for day1, PM for day2


title: ART4

description: Library name: ART4


title: ESI017, DE(a)-LM, 48hr, rep1

description:
Library name: day2_9
RNASeq1ExpressionMat.csv
column name: counts.DE.a..LM..48hr.

value: human pluripotent stem cells

value: DE(a) for day1, LM for day2


title: ESI017, PPS-DE(b), 48hr, rep1

description:
Library name: day2_4
RNASeq1ExpressionMat.csv
column name: counts.PPS.DE.b...48hr.

value: PPS for day1, DE(b) for day2


title: ESI017, APS-DE(b), 48hr, rep1

description:
Library name: day2_2
RNASeq1ExpressionMat.csv
column name: counts.APS.DE.b...48hr.

value: APS for day1, DE(b) for day2


title: ESI017, MPS-PM, 48hr, rep1

description:
Library name: day2_7
RNASeq1ExpressionMat.csv
column name: counts.MPS.PM..48hr.

value: MPS for day1, PM for day2


title: ESI017, DE(a)-DE(b), 48hr, rep1

description:
Library name: day2_1
RNASeq1ExpressionMat.csv
column name: counts.DE.a..DE.b...48hr.

value: wild type

value: DE(a) for day1, DE(b) for day2


title: VEH1

description: Library name: VEH1

value: heart

value: WT

value: LPS+Vehicle


title: ESI017, MPS, 24hr, rep1

description:
Library name: day1_3
RNASeq1ExpressionMat.csv
column name: counts.MPS..24hr.

value: MPS for day1


title: ESI017, DE(a)-PM, 48hr, rep1

description:
Library name: day2_5
RNASeq1ExpressionMat.csv
column name: counts.DE.a..PM..48hr.

value: DE(a) for day1, PM for day2


title: scRNA-seq of thioglycollate-elicited peritoneal cells from S1pr1 GOF mice without Cre

description:
Library name: GOF_Cre_minus
Single-cell RNA sequencing of thioglycollate-elicited peritoneal cells. Downstream analyses focused on neutrophil populations identified based on canonical marker expression.

value: S1pr1 gain-of-function (Cre-negative)


title: ESI017, PPS, 24hr, rep1

description:
Library name: day1_4
RNASeq1ExpressionMat.csv
column name: counts.PPS..24hr.

value: PPS for day1


title: scRNA-seq of thioglycollate-elicited peritoneal cells from S1pr1 floxed mice

description:
Library name: KO_Cre_minus
Single-cell RNA sequencing of thioglycollate-elicited peritoneal cells. Downstream analyses focused on neutrophil populations identified based on canonical marker expression.

value: Peritoneal cavity

value: S1pr1 floxed (Cre-negative)


title: scATACseq of day9 STIA myeloid cells

city: Berlin

first: Gerhard

last: Krönke

address: Virchowweg 11

department: Rheumatology and clinical immunology

country: Germany

institute: Charite Berlin

description: Library name: M_day9

library_source: genomic single cell

data_processing:
Sequencing reads were processed using the Cell Ranger ARC (10x Genomics) and the cellranger atac count function (v2.1.0) pipeline with default parameters to obtain fragment files and count matrices, which were subsequently used as input for ArchR (v1.0.3). Single cell ATAC sequencing (scATACseq) analysis
Assembly: mm10
Supplementary files format and content: scATAC fragment file

source_name: Paw

extract_protocol:
Single-cell (sc) ATAC-seq libraries were generated from sorted CD45+CD11b+Ly6G- cells isolated from synovial tissue of K/BxN serum transfer arthritis (STA) mice at day 0, day 5, and day 9 of disease according to the demonstrated protocol for nuclei isolation (10x Genomics, CG000169 • Rev D).
Isolated nuclei were further processed as described in Chromium Next GEM Single Cell ATAC Reagent Kits v1.1 (10x Genomics, CG000209 Rev A). The library was sequenced by Novogene with a depth of 20,000 reads per nuclei.

treatment_protocol: Mice were injected intraperitoneally with 200 µl of serum from K/BxN arthritic mice. Their well-being was monitored daily and the course of arthritis was evaluated using a clinical score together with the measurement of the hind-paw swelling using a thickness gauges (Peacock). The score for each paw ranged from 0 to 4, with 0 = no signs of inflammation; 1 = minor swelling and reddening of a paw, or affecting only single digits; 2 = moderate swelling and erythema, or affecting multiple digits per paw; 3 = severe swelling and erythema affecting the whole paw; 4 = maximum swelling and erythema and was cumulated to a minimal clinical score of 0 and a maximum of 16. The clinical index gave an indication of inflammation in the paws and was used to follow the course of STA at different timepoints after induction.

value: Paw

value: day 9 after STIA


title: ESI017, PPS-PM, 48hr, rep1

description:
Library name: day2_8
RNASeq1ExpressionMat.csv
column name: counts.PPS.PM..48hr.

value: human pluripotent stem cells

value: PPS for day1, PM for day2


title: ESI017, APS, 24hr, rep1

description:
Library name: day1_2
RNASeq1ExpressionMat.csv
column name: counts.APS..24hr.

value: APS for day1


title: scATACseq of day5 STIA myeloid cells

description: Library name: M_day5

value: day 5 after STIA


title: scATACseq of steady state myeloid cells

description: Library name: M_day0

value: naive


title: scRNA-seq of thioglycollate-elicited peritoneal cells from LysM-S1pr1 GOF mice

description:
Library name: GOF_Cre_plus
Single-cell RNA sequencing of thioglycollate-elicited peritoneal cells. Downstream analyses focused on neutrophil populations identified based on canonical marker expression.

value: LysM-S1pr1 gain-of-function

value: Thioglycollate elicitation, 10 h


title: EA.HY926, ENO1 knockdown with siRNA, rep1

value: Endothelial cell

value: ENO1 knockdown


title: CJ_XC_1027LR_019_L

first: Joshua

middle: D.

last: Campbell

state: MA

address: 72 East Concord Street

institute: Boston University Chobanian & Avedisian School of Medicine

description:
Library name: Patient10, LN
Multiplexed CITE-seq data from Patient10, lymph node

data_processing:
Transcriptomic reads were aligned to the GRCh38-1.2.0 reference genome and quantified using 10X CellRanger.
CITE-seq ADT and HTO reads were examined for antibody-oligonucleotide conjugate specific sequence barcodes through CellRanger’s feature indexing function.
Demultiplexing of HTO-multiplexed samples was achieved through the Seurat HTODemux algorithm.
Cells with high mitochondrial gene expression (>15% of entire gene expression counts), displaying a high level of ambient RNA contamination (> 0.9), or expressing less than 50 antibodies out of the 128-antibody panel were discarded prior to analysis.
Assembly: hg19
Supplementary files format and content: counts
Library strategy: CITE-seq

source_name: Lymph node

extract_protocol:
Cell suspensions were then washed, counted, pooled, concentrated, and subjected to 5′ single-cell RNA sequencing using the Chromium Next GEM Single Cell 5′ Kit v2 and Chromium Next GEM Chip K Single Cell Kit (10x Genomics, Pleasanton, CA, USA), targeting a recovery of 10,000 cells using manufacturer’s protocols. Sequencing libraries were prepared using the Library Construction Kit (10x Genomics, Pleasanton, CA, USA) and sequenced on an Illumina NextSeq 2000. Cells were stained using TotalSeq-C hashtag and CITE-Seq antibodies. Cell suspensions were then washed, counted, pooled, concentrated, and subjected to 5′ single-cell RNA sequencing using the Chromium Next GEM Single Cell 5′ Kit v2 and Chromium Next GEM Chip K Single Cell Kit, targeting a recovery of 10,000 cells.
Sequencing libraries were prepared using the 10X Genomics Library Construction Kit and sequenced on an Illumina NextSeq 2000.

value: Lymph node

value: Immune, epithelial

tag: subject

tag: Sex

value: Male

tag: age

tag: smoking status

value: Current

tag: race

value: Hispanic or Latino


title: EA.HY926, ENO1 knockdown with siRNA, rep3


title: EA.HY926, with LPS+lactate stimulation, rep3

value: WT


title: ESI017, DE(a), 24hr, rep1

description:
Library name: day1_1
RNASeq1ExpressionMat.csv
column name: counts.DE.a...24hr.

value: wild type

value: DE(a) for day1


title: ESI017, MPS-DE(b), 48hr, rep1

description:
Library name: day2_3
RNASeq1ExpressionMat.csv
column name: counts.MPS.DE.b...48hr.

value: human pluripotent stem cells

value: MPS for day1, DE(b) for day2


title: EA.HY926, with LPS+lactate stimulation, rep2


title: CJ_XC_LR_018_T

description:
Library name: Patient 9, Tumor + Normal Lung
Multiplexed CITE-seq data from Patient9, tumor and normal lung

source_name: Tumor and normal lung

value: Tumor and normal lung

value: Former

value: Caucasian


title: RNA-seq of mus musculus: isolated primary clear cell renal carcinoma cells dopamine treated3

first: Junhui

last: Su

address: zhangheng Street

department: Pharmacology

institute: Fudan University

description:
Library name: sample6
Dopa3

data_processing:
input files (FASTQ) are processed and transformed into splicing graphs, and an .rmats file is saved to store information of weighted splicing graphs for each RNA-seq sample.
Assembly: GRCm39

source_name: KVTR cells

extract_protocol:
Total RNA was extracted from the indicated cells using the SMART-Seq HT Kit (Takara Bio) following the manufacturer’s instructions.
RNA-seq libraries were constructed with the DNA Library Prep Kit V2 for Illumina (Vazyme) according to the recommended protocol. Paired-end sequencing (150 bp read length) was performed on an Illumina NovaSeq 6000 platform.

value: KVTR cells

value: dopamine


title: EA.HY926, LPS+lactate stimulation after ENO1 knockdown with siRNA, rep1

value: Endothelial cell


title: CJ_XC_LR_017_T

description:
Library name: Patient 8, Tumor
Multiplexed CITE-seq data from Patient8, tumor

source_name: Tumor

value: Tumor

value: Female

value: Never


title: ART1

description: Library name: ART1

value: heart

value: LPS+ART


title: RNA-seq of mus musculus: isolated primary clear cell renal carcinoma cellsdopamine treated2

description:
Library name: sample5
Dopa2


title: EA.HY926, without stimulation, rep2

value: EA.HY926, without stimulation, rep2


title: CJ_XC_1027LR_020_L

description:
Library name: Patient11, LN
Multiplexed CITE-seq data from Patient11, lymph node

value: Lymph node

value: Immune, epithelial

value: Male


title: CJ_XC_LR_017_L

description:
Library name: Patient 8, LN
Multiplexed CITE-seq data from Patient8, lymph node


title: EA.HY926, with LPS+lactate stimulation, rep1

value: WT


title: RNA-seq of mus musculus: isolated primary clear cell renal carcinoma cells blank3

description:
Library name: sample3
blank3

value: blank


title: XC_CJ_LR_015_T

description:
Library name: Patient 6, Tumor
Multiplexed CITE-seq data from Patient6, tumor


title: CJ_XC_1027LR_020_T

description:
Library name: Patient11, Tumor + Normal Lung
Multiplexed CITE-seq data from Patient11, tumor and normal lung

value: Tumor and normal lung


title: CJ_XC_LR_018_L

description:
Library name: Patient 9, LN
Multiplexed CITE-seq data from Patient9, lymph node

value: Former


title: EA.HY926, without stimulation, rep3

value: EA.HY926, without stimulation, rep3


title: CJ_XC_LR_014_T

description:
Library name: Patient 5, Tumor
Multiplexed CITE-seq data from Patient5, tumor

value: Black or African American


title: RNA-seq of mus musculus: isolated primary clear cell renal carcinoma cells dopamine treated1

description:
Library name: sample4
Dopa1

value: KVTR cells

value: dopamine


title: RNA-seq of mus musculus: isolated primary clear cell renal carcinoma cells blank2

description:
Library name: sample2
blank2


title: CJ_XC_1027LR_019_T

description:
Library name: Patient10, Tumor + Normal Lung
Multiplexed CITE-seq data from Patient10, tumor and normal lung

value: Current

value: Hispanic or Latino


title: MDA-MB-231 shE2F1 replicate 1 [RNA-seq]

data_processing:
Reads were mapped to the genome (Ensembl GRCh38 release108) using STAR-v2.7.2b with ENCODE option.
RSEM-v1.3.1 was used to calculate read counts and normalization.
Assembly: hg38
Supplementary files format and content: tab separated RSEM results
Supplementary files format and content: bigWig

source_name: Breast

extract_protocol:
RNA was extracted from cells using Trizol reagent (Invitrogen, 15596026) according to manufacturer’s guide line.
The mRNA-seq libraries were made using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S) and the mRNA Magnetic Isolation Module (NEB, E7490S) following the manufacturer’s instructions.

value: Breast

value: Immortalized Breast Cancer


title: CJ_XC_LR_014_L

description:
Library name: Patient 5, LN
Multiplexed CITE-seq data from Patient5, lymph node

value: Female

value: Never


title: XC_CJ_LR_016_L

description:
Library name: Patient 7, LN
Multiplexed CITE-seq data from Patient7, lymph node

value: Lymph node


title: XC_CJ_LR_016_T

description:
Library name: Patient 7, Tumor
Multiplexed CITE-seq data from Patient7, tumor

value: Tumor

value: Immune, epithelial


title: EA.HY926, ENO1 knockdown with siRNA, rep2

value: Endothelial cell

value: ENO1 knockdown


title: CJ_XC_LR_012_L

description:
Library name: Patient 3, LN
Multiplexed CITE-seq data from Patient3, lymph node

value: Male

value: Caucasian


title: EA.HY926, without stimulation,rep1

value: WT

value: EA.HY926, without stimulation,rep1


title: sc-seq of mus musculus: isolated primary clear cell renal carcinoma cells PO3

description:
Library name: sample6
PO-harmony.rds

data_processing:
To recover barcodes from each single cell, the raw reads from the barcode libraries were filtered for those containing the designated anchor sequence (“AATCCAGCTAGCTGTGCAGC”) as a prefix to the unique barcode region. For each unique cell barcode identified in scRNA-seq data, all corresponding barcode-labeled reads were grouped. The final clonal identity for each single cell was assigned based on the dominant barcode sequence found in at least 95% of barcode reads for that cell, ensuring robust clonal attribution and enabling direct lineage tracing of cells between pre-treatment and post-treatment conditions. This approach enabled quantification of the degree of clonal contraction or persistence after therapy; for example, barcode recovery from PO tumors allowed the comparison of the number and identity of surviving clones relative to the total clonal pool at baseline. Gene expression matrices were generated from raw sequencing data using CeleScope (v1.5.2). Quality control filters were applied to remove low-quality cells (<30,000 UMIs, <200 or >5,000 genes, >20% mitochondrial reads). Data normalization, identification of highly variable genes, scaling, principal component analysis, clustering, and UMAP visualization were performed using Seurat (v3.1.2).
Assembly: GRCm39
Supplementary files format and content: Harmonized merged PO group sample RDS files provided as “PO-harmony.rds”
Supplementary files format and content: Harmonized merged PR group sample RDS files provided as “PR-harmony.rds”

source_name: tumor

extract_protocol:
For clonal tracing experiments, FACS-sorted GFP-positive KVTR cells, representing approximately 10⁵ unique barcoded clones, were further labeled with a luciferase reporter and orthotopically implanted into syngeneic C57BL/6 mice. Successful engraftment was monitored via imaging, after which tumor-bearing mice were randomized to receive either anti-PD-1 monoclonal antibody (mAb) or IgG control twice weekly over a 21-day course. Tumors were harvested both prior to therapy initiation (PR) and after completion of the 3-week regimen (PO). At each timepoint, tumors were surgically excised, enzymatically dissociated using collagenase IV (Sigma, #C5138) and DNase I (Meilunbio, #MB3069) for 30min at 37°C with agitation, and filtered through a 70µm strainer. GFP⁺PI⁻ live tumor cells were isolated using a BD FACSAria cell sorter (BD Biosciences).
Single-cell suspensions in PBS were loaded onto microwell chips (Singleron Matrix® Single Cell Processing System) for simultaneous construction of barcode and scRNA-seq libraries using the GEXSCOPE® Single Cell RNA Library Kits (Singleron), following the manufacturer’s protocol.

value: tumor


title: MDA-MB-231 shEZH2 replicate 1 [RNA-seq]


title: sc-seq of mus musculus: isolated primary clear cell renal carcinoma cells PO1

description:
Library name: sample4
PO-harmony.rds

value: after completion of the 3-week regimen (PO)


title: MDA-MB-231 Control shRNA replicate 2 [RNA-seq]

value: Control shRNA


title: MDA-MB-231 shEZH2 replicate 2 [RNA-seq]


title: M-CSF MACRO 2 Days, EGR1 (CUT&RUN)

city: PHILADELPHIA

first: Sandra

last: Deliard

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

description: Library name: MCSF_MACRO_2_days_CR

data_processing:
For analysis, sequencing files were demultiplexed and QC was performed on FASTQ files with FASTQC. Adaptors were trimmed from sequencing reads with TrimGalore, which were then aligned to the human genome (hg19) with BWA-MEM. Alignment files were sorted, filtered for a mapping quality > 10. Peak calling was done with MACS2. Motif analysis on peaks was done using MEME-ChIP
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: macrophage

extract_protocol:
CUT&RUN was performed according to the published protocol by Skene and Henikoff with some modifications. Experiments were performed with primary monocytes and macrophages using antibodies for CTCF (Cell Signaling), SMC1 (Bethyl), PU.1 (Santa Cruz), and EGR1 (Bethyl). Approximately 250-500, 000 cells were used. For digestion, 1.5uL of pAG-mnase (Cell Signaling) was used. The alternative DNA extraction method was used to extract the final DNA product.
Sequencing libraries were generated with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

value: macrophage


title: CJ_XC_LR_013_T

description:
Library name: Patient 4, Tumor
Multiplexed CITE-seq data from Patient4, tumor

value: Current

value: Native American


title: CJ_XC_LR_010_TL

description:
Library name: Patient 1, LN + Normal Lung
Multiplexed CITE-seq data from Patient1, tumor and lymph node

source_name: Tumor and lymph node

value: Tumor and lymph node


title: MDA-MB-231 shE2F1 replicate 2 [RNA-seq]

value: Breast

value: Immortalized Breast Cancer


title: RNA-seq of mus musculus: isolated primary clear cell renal carcinoma cells blank1

description:
Library name: sample1
blank1

value: KVTR cells

value: blank


title: KT-47 Resistance 1, H3K4me3_1

first: Hongjian

last: Jin

department: Center for Applied Bioinformatics

description: Library name: 3140071_CMJ_R_H3K4me3_052

data_processing:
Trim_Galore(v0.4.4) is used to quality trim 3’ reads raw reads with the cutadapt (DOI: 10.14806/ej.17.1.200) program. A default quality score cutoff of Q20 is used and first 15bp from both paired-end reads were removed due to Tn5 bias("--paired --clip_R1 15 --clip_R2 15").
Trimmed reads are mapped to the hg38 reference genome by bwa(v0.7.12-r1039, PMID: 19451168) and converted to a bam file(a binary version of sam file) by samtools(v1.2, PMID: 19505943).
biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) was used to mark duplicated reads and non-duplicated reads were kept by samtools (parameter “-q 1 -F 1804” version 1.2). All samples have more than 5 million fragments as suggested by CUT&RUN protocol paper.
We generated bigwig files using the center 80 bp of fragments smaller than 2000 bp and normalized to 10 million fragments. We confirmed the replicability between replicates.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: kidney tumor

growth_protocol: KT-47 was heterotopically engrafted into the flanks of C.B-17 scid (C.B-Igh-1b/IcrTac-Prkdcscid) mice (6–8 weeks old; Taconic Farms, Hudson, NY, USA) without cell culture intermediates.

extract_protocol:
Snap frozen PDX tumor chunks from either KT47 Pretreatment or KT47R1 were using a dounce homogenizer.  Homogenized cells were processed according to manufacturer protocol using the EpiCypher CUTANA CUT&TAG assay kit (cat# 14-11-2) using 100,000 nuclei per reaction per sample.
CUT&TAG was performed by homogenizing snap frozen PDX tumor chunks from either KT47 Pretreatment or KT47R1 using a dounce homogenizer.  Homogenized cells were processed according to manufacturer protocol using the EpiCypher CUTANA CUT&TAG assay kit (cat# 14-11-2) using 100,000 nuclei per reaction per sample.  Antibodies include: IgG control (EpiCypher cat# 13-0042), H3K27ac (EpiCypher cat# 13-0059), H3K27me3 (EpiCypher cat# 13-0055), H3K4me1 (EpiCypher cat# EpiCypher 13-0057), H3K4me3 (Active Motif cat# 39159), H3K9me1 (Invitrogen cat# MA5-333-85), and H3K9me3 (Invitrogen cat# 720093).

treatment_protocol: Tumor-bearing mice were treated with actinomycin-D (0.30 mg/kg intraperitoneal q21 days x 3; Baxter Oncology, Lebanon, NJ), vincristine (1 mg/kg intraperitoneal q7 days x 8; Hospira, Lake Forest, IL), and doxorubicin (4 mg/kg IV q7 days x 8; Pfizer, New York, NY, USA). Three timepoints were selected as experimental groups during this treatment schema for further inquiry: pre-treatment (no VAD chemotherapy exposure in WTPDX model), pre-resistance (VAD chemotherapy exposure without evidence of complete chemoresistance), and resistance (VAD chemotherapy exposure with complete chemotherapy resistance documented). The resistance timepoint was separated into resistance clone 1 and resistance clone 2 (KT-47R1, KT-47R2) which were originally derived from two different mice.

value: kidney tumor

value: Wilms tumor patient-derived xenograft

value: VAD


title: M-CSF MACRO 5 Days, EGR1 (CUT&RUN)

description: Library name: MCSF_MACRO_5_days_CR


title: CJ_XC_LR_012_TL

description:
Library name: Patient 3, Tumor
Multiplexed CITE-seq data from Patient3, tumor and lymph node

value: Tumor

value: Immune, epithelial

value: Male

value: Former

value: Caucasian


title: GM-CSF MACRO 5 Days, EGR1 (CUT&RUN)

description: Library name: GMCSF_MACRO_5_days_CR


title: sc-seq of mus musculus: isolated primary clear cell renal carcinoma cells PO2

description:
Library name: sample5
PO-harmony.rds

value: tumor

value: after completion of the 3-week regimen (PO)


title: sc-seq of mus musculus: isolated primary clear cell renal carcinoma cells PR2

description:
Library name: sample2
PR-harmony.rds

value: prior to therapy initiation (PR)


title: XC_CJ_LR_015_L

description:
Library name: Patient 6, LN
Multiplexed CITE-seq data from Patient6, lymph node

value: Lymph node


title: GM-CSF MACRO 2 Days, EGR1 (CUT&RUN)

description: Library name: GMCSF_MACRO_2_days_CR

value: macrophage


title: KT-47 Resistance 1, H3K4me3_2

description: Library name: 3140073_CMJ_R_H3K4me3_054


title: MDA-MB-231 GSK126 E2F1 [ChIP-seq]

value: Breast

value: E2F1 (Santa cruz, sc-251)

value: GSK126, 1uM


title: MDA-MB-231 Control shRNA replicate 1 [RNA-seq]

value: Immortalized Breast Cancer

value: Control shRNA


title: KT-47 Resistance 1, H3K4me1_2

description: Library name: 3140064_CMJ_R_H3K4me1_045

value: kidney tumor

value: Wilms tumor patient-derived xenograft


title: sc-seq of mus musculus: isolated primary clear cell renal carcinoma cells PR3

description:
Library name: sample3
PR-harmony.rds


title: KT-47 Resistance 1, H3K4me1_1

description: Library name: 3140062_CMJ_R_H3K4me1_043

value: VAD


title: MDA-MB-231 shE2F1 H3K27me3 [ChIP-seq]

value: H3K27me3 (Active motif, 39155)


title: sc-seq of mus musculus: isolated primary clear cell renal carcinoma cells PR1

description:
Library name: sample1
PR-harmony.rds


title: KT-47 Resistance 1, H3K9me3_1

description: Library name: 3140059_CMJ_R_H3K9me3_040


title: MDA-MB-231 DMSO E2F1 [ChIP-seq]

value: DMSO


title: KT-47 Resistance 1, H3K9me1_1

description: Library name: 3140056_CMJ_R_H3K9me1_037


title: C2C12 cells, Day4, 4-PBA, rep2

city: Yamaguchi

first: Kana

last: Tominaga

address: 1-1-1 Minami-kogushi, Ube

country: Japan

institute: Yamaguchi University Graduate School of Medicine

description:
Library name: Sample6
Column name in raw_counts_C2C12.txt: 4PBA_D4_rep2

data_processing:
CLC Genomics Workbench 23.0.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC Genomics Workbench (parameter- Quality limit = 0.05).
Trimmed sequence reads were mapped to Mus musculus (GRCm39) release-110 database using CLC Genomics Workbench (parameters-Mismatch cost = 2, Insertion cost =  3, Deletion cost = 3, Length faction =  0.8, similarity fraction = 0.8).
Read count extraction counted according to default settings using a CLC Genomics Workbench.
Assembly: GRCm39 release-110
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

source_name: skeletal muscle

growth_protocol: C2C12 cells were cultured in growth medium containing Dulbecco's Modified Eagle Medium (DMEM) containing 10 % fetal bovine serum (FBS), 100 units/ml penicillin, and 100 µg/ml streptomycin. Cell lines were cultured in a humidified atmosphere at 37C in 5% CO2.

extract_protocol:
Total RNA using an Maxwell RSC simply RNA　Cell　Kit　(Promega), followed by DNase treatment. 100ng of total RNA was used for generate cDNA libraries for Illumina sequencing.
RNA Libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacture's protocol.

treatment_protocol: C2C12 cells were washed with PBS, then changed to differentiation medium containing DMEM containing 5 % horse serum, and 100 units/ml penicillin, and 100 µg/ml streptomycin. 1mM 4-PBA (Sigma), and DMSO in differentiation medium for 4 days.

value: skeletal muscle

value: myoblast cell line

value: WT

value: 4-PBA, myoblast differentiation


title: MDA-MB-231 Contorl shRNA H3K27me3 [ChIP-seq]

first: Tae-Young


title: KT-47 Resistance 1, H3K27ac_1

description: Library name: 3140053_CMJ_R_H3K27ac_034


title: KT-47 Resistance 1, H3K27ac_2

description: Library name: 3140055_CMJ_R_H3K27ac_036


title: KT-47 Resistance 1, H3K27me3_2

description: Library name: 3140051_CMJ_R_H3K27me3_032


title: primary GBM patient 62

city: Seongnam-si

first: Jaejoon

last: Lim

address: 59 Yatap-ro, Bundang-gu

department: College of Medicine

institute: CHA University

data_processing:
At first, reads for each sample were mapped to the reference genome(Mouse mm10) by Tophat(v2.0.13) . The aligned results were added to Cuffdiff(v2.2.1)  to report differentially expressed genes. For library normalization and dispersion estimation, geometric and pooled (“blind” when each condition has single replicates, or “pooled” when multiple replicates are available) methods  were applied.
Assembly: mm10
Supplementary files format and content: gz format

source_name: Brain tissue

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. RNA purity was determined by assaying 1 µl of total RNA extract on a NanoDrop8000 spectrophotometer. RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer with an RNA Integrity Number (RIN) value.
Total RNA sequencing libraries were prepared according to the manufacturer’s instructions (Illumina Truseq Stranded Total RNA Sample prep kit with Ribo-zero Human/mouse/rat).  Total RNA 400ng was subjected to ribosomal RNA depletion, with Ribo-zero Human/mouse/rat reagent using biotinylated probes that selectively bind rRNA species. Following purification, the rRNA-depleted total RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand. cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were purified and enriched with PCR to create the final cDNA library. The quality of the amplified libraries was verified by automated electrophoresis (Tapestation, Agilent). After QPCR using KAPA SYBR FAST qPCR Master Mix(Kapa Biosystems), we combined libraries that index tagged in equimolar amounts in the pool. RNA sequencing is performed using an Illumina NovaSeq 6000 system following provided protocols for 2x100 sequencing.

value: Brain tissue

value: IDH1 wild type


title: KT-47 Resistance 1, IgG_1

description: Library name: 3140047_CMJ_R_Ctrl_028


title: C2C12 cells, Day4, DMSO, rep1

description:
Library name: Sample3
Column name in raw_counts_C2C12.txt: DMSO_D4_rep1

value: DMSO, myoblast differentiation


title: KT-47 Resistance 1, IgG_2

description: Library name: 3140048_CMJ_R_Ctrl_029


title: KT-47 pretreatment, H3K4me3_2

description: Library name: 3140045_CMJ_H3K4me3_026


title: C2C12 cells, Day4, DMSO, rep2

description:
Library name: Sample4
Column name in raw_counts_C2C12.txt: DMSO_D4_rep2


title: primary GBM patient 61


title: C2C12 cells, Day0, rep1

description:
Library name: Sample1
Column name in raw_counts_C2C12.txt: D0_rep1

value: Non-treated


title: KT-47 Resistance 1, H3K9me3_2

description: Library name: 3140060_CMJ_R_H3K9me3_041


title: primary GBM patient 59


title: KT-47 pretreatment, H3K4me1_1

description: Library name: 3140035_CMJ_H3K4me1_016


title: KT-47 pretreatment, H3K4me1_2

description: Library name: 3140037_CMJ_H3K4me1_018


title: KT-47 pretreatment, H3K4me3_1

description: Library name: 3140044_CMJ_H3K4me3_025


title: C2C12 cells, Day0, rep2

description:
Library name: Sample2
Column name in raw_counts_C2C12.txt: D0_rep2


title: C2C12 cells, Day4, 4-PBA, rep1

description:
Library name: Sample5
Column name in raw_counts_C2C12.txt: 4PBA_D4_rep1


title: primary GBM patient 58 tumor normal region


title: KT-47 pretreatment, H3K9me3_2

description: Library name: 3140034_CMJ_H3K9me3_015


title: KT-47 pretreatment, H3K9me1_2

description: Library name: 3140031_CMJ_H3K9me1_012


title: KT-47 Resistance 1, H3K9me1_2

description: Library name: 3140057_CMJ_R_H3K9me1_038


title: primary GBM patient 63


title: rip_helz2

city: Dallas

first: Zhao

last: Zhang

state: Texas

address: 5323 Harry Hines Blvd.

department: Center for the Genetics of Host Defense

institute: The University of Texas Southwestern Medical Center

description: Library name: 2

data_processing:
Reads were trimmed with Trimmomatic v0.39 (phred+33; TruSeq3-PE-2 adapters; sliding window 4:15; minimum length 36 nt) and quality checked with FastQC v0.11.2.
Trimmed reads were aligned to mouse GRCm38 (mm10) using TopHat v2.0.12 with Bowtie2 v2.2.3 and SAMtools v0.1.19, library type fr unstranded.
Both paired reads and merged singleton reads were aligned; as a basic QC threshold, libraries with overall mapping at least 50 percent were retained (Control 60.5%, HELZ2 74.6%).
Quantification used the Cufflinks suite v2.2.1 (Cufflinks, Cuffmerge, Cuffquant, Cuffnorm).
Differential analysis used Cuffdiff v2.2.1 with bias correction and multi-read correction; results are presented as HELZ2 pull down over control pull down gene-level FPKM enrichment ratios.
Assembly: Mouse GRCm38 (mm10)
Supplementary files format and content: Tab-delimited Cufflinks file: one row per gene with identifiers and locus; contains Control_FPKM, Helz2_FPKM, confidence bounds (conf_lo, conf_hi) for each condition, status, length, and coverage.

source_name: Liver

extract_protocol:
Mouse livers were collected after euthanasia and extracted using Tissue Lyser (Qiagen) in Nonidet P-40 lysis buffer supplemented with 1 U/μl RNase Inhibitor (FEREO0381PM, Fisher Scientific) and extracted for 10 min. The lysate was centrifuged for 10 min at 16,800g, and supernatant was transferred to a fresh 1.5-ml tube. Total protein was measured by Bradford assay and 2 mg of cytoplasmic lysate protein was subjected to immunoprecipitation. Lysates were incubated with Flag antibody-conjugated beads for 6-8 hours at 4°C. The beads were subsequently washed three times with 1 mL of Nonidet P-40 lysis buffer supplemented with 1 U/μl RNase Inhibitor. The RNA and protein on beads were isolated using TRIzol according to the manufacturer’s instructions. The RNA fraction was subjected to qPCR analysis and RNA sequencing (RNA-seq).
With the RNA from RIP, cDNA synthesis and library preparation were carried out using the SMART-Seq mRNA LP kit (Takara, 634768).

value: Liver


title: KT-47 Resistance 1, H3K27me3_1

description: Library name: 3140050_CMJ_R_H3K27me3_031


title: rip_ctrl

description: Library name: 1


title: primary GBM patient 58 tumor core region


title: KT-47 pretreatment, H3K9me1_1

description: Library name: 3140030_CMJ_H3K9me1_011


title: KT-47 pretreatment, H3K9me3_1

description: Library name: 3140032_CMJ_H3K9me3_013


title: DDKC_9804_S164339

city: Ulm

first: Alexander

last: Kleger

address: Albert einstein allee 23

department: Institute for Molecular Oncology and Stem Cell biology

institute: Universitaetsklinikum Ulm

description:
Library name: DDKC_9804_S164339
Column name in rnaseq_deseq_rdkk3_counts_raw.tsv: DDKC_9804_S164339

data_processing:
Illumina NovaSeq Control Software (NVCS) 1.8.1 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 3.4.4.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm39 (UCSC Genome Browser mm39) and GENCODE reference transcriptome M32 (February 2023) with STAR 2.7.9a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.16 package DESeq2 1.38.0, running under R 4.2.2.
Assembly: UCSC mm39 based on GRCm39
Supplementary files format and content: tsv file includes raw counts for each sample

source_name: Pancreas

growth_protocol: Pancreatic tumor cells were cultured using Dulbecco's Modified Eagle Medium supplemented with 10% FBS  and 1% Pencillin/ streptomycin

extract_protocol:
RNA isolation was done using Rneasy Plus Mini kit from Qiagen
The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the NEBNext® Ultra™ II Directional RNA sample preparation kit (New England Biolabs, Inc., Ipswich, MA, USA). Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). For sequencing, samples were diluted and pooled into NGS libraries in equimolar amounts.

treatment_protocol: Dkk3 null tumor cells were treated with recombinant form of soluble DKK3 commercially available to assess its oncogenic properties

value: Pancreas

value: Pancreatic cancer cells

value: DKK3 knockout


title: KT-47 pretreatment, H3K27ac_2

description: Library name: 3140027_CMJ_H3K27ac_008

value: kidney tumor


title: KT-47 pretreatment, H3K27ac_1

description: Library name: 3140026_CMJ_H3K27ac_007

value: Wilms tumor patient-derived xenograft


title: primary GBM patient 57


title: primary GBM patient 58 peripheral region


title: primary GBM patient 55


title: DDKC_9804_plus_rDKK3_S164334

description:
Library name: DDKC_9804_plus_rDKK3_S164334
Column name in rnaseq_deseq_rdkk3_counts_raw.tsv: DDKC_9804_plus_rDKK3_S164334

value: recombinant DKK3


title: KT-47 pretreatment, IgG_2

description: Library name: 3140021_CMJ_Ctrl_002


title: DDKC_9804_S164323

description:
Library name: DDKC_9804_S164323
Column name in rnaseq_deseq_rdkk3_counts_raw.tsv: DDKC_9804_S164323


title: primary GBM patient 54 tumor core region


title: Control Subject 23

city: Angers

first: Benoit

last: BRILLAND

address: 4 rue Larrey

country: France

institute: Angers University Hospital

hyb_protocol: 100 ng of the resulting RNA was then hybridised to probes from the nCounter XT autoimmune profiling panel (NS_Hs_AI_Pro_v1.1, NanoString Technologies, 750 genes involved in 35 pathways and processes + 20 housekeeping genes + 14 internal controls), according to the manufacturer’s guidelines using an 19-hour hybridisation.

scan_protocol: Sample slides were prepared, and absolute counts generated using the nCounter FLEX analysis system.

data_processing:
Raw gene expression data were analyzed using nSolver Analysis Software v4.0 (NanoString Technologies) with the Advanced Analysis Module v2.0. The software first identifies and checks standard quality controls such as imaging, binding density, and positive controls to ensure the samples were read and reported properly.
For gene expression data, raw counts were normalized to the positive controls and then log2 transformed. To reduce technical bias, background thresholding was performed using the eight negative controls included within the panel. Genes with counts below a threshold of three standard deviations above the mean background signal were excluded from subsequent analysis. Data normalization was performed on background-thresholded samples using internal positive controls and selected housekeeping genes that were identified using the geNorm algorithm. Data were normalized for hybridization and counting efficiency and kept within the range of 0.3–3 (Nanostring recommended).

source_name: kidney biopsy

extract_protocol: Kidney biopsies containing at least 4 glomeruli and sufficient tissue after clinical use were selected for subsequent mRNA extraction. This pragmatic cutoff was chosen to reflect the broad range of biopsies encountered in clinical practice. Ten-micrometer sections were cut from the formalin-fixed paraffin-embedded (FFPE) blocks and placed in 2 ml microcentrifuge tubes after discarding the first two sections (to avoid collecting RNA that would have been damaged by contact with air). Whole sections, including glomeruli and tubulo-interstitium were used. The number of sections per sample was dependent on the size of the FFPE tissue. Preliminary studies allowed us to determine that 3 to 6 sections were necessary to obtain a minimum of 100 ng of total RNA.  Extraction of total RNA from FFPE specimens was performed using the High Pure FFPE RNA Isolation Kit (Roche Molecular Diagnostics, Rotkreuz, Switzerland) according to the manufacturer’s instructions. Extraction of RNA was either performed immediately after FFPE sectioning or sections were frozen at -20°C until the extraction was performed.  RNA purity and quantification were assessed by spectrophotometry (NanoDrop 2000; Thermo Fisher Scientific, Waltham, MA): RNA with a 260/280 ratio of 1.7–2.0 as well as a 260/230 ratio in the range of 1.8–2.3 were considered to be of acceptable quality for downstream assays). RNA quality analysis (fragmentation analysis) was performed to assess the integrity of RNA by measuring the proportion of RNA fragments greater than 200 base pairs (DV200) (TapeStation; Agilent, Santa Clara, CA). The resulting data were used to calculate the corrected RNA input for each NanoString hybridization reaction following the manufacturer’s instructions. Only samples with DV200 > 30% were considered for subsequent analyses. RNA was stored at −80 °C prior to NanoString assays. RNA was diluted in nuclease free water at a concentration of 20 ng/μL immediately before the assay, and 100 ng (5 µL) of total RNA per sample were used for quantification.

value: kidney

tag: disease group

value: CTRL


title: KT-47 pretreatment, H3K27me3_1

description: Library name: 3140023_CMJ_H3K27me3_004


title: DDKC_9790_S164341

description:
Library name: DDKC_9790_S164341
Column name in rnaseq_deseq_rdkk3_counts_raw.tsv: DDKC_9790_S164341


title: Control Subject 22


title: DDKC_9804_plus_rDKK3_S164326

description:
Library name: DDKC_9804_plus_rDKK3_S164326
Column name in rnaseq_deseq_rdkk3_counts_raw.tsv: DDKC_9804_plus_rDKK3_S164326


title: KT-47 pretreatment, IgG_1

description: Library name: 3140020_CMJ_Ctrl_001


title: primary GBM patient 54 peripheral region


title: Control Subject 21


title: primary GBM patient 53 tumor core region


title: Control Subject 20


title: Control Subject 18


title: Control Subject 16


title: primary GBM patient 53 peripheral region


title: KT-47 pretreatment, H3K27me3_2

description: Library name: 3140024_CMJ_H3K27me3_005


title: Control Subject 17


title: DDKC_9790_plus_rDKK3_S164340

description:
Library name: DDKC_9790_plus_rDKK3_S164340
Column name in rnaseq_deseq_rdkk3_counts_raw.tsv: DDKC_9790_plus_rDKK3_S164340


title: DDKC_9790_S164325

description:
Library name: DDKC_9790_S164325
Column name in rnaseq_deseq_rdkk3_counts_raw.tsv: DDKC_9790_S164325


title: primary GBM patient 52 ventricle wall


title: Control Subject 15


title: Control Subject 19


title: primary GBM patient 52 peripheral region_2


title: Control Subject 11


title: Control Subject 12


title: primary GBM patient 52 peripheral region


title: Control Subject 8


title: primary GBM patient 52 tumor core region


title: DDKC_9750_S164322

description:
Library name: DDKC_9750_S164322
Column name in rnaseq_deseq_rdkk3_counts_raw.tsv: DDKC_9750_S164322


title: DDKC_9750_plus_rDKK3_S164333

description:
Library name: DDKC_9750_plus_rDKK3_S164333
Column name in rnaseq_deseq_rdkk3_counts_raw.tsv: DDKC_9750_plus_rDKK3_S164333


title: Control Subject 10


title: primary GBM patient 51 cortex


title: Control Subject 9


title: Control Subject 7


title: DDKC_9790_plus_rDKK3_S164327

description:
Library name: DDKC_9790_plus_rDKK3_S164327
Column name in rnaseq_deseq_rdkk3_counts_raw.tsv: DDKC_9790_plus_rDKK3_S164327


title: Control Subject 4


title: primary GBM patient 51 peripheral region


title: Control Subject 3


title: Control Subject 6