title: AP2gama-control-2

city: Shanghai

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

description: Library name: AP2gama-control-2

data_processing:
Raw sequencing reads were trimmed with Trim Galore (version 0.6.10) to remove adapter sequences and low-quality bases. The cleaned reads were then aligned to the mm10 reference genome using Bowtie2 (version 2.5.1) with the following parameters: -N 1 -X 1000 --no-mixed --no-discordant. Unmapped reads, multiple mapped reads, and PCR duplicates were subsequently filtered out using Sambamba (version 0.8.2). Peaks were called using MACS2 (version 2.2.6) with  -q 0.05 --nomodel --nolambda.To normalize read counts, RPKM (Reads Per Kilobase of transcript per Million mapped reads) was calculated in 100 bp bins using bamCoverage from deepTools (version 3.5.1).
Assembly: mm10
Supplementary files format and content: Bw files include the raw counts for each sample.
Library strategy: CUT&RUN

source_name: E9.25 embryo

extract_protocol:
E9.25 control and Trim37ko embryos carrying Nanog-EGFP transgene were dissected from recipient mice and digested with 0.25% Trypsin-EDTA (Thermo Fisher Scientific, Cat#25200072) at 37 °C. Following digestion, Nanog-EGFP positive PGCs were isolated from the suspension via FACS.
Cleavage Under Targets and Tagmentation (CUT&Tag) was performed to detect  H3K27ac (anti-H3K27ac antibody, Abcam, Cat#ab4729) modification in the genomes of E9.0 control and Trim37ko PGCs. Approximately 1000 PGCs per sample were transferred into a 1.5 mL tube containing 500 µL of wash buffer. The samples were then processed and libraries constructed according to the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, Cat#TD904). All libraries were sequenced on the Illumina NovaSeq 6000 platform at Genergy Biotechnology Co. Ltd. (Shanghai, China).
For CUT&Tag, all libraries were sequenced on the Illumina NovaSeq 6000 platform at Genergy Biotechnology Co. Ltd. (Shanghai, China). For CUT&RUN, after ligation and USER enzyme treatment, samples were purified with AMPure beads, PCR amplified, and sequenced on an Illumina NovaSeq X Plus.

value: E9.25 embryo

tag: strain

tag: genetic modification

value: Control

tag: time

tag: antibody


title: DNNK-4

status: Public on Jun 26 2026

type: SRA

city: Houston

first: Katayoun

last: Rezvani

state: Texas

address: 1515 Holcombe Blvd

department: Department of Stem Cell Transplantation and Cellular Therapy

country: USA

institute: The University of Texas MD Anderson Cancer Center

description: Library name: DNNK-4

library_source: transcriptomic single cell

data_processing:
Sequencing raw data were converted into fastq files by running Illumina’s bcl2fastq. The data were aligned to reference genome (GRCh38-2024-A) using Cell Ranger (10x Genomics Cell Ranger 9.0.1). After mapping, Seurat was used as the primary R package for quality control, transformation and most of the visualization of the gene expression data (PMID: 29608179). Quality control steps were first carried out using GEX assay whereby cells not expressing a minimum of 500 genes and genes expressed less than 3 cells were removed. The number of genes expressed, and the percentage of mitochondrial reads mapped were capped at 7500 and 5%, respectively.
Assembly: GRCh38
Supplementary files format and content: 10X Genomics Cell Ranger (9.0.1) output

molecule: total RNA

organism: Homo sapiens

source_name: ex vivo expanded cord blood NK cells

extract_protocol:
NK cells were isolated from thawed CBUs after purification of CBMCs via Ficoll gradient centrifugation, as described above. The isolated NK cells were then subjected to FACS to obtain purified NK cell subsets. First, Fc receptors were blocked using Human TruStain FcX (BioLegend; 1:50) for 15 min at 4 °C. Cells were then stained for 30 min at 4 °C  with the following fluorochrome-conjugated antibodies: anti-human CD45-Krome Orange (Beckman Coulter; 1:40), DAPI (ThermoFisher; 1:1000), anti-human CD56-BV510 (Biolegend; 1:200), anti-human CD16-FITC (Biolegend; 1:100), anti-human CD161-APC (Miltenyi Biotec; 1:100), anti-human CD3-PE (Biolegend; 1:200), anti-human CD33-PE (Biolegend; 1:200), anti-human CD14-PE (Biolegend; 1:200). Live CD56+CD3-CD33-CD14- NK cells were sorted to subsets expressing both CD16 and CD161, denoted as the double positive (DP) NK cell subset; or subsets that lacked both CD16 and CD161 expression, denoted as the double negative (DN) NK cell subset. Sorted NK cell subsets were expanded by co-culture with uAPCs and exogenous IL-2 (200 U/ml) for two weeks. DP/DN-derived NK cells were then stained with combinations of the following nucleotide barcode-labeled antibodies (BioLegend) for epitope labeling: TotalSeq-C1290 anti-human CD3 (HIT3a; 1:200), TotalSeq-C0168 anti-human CD57 (QA17A04; 1:200), TotalSeq-C0166 anti-human CD66b (6/40c; 1:200) , TotalSeq-C0100 anti-human CD20 (2H7; 1:200), TotalSeq-C0083 anti-human CD16 (3G8; 1:200), TotalSeq-C0051 anti-human CD14 (63D3; 1:200), TotalSeq-C0050 anti-human CD19 (HIB19; 1:200), TotalSeq-C0251 anti-human Hashtag 1 (2M2; 1:200), TotalSeq-C0252 anti-human Hashtag 2 (2M2; 1:200), TotalSeq-C0253 anti-human Hashtag 3 (2M2; 1:200), TotalSeq-C0254 anti-human Hashtag 4 (2M2; 1:200), TotalSeq-C0052 anti-human CD33 (P67.6; 1:150), TotalSeq-C0048 anti-human CD45 (2D1; 1:150), TotalSeq-C5100-custom-CD161 (REA631; 1:150), TotalSeq-C0047 anti-human CD56 (5.1H11; 1:150), TotalSeq-C0149 anti-human CD161 (HP-3G10; 1:150). As described in the GEM-X Flex gene expression protocols provided by the manufacturer (10x Genomics), cells were fixed with fixation buffer overnight in 4°C. Fixation was quenched with additive C and quenching buffer. Cells were then washed twice with quenching buffer and counted, 500,000 cells from each sample were loaded.
Libraries were prepared using the GEM-X Flex Gene Expression Reagent Kit (10x Genomics, Chromium Human Transcriptome Probe Set v1.1.0) following the manufacturer’s instructions. Briefly, each sample was subjected to probe hybridization for their gene expression (GEX) and TotalSeq antibody-derived epitope tags (ADT), respectively. Samples were then pooled for GEM generation and library preparation of both GEX and ADT fractions. Library size and quality were determined using a Fragment Analyzer (Agilent TapeStation Traces) before fragmentation and after final purification. Final library concentrations were measured on a Qubit 2.0 fluorometer (Thermo Fisher). For each sequencing reaction, pooling was performed with the aim to yield ~30,000 reads per cell for the GEX libraires and ~10,000 reads per cell for the ADT libraries. The pooled GEM-X Flex libraries were sequenced on the Illumina NovaSeq X Plus instrument using R1-i7-i5-R2 parameters of 28+10+10+90 cycles.

tag: tissue

value: ex vivo expanded cord blood NK cells

tag: cell type

value: NK cells

tag: batch


title: OM input#1

city: Taipei

first: Pinghsing

last: Tsai

state: Taiwan

address: Rm. 825, 7F., No.322, Sec. 2, Shipai Rd., Beitou D

country: Taiwan

institute: Taipei Veterans General Hospital

description:
Library name: OM1inp_eCLIP
RNA input, METTL3 knockdown endothelial cells under oscillatory flow#1

library_source: transcriptomic

data_processing:
FASTQ files were aligned to the GRCh37 reference genome using Kallisto and quantified to gene-level counts. Counts were normalized using edgeR.
Supplementary Files: Comma-delimited text file containing raw and normalized gene counts for each sample.
Assembly: GRCh37
Supplementary files format and content: excel files include TPM values for each Sample
Library strategy: iCLIP

molecule: polyA RNA

source_name: HUVEC

growth_protocol: HUVECs was maintained in DMEM (Sigma-Aldrich) supplemented with 10% Clonetics Endothelial Growth Medium (Lonza), 10% FBS (Gibco), 1% L-glutamate, and 1% sodium pyruvate.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Plus Kit (Qiagen) following the manufacturer's instructions.
RNA libraries for circRNA sequencing were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina, with modifications to enrich for circRNAs following RNase R treatment. Libraries were constructed according to the manufacturer's protocols.

treatment_protocol: Cells were collected and resuspended in electroporation buffer, followed by the addition of plasmid or siRNA. Electroporation was performed using the A-034 program on an Amaxa Nucleofector device (Lonza), and cells were subsequently seeded onto collagen I–coated slides or culture plates.

tag: cell line

value: HUVEC

value: Endothelial cells

tag: genotype

value: METTL3 knockdown


title: breast cancer_SM024

type: RNA

first: William

middle: Fraser

last: Symmans

state: TX

address: 2130 W Holcombe Blvd #11.4000

institute: University of Texas MD Anderson Cancer Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX.

data_processing:
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).
MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 600 breast cancer specific genes.

label: biotin

source_name: breast cancer sample

label_protocol: A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization. At least 1 ug of RNA is required for cRNA synthesis.

extract_protocol: Total RNA was extracted from tissue using Qiagen Rneasy columns

treatment_protocol: Patients consented to future tissue-based research sample collections from either prospective biopsy or surgical resection.

tag: er status

value: P

tag: pr status

value: N

tag: her2 status

tag: ajcc stage

value: III

tag: sample collection type

value: Tissue

tag: setting of sample collection

value: Needle Biopsy Sample


title: DNNK-3

description: Library name: DNNK-3


title: AP2gama-control-1

country: China

description: Library name: AP2gama-control-1

library_source: genomic

molecule: genomic DNA

organism: Mus musculus


title: OC eCLIP#2

description:
Library name: OC2IP_eCLIP
IP, control endothelial cells under oscillatory flow#2

value: WT


title: DNNK-2

description: Library name: DNNK-2


title: Non-diabetic, myocardial biopsy from patient, biol rep 15

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

data_processing:
Illumina
Base Calling and quality assessement were performes using NCS v4.0.1 & RTA v2.4.11. demultiplexing was realized usign Bxl2fastq v2.17.1.14.Quality Analysis was performed using FastQC tool v0.11.9. Sequenced reads were trimmed for adapters using cutadapt v4.0 with default parameters. Mapping to Homo Sapiens GRCHh38  was performed using STAR v2.7.5a.  Gene count Table was realized using STAR v2.7.5a
raw Reads
Assembly: GRCHh38
Supplementary files format and content: tab-delimited text files include raw count for each sample

source_name: Left cardiac ventricular biopsy from patient

extract_protocol:
Total RNA extraction was performed using miRNeasy mini kit (Qiagen) following manufacturer’s instructions
100ng of total RNA were used for library construction using Lexogen QuantSeq 3 mRNA seq Library Prep kit (Illumina) following manufacturer's instruction
RNA-Seq SingleEnd 75bp with Illumina NextSeq500

value: Left Ventricular myocardial biopsy

tag: disease state

value: Non  diabetic


title: TRIM28-T37KO-2

description: Library name: TRIM28-T37KO-2

value: Trim37 knockout


title: breast cancer_SM023

value: IIB

value: Surgical Tissue Sample


title: DNNK-1

description: Library name: DNNK-1


title: TRIM28-T37KO-1

description: Library name: TRIM28-T37KO-1

value: E9.25 embryo


title: breast cancer_SM022

value: IIA

value: Cytology


title: OC input#2

description:
Library name: OC2inp_eCLIP
RNA input, control endothelial cells under oscillatory flow#2

value: HUVEC


title: breast cancer_SM019


title: hBMEC treated with 10μM Yoda1 for 24h (Replicate 4)

city: Harbin

first: Haoran

last: Zhang

state: Heilongjiang

address: 246 Xuefu Road

institute: Harbin Medical University

description: Library name: hBMEC-Yoda1-Rep4

data_processing:
Raw reads were quality-controlled and adapters trimmed using default Illumina protocols.
Transcript-level quantification was performed using Salmon in quasi-mapping mode against the transcriptome index built from GENCODE v41 (human) annotations.
Tximport was used to summarize transcript-level abundance to gene-level counts based on consistent annotation files.
Differential expression analysis was conducted using DESeq2, with significance defined as adjusted p-value < 0.05 and |log2 fold change| > 0.5.
Variance stabilizing transformation (VST) normalization was applied before downstream visualization (PCA, heatmaps, volcano plots) using ggplot2, pheatmap, and factoextra.
Assembly: GRCh38 (GENCODE v41)
Supplementary files format and content: Processed data files include gene-level count matrices (CSV or XLSX) from tximport and normalized expression data (TPM matrices, XLSX format). Differential expression results for pairwise group comparisons are provided as XLSX files, including gene identifiers, log2 fold change, p-values, adjusted p-values, and gene symbols. Visualization outputs (PCA plots, heatmaps, volcano plots) are provided as PDF files.
Supplementary files format and content: MD5 checksum files provided for data integrity verification.

source_name: Bone marrow

growth_protocol: Human bone microvascular endothelial cells (hBMEC) were maintained in hBMEC growth medium in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using RNAeasy Animal RNA Isolation Kit (Byotime, Cat# R0027). Three micrograms of RNA were used as input material for the RNA sample preparations.
Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

treatment_protocol: hBMEC were cultured until reaching approximately 80% confluence, then treated with 10μM Yoda1 (10mM Yoda1 dissolved in DMSO, 1:1000) for 24 hours.

value: Bone marrow

value: Human bone marrow microvascular endothelial cells

tag: treatment

value: 10 μM Yoda1 for 24 h


title: OC input#1

description:
Library name: OC1inp_eCLIP
RNA input, control endothelial cells under oscillatory flow#1

value: Endothelial cells


title: breast cancer_SM018

value: P

value: L

value: N


title: TRIM28-control-2

description: Library name: TRIM28-control-2

tag: strain

value: Control


title: hBMEC treated with 10μM Yoda1 for 24h (Replicate 3)

description: Library name: hBMEC-Yoda1-Rep3


title: TRIM28-control-1

description: Library name: TRIM28-control-1

tag: genetic modification


title: PC_RNA#3

description:
Library name: PC3_RNA
Control endothelial cells under pulsatile shear flow#3

data_processing:
FASTQ files were aligned to the GRCh37 reference genome using Kallisto and quantified to gene-level counts. Counts were normalized using edgeR.
Supplementary Files: Comma-delimited text file containing raw and normalized gene counts for each sample.
Assembly: GRCh37
Supplementary files format and content: excel files include TPM values for each Sample

value: WT


title: breast cancer_SM016

value: Tissue


title: hBMEC treated with 10μM Yoda1 for 24h (Replicate 2)

description: Library name: hBMEC-Yoda1-Rep2


title: OC eCLIP#1

description:
Library name: OC1IP_eCLIP
IP, control endothelial cells under oscillatory flow#1


title: hBMEC treated with 10μM Yoda1 for 24h (Replicate 1)

description: Library name: hBMEC-Yoda1-Rep1


title: EscV2 IFNy

city: Minneapolis

first: Ingunn

last: Stromnes

state: Minnesota

address: 2-186 Wallin Medical Biosciences Building, 2101 6th St SE

department: Medical School

institute: University of Minnesota

description: Library name: EscV2 IFNy

data_processing:
The sequence reads were aligned to the reference genome Mus_musculus-113/GRCm39 using Bowtie2 (bowtie2/2.3.4.1) in local alignment mode with single end mode (using only R1) and one mismatch allowed in the seed (-L 22, -N 1, -k 100). Resulting SAM files were converted to sorted BAM files using SAMtools (samtools/1.21). Peak calling was performed using MACS3 (v3.0.1) with default parameters. Peaks were called separately for each treatment and control sample, and signal tracks were generated using the MACS3 -B option.
Assembly: Mus_musculus-113/GRCm39

source_name: murine tumor

growth_protocol: Cells were grown in DMEM-F12 supplemented with 10%FBS, 1% pen/strep, 1% fungizone, and 0.5% w/v dextrose. Cells were cultured at 37C, 5% CO2 in a humidified atmosphere and routinely monitored for mycoplasma contamination.

extract_protocol:
Nucleic DNA was extracted from 50,000 cultured tumor cells per sample. Cells were pelleted, washed once in cold PBS, and lysed in 50 µl ice-cold lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Igepal CA-630) to isolate nuclei. Nuclei were immediately pelleted (500 × g, 10 min, 4°C) and resuspended in a 50 µl transposition reaction containing 25 µl 2× TD buffer, 2.5 µl TDE1 Tn5 transposase (Illumina 20034197), and 22.5 µl nuclease-free water. Transposition was carried out at 37°C for 30 min with gentle shaking (100 rpm). DNA was purified using a Qiagen MinElute PCR Purification Kit and eluted in 10 µl Buffer EB (10 mM Tris-Cl). DNA was given to the University of Minnesota Genomics Center for library preparation and sequencing.
Created 6 unique dual-indexed ATAC-seq libraries from transposed DNA. Element Adept Rapid PCR+ kit was used to convert the pooled ATAC libraries into Aviti compatible libraries. Libraries were sequences on an Element Bioscience Aviti Cloudbreak Low 2x150-bp run.

treatment_protocol: Following thaw from frozen stocks, cell lines were passaged twice before use. Cells were plated at a density of 2e5 in 6-well culture dishes, then allowed to settle. After 24hrs, cultures were treated with 10ng/mL mouse interferon-gamma for 24 hours.

value: murine tumor

value: interferon-gamma


title: Lung cancer cfRRBS Patient #1

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

description:
Library name: L-ES-1
The standard reduced representation bisulfite sequencing (RRBS) enriches for CpG-rich regions by size-selecting fragments between 40 and 220 bp after restriction digestion with enzymes such as MspI. However, this size range overlaps with the average size of cfDNA (150 – 200 bp), complicating CpG enrichment in cfDNA samples. Cell-free reduced representation bisulfite sequencing (cfRRBS) addresses this limitation by dephosphorylating the 5’ ends of the DNA. This is followed by the ligation of a custom adaptor that differentially binds cfDNA with MspI cut sites at both ends, thus making it possible to isolate on-target (CpG-rich) from off-target regions in the sample.

library_source: other

data_processing:
The preprocessing of raw cfRRBS data began with quality assessment using a QC tool developed by Wingett and Andrews (2018) to ensure suitability for downstream analysis. Adapter sequences were then removed using Trim Galore (Krueger), resulting in cleaner reads for alignment.   These cleaned reads were aligned to the human reference genome (GRCh37/hg19) using Bismark (Krueger and Andrews, 2011), generating BAM files that contain detailed alignment information.  Reference genome sequences and RefSeq gene annotations were obtained from the UCSC Genome Browser  (hg19 version) to support read interpretation.   To extract methylation-relevant features from the BAM files,we used the Pysam library (Li et al., 2009). Each BAM file included information such as chromosome, start and end positions, bisulfite-converted read sequence, methylation call string (XM tag), and strand alignment.  For each read, we extracted the corresponding genomic sequence and methylation counts (methylated and unmethylated cytosines) along with other relevant information, and stored the output in a structured text file to facilitate downstream quantification.  For each candidate region, we computed MM (Mean Methylation) to quantify average methylation levels, and MHL (Methylation Haplotype Load) to capture the distribution of methylation patterns across cfDNA fragments.  The final output for each region included the following fields: Sample name, Chromosome number, Start Position, End Position,  DNA reference sequence, Methylation Pattern Summary, Sequence Length, Number of CpGs, Coverage, Mean Methylation Value, Methylation Haplotype Load Value, and Number of Haplotype Patterns.
Assembly: GRCh37/hg19
Supplementary files format and content: .txt format (contains Sample name, Chromosome number, Start Position, End Position,  DNA reference sequence, Methylation Pattern Summary, Sequence Length, Number of CpGs, Coverage, Mean Methylation Value, Methylation Haplotype Load Value, and Number of Haplotype Patterns.

molecule: other

source_name: Plasma

extract_protocol:
cfDNA was extracted using Qiagen ccfDNA Midi Kit
Cell-free DNA was extracted from 2-5 mLs of plasma using the QIAamp MinElute ccfDNA Midi Kit according to the manufacturer's instructions. cfDNA was quantified using the Qubit 4 fluorometer according to the Qubit dsDNAhigh-sensitivity assay kit protocol. An Agilent 2100 Bioanalyser instrument was used to assess the cfDNA quality to rule out possible genomic DNA contamination.
4-10 ng of cfDNA was dephosphorylated using recombinant shrimp alkaline phosphatase (rSAP). This was followed by endonuclease digestion suing the MspI restriction enzyme, then enr-repair and adenylation of the 3' ends. Followiing the ligation of custom adapters, exonucleases were used to degrade unligated and partially ligated DNA fragments. This was followed by the cleavage of adaptor hairpin using antarctic thermolabile UDG and endonuclease VII, thus generating single-stranded DNA required for bisultte conversion. The DNA was bisulfite-converted twice using the Epitect plus bisulfite kit. This was followed by PCR amplification and 2.5x Ampure bead purification. The purified DNA was assessed for quality using a Qubit 4 fluorometer (Thermofisher Scientific, USA) and BioAnalyser (Agilent, USA).

tag: Stage

value: Stage II

value: Plasma

tag: extract molecule

value: cell-fee DNA


title: PC_RNA#2

description:
Library name: PC2_RNA
Control endothelial cells under pulsatile shear flow#2


title: EscV2 PBS

description: Library name: EscV2 PBS

value: control


title: PC_RNA#1

description:
Library name: PC1_RNA
Control endothelial cells under pulsatile shear flow#1

value: HUVEC


title: breast cancer_SM013

value: IIA

value: Cytology

value: Needle Biopsy Sample


title: hBMEC treated with DMSO for 24h (Replicate 4)

description: Library name: hBMEC-DMSO-Rep4

tag: tissue

value: Bone marrow

value: Human bone marrow microvascular endothelial cells

value: DMSO


title: KPC2a IFNy

description: Library name: KPC2a IFNy

tag: cell type


title: OM_RNA#3

description:
Library name: OM3_RNA
METTL3 knockdown endothelial cells under oscillatory flow#3

value: Endothelial cells

value: METTL3 knockdown

tag: batch


title: breast cancer_SM012

value: P

value: N


title: Casp3⁻/⁻ P815 cells Control, rep1

city: Lørenskog

first: Shixiong

last: Wang

address: Sykehusveien 25

country: Norway

institute: Akershus University Hospital

description: Library name: Sample1

data_processing:
Screening data were analyzed using MAGeCK-VISPR  to identify significantly enriched or depleted sgRNAs/genes. In brief, sgRNA counting was first performed with mageck count function on Fastq files with option --trim-5 22,23,24,25,26,28,29,30 to trim the 5 prime stagger sequences.
CD8 T cells treated and control treatments were compared with mageck test function, and the normalization was performed by using control sgRNAs.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with gene ranking summary
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA was extracted from 2 × 10⁷ cells per replicate using the NucleoSpin™ Blood L Midi kit (Macherey-Nagel; #740954.20).
sgRNA sequences were amplified and prepared for next-generation sequencing (NGS) using a two-step PCR strategy. In the first PCR (30–45 cycles), sgRNA-containing regions were amplified from genomic DNA using eight staggered forward primers (PCR1_Fwd_1–8) together with a vector-specific reverse primer, using Q5® High-Fidelity DNA Polymerase (New England Biolabs; M0491S). PCR products were pooled and purified using the NucleoSpin™ Gel and PCR Clean-up Midi kit (Macherey-Nagel; #740986.20). In the second PCR (8 cycles), Illumina P5 and P7 adapters and sample-specific indices were added. Final libraries were purified using SpeedBeads (GE65152105050250, Cytiva), quantified using a Qubit fluorometer (Thermo Fisher Scientific), and quality-checked using TapeStation system with D1000 ScreenTape (5067-5582, Agilent). Libraries were pooled equimolarly and sequenced on a NovaSeq X platform (Illumina), targeting a depth of 20–30 million reads per sample.

treatment_protocol: 7.5 × 10⁷ Casp3⁻/⁻ P815 cells were transduced with the Brie lentiviral library at a multiplicity of infection (MOI) of 0.3 to ensure single integration events per cell. 48 hours post-transduction, cells were selected with puromycin (0.6 µg/mL). After 48 h of selection, surviving cells were pooled, cultured in puromycin-free medium, and subjected to cytotoxic T lymphocyte (CTL) selection. For CTL selection, 8 × 10⁶ target cells were co-cultured with activated human CD8⁺ T cells at equal effector-to-target ratios in the presence of 5 µg/mL anti-CD3 antibody. After 24 h of co-culture, cells were collected and treated with puromycin to eliminate residual CD8⁺ T cells. Surviving P815 cells were expanded, and CTL selection was repeated three times. Following selection, surviving cells were expanded, and genomic DNA was extracted from 2 × 10⁷ cells per replicate.

tag: cell line

value: Mastocytoma

value: Control


title: breast cancer_SM270

value: L

value: Tissue


title: hBMEC treated with DMSO for 24h (Replicate 3)

description: Library name: hBMEC-DMSO-Rep3


title: PC input#2

description:
Library name: PC2inp_eCLIP
RNA input, control endothelial cells under pulsatile shear flow#2

tag: genotype

value: WT


title: CD8+ T cell transduced with Runx3 wt construct replicate 2

city: Jupiter

first: Wuyue

last: Zhou

address: 110 Scripps Way

institute: The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology

description:
Library name: WT_REP2
See corresponding column

data_processing:
Reads were processed using nf-core/rnaseq v3.14.0. Briefly, raw read quality was assessed with FastQC v0.12.1, and adapter sequences and low-quality bases were trimmed using Trim Galore! v0.6.7. Trimmed reads were aligned to the GRCm38 reference genome with STAR, and the resulting transcriptome-level alignments were quantified with Salmon v1.10.1. Genome alignments were coordinate-sorted and indexed with SAMtools v1.17, duplicate reads were marked with Picard v3.0.0, and normalized genome coverage tracks were generated with BEDTools v2.30.0. Post-alignment quality control included read distribution, gene-body coverage, and strand-specificity metrics (RSeQC, Qualimap, and inference via Salmon), duplication assessment (dupRadar), library-complexity estimation (Preseq), and gene-biotype quantification with featureCounts (Subread v2.0.1). Sample-to-sample similarity was evaluated by principal component analysis and hierarchical clustering of regularized log-transformed counts using DESeq2 v1.40.2. Differential gene expression analysis was performed in R using DESeq2 v1.40.2. Gene-level counts from the star_salmon quantification were filtered to retain genes with a mean raw count ≥ 5 across all samples, and a model of the form “~ group” was fit to test pairwise contrasts between each RUNX3 fusion construct (FT, LOV, APEX, ULTRA, MINI, TID) and the empty-vector (EV) and wild-type RUNX3 (WT) controls using the Wald test. Genes with a Benjamini–Hochberg-adjusted p-value ≤ 0.05 and |log₂ fold-change| ≥ 1 were considered differentially expressed.
Assembly: GRCm38 (mouse)
Supplementary files format and content: Tab-separated values (TSV) file containing gene-level raw counts from Salmon/STAR quantification. Rows represent genes (n = 45,706), with columns for Ensembl gene ID, gene name, and raw read counts for 2 biological replicates across 7 conditions (APEX, EV, FT, LOV, MINI, TID, ULTRA, WT)

source_name: primary cell

growth_protocol: CD8+ T cells were isolated from splenocytes and cultured ex vivo with anti-CD3/CD28 stimulation and transduced with RUNX3 retroviral constructs as described in the CD8+ T cell transduction protocol.

extract_protocol:
T cells were collected and centrifuged at 750 × g for 5 minutes. Cells were lysed with DNA/RNA Shield (Zymo Research, #1100-50) at a density of 1 × 10⁶ cells per 50 µL. Lysed samples were submitted to Plasmidsaurus for library construction and sequencing.
Library construction and RNA-seq sequencing (10 million reads/sample) were performed by Plasmidsaurus. In brief, they converted mRNA into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation and library indexing and amplification.

treatment_protocol: Sixteen hours post-activation, cells were spinfected with retroviral supernatant to express different Runx3-tagged constructs: FT(FlAsH-tag), LOV*, APEX2, ultraID, miniTurbo, TurboID, WT, and Empty vector control.

value: primary cell

value: primary CD8+ T cells were isolated from splenocytes

value: C57BL/6J mice

value: transduced with Runx3 wt construct


title: breast cancer_SM015

tag: er status

value: I

value: Surgical Tissue Sample


title: breast cancer_SM011

tag: pr status

value: IV

value: Cytology

value: Needle Biopsy Sample


title: KPC2a PBS

description: Library name: KPC2a PBS

value: murine tumor

value: control


title: Casp3⁻/⁻ P815 cells Control, rep3

description: Library name: Sample3


title: breast cancer_SM010

value: P

tag: her2 status

value: N

value: IIA


title: hBMEC treated with DMSO for 24h (Replicate 2)

description: Library name: hBMEC-DMSO-Rep2

value: Bone marrow

value: Human bone marrow microvascular endothelial cells

value: DMSO


title: Parental PBS

description: Library name: Parental PBS


title: hBMEC treated with DMSO for 24h (Replicate 1)

description: Library name: hBMEC-DMSO-Rep1


title: OM_RNA#2

description:
Library name: OM2_RNA
METTL3 knockdown endothelial cells under oscillatory flow#2

value: HUVEC

value: Endothelial cells

value: METTL3 knockdown


title: Parental IFNy

description: Library name: Parental IFNy

value: interferon-gamma


title: OC_RNA#3

description:
Library name: OC3_RNA
Control endothelial cells under oscillatory flow#3

value: WT


title: breast cancer_SM009

tag: ajcc stage

value: Tissue

value: Surgical Tissue Sample


title: OM_RNA#1

description:
Library name: OM1_RNA
METTL3 knockdown endothelial cells under oscillatory flow#1


title: MDA-MB-231 siENO1, RNA-seq, rep2

city: Dalian city

first: Yujie

last: Zeng

state: Liaoning province

address: No. 9, West Section, Lvshun South Road

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

description:
Library name: 231_siENO1_rep2
Strand-specific poly(A) mRNA-seq of MDA-MB-231; siRNA targeting ENO1; not SDorm-sorted; PE150.

data_processing:
Raw reads were processed to generate gene-level expression matrices.
For the A-BCSCs vs Q-BCSCs dataset, gene-level quantification was generated using Homo sapiens Ensembl release 94 annotation.
For the siENO1 vs siNC dataset, gene-level quantification was generated using Homo_sapiens.GRCh38.110 annotation.
Because different Ensembl annotation releases were used for the two experiments, processed data are deposited as separate experiment-specific matrices rather than as a single unified matrix.
Processed files include raw counts matrices, FPKM matrices, and matching gene annotation tables.
Assembly: Homo sapiens GRCh38; A-BCSCs vs Q-BCSCs quantified with Ensembl release 94 annotation, and siENO1 vs siNC quantified with Homo_sapiens.GRCh38.110 annotation.
Supplementary files format and content: Supplementary processed data are provided as gzipped tab-delimited text files. For the A-BCSCs vs Q-BCSCs dataset, files include a gene-level raw counts matrix, an FPKM matrix, and a matching gene annotation table. For the siENO1 vs siNC dataset, files include a gene-level raw counts matrix, an FPKM matrix, and a matching gene annotation table.
Supplementary files format and content: Gene features are identified by Ensembl gene IDs and are traceable through the accompanying annotation tables.

growth_protocol: MDA-MB-231 human breast cancer cells (ATCC HTB-26) were maintained in DMEM supplemented with 10% FBS and 1% penicillin–streptomycin at 37℃ in 5% CO₂. For BCSC-state profiling, activated (A-BCSCs; SDorm-high) and quiescent (Q-BCSCs; SDorm-low) subpopulations were isolated by FACS using the SDorm dual-reporter system (NANOG-EGFP with H2B-mCherry pulse-chase) and collected for RNA-seq.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen). Genomic DNA was removed by on-column DNase I digestion when needed. RNA quantity was measured by Qubit/NanoDrop and integrity assessed by Bioanalyzer; only samples with RIN ≥ 7 were used for library construction.
Strand-specific, poly(A)-selected mRNA-seq libraries were prepared from 1 µg total RNA with Illumina-compatible kits (UTP method). cDNA was synthesized with oligo-dT priming, end-repaired, A-tailed, adaptor-ligated, and PCR-amplified. Libraries with ~300 bp inserts were sequenced as paired-end 150 bp reads on an Illumina NextSeq 2000.

treatment_protocol: For ENO1 silencing, cells were transfected with siRNA targeting ENO1 (siENO1) or a non-targeting control (siNC) using a standard liposome-based reagent following the manufacturer’s instructions. Cells were harvested 48 h post-transfection for RNA extraction; these samples were not SDorm-sorted.

value: breast cancer cell line

value: siRNA targeting ENO1


title: KPC2a cells, treated with interferon gamma and decitabine

description:
Library name: KPC2a_IFNg_DEC
NEBNEXT Enzymatic methyl-seq

data_processing:
Raw paired-end reads were trimmed using Trim Galor with Cutadapt, removing 10bp from both 5' and 3' ends of each read.
Quality control was performed post-trimming using FastQC.
Trimmed reads were aligned to the mouse reference genome (mm10) using Bismark with Bowtie2 in paired-end mode.
Aligned BAM files were name-sorted with SAMtools, and BCR duplicates were removed using deduplicate_bismark.
Methylation calls were extracted using bismark_methylation_extractor in paired-end mode, and quality metrics aggregated using MultiQC.
Assembly: mm10
Supplementary files format and content: per-sample bedGraph includes methylation % at genomic coordinates
Library strategy: EM-seq

extract_protocol:
Genomic DNA was extracted using the Qiagen Dneasy Blood&Tissue kit.
Libraries were constructed using the NEBNext Enzymatic Methyl-seq kit following manufacturer protocols.

treatment_protocol: Following thaw from frozen stocks, cell lines were passaged twice before use. Cells were plated at a density of 5e5 in 10cm culture dishes, then allowed to settle. After 24hrs, cultures were treated with 1. DMSO vehicle, 2. 50ng/ml IFNg, or 3. 50ng/ml IFNg+250nM decitabine. After 48 hours of drug treatment, cells were harvested via trypsinization and genomic DNA was extracted.

value: pancreatic ductal adenocarcinoma

value: KPC-derived cancer cells

value: Interferon gamma and decitabine


title: breast cancer_SM008

value: P

value: N

value: III

tag: sample collection type

value: Needle Biopsy Sample


title: OC_RNA#2

description:
Library name: OC2_RNA
Control endothelial cells under oscillatory flow#2


title: breast cancer_SM007

value: L

value: IIA

tag: setting of sample collection


title: MDA-MB-231 siNC, RNA-seq, rep2

description:
Library name: 231_siNC_rep2
Strand-specific poly(A) mRNA-seq of MDA-MB-231; siRNA negative control; not SDorm-sorted; PE150.

value: siRNA negative control


title: KPC2a cells, treated with interferon gamma

description:
Library name: KPC2a_IFNg
NEBNEXT Enzymatic methyl-seq

tag: disease state

value: Interferon gamma


title: ZT1, replicate 4

city: Genève

first: Christoph

last: Scheiermann

address: 1, rue Michel Servet

country: Switzerland

institute: UNIGE

description:
Library name: ZT1x4
ZT1x4_S9

data_processing:
RNA sequencing quality was checked by FastQC. Fastq files were aligned to the GRCm38 reference by STAR v2.7.10b (Dobin et al., 2013) and counted by featureCounts in Subread v2.0.3 package (Liao et al., 2014). Raw counts were analyzed and differentially expressed genes were calculated using DESeq2 v1.46.0 (Love et al., 2014). The genes were considered as differentially expressed when the fold change (FC) was at least 1.5-fold with a 5% false discovery rate (FDR). Principal component analysis (PCA) was performed using the plotPCA function from DESeq2. Gene ontology (GO) and cluster enrichment was performed using Database for Annotation, Visualization, and Integrated Discovery (DAVID, https://davidbioinformatics.nih.gov/). Default parameters were used, except when indicated.
Assembly: GRCm38
Supplementary files format and content: csv of raw counts

source_name: Neutrophils

extract_protocol:
Spinal cords were collected from EAE-induced mice and harvested at 2 time points (ZT1 and ZT13).  Spinal cords were digested as described above, and CD45+CD11b+Ly6G+ cells were sorted using an Astrios sorter (Beckman). Flow cytometry sorted neutrophils (11’000-50’000 per mouse) were collected in RNAprotect Cell Reagent (cat. #76526, Qiagen). RNA was isolated using an RNeasy Plus Micro Kit (cat. #74034, Qiagen) according to the manufacturer’s instructions. RNA integrity and quantity were assessed with a Bioanalyzer (Agilent Technologies).
cDNA libraries were constructed by the Genomic platform of the University of Geneva. The SMART-Seq v4 kit from Clontech was used for the reverse transcription and cDNA amplification according to the manufacturer’s specifications, starting with 1 ng of total RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina. Library molarity and quality were assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled and loaded for clustering on 2 lanes of a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer.

value: Neutrophils

value: Neutrophils from Spinal cord

tag: time point


title: MDA-MB-231 siENO1, RNA-seq, rep1

description:
Library name: 231_siENO1_rep1
Strand-specific poly(A) mRNA-seq of MDA-MB-231; siRNA targeting ENO1; not SDorm-sorted; PE150.

tag: treatment


title: OC_RNA#1

description:
Library name: OC1_RNA
Control endothelial cells under oscillatory flow#1

value: HUVEC

value: Endothelial cells

value: WT


title: breast cancer_SM006

value: Tissue

value: Surgical Tissue Sample


title: KPC2a cells, vehicle control

description:
Library name: KPC2a_DMSO
NEBNEXT Enzymatic methyl-seq

value: pancreatic ductal adenocarcinoma

value: KPC-derived cancer cells

value: DMSO vehicle


title: MDA-MB-231 siNC, RNA-seq, rep1

description:
Library name: 231_siNC_rep1
Strand-specific poly(A) mRNA-seq of MDA-MB-231; siRNA negative control; not SDorm-sorted; PE150.

value: breast cancer cell line


title: breast cancer_SM005

value: P

value: N

value: III


title: MDA-MB-231 Q-BCSCs, RNA-seq, rep3

description:
Library name: 231_Q-BCSCs_rep3
Strand-specific poly(A) mRNA-seq; FACS-sorted quiescent BCSCs (SDorm-low); PE150.

value: breast cancer stem-like cells (quiescent)

value: FACS-sorted using SDorm reporter


title: ZT1, replicate 3

description:
Library name: ZT1x3
ZT1x3_S8


title: EscV2 cells, treated with interferon gamma

description:
Library name: EV2_IFNg
NEBNEXT Enzymatic methyl-seq

value: Interferon gamma


title: ZT1, replicate 2

description:
Library name: ZT1x2
ZT1x2_S7

value: Neutrophils


title: EscV2 cells, treated with interferon gamma and decitabine

description:
Library name: EV2_IFNg_DEC
NEBNEXT Enzymatic methyl-seq

value: Interferon gamma and decitabine


title: MDA-MB-231 Q-BCSCs, RNA-seq, rep2

description:
Library name: 231_Q-BCSCs_rep2
Strand-specific poly(A) mRNA-seq; FACS-sorted quiescent BCSCs (SDorm-low); PE150.


title: breast cancer_SM004

value: Cytology

value: Needle Biopsy Sample


title: EscV2 cells, vehicle control

description:
Library name: EV2_DMSO
NEBNEXT Enzymatic methyl-seq


title: ZT1, replicate 1

description:
Library name: ZT1x1
ZT1x1_S6

value: Neutrophils from Spinal cord


title: breast cancer_SM002

value: I

value: Tissue


title: MDA-MB-231 Q-BCSCs, RNA-seq, rep1

description:
Library name: 231_Q-BCSCs_rep1
Strand-specific poly(A) mRNA-seq; FACS-sorted quiescent BCSCs (SDorm-low); PE150.


title: CD8+ T cell transduced with Runx3-ultraID construct replicate 2

description:
Library name: ULTRA_REP2
See corresponding column

value: primary cell

value: primary CD8+ T cells were isolated from splenocytes

value: C57BL/6J mice

value: transduced with Runx3-ultraID construct


title: lung alveolar organoid, Ager knockout, plate1-2 well F04

city: South San Francisco

first: Anne

last: Biton

state: CA

address: 1 DNA way

institute: Genentech

description: Library name: 1-2_F04_AGER

data_processing:
The sequencing reads in each fastq file were first split between mouse and human using Xenome (Conway et al., 2012). Only reads unambiguously assigned to either mouse or human were kept and respectively aligned to their reference genome (mouse: GRCm38.p5, human: GRCh38.p10) through the HTSeqGenie v4.35 Bioconductor package (Pau and Reeder, 2012, https://doi.org/10.18129/B9.bioc.HTSeqGenie). First, reads with low nucleotide qualities (70% of bases with quality <23) or matches to rRNA and adapter sequences were removed. Then, reads were aligned using GSNAP (Wu et al., 2010; Wu et al., 2016) version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap'). Transcript annotation was based on the Gencode genes database (human: GENCODE 27, mouse: GENCODE M15). Reads unambiguously mapping to exons were counted to get gene-level read counts.
Assembly: GRCm38.p5, GRCh38.p10
Supplementary files format and content: gene_counts.xlsx provides gene-level counts of reads unambiguously mapping to exons. There is one table for the reads assigned by Xenome to the Mus Musculus genome (originating from the mouse alveolar type 2 cells of the organoids in the well), and one table for the reads assigned to the Homo Sapiens genome (originating from the human fibroblasts of the organoids in the well).
Supplementary files format and content: plate_design.csv contains the sgRNA sequences used to target each gene and their location on the four plates.
Supplementary files format and content: imaging_outputs.csv contains the main outputs of the image analysis performed on each well at day 7 and day 14, in terms of number or organoids in the well, average area of the organoids in the well, and estimate of the percentage of the well covered by organoids.
Supplementary files format and content: xenome_stats.csv contains the summary of the sequencing read assignment made by Xenome (Conway et al., 2012).

organism:
Homo sapiens
Mus musculus

source_name: lung mouse alveolar type 2 cells and primary human fibroblasts

extract_protocol:
Libraries were prepared from extracted RNA using a modified Smart-seq3 protocol ( Hagemann-Jensen, M., Ziegenhain, C., Chen, P. et al. Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nat Biotechnol 38, 708–714 (2020). https://doi.org/10.1038/s41587-020-0497-0) Annealing reaction was performed with 4ul purified RNA, 0.8 ul 40% PEG 8000, 0.08 ul RNAse Inhibitor, 0.04 ul Smart-seq3 oligo dT (100µM), 0.3 ul dNTP (25mM each) and 1 ul water per 384 well reaction. 10 ul mineral oil was added on top to prevent evaporation. Reaction was sealed, spun and incubated at 70˚C for 10 min. Reverse translation was performed by adding 2 ul of RT mix (0.2ul Tris HCl, pH8.0 (1M), 0.24 ul NaCl (1M), 0.2 ul MgCl2 (100mM), 0.08 ul GTP (10mM), 0.64 ul DTT (100mM), 0.16 ul TSO (100µM), 0.08 ul Maxima H Minus RTase and 0.4 ul water) to each 384 well reaction. The RT reaction was incubated at 42°C for 90 min and repeated the following steps for 10 cycles: 50˚C for 2 min and 42˚C for 2 min, and was terminated at 85°C for 5 min.
cDNA amplification was performed by adding 12ul of PCR mix (0.1 ul cDNA fwd (100µM), 0.02 ul cDNA rev (100µM), 0.1 ul MgCl2 (100mM), 10 ul 2X Kapa HiFi Hotstart Readymix  and 1.78 ul water) to the RT reaction for a total of 20 ul. Reaction was thermal cycled at 95°C for 3 min, [98°C for 20 sec, 65°C for 30 sec, 72°C for 4 min] x 14 cycles, 72 °C 4min. cDNA was diluted 1:10 in water. 1 ul of each sample was transferred to a new 384 well plate to perform tagmentation. 3 ul of tagmentation mix (0.8 ul 5X TAPS Mg buffer, 0.1 ul Tn5 enzyme, 2.1 ul water) was added to each sample on ice. Plate was sealed, vortexed for 15 seconds and spun. The reaction mixture was incubated at 55 °C for 10 min. Reaction was quenched by adding 0.5µl of 0.2% SDS to each well, sealing, vortexing for 15 seconds, and spinning the plate. The plate was  incubated at room temperature for 5 min. Libraries were indexed by added 3.5 ul of PCR mix and 2 ul indexing primers  to each sample.  Reaction was thermal cycled at 72°C for 5 min, 95°C for 3 min, [98°C for 20 sec, 65°C for 30 sec, 72°C for 30 sec] x 10 cycles, 72 °C 4min. Libraries were pooled and sequenced on an Illumina NovaSeq X Plus system, targeting 8M reads per library.

value: Ager CRISPR/Cas9 knockout


title: ZT13, replicate 4

description:
Library name: ZT13x5
ZT13x5_S5


title: breast cancer_SM001

value: P

value: N

value: IIA


title: NICD-OE 3rd instar brain, Hypoxia

city: La Jolla

first: Dan

address: 9500 Gilman Drive

institute: UCSD

description:
Library name: 4GGH-HN
Brain sample isolated from 3rd instar larvae with NICD-OE in Eaat1-positive cells reared in 3.5% hypoxia.

data_processing:
Cell Ranger Count v9.0.0
Assembly: Dmel Release 6.56/dm6
Supplementary files format and content: raw matrix files

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: 3rd instar larval brain

growth_protocol: Drosophila melanogaster larvae were raised on standard cornmeal-yeast-agar medium at 25°C on a 12:12 hour light:dark cycle.

extract_protocol:
Following hypoxia and room air treatment, brains were rapidly dissected in ice-cold Schneider's Insect Medium supplemented with 10% FBS. Tissues were transferred to 1 mL of ice-cold Nuclei EZ Lysis Buffer (Sigma-Aldrich, NUC101) supplemented with 0.1% Triton X-100, RNase inhibitor (0.5 U/μL), and dithiothreitol (DTT, 1 mM). Tissues were homogenized with a Dounce homogenizer (15 strokes with loose pestle, 15 strokes with tight pestle) on ice. The homogenate was incubated on ice for 5 minutes, then filtered through a 40 μm cell strainer. The filtered suspension was centrifuged at 500 x g for 5 minutes at 4°C. The supernatant was discarded, and the nuclear pellet was gently resuspended in 500 μL of Nuclei Wash and Resuspension Buffer (NWRB; 1x PBS, 1.0% BSA, 0.2 U/μL RNase inhibitor). The nuclei were centrifuged again, resuspended in NWRB, and filtered through a 20 μm strainer. Nuclei concentration and quality were assessed using a Countess II Automated Cell Counter with trypan blue staining.
The isolated nuclei suspension was processed using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to the manufacturer's protocol.

treatment_protocol: For hypoxia experiments, third-instar larvae were placed in a computer-controlled hypoxia chamber (Coy Laboratory Products) and exposed to a gas mixture of 3.5% O₂ and 96.5% N₂ for 24 hours. Room air controls were maintained in parallel in ambient air (21% O₂).

value: 3rd instar larval brain

value: NICD-OE

value: Hypoxia


title: MDA-MB-231 A-BCSCs, RNA-seq, rep3

description:
Library name: 231_A-BCSCs_rep3
Strand-specific poly(A) mRNA-seq; FACS-sorted activated BCSCs (SDorm-high); PE150.

value: breast cancer stem-like cells (activated)

value: FACS-sorted using SDorm reporter


title: NICD-OE 3rd instar brain, Normoxia

description:
Library name: 3GGH-NN
Brain sample isolated from 3rd instar larvae with NICD-OE in Eaat1-positive cells reared in room air.

value: Normoxia


title: ZT13, replicate 3

description:
Library name: ZT13x4
ZT13x4_S4

value: Neutrophils

value: Neutrophils from Spinal cord


title: MDA-MB-231 A-BCSCs, RNA-seq, rep2

description:
Library name: 231_A-BCSCs_rep2
Strand-specific poly(A) mRNA-seq; FACS-sorted activated BCSCs (SDorm-high); PE150.


title: ZT13, replicate 2

description:
Library name: ZT13x2
ZT13x2_S2


title: RMT1EV1

city: Tokyo

first: Takaaki

last: Tamura

address: 6-7-1 Nishishinjuku, Shinjyuku-ku

country: Japan

institute: Tokyo Medical University

description:
Library name: Sample1
EV-microRNA

data_processing:
GeneGlobe/Strand NGS v4.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped
Read count extraction and normalization were performed
Assembly: UCSC Rat mm10
Supplementary files format and content: tab-delimited file includes raw counts for each sample
Supplementary files format and content: tab-delimited file includes RPKM values for each sample

organism: Rattus norvegicus

source_name: EVs

extract_protocol:
EV-associated miRNA were isolated from cultured cells and purified EVs by QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocols.
Small RNA libraries were prepared using QIAseq miRNA library Kit and QIAseq miRNA NGS 96 Index IL for Illumina, and yields were evaluated using Agilent 2100 BioAnalyzer.

value: EVs

value: breast cancer cell


title: MDA-MB-231 A-BCSCs, RNA-seq, rep1

description:
Library name: 231_A-BCSCs_rep1
Strand-specific poly(A) mRNA-seq; FACS-sorted activated BCSCs (SDorm-high); PE150.


title: Wildtype Control 3rd instar brain, Normoxia

description:
Library name: 1GGH-NC
Brain sample isolated from Wildtype Control 3rd instar larvae reared in room air.

value: control


title: GE97_0Gy_d2, CT, batch_2

status: Public on Jun 25 2026

city: Mannheim

first: Ahmad

last: Sami

state: Baden-Württemberg

address: Theodor-Kutzer-Ufer 1-3

department: Department of Radiation Oncology

country: Germany

institute: Medical Faculty Mannheim, Heidelberg University

description: Library name: GE97_0Gy_d2

data_processing:
Cleaned raw data after index sequences removal were provided by BGI Genomics
Gene raw read counts from the RNA-seq data were calculated with the Kallisto (pseudoalignment) program
Low count reads were removed with the filterByExpr function, followed by TMM normalisation with EdgeR library
Normalised log2 CPM values were obtained with the voomWithQualityWeights function from the limma pacage
Assembly: Homo_sapiens GRCh38 cdna collection
Supplementary files format and content: Raw counts and log2 CMP normalised data are saved as .csv files, containing data for all samples

source_name: in-vitro fibroblasts

growth_protocol: Early-passage fibroblast cultures were grown in AmnioMAXTM C-100 medium (Thermo Fisher, Darmstadt, Germany), supplemented with 7.5% AmnioMAXTM C-100 supplement, 7.5% fetal bovine serum (HyClone, Fisher Scientific GmbH, Schwerte, Germany, 2 mM glutamin and penicillin/streptomycin.

extract_protocol:
Total cellular RNA was extracted on day 0 from non-irradiated fibroblasts and on day 2 from irradiated and non-irradiated fibroblasts using Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.
Libraries were prepared by the BGI Genomics company as a commercial service

treatment_protocol: At passage 6, cell irradiation was performed with 4 Gy (6 MV) X-rays from a clinical therapy machine.

value: in-vitro fibroblasts

value: primary dermal fibroblast strain

value: CT


title: GE97_0Gy_d0, CT, batch_2

description: Library name: GE97_0Gy_d0


title: GE96_0Gy_d0, TT, batch_1

description: Library name: GE96_0Gy_d0

value: TT


title: GE94_4Gy_d2, CC, batch_2

description: Library name: GE94_4Gy_d2

value: CC


title: GE94_0Gy_d2, CC, batch_2

description: Library name: GE94_0Gy_d2


title: GE94_0Gy_d0, CC, batch_2

description: Library name: GE94_0Gy_d0


title: GE9_0Gy_d0, TT, batch_1

description: Library name: GE9_0Gy_d0


title: GE8_4Gy_d2, CC, batch_2

description: Library name: GE8_4Gy_d2


title: GE9_0Gy_d2, TT, batch_1

description: Library name: GE9_0Gy_d2


title: GE8_0Gy_d0, CC, batch_2

description: Library name: GE8_0Gy_d0


title: GE70_4Gy_d2, CC, batch_1

description: Library name: GE70_4Gy_d2


title: GE70_0Gy_d0, CC, batch_1

description: Library name: GE70_0Gy_d0


title: GE67_4Gy_d2, CT, batch_2

description: Library name: GE67_4Gy_d2


title: GE70_0Gy_d2, CC, batch_1

description: Library name: GE70_0Gy_d2


title: GE67_0Gy_d2, CT, batch_2

description: Library name: GE67_0Gy_d2


title: GE9_4Gy_d2, TT, batch_1

description: Library name: GE9_4Gy_d2


title: GE96_4Gy_d2, TT, batch_1

description: Library name: GE96_4Gy_d2


title: GE65_0Gy_d0, TT, batch_1

description: Library name: GE65_0Gy_d0


title: GE66_0Gy_d2, CT, batch_1

description: Library name: GE66_0Gy_d2


title: GE6_0Gy_d0, TT, batch_1

description: Library name: GE6_0Gy_d0


title: GE65_0Gy_d2, TT, batch_1

description: Library name: GE65_0Gy_d2


title: GE6_4Gy_d2, TT, batch_1

description: Library name: GE6_4Gy_d2


title: GE56_4Gy_d2, CC, batch_1

description: Library name: GE56_4Gy_d2


title: GE66_0Gy_d0, CT, batch_1

description: Library name: GE66_0Gy_d0


title: GE56_0Gy_d2, CC, batch_1

description: Library name: GE56_0Gy_d2


title: GE44_4Gy_d2, CT, batch_1

description: Library name: GE44_4Gy_d2


title: GE44_0Gy_d2, CT, batch_1

description: Library name: GE44_0Gy_d2


title: GE56_0Gy_d0, CC, batch_1

description: Library name: GE56_0Gy_d0


title: GE65_4Gy_d2, TT, batch_1

description: Library name: GE65_4Gy_d2


title: GE4_4Gy_d2, CC, batch_2

description: Library name: GE4_4Gy_d2


title: GE4_0Gy_d2, CC, batch_2

description: Library name: GE4_0Gy_d2


title: GE44_0Gy_d0, CT, batch_1

description: Library name: GE44_0Gy_d0


title: GE4_0Gy_d0, CC, batch_2

description: Library name: GE4_0Gy_d0


title: GE28_4Gy_d2, TT, batch_1

description: Library name: GE28_4Gy_d2


title: GE28_0Gy_d2, TT, batch_1

description: Library name: GE28_0Gy_d2


title: GE30_0Gy_d0, CT, batch_2

description: Library name: GE30_0Gy_d0


title: GE28_0Gy_d0, TT, batch_1

description: Library name: GE28_0Gy_d0


title: GE11_4Gy_d2, CT, batch_1

description: Library name: GE11_4Gy_d2


title: GE11_0Gy_d2, CT, batch_1

description: Library name: GE11_0Gy_d2


title: GE19_0Gy_d0, CC, batch_1

description: Library name: GE19_0Gy_d0


title: GE11_0Gy_d0, CT, batch_1

description: Library name: GE11_0Gy_d0


title: GE19_0Gy_d2, CC, batch_1

description: Library name: GE19_0Gy_d2


title: 319 STING 1

city: Lausanne

first: Andrea

last: Ablasser

address: Rte Cantonale

institute: EPFL

description: Library name: 319 STING 1

data_processing:
The analysis of the RNA-seq was performed in the Galaxy server (https://usegalaxy.eu/). Briefly, RNA was mapped to human genome assembly GRCh38 using STAR aligner (Version 2.7.11b) and the counts were generated with featureCounts (Version 2.1.1).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containg raw counts for each sample

extract_protocol:
RNA was isolated with RNeasy micro kit (Qiagen, 74004)
Samples were prepared with NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, E7760L) with ribodepletion starting from 750 ng of RNAs.

treatment_protocol: THP-1 SKO cells reconstituted with EGFP tagged WT or mutant STING were treated with doxycycline for 24h

value: Human monocytic leukemia cells (monocyte-like)

value: THP-1 STING1-knockout

value: D319K/D310K STING overexpression


title: WT STING 3

description: Library name: WT STING 3

value: WT STING overexpression


title: 119 STING 1

description: Library name: 119 STING 1

value: W119K/M120K STING overexpression


title: WT STING 2

description: Library name: WT STING 2


title: WT STING 1

description: Library name: WT STING 1


title: ult1-3clf-28,R2,Input

city: Grenoble

first: Christel

last: Carles

state: Auvergne/Rhone Alpes

address: 17 rue des Martyrs, bât. C2

department: Laboratoire Physiologie Cellulaire Végétale (LPCV)

institute: University Grenoble Alpes

description: Library name: ult1-3clf-28_R2_Input

data_processing:
For single read samples (Ler WT, ult1-2, ult1-3, 35S::ULT1, Col-0 WT and ref6-3): reads were aligned using bwa 0.6.2-r126; For paired-end sampled (WT, ult1-3, clf-28, swn-7, ult1-3 clf-28 and ult1-3 swn-7): reads were aligned using bwa 0.7.17-r1188
For single read samples (Ler WT, ult1-2, ult1-3, 35S::ULT1, Col-0 WT and ref6-3): files were converted into bam formate using samtools 0.1.19+; For paired-end sampled (WT, ult1-3, clf-28, swn-7, ult1-3 clf-28 and ult1-3 swn-7): files were converted into bam formate using samtools 1.16.1
For single read samples (Ler WT, ult1-2, ult1-3, 35S::ULT1, Col-0 WT and ref6-3): duplicated reads were removed using Picard-tools 1.93 (not for R3 due to saturation); For paired-end sampled (WT, ult1-3, clf-28, swn-7, ult1-3 clf-28 and ult1-3 swn-7): duplicated reads were removed using Picard-tools 2.26.10
For single read samples (Ler WT, ult1-2, ult1-3, 35S::ULT1, Col-0 WT and ref6-3): bed files were generated using bedtools v2.17.0-97-ge80528b; For paired-end sampled (WT, ult1-3, clf-28, swn-7, ult1-3 clf-28 and ult1-3 swn-7): ChIP and input samples with more than 30% higher read numbers than the replicates average were down-sampled to fall within the average (this concerned the input ult1 and IP WT for Rep.1) using samtools. Bam files were converted into BEDPE format using bedtools (Quinlan and Hall, 2010) (v2.30.0). Paired reads were merged into one fragment using awk (4.1.4). Sub-nucleosomal fragments (<146 bases), large undigested fragments (>500bp), reads mapping to regions prone for artificial signals (Klasfeld et al., 2022), a region surrounding the centromere of chromosome 4 (low signal in input of clf-28, putative inversion caused by T-DNA) and all reads mapping to the plastid or mitochondria genome were removed at this step. To avoid normalisation problems due to differences in fragment size, all fragments were set to a length of 146 bases around the fragment center and reads of both replicates were merged for further analysis.
H3K27me3 and H3K4me3 positive islands were determined using SICER V1.1 with window size 200 bp, gap size 400 bp and effective genome size of 90 % , a FDR-cutt-off of 0.0001 was employed
Assembly: tair10
Supplementary files format and content: bed files containing regions of significant enrichment of the H3K4me3 or H3K27me3 histone mark over input
Supplementary files format and content: bw files containing normalised (CPM) counts in bigwig format

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seedlings were grown in long day (LD) conditions of 16 h light (18 degrees) and 8 h darkness (16 degrees) on Murashige and Skoog medium (Sigma-Aldrich, Lyon, France) supplemented with 0.3% sucrose in growth cabinets (Percival, Percival Scientific Incorporated, provided by CLF Plant Climatics, Emersacker, Germany) for 8 days.

extract_protocol:
For single read samples ( Ler WT, ult1-2, ult1-3, 35S::ULT1, Col-0 WT and ref6-3):Formaldehyde cross-linking and extraction of nuclei was performed as described in Carles and Fletcher (2009) with the following modifications: infiltration time was prolongated (6 min), filtration of the extract after grinding was performed through 75 µm and 50 µm nylon meshes and sonication was done for 13x 30 sec on, 1 min off, position H. Immunoprecipitation reactions were set up as described in Carles and Fletcher (2009) except that 15 µg of chromatin was used and the chromatin was incubated with the antibody alone for 5 hours prior to addition of Protein A Agarose beads without salmon sperm DNA (Millipore). Washing of the ChIP reaction was performed using binding/wash buffer as described in Carles and Fletcher (2009) but for four times 10 min at 4°C and once 10 min at room temperature (RT).  Elution and reverse cross-linking was performed as described in Kaufmann et al. (2010) except that the elution was done by vortex mixing for 1 min at RT and input samples (1/3 of the chromatin used for one ChIP sample) were brought to the same volume by adding elution buffer and Tris pH9 in the same ratio as to the ChIP samples. Reverse cross-linked samples were purified using the MinElute Reaction Cleanup Kit (Quiagen) and DNA was eluted in 30 µl Elution buffer. Three technical replicates of ChIP were performed on the same nuclear extract and pooled on one MinElute column.   For paired-end sampled (WT, ult1-3, clf-28, swn-7, ult1-3 clf-28 and ult1-3 swn-7): chromatin preparation and immuno-precipitation was performed as described in (Zhu et al., New Phytol, 2024)
For single read samples ( Ler WT, ult1-2, ult1-3, 35S::ULT1, Col-0 WT and ref6-3): ChIP-seq library preparation was performed using the Truseq ChIP sample preparation kit (Illumina, ref. IP-202-1012) according to the manufacturer's instructions except that PCR amplification was performed prior to size selection. Briefly, sonicated chromatin was repaired prior to 3' ends adenylation. Illumina's indexed adapters were ligated to the adenylated double-stranded DNA fragments. A 18-cycles PCR was performed on the ligated DNA using Illumina's PCR primers. The libraries were then size-selected between 300 and 700 bp on a 2% agarose gel. Each library was validated using high sensitivity chip (Agilent, ref. 5067-4626) on an Agilent Bioanalyzer and quantified using the Kapa library quantification kit (Clinisciences, ref. KK4824). Equimolar amounts of 4 libraries were pooled, diluted to 10 nM, denatured, and diluted again to 7 pM. 100 µl of the diluted pool were hybridized on one lane of an Illumina's Flow Cell. Clustering and 50 cycles sequencing were performed according to Illumina's instructions on a Hiseq2000. Libraries were multiplexed by three (H3K4me3 samples) or four and sequenced on a HiSeq2000 (Illumina) sequencer, yielding 50 bp single-end reads.  For paired-end sampled (WT, ult1-3, clf-28, swn-7, ult1-3 clf-28 and ult1-3 swn-7): Library preparation was performed as described in (Zhu et al., New Phytol, 2024) with 100-300bp insert size at BGI, China.

value: seedlings

value: ult1-3 clf-28


title: ult1-3clf-28,R1,Input

description: Library name: ult1-3clf-28_R1_Input


title: ult1-3swn-7,R2,Input

description: Library name: ult1-3swn-7_R2_Input

value: ult1-3 swn-7


title: ult1-3swn-7,R1,Input

description: Library name: ult1-3swn-7_R1_Input


title: clf-28,R2,Input

description: Library name: clf-28_R2_Input


title: swn-7,R2,Input

description: Library name: swn-7_R2_Input


title: swn-7,R1,Input

description: Library name: swn-7_R1_Input


title: ult1-3,R2,Col-0,Input

description: Library name: ult1-3_R2_Col-0_Input


title: ult1-3,R1,Col-0,Input

description: Library name: ult1-3_R1_Col-0_Input


title: WT,R1,Input

description: Library name: WT_R1_Input


title: WT,R2,Input

description: Library name: WT_R2_Input


title: ult1-3clf-28,R2,K27

description: Library name: ult1-3clf-28_R2_K27


title: ult1-3swn-7,R2,K27

description: Library name: ult1-3swn-7_R2_K27


title: clf-28,R2,K27

description: Library name: clf-28_R2_K27


title: ult1-3swn-7,R1,K27

description: Library name: ult1-3swn-7_R1_K27


title: clf-28,R1,K27

description: Library name: clf-28_R1_K27


title: swn-7,R2,K27

description: Library name: swn-7_R2_K27


title: ult1-3,R1,Col-0,K27

description: Library name: ult1-3_R1_Col-0_K27


title: WT,R2,K27

description: Library name: WT_R2_K27


title: swn-7,R1,K27

description: Library name: swn-7_R1_K27


title: WT,R1,K27

description: Library name: WT_R1_K27


title: SM4

city: Dalian

first: Xiang

address: No. 467, Zhongshan Road, Shahekou District

institute: The Second Hospital of Dalian Medica

description:
Library name: sample8
C_4

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Homo sapiens, GRCh38 (hg38)
Supplementary files format and content: FPKM values for each Sample

organism: Homo

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: SM for 24h


title: SM2

description:
Library name: sample6
C_2


title: SM1

description:
Library name: sample5
C_1


title: CON4

description:
Library name: sample4
A_4


title: CON3

description:
Library name: sample3
A_3


title: CON1

description:
Library name: sample1
A_1


title: CON2

description:
Library name: sample2
A_2


title: Extracted Human reads from AAP16 PDX Model treated with Vehicle control (Replicate 3)

city: HOUSTON

first: John Paul

last: Shen

address: 1515 Holcombe Blvd

department: Gastrointestinal Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

description: Library name: AAP16_VC3_Human

data_processing:
Xenome (version 1.0.1-r) was used to segregate mouse and human reads from raw RNAseq files of PDX models. Mouse reference genome (GRCm39) and gene annotation file (Gencode.vM26) were used for mapping and annotating mouse reads. Extracted human reads for each PDX sample were stored in FASTQ files and input to the downstream STAR (version 2.7.2b) RNASeq alignment tool. Raw FASTQ files were mapped to the human reference genome (hg38) and mouse reference genome (GRCm39) separately using STAR (version 2.7.2b) RNASeq alignment tool. Biobambam (version 0.0.191) was used to mark duplicates and index raw files before alignment.
HTSeq (version 0.11.0) was utilized to extract raw read counts from STAR-aligned RNAseq BAM files of PDX models.
Assembly: hg38, GRCm39
Supplementary files format and content: tab-delimited csv file include raw counts of human and mouse reads for each sample

source_name: Appendiceal Adenocarcinoma

growth_protocol: Female NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice, 5–7 weeks of age, were purchased from The Jackson Laboratory (Bar Harbor, ME, USA), and used for tumor implantation. The animals were maintained under specific pathogen-free conditions. Housing and all procedures involving animals were performed according to protocols approved by the Institutional Animal Care and Use Committee of MD Anderson Cancer Center and conducted in accordance with U.S. Common Rule. AA tumors from The Jackson Laboratory for TM00351 (KRASG12D) and the University of Texas MD Anderson Cancer Center for AAPDX-16 (KRASG12V) were implanted into NSG mice in the peritoneal cavity. The well-being of the mice was carefully monitored, and mice were sacrificed when signs of disease, mainly abdominal distension together with a rough coat and reduced mobility, were seen. The tumor was harvested, cut into ~ 25–30 mm3 fragments, six of which were placed in the peritoneal cavity, both upper and lower abdominal quadrants, and both flank sides, of NSG mice.

extract_protocol:
Bulk RNA sequencing was performed on tumor tissue harvested from the AAPDX-01 (KRASG12D) and AAPDX-16 (KRASG12V) IP-PDX models following four weeks of treatment with MRTX1133, RMC-6236, or vehicle control, respectively. RNA was extracted using RNAqueous™ Total RNA Isolation Kit (Catalog number: AM1912). RNA concentraction ≥ 20 ng/µl for each sample was used for library construction.
Before library construction, quality control for each RNA samples was performed to guarantee the reliability of the data. RNA degradation and potential contamination were tested by Agarose Gel Electrophoresis. Agilent 2100 was used to check the RNA integrity and quantitation. After the QC procedures, mRNA from each smaple was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: MRTX1133 (synthesized in in TRACTION, the University of Texas MD Anderson Cancer Center) were freshly dissolved in 10% Captisol in 50 mM citrate buffer pH 5.0. PDX mice were intraperitoneally (IP) injected with MRTX1133 (15 mg/kg), twice a day. RMC-6236 (Selleck Chemicals, Houston, TX, USA) were dissolved in DMSO, PEG300, and Tween80, then added with ddH2O to adjust volume to 0.5 mL per mouse (final concentration of 5%DMSO/40%PEG300/5%Tween/50%ddH2O). PDX mice were IP injected with RMTRACTION, the University of Texas MD Anderson Cancer Center) was freshly dissolved in 10% Captisol in 50 mM citrate buffer,C-6236 (20 mg/kg, an equal mole of MRTX1133) daily. As a control, mice were IP injected with the same amount of vehicle at the same schedule.

value: Appendiceal Adenocarcinoma

value: Vehicle Control


title: Extracted Human reads from AAP16 PDX Model treated with Vehicle control (Replicate 1)

description: Library name: AAP16_VC1_Human


title: Extracted Human reads from AAP16 PDX Model treated with RMC-6236 (Replicate 2)

description: Library name: AAP16_RMC2_Human


title: Extracted Human reads from AAP16 PDX Model treated with RMC-6236 (Replicate 1)

description: Library name: AAP16_RMC1_Human


title: Killifish-Zebrafish barnyard 8-somite stage (115 hpf, 12 hpf)

city: Seattle

first: Sydney

middle: Marie

last: Sattler

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description:
Library name: 115 hpf
V4 T20 PIPseq

data_processing:
Reads were aligned to the N. furzeri (Nfu_20140520) or the D. rerio (GRCz11.108) genomes and gene-count matrices were generated using PIPseeker software (v1.1.7, Fluent Bio). For the 115hpf timepoint only, cells with >90% reads mapping to the killifish genome were labelled killifish cells and computationally isolated from the barnyard mix. Doublets were removed using scrublet (v0.2.3). Cells with >12% mitochondria reads and >5000 reads/cell were removed. The downstream analysis was performed with Seurat (v5.4.0).
Assembly: Nfu_20140520, GRCz11.108
Supplementary files format and content: Single Cell Experiment .RDS files

organism:
Danio rerio
Nothobranchius furzeri

source_name: whole embryo

growth_protocol: An inbred strain of Nothobranchius furzeri, originating from Gonarezhou National Park, Zimbabwe was used in each experiment. An inbred strain (AB or WIK) of Danio rerio was used in each experiment. Both species were maintained at 28°C under 15:9 light:dark cycles including a 1-hour ramp up/down period. Killifish (GRZ) were crossed for 2 hours. Zebrafish (WIK) were crossed for 30 minutes. Using the mid-point as 0 hours post fertilization, clutches of killifish embryos from 52, 72, 96, and 115hpf, and zebrafish embryos at 12 hpf, consisting of 132, 90, 80, 35, and 35 embryos, respectively, were visually confirmed to be at 100% dispersed, incipient aggregate, bud, and 8-somite stages.

extract_protocol:
Embryos were manually dechorionated with forceps in ice cold DMEM/F12 (Gibco, 21-041-025) and transferred to lo-bind 1.5 mL Eppendorf tubes on ice. Cells were spun down at 500xg for 3 min at 4°C. Cells were dissociated in Accutase (Innovative Cell Technologies, AT104) at 37°C for 7-20 min depending on embryo stage (older embryos required longer dissociation). Percent viability was determined by counting DAPI+, Calcein-AM+ (Invitrogen, C1430) live cells and DAPI+, Calcein-AM- dead cells on a disposable hemocytometer (Bulldog Bio, DHC-N420). 40,000 cells were loaded onto the V4 T20 PIP-seq kit (formerly Fluent Bio, now the Illumina Single Cell 3’RNA Prep Kit) for each timepoint except for the 115hpf timepoint which consisted of a 1:1 mix of killifish and stage-matched zebrafish cells used to initially assess the efficacy of the PIP-seq kit which, at that time, had not yet been used on teleosts.
Followed V4 P20 PIPseq protocol. cDNA fragment analysis of scRNAseq libraries was performed using the 4200 TapeStation System. Libraries were sequenced with a NextSeq 2000 P3 100 cycle kit (52hpf, 72hpf, 96hpf) or NovaSeq 6000 S4 300 cycle kit (115hpf, a gift from Fluent Biosciences) using the following configuration: read 1: 54, i7 index: 8, i5 index: 8, read 2: 68.

value: whole embryo

value: GRZ, WIK

tag: hours post_fertilization


title: Extracted Human reads from AAP01 PDX Model treated with Vehicle control (Replicate 3)

description: Library name: AAP01_VC3_Human


title: Extracted Human reads from AAP01 PDX Model treated with Vehicle control (Replicate 2)

description: Library name: AAP01_VC2_Human


title: Extracted Human reads from AAP01 PDX Model treated with Vehicle control (Replicate 1)

description: Library name: AAP01_VC1_Human


title: Extracted Human reads from AAP01 PDX Model treated with MRTX1133 (Replicate 3)

description: Library name: AAP01_MRTX3_Human


title: Extracted Human reads from AAP01 PDX Model treated with MRTX1133 (Replicate 2)

description: Library name: AAP01_MRTX2_Human


title: SM3

description:
Library name: sample7
C_3


title: Extracted Human reads from AAP01 PDX Model treated with MRTX1133 (Replicate 1)

description: Library name: AAP01_MRTX1_Human


title: hAO_Re

city: New haven

first: Woo Sub

last: Yang

state: CT

address: 10 Amistad St, Room 214j

institute: Yale University

description:
Library name: scRNA-seq sample1
10x Genomics

data_processing:
For RNA-seq, Sequencing reads were first quality-trimmed using fastp (v0.20.1) with adapter detection enabled and a minimum length cutoff of 25 bp. The quality of the trimmed reads was evaluated with FastQC (v0.11.9). Trimmed paired-end reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.9a), with the primary assembly FASTA file and GTF annotations obtained from Ensembl (release 112). The alignment included both transcriptome and gene count quantification modes. Parameters allowed for a maximum of 20 multimapping reads and required a minimum overhang of 8 bp for splice junctions. Aligned reads were sorted and indexed using samtools (v1.10), and transcript quantification was performed with Salmon (v1.5.2) in alignment-based mode using the sorted BAM files, accounting for sequence and GC biases.  For scRNA-seq, The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-in)
Assembly: GRCh38
Supplementary files format and content: For RNA-seq, csv file including TPM. For scRNA-seq, matrix, features and barcode files.

source_name: Brain organoid

extract_protocol:
for RNAseq, RNA was extracted using RNeasy plus universal mini prep kit (Quiagen). 1 ug total RNA was used for construction of sequencing libraries. For scRNA-seq organoids were dissociated with Papain dissociation system (worthington biochemical). And total 20,000 cells were used for library contruction.
for RNA-seq, Truseq stranded mRNA library prep kit (Illumina) was used following manufacture's protocol. For scRNA-seq, Library prep was performed following 3P v4 (GEM-X)  protocol (10X Genomics)

value: Brain organoid


title: HepG2 siNAT10 knockdown replicate 4

city: Yushima, Bunkyo-ku, Tokyo

first: Ryota

last: Kurimoto

state: Tokyo

department: Systems BioMedicine

institute: Tokyo Medical and Dental University

description:
Library name: HepG2_siNAT10_rep4
Column S8 in SLAM_count_matrix_fc.tsv

data_processing:
Raw FASTQ files were adapter-trimmed and quality-filtered using Trim Galore v0.6.10 with Cutadapt v3.5 (quality Phred cutoff: 20, minimum read length: 20 bp, Illumina TruSeq adapter removal).
Trimmed reads were aligned to the human reference genome (GRCh38 primary assembly) using STAR v2.7.9a with GENCODE v38 annotation (sjdbOverhang=74).
Gene-level read counts were quantified using featureCounts from the Subread package with GENCODE v38 annotation (gene-level summarization, Ensembl gene IDs).
Assembly: GRCh38 (hg38)
Supplementary files format and content: Count_matrix_fc.tsv: Tab-separated values file. Rows represent genes (ENSEMBL gene IDs), columns represent samples (S1=HepG2_siCtrl_rep1, S2=HepG2_siCtrl_rep2, S3=HepG2_siNAT10_rep1, S4=HepG2_siNAT10_rep2, S5=HepG2_siCtrl_rep3, S6=HepG2_siCtrl_rep4, S7=HepG2_siNAT10_rep3, S8=HepG2_siNAT10_rep4). Values are raw read counts.

source_name: liver

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using TRI reagent (Sigma-Aldrich) according to the manufacturer's instructions. RNA quantity and quality were assessed by spectrophotometry.
3' mRNA-seq libraries were prepared using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit REV according to the manufacturer's protocol. Libraries were sequenced on Illumina NovaSeq 6000 (paired-end, 150 bp).

treatment_protocol: Cells were transfected with siRNA targeting NAT10 (siNAT10) or negative control siRNA (siCtrl) using a lipofection reagent. Total RNA was harvested 2 days after transfection.

value: liver

value: hepatocellular carcinoma


title: HepG2 siNAT10 knockdown replicate 3

description:
Library name: HepG2_siNAT10_rep3
Column S7 in SLAM_count_matrix_fc.tsv


title: Wildtype Control 3rd instar brain, Hypoxia

description:
Library name: 2GGH-HC
Brain sample isolated from Wildtype Control 3rd instar larvae reared in 3.5% hypoxia.

value: 3rd instar larval brain

value: control

value: Hypoxia


title: RMT1EV2

description:
Library name: Sample2
EV-microRNA

value: EVs

value: breast cancer cell


title: HepG2 siControl replicate 4

description:
Library name: HepG2_siCtrl_rep4
Column S6 in SLAM_count_matrix_fc.tsv

value: siControl


title: GE97_4Gy_d2, CT, batch_2

description: Library name: GE97_4Gy_d2

value: in-vitro fibroblasts

value: primary dermal fibroblast strain

value: CT


title: ZT13, replicate 1

description:
Library name: ZT13x1
ZT13x1_S1

value: Neutrophils

value: Neutrophils from Spinal cord


title: Extracted Human reads from AAP16 PDX Model treated with Vehicle control (Replicate 2)

description: Library name: AAP16_VC2_Human

value: Appendiceal Adenocarcinoma

value: Vehicle Control


title: HepG2 siControl replicate 3

description:
Library name: HepG2_siCtrl_rep3
Column S5 in SLAM_count_matrix_fc.tsv


title: GE96_0Gy_d2, TT, batch_1

description: Library name: GE96_0Gy_d2

value: TT


title: HepG2 siNAT10 knockdown replicate 2

description:
Library name: HepG2_siNAT10_rep2
Column S4 in SLAM_count_matrix_fc.tsv


title: HepG2 siNAT10 knockdown replicate 1

description:
Library name: HepG2_siNAT10_rep1
Column S3 in SLAM_count_matrix_fc.tsv


title: GE8_0Gy_d2, CC, batch_2

description: Library name: GE8_0Gy_d2

value: CC


title: HepG2 siControl replicate 2

description:
Library name: HepG2_siCtrl_rep2
Column S2 in SLAM_count_matrix_fc.tsv

value: liver


title: HepG2 siControl replicate 1

description:
Library name: HepG2_siCtrl_rep1
Column S1 in SLAM_count_matrix_fc.tsv

value: hepatocellular carcinoma


title: GE67_0Gy_d0, CT, batch_2

description: Library name: GE67_0Gy_d0


title: GE66_4Gy_d2, CT, batch_1

description: Library name: GE66_4Gy_d2


title: dHL-60 cells, SUD2core-expression,  rep2

city: Chengdu

first: Ying

last: Li

address: No. 17 Gaopeng Dadao

institute: Sichuan University

description: Library name: Sample 5

data_processing:
HISAT2 software was used (hisat2-2.0.4) to map reads to the genome.
Assembly: GRCh38_release110
Supplementary files format and content: csv files include FPKM values for each sample

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0.
Poly (A) RNA was purified from 1 μg of total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher Scientific) for two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, e6150) under 94 °C for 5-7 min. Then the cleaved RNA fragments were reverse transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Thermo Fisher Scientific, 1896649). These were then used to synthesize U-labeled second-stranded DNA with E. coli DNA polymerase I (NEB, m0209), RNase H (NEB, m0297) and dUTP Solution (Thermo Fisher Scientific, R0133). Single or dual index adapters were ligated to the fragments. After heat-labile UDG enzyme (NEB, m0280) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR in the following conditions: initial denaturation at 95 °C for 3 min, 8 cycles of denaturation at 98 °C for 15 sec, annealing at 60 °C for 15 sec, and extension at 72 °C for 30 sec, and then final extension at 72 °C for 5 min. The average insert size for the final cDNA library was 300 ± 50 bp.

value: promyeloblast

value: SARS-CoV-2 trVLP


title: dHL-60 cells, SUD2core-expression,  rep1

description: Library name: Sample 4


title: dHL-60 cells, SUD2core-expression,  rep3

description: Library name: Sample 6


title: dHL-60 cells, control,  rep3

description: Library name: Sample 3


title: dHL-60 cells, control,  rep2

description: Library name: Sample 2


title: dHL-60 cells, control,  rep1

description: Library name: Sample 1


title: dHL-60 cells, HEBP2-knockout,  rep3

description: Library name: Sample 6


title: dHL-60 cells, HEBP2-knockout,  rep2

description: Library name: Sample 5


title: dHL-60 cells, HEBP2-knockout,  rep1

description: Library name: Sample 4


title: GE6_0Gy_d2, TT, batch_1

description: Library name: GE6_0Gy_d2


title: dHL-60 cells, control sgRNA,  rep3

description: Library name: Sample 3


title: dHL-60 cells, control sgRNA,  rep2

description: Library name: Sample 2


title: lung alveolar organoid, Nr1d2 knockout, plate1-1 well G07

description: Library name: 1-1_G07_NR1D2

value: lung mouse alveolar type 2 cells and primary human fibroblasts

value: Nr1d2 CRISPR/Cas9 knockout


title: Salmoenlla infected SpiB+ epithelila cells, scRNAseq, rep2

city: Brisbane

first: M. Zeeshan

last: Chaudhry

state: Queensland

address: 37 Kent Street

country: Australia

institute: The University of Queensland

data_processing:
RunHarmony 19 wrapped in Seurat was performed using the 30PCs to integrate data sets from each batch. The first 40 harmony dimension reductions were applied to construct a shared nearest neighbour graph and FindClusters with Louvain algorithms using a standard Seurat analysis pipeline. Uniform manifold approximation and projection (UMAP) was also generated with the first 40 harmony dimension reductions to embed the data sets into two dimensions for visualization.
To annotate each cluster, we used FindAllMarkers in Seurat to find marker genes for each cluster. We also checked the expression level of marker genes of expected cell type cells from literatures.
Differential expression (DE) analysis between M cells and Tuft cells, and between cells from different locations including PP, SI and LI compared to other M cells without any stimulus was performed with MAST 20. Genes with P values < 0.01 were regarded as DE genes. Adjusted P values were then used in volcano plots. GO analysis was conducted on up-regulated genes using goana in limma (3.50.3)
Assembly: ScRNA-sequencing reads were mapped to the GRCm38.p8 mouse genome and external RNA controls consortium (ERCC) spike-in sequences using the Subread aligner (v2.4.3)13 and assigned to genes using scPipe (v1.12.0) 14 with GENCODE 38 primary assembly annotation
Supplementary files format and content: sce file containing the raw count for each individual cell
Supplementary files format and content: sce file containing the raw count for each individual cell

source_name: Peyer's patch, small intestine and large intestine

extract_protocol:
Single-cell (sc)-RNA-seq using a modified CEL-Seq2 protocol. Cell were sorted into into a chilled 384-well PCR plate (Greiner, 785290) containing 1.2μl of primer/lysis mix [20 nM indexed polydT primer (custom made, IDT), 1:6.000.000 dilution of ERCC RNA spike-in mix (Ambion - 4456740), 1 mM dNTPs (NEB - N0446S), 1.2 units SUPERaseIN Rnase Inhibitor (Thermo Fisher - AM2696), 0.2 % Triton X-100 solution (Sigma Aldrich – 93443-100ml), DEPC water (Thermo Fisher - AM9920)]
Single cell transcriptome libraries were generated by adapting the CelsSeq2 protocol [Hashimshony et al., 2016] as follows: Samples were pooled after first strand cDNA synthesis, treated with Exonuclease 1 for 30 minutes, followed by a 1.2X bead clean-up. Second strand synthesis was performed using NEBNext Second Strand Synthesis module (NEB #E6111S) in a final reaction volume of 20 ul and NucleoMag NGS Clean-up and Size select magnetic beads (Macherey-Nagel - 7449970.5) were used for all DNA purification and size selection steps.]

value: Salmoenella


title: naïve SpiB+ epithelila cells, scRNAseq, rep4

value: Peyer's patch, small intestine and large intestine


title: moDCs_LPS_IgG_5

city: Heraklion

first: Prodromos

last: Sidiripoulos

address: Andrea Kalokerinou 13

country: Greece

institute: University of Crete

description: Library name: 6A

data_processing:
Raw FASTQ files were quality checked using FastQC and summarized with MultiQC.
Reads were aligned to the Homo sapiens reference genome (hg38) using HISAT2 v2.1.0 with default parameters.
Alignment files were sorted with SAMtools v1.9.
Reads were assigned to genomic features using featureCounts v1.5.0-p1 with GENCODE v34 primary assembly annotation.
Assembly: hg38, GENCODE v34 primary assembly annotation
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts for all samples

source_name: monocyte-derived dendritic cell

growth_protocol: Magnetically isolated CD14+ monocytes were cultured in RPMI 1640 supplemented with 10% heat-inactivated FBS, 100 IU/mL penicillin and 100 μg/mL streptomycin, 0.01 M Hepes and 50 μM 2-mercaptoethanol in the presence of 100 ng/ml IL4 and 100 ng/ml GM-CSF for 6 days at 1× 10^6 cells/ml. Cells were maintained at 37°C in a humidified atmosphere containing 5% CO2.  On day 3, culture medium was refreshed and supplemented with 50 ng/ml IL4 and GM-CSF.

extract_protocol:
Total RNA from treated DCs was isolated using the PureLink RNA mini kit (catalog no. 12183018A, Invitrogen) according to the manufacturer’s instructions. RNA quantity was assessed by NanoDrop spectrophotometry, and RNA integrity was evaluated using the Agilent Bioanalyzer RNA Nano Kit. 1ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer's instructions.100-bp single-end reads were generated per sample on an Illumina NovaSeq 6000 instrument.

treatment_protocol: On day 6, cells were stimulated with LPS (100 ng/ml) in the presence of either CTLA4-Ig (50 μg/ml) or control IgG (50 μg/ml) for 18 hours.

value: monocyte-derived dendritic cell

value: LPS + IgG

tag: time

value: 18 hours


title: moDCs_LPS_CTLA4Ig_4

description: Library name: 5B

value: LPS + CTLA4-Ig


title: dHL-60 cells, control sgRNA,  rep1

description: Library name: Sample 1


title: moDCs_LPS_CTLA4Ig_5

description: Library name: 6B


title: moDCs_LPS_CTLA4Ig_3

description: Library name: 3B


title: moDCs_LPS_IgG_3

description: Library name: 3A


title: moDCs_LPS_IgG_4

description: Library name: 5A


title: GE30_4Gy_d2, CT, batch_2

description: Library name: GE30_4Gy_d2

value: in-vitro fibroblasts

value: primary dermal fibroblast strain

value: CT


title: moDCs_LPS_IgG_2

description: Library name: 2A


title: IgG Control sample-CTB (Cut & Run)

city: Kansas city

first: Soumen

last: Paul

state: Kansas

address: Rainbow Blvd

institute: University of Kansas Medical center

description: Library name: CTB IgG

data_processing:
nf-core chipseq pipeline
Assembly: hg38(human)
Supplementary files format and content: peaks file in bed format
Supplementary files format and content: Coverage in bigwig file
Library strategy: CUT&Run

source_name: Placenta

growth_protocol: Primary CTBs isolation from placenta tissues was published earlier (PMID: 36037374).

extract_protocol:
CUT&RUN experiments was performed according to the published protocol (PMID: 38346193). 1 X 105 freshly isolated and selected CTBs were used per condition, and CUT&RUN assay was performed using Cell Signaling Technology (86652) kit. For our experiment, primary antibodies against PRMT1 (Cell Signaling Technology 2449) or IgG (Cell Signaling Technology 66362) were used. Finally, DNA fragments were isolated and used for library preparation using Illumina TruSeq ChIP. (PMID: 29651053,PMID: 31232687.
For library preparation TruSeq RNA Library Prep Kit v2 was used. Finally, deep sequencing was performed using the Illumine NovaSeq 6000 sequencing system at the University of Kansas Genome Sequencing Facility to generate pair-end reads with read length 101 bp.

treatment_protocol: No

value: Placenta


title: moDCs_LPS_IgG_1

description: Library name: 1A


title: PRMT1 Control sample-CTB (Cut & Run)

description: Library name: CTB PRMT1


title: moDCs_LPS_CTLA4Ig_1

description: Library name: 1B


title: HD8HD9_skinV; HD31HD32_spatial

city: Taoyuan

first: Chuang-Wei

last: Wang

address: No. 5, Fusing St

institute: cgmh

description:
Library name: HD8HD9Visium
Visium for FFPE v2

data_processing:
FASTQ files were processed with Cell Ranger (10x Genomics) and Space Ranger (10x Genomics). Downstream analyses were performed using Seurat. For scRNA-seq quality control, cells with >20% mitochondrial gene content, fewer than 200 detected genes, or a number of detected genes greater than the upper quartile plus 1.5 × interquartile range (UQ + 1.5 × IQR) were excluded. For spatial analysis, spots located outside the tissue were removed.
Assembly: Human GRCh38 (GENCODE v32/Ensembl98); GRCh38-2020-A
Supplementary files format and content: For scRNA-seq, filtered barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz were provided. For the TCR library, filtered_contig_annotations.csv.gz was also provided.
Supplementary files format and content: For Visium, filtered barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz, as well as spatial information generated by Space Ranger, were provided.
Library strategy: Spatial Transcriptomics

source_name: skin

extract_protocol:
scRNA-seq: Lesional blister fluid collected from acute-stage patients was centrifuged at 750 × g for 10 minutes to isolate lesional blister cells (BC). Peripheral blood mononuclear cells (PBMCs) were isolated from ethylenediaminetetraacetic acid (EDTA)–anticoagulated blood by Ficoll density-gradient centrifugation (Cytiva).  Visium: FFPE skin sections (5 µm) were cut using a microtome and processed according to the Visium protocol.
scRNA-seq: Library preparation, including cDNA synthesis and library construction, was performed according to the manufacturer's Single Cell 5' v2 protocol (10x Genomics). Library quality was assessed using the Agilent 2200 TapeStation system, and sequencing was performed on the Illumina NovaSeq 6000 platform with a 150-bp read length. Abbreviations: GEX — gene expression library; TCR — T cell receptor library; CSP — multiplexed sample library.  Visium: Spatial transcriptome sequencing libraries were prepared using the 10x Genomics Visium Spatial Gene Expression for FFPE kit (v1 and v2), following the manufacturer's protocol.

value: skin

tag: disease

value: HD


title: skin_HD13, skin_HD14, skin_HD15; HD27_skin, HD28_skin, HD29_skin [CSP]

description:
Library name: KE-HDCSP
10x Genomics 5'

data_processing:
FASTQ files were processed with Cell Ranger (10x Genomics) and Space Ranger (10x Genomics). Downstream analyses were performed using Seurat. For scRNA-seq quality control, cells with >20% mitochondrial gene content, fewer than 200 detected genes, or a number of detected genes greater than the upper quartile plus 1.5 × interquartile range (UQ + 1.5 × IQR) were excluded. For spatial analysis, spots located outside the tissue were removed.
Assembly: Human GRCh38 (GENCODE v32/Ensembl98); GRCh38-2020-A
Supplementary files format and content: For scRNA-seq, filtered barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz were provided. For the TCR library, filtered_contig_annotations.csv.gz was also provided.
Supplementary files format and content: For Visium, filtered barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz, as well as spatial information generated by Space Ranger, were provided.

tag: tissue


title: HD4_skinV; HD30_spatial

description:
Library name: HD4Visium
Visium for FFPE v1


title: skin_HD13, skin_HD14, skin_HD15; HD27_skin, HD28_skin, HD29_skin [GEX]

description:
Library name: KE-HDGEX
10x Genomics 5'


title: AdrD9292_10_PBMC, AdrD10022_13_PBMC; STP5_post, STP6_post [GEX]

description:
Library name: A9292GEX
10x Genomics 5'

source_name: PBMC

tag: cell type

value: PBMC


title: AdrD9292_10_PBMC, AdrD10022_13_PBMC; STP5_post, STP6_post [CSP]

description:
Library name: A9292CSP
10x Genomics 5'


title: AdrD11588_skinV; SJS24_spatial

description:
Library name: A11588Visium
Visium for FFPE v2

value: SJS/TEN


title: AdrD9292_10_PBMC, AdrD10022_13_PBMC; STP5_post, STP6_post [TCR]

description:
Library name: A9292TCR
10x Genomics 5'


title: AdrD9316_PBMC, AdrD9316_10_PBMC; STP4, STP4_post [TCR]

description:
Library name: A9316TCR
10x Genomics 5'

value: SJS/TEN, SJS/TEN_recovery


title: AdrD10022_BC, AdrD10022_PBMC; STB6, STP6 [TCR]

description:
Library name: A10022PBTCR
10x Genomics 5'

source_name: Blister cell, PBMC

value: Blister cell, PBMC


title: AdrD10022_BC, AdrD10022_PBMC; STB6, STP6 [CSP]

description:
Library name: A10022PBCSP
10x Genomics 5'


title: breast cancer_SM181

city: Houston

first: William

last: Symmans

address: 2130 W Holcombe Blvd #11.4000

institute: University of Texas MD Anderson Cancer Center

data_processing:
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).
MAS5.0 signal intensity for each array was log2 transformed and scaled to a reference distribution of 600 breast cancer specific genes.

source_name: breast cancer sample

extract_protocol: Total RNA was extracted from tissue using Qiagen Rneasy columns

value: P

value: N

value: IIB

value: Tissue

value: Surgical Tissue Sample