title: platelet-derived extracellular vesicles 1

description: Library name: PEV_6


title: TEB-011;N1

status: Public on Dec 17 2024

type: SRA

city: Krems

first: Christine

last: Hafner

address: Dr.-Karl-Dorrek-Straße 30

country: Austria

institute: Karl Landsteiner University of Health Sciences

description:
SS01017
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

library_source: transcriptomic

data_processing:
On average, 12 million and 7.6 million reads per sample were generated for allergic and healthy individuals, respectively. Reads in fastq format were generated using the Illumina bcl2fastq command line tool (v2.19.1.403).
Reads were trimmed and filtered using cutadapt version 2.8 to trim polyA tails, remove reads with N’s and trim bases with a quality of less than 30 from the 3’ ends of the reads. On average, 7 million and 5 million reads were left after this procedure for allergic and healthy individuals, respectively.
Trimmed reads in fastq format were aligned to the human reference genome version GRCh38 with Gencode 29 annotations  using STAR aligner version 2.6.1a in 2-pass mode. Raw reads per gene were counted by STAR.
Differential gene expression was calculated using DESeq2 version 1.22.2.
Assembly: Genome version GRCh38 with Gencode 29 annotations
Supplementary files format and content: Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv: File containing raw counts per gene from ReadsPerGene.out.tab generated by STAR aligner (allergic samples); Columns: GeneType, GeneSymbol Ensembl Gene ID , sampleIDs with raw counts (all integer numbers)
Supplementary files format and content: Nonallergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv:File containing raw counts per gene from ReadsPerGene.out.tab generated by STAR aligner (nonallergic samples); Columns: GeneType, GeneSymbol Ensembl Gene ID , sampleIDs with raw counts (all integer numbers)
Supplementary files format and content: Allergic_vst_transf_counts_GeneSymbols_GeneTypes.tsv: File containing variance-stabilizing-transformed count data (allergic samples), generated by DESeq2 function vst . Columns: GeneType, GeneSymbol, Ensembl Gene ID, sampleIDs with vst transformed counts
Supplementary files format and content: Nonllergic_vst_transf_counts_GeneSymbols_GeneTypes.tsv: File containing variance-stabilizing-transformed count data (nonallergic samples), generated by DESeq2 function vst . Columns: GeneType, GeneSymbol, Ensembl Gene ID, sampleIDs with vst transformed counts
Supplementary files format and content: Allergic_paired_T15.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (allergic samples; provocation 15 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Allergic_paired_T30.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (allergic samples; provocation 30 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Allergic_paired_T60.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (allergic samples; provocation 60 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Allergic_paired_T120.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (allergic samples; provocation 120 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Non-allergic_paired_T15.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (non-allergic samples; provocation 15 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Non-allergic_paired_T30.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (non-allergic samples; provocation 30 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Non-allergic_paired_T60.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (non-allergic samples; provocation 60 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)
Supplementary files format and content: Non-allergic_paired_T120.tsv: File containing the results of the differential gene expression test performed by DESeq2 functions DESeq and results (non-allergic samples; provocation 120 min vs. baseline); Columns: GeneType, GeneSymbol, Ensembl Gene ID, baseMean intermediate mean of normalized counts for all samples, log2FoldChange log2 fold change (maximum likelihood estimate) for group 2 vs group 1, lfcSE standard error for group 2 vs group 1, stat Wald statistic group 2 vs group 1, pvalue Wald test p-value group 2 vs group 1, padj Benjamini-Hochberg adjusted p-values, sampleIDs with normalized counts (normalized by size factors)

molecule: total RNA

organism: Homo sapiens

source_name: Nasal mucosa

extract_protocol:
The nasal scrapings were immediately transferred to lysis buffer (RLT buffer, RNeasy micro kit, Qiagen, Germany) and kept on ice until total RNA was isolated using the protocol as described by the manufacturer. The RNA quality and concentration was determined by 2100 Bioanalyser instrument (Agilent).
Sequencing libraries from total RNA were prepared at the Core Facility Genomics, Medical University of Vienna, using the QuantSeq FWD protocol (Lexogen). 21 PCR cycles were used for library prep, as determined by qPCR according to the library prep manual. Libraries were QC-checked on a Bioanalyzer 2100 (Agilent) using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay (Invitrogen). Pooled libraries were sequenced on a NextSeq500 instrument (Illumina) in 1x75bp single-end sequencing mode.

tag: tissue

value: Nasal mucosa

tag: disease state

value: Allergic

tag: treatment

value: Saline nasal spray

tag: time point

value: 15 min

tag: Sex

value: male

tag: age

tag: date of_sample_acquisition


title: TEB-011;N2

description:
SS01018
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Birch pollen extract

value: 30 min


title: TEB-012;N2

description:
SS01020
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: 60 min

value: female


title: Tam_F_ct42_541

city: Gainesville

first: Spencer

last: Procopio

state: FL

address: 1345 Center Drive

country: USA

institute: University of Florida

data_processing:
HiPerGator
Alignment: hisat2 with reference Mus_musculus.GRCm38.97.chr.gtf
Deduplication: picard
Raw Counts: htseq
Assembly: mm10 (GRCm38)
Supplementary files format and content: .csv of raw counts from each sample

molecule: polyA RNA

organism: Mus musculus

source_name: mouse ventricle

extract_protocol:
Qiagen RNeasy Mini Kit
Preparation of poly-A tail selected RNA libraries (Illumina mRNA Prep kit (Illumina, Inc. CA, USA)) and whole transcriptome sequencing (Novaseq 6000 (Illumina, Inc. CA, USA)),

value: mouse ventricle

tag: genotype

value: iCSBmal1 KO

value: Tamoxifen


title: premenopausal platelet-derived extracellular vesicles 2

city: Jacksonville

first: DeLisa

last: Fairweather

address: 4500 San Pablo Rd S

department: Cardiovascular Medicine

institute: Mayo Clinic

description: Library name: pmPEV_2

data_processing:
Cutadapt, miRDeep2 mapper, miRDeep2 module, edgeR
Assembly: hg38
Supplementary files format and content: Processed data is log2 normalized counts

source_name: Plasma

extract_protocol:
QIAseq miRNA Library Kit
Illumina cBot, HiSeq 3000/4000 PE Cluster Kit

value: Plasma


title: CD45+ immune cells from post-treatment adjacent normal liver tissue of patient P16 (NR/PD)

city: Hangzhou

first: Chen

last: Dong

state: Zhejiang

address: Shilongshan Street No.18, Xihu District

country: China

institute: Westlake University

data_processing:
For scRNA-seq samples, reads were aligned and quantified using the Cell Ranger Single-Cell toolkit (v.6.1.2) against the GRCh38 human reference genome (refdata-gex-GRCh38-2020-A). Preliminary filtered raw count data generated from Cell Ranger were used for downstream analysis. Further quality control was applied to filter out low-quality cells with either (1) <500 expressed genes, (2) >6,000 expressed genes, (3) >20% mitochondrial UMI counts, or <1% hemoglobin UMI counts (sum of UMI counts of HBA1, HBA2 and HBB genes) and filter out genes detected in less than 3 cells. Scrublet (v.0.2.3) was applied to each sequencing library to remove potential doublets with default setting.
For 10X dCODE dextramer experiments, data
For scTCR-seq samples, reads were aligned and quantified using Cell Ranger Single-Cell toolkit (v.6.1.2) with the manufacturer-supplied human VDJ reference genome (refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0). For each sample, the output file all_contig_annotations.csv, containing TCR α- and β-chain complementarity determining region 3 (CDR3) amino acid sequence, was used for downstream analysis. These files were combined using scirpy (v.0.11.0) and quality control was performed with the following criterions: 1) low-confidence, non-productive chains or those with UMIs < 2 were discarded; 2) cells with more than four productive chains: two VJ and two VDJ chains were discarded; 3) cells with only one VD or only one VDJ chain were discarded; 4) for T cells with two α- or β- chains assembled, the α-β pair showing the highest expression level (UMIs) was defined as the domain α- β pair in the corresponding T cells. For each patient, T cells comprising the same VJ and VDJ CDR3 amino acid sequences for each patient were considered as having originated from the same clone and were therefore identified as clonal cells.
For bulk RNA-seq samples, we applied FastQC (v.0.11.9) to determine the quality of the raw sequencing data. Adapters, low quality bases and reads were removed using 'Trim Galore' (v.0.6.5). Then, the expression levels of transcripts were quantified by Salmon (v.1.9.1). The gene expression levels of genes, including raw count and transcript per million (TPM), were generated by tximport (v.1.18.0) with the inputs from Salmon.
Assembly: hg38
Supplementary files format and content: csv and txt files for TCR summary, and deCODE dextramer summary.
Supplementary files format and content: h5ad files for expression matrices

source_name: HBV+ HCC

extract_protocol:
To perform single-cell sequencing, single-cell suspensions from tumor and blood samples were stained with antibodies against CD45 and sorted using a BD FACSAriaTM III instrument. Based on FACS analysis, single cells were sorted into 15 ml tubes (Nest) and manually counted under a microscope. To perform bulk RNA analysis, small fragments of tumor tissues were first preserved in RNAlater RNA stabilization reagent (QIAGEN) immediately after surgical resection, and stored on ice to prevent RNA degradation. The RNA was then extracted from the tumor tissue samples using the RNeasy Mini Kit (QIAGEN), following the manufacturer's specifications. The concentration of RNA was quantified using the NanoDrop instrument (Thermo), and the quality of RNA was evaluated using the fragment analyzer (AATI).
To construct scRNA-seq libraries, the concentration of single cell suspensions was adjusted to 1,000 cells/ul, and cells were loaded between 5,000 and 20,000 cells/reaction using 10X Chromium Single Cell 5' and human variable, diversity, and joining (VDJ) (10X Genomics). All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina NovaSeq 6000 sequencer with 150-bp paired-end reads. The bulk RNA-seq libraries were constructed using the NEBNext Poly (A) mRNA Magnetic Isolation Module kit (NEB) and the NEBNext Ultra RNA Library Prep Kit for Illumina Paired-end Multiplexed Sequencing Library (NEB). Finally, the samples were sequenced on the Illumina Hiseq 4000 sequencer with 150 bp paired-end reads.
10x Chromium Single cell 5’ + VDJ library; 10x Chromium Single cell 5’ + VDJ library + deCODE dextramer library; bulk RNA-seq

treatment_protocol: All patients included in this study were pathologically diagnosed with HBV-infected hepatocellular carcinoma and received lenvatinib (12 mg/day for bodyweight ≥ 60 kg or 8 mg/day for bodyweight < 60 kg) orally once daily and a PD-1 inhibitor intravenously on day 1 of a 21-day treatment cycle. The anti-PD-1 antibodies and their single-dose infusion were sintilimab 200 mg, pembrolizumab 200 mg, tislelizumab 200 mg, or toripalimab 240 mg.

value: adjacent normal liver tissue

tag: patient

tag: response

value: PD, non-responder

tag: cell type

value: CD45+ immune cells

tag: library type

value: scRNA-seq & scTCR-seq & deCODE-Dextramer-seq

value: anti-PD-1 plus lenvatinib combination therapy


title: Tam_F_ct38_536


title: CD45+CD3+CD8+ immune cells from pre-treatment tumor of patient P16 (NR/PD)

value: liver tumor

value: CD45+CD3+CD8+ immune cells


title: premenopausal platelet-derived extracellular vesicles 3

description: Library name: pmPEV_3


title: Tam_F_ct34_530


title: premenopausal platelet-derived extracellular vesicles 1

description: Library name: pmPEV_1


title: Chimp A4A014 Health Check

city: Madison

last: Wooddell

state: WI

address: 502 S Rosa Rd

institute: Arrowhead Pharmaceuticals

data_processing:
Subreads were collapsed to circular consensus sequence (CCS) reads using Pacbio’s internal CCS tool using default parameters (https://github.com/PacificBiosciences/ccs). Lima was used  with the argument –peek-guess to discover primer sequences and demultiplex CCS reads to individual samples(https://github.com/pacificbiosciences/barcoding/). FLNC transcripts were produced from demultiplexed reads using isoseq3 with the refine subcommand requiring poly-A sequences. Finally, FLNC transcripts were clustered into complete transcripts which were guided by FLNC quality (https://github.com/PacificBiosciences/IsoSeq). Following production,FLNC reads were aligned, sorted and indexed using PBMM2 (https://github.com/PacificBiosciences/pbmm2) with the default conditions for --preset "ISOSEQ".
Assembly: The consensus sequences for the six chimpanzee HBV genomes in this study were determined by next generation sequencing of both their genomic HBV DNA and their HBV RNA in liver samples after ETV lead-in but prior to ARC-520 treatment (“ARC-520 Day 1”) as previously described [13]. The HBV sequences of the six chimpanzees differed by only 2-4 bases from that of chimpanzee ID 88A010, and all HBV transcripts from each animal in this study were aligned to the sequence of chimpanzee 88A010. HBV from chimpanzees and the human reference GenBank accession number V01460 have a circular genome of 3,182 base-pairs (bp) that is transcribed more than one genome length to produce the precore and pgRNA transcripts generally named “3.5 kb”. From precore transcription start site at HBV position 1781 to the end of the HBV PAS at 1919, the sequence comprises positions 1781-3182 + 1-1919 (3321 bases) plus variable sequence beyond the PAS and a polyadenylated tail. To get accurate full transcript alignment, it is necessary to construct a hybrid genome sequence containing >1X content. Based on the known start and end of HBV transcripts that are greater than one genome length, we concatenated the genome sequence from coordinates 2700-3182 + 1-3182 + 1-2100 (“2700-2100”) into a single genome fasta file. This was easily achieved by constructing the sequence in the DNA sequence editor SnapGene and then converting to text using a quality text editor (VScode) because the final genome sequence was small (~5.7 kb).
Supplementary files format and content: normalized_transcript_counts
Library strategy: Iso-Seq

organism: Pan troglodytes

source_name: Liver

extract_protocol:
Total mRNA was extracted from tissues via the NucleoSpin RNA kit from Takara Biosciences using the manufacturers recommended protocol
Iso-seq library was prepared according to PacBio’s standard protocol. Briefly, cDNA was synthesized using the SMARTer PCR cDNA Synthesis Kit (Clontech) and was PCR-amplified. Following Blue Pippin size selection to create four size bins (<1kb, 1-2kb, 2-3kb, and 3-6kb), the cDNA was further amplified with PCR, ligated to hairpin adapters to create the SMRTbell Template, annealed to sequencing primer, and bound to polymerase for sequencing on the RSII sequencer by generation of concatemers. For chimpanzee 88A010, the size bins were 1-2kb, 2-3kb, 3-6kb and >6kb.

value: Liver

tag: cell line

value: Primary Hepatocyte


title: CD45+CD3+CD8+ immune cells from pre-treatment blood of patient P16 (NR/PD)

value: blood


title: TEB-012;N1

description:
SS01019
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Nasal mucosa

value: Allergic

value: Saline nasal spray

value: 15 min


title: TEB-010;N2

description:
SS01016
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Birch pollen extract

value: 30 min

value: female


title: Tam_F_ct38_535

value: mouse ventricle

value: iCSBmal1 KO

value: Tamoxifen


title: TEB-009;N2

description:
SS01014
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv


title: TEB-010;N1

description:
SS01015
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv


title: Chimp A3A006 day 351

value: Entecavir + ARC-520


title: Tam_F_ct30_524


title: CD45+CD8- immune cells from pre-treatment blood of patient P16 (NR/PD)

value: PD, non-responder

value: CD45+ immune cells exclude CD45+CD3+CD8+ cells

value: scRNA-seq & scTCR-seq & deCODE-Dextramer-seq

value: anti-PD-1 plus lenvatinib combination therapy


title: Tam_F_ct26_518


title: CD45+CD8- immune cells from pre-treatment tumor of patient P16 (NR/PD)

value: liver tumor


title: Post-treatment liver tumor of patient P26 (NR/PD)

value: CD45+ immune cells

value: scRNA-seq & scTCR-seq


title: TEB-009;N1

description:
SS01013
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Nasal mucosa

value: Allergic


title: Post-treatment blood of patient P26 (NR/PD)

value: blood


title: TEB-008;N2

description:
SS01012
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Birch pollen extract

value: 120 min

value: male


title: Tam_F_ct34_583

value: mouse ventricle


title: Tam_F_ct22_511

value: iCSBmal1 KO


title: Chimp A3A006 day 141

value: Liver

value: Primary Hepatocyte


title: Chimp A3A006 Health Check


title: Chimp A2A004 day 351

value: Entecavir + ARC-520


title: Tam_F_ct30_581

value: Tamoxifen


title: Tam_F_ct26_517


title: Chimp A2A004 day 323


title: TEB-007;N2

description:
SS01010
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: 15 min


title: Tam_F_ct22_510


title: TEB-008;N1

description:
SS01011
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Saline nasal spray


title: Tam_F_ct18_575


title: TEB-004;N2

description:
SS01008
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: 60 min


title: Post-treatment blood of patient P15 (NR/PD)

value: PD, non-responder

value: CD45+ immune cells

value: anti-PD-1 plus lenvatinib combination therapy


title: TEB-007;N1

description:
SS01009
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Nasal mucosa

value: Allergic


title: XCKO 3

city: nanjing

first: Qi

last: Wang

state: Jiangsu

address: The First Affiliated Hospital of Nanjing Medical University, 300 Guang Zhou Road

institute: The first affliated hospital of nanjing medical university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced of library size (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Hepatocytes were isolated from mice fed with HFD for 26 weeks,and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Cat#E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: 32-34 weeks

value: primary mouse hepatocytes


title: Chimp 95A010 day 57


title: Tam_F_ct18_504


title: Chimp A2A004 Health Check


title: Pre-treatment liver tumor of patient P26 (NR/PD)

value: liver tumor

value: scRNA-seq & scTCR-seq


title: Pre-treatment blood of patient P15 (NR/PD)

value: blood


title: XCKO 2


title: Chimp 89A008 day 379

value: Liver


title: TEB-004;N1

description:
SS01007
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: male


title: TEB-003;N2

description:
SS01006
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Birch pollen extract

value: female


title: Pre-treatment blood of patient P26 (NR/PD)


title: Post-treatment blood of patient P1 (NR/SD)

value: SD, non-responder


title: Post-treatment liver tumor of patient P1 (NR/SD)


title: XCKO 1


title: Pre-treatment blood of patient P1 (NR/SD)


title: Pre-treatment liver tumor of patient P15 (NR/PD)


title: Chimp 89A008 Health Check

value: Primary Hepatocyte


title: Chimp A2A004 day 85

value: Entecavir + ARC-520


title: TEB-002;N2

description:
SS01004
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: 15 min


title: XCON 2


title: Chimp 88A010 day 57


title: TEB-002;N1

description:
SS01003
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Saline nasal spray


title: TEB-001;N2

description:
SS01002
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: 120 min


title: TRdko61_Tail,1 day after amputation;rep1 [TRdko61_1dpa-1]

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description: featureCounts.txt

data_processing:
Raw read sequence were trimmed with cutadapt 3.2 to remove adapter sequence.
Trimmed reads were mapped to genome with STAR 2.7.7a
Mapped reads were counted with featureCounts from subread 2.0.1.
Assembly: Xenopus_tropicalis (Xenbase v10.0)
Supplementary files format and content: Tab-delimited text file with read counts for each gene.

organism: Xenopus tropicalis

source_name: Tail

extract_protocol:
RNA was harvested using Direct-zol RNA MiniPrep kit (Zymo research, Catalog No: ZR2052).
RNA libraries for RNA-seq were prepared using  TruSeq Stranded Total RNA Library Prep Kit following manufacturer's protocols. Two biological replica RNA samples were prepared for RNA-seq analysis on a NovaSeq 6000 System (Illumina).

treatment_protocol: Amputation  the tail of widl type and TRdko tadpoles at stage 56 and stage 61, then harvest the tail tissue (including the newly formed tissue plus  about 250 μm proximal to the site of amputation at 0hr, 6hr and 1d  after cutting

value: Tail

value: whole tissue

value: 1 day after amputation

value: TRdko

value: tail cutting


title: Post-treatment blood of patient P27 (R/PR)

value: PR, responder

value: CD45+ immune cells

value: scRNA-seq & scTCR-seq

value: anti-PD-1 plus lenvatinib combination therapy


title: TRdko61_Tail,1day after amputation;rep2 [TRdko61_1dpa-2]

description: featureCounts.txt

value: 1day after amputation


title: Pre-treatment liver tumor of patient P27 (R/PR)

value: liver tumor


title: TEB-003;N1

description:
SS01005
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: Nasal mucosa

value: Allergic

value: female


title: TEB-001;N1

description:
SS01001
Allergic_raw_gene_counts_GeneSymbols_GeneTypes.tsv

value: 15 min

value: male


title: XCON 3

value: 32-34 weeks

value: primary mouse hepatocytes


title: XKO 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced of library size (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: readcount, fpkm values for each Sample

source_name: Xbp1ΔMf _BMDMs

extract_protocol:
LPS-primed Xbp1FL/FL（XWT）or Xbp1ΔMf（XKO）bone marrow-derived macrophages were incubated with WT primary hepatocytes conditioned media (CM) for 48 h, and then Xbp1FL/FL or Xbp1ΔMf BMDMs RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Cat#E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow-derived macrophages


title: Post-treatment liver tumor of patient P27 (R/PR)


title: XCON 1


title: Pre-treatment blood of patient P27 (R/PR)

value: blood


title: Post-treatment liver tumor of patient P18 (R/CR)

value: CR, responder


title: TRdko61_Tail,6 hour after amputation;rep2 [TRdko61_6hpa-2]

description: featureCounts.txt

value: Tail

value: whole tissue

value: 6 hour after amputation

value: TRdko

value: tail cutting


title: TRdko61_Tail,6 hour after amputation;rep1 [TRdko61_6hpa-1]

description: featureCounts.txt


title: XKO 1


title: Participant 5, uninfected population

city: Amsterdam

first: Neeltje

last: Kootstra

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC, AMC

description: Sequencing and data processing was performed by Qiagen (Hilden, Germany)

data_processing:
CLC Genomics Workbench 12.0.4
The bcl2fastq Conversion Software (Illumina, San Diego, CA, USA) was used to demultiplex raw data and generate FASTQ files
Raw sequencing reads were demultiplexed using the "Demultiplex QIAseq UPX 3' reads" tool of the CLC Genomics Workbench (version 12.0.4; Qiagen), and demultiplexed sequencing reads were processed using the "Quantify QIAseq UPX 3' workflow" with default settings.
The reads were then mapped to the Human genome GRCh38 and annotated using the NCBI RefSeq GRCh38.p11 gene annotation.
Assembly: Human genome GRCh38
Supplementary files format and content: Mapped read counts for each sample

source_name: white blood cell

extract_protocol:
RNA was extracted using Qiaseq 3’ Transcriptome Kit following manufacturer's protocols
Libraries were prepared using Qiaseq 3’ Transcriptome Kit following manufacturer's protocols

value: white blood cell


title: Participant 5, active population


title: TRdko61_Tail,0 hour after amputation;rep2 [TRdko61_0hpa-2]

description: featureCounts.txt

value: 0 hour after amputation


title: XKO 3


title: XWT 2


title: Post-treatment blood of patient P18 (R/CR)

value: CD45+ immune cells

value: scRNA-seq & scTCR-seq

value: anti-PD-1 plus lenvatinib combination therapy


title: TRdko61_Tail,0 hour after amputation;rep1 [TRdko61_0hpa-1]

description: featureCounts.txt


title: Participant 5, latent population


title: Pre-treatment liver tumor of patient P18 (R/CR)

value: liver tumor


title: Participant 4, uninfected population


title: XWT 1


title: XWT 3


title: Pre-treatment blood of patient P18 (R/CR)


title: TRdko56_Tail,1 day after amputation;rep1 [TRdko56_1dpa-1]

description: featureCounts.txt

value: 1 day after amputation


title: Participant 4, active population


title: Post-treatment liver tumor of patient P11 (R/PR)

value: PR, responder


title: TRdko56_Tail,1day after amputation;rep2 [TRdko56_1dpa-2]

description: featureCounts.txt

value: 1day after amputation


title: Participant 4, latent population


title: Cortex PlyA-KI rep2

city: Suzhou

first: shaojun

last: Qi

address: B8, Lane 21, Dong Yan Li Rd, Suzhou Industry Park,Suzhou ,Jiang Su, China

department: Department of mRNA Sciences

institute: Suzhou Abogen Biosciences Co., Ltd.

data_processing:
Illumina bcl2fastq2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then the clean data were further processed on https://usegalaxy.org/ online website. Firstly, sequence reads were trimmed for low-quality sequence using Trimmomatic with parameters LEADING 20/TRAILING 20/SLIDING WINDOW bases 4 quality 20/MINLEN 35, then mapped to mm10 whole genome using HISAT2 with default parameters. Finally, the output BAM file were calculated to counts using featurecounts with parameters only count primary alignments TRUE.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell et al., Nature Biotechnology, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts and abundance for every gene and every sample

source_name: E13.5 cortex

extract_protocol:
500-1000ng total RNA were extracted following the TRIzol® reagent protocol (Cat#15596018, Invitrogen)
The mRNA library preparation including mRNA capturing, fragmentation (200-300bp), adaptor (Cat#E7775, NEB) ligation, and library amplification and purification was finished following the manufacturer’s protocols of KAPA Hyper Prep Kit (Cat#KK8504, Kapa Biosystems).

treatment_protocol: For ICR mice, 3μg/μl control or Lockd-shRNA expressing plasmids was electroporated into the lateral ventricle of brains at embryonic (E) 14.5,  and the embryos were placed back into the abdorminal of the pregnant mice for normal development, the cortices were dissociated at E16.5.

value: brain cortex

tag: strain

value: PlyA-KI


title: Post-treatment blood of patient P11 (R/PR)

value: blood


title: TRdko56_Tail,6 hour after amputation;rep2 [TRdko56_6hpa-2]

description: featureCounts.txt

value: Tail


title: Participant 3, uninfected population


title: Cortex PlyA-KI rep1


title: Pre-treatment liver tumor of patient P11 (R/PR)


title: Participant 3, active population


title: Cortex WT rep1

value: wild type


title: Cortex WT rep2


title: Pre-treatment blood of patient P11 (R/PR)


title: IUE Lockd-KD-2

value: ICR

value: Lockd knockdown


title: TRdko56_Tail,0 hou after amputationr;rep1 [TRdko56_0hpa-1]

description: featureCounts.txt

value: whole tissue

value: 0 hou after amputationr

value: TRdko

value: tail cutting


title: IUE Lockd-KD-1


title: Post-treatment liver tumor of patient P5 (R/PR)

value: CD45+ immune cells

value: scRNA-seq & scTCR-seq


title: TRdko56_Tail,6 hour after amputation;rep1 [TRdko56_6hpa-1]

description: featureCounts.txt

value: 6 hour after amputation


title: wt61_Tail,1day after amputation;rep2 [wt61_1dpa-2]

description: featureCounts.txt

value: WT


title: Post-treatment blood of patient P5 (R/PR)

value: PR, responder

value: anti-PD-1 plus lenvatinib combination therapy


title: Participant 2, uninfected population

value: white blood cell


title: wt61_Tail,1 day after amputation;rep1 [wt61_1dpa-1]

description: featureCounts.txt

value: 1 day after amputation


title: wt61_Tail,6 hour after amputation;rep2 [wt61_6hpa-2]

description: featureCounts.txt


title: Participant 3, latent population


title: IUE Control-2

value: brain cortex

value: control


title: Participant 2, active population


title: TRdko56_Tail,0 hour after amputation;rep2 [TRdko56_0hpa-2]

description: featureCounts.txt

value: Tail

value: 0 hour after amputation


title: Pre-treatment blood of patient P5 (R/PR)

value: blood


title: Participant 1, uninfected population


title: Pre-treatment liver tumor of patient P5 (R/PR)

value: liver tumor


title: trxKD, naïve, rep3

city: Nijmegen

first: Nicholas

last: Raun

address: Geert Grooteplein 10

institute: Radboudumc

data_processing:
Raw sequence reads were trimmed using Prinseq (version 0.20.4) quality trimming to a minimum base quality score of 30.
Trimmed reads were aligned to D. melanogaster genome (dm6) using STAR (version 2.5.3a). Reads were also aligned to C. elegans unc-84 gene (NC_003284.9).
Reads that aligned to multiple loci, or to one loci with >4 mismatches, and genes that mapped to Drosophila rRNA were removed.
Gene counts were obtained using HTSeq-count (version 0.7.1) using union setting to generate genic regions.
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Mushroom body

extract_protocol:
Fly heads were obtained from samples of 50-60 flies through flash freezing with liquid nitrogen, followed by vortexing and separation through a series of a sieves. Fly heads were then suspended in homogenization buffer and nuclei released into solution through chemical and physical agitation of the cell membrane. Anti-GFP bound beads were then used to isolate GFP-positive nuclei from the whole head homogenate to represent the mushroom body-specific fraction (MB). RNA was then isolated from MB-fractions using a PicoPure RNA Isolation Kit (Invitrogen:KIT0204) according to the manufacturer instructions.
RNA libraries were generated using the Nugen Ovation Drosophila RNA-Seq System 1-16 (Nugen: NU035032) according to manufacturer instructions.

value: Mushroom body

value: naïve


title: IUE Control-1

value: ICR

value: wild type


title: Participant 2, latent population


title: wt61_Tail,6 hour after amputation;rep1 [wt61_6hpa-1]

description: featureCounts.txt

value: whole tissue

value: tail cutting


title: shZDHHC15 2

city: Dalian

first: Jianxin

state: Liaoning

address: West Lushun South Road

institute: Dalian Medical University

description: Knowdown ZDHHC15 gene

data_processing:
hisat2 for sequence alignment
stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
samtools tools for related file processing
Assembly: hg38
Supplementary files format and content: Comma-separated csv files include count values for each Sample

growth_protocol: Human breast cancer cell lines HCC1954 were purchased from the American Type Culture Collection. Cells were cultured at 37℃ in 5% CO2 with RPMI-1640 (Gibco) medium supplemented with 10% fetal bovine serum, 100 unit/mL penicillin and 100 mg/mL streptomycin

extract_protocol:
After the total RNA extraction,RNA degradation and contamination was detected by 1% agarose gels; RNA purity and concentration was checked by Nanodrop2000（Thermo Fisher Scientific，MA，USA）；RNA concentration was checked using the Qubit® 3.0 Flurometer（Thermo Fisher Scientific，MA，USA）；RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The lentiviral vectors encoding short hairpin RNAs (GIPZ shRNAs) targeting ZDHHC15 and scrambled shRNA were purchased from Dharmacon (America). The plasmids were transiently transfected into cells with Lipofectamine 3000 (Invitrogen, CA) according to the manufacturer’s protocol. Cells were harvested and analyzed 36 h after transfection.

value: Breast cancer

value: Knockdown ZDHHC15 gene


title: wt61_Tail,0 hour after amputation;rep2 [wt61_0hpa-2]

description: featureCounts.txt

value: WT


title: trxKD, naïve, rep2


title: shZDHHC15 1

description: Knowdown ZDHHC15 gene


title: Participant 1, active population

value: white blood cell


title: trxKD, naïve, rep1


title: wt56_Tail,1day after amputation;rep2 [wt56_1dpa-2]

description: featureCounts.txt

value: 1day after amputation


title: wt61_Tail,0 hour after amputation;rep1 [wt61_0hpa-1]

description: featureCounts.txt


title: trxKD, trained, rep4

value: trained


title: shCON 1

description: Negative Control

value: control


title: Participant 1, latent population


title: Resistant_304-rep2

city: San Fransisco

first: Xiaosai

last: Yao

state: CA

address: 1 DNA Way

department: Oncology Bioinformatics

institute: Roche/Genentech

library_source: genomic

data_processing:
ATAC-seq reads were analyzed using the ENCODE ATAC-seq pipeline (version 1). Briefly, reads were trimmed of adapters using cutadapt (version 1.9.1) and mapped to hg38 using Bowtie 2 (version 2.2.6). Bam files were converted to tagAlign format, which was then adjusted for Tn5 by shifting +4 bp for positive strands and −5 bp for negative strands. TagAlign files were used to call peaks using MACS2 (version 2.1.0), and those peaks with P < 1 × 10−6 were retained for differential analysis with DiffBind (version 3.0.13). For subsequent comparative analyses, only peaks called in at least two samples were retained. Differential accessibility analysis was performed using either the R package DiffBind (version 3.0.13). Differential peaks were defined by an absolute fold change of >2 and called peaks by MACS2 in at least two samples with gained accessibility (the Benjamini–Hochberg procedure was used for multiple hypothesis correction with a cut-off of FDR < 0.01). The genomic distribution of differential peaks was annotated with ChIPpeakAnno (version 3.24.1). Bigwigs corresponding to a fold change against the background control were generated by MACS2 and used to generate heatmaps with the heatmap function of deepTools (version 3.5.0). Motif enrichment analysis was performed using either HOMER (version 4.10) with all peaks as the background. The peaks were assigned using Poly-Enrich with distal enhancer–gene target links (>5 kilobases from the transcription start site) plus 5-kilobase locus definitions. Gene set enrichment was searched against Gene Ontology, MsigDB Oncogenic and Hallmark.
Assembly: hg38.p10
Supplementary files format and content: bigWig, Macs2 peaks

molecule: genomic DNA

source_name: Pancreas

growth_protocol: PATU-8902 shNTC and shYAP/WWTR1 were maintained in vitro as a monolayer culture in RPMI medium supplemented with 10% Tet free fetal bovine serum, and L-glutamine (2 mM) at 37C in an atmosphere of 5% CO2 in air. Cell culture medium did not contain any antibiotics. The tumor cells were routinely subcultured twice weekly by trypsin-EDTA treatment. The cells growing in an exponential growth phase were harvested and counted for tumor inoculation. Animals: 40 Nu/Nu nude mice, female, 6-8 weeks, weighing approximately 20-22g, were used for each cell line. Animals were purchased from Beijing Vital River Laboratory Animal Technology Co., Ltd Tumor Inoculation: Each mouse was inoculated subcutaneously at the right flank with PA-TU-8902 tumor cells (5 x 106) in 0.2 ml of HBSS with Matrigel (1:1) for tumor development. Cells from the shYAP/WWTR1 resistant tumor were propagated in vitro to establish a cell line.  ATAC-seq was performed on the resistance cell line generated from the collected tumor (under doxycycline treatment). Parental PATU-8902 cells transfected with shNTC and shYAP/WWTR1 were used as a control.

extract_protocol:
Cell lines were lysed on-plate for RNA isolation using the Qiagen RNeasy Plus Mini kit (Cat. No. 74034), and RNA concentration was determined using a NanoDrop 8000 (Thermo Fisher Scientific).  RNA integrity was confirmed using a “Bioanalyzer 2100 (Agilent Technologies).
Briefly, cryo-preserved cells were thawed, washed with 1X PBS and counted. About 100,00 cells were then lysed for 5 min on ice in 100 µl lysis buffer (10 mM Tris (pH 7.5), 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween- 20 and 0.01% digitonin). 1ml wash buffer (10 mM Tris (pH 7.5), 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20) was then added and the pellets were spun down at 500g for 10 min at 4°C. The supernatant was discarded and the pellet was resuspended in 50 µl tagmentation buffer (25 µl 2X TD buffer, 16.5 µl PBS, 0.5 µl 10% Tween-20, 0.5 µl 1% digitonin, 2.5 µl Tn5 transposase and 5 µl H2O). The tubes were incubated at 37 °C for 30 min, followed by DNA isolation using the Qiagen MinElute Cleanup Kit (catalog number 28206). The DNA was then amplified using NEBNext 2X PCR Master mix (catalog number M0541L) and analyzed by TapeStation (Agilent) before submission for sequencing.

value: Pancreas

value: Adenocarcinoma

value: Resistant to TEAD inhibitor GNE-7883


title: shCON 2

description: Negative Control


title: wt56_Tail,1 day after amputation;rep1 [wt56_1dpa-1]

description: featureCounts.txt

value: Tail

value: 1 day after amputation


title: Resistant_304-rep1


title: trxKD, trained, rep2

value: Mushroom body


title: trxKD, trained, rep3


title: PDX6-B16-3

city: Shenzhen

first: Suping

last: Zhang

state: Guangdong

address: No. 3688, Nanhai Road, Nanshan District

institute: Shenzhen University

data_processing:
Illumina Casava software used for basecalling
（1）Trim adapter sequences from the raw reads（2）Remove low-quality bases from the 3' end of the reads.（3）Remove reads that are shorter than 30 bp.
STAR was used to align the reads to human genome hg38 and mouse genome mm 10, and XenofilteR was used to filter out mouse contamination.
RSEM was used to count the reads.
DESeq2 was used for differential gene expression analysis between two samples with biological replicates. Genes with q≤0.1 and |log2_ratio|≥0.5 are identified as candidate differentially expressed genes.
Genome_build: Homo_sapiens.GRCh38.91.chr
Supplementary_files_format_and_content: Excel files include nomalized counts for each Sample ...
Supplementary_files_format_and_content: Excel files include differentially expressed genes of B16-treatment group VS control group

source_name: patient derived xenograft cells

growth_protocol: 1x10^6 single cells isolated from PDX5 or PDX6 and were injected into the second mammary pads of 4 to 6-week-old female NOD-Prkdcem26Cd52 Il2rgem26Cd22 /NjuCrl (NCG) mice.

extract_protocol:
Primary tumor tissues from these PDX models were dissociated enzymatically/mechanically using GentleMACS Dissociator (Miltenyi Biotec), as per the manufacturer’s guidelines. live cells were isolated via density gradient centrifugation in Percoll Plus (GE Healthcare Life Sciences, CC-17-5442-01). RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 mg/kg B16 were delivered via intravenous injection biweekly. Control groups were similarly treated instead with human IgG or irrelevant specificity.

value: breast cancer cells

value: B16 (anti-ROR2 antibody)


title: PDX6-B16-4


title: Sensitive_shYAP-TAZ-rep1

value: Sensitive to TEAD inhibitor GNE-7883


title: control, naïve, rep4

value: naïve


title: wt56_Tail,6 hour after amputation;rep2 [wt56_6hpa-2]

description: featureCounts.txt

value: whole tissue

value: 6 hour after amputation

value: tail cutting


title: Sensitive_shNTC-rep2


title: Sensitive_ShYAP-TAZ-rep2


title: wt56_Tail,0 hour after amputation;rep2 [wt56_0hpa-2]

description: featureCounts.txt

value: 0 hour after amputation

value: WT


title: Chimp 89008 day 141

value: Liver

value: Primary Hepatocyte

value: Entecavir + ARC-520


title: PDX6-B16-2


title: PDX6-B16-1


title: wt56_Tail, 6 hour after amputation;rep1 [wt56_6hpa-1]

description: featureCounts.txt


title: wt56_Tail, 0 hour after amputation;rep1 [wt56_0hpa-1]

description: featureCounts.txt


title: control, naïve, rep3


title: control, naïve, rep2


title: PDX6-control-4

value: IgG


title: IgG_P_7883

data_processing:
For each sequence library, raw reads were aligned on the hg38 human genome reference using Bowtie2  (v2.4.1) followed by alignments sorting (samtools v1.9) of resulting bam files with filtering out of unmapped  reads and keeping reads with mapping quality higher than 30. Duplicates were removed with Picard’s  (v2.23.9) MarkDuplicates function followed by indexation of resulting bam files with samtools. For each bam  file, genome coverage was computed with bedtools (v2.29.2) followed by generation of bigwig  (wigToBigWig v357) files. Peaks were called with macs2 (v2.7.1) for each treatment sample using their  corresponding IgG control. Downstream analyses were performed with DiffBind v3.11.1 with default  parameters, except for summits=250 in dba.count(). dba.contrast() and dba.analyzed() were used to  compute significant differential peaks with DESeq2.
Assembly: hg38.p10
Supplementary files format and content: bigWig, Macs2 peaks
Library strategy: CUT&Run

source_name: Lung, Epithelial

growth_protocol: Cell lines were maintained in RPMI 1640 supplemented with 10% FBS and 2 mM L-glutamine in a humidified incubator maintained at 37 °C with 5% CO2. TEAD SMI resistant NF2 null NCI-H226 (i.e. NCI-H226_CL3) cells were generated by incubation with increasing concentrations of TEAD SMI over time (0.25 μM to 3 μM at bi-weekly with 0.1-0.5 μM increments), ensuring at least a 25% confluence at all times.

extract_protocol:
H226/ H226-7883R cells were trypsinized into single-cell suspension with 0.05% Trypsin, EDTA 0.5 mM.  500k cells were used for each reaction.
We used the CUTANA ChIC/CUT&RUN Kit from Epicypher (#14- 1048) following manufacturer’s instructions. ConA Beads were briefly resuspended and 11 μl of beads per  reaction was transferred to a 1.5 ml tube. Beads were resuspended in 100 μl bead activation buffer per  reaction and washed 2✕. Then resuspended in 11 μl buffer per reaction and aliquoted 10 μl into 8-strip PCR  tubes, and kept on ice. Harvested cells were spun down at 600 × g for 3 min at room temperature. Cells  were then resuspended in 100 μl/reaction of wash buffer and aliquoted into 8 strip tubes with the 10 μl of  activated ConA beads. After 10 mins incubation, 50 μl of cold antibody buffer was added. YAP antibody  (CST Cat. #14074) was used at 1:50 dilution, TEAD1 antibody (BD Cat. #610923) or FOSL1 antibody  (ThermoFisher Cat. #PA5-66880) was added at 0.5 μg per reaction. Tubes were incubated on nutator  overnight at 4 °C. The next day, tubes were collected and washed 2✕ with 200 μl cell permeabilization  buffer. Beads were resuspended in 50 μl cell permeabilization buffer and 2.5 μl pAG-MNase was added.  After 10 min incubation at room temperature, beads were washed with another 200 μl cell permeabilization  buffer 2✕. Finally beads were resuspended in 50μl cell permeabilization buffer. 1 μl of 100 mM CaCl2 was  added to activate the enzyme. Tubes were then incubated for 2 h on nutator at 4 °C. Finally, the reaction  was stopped with 33 μl of stop master mix. DNA was then purified and quantified using a Qubit fluorometer.  For library preparation, we used the CUTANA CUT&RUN Library Prep Kit from Epicypher (#14-1001). End  Repair step, Adapter ligation and U-excision were performed following manufacturer’s instructions. We  used 1✕ SPRIselect beads for DNA cleanup. After indexing PCR, we then used 1✕ SPRIselect beads for  DNA cleanup prior to sequencing. Analysis of the library fragment size was done using Tapestation.  10 million Paired End Reads (PE) per sample.

value: Lung, Epithelial

value: Mesothelioma

tag: cutnrun antibody


title: control, naïve, rep1


title: PDX6-control-2


title: erf114, JA, 3h, rep3

city: Qingdao

first: XUAN

middle: JIA]

last: SUI

state: 山东省

address: Binhai Road

institute: ShanDong university

data_processing:
Select the corresponding testing methods for quality inspection according to the requirements of samples and products
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
Assembly: The corresponding library quality control protocol will be selected depending upon product requirements.
Supplementary files format and content: Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
Supplementary files format and content: Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Arabidopsis seeds were planted in a culture dish containing 1/2 ms medium at 4 ° C for two days and germinated at 22 ° C for five days

extract_protocol:
RNAsimple Total RNA Kit (TIANGEN) DP419
RNA-Seq (Quantification) uses a new generation of high-throughput sequencing technology to study the gene expression pattern of eukaryotic cells and provide accurate digital expression profile detection by sequencing and comparing transcripts.
Transcriptome research is the basis and starting point of gene function and structure research. Through the new generation of high-throughput sequencing, almost all transcripts of a specific tissue or organ of a species can be obtained comprehensively and quickly.

treatment_protocol: 15μM MeJA (Sigama)

value: root

value: MeJA


title: erf114, JA, 3h, rep2


title: PDX6-control-3

value: breast cancer cells


title: Sensitive_shNTC-rep1

value: Pancreas

value: Adenocarcinoma


title: control, trained, rep4

value: Mushroom body

value: trained


title: erf114, JA, 3h, rep1


title: IgG_P7883R_CL3

value: Resistant to TEAD inhibitor GNE-7883


title: IgG_P_DMSO

value: Sensitive to TEAD inhibitor GNE-7883


title: H226-7883R_CL3_FOSL1

value: ThermoFisher Cat. #PA5-66880)


title: control, trained, rep3


title: PDX6-control-1


title: erf114, ck, rep3

value: MS


title: trxKD, trained, rep1


title: H226-7883R_CL3_YAP


title: PDX5-B16-4

value: B16 (anti-ROR2 antibody)


title: control, trained, rep2


title: control, trained, rep1


title: PDX5-B16-2


title: PDX5-B16-3


title: H226-7883R_CL3_TEAD1


title: erf114, ck, rep2


title: H226-P_7883_FOSL1


title: erf114, ck, rep1


title: PDX5-control-4


title: H226-P_7883_TEAD1


title: PDX5-control-3


title: Col, JA, 3H, rep2

value: col


title: Col, JA, 3H, rep1


title: Aspergillus terreusmycelia under optimized metal ion, Sample 3, Day2

city: Changzhou

first: Xia

last: Yi

address: Gehu Middle Road #21

institute: Changzhou University

data_processing:
In briefly, the enriched mRNA was fragmented into approximately 200 nt RNA inserts, which were used to synthesize the first-strand cDNA and the second cDNA. The double-stranded cDNA were performed end-repair/dA-tail and adaptor ligation. The suitable fragments were isolated by Agencourt AMPure XP beads (Beckman Coulter, Inc.), and enriched by PCR amplification. Finally, the constructed cDNA libraries of A. terreus were sequenced on a flow cell using an Illumina HiSeq™ sequencing platform. Low quality reads, such as only adaptor, unknown nucleotides>5%, or Q20 <20% (percentage of sequences with sequencing error rates <1%), were removed by perl script.Differential gene analysis was performed using DESeq under the conditions of Fold Change ≥ 2.0 and Adjusted Pvalue ≤ 0.001. Using the pheatmap function on the differential gene set to draw a heatmap of differential gene clusters. According to the GO and KEGG annotation results and official classifications, the differentially expressed genes were functionally classified, and the phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) in R software was used for KEGG enrichment analysis, and the TermFinder package was used for GO Enrichment analysis (https://metacpan.org/pod/GO::TermFinder). With a Q value of  ≤ 0.05 as the threshold, candidate genes that met this condition was defined as being significantly enriched.
Assembly: The clean reads that were filtered from the raw reads were mapped to the genome of Aspergillus_terreus (GCA_034642025.1) using Tophat2 software.
Supplementary files format and content: ASM3464202v1
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Aspergillus terreus

source_name: mycelia

growth_protocol: A. terreus mycelia were cultured in fermentation medium at 32 oC 180 rpm.

extract_protocol:
The total RNA was isolated from all A. terreus samples using the TRIzol Reagent (Life technologies, California, USA) according to the instructions.
RNA was harvested using TRlzol Reagent (Life technologies, California, USA). 0.1-1.0 μg of total RNA was used for the construction of sequencing libraries.
The library was constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530) and NEBNext Multiplex Oligos for Illumina (NEB, E7500).

treatment_protocol: A. terreus mycelia were cultured in fermentation medium at 32 oC 180 rpm adding the certain concentration of taurine.

value: mycelia

value: Aspergillus terreus AT2022

value: WT

value: treated with 0.25 g/L ZnSO4·2H2O and 0.40 g/L FeSO4·2H2O


title: Col, ck, rep3

value: root


title: Aspergillus terreus mycelia, Control 2, day2

value: Untreated with 0.15 g/L ZnSO4·2H2O and 0.16 g/L FeSO4·2H2O


title: PDX5-control-1

value: breast cancer cells

value: IgG


title: Aspergillus terreus mycelia, Control 1, day2


title: Col, ck, rep1


title: PDX5-B16-1


title: Aspergillus terreus mycelia under optimized metal ion, Sample 2, Day2


title: H226-P_7883_YAP

value: Lung, Epithelial

value: Mesothelioma


title: Aspergillus terreus mycelia under optimized metal ion, Sample 1, Day2


title: PDX5-control-2


title: H226-P_DMSO_FOSL1


title: Aspergillus terreus mycelia, Control 3, day2


title: 1858_postTreatment

status: Public on Dec 16 2024

type: genomic

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

description:
1858_Sx_BrM
Sample from resection post-treatment

hyb_protocol: Genomic DNA was bisulfite converted using the Infinium Methylation EPIC array with the Infinium MethylationEPIC v1.0 B5 manifest published by Illumina.

scan_protocol: Microarray chips were scanned using the Illumina HiScan system. Array processing and Beadstudio analysis were conducted through Genuity Science Ltd (Ireland) and Beaumont Hospital (Dublin, Ireland).

data_processing:
Quality control was performed on the raw data (idat files); probes were filtered with a detection P value above 0.01 in all samples. Furthermore, probes with a bead count of less than 3 in at least 5% of the samples were removed. Also, probe sequences which aligned at multiple sites and potential probes with SNPs were excluded from the analysis using the ChAMP package. The raw data were normalized using Beta-mixture quantile normalization (BMIQ), and batch correction was performed using the combat function from the SVA package within the ChAMP pipeline. Differential methylated probe analysis was performed using the champ.DMP function in the ChAMP package, which utilizes the limma package, where the threshold for the Benjamini-Hochberg adjusted P values threshold was set to 0.05. A CpG was considered differentially methylated if the methylation difference between conditions (the beta value difference) was at least 0.2.
Beta (β) intensity value, normalized and batch corrected.

label: Cy3 and Cy5

source_name: Breast cancer tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue from patient-matched, pre-treatment breast tumors (Bx), post-treatment resection specimen (Sx), and subsequent metastasis (Rx). This extraction was performed using the Qiagen QiAMP DNA FFPE kit and run on the QIAcube, following manufacturer’s standard protocols.

value: Breast cancer tissue

tag: sample type

value: Resection


title: 1598_postTreatment

description:
1598_Sx_LN
Sample from resection post-treatment

tag: tissue


title: 496_preTreatment

description:
496_Bx_Bone
Sample from biopsy pre-treatment

value: Biopsy


title: 1858_metastasis_BrM

description:
1858_Rx_BrM
Sample from metastasis

source_name: Breast cancer brain metastasis tissue

value: Breast cancer brain metastasis tissue

value: Metastasis


title: 2151_preTreatment

description:
2151_Bx
Sample from biopsy pre-treatment


title: Col, ck, rep2

value: MS


title: H226-P_DMSO_TEAD1

value: Sensitive to TEAD inhibitor GNE-7883


title: 220_preTreatment

description:
220_Bx
Sample from resection pre-treatment


title: 316_postTreatment

description:
316_Sx
Sample from resection post-treatment


title: 645_metastasis_BrM

description:
645_Rx_BrM
Sample from metastasis


title: H226-P_DMSO_YAP


title: 165_preTreatment

description:
165_Bx_LN
Sample from biopsy pre-treatment


title: 165_metastasis_LN

description:
165_Rx_LN
Sample from metastasis

source_name: Breast cancer lung metastasis tissue

value: Breast cancer lung metastasis tissue


title: 187_metastasis_BrM

description:
187_Rx_BrM
Sample from metastasis


title: 2151_postTreatment

description:
2151_Sx
Sample from resection post-treatment


title: 165_postTreatment

description:
165_Sx_LN
Sample from resection post-treatment


title: Thyroid_Wistar, 1w old, control #1

city: Hiroshima

first: Nariaki

last: FUJIMOTO

state: Hiroshima

address: 1-2-3 Kasumi

department: RIRBM

country: Japan

institute: Hiroshima University

description:
Library name: W375
2x100 bp

data_processing:
The genomic mapping was performed with hisat2 (ver. 2.2.1) . The reads were counted with featureCounts (ver. 2.0.0) and normalized as Transcripts Per Million (TPM)
Assembly: The genomic mapping was performed with hisat2 (ver. 2.2.1) . The reads were counted with featureCounts (ver. 2.0.0) and normalized as Transcripts Per Million (TPM)
Supplementary files format and content: A csv file containing raw counts, RPKMs, and TPMs for each sample

organism: Rattus norvegicus

source_name: Thyroid

extract_protocol:
Total RNA was isolated from the thyroid tissue with Isogen II (Nippon Gene Co., Tokyo, Japan) according to the manufacturer’s instructions.
cDNA libraries were prepared with MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd, Shenzhen, China.) and circularized with MGIEasy Circularization Kit (MGI Tech Co.).

value: Thyroid

value: Wistar

value: male

value: 1 week old

value: Sham-irradiation


title: 1598_preTreatment

description:
1598_Bx_LN
Sample from biopsy pre-treatment


title: 1598_metastasis_LN

description:
1598_Rx_LN
Sample from metastasis


title: Thyroid_Wistar, 4m old,4Gy #1

description:
Library name: W368
2x100 bp

value: 4 months old

value: X-irradiation, Cervical, 4Gy


title: Thyroid_Wistar, 4m old,4Gy #2

description:
Library name: W370
2x100 bp


title: 496_metastasis_Bone

description:
496_Rx_Bone
Sample from metastasis

source_name: Breast cancer bone metastasis tissue

value: Breast cancer bone metastasis tissue


title: Thyroid_Wistar, 4m old, control #2

description:
Library name: W366
2x100 bp


title: 645_preTreatment

description:
645_Bx_BrM
Sample from biopsy pre-treatment


title: Spheroplasts incubated with TMP without 5s of UV treatment

city: Ithaca

first: Michelle

middle: D.

state: NY

address: 142 Sciences Dr B08

department: LASSP

institute: Cornell University, HHMI

description:
Library name: Sphero_UV5s
Raw bigwig files for the condition

data_processing:
Sequencing, demultiplexing and Fastq generation were performed by the Cornell Biotechnology Resource Center. Fastq files were aligned to the SacCer3 Genome using BWA-mem2 with default settings for paired-end reads. Sam files were converted to BAM files followed by fixmate and duplicate marking using Samtools. Duplicates were again marked using picard-MarkDuplicates, and duplicates were removed using Samtools-view. Bedgraph files were generated using deeptools bamCoverage with 10 bp bins using the following settings (--samFlagInclude 64 --Offset 1) yielding the coverage of the 5’ end of Read_1 where the ICL was located.
Bedgraph files were further processed in MATLAB to ensure one bin per 10 bp interval, and normalized to the mean number of reads per bin.  Replicate bedgraphs were averaged, and indicated subtractions were done using MATLAB.  Normalized bedgraphs were converted to bigwig files using ucsc-bedGraphToBigWig.  Heatmaps and composite plots were generated using deeptools computeMatrix, and visualized using Origin Lab.  Bed files containing coordinates of verified s. cerevisiae ORFs were downloaded from the Saccharomyces Genome Database (SGD), and a region blacklist was downloaded from the yeastepigenome.org.  Bed files for each gene configuration in Figure 3 were generated by considering the boundaries of nearest neighbor verified ORFs and classifying them based on their strand configuration.  Regions that had any annotations according to the list of all yeast genes from the SGD were removed to isolate true intergenic regions.  The resulting Bed files were used to make heatmaps and composite plots as described above.
Assembly: SacCer3
Supplementary files format and content: BigWig

organism: Saccharomyces cerevisiae

growth_protocol: The Saccharomyces cerevisiae strain BY4741 (MAT a his3Δ1 leu2Δ0 met15Δ0 ura3Δ0 bar1::NatMX his3∆1::HIS3-ADH1pr-hENT-GPDpr-HSV-TK)58 was used for all experiments. Cells were grown at 30°C in YPD media until the OD600 reached ~0.6, and then processed for different conditions as described below.

extract_protocol:
Directly after TMP photobinding, the cells were fixed in 95 ml 70% -20 °C ethanol and placed at -20°C overnight. Cells were then harvested by centrifugation at 10,000 g for 10 minutes, resuspended in 500 µl of 50 mM sodium citrate (Sigma, 567446), pH 7.4, and incubated at room temp for 10 minutes. Centrifugation and wash steps were repeated once more, followed by a 20-minute Zymolyase treatment as detailed above. Spheroplasts were harvested by centrifugation and resuspended in 100 µl of lysis buffer (300 mM NaCl (Fisher, BP358), 50 mM EDTA (Fisher, AM9260G), 2% SDS (Sigma, 71725), and 5 % (v/v) RNase A (Thermo , 12091021) for ~2 hours and then vortexed for 2 minutes. 10 µl of Proteinase K (NEB, P8107S) was added, and cells were incubated for 2 hours at 65 °C.  Zero torsion samples were harvested 10,000 g at 4°C, the supernatant was removed, and they were resuspended in 100 µl of Lysis buffer containing 10 µl Proteinase K. The zero torsion samples were incubated at 65°C overnight to reverse formaldehyde crosslinks. After lysis, genomic DNA was extracted from all samples via 2X phenol-chloroform (Sigma, 77617) extraction followed by isopropanol (Sigma, 59304) precipitation.
Extracted genomic DNA was sonicated to ~400 bp fragments using appropriate settings on a Covaris E200 sonicator.  Following sonication, DNA was treated with 5 µl RNase A and purified using a Zymoclean DNA  Clean and Concentrator-5 kit according to the manufacturer’s protocol using a 7:1 binding buffer:sample ratio. After quantification using a Biotum HS DNA quantification kit, 250 ng of DNA was diluted into 86 µl of 10 mM Tris-Cl pH 8.5, incubated at 98°C for 15 minutes, and then directly moved to ice for 2 minutes. DNA was then digested with 4 µl of ExoI (NEB, M0293) in 1X ExoI reaction buffer at 37°C for 1 hour. This digestion process was repeated by incubating at 98°C for 1 hour and then adding an additional 4 µl of ExoI followed by another incubation at 37°C for 1 hour. Digested samples were purified using a Zymo DNA Clean and Concentrator-5 kit using a 7:1 binding buffer: sample ratio. DNA was again quantified using the Biotum HS DNA assay. Illumina adaptors were ligated to the digested samples using the NEBNext Ultra II DNA library prep kit for Illumina (NEB, E7645) at half the standard total reaction volume of the manufacturer’s protocol. Adapter ligated DNA was purified with 2X Ampure beads (Beckman Coulter) and eluted in 40 µl of 10 mM Tris-Cl pH 8.5.  DNA was stored at -20 C until further processing.  To locate psoralen interstrand crosslinks, DNA from the previous step was incubated with 5 µl of lambda exonuclease (NEB, M0262) in the provided buffer in a 50 µl total reaction volume at 37°C for 1 hour, purified with 1.8X Ampure beads, and eluted with 30 µl of 10 mM Tris pH 8.5. Lambda-digested DNA was then subjected to 10 rounds of primer extension with Q5 DNA polymerase (NEB, M0491), using 10 nM of the primer (ID): 5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T on a thermocycler (98°C for 10s à 10 rounds (98°C, 10s à 65°C, 2 min)à 65°C, 5min à 95°C 1min à 4°C). Products were purified using 1.8x Ampure beads and eluted in 40 µl 10mM Tris pH 8.5. Primer extension products were ribotailed using 1.4 µl Terminal Transferase (NEB, M0315) and 0.4 mM rGTP (Roche, 11277057001) in Terminal Transferase buffer supplemented with 0.25 mM CoCl2 by incubating at 37°C for 30 minutes followed by incubation at 75°C for 20 min. Ribotailed products were purified with 1.8X Ampure beads, eluted with 30 µl 10mM Tris pH 8.5. Purified ribotailed products were ligated with 0.33 µM annealed adapter oligos (IDT) (Top: 5’p-AGA TCG GAA GAG CGT CGT GTA GGG AAA GAG TGT-3’, Bottom: 5’ ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CCC -3’) using 1.2 µl T4 DNA ligase (NEB, M0202S) in the provided buffer for 1 hour at 16 °C, and subsequently purified with 1.8X Ampure beads and eluted in 20 µl 10mM Tris pH 8.5. Finally, products were indexed and amplified using NEBNEXT Multiplex Oligos for Illumina set 1 (NEB, E7600) following the manufacturers protocol with a total of 12 PCR cycles. The PCR products were purified using 0.8X Ampure beads and eluted in TE (Invitrogen). Samples were pooled at equimolar concentrations and empty adapters were removed from the pool.  Pooled libraries were sequenced on a NextSeq 2000 (Illumina) using a NextSeq 2K P2 100 bp kit (Illumina) in paired-end mode with a 63 bp Read_1 and 59 bp Read_2.

treatment_protocol: Zero torsion state preparation Cells designated as zero torsion state controls were crosslinked with 1% (v/v) formaldehyde (Fisher, F79-500) for 15 minutes at 30°C. Formaldehyde was quenched with 0.4 M glycine (Sigma, 357002) for 5 minutes at room temperature. Following quenching, cells were pelleted and washed 2X with PBS at 4˚C. Next, cells were spheroplasted via 0.01% (v/v) 10 mg/µl zymolyase (Sunrise Science Products, N0766391) treatment in 1 M sorbitol (Sigma, S6021), 0.5 mM 2-mercaptoethanol (Sigma, 444203) for 20 minutes. Spheroplasts were confirmed to be >90% of cells using microscopy. Formaldehyde-fixed spheroplasts were centrifuged at 1,000 g for 10 minutes at 4˚C, washed with 25 ml of cold PBS (Thermo, AM9624), and resuspended in 100 µl of 1x DpnII reaction buffer (NEB, R0543) containing 100 units of DpnII (NEB, R0543) and supplemented with 0.1% (v/v) NP-40 (Thermo, 85124), and 10 µM TMP (Sigma, T6137). Samples were incubated for 2 hours at 37°C followed by TMP photobinding as described below. Trimethylpsoralen Photobinding The 4,5′, 8-trimethylpsoralen (TMP) was dissolved in 100% ethanol at a final stock solution of 2 mM. TMP was added to growing cells at a final concentration of 10 µM and cells were further incubated at 30°C for 1 hour. Twenty-five mL of cell solution was placed in a 10 cm petri dish and exposed to ~0.15 W/cm2 of 365-nm light for 20 seconds. Zero torsion samples followed a similar photobinding protocol but were exposed to UV light at ~0.35 W/cm2 for 10 seconds in a 1.5 ml Eppendorf tube. Samples were harvested at 10,000 g at 4°C, the supernatant was removed, and they were resuspended in 100 µl of Lysis buffer containing 10 µl Proteinase K. The zero torsion samples were incubated at 65°C overnight to reverse formaldehyde crosslinks. After lysis, genomic DNA was extracted from all samples via 2X phenol-chloroform (Sigma, 77617) extraction followed by isopropanol (Sigma, 59304) precipitation.


title: 496_postTreatment

description:
496_Sx_Bone
Sample from resection post-treatment


title: Cells treated with psoralen and exposed to UV for 80s

description:
Library name: Cells_UV_80s
Raw bigwig files for the condition


title: Sheared Genomic DNA Treated with 0.1 uM TMP

description:
Library name: DNA_0p1uM_TMP
Raw bigwig files for the condition


title: 645_postTreatment

description:
645_Sx_BrM
Sample from resection post-treatment


title: Thyroid_Wistar, 1w old,4Gy #1

description:
Library name: W382
2x100 bp


title: 316_preTreatment

description:
316_Bx
Sample from biopsy pre-treatment


title: Cells treated with psoralen and exposed to UV for 10s

description:
Library name: Cells_UV_10s
Raw bigwig files for the condition


title: Col, JA, 3H, rep3

value: root

value: col

value: MeJA


title: Cells treated with psoralen and not exposed to UV

description:
Library name: Cells_UV_0s
Raw bigwig files for the condition


title: Thyroid_Wistar, 4m old, control #1

description:
Library name: W364
2x100 bp


title: Thyroid_Wistar, 1w old, control #2

description:
Library name: W377
2x100 bp


title: 1858_preTreatment

description:
1858_Bx_BrM
Sample from biopsy pre-treatment

value: Breast cancer tissue

value: Biopsy


title: psoralen binding to Naked Genomic DNA after DpnII treatment bioloigcal replicate 2

description:
Library name: DPNII_DNA_Rep2
Raw, and Averaged bigwig files for DNA treated with psoralen after DpnII treatment and sonication


title: Spheroplasts incubated with TMP without UV treatment

description:
Library name: Sphero_UV0s
Raw bigwig files for the condition


title: Spheroplasts incubated with TMP without 30s of UV treatment

description:
Library name: Sphero_UV30s
Raw bigwig files for the condition


title: Spheroplasts treated with DpnII before psoralen photobinding biological replicate 3

description:
Library name: Sphero_DPNII_UV_Rep3
Raw, Averaged, and DNA subtracted bigwig files for spheroplasts treated with psoralen and DpnII


title: cells after psoralen photobinding biological replicate 1

description:
Library name: Cells_UV_20s_Rep1
Raw, Averaged, DNA subtracted, and Spheroplast subtracted bigwig files for Cells treated with psoralen


title: cells after psoralen photobinding biological replicate 2

description:
Library name: Cells_UV_20s_Rep2
Raw, Averaged, DNA subtracted, and Spheroplast subtracted bigwig files for Cells treated with psoralen


title: Spheroplasts incubated with TMP without 10s of UV treatment

description:
Library name: Sphero_UV10s
Raw bigwig files for the condition


title: Spheroplasts treated with DpnII before psoralen photobinding biological replicate 2

description:
Library name: Sphero_DPNII_UV_Rep2
Raw, Averaged, and DNA subtracted bigwig files for spheroplasts treated with psoralen and DpnII


title: Sheared Genomic DNA Treated with 0.4 uM TMP

description:
Library name: DNA_0p4uM_TMP
Raw bigwig files for the condition, The top 2 concentrations were used as Cell_DNA_Avg


title: Sheared Genomic DNA Treated with 0.2 uM TMP

description:
Library name: DNA_0p2uM_TMP
Raw bigwig files for the condition, The top 2 concentrations were used as Cell_DNA_Avg


title: Spheroplasts treated with DpnII before psoralen photobinding biological replicate 1

description:
Library name: Sphero_DPNII_UV_Rep1
Raw, Averaged, and DNA subtracted bigwig files for spheroplasts treated with psoralen and DpnII


title: Thyroid_Wistar, 1w old,4Gy #2

description:
Library name: W384
2x100 bp


title: 187_postTreatment

description:
187_Sx_BrM
Sample from resection post-treatment

value: Resection


title: Cells treated with psoralen and exposed to UV for 40s

description:
Library name: Cells_UV_40s
Raw bigwig files for the condition


title: MHCC-97H GK921-rep 2

city: Wuhan

first: Tian Ci

state: Hubei

address: No. 1095 Jiefang Avenue, Wuhan, China

department: Hepatic Surgery Center

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Library name: Sample5

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTQC version 0.11.5 and Linux version 6.8.0
RNA-seq reads were aligned to the hg38 genome assembly using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.1-beta).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Feature Counts version v1.6.0 was used to count the fragment within each gene, and TMM algorithm was used for normalization
Differential expression analysis for RNA was performed using R package edgeR（3.4.3）.
Assembly: hg38
Supplementary files format and content: RNAseq all sample FPKM.txt

growth_protocol: MHCC-97H cells were grown in complete DMEM(Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 1% penicillin/ streptomycin(Gibco)

extract_protocol:
Total RNAs were isolated from MHCC-97H cells by Trizol reagent (Life Technologies, Carlsbad, California, USA) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: MHCC-97H cells(1×106) were treated with DMSO(control) or 2μM GK921 for 24h.

value: Liver

value: Hepatocellular Carcinoma

value: WT


title: MHCC-97H DMSO-rep 3

description: Library name: Sample3

value: DMSO 24H


title: CHGA-Venus, duodenum, scRNA-seq

city: Cambridge

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

country: United Kingdom

institute: University of Cambridge

description:
Library name: Duodenum
10x Genomics

library_source: transcriptomic single cell

data_processing:
Quality controls, read alignment, and raw count quantification for each cell were generated using the CellRanger pipeline (v6.1.2, 10x Genomics).
Assembly: hs38 genome, downloaded from the UCSC genome browser.
Supplementary files format and content: Count matrices, exported by CellRanger, are H5 format.
Supplementary files format and content: Seurat objects are in RDS format, for import into R, including normalised data, and UMAP maps.

source_name: duodenum

growth_protocol: Organoids were passaged every 10–14 days, maintained, and differentiated for maximum generation of EECs. Human organoid growth medium consisted of advanced DMEM:F12 (ADF) medium, conditioned Wnt3A and RSPO-1 medium, murine noggin (100 ng/ml, Peprotech), B27 supplement (Invitrogen), N2 supplement (Invitrogen), L-glutamine (2 mm, Sigma–Aldrich), penicillin-streptomycin (50 U/ml and 50 μg/ml, respectively, Sigma–Aldrich), N-acetyl-L-cysteine (1 mm, Sigma–Aldrich), murine epidermal growth factor (EGF, 50 ng/ml, Invitrogen), A83-01 (500 nm, Tocris), human [Leu15]-gastrin I (10 nm, Sigma–Aldrich), human insulin-like growth factor 1 (IGF-1, 100 ng/ml, Biolegend) and human fibroblast growth factor 2 (FGF-2, 50 ng/ml Peprotech). Y-27632 (10 μm, Tocris) was added to human organoid medium for 3–4 days after passaging. The differentiation medium consisted of human organoid medium without EGF.

extract_protocol:
Human duodenum and ileum organoids were generated from fully anonymised specimens provided by Addenbrooke's Hospital Tissue Bank. Human small intestinal organoids were cultured in a differentiation medium for 5–10 days before enzymatic and mechanical dissociation to single cells. Single cells were sorted for Venus fluorescence using an Influx Cell Sorter (BD Biosciences) at the Cambridge Institute of Medical Research (CIMR) Flow Cytometry Core Facility. DAPI and DRAQ5 staining, side scatter, forward scatter and pulse width gates were used to remove debris and cell clusters.
cDNA library preparations were performed using the Chromium system (10X Genomics) by the Genomics and Transcriptomic Core at the Institute of Metabolic Science.

value: duodenum

value: CHGA-Venus


title: CHGA-Venus, ileum, scRNA-seq

description:
Library name: Ileum
10x Genomics

source_name: ileum

value: ileum


title: MHCC-97H DMSO-rep 2

description: Library name: Sample2

source_name: Liver


title: Cells treated with psoralen and exposed to UV for 5s

description:
Library name: Cells_UV_5s
Raw bigwig files for the condition


title: Sheared Genomic DNA Treated with 0.05 uM TMP

description:
Library name: DNA_0p05uM_TMP
Raw bigwig files for the condition


title: MHCC97H-GK921-H3K4me3Q5ser-rep2

description: Library name: MHCC97H-GK921-H3K4me3Q5ser-rep2

data_processing:
Sequencing reads were quality controlled using FASTQC version 0.11.5 and Linux (version 6.8.0).
Reads were aligned to hg38 using Bowtie2 (version 2.5.4)
Sam files were converted to bam files and sorted using Samtools view and sort (version 1.19.2)
Identical equence reads were collapsed to avoid PCR duplicates using Picard Tools MarkDuplicates(version 2.25.5)
Bedgraph files averaging replicates were constructed from deduplicated bam files using Deeptools (version 2.27.0) bamCompare with -normalizeUsing RPKM --operation log2 --scaleFactorsMethod None -of bedgraph --binSize 50 --extendReads 300
Assembly: hg38
Supplementary files format and content: bigWig cut and tag signal files
Supplementary files format and content: DMSO-H3K4me3_1.bw
Supplementary files format and content: DMSO-H3K4me3_2.bw
Supplementary files format and content: DMSO-H3K4me3Q5ser_1.bw
Supplementary files format and content: DMSO-H3K4me3Q5ser_2.bw
Supplementary files format and content: GK921-H3K4me3_1.bw
Supplementary files format and content: GK921-H3K4me3_2.bw
Supplementary files format and content: GK921-H3K4me3Q5ser_1.bw
Supplementary files format and content: GK921-H3K4me3Q5ser_2.bw
Library strategy: CUT&Tag

extract_protocol:
The CUT & Tag assay was conducted following the protocol outlined by the manufacturer of the Hyperactive Universal CUT & Tag Assay Kit (TD903, Vazyme, China). In brief, 1 × 105 cells were collected and washed. Subsequently, Concanavalin A-coated magnetic beads were added and allowed to incubate for 10 minutes. The cells attached to the beads were then suspended in dig-wash buffer along with the primary antibodies overnight at 4 °C. Following this, the cells were treated with pA/G-Tnp at room temperature for 1 hour. The cells were further suspended in tagmentation buffer and incubated at 37 °C for 1 hour. To halt tagmentation, a mixture of 20 mg/mL proteinase K, 10% SDS, and 0.5 mol/L EDTA was added to the sample, which was then incubated at 55 °C for 10 minutes. Subsequently, DNA extraction was carried out, followed by suspension in RNase-free water. The DNA underwent PCR amplification and purification.
DNA was used to construct sequencing libraries following the protocol provided by the TruePrep Index Kit V2 for Illumina (TD202, Vazyme, China).


title: psoralen binding to Naked Genomic DNA after DpnII treatment bioloigcal replicate 1

description:
Library name: DPNII_DNA_Rep1
Raw, and Averaged bigwig files for DNA treated with psoralen after DpnII treatment and sonication


title: MHCC97H-GK921-H3K4me3-rep2

description: Library name: MHCC97H-GK921-H3K4me3-rep2


title: MHCC97H-GK921-H3K4me3Q5ser-rep1

description: Library name: MHCC97H-GK921-H3K4me3Q5ser-rep1


title: MHCC-97H GK921-rep 1

description: Library name: Sample4


title: MHCC97H-DMSO-H3K4me3Q5ser-rep2

description: Library name: MHCC97H-DMSO-H3K4me3Q5ser-rep2


title: MHCC97H-GK921-IgG-rep2

description: Library name: MHCC97H-GK921-IgG-rep2


title: CRC_ST_V11Y04-378-A1

city: Philadelphia

first: Jiazhen

last: Rong

state: PA

address: Academic Research Building

department: Genomics and Computational Biology

institute: University of Pennsylvannia

description:
Library name: V11Y04-378-A1
formalin-fixed paraffin-embedded (FFPE) Spatial Transcirptomics

data_processing:
Raw sequencing data were processed using 10x Genomics Space Ranger to generate FASTQ files.
10x Genomics Space Ranger's count pipeline with default settings aligned the FASTQ file to generate the bam file and the final gene expression count matrix.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of genes
Supplementary files format and content: matrix.mtx.gz: gene expression count matrix
Supplementary files format and content: filtered_feature_bc_matrix.h5: h5 format of filtered count matrix
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and their spatial coordinates
Supplementary files format and content: aligned_fiducials.jpg: aligned fluducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of the tissue and spots
Supplementary files format and content: scalefactors_json.json: image scale factors in json format
Supplementary files format and content: tissue_hires_image.png: high resolution image of the tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image of the tissue
Library strategy: Spatial Transcriptomics

source_name: Colorectal Cancer

extract_protocol:
The formalin-fixed paraffin-embedded (FFPE) tissue was extracted following the standard 10x Visium guideline.
The sequencing libraries were prepared based on the instruction of 10x Genomics Visium Spatial Gene Expression Reagent Kits.

value: Colorectal Cancer


title: MHCC-97H DMSO-rep 1

description: Library name: Sample1


title: MHCC97H-GK921-H3K4me3-rep1

description: Library name: MHCC97H-GK921-H3K4me3-rep1


title: MHCC-97H GK921-rep 3

description: Library name: Sample6


title: MHCC97H-DMSO-H3K4me3-rep2

description: Library name: MHCC97H-DMSO-H3K4me3-rep2


title: MHCC97H-GK921-IgG-rep1

description: Library name: MHCC97H-GK921-IgG-rep1


title: MHCC97H-DMSO-H3K4me3-rep1

description: Library name: MHCC97H-DMSO-H3K4me3-rep1


title: MHCC97H-DMSO-IgG-rep2

description: Library name: MHCC97H-DMSO-IgG-rep2


title: MHCC97H-DMSO-H3K4me3Q5ser-rep1

description: Library name: MHCC97H-DMSO-H3K4me3Q5ser-rep1


title: HA102AC_inf

city: Dallas

first: Bingqing

last: Xie

state: Texas

address: 6001 Forest Park Rd

department: Internal medicine

institute: University of Texas Southwestern medical center

description:
Library name: HA102AC_inf
10x RNA

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software (v7.0.1)
Extract high-quality cells with 200-6000 genes and greater than 1000 UMIs per cell and mitochondria percentage less than 50 using Seurat V4.3
Assembly: hg38
Supplementary files format and content: Each process sample contains the following files: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene features), and matrix.mtx.gz (sparse count matrix).

growth_protocol: No growth

extract_protocol:
Tissues were incubated in buffered EGTA at 37 Celsius for 15 minutes to separate epithelium from lamina propria. Epithelium was digested in TrypLE express at 37 Celsius for 5 minutes. Lamina propria was digested in liberase TM at 37 Celsius for 20 minutes.
Amplication product of cDNA was processed with Dnase fragmentation, A tailling, ligation of adaptors and index PCR per 10x Genomics 3'RNA v3.1 library construction protocol.

treatment_protocol: No treatment

tag: condition

value: CD

tag: race

value: casusasian

tag: history

value: Ileocolonic CD

tag: treatment (biological)

value: anti-TNF

tag: sample region

value: inf


title: HA104AC_inf

description:
Library name: HA104AC_inf
10x RNA

tag: age

value: Colonic and Perianal CD


title: MHCC97H-DMSO-IgG-rep1

description: Library name: MHCC97H-DMSO-IgG-rep1

tag: genotype

tag: treatment


title: HA98AC_ad

description:
Library name: HA98AC_ad
10x RNA

tag: patient

value: Ileal-colonic and perianal CD

value: adjacent


title: HA98AC_inf

description:
Library name: HA98AC_inf
10x RNA


title: HA104AC_ad

description:
Library name: HA104AC_ad
10x RNA


title: HA102AC_ad

description:
Library name: HA102AC_ad
10x RNA


title: DIFI_SEC_F7

city: Houston

first: exRNA

last: BRL

state: TX

address: One Baylor Plaza

department: Molecular & Human Genetics - Milosavljevic

institute: Baylor College of Medicine

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: cell culture

extract_protocol:
RNA Isolation method was "500uL of biofluid was incubated with 100uL warmed Slurry and 900uL warmed Lysis Buffer A (containing 2-Mercaptoethanol) for 10 min at 60C. To this 1.5 mL of 100% ethanol was added and centrifuged for 2min at 1000rpm. To the pellet 300uL Lysis Buffer A was added and incubated for 10 min at 60C. 300uL 100% Ethanol was added, loaded onto the filter column and centrifuged for 30sec at 1000xg followed by 1 min at 16000xg. The column was washed thrice with 400uL Wash Solution for 1 min at 16000 xg and then centrifuged once again for 3 min to dry the membrane. RNA was eluted in 14uL water with a slow spin for 2 mins at 300 xg followed by a spin for 3 min at 16000 xg.". RNA Isolation kit was Plasma/Serum Circulating and Exosomal RNA Purification Kit(Norgen Biotek).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were multiplexed. Type of Starting Material was total RNA.

value: Colorectal Carcinoma

tag: anatomical location

value: Colon structure

tag: rna source

value: other


title: DIFI_SEC_F11


title: DIFI_SEC_F6


title: DIFI_CRUDE_INPUT

value: total cell-free biofluid RNA


title: DIFI_SEC_F10


title: DIFI_SEC_F3


title: DIFI_SEC_F5


title: DIFI_SEC_F12


title: DIFI_SEC_F2


title: DIFI_SEC_F4


title: DIFI_SEC_F9


title: DIFI_SEC_F8


title: DiFi_TC2_01d_3


title: Hepa1-6 TIL tTreg_rep3

city: Zhejiang

first: Sang Nee

last: Tan

address: Hangzhou

department: School of Medicine

institute: Westlake University

description: Library name: t4A

data_processing:
BGISEQ-500 was used to obtain sequence reads. The clean paired end reads were aligned to the Mus musculus reference genome (GRCm38) using STAR v2.7.11a via RSEM v1.3.3 with default parameters.
The reads count matrix and fragments per kilobase of exon model per million mapped fragments (FPKM) matrix was quantified using RSEM, with Gencode vM25 for gene annotation.
Differential expression analysis was performed by DESeq2, and ClusterProfiler was used for GSEA analysis.
Differentially expressed genes (DEGs) in Hepa1-6 intra-tumoral pTreg cells versus Hepa1-6 intra-tumoral tTreg cells were identified by a fold-change higher than 2 and adjusted p value lower than 0.05.
DEGs in Hepa1-6 intra-tumoral pTreg or Hepa1-6 intra-tumoral tTreg cells versus LN-derived Treg cells were identified by a fold-change higher than 4 and adjusted p value lower than 0.01.
Assembly: mm10
Supplementary files format and content: txt file including counts
Supplementary files format and content: txt file including FPKM value

source_name: Tumors

growth_protocol: Intra-tumoral Treg cells were sorted from Hepa1-6 tumor-bearing TCRbd-/- mice on day 18 post-inoculation. Treg cells sorted from lymph nodes of tumor-free mice were included as a control.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) according to manufacturer’s instructions.
RNA-seq library was constructed by BGI Genomics. BGISEQ-500 was used to obtain sequence reads.

treatment_protocol: We sorted tTreg cells from spleen and lymph nodes (LNs) of CD45.1 Foxp3YFP-cre mice, and sorted conventional Foxp3- CD4+ T cells and CD8+ T cells from CD45.2 Foxp3YFP-cre mice. We then co-transferred tTreg cells, conventional CD4+ T cells and CD8+ T cells at ratios of 1: 10: 8 into TCRbd-/- mice, followed by the inoculation of Hepa1-6 tumor cells 3 days later. The Hepa1-6 tumor-bearing mice were sacrificed on day 18 post-inoculation. Tumors were subjected to tumor-infiltrating lymphocytes (TIL) isolation. Intra-tumoral Treg cells were sorted from the isolated CD4+ T cells by using BD FACSAria Cell Sorter. Treg cells sorted from lymph nodes of tumor-free mice were included as a control.

value: Tumors

tag: cell line

tag: cell type

value: Treg cells

value: Foxp3YFP-cre and TCRbd-/- mice

value: Hepa1-6 tumor inoculation


title: Hepa1-6 TIL tTreg_rep2

description: Library name: t3A


title: Hepa1-6 TIL tTreg_rep5

description: Library name: t6A


title: DiFi_TC1_01w_2


title: Hepa1-6 TIL tTreg_rep4

description: Library name: t5A


title: DiFi_2500_HollowFiber2_2


title: Hepa1-6 TIL tTreg_rep1

description: Library name: t2A


title: DiFi_TC2_05d_1


title: Hepa1-6 TIL pTreg_rep3

description: Library name: P4A


title: DiFi_TC2_02h_3


title: Hepa1-6 TIL pTreg_rep2

description: Library name: P3A

value: Foxp3YFP-cre  and TCRbd-/- mice


title: Hepa1-6 TIL pTreg_rep1

description: Library name: P2A


title: Tumor-free LN total Treg_rep3

description: Library name: L11A

source_name: Lymph nodes

value: Lymph nodes

value: Not applicable

value: Foxp3YFP-cre  and TCRbd-/-mice


title: Tumor-free LN total Treg_rep4

description: Library name: L12A


title: DiFi_TC2_04d_1


title: DiFi_TC2_05d_3


title: DiFi_TC2_04d_3


title: DiFi_2500_HollowFiber1_1


title: DiFi_TC1_00h_2


title: Tumor-free LN total Treg_rep1

description: Library name: L9A


title: DiFi_TC1_00h_1


title: DiFi_TC2_02h_2


title: DiFi_TC2_03d_1


title: DiFi_TC1_02w_3


title: DiFi_TC2_00h_3


title: DiFi_2500_HollowFiber1_2


title: DiFi_TC2_02h_1


title: DiFi_TC2_00h_2


title: Tumor-free LN total Treg_rep2

description: Library name: L10A


title: DiFi_250_HollowFiber1_2


title: DiFi_TC2_10d_2


title: DiFi_250_HollowFiber1_1


title: DiFi_TC1_02w_2


title: DiFi_2500_HollowFiber1_3


title: DiFi_TC2_03d_3


title: DiFiP3C2


title: DiFiP2C1


title: DiFi_TC2_07d_2


title: DiFi_TC2_06d_2


title: DiFi_TC2_07d_1


title: VAESBJ_.12C_nDOX

type: RNA

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Affymetrix Clariom D Array one-color based hybridization protocol, cDNA samples were hybridized at 45°C for 16 h on separate Affymetrix Human Clariom D™ Arrays

scan_protocol: Affymetrix GeneChip 3000 Scanner

data_processing:
Raw data (.CEL files) were processed using the RMA (Robust Multi-array Average) normalization method implemented in the `oligo` package in R (version 4.0.3). Background correction and probe summarization were performed as described in the Affymetrix Clariom D Human array documentation. ProbeIDs were matched to Gene Symbols using the R package clariomdhumantranscriptcluster.db.
Clariom_D_Human.r1.pgf
Clariom_D_Human.r1.mps

label: biotin

source_name: Epithelioid Sarcoma cell line

label_protocol: Affymetrix GeneChip WT PLUS Reagent Kit, according to the manufacturer's protocol

growth_protocol: All cell lines were cultured in RPMI 1640 with stable glutamine (Gibco) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin (Sigma-Aldrich) at 37°C in a fully humidified 5% CO2 atmosphere. Cell lines were routinely tested for Mycoplasma contamination using a custom nested PCR protocol.

extract_protocol: For RNA extraction, the NucleoSpin RNA kit from Macherey-Nagel (Duren, Germany) was used following the manufacturer’s protocol.

treatment_protocol: 96h Dox or no Dox, BRM014 (1µM) or DMSO

value: VAESBJ

tag: cell model type

value: isogenic SMARCB1 tetON

value: No DOX


title: VAESBJ_MCS_nDOX

value: bulk empty (MCS) vehicle


title: VAESBJ_MCS_DOX

value: DOX


title: VAESBJ_.12C_DOX


title: DiFi_TC2_10d_3

value: Colorectal Carcinoma


title: DiFi_TC2_00h_1

value: Colon structure


title: DiFi_TC1_01w_1

value: other


title: NEPS_MCS_DOX

value: NEPS


title: NEPS_DMSO_4

value: DMSO


title: VAESBJ_.12_nDOX


title: NEPS_DMSO_3


title: NEPS_.20_DOX


title: DiFi_TC2_06d_1


title: VAESBJ_.12_DOX


title: NEPS_DMSO_1


title: DiFi_TC1_03w_3


title: DiFi_TC1_00h_3


title: DiFi_TC2_03d_2


title: DiFiP1C2


title: NEPS_MCS_nDOX


title: NEPS_.2_DOX


title: NEPS_DMSO_2


title: NEPS_BRM_1

value: BRM


title: NEPS_BRM_2


title: NEPS_BRM_3


title: DiFi_250_HollowFiber2_2


title: DiFi_TC2_02d_2


title: HSES2R_DMSO_2


title: HSES2R_DMSO_4


title: DiFi_TC1_04w_3


title: NEPS_.2_nDOX


title: DiFiP1C1


title: HSES2R_BRM_3


title: DiFi_TC2_07d_3


title: HSES2R_DMSO_1


title: DiFi_TC1_04w_2


title: HSES2R_BRM_1


title: HSES2M_DMSO_3


title: DiFi_TC2_21d_2


title: NEPS_.20_nDOX


title: HSES2R_BRM_2


title: DiFi_TC2_06d_3


title: DiFi_250_HollowFiber2_1


title: T-1

city: Shanghai

first: Lei

last: Hou

state: Shanghai

address: 746 Zhongshan Middle Road

department: Department of Cardiology

institute: Songjiang Hospital and Songjiang Research Institute, School of Medicine, Shanghai Jiao Tong University

description:
Library name: Sample 4
T-1 in tpm_allsamples.txt

data_processing:
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters - mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Assembly: NCBI_GCF_000001635.27_GRCm39
Supplementary files format and content: tab-delimited text file includes TPM for each Sample

source_name: Primary ADSCs

extract_protocol:
RNA was harvested using Trizol (Takara). 800 ug of total RNA was used for the construction of sequencing libraries.
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments.

value: Primary ADSCs

value: WT

value: Treg co-culture treatment

tag: batch

value: batch 1


title: T-2

description:
Library name: Sample 5
T-2 in tpm_allsamples.txt

value: batch 2


title: T-3

description:
Library name: Sample 6
T-3 in tpm_allsamples.txt

value: batch 3


title: DiFi_TC2_21d_1


title: DiFi_250_HollowFiber1_3


title: HSES2M_DMSO_1


title: HSES2M_DMSO_4


title: HSES2R_BRM_4


title: C-3

description:
Library name: Sample 3
C-3 in tpm_allsamples.txt

value: Ctrl


title: DiFi_TC2_01d_2