title: p312dwt_IMM+B48_GEX

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

description:
Library name: p312dwt
the gene expression of  samples 21 days after vaccination, and treated with CD4CD8 antibodies samples 21 days after vaccination

data_processing:
scRNA-seq.  Libraries were sequenced on the Illumina NovaSeq X Plus platform (Illumina, San Diego, CA). Raw sequencing data were processed using the BD Rhapsody Analysis Pipeline (v2.2.1) on VELSERA cloud platform, aligned to the GRCm39 reference genome ( scATAC-seq Sequencing data was processed using BD Rhapsody Sequence Analysis Pipeline v2.2.1 ATAC Large Input  on the Seven Bridges Genomics (SBG, now VELSERA) cloud platform (San Francisco, CA). the output files were generated for secondary analysis and visualization. Spatial Transcriptomic The single nuclei whole transcriptome (snWT) seq data was uploaded to the BD Rhapsody SBG for gene expression analysis, and the RSEC_MolsPerCell_MEX.zip output files folder, along with the Trekker seq data,  were uploaded to the LatchBio cloud platform for the CurioTrekker v1.1.0 spatial single cell seq pipeline  analysis.
Assembly: GRCm39
Supplementary files format and content: CITE-Seq pipeline output: MEX.tar.gz files with matrix.mtx, barcodes.tsv, features.tsv; ATAC-seq pipeline output: 1. MEX.tar.gz files with matrix.mtx, barcodes.tsv, features.tsv. 2 peak.bed files, 3 fragment.bed files.;  Spatial Transcriptomics: 1. spatial positions: coordinates.csv. 2  Curio Trekker output: matrix.mtx, barcodes.tsv, features.tsv. 3. Curio Trekker output: anndata files for the final pipeline output
Library strategy: Spatial Transcriptomics

extract_protocol:
Lung immune and epithelial cells were isolated using a modified enzymatic digestion protocol from a previous study with minimal modification (17). Mice were euthanized and lungs were perfused and lavaged with digestion buffer composed of RPMI-1640 supplemented with elastase (Worthington), dispase II (Sigma-Aldrich), and DNase I (Sigma-Aldrich). Lung tissues were then excised, minced into small fragments, and further digested in RPMI-1640 containing liberase (Sigma-Aldrich) and DNase I at 37°C for 30 minutes. Following enzymatic digestion, single-cell suspensions were obtained by passing the mixture through a 100 μm cell strainer and red blood cells were lysed using ACK lysis buffer. To enrich for specific cell subsets, cells were stained with surface markers targeting CD11b⁺, EpCAM⁺, and CD11c⁺ populations using a customized innate immune panel. CD3⁺ T cells were enriched following FACS protocol. Cells were sorted using a FACSAria cell sorter (BD Biosciences) after staining with oligo antibodies (Table S2). CD11b⁺, EpCAM⁺, CD11c⁺, CD3⁺ cells and the non-sorted fraction at a 1:1:1:1:6 ratio and resuspended in cold PBS supplemented with 1% BSA (Miltenyi Biotec) and 0.5 U/μL RNase inhibitor (Sigma-Aldrich) for scRNA-seq. CD11b⁺, EpCAM⁺, CD11c⁺ and the non-sorted fraction at a 1:1:1:7 ratio and resuspended in BD OMICS Guard™ buffer (BD Biosciences, Cat. 570911).Spatial transcriptomics Lung tissues from C57BL/6 mice were freshly harvested, embedded in optimal cutting temperature (OCT) compound, and immediately snap-frozen in liquid nitrogen. Samples were stored at −80 °C until sectioning.
scRNA-seq analysis To simultaneously assess whole-transcriptome and targeted surface protein expression at the single-cell level, BD Rhapsody™ single-cell multi-omics technology was employed. Mouse lung cells were thawed and resuspended in FACS buffer prior to dextramer-based flow cytometric sorting for antigen-specific T cells. Sorted cells were collected into staining buffer at a concentration of 200–800 cells/μL in ~600 μL per sample. Approximately half of the collected cells were loaded onto the BD Rhapsody Cartridge (BD Biosciences, Cat. #633733) using the associated BD Rhapsody Cartridge Reagent Kit (Cat. #633731). Cells were captured in microwell arrays with barcoded beads, followed by cell lysis, bead retrieval, cDNA synthesis, template switching, and Klenow extension. Full-length cDNA containing unique molecular identifiers (UMIs) and cell barcodes was PCR-amplified. Whole-transcriptome was prepared using the BD Rhapsody Whole Transcriptome Amplification Kit (Cat. #633801) following the manufacturer’s instructions. scATAC-seq analysis Cryopreserved cells stored in BD OMICS-Guard™ buffer (Cat. #570911) for less than 48 hours were centrifuged at 800 × g for 5 minutes to remove the preservation buffer. Without additional washing, cells were resuspended in BD sample buffer at ~800 cells/μL for downstream ATAC-seq processing. Splint beads were prepared using a custom splint oligonucleotide specific to V3 capture beads provided by BD Biosciences. Nuclei were isolated following a modified protocol (62). Briefly, cell pellets were lysed and resuspended in Nuclei Buffer using a wide-bore pipette, aiming for a concentration of 10,000 nuclei/μL. In situ tagmentation was performed by incubating the nuclei with a Tagmentase mix that targets accessible chromatin regions, generating DNA fragments with preloaded adapter sequences. An aliquot of tagmented nuclei was stained with DyeCycle™ Green (1 mM) and counted using the BD Rhapsody™ Scanner. Single-nucleus capture, cell lysis, and genomic DNA processing were performed according to the BD Rhapsody manufacturer’s protocol. DNA fragments were captured via splint-oligo-bonded TSO (template-switch oligo) strands. Ligase was used to ligate the bead-bound oligos to the tagmented DNA, followed by gap filling and extension using a specific enzyme mix. Final denaturation removed DNA templates from beads, and Illumina-compatible adapters and sample indices were introduced during amplification. Libraries were prepared with the following sequencing parameters: Read 1: 50 cycles, Read 2: 50 cycles, Index 1: 8 cycles, and Index 2: 60 cycles. Sequencing data were analyzed using the BD Rhapsody ATAC Large Input pipeline (v2.2.1) on VELSERA cloud platform. Processed output files were used for secondary analysis and visualization using the Signac package (v1.14.0). In brief, fragment files were imported and used to create a Seurat object with a chromatin assay via the CreateChromatinAssay function. Spatial transcriptomics Lung tissues from C57BL/6 mice were freshly harvested, embedded in optimal cutting temperature (OCT) compound, and immediately snap-frozen in liquid nitrogen. Samples were stored at −80 °C until sectioning. Spatially resolved single-nucleus transcriptomic profiling was performed using the Curio Trekker Single-Cell Spatial Mapping Kit (Cat. Nos. SK017 and SK020; Takara Bio). Briefly, 25 μm cryosections of mouse lung tissue were placed onto Trekker 10 × 10 mm glass tiles, each embedded with a monolayer of uniquely DNA-barcoded microparticles (beads). Upon exposure to ultraviolet (UV) light, the spatial DNA barcodes were photocleaved and internalized into the overlying tissue. Following UV exposure and barcode incorporation, the tissue was dissociated from the tile into single-nucleus suspensions. These spatially tagged nuclei were then loaded onto the BD Rhapsody™ Single-Cell system (BD Biosciences) for single-nucleus capture and transcriptomic profiling.

value: Lung

value: GLA-3M-052-LS+OVA, and anti-cd4cd8 treatment

tag: library type

value: mRNA


title: mESCs, CKO2-MCM2

status: Public on Feb 23 2026

type: SRA

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

country: USA

institute: UCSF

library_source: genomic

data_processing:
Nextflow/chip
Fastq files were mapped and quality controlled using the nfcore/chip pipeline. Merged bigwig files were generated from bam files using multiBamSummary function of deepTools2.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

source_name: mESCs

growth_protocol: Mouse ESCs were grown in the presence of Lif+2i.

extract_protocol:
SimpleChIP Plus Sonication Chromatin IP Kit
NEBNext Ultra II

tag: cell type

value: mESCs

tag: culture conditions

value: Naive

tag: genotype

tag: treatment

tag: chip antibody

value: MCM2 (MCM2 3619 Cell Signaling)


title: U20_siLuc_Rep1

city: Vienna

first: Dominik

last: Handler

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA-Institute of Molecular Biotechnology of Austrian Academy of Sciences

description:
Library name: U20_siLuc_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells

library_source: other

data_processing:
Illumina reads were processed by removing 3′ adapters with cutadapt {Martin, 2011 #646}, trimming 4 random nucleotides from each end and filtering for minimal length (>18 nt) and sequence complexity (bbduk, entropy = 0.35, entropy window = 18, k = 4) . Reads were first aligned to Drosophila rRNA precursor sequences and the mitochondrial genome using bowtie {Langmead, 2009 #656}. Remaining unmapped reads were mapped to the OSC_r1.01 genome using bowtie allowing for 1 mismatch. Alignments were separated into uniquely and all‑mapping fractions. For visualization, HOMER was used to generate tag directories (makeTagDirectory … -format bed -keepAll -single -fragLength given) and UCSC‑compatible tracks (makeUCSCfile … -fsize 1e20 -strand +/- -fragLength given -noadj -normLength 0) were generated per strand. Counts were normalized to 1M miRNAs and final BigWig tracks were created with bedGraphToBigWig (Kent Utilities), producing strand‑specific (sense and antisense) coverage profiles for genome browser display. For transposon histogram analysis, piRNA reads longer than 23 nucleotides were aligned to transposable element consensus sequences using bowtie (--best --strata -f -v 2 -a), permitting multiple mappings. Alignments were subsequently filtered to retain reads that mapped either uniquely or at most twice to a single transposon consensus, to account for long terminal repeat (LTR) redundancy. Reads mapping twice were assigned a fractional count of 0.5 to each location.
Assembly: OSC_r1.01
Supplementary files format and content: All mapping and unique mapping bigwig files for sense and antisense

molecule: other

organism: Drosophila melanogaster

source_name: OSC

growth_protocol: Ovarian somatic cells (OSCs) were maintained at 27 °C in a humidified incubator with 2.5% CO₂, as previously described (Niki, Yamaguchi et al. 2006, Saito, Inagaki et al. 2009) Cells were cultured in M3 basal medium supplemented with 10% fetal bovine serum (FBS), insulin, glutathione, and fly extract.

extract_protocol:
sRNAseq libraries were prepared by first purifying Argonaute–sRNA complexes with TraPR resin columns. OSCs were harvested using trypsin, washed 2x with PBS and stored at -70°C after snap freezing cell-pellets in liquid nitrogen. OSCs were lysed by adding 330 µL of TraPR lysis buffer. OSC lysates were clarified, normalized to equal protein amounts (depending on the experiment 70-120 µg total protein) after Bradford measurements, applied to TraPR columns, and Argonaute-bound RNAs were eluted, followed by phenol–chloroform extraction and precipitation.
To minimize ligation bias and facilitate library multiplexing, adaptors were designed with random nucleotides placed adjacent to the ligating end. The 3′ adaptor carried six random bases at its 5′ terminus and contained sample barcodes (X) for multiplexing (5rApp/NNNNNNXXXX–Adaptor–/3ddC). The 5′ adaptor was an RNA oligo bearing four random nucleotides at its 3′ terminus (…UCUNNNN). After 3′ adaptor ligation with T4 RNA ligase 2, truncated KQ, samples were pooled as necessary, spiked with fluorescently labeled and ligation-blocked oligos as size controls, and gel-purified on a 12.5% polyacrylamide–urea gel. Small RNAs were isolated using the Zymo ZR small RNA PAGE Recovery kit and subjected to 5′ adaptor ligation with T4 RNA ligase 1. Following cleanup with Zymo RCC5 columns, reverse transcription was performed. Libraries were PCR-amplified with KAPA HiFi polymerase and dual-index barcoded primers. Amplification was monitored in real time with EvaGreen, and reactions were stopped upon reaching 3,500–4,000 RFU to prevent overamplification. Final libraries were size-selected on low-melt agarose gels, gel-purified (Zymo), quantified with Qubit, multiplexed and sequenced (SE50, Illumina NovaSeq6000).

tag: cell line

value: OSC

value: ovarian somatic cells

value: OSC cells with indicated piRNA biogenesis reporter stably integrated on chromosome 3R

value: Transfection with siRNA at 0 and 48h. Harvested after 96h


title: Dissociated organoids, 59XY, batch 3

city: London

first: Adam

last: Pavlinek

address: Maurice Wohl Clinical Neuroscience Institute 5 Cutcombe Road

department: Basic and Clinical Neuroscience

country: United Kingdom

institute: King's College London

description: Library name: Sample_13

library_source: transcriptomic

data_processing:
FASTQ files were processed using command line tools on the King’s College London CREATE high-performance computing cluster. Alignment of reads to the human genome (Assembly GRCh38.p14, accession GCF_000001405.40, NCBI RefSeq) was performed using STAR (version 2.7.10b). After alignment, the output BAM files were sorted by chromosome and position coordinates using Samtools (version 1.17) and Picard (version 2.26.2) was used to mark duplicates in the BAM files.
The duplicate checked BAMs were downloaded from CREATE and subsequent analysis was carried out in R (version 4.2.2). A raw counts table was generated using the featureCounts function from the Rsubread package. Gene symbols were annotated using the getBM function from the biomaRt package.
Differential gene expression analysis was performed using the DESeq2 1.38.3 package, which was used to generate DESeq2 normalized counts.
Assembly: GRCh38.p14
Supplementary files format and content: CSV files containing DESeq2 normalized counts for each sample
Supplementary files format and content: CSV files containing raw counts generated using Rsubread for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Dissociated unguided cerebral organoid

growth_protocol: Cerebral organoids were generated from stem cells maintained in Stemflex medium using the commercially available STEMdiff Cerebral Organoid Kit (Stem Cell Technologies; 08570).

extract_protocol:
The culture medium was aspirated and the cells were lifted with accutase and washed with HBSS. The cells were resuspended in TRIzol and RNA was precepitated from the aqueous phase following phase sepration of TRIzol with chloroform.
Purified RNA samples were sent for sequencing to Genewiz Inc (Azenta Life Sciences). Illumina sequencing libraries with PolyA selection were prepared in-house by Azenta.

treatment_protocol: Whole organoids were dissociated at 45-47 DIV using the Neural Tissue Dissociation Kit (P, Papain) (Miltenyi Biotec; 130-092-628). The cells were then resuspended in medium with 445 ml high-glucose DMEM supplemented with GlutaMAX (Gibco; 10569010), 50 ml FBS (Gibco; 10270-106) and 5 ml of 50% (wt/vol) glucose solution without antibiotic-antimycotic. The cells were cultured on polyethyleneimine and laminin-coated plates with BrainPhys medium and SM1 supplement for a further 37 days.

tag: tissue

value: Dissociated unguided cerebral organoid

tag: batch


title: U20_siYB_Rep2

description:
Library name: U20_siYB_Rep2
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: PBMC, Group 1, Baseline, rep 2

city: New Orleans

first: Xuebin

last: Qin

state: LA

address: 1430 Tulane Avenue

department: Pathology

institute: Tulane University

description:
Library name: Sample 2
10x Genomics

data_processing:
Raw reads were evaluated with FastQC and aligned to Mmul10 using Hisat2. Transcript assembly and abundance estimation were performed with the featurecounts R package. Gene-level differential expression was analyzed with DESeq2. Volcano plots were created with the Enhanced Volcano package (v1.16.0) to visualize gene-level changes. Gene ontology (GO) analysis used DAVID Functional Annotation Bioinformatics Microarray Analysis; gene sets with p-value < 0.05 were deemed significantly enriched, and results were visualized with enrichplot, ggplot2, and base R graphics.
Assembly: Mmul10
Supplementary files format and content: matrix files of featurecounts

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
Blood collected in EDTA tubes (Sarstedt) was processed immediately. PBMCs were isolated by density gradient centrifugation (Lymphocyte Separation Medium, MP Biomedicals) at 1500 rpm for 45 min for phenotyping and functional assays. Tissues were collected in 1 mL Trizol reagent (15596026; Invitrogen) and extracted with RNeasy Mini Kit (Cat. No.74104; QIAGEN, Hilden, Germany) following the manufacturer’s protocol. The concentration of RNA was determined by NanoDrop 2000.
Final cDNA libraries carrying TruSeq RNA CD indexes (Illumina, 20019792) were quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854). Library quality was assessed on an Agilent TapeStation 4150 using Agilent D1000 ScreenTape (Agilent, 5067-5582). Smear analysis (Agilent TapeStation Software, Version 4.1.1) with a 600 bp window was used to determine the average library size. Library molarity was then calculated from the measured size and concentration. Libraries were pooled to a final concentration of 750pM with a 2% spike-in of PhiX control library v3 (Illumina, FC-110-3001). The pooled mixture was loaded onto an Illumina NextSeq P1 (300) reagent cartridge (Illumina, 20050264). Paired-end, dual-index sequencing (150×8×8×150) was run on the NextSeq2000, generating ~20 M paired-end reads per sample. Fastq files produced by Illumina BaseSpace DRAGEN Analysis Software (Version 1.2.1) were used for downstream analyses.

value: PBMC

value: Wild-type

value: Baseline


title: mESCs, CKO2-IgG

description: CKO-merged-IgG.mLb.clN.sorted.bw

value: IgG (Rabbit IgG ab171870 Abcam)


title: PBMC, Group 1, Baseline, rep 3

description:
Library name: Sample 3
10x Genomics


title: Dissociated organoids, 272XX, batch 3

description: Library name: Sample_12


title: MGO.53 biol rep 4

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

description:
Library name: MGO53_4_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.

data_processing:
Raw reads were aligned to the mouse transcriptome and genome version GRCh39 with annotations from Ensembl release 106 using STAR aligner v.2.7.10a. Counts per gene quantification was done using htseq-count v2.01 (ref. 2). Genes with a sum of counts below 10 over all samples were filtered out. Base mean counts (mormc) were calculated using DESeq2 package
Assembly: GRCh39
Supplementary files format and content: raw and norm counts per gene per sample.xlsx

molecule: polyA RNA

source_name: skin

growth_protocol: B16 were all grown in complete DMEM (supplemented with 10% fetal bovine serum (FBS), 1 % penicillin/streptomycin, and 1 % L-glutamine, Gibco). Cells were grown at 37C with 5 % CO2

extract_protocol:
MicroPure™ RNA Isolation Kit
Poly(A)+ RNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module. Strand-specific RNA-seq libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit according to the manufacturer’s protocol, with an expected fragment length of approximately 350 bp including adapters.

treatment_protocol: 4 antibodies were incubated (Mel321-31, Mel322-34, Mel321-35 and isotype control-MGO.53) with B16 cancer line and RNA was produced following 24 hours

value: skin

value: melanoma

value: wild type

value: batch 1


title: U20_siYB_Rep1

description:
Library name: U20_siYB_Rep1
Sequencing of TraPR isolated Argonaute bound small RNAs from OSC cells


title: mESCs, CKO1-pMCM2

value: pMCM2 (MCM2-S40P ab133243 Abcam)


title: PBMC, Group 1, Baseline, rep 1

description:
Library name: Sample 1
10x Genomics


title: p312btk_B48_spatial-barcode

description:
Library name: p312btk
sequence of bacorde of samples treated with CD4CD8 antibodies 21 days after vaccination

source_name: Lung

value: Lung

value: anti-cd4cd8 treatment

value: other


title: Mel321-35 biol rep 2

description:
Library name: ab35_2_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.

value: Mel321-35 mAb


title: SNB19 TES-expressing, biological replicate 1

city: Milan

first: Michal

last: Kubacki

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

description:
Library name: ASE01_TES1
SNB19 glioblastoma cells expressing TES (synthetic TEAD1-targeting transcriptional silencer), biological replicate 1. Column name in count_matrix.txt: ASE01_TES1

data_processing:
Raw reads were assessed for quality using FastQC. Adapter sequences and low-quality bases were removed using Trim Galore with parameters: Phred33 quality encoding (--phred33), quality threshold Phred 20, minimum read length 20 bp, adapter detection stringency 3 bp (--stringency 3), automatic Illumina adapter detection for paired-end reads (--paired). FastQC was run on trimmed reads (--fastqc).
Trimmed reads were aligned to GRCh38 using STAR in two-pass mode (--twopassMode Basic). Parameters: splice junction filtering (--outFilterType BySJout), max 20 multi-mapping locations (--outFilterMultimapNmax 20), mismatch rate 4% per read length (--outFilterMismatchNoverReadLmax 0.04, --outFilterMismatchNmax 999), min intron 20 bp, max intron 1000000 bp, min unannotated SJ overhang 8 bp (--alignSJoverhangMin 8), min annotated SJ overhang 1 bp (--alignSJDBoverhangMin 1). Gene annotations from GENCODE v44.
Gene-level read counts generated using STAR --quantMode GeneCounts. Unstranded counts (column 2 of ReadsPerGene.out.tab) were extracted and assembled into a count matrix for all samples using Ensembl gene IDs.
Differential expression analysis performed using DESeq2 with design ~condition (TES vs GFP, GFP as reference). Genes with < 10 total counts filtered. P-values adjusted by Benjamini-Hochberg. Genes with adjusted p < 0.05 considered significant. VST applied for PCA and heatmaps. Gene symbols mapped via org.Hs.eg.db.
Transcription factor binding site enrichment at DEG promoters performed using HOMER findMotifsGenome.pl. Promoters defined as TSS +/- 2000 bp (GENCODE v44). DEGs split into up/downregulated sets. De novo motif discovery for lengths 8, 10, 12 bp (-len 8,10,12), using exact BED coordinates (-size given), hg38 genome, top 25 motifs reported.
Assembly: hg38
Supplementary files format and content: count_matrix.txt: tab-delimited text file with raw gene-level read counts for all samples, rows are Ensembl gene IDs, columns are sample names
Supplementary files format and content: normalized_counts.txt: tab-delimited text file with DESeq2 normalized counts for all samples

source_name: brain

growth_protocol: SNB19 human glioma cells were cultured in plastic-adherence condition in DMEM medium (Dulbecco Modified Eagle Medium - high glucose, Sigma-Aldrich) containing 10% fetal bovine serum (FBS, Sigma-Aldrich), 1% penicillin/streptomycin (Sigma-Aldrich), 2 mM Glutamine (Sigma-Aldrich), 1% non-essential amino acids (MEM NEAA, ThermoFisher Scientific), 1% sodium pyruvate solution (Sigma-Aldrich). Cells were maintained in humidified atmosphere of 5% CO2 at 37C under atmospheric oxygen conditions.

extract_protocol:
Total RNA was extracted from SNB19 cells using the TRIzol reagent isolation system (Sigma-Aldrich) according to manufacturer instructions. RNA quantity and quality were assessed using a TapeStation instrument (Agilent Technologies), and only samples with RNA integrity number (RIN) > 8 were used for library preparation.
RNA-seq libraries were generated from 1 ug of total RNA. RNA quantity and quality were assessed using a TapeStation instrument (Agilent Technologies), and only samples with an RNA integrity number (RIN) > 8 were used. RNA was processed according to the TruSeq Stranded mRNA Library Prep Kit protocol (Illumina), following the manufacturer instructions. Libraries were quantified, pooled, and sequenced on an Illumina HiSeq 3000 platform to generate 76-bp stranded paired-end reads using Illumina TruSeq technology.

treatment_protocol: SNB19 cells were transduced with lentiviral constructs (MOI 33) expressing either TES (KRAB-hTEAD1(1-166)-DNMT3A/3L, a synthetic TEAD1-targeting transcriptional silencer with V5 epitope tag, driven by EF1aL promoter) or GFP (control, same EF1aL promoter). RNA was harvested 48 hours after lentiviral administration. Three biological replicates were prepared for each condition.

value: brain

value: glioblastoma

value: TES


title: Mel321-35 biol rep 1

description:
Library name: ab35_1_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.

value: batch 2


title: SNB19 GFP control, biological replicate 3

description:
Library name: ASE01_GFP3
SNB19 glioblastoma cells expressing GFP control, biological replicate 3. Column name in count_matrix.txt: ASE01_GFP3

value: GFP


title: wor-GAL4>UAS-mCD8-GFP+ cells isolated by FACS, at embryonic stage 17

city: New York

first: Jocelyn L.Y.

last: Tang

address: 540 1st Avenue

institute: NYU School of Medicine

description: Library name: Embryo_St17_biolrep1

library_source: transcriptomic single cell

data_processing:
Reads were processed using Cell Ranger v3
Assembly: dm6
Supplementary files format and content: Each single cell sample contains a barcodes.tsv, features.tsv and matrix.mtx file generated from Cell Ranger

molecule: cytoplasmic RNA

source_name: Brain

extract_protocol:
Brains from stage 17 embryos were dissociated and 24ALH larval brains were dissected and dissociated. These samples were kept separate and NSCs were enriched for by sorting for GFP+ cells via flow cytometry (using wor-GAL4>UAS-mCD8-GFP).
Cells isolated by FACS were processed using the 10X Genomics Chromium Platform, using v3 chemistry (3' end gene expression), with the exception of Embryo_St17_biolrep1, which used v2 chemistry.

value: Brain

value: NSCs, neurons, glia


title: Dissociated organoids, 59XY, batch 2

description: Library name: Sample_11

value: Dissociated unguided cerebral organoid


title: Dissociated organoids, 272XX, batch 1

description: Library name: Sample_8


title: MGO.53 biol rep 1

description:
Library name: MGO53_1_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.

value: skin


title: p312dtk_IMM+B48_spatial-barcode

description:
Library name: p312dtk
sequence of bacorde of samples 21 days after vaccination, and treated with CD4CD8 antibodies samples 21 days after vaccination

value: GLA-3M-052-LS+OVA, and anti-cd4cd8 treatment


title: p312ctk_naive_spatial-barcode

description:
Library name: p312ctk
sequence of bacorde of naïve mice

value: NAÏVE


title: SNB19 TES-expressing, biological replicate 3

description:
Library name: ASE01_TES3
SNB19 glioblastoma cells expressing TES (synthetic TEAD1-targeting transcriptional silencer), biological replicate 3. Column name in count_matrix.txt: ASE01_TES3


title: Mel321-35 biol rep 4

description:
Library name: ab35_4_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.

value: melanoma

value: wild type

value: batch 1


title: Dissociated organoids, H9, batch 2

description: Library name: Sample_7


title: p312cwt_naive_GEX

description:
Library name: p312cwt
the gene expression of naïve mice

molecule: nuclear RNA

value: Lung

value: mRNA


title: NbD413_508_mouse_2

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

description:
Library name: NbD413_508
10X Genomics chromium

data_processing:
Illumina sequencing was performed on the PDX tumor samples using Illumina NovaSeq X 1.5B platform with paired-end 150 bp reads. The reads were aligned and counted using STARSolo version 2.7.11b, with --featureType Gene, and --soloCellFilter EmptyDrops_CR.  The genome and GTF were taken from the cellranger ref-GRCH38-2024-A, which is derived from GENCODEv44.
To generate feature-barcode matrices analysis was conducted in R (v4.1.2) with Seurat (v4.3.0). Quality control excluded cells expressing fewer than 500 genes, fewer than 1,000 total RNA counts, more than 50,000 features, or with >10% mitochondrial content. Data were normalized, and highly variable features were identified for downstream analysis. Batch effects were corrected with the Harmony package in RStudio (v0.1.1), grouping by experimental conditions. Gene symbols were annotated using biomaRt.
Assembly: GRCh38
Supplementary files format and content: cellranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: mouse spleen

extract_protocol:
Single-cell suspensions were processed using the 10x Genomics Chromium Controller for single-cell partitioning and barcoding. The samples were processed using 10X chromium platform (Chromium Next GEM Immune Profiling 5'HT kit v2, 1000374). Cells were encapsulated into Gel Beads-in-Emulsion (GEMs) for droplet-based lysis and reverse transcription. Barcoded cDNA was then synthesized within the droplets, followed by amplification and purification according to the manufacturer’s protocol (10x Genomics)
Library construction was performed using the 10x Chromium Next GEM Immune Profiling 5' HT Kit v2 (Catalog #1000374) following the manufacturer’s protocol (10x Genomics).

value: Mantle cell lymphoma

value: mouse spleen

value: NbD413 CAR


title: p312atk_IMM_spatial-barcode

description:
Library name: p312atk
sequence of bacorde of samples 21 days after vaccination

value: other


title: Mel322-34 biol rep 4

description:
Library name: ab34_4_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.

value: Mel322-34 mAb


title: Mel321-35 biol rep 3

description:
Library name: ab35_3_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.

value: Mel321-35 mAb


title: SNB19 TES-expressing, biological replicate 2

description:
Library name: ASE01_TES2
SNB19 glioblastoma cells expressing TES (synthetic TEAD1-targeting transcriptional silencer), biological replicate 2. Column name in count_matrix.txt: ASE01_TES2

value: brain

value: glioblastoma

value: TES


title: p312bwt_B48_GEX

description:
Library name: p312bwt
the gene expression of sample treated with CD4CD8 antibodies 21 days post vaccinations

value: anti-cd4cd8 treatment


title: Day-10 differentiated TSCs-2

city: Columbia

first: Andrew

last: Kelleher

state: MO

address: 1030 Hitt Street

department: Ob, Gyn Womens Health

institute: University of Missouri

description:
Library name: B4D10
B4D10

data_processing:
Bulk RNA seq workflow
Trimming: Trim data using fastp with default parameters
Alignment: Align reads using STAR with default parameters
Counting: Generate raw counts using featureCounts with parameters: -p -B
Assembly: Bos_taurus.ARS-UCD1.3
Supplementary files format and content: csv file includes raw counts for all Samples
Supplementary files format and content: csv file include TPM values for all Samples

organism: Bos taurus

source_name: Trophoblast cells

growth_protocol: These cells either cultured on MEFs in LCDM condition ( the undifferentiated TSC) or on collagen IV coated plate in forskolin and ROCK inhibitor containing media.

extract_protocol:
RNeasy Micro Kit Protocol
Libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina

treatment_protocol: Undifferentiated TSC, day-4 differentiated TSC and day-10 differentiated TSC.

value: Trophoblast cells

value: Day-10 differentiated TSCs-2


title: NbD413_505_mouse_1

description:
Library name: NbD413_505
10X Genomics chromium


title: Dissociated organoids, 59XY, batch 1

description: Library name: Sample_9

value: Dissociated unguided cerebral organoid


title: Mel322-34 biol rep 3

description:
Library name: ab34_3_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.

value: skin

value: melanoma

value: wild type


title: SNB19 GFP control, biological replicate 2

description:
Library name: ASE01_GFP2
SNB19 glioblastoma cells expressing GFP control, biological replicate 2. Column name in count_matrix.txt: ASE01_GFP2

value: GFP


title: SNB19 GFP control, biological replicate 1

description:
Library name: ASE01_GFP1
SNB19 glioblastoma cells expressing GFP control, biological replicate 1. Column name in count_matrix.txt: ASE01_GFP1


title: Mel322-34 biol rep 1

description:
Library name: ab34_1_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.

value: batch 1


title: p312awt_IMM_GEX

description:
Library name: p312awt
the gene expression of sample 21 days post vaccinations

value: Lung

value: mRNA


title: Dissociated organoids, 272XX, batch 2

description: Library name: Sample_10


title: Mel321-31 biol rep 4

description:
Library name: ab31_4_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.

value: Mel321-31 mAb


title: Dissociated organoids, SCTi003-A, batch 2

description: Library name: Sample_6

data_processing:
FASTQ files were processed using command line tools on the King’s College London CREATE high-performance computing cluster. Alignment of reads to the human genome (Assembly GRCh38.p14, accession GCF_000001405.40, NCBI RefSeq) was performed using STAR (version 2.7.6a). After alignment, the output BAM files were sorted by chromosome and position coordinates using Samtools (version 1.17) and Picard (version 2.26.2) was used to mark duplicates in the BAM files.
The duplicate checked BAMs were downloaded from CREATE and subsequent analysis was carried out in R (version 4.2.2). A raw counts table was generated using the featureCounts function from the Rsubread package. Gene symbols were annotated using the getBM function from the biomaRt package.
Differential gene expression analysis was performed using the DESeq2 1.38.3 package, which was used to generate DESeq2 normalized counts.
Assembly: GRCh38.p14
Supplementary files format and content: CSV files containing DESeq2 normalized counts for each sample
Supplementary files format and content: CSV files containing raw counts generated using Rsubread for each sample


title: H24_513_mouse_3

description:
Library name: H24_513
10X Genomics chromium

value: Mantle cell lymphoma

value: mouse spleen

value: H24 CAR


title: Mel322-34 biol rep 2

description:
Library name: ab34_2_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.

value: Mel322-34 mAb


title: Dissociated organoids, KOLF2.1J, batch 2

description: Library name: Sample_3


title: H24_507_mouse_1

description:
Library name: H24_507
10X Genomics chromium


title: Dissociated organoids, SCTi003-A, batch 1

description: Library name: Sample_4


title: Mel321-31 biol rep 2

description:
Library name: ab31_2_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.


title: Day-10 differentiated TSCs-1

description:
Library name: C1D10
C1D10

value: Day-10 differentiated TSCs-1


title: Dissociated organoids, H1, batch 1

description: Library name: Sample_5


title: Dissociated organoids, H9, batch 1

description: Library name: Sample_2


title: Dissociated organoids, KOLF2.1J, batch 1

description: Library name: Sample_1


title: Mel321-31 biol rep 1

description:
Library name: ab31_1_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.


title: Mel321-31 biol rep 3

description:
Library name: ab31_3_counts
B16 murine melanoma cells incubated with monoclonal antibody for 24 hours prior to RNA extraction.


title: H24_511_mouse_2

description:
Library name: H24_511
10X Genomics chromium


title: Undifferentiated TSCs-1

description:
Library name: C1Ctrl
C1Ctrl

value: Undifferentiated TSCs-1


title: Day-4 differentiated TSCs-1

description:
Library name: C1D04
C1D04

value: Trophoblast cells

value: Day-4 differentiated TSCs-1


title: Day-4 differentiated TSCs-2

description:
Library name: B4D04
B4D04

value: Day-4 differentiated TSCs-2


title: Undifferentiated TSCs-2

description:
Library name: B4Ctrl
B4Ctrl

value: Undifferentiated TSCs-2


title: EmptyCAR_574_mouse_2

description:
Library name: EmptyCAR_574
10X Genomics chromium

value: Empty CAR


title: NCI-H295R cells, shCtrl_2

status: Public on Feb 22 2026

city: Chongqing

first: Ling

last: Xie

address: No. 1 Youyi St

country: China

institute: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

description:
Library name: shCtrl_2
Column name in FPKMs_All_Samples.txt: shCtrl_2

data_processing:
Quality Control: Raw FASTQ reads were processed using custom Perl scripts to remove adapter sequences and filter out low-quality reads (where >60% of bases had quality ≤25) and reads with >5% ambiguous bases (N), resulting in clean reads for downstream analysis.
Mapping: Clean reads were aligned to the GRCh38 (hg38) human reference genome using HISAT2 (v2.2.1) with default parameters to generate mapped reads.
Gene Expression Quantification: Gene-level read counts were quantified using featureCounts (v2.0.3). FPKM values were then calculated for each gene based on its annotated length and the number of fragments mapped to it.
Assembly: GRCh38
Supplementary files format and content: FPKMs_All_Samples.txt file includes gene expression matrix with FPKM values for all samples

source_name: adrenal cortex

growth_protocol: NCI-H295R cells were cultured in DMEM/F12 medium  supplemented with 10% fetal 10% fetal bovine serum  and 1% insulin-transferrin-selenium (ITS) at 37°C in 5% CO2

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer's instructions
Paired-end libraries were prepared using a VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina（Vazyme） following the manufacturer’s instructions.

treatment_protocol: Transduced with lentivirus carrying non-targeting control shRNA or shRNA targeting TPD52

value: adrenal cortex

value: adrenocortical carcinoma cell

value: lentiviral transduction with control shRNA


title: EmptyCAR_573_mouse_1

description:
Library name: EmptyCAR_573
10X Genomics chromium


title: Blood, SAD Responder3, LowBAFFR, P17

city: Leeds

first: Sinisa

last: Savic

address: St James's University Hospital

institute: University of Leeds

description: Library name: P17

data_processing:
QC was done using Fastqc
Fastq files were trimmed for adapters using Cutadapt
Reads were mapped onto reference genome using Salmon
Counts were exported to Rstudio and analysed using DESeq2
Results were visualised using ggplot2
Assembly: hg38
Supplementary files format and content: Processed data contains raw reads generated from Salmon

source_name: Blood

extract_protocol:
Total RNA was extracted from PAXGene blood tubes using the PAXgene Blood RNA Kit
Strand-specific RNAseq libraries were prepared with rRNA and globin depletion, sequenced at 20M reads per sample

value: Blood

value: Responder, LowBAFFR


title: Blood, SAD Responder2, LowBAFFR, P15

description: Library name: P15


title: Blood, CVID Responder3, LowBAFFR, P14

description: Library name: P14


title: NCI-H295R cells, shTPD52_3

description:
Library name: shTPD52_3
Column name in FPKMs_All_Samples.txt: shTPD52_3

value: lentiviral transduction with shRNA targeting TPD52


title: NCI-H295R cells, shTPD52_1

description:
Library name: shTPD52_1
Column name in FPKMs_All_Samples.txt: shTPD52_1


title: Blood, Hypogammaglobinaemia Responder1, HighBAFFR, P13

description: Library name: P13

value: Responder, HighBAFFR


title: Blood, CVID Responder4, HighBAFFR, P18

description: Library name: P18


title: NCI-H295R cells, shTPD52_2

description:
Library name: shTPD52_2
Column name in FPKMs_All_Samples.txt: shTPD52_2


title: Human FL FFPE section for spatial-FFPE-CUT&Tag at a resolution of 50um_H3K27me3

city: New Haven

first: Haikuo

last: Li

state: CT

address: 55 Prospect St

institute: Washington University in St. Louis

description: Library name: human_FL_H3K27me3

data_processing:
Read 2 fastq sequences were first filtered based on linker oligo sequences using bbduk, followed by extraction of spatial Barcode A (8 bp) and spatial Barcode B (8 bp) sequences. Then, The Read 2 fastq file was split into two new fastq files, which indicate genomic DNA sequences and the Barcode A/B sequences, respectively. A reference genome index file was created using chromap (version 0.2.6-r490) against the GRCm38 or GRCh38 primary assembly fasta files. Genome mapping was performed using chromap (chromap --preset atac) against the created index file, in which the 16-bp spatial barcode fastq is set as the barcode file. This pipeline generates a fragment .bed file, which is then compressed with gzip and tabix indexed for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: .h5ad: Anndata format for data matrix
Library strategy: CUT&Tag

source_name: human lymph node FL

extract_protocol:
ATAC-seq and CUT&Tag are performed in situ on tissue sections. The tissue is then lysed for library preparation.
Library is constructed with standard Nextera adapters.

value: human lymph node FL

value: Yale Pathology


title: Blood, CVID Non Responder2, LowBAFFR, P16

description: Library name: P16

value: Non Responder, LowBAFFR


title: NCI-H295R cells, shCtrl_3

description:
Library name: shCtrl_3
Column name in FPKMs_All_Samples.txt: shCtrl_3


title: Blood, SAD Responder1, HighBAFFR, P12

description: Library name: P12


title: Human DLBCL FFPE section for spatial-FFPE-CUT&Tag at a resolution of 50um_H3K4me3

description: Library name: human_DLBCL_H3K4me3

source_name: human lymph node DLBCL

value: human lymph node DLBCL


title: NCI-H295R cells, shCtrl_1

description:
Library name: shCtrl_1
Column name in FPKMs_All_Samples.txt: shCtrl_1


title: TSN051_S46_R1_001

city: Augusta

first: Ashok

last: Sharma

state: GA

address: 1120 15th Street

department: Ophthalmology

institute: Augusta University

description: Library name: Sample 31

data_processing:
The libraries were pooled with the correspondingly identified bar-codes for each sample and run on the Novaseq6000 sequencing system using a 72-cycle single end protocol.
FastQC was used to assess the raw reads, and Cutadapt (version 4.0) was used to trim the Illumina Universal Adapter sequences.
Reads were filtered to miRNA lengths (21-24 nt) and mapped to miRBase (v22.1) using the bowtie1 (v1.3.1) short read aligner, not allowing for any mismatches.
Counts for each miRNA were derived using samtools
Assembly: miRBase (v22.1)
Supplementary files format and content: CSV files with raw miRNA expression values

source_name: Tear fluid

growth_protocol: Tear samples were collected using Schirmer strips without the application of topical anesthesia. Using a gloved hand, the Schirmer strip (TearFlo, USA) was placed under the lower eyelid of one eye for 5 minutes, with the patient’s eyes remaining closed. After the strip was inserted, the collection tube was removed from cold storage and allowed to thaw at room temperature as the sample was collected. Once the strip was removed, it was immediately placed in the prepared collection tube. The tube was then inverted to allow the solution to completely wet the strip before being stored at -80° C.

extract_protocol:
Once thawed, the Schirmer strips were removed from the tube using RNase-free pipette tips (Fisher Scientific), placed in a 0.22-µm cellulose-acetate filter tube (Fisher Scientific), and centrifuged at 12,000 x g for 15 minutes at 4 °C. The eluate from the filter tube was collected and returned to the original collection tube containing any leftover volume not absorbed by the Schirmer strip. RNA extraction was performed using the miRNeasy Serum/Plasma Kit (Qiagen) according to the manufacturer’s protocol
Briefly, the mature miRNAs from 10 ng of total RNA were ligated sequentially with the specially designed 3’ and 5’ adaptors and converted to cDNA using RT primer integrated with unique molecular indices (UMI) to enable quantification of individual sncRNA molecules. The cDNA products were then purified, enriched by PCR, and purified using QMN Beads (Qiagen) to create the final cDNA library.

value: Tear fluid

tag: Sex

value: F

tag: race

value: White


title: TSN028_S28_R1_001

description: Library name: Sample 28

value: Black


title: Blood, CVID Non Responder1, LowBAFFR, P10

description: Library name: P10


title: TSN039_S35_R1_001

description: Library name: Sample 29


title: Blood, Control2, HighBAFFR, HC2

description: Library name: HC2

value: Control, HighBAFFR


title: Blood, CVID Responder2, HighBAFFR, P6

description: Library name: P6


title: Blood, CVID Responder1, HighBAFFR, P5

description: Library name: P5


title: Human FL FFPE section for spatial-FFPE-ATAC at a resolution of 50um

description: Library name: human_FL_ATAC

data_processing:
Read 2 fastq sequences were first filtered based on linker oligo sequences using bbduk, followed by extraction of spatial Barcode A (8 bp) and spatial Barcode B (8 bp) sequences. Then, The Read 2 fastq file was split into two new fastq files, which indicate genomic DNA sequences and the Barcode A/B sequences, respectively. A reference genome index file was created using chromap (version 0.2.6-r490) against the GRCm38 or GRCh38 primary assembly fasta files. Genome mapping was performed using chromap (chromap --preset atac) against the created index file, in which the 16-bp spatial barcode fastq is set as the barcode file. This pipeline generates a fragment .bed file, which is then compressed with gzip and tabix indexed for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: .h5ad: Anndata format for data matrix


title: TSN053_S48_R1_001

description: Library name: Sample 32

value: M


title: TSN043_S39_R1_001

description: Library name: Sample 30


title: TSN011_S11_R1_001

description: Library name: Sample 26


title: Blood, Control1, HighBAFFR, HC1

description: Library name: HC1


title: TRNA66_S48_R1_001

description: Library name: Sample 21


title: TSN007_S7_R1_001

description: Library name: Sample 25

value: Asian


title: TRNA78_S55_R1_001

description: Library name: Sample 24


title: TRNA74_S52_R1_001

description: Library name: Sample 23


title: TSN017_S17_R1_001

description: Library name: Sample 27


title: TRNA70_S50_R1_001

description: Library name: Sample 22


title: TRNA58_S42_R1_001

description: Library name: Sample 16


title: TRNA60_S43_R1_001

description: Library name: Sample 17


title: TRNA44_S32_R1_001

description: Library name: Sample 12


title: TRNA63_S45_R1_001

description: Library name: Sample 18


title: TRNA52_S38_R1_001

description: Library name: Sample 15


title: TRNA49_S36_R1_001

description: Library name: Sample 14


title: TRNA64_S46_R1_001

description: Library name: Sample 19


title: TRNA65_S47_R1_001

description: Library name: Sample 20


title: TRNA27_S21_R1_001

description: Library name: Sample 8


title: TRNA22_S17_R1_001

description: Library name: Sample 6


title: TRNA11_S62_R1_001

description: Library name: Sample 4


title: TRNA45_S33_R1_001

description: Library name: Sample 13


title: TRNA26_S20_R1_001

description: Library name: Sample 7


title: TRNA42_S30_R1_001

description: Library name: Sample 10


title: TRNA29_S23_R1_001

description: Library name: Sample 9


title: TRNA43_S31_R1_001

description: Library name: Sample 11


title: Human DLBCL FFPE section for spatial-FFPE-CUT&Tag at a resolution of 50um

description: Library name: human_DLBCL_H3K27me3

data_processing:
Read 2 fastq sequences were first filtered based on linker oligo sequences using bbduk, followed by extraction of spatial Barcode A (8 bp) and spatial Barcode B (8 bp) sequences. Then, The Read 2 fastq file was split into two new fastq files, which indicate genomic DNA sequences and the Barcode A/B sequences, respectively. A reference genome index file was created using chromap (version 0.2.6-r490) against the GRCm38 or GRCh38 primary assembly fasta files. Genome mapping was performed using chromap (chromap --preset atac) against the created index file, in which the 16-bp spatial barcode fastq is set as the barcode file. This pipeline generates a fragment .bed file, which is then compressed with gzip and tabix indexed for downstream analysis.
Patho-DBiT Read 1 sequences were aligned to the reference genome GRCh38 with STAR (version 2.7.7a) and unique molecular identifier (UMI) and spatial barcode sequences were extracted from Read 2 using published scripts (https://github.com/Zhiliang-Bai/Patho-DBiT), followed by generation of a gene-by-pixel count matrix by ST_Pipeline (version 1.7.6).
Assembly: GRCm38 or GRCh38
Supplementary files format and content: .h5ad: Anndata format for data matrix
Supplementary files format and content: .txt: positions of pixels used for analysis; otherwise, the region is blank with no tissues
Library strategy: CUT&Tag


title: Human MALT FFPE section for spatial-FFPE-ATAC at a resolution of 20um

description: Library name: human_MALT

data_processing:
Read 2 fastq sequences were first filtered based on linker oligo sequences using bbduk, followed by extraction of spatial Barcode A (8 bp) and spatial Barcode B (8 bp) sequences. Then, The Read 2 fastq file was split into two new fastq files, which indicate genomic DNA sequences and the Barcode A/B sequences, respectively. A reference genome index file was created using chromap (version 0.2.6-r490) against the GRCm38 or GRCh38 primary assembly fasta files. Genome mapping was performed using chromap (chromap --preset atac) against the created index file, in which the 16-bp spatial barcode fastq is set as the barcode file. This pipeline generates a fragment .bed file, which is then compressed with gzip and tabix indexed for downstream analysis.
Patho-DBiT Read 1 sequences were aligned to the reference genome GRCh38 with STAR (version 2.7.7a) and unique molecular identifier (UMI) and spatial barcode sequences were extracted from Read 2 using published scripts (https://github.com/Zhiliang-Bai/Patho-DBiT), followed by generation of a gene-by-pixel count matrix by ST_Pipeline (version 1.7.6).
Assembly: GRCm38 or GRCh38
Supplementary files format and content: .h5ad: Anndata format for data matrix
Supplementary files format and content: .txt: positions of pixels used for analysis; otherwise, the region is blank with no tissues

source_name: human lymph node MALT

value: human lymph node MALT


title: TRNA10_S8_R1_001

description: Library name: Sample 3


title: TRNA15_S12_R1_001

description: Library name: Sample 5


title: Human DLBCL FFPE section for Patho-DBiT at a resolution of 50um

description: Library name: human_DLBCL_Patho_DBiT


title: WT siHDAC4 UNT 1

city: Udine

first: Nicolò

last: Gualandi

state: Italy

address: P.le Kolbe, 4

department: Department of Medicine

institute: Università degli studi di Udine

description: esiCT+PROTAC#11 10µM+OxPt 50µM

data_processing:
Reads were trimmed to remove sequencing adapters and low quality base calls using Trimmomatic (v 0.39)
RNA-seq reads were aligned to the reference human genome using STAR (v 2.7.11a)
The number of reads per gene were counted using STAR (--quantMode GeneCounts)
Assembly: hg38
Supplementary files format and content: tab delimited files including reads per gene counts in each sample

source_name: Colorectal cancer

growth_protocol: HCT-116 cells were cultured in Dulbecco modified Eagle medium (Euroclone, Milan, Italy), supplemented with 10% of fetal bovine (FBS, Sigma Aldrich, Germany), L-glutamine 2 mM; penicillin 100 U/mL, and streptomycin, 100 μg/mL; (Euroclone). Cells were grown at 37°C in 5% CO2

extract_protocol:
Total RNA was extracted with TriReagent (Sigma Aldrich). DNAseI digestion (Ambion) was performed to exlude gDNA contaminations.
Libraries were prepared according to Illumina's instructions of Illumina Stranded mRNA Prep to enrich for polyA mRNA.

treatment_protocol: HCT-116 WT or KO for FBXW7 were transfected for 48h with esiRNAs directed against CT or HDAC4 or PROTAC #11 1µM. Cells were treated or not for the last 24h with OxPt (50 µM).

value: Colorectal cancer

value: wt

value: esiCT+PROTAC#11 1uM+OxPt 50uM


title: TRNA1_S1_R1_001

description: Library name: Sample 1


title: WT siHDAC4 OXPT 1

description: esiCT+PROTAC#11 10µM

value: esiCT+PROTAC#11 1uM


title: WT siHDAC4 OXPT 2

description: esiCT+PROTAC#11 10µM


title: WT siHDAC4 OXPT 3

description: esiCT+PROTAC#11 10µM


title: WT siHDAC4 UNT 3

description: esiCT+PROTAC#11 10µM+OxPt 50µM


title: TRNA5_S4_R1_001

description: Library name: Sample 2


title: WT siCT OXPT 2

description: esiHDAC4+Oxaliplatin 50µM

value: esiHDAC4+Oxaliplatin 50uM


title: WT siCT UNT 2


title: WT siCT OXPT 1

description: esiHDAC4+Oxaliplatin 50µM


title: WT siCT UNT 1


title: WT PROTAC11 OXPT 3

description: esiCT

value: esiCT


title: WT siCT UNT 3


title: WT siHDAC4 UNT 2

description: esiCT+PROTAC#11 10µM+OxPt 50µM


title: WT PROTAC11 OXPT 2

description: esiCT


title: WT PROTAC11 3

description: esiCT+Oxaliplatin 50µM

value: esiCT+Oxaliplatin 50uM


title: WT PROTAC11 2

description: esiCT+Oxaliplatin 50µM


title: WT PROTAC11 OXPT 1

description: esiCT


title: WT PROTAC11 1

description: esiCT+Oxaliplatin 50µM


title: KO PROTAC11 OXPT 3

description: esiCT+PROTAC#11 10µM+OxPt 50µM


title: WT siCT OXPT 3

description: esiHDAC4+Oxaliplatin 50µM


title: KO PROTAC11 3

description: esiCT+PROTAC#11 10µM


title: KO PROTAC11 OXPT 1

description: esiCT+PROTAC#11 10µM+OxPt 50µM


title: KO PROTAC11 OXPT 2

description: esiCT+PROTAC#11 10µM+OxPt 50µM


title: FBXW7KO siHDAC4 UNT 3


title: KO PROTAC11 1

description: esiCT+PROTAC#11 10µM


title: FBXW7KO siHDAC4 UNT 1


title: FBXW7KO siCT UNT 2

description: esiCT


title: FBXW7KO siHDAC4 OXPT 1

description: esiHDAC4+Oxaliplatin 50µM


title: KO PROTAC11 2

description: esiCT+PROTAC#11 10µM


title: FBXW7KO siHDAC4 OXPT 2

description: esiHDAC4+Oxaliplatin 50µM


title: FBXW7KO siCT OXPT 2

description: esiCT+Oxaliplatin 50µM


title: FBXW7KO siHDAC4 UNT 2


title: FBXW7KO siCT UNT 1

description: esiCT


title: FBXW7KO siCT OXPT 1

description: esiCT+Oxaliplatin 50µM


title: JIA-ERA-5-PBMC TCR

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Cell Ranger count or vdj pipelines scTCR-seq (10X Genomics).
A CSV file containing Cell Ranger vdj pipeline output for all or filtered alpha-beta TCR clonotype data: columns contain cells; rows contain TCR clonotype parameters quantified.
Assembly: GRCh38
Supplementary files format and content: TSV files with genes and barcode sequences corresponding to row and column indices, respectively.
Supplementary files format and content: CSV files containing filtered_contig_annotations and  clonotypes
Library strategy: TCR-seq

source_name: Peripheral blood

extract_protocol:
Fresh synovial fluid and peripheral blood samples were collected prior to the treatment of intra-articular injection into EDTA anticoagulant tubes and subsequently isolated mononuclear cells by density gradient centrifugation.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5' Kit v2 and Chromium Single Cell V(D)J Reagent Kits V1.0, 10× Genomics).

value: Mononuclear cells

value: Peripheral blood

tag: disease state

value: JIA

tag: disease subtype

value: ERA

tag: age


title: JIA-ERA-3-SFMC TCR

description: 10x Genomics

source_name: synovial fluid

value: synovial fluid


title: JIA-ERA-4-PBMC TCR

description: 10x Genomics


title: FBXW7KO siCT OXPT 3

description: esiCT+Oxaliplatin 50µM


title: JIA-ERA-2-SFMC TCR

description: 10x Genomics


title: JIA-ERA-4-SFMC TCR

description: 10x Genomics


title: FBXW7KO siHDAC4 OXPT 3

description: esiHDAC4+Oxaliplatin 50µM


title: JIA-ERA-2-PBMC TCR

description: 10x Genomics


title: JIA-ERA-3-PBMC TCR

description: 10x Genomics


title: JIA-ERA-1-SFMC TCR

description: 10x Genomics


title: FBXW7KO siCT UNT 3

description: esiCT


title: JIA-OligoA-6.1-SFMC TCR

description: 10x Genomics

value: OligoA


title: JIA-ERA-1-PBMC TCR

description: 10x Genomics


title: JIA-OligoA-7-PBMC TCR

description: 10x Genomics


title: JIA-OligoA-5-SFMC TCR

description: 10x Genomics


title: JIA-OligoA-6-SFMC TCR

description: 10x Genomics


title: JIA-OligoA-6-PBMC TCR

description: 10x Genomics


title: JIA-OligoA-5-PBMC TCR

description: 10x Genomics


title: JIA-OligoA-4-SFMC TCR

description: 10x Genomics


title: JIA-OligoA-4-PBMC TCR

description: 10x Genomics


title: JIA-OligoA-2-SFMC TCR

description: 10x Genomics


title: JIA-OligoA-1-SFMC TCR

description: 10x Genomics


title: JIA-OligoA-2-PBMC TCR

description: 10x Genomics


title: JIA-OligoA-7-SFMC TCR

description: 10x Genomics


title: JIA-ERA-4-SFMC 5'

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Cell Ranger count or vdj pipelines scTCR-seq (10X Genomics).
A CSV file containing Cell Ranger vdj pipeline output for all or filtered alpha-beta TCR clonotype data: columns contain cells; rows contain TCR clonotype parameters quantified.
Assembly: GRCh38
Supplementary files format and content: TSV files with genes and barcode sequences corresponding to row and column indices, respectively.
Supplementary files format and content: CSV files containing filtered_contig_annotations and  clonotypes


title: JIA-ERA-4-PBMC 5'

description: 10x Genomics


title: JIA-OligoA-1-PBMC TCR

description: 10x Genomics


title: JIA-ERA-5-PBMC 5'

description: 10x Genomics


title: JIA-ERA-3-SFMC 5'

description: 10x Genomics


title: JIA-ERA-3-PBMC 5'

description: 10x Genomics


title: JIA-ERA-1-SFMC 5'

description: 10x Genomics


title: JIA-ERA-2-SFMC 5'

description: 10x Genomics


title: JIA-ERA-2-PBMC 5'

description: 10x Genomics


title: JIA-OligoA-7-SFMC 5'

description: 10x Genomics


title: JIA-OligoA-7-PBMC 5'

description: 10x Genomics


title: JIA-OligoA-3-PBMC TCR

description: 10x Genomics


title: JIA-OligoA-6.1-SFMC 5'

description: 10x Genomics


title: JIA-OligoA-6-SFMC 5'

description: 10x Genomics


title: JIA-OligoA-5-PBMC 5'

description: 10x Genomics


title: JIA-OligoA-3-PBMC 5'

description: 10x Genomics


title: JIA-OligoA-4-PBMC 5'

description: 10x Genomics


title: JIA-ERA-1-PBMC 5'

description: 10x Genomics


title: JIA-OligoA-5-SFMC 5'

description: 10x Genomics


title: JIA-OligoA-4-SFMC 5'

description: 10x Genomics


title: JIA-OligoA-6-PBMC 5'

description: 10x Genomics


title: JIA-OligoA-2-SFMC 5'

description: 10x Genomics


title: JIA-OligoA-1-PBMC 5'

description: 10x Genomics


title: JIA-OligoA-1-SFMC 5'

description: 10x Genomics


title: JIA-OligoA-2-PBMC 5'

description: 10x Genomics


title: Participant 058, Batch 3, 12h post-challenge

type: RNA

city: Oxford

first: Amber

last: Barton

state: Oxfordshire

address: Old Road

institute: Oxford Vaccine Group

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Data were quantile normalized, background subtracted and log2 transformed using neqc() in R.
Fluorescent probe intensities output from GenomeStudio

label: biotin

source_name: Whole blood

label_protocol: Standard Illumina TotalPrep RNA Amplification kits

growth_protocol: NA - whole blood samples from clinical study

extract_protocol: Tempus tube RNA isolation kit

tag: challenge dose

value: High

tag: hours post-challenge

tag: outcome

value: Developed enteric fever

tag: study

value: Typhoid oral vaccine trial (placebo arm)

tag: participant


title: Participant 059, Batch 3, 12h post-challenge

treatment_protocol: NA - whole blood samples from clinical study


title: Participant 054, Batch 3, 12h post-challenge


title: Participant 049, Batch 3, 12h post-challenge


title: Participant 051, Batch 3, 12h post-challenge

value: Remained healthy


title: Participant 056, Batch 3, 12h post-challenge


title: Participant 055, Batch 3, 12h post-challenge


title: Participant 061, Batch 3, 12h post-challenge


title: Participant 050, Batch 3, 12h post-challenge


title: Participant 060, Batch 3, 12h post-challenge


title: Participant 046, Batch 3, 12h post-challenge


title: Participant 043, Batch 3, 12h post-challenge


title: Participant 045, Batch 3, 12h post-challenge


title: Participant 056, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092344


title: Participant 055, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092330


title: Participant 053, Batch 3, 12h post-challenge


title: Participant 059, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092368


title: Participant 057, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092358


title: Participant 047, Batch 3, 12h post-challenge


title: Participant 054, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092326


title: Participant 053, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092313


title: Participant 050, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092297


title: Participant 047, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092280


title: Participant 057, Batch 3, 12h post-challenge


title: Participant 048, Batch 3, 12h post-challenge


title: Participant 049, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092286


title: Participant 058, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092360


title: Participant 051, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092301


title: Participant 045, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092268


title: Participant 048, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092284


title: Participant 017, Batch 2, 24h post-challenge

value: Low

value: Typhoid dose-finding study


title: Participant 043, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092254


title: Participant 052, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092309


title: Participant 044, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092258


title: Participant 046, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092274


title: Participant 015, Batch 2, 24h post-challenge


title: Participant 041, Batch 2, 24h post-challenge


title: Participant 040, Batch 2, 24h post-challenge


title: Participant 019, Batch 2, 24h post-challenge


title: Participant 014, Batch 2, 24h post-challenge


title: Participant 027, Batch 2, 24h post-challenge


title: Participant 018, Batch 2, 24h post-challenge


title: Participant 016, Batch 2, 24h post-challenge


title: Participant 036, Batch 2, 24h post-challenge


title: Participant 042, Batch 3, 0h post-challenge

description: Re-analysis of GSM3092248


title: Participant 035, Batch 2, 24h post-challenge


title: Participant 012, Batch 2, 24h post-challenge


title: Participant 039, Batch 2, 24h post-challenge


title: Participant 026, Batch 2, 24h post-challenge


title: Participant 009, Batch 2, 24h post-challenge


title: Participant 011, Batch 2, 24h post-challenge


title: Participant 025, Batch 2, 24h post-challenge


title: Participant 006, Batch 2, 24h post-challenge


title: Participant 004, Batch 2, 24h post-challenge


title: Participant 038, Batch 2, 24h post-challenge


title: Participant 032, Batch 2, 24h post-challenge


title: Participant 037, Batch 2, 24h post-challenge


title: Participant 030, Batch 2, 24h post-challenge


title: Participant 013, Batch 2, 24h post-challenge


title: Participant 022, Batch 2, 24h post-challenge


title: Participant 028, Batch 2, 24h post-challenge


title: Participant 034, Batch 2, 24h post-challenge


title: Participant 005, Batch 2, 24h post-challenge


title: Participant 008, Batch 2, 24h post-challenge


title: Participant 010, Batch 2, 24h post-challenge


title: Participant 007, Batch 2, 24h post-challenge


title: Participant 017, Batch 2, 12h post-challenge


title: Participant 003, Batch 2, 24h post-challenge


title: Participant 002, Batch 2, 24h post-challenge


title: Participant 016, Batch 2, 12h post-challenge


title: Participant 018, Batch 2, 12h post-challenge


title: Participant 024, Batch 2, 24h post-challenge


title: Participant 033, Batch 2, 24h post-challenge


title: Participant 014, Batch 2, 12h post-challenge


title: Participant 015, Batch 2, 12h post-challenge


title: Participant 029, Batch 2, 24h post-challenge


title: Participant 031, Batch 2, 24h post-challenge


title: Participant 021, Batch 2, 24h post-challenge


title: Participant 020, Batch 2, 24h post-challenge


title: Participant 001, Batch 2, 24h post-challenge


title: Participant 026, Batch 2, 12h post-challenge


title: Participant 025, Batch 2, 12h post-challenge


title: Participant 027, Batch 2, 12h post-challenge


title: Participant 038, Batch 2, 12h post-challenge


title: Participant 041, Batch 2, 12h post-challenge


title: Participant 024, Batch 2, 12h post-challenge


title: Participant 037, Batch 2, 12h post-challenge


title: Participant 013, Batch 2, 12h post-challenge


title: Participant 035, Batch 2, 12h post-challenge


title: Participant 019, Batch 2, 12h post-challenge


title: Participant 039, Batch 2, 12h post-challenge


title: Participant 010, Batch 2, 12h post-challenge


title: Participant 011, Batch 2, 12h post-challenge


title: Participant 009, Batch 2, 12h post-challenge


title: Participant 012, Batch 2, 12h post-challenge


title: Participant 005, Batch 2, 12h post-challenge


title: Participant 036, Batch 2, 12h post-challenge


title: Participant 034, Batch 2, 12h post-challenge


title: Participant 007, Batch 2, 12h post-challenge


title: Participant 032, Batch 2, 12h post-challenge


title: Participant 023, Batch 2, 12h post-challenge


title: Participant 030, Batch 2, 12h post-challenge


title: Participant 033, Batch 2, 12h post-challenge


title: Participant 008, Batch 2, 12h post-challenge


title: Participant 020, Batch 2, 12h post-challenge


title: Participant 027, Batch 1, 12h post-challenge


title: Participant 002, Batch 2, 12h post-challenge


title: Participant 003, Batch 2, 12h post-challenge


title: Participant 026, Batch 1, 12h post-challenge


title: Participant 022, Batch 2, 12h post-challenge


title: Participant 014, Batch 1, 12h post-challenge


title: Participant 006, Batch 2, 12h post-challenge


title: Participant 040, Batch 2, 12h post-challenge


title: Participant 004, Batch 2, 12h post-challenge


title: Participant 029, Batch 2, 12h post-challenge


title: Participant 031, Batch 2, 12h post-challenge


title: Participant 012, Batch 1, 12h post-challenge


title: Participant 011, Batch 1, 12h post-challenge


title: Participant 023, Batch 2, 24h post-challenge


title: Participant 009, Batch 1, 12h post-challenge


title: Participant 021, Batch 2, 12h post-challenge


title: Participant 028, Batch 2, 12h post-challenge


title: Participant 007, Batch 1, 12h post-challenge


title: Participant 006, Batch 1, 12h post-challenge


title: Participant 001, Batch 2, 12h post-challenge


title: Participant 018, Batch 1, 12h post-challenge


title: Participant 004, Batch 1, 12h post-challenge


title: Participant 019, Batch 1, 12h post-challenge


title: Participant 017, Batch 1, 12h post-challenge


title: Participant 002, Batch 1, 12h post-challenge


title: Participant 015, Batch 1, 12h post-challenge


title: Participant 025, Batch 1, 12h post-challenge


title: Participant 013, Batch 1, 12h post-challenge


title: Participant 022, Batch 1, 12h post-challenge


title: Participant 021, Batch 1, 12h post-challenge


title: Participant 016, Batch 1, 12h post-challenge


title: Participant 001, Batch 1, 12h post-challenge


title: Participant 005, Batch 1, 12h post-challenge


title: Participant 024, Batch 1, 12h post-challenge


title: Participant 008, Batch 1, 12h post-challenge


title: Participant 017, Batch 1, 0h post-challenge


title: Participant 014, Batch 1, 0h post-challenge


title: Participant 010, Batch 1, 12h post-challenge


title: Participant 009, Batch 1, 0h post-challenge


title: Participant 003, Batch 1, 12h post-challenge


title: Participant 023, Batch 1, 12h post-challenge


title: RNA27tiles_TotalCells_C

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

institute: Weizmann Institute

description: Library name: Sample 104

data_processing:
The reads of the ribo-seq libraries was trimmed to remove the linker CTGTAGGCACCATCAAT by using cutadapt. For the Shishkin protocol libraries the linker was AGATCGGAAGAGCACACGT
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from our STAR runs.
The alignments above was made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
genome build: Host: hg19, Merlin: NC_006273.2, TB40: EF999921.1
Supplementary files format and content: csv files of the cytosolic to nuclear ratio, half-life, and footprints of transcripts and the read counts of all transcripts in each experiment. For the tiles screen, a table with the read counts of different tiles in different flow cytometry defined categories.

extract_protocol:
For RNA-seq, cells were harvested with Tri-Reagent (Sigma-Aldrich), total RNA was extracted, and poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For ribosome profiling, medium was aspirated from dishes, which were immediately placed on ice and rinsed with 10 ml ice-cold PBS supplemented with drugs used in pretreatment of the cells. PBS was aspirated and 800 μl ice-cold lysis buffer (20 mM Tris, pH 7.4, 250 mM NaCl, 15 mM MgCl2, 1 mM dithiothreito, 0.5% Triton X-100 and 24 U / ml Turbo DNase (Ambion, AM2239), along with any drugs used for sample treatment) was dripped onto dishes. Cells were scraped and the lysate was removed and incubated 10 min on ice. The lysate was then clarified by centrifugation for 10 min at 20,000 × g, 4°C and ∼1.1 ml supernatant was recovered.
RNA-seq: mRNA samplewas subjected to DNAseI treatment and 3’ dephpsphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3’ adaptor ligation using T4 ligase (NEB). The ligated products used for reverse transcription with SSIII (Invitrogen) for first strand cDNA synthesis. The cDNA products were 3’ ligated with a second adaptor using T4 ligase and amplified for 8 cycles in a PCR for final library products of 200-300bp. For the tiles screen DNA was extracted from sorted cells and the transfected plasmids were amplified with primers containing the illumina adaptors.
ribosome profiling and targeted PCR of transfected DNA

treatment_protocol: For Ribo-seq libraries, all samples were treated with 100μg/mL CHX for 1 minute. Cells were placed on ice immediately after treatment, washed twice with PBS containing 100μg/mL CHX.

tag: virus strain

tag: hours post infection


title: Participant 006, Batch 1, 0h post-challenge


title: Participant 019, Batch 1, 0h post-challenge


title: RNA27tiles_TotalCells_A

description: Library name: Sample 102


title: Participant 005, Batch 1, 0h post-challenge


title: Participant 016, Batch 1, 0h post-challenge


title: Participant 015, Batch 1, 0h post-challenge


title: Participant 020, Batch 1, 12h post-challenge


title: Participant 018, Batch 1, 0h post-challenge


title: Participant 004, Batch 1, 0h post-challenge


title: Participant 010, Batch 1, 0h post-challenge


title: RNA27tiles_G0G1_C

description: Library name: Sample 98


title: Participant 011, Batch 1, 0h post-challenge


title: RNA27tiles_G0G1_B

description: Library name: Sample 97


title: Participant 012, Batch 1, 0h post-challenge


title: Participant 008, Batch 1, 0h post-challenge


title: Participant 013, Batch 1, 0h post-challenge


title: RNA27tiles_TotalCells_B

description: Library name: Sample 103


title: Participant 007, Batch 1, 0h post-challenge


title: RNA27tiles_G2M_B

description: Library name: Sample 100


title: Participant 003, Batch 1, 0h post-challenge


title: RNA27tiles_G2M_A

description: Library name: Sample 99


title: Participant 001, Batch 1, 0h post-challenge


title: HFF_rRNAdepletion_Delta27_C

description: Library name: Sample 91

source_name: HFF

value: HFF


title: MRC5_rRNAdepletion_WT_B

description: Library name: Sample 93


title: Participant 002, Batch 1, 0h post-challenge


title: HFF_rRNAdepletion_WT_B

description: Library name: Sample 87


title: HFF_rRNAdepletion_Delta27_B

description: Library name: Sample 90


title: RNA27tiles_G0G1_A

description: Library name: Sample 96


title: MRC5_rRNAdepletion_Delta27_A

description: Library name: Sample 94


title: RNA27tiles_G2M_C

description: Library name: Sample 101


title: MRC5_rRNAdepletion_Delta27_B

description: Library name: Sample 95


title: HFF_rRNAdepletion_WT_C

description: Library name: Sample 88


title: HFF_rRNAdepletion_WT_A

description: Library name: Sample 86


title: HFF_Footprints_WT_72hpi_A

description: Library name: Sample 82


title: HFF_rRNAdepletion_Delta27_A

description: Library name: Sample 89


title: MRC5_SLAMseq_RNA27_Uninfected_4sU3hr_72hpi__B

description: Library name: Sample 81


title: HFF_Footprints_Delta27_72hpi_A

description: Library name: Sample 84


title: MRC5_SLAMseq_RNA27_Delta_4sU3hr_72hpi__B

description: Library name: Sample 79


title: MRC5_rRNAdepletion_WT_A

description: Library name: Sample 92


title: MRC5_SLAMseq_RNA27_Uninfected_4sU3hr_72hpi__A

description: Library name: Sample 80


title: HFF_Footprints_Delta27_72hpi_B

description: Library name: Sample 85


title: MRC5_SLAMseq_RNA27_Uninfected_4sU2hr_72hpi__B

description: Library name: Sample 75


title: MRC5_SLAMseq_RNA27_Delta_4sU3hr_72hpi__A

description: Library name: Sample 78


title: HFF_Footprints_WT_72hpi_B

description: Library name: Sample 83


title: MRC5_SLAMseq_RNA27_WT_4sU3hr_72hpi__B

description: Library name: Sample 77


title: MRC5_SLAMseq_RNA27_Delta_4sU2hr_72hpi__B

description: Library name: Sample 73


title: MRC5_SLAMseq_RNA27_Delta_4sU2hr_72hpi__A

description: Library name: Sample 72


title: MRC5_SLAMseq_RNA27_WT_4sU3hr_72hpi__A

description: Library name: Sample 76


title: MRC5_SLAMseq_RNA27_WT_4sU2hr_72hpi__A

description: Library name: Sample 70


title: MRC5_SLAMseq_RNA27_WT_4sU2hr_72hpi__B

description: Library name: Sample 71


title: MRC5_SLAMseq_RNA27_Uninfected_4sU2hr_72hpi__A

description: Library name: Sample 74


title: MRC5_SLAMseq_RNA27_Uninfected_72hpi__A

description: Library name: Sample 68


title: MRC5_SLAMseq_RNA27_Uninfected_72hpi__B

description: Library name: Sample 69


title: MRC5_SLAMseq_RNA27_WT_72hpi__A

description: Library name: Sample 64


title: MRC5_SLAMseq_RNA27_Delta_72hpi__A

description: Library name: Sample 66


title: MRC5_SLAMseq_RNA27_Delta_72hpi__B

description: Library name: Sample 67


title: HFF_SLAMseq_RNA27_Uninfected_4sU3hr_72hpi__B

description: Library name: Sample 63


title: HFF_SLAMseq_RNA27_WT_4sU3hr_72hpi__B

description: Library name: Sample 59


title: HFF_SLAMseq_RNA27_Delta_4sU3hr_72hpi__B

description: Library name: Sample 61


title: HFF_SLAMseq_RNA27_Delta_4sU3hr_72hpi__A

description: Library name: Sample 60


title: HFF_SLAMseq_RNA27_WT_4sU3hr_72hpi__A

description: Library name: Sample 58


title: HFF_SLAMseq_RNA27_Delta_4sU2hr_72hpi__B

description: Library name: Sample 55


title: MRC5_SLAMseq_RNA27_WT_72hpi__B

description: Library name: Sample 65


title: HFF_SLAMseq_RNA27_WT_4sU2hr_72hpi__B

description: Library name: Sample 53


title: HFF_SLAMseq_RNA27_Delta_72hpi__B

description: Library name: Sample 49


title: HFF_SLAMseq_RNA27_Delta_4sU2hr_72hpi__A

description: Library name: Sample 54


title: HFF_SLAMseq_RNA27_Uninfected_4sU3hr_72hpi__A

description: Library name: Sample 62


title: HFF_SLAMseq_RNA27_Uninfected_4sU2hr_72hpi__B

description: Library name: Sample 57


title: HFF_SLAMseq_RNA27_WT_4sU2hr_72hpi__A

description: Library name: Sample 52


title: HFF_SLAMseq_RNA27_Uninfected_72hpi__A

description: Library name: Sample 50


title: HFF_SLAMseq_RNA27_WT_72hpi__A

description: Library name: Sample 46


title: HFF_SLAMseq_RNA27_Delta_72hpi__A

description: Library name: Sample 48


title: HFF_SLAMseq_RNA27_WT_72hpi__B

description: Library name: Sample 47


title: HFF_SLAMseq_RNA12_Delta_4sU3hr_72hpi__B

description: Library name: Sample 43


title: DSS treated, ketogenic diet-fed mice

city: Shanghai

first: Yameng

last: Liu

address: No.555 Zuchongzhi Road, Pudong New Area

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

description:
Library name: IBD_KD
10x Genomics

data_processing:
Data analysis performed by Genergy Biotech
Assembly: Mouse mm10
Supplementary files format and content: Raw data

source_name: Colon

extract_protocol:
Colon tissues were washed with PBS, minced into 0.5-1 cm pieces, and digested in 0.5 M EDTA (20 mL/tube, 4°C, 5000 ×g, 15 min; repeated once). Tissue fragments were then enzymatically digested with 3 mL Type IV collagenase (37°C, 30 min). The cell suspension was washed 3× with PBS, treated with DNAzyme (15 mL, 20 min), and filtered through a 70 μm strainer. After centrifugation (150 ×g, 5 min, 4°C), the pellet was resuspended for flow cytometric sorting (BD FACS Aria II) to isolate viable single cells.
Cell suspensions were adjusted to 700-1200 cells/μL and processed using microfluidic technology. Single cells were co-encapsulated with barcoded gel beads in droplets to generate Gel Bead-in-Emulsions (GEMs). Within each GEM, reverse transcription was performed to produce barcoded cDNA. The cDNA was then fragmented (200-300 bp), adapter-ligated, and PCR-amplified to construct sequencing libraries. Final libraries were sequenced on an Illumina NovaSeq platform (paired-end). Experimental procedures were conducted by Personalbio.

value: Colon

value: not included

tag: cell type

value: epithelial cells, endothelial cells, B cells, macrophages, dendritic cells, granulocytes, monocytes, fibroblasts, and T cell subsets

value: 10- to 12-week-old,

value: male

tag: stain

value: wild-type C57BL/6JNarl mice


title: HFF_SLAMseq_RNA27_Uninfected_72hpi__B

description: Library name: Sample 51

tag: cell line


title: CKO3

city: Guangzhou

first: Li

last: Zhao

state: Guangdong

address: 1838 North Guangzhou Avenue,

department: Department of Cardiovascular Surgery

institute: Nanfang Hospital, Southern Medical University

description: Library name: Sample 6

data_processing:
TruSeq PE Cluster Kit v3 cBot HS
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: abdominal aorta

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

extract_protocol:
Total RNA was extracted from the samples, and the integrity of the extracted RNA was assessed by agarose gel electrophoresis. The concentration of RNA was accurately determined using NanoDrop.
RNA libraries for RNA-seq were preparded using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Vascular smooth muscle cells were treated with ang II

tag: tissue

value: abdominal aorta

value: vascular smooth muscle cells

tag: genotype

tag: treatment

value: Ang II


title: HFF_SLAMseq_RNA12_WT_4sU3hr_72hpi__A

description: Library name: Sample 40


title: HFF_SLAMseq_RNA12_Delta_4sU3hr_72hpi__A

description: Library name: Sample 42


title: Input FBXW7 KO B

description: Pooling of KO Replicate B

data_processing:
ChIP-seq reads were trimmed using Trimmomatic (v 0.39) in order to remove sequencing adapters and low quality bases
ChIP-seq reads were aligned to the reference hman genome using bowtie (v 2.4.4)
Reads with a mapping quality below 10 were removed with samtools (v 1.18)
Duplicate reads were removed with samtools (v 1.18)
Peaks were called using macs2 (v 2.2.7.1)
Super enhancers were identified using ROSE
Assembly: hg38
Supplementary files format and content: narrowPeak, peak location
Supplementary files format and content: BED, Superenhancers location

extract_protocol:
After 10 minutes fixation with 1% formaldeyde, chromatin was extracted and shared with Bioruptor Plus (Diagenode). DNA was purified with Zymo ChIP columns. Three independent experiments were pulled.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, 5 μg of DNA were used. DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: HCT-116 WT or KO for FBXW7 were transfected for 48h with esiRNAs directed against CT or HDAC4. Cells were treated or not for the last 24h with OxPt (50 µM).

value: Colorectal cancer

value: Pooling of KO


title: Input WT B

description: Pooling of WT Peplicate A

value: wt

value: Pooling of WT


title: CKO2

description: Library name: Sample 5


title: HFF_SLAMseq_RNA27_Uninfected_4sU2hr_72hpi__A

description: Library name: Sample 56


title: H3K27ac FBXW7 KO SIHDAC4 OXPT B

description: FBXW7KO esiHDAC4 OxPt Replicate B

value: Oxaliplatin 50uM


title: HFF_SLAMseq_RNA12_Uninfected_4sU3hr_72hpi__B

description: Library name: Sample 45


title: HFF_SLAMseq_RNA12_WT_4sU3hr_72hpi__B

description: Library name: Sample 41


title: DSS treated, control diet-fed mice

description:
Library name: IBD_CD
10x Genomics

tag: Sex


title: HFF_SLAMseq_RNA12_Uninfected_4sU3hr_72hpi__A

description: Library name: Sample 44


title: H3K27ac FBXW7 KO SIHDAC4 UNT B

description: FBXW7KO esiHDAC4 untreated Replicate B

value: Untreated


title: HFF_SLAMseq_RNA12_Uninfected_4sU2hr_72hpi__A

description: Library name: Sample 38


title: H3K27ac FBXW7 KO SICT OXPT B

description: FBXW7KO esiCT OxPt Replicate B


title: HFF_SLAMseq_RNA12_Uninfected_4sU2hr_72hpi__B

description: Library name: Sample 39


title: Flox3

description: Library name: Sample 3


title: HFF_SLAMseq_RNA12_Delta_4sU2hr_72hpi__A

description: Library name: Sample 36


title: H3K27ac FBXW7 KO SICT UNT B

description: FBXW7KO esiCT untreated Replicate B


title: H3K27ac WT SIHDAC4 UNT B

description: wt esiHDAC4 untreated Replicate B


title: HFF_SLAMseq_RNA12_Delta_4sU2hr_72hpi__B

description: Library name: Sample 37


title: H3K27ac WT SICT UNT B

description: wt esiCT untreated Replicate B


title: H3K27ac WT SIHDAC4 OXPT B

description: wt esiHDAC4 OxPt Replicate B


title: Flox2

description: Library name: Sample 2


title: CKO1

description: Library name: Sample 4


title: Flox1

description: Library name: Sample 1


title: HFF_SLAMseq_RNA12_WT_4sU2hr_72hpi__A

description: Library name: Sample 34


title: HFF_SLAMseq_RNA12_WT_4sU2hr_72hpi__B

description: Library name: Sample 35


title: Input FBXW7 KO

description: Pooling of KO Replicate A


title: Input WT

description: Pooling of WT Peplicate A


title: H3K27ac FBXW7 KO SIHDAC4 OXPT

description: FBXW7KO esiHDAC4 OxPt Replicate A


title: HFF_SLAMseq_RNA12_Uninfected_72hpi__B

description: Library name: Sample 33


title: BMDMs Ezh2 KO, Hepa1-6 CM-treated, R1

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

description:
Library name: KO_CM_R1
Column name in raw_counts.txt: KO_CM_R1

data_processing:
Sequencing reads were mapped against the Mus musculus reference genome mm10. Reads were mapped ana aligned with HISAT2. Reads were counted by Rsubread.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Bone marrow-derived macrophage

growth_protocol: BMDMs were harvested from the femurs and tibias of Ezh2fl/fl;LysM-Cre+/- (Ezh2 KO) mice and its littermate control mice by flushing. Bine marrow cells were cultured for 7-10 days in Dulbecco's modified Eagle's medium (DMEM, HyClone, Logan, UT, USA) supplemented with 10% fetal bovine serum (Gibco, Grand Island, NY, USA), 1% sodium pyruvate, 1% HEPES, 100 U/ml penicillin/streptomycin, 20% L929 cell conditioned media and 5% horse serum.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen).
cDNA libraries were prepared with the QIAseq Stranded mRNA Select Kit (Qiagen). The quantuty and quality of the libraries were determined using a 2100 Bioanalyzer. Sequencing was carried out on the Illumina NovaSeq 6000 (Illumina, San Diego, USA) (2 x 150 bp paired end reads). Library construction and sequencing were performed at the Omics Sciences and Bioinformatics Center (Chulalongkorn University, Bangkok, Thailand).

treatment_protocol: BMDMs were treated with Hepa1-6 conditioned media for 24 hours. For the control condition, BMDMs were cultured in DMEM complete medium for 24 hours.

value: Bone marrow-derived macrophage

value: Ezh2 KO

value: Hepa1-6 CM


title: HFF_SLAMseq_RNA12_Uninfected_72hpi__A

description: Library name: Sample 32

value: HFF


title: H3K27ac FBXW7 KO SICT OXPT

description: FBXW7KO esiCT OxPt Replicate A


title: BMDMs Ezh2 KO, Hepa1-6 CM-treated, R3

description:
Library name: KO_CM_R3
Column name in raw_counts.txt: KO_CM_R3


title: BMDMs Ezh2 KO, Hepa1-6 CM-treated, R2

description:
Library name: KO_CM_R2
Column name in raw_counts.txt: KO_CM_R2


title: WL-COL-ABA1

city: Shenzhen

first: Yao

last: Peng

address: 1066 Xueyuan Avenue, Nanshan District

institute: Shenzhen University

data_processing:
Majorbio cloud (https://cloud.majorbio.com/) was used to analyze differentially expressed genes (DEG). Genes with a corrected p-value < 0.05 and absolute log2 fold change > 2 were interpreted as differentially expressed. Venn diagrams, heatmaps and GO enrichment analysis were conducted by R packages.
Assembly: TAIR10.1_NCBI
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: 10-d-old seedlings

growth_protocol: 10-d-old Col-0 and uvr8 seedlings grown in long-day conditions(16 hour light/8 hour dark)

extract_protocol:
Total RNA was isolated using the RNAiso Plus (Takara) kit. RNA quality control was performed by gel electrophoresis. Three biological replicates were independently prepared throughout the processes, from the induction of seed germination to the preparation of RNA-seq libraries.
Generation of RNA libraries using Illumina TruseqTM RNA sample prep Kit followed the manufacturer’s instructions. The average RNA fragment was 300 bp and a 15-cycle PCR amplification was carried out with the primer mixture provided in the kit. Libraries were sequenced using an Illumina Hiseq4000 instrument with 2× 150-bp paired-ends reads by Majorbio.

treatment_protocol: treated with or without 50 uM ABA in white light or white light plus UV-B (5 umol m-2 sec-1)for 3 h.

value: 10-d-old seedlings

value: seedlings

value: white light with ABA


title: H3K27ac WT SICT OXPT B

description: wt esiCT OxPt Replicate B


title: WL-COL-ABA2


title: BMDMs Ezh2 KO, control, R2

description:
Library name: KO_DMEM_R2
Column name in raw_counts.txt: KO_DMEM_R2

value: DMEM (control)


title: HFF_SLAMseq_RNA12_Delta_72hpi__A

description: Library name: Sample 30


title: HFF_SLAMseq_RNA12_Delta_72hpi__B

description: Library name: Sample 31


title: H3K27ac FBXW7 KO SICT UNT

description: FBXW7KO esiCT untreated Replicate A


title: BMDMs Ezh2 KO, control, R1

description:
Library name: KO_DMEM_R1
Column name in raw_counts.txt: KO_DMEM_R1


title: BMDMs Ezh2 KO, control, R3

description:
Library name: KO_DMEM_R3
Column name in raw_counts.txt: KO_DMEM_R3


title: UVB-uvr8-MOCK3

value: white light or white light plus UV-B


title: H3K27ac FBXW7 KO SIHDAC4 UNT

description: FBXW7KO esiHDAC4 untreated Replicate A


title: WL-COL-ABA3


title: HFF_SLAMseq_RNA12_WT_72hpi__B

description: Library name: Sample 29


title: H3K27ac WT SIHDAC4 OXPT

description: wt esiHDAC4 OxPt Replicate A


title: BMDMs WT, Hepa1-6 CM-treated, R3

description:
Library name: WT_CM_R3
Column name in raw_counts.txt: WT_CM_R3

value: WT


title: UVB-uvr8-MOCK1


title: HFF_SLAMseq_RNA12_WT_72hpi_A

description: Library name: Sample 28


title: H3K27ac WT SIHDAC4 UNT

description: wt esiHDAC4 untreated Replicate A


title: H3K27ac WT SICT OXPT

description: wt esiCT OxPt Replicate A


title: BMDMs WT, Hepa1-6 CM-treated, R4

description:
Library name: WT_CM_R4
Column name in raw_counts.txt: WT_CM_R4


title: UVB-COL-MOCK3


title: H3K27ac WT SICT UNT

description: wt esiCT untreated Replicate A


title: UVB-uvr8-MOCK2


title: HFF_Fractionation_Uninfected_Nuclear_72hpi_C

description: Library name: Sample 27


title: UVB-COL-MOCK2


title: HFF_Fractionation_Uninfected_Nuclear_72hpi_B

description: Library name: Sample 26


title: HFF_Fractionation_Uninfected_Nuclear_72hpi_A

description: Library name: Sample 25


title: BMDMs WT, control, R4

description:
Library name: WT_DMEM_R4
Column name in raw_counts.txt: WT_DMEM_R4


title: Tim3 agonist3

city: Los Angeles

first: Yoshihiro

last: Sakano

address: 1450 Biggy street

department: Molecular Microbiology & Immunology

institute: Unversity of Southern California

description:
Library name: Sample_6
21079R-06-20P1_S0

data_processing:
Partek Flow, version 10.0
Sequence reads were trimmed by quality score (min Phred score 20 from both end, and trimmed reads shorter than 25bp were discarded).
Trimmed reads were mapped to mm10 with GENECODE M25 annotation as a guidance by STAR 2.7.8.
Aligned reads were further quantified to GENCODE M25 with Partek E/M algorithm.
Genes with less than 10 counts in all samples were removed from the analysis. The remaining genes were subjected to differential expression analysis by DESeq2 with median ratio normalization
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw read counts per gene per sample

source_name: lung

extract_protocol:
Cultured ILC2s were recovered, lysed in RLT buffer (Qiagen) and RNA was extracted using the MicroRNeasy kit (Qiagen)
For each sample, a total of 10pg of RNA was used to generate cDNA (SMARTer Ultra Low Input RNA v3 kit, Clontech) for library preparation

value: lung

value: sorted ILC2s

tag: strain

value: Tim-3 agonist


title: BMDMs WT, Hepa1-6 CM-treated, R2

description:
Library name: WT_CM_R2
Column name in raw_counts.txt: WT_CM_R2


title: MMTV-R26Met syngeneic graft tumor S34

city: Marseille

first: Olivier

last: Castellanet

address: 27 boulevard Lei Roure

country: France

institute: Aix Marseille University, CNRS, INSERM

description:
Library name: Tumor_TNBC34
10x Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger (v6.1.1, 10x Genomics). The cellranger mkfastq command was employed to demultiplex the raw base call files into FASTQ files, followed by alignment to the mouse reference genome (mm10) using the “cellranger count” command, which also produced gene-cell expression matrices for each sample. Quality Control (QC) was performed using multiple approaches to ensure high-quality cell and gene selection. Ambient RNA contamination and cell barcode calling were initially assessed using the knee detection method implemented in Cell Ranger. Barcode rank plots were inspected to confirm appropriate cell versus background separation. Mitochondrial and ribosomal genes were identified based on gene symbols, where mitochondrial genes were defined by the prefix “mt-” and ribosomal genes by the prefix “Rpl” or “Rps,” using pattern matching on the gene annotation metadata. The scater package (v1.26.0) was then used to calculate per-cell quality metrics with “perCellQCMetrics” function, including the percentage of mitochondrial and ribosomal gene expression per cell. Outlier cells were identified and filtered based on library size, number of detected genes, and mitochondrial and ribosomal gene content using the “isOutlier” function from the scater package. This method flags cells that deviate beyond three median absolute deviations (MADs) from the median. Cells identified as outliers were excluded from downstream analyses to ensure data quality. Doublet detection was performed with the DoubletFinder package (v2.0.3), assuming an expected doublet rate of 10%, and clusters with more than 80% predicted doublets were removed. Cell cycle phase assignment was conducted using the “cyclone” function from the scran package (v1.26.0) with the mouse cell cycle marker dataset, categorizing cells into G1, S, and G2/M phases. These QC filters were applied using the Seurat R package (v5), and cells meeting all the criteria were considered high-confidence cells for downstream analysis. Raw sequencing data processing, mappings, and QC were performed at the Cancer Research Center of Marseille Integrative BioInformatics (Cibi) facility.
Assembly: mouse mm10
Supplementary files format and content: RDS file of a Seurat object with all samples integrated, including expression, metadata, clustering, and embeddings

source_name: mammary gland tumor

extract_protocol:
MMTV-R26Met syngeneic tumors were dissected at passage 7 and minced into small fragments, followed by enzymatic digestion for 20-35 min at 37°C. The digestion solution consisted of type IV collagenase (2 mg/ml, Sigma), hyaluronidase (1 mg/ml, Sigma), and DNase I (20 µg/ml, Roche) in DMEM/F12 (Dulbecco's modified Eagle's media/F12, 1/1, ThermoFisher Scientific) supplemented with 10% fetal bovine serum (FBS, Sigma) and penicillin–streptomycin (P/S, 100 U/ml / 0.1 mg/ml, ThermoFisher Scientific). After digestion, samples were centrifuged, and the pellet was incubated on ice for 1 min with red blood cell lysis buffer (ThermoFisher Scientific). They were then washed in PBS and further incubated for 5 min at 37°C with trypsin (0.05%, Gibco). Subsequently, the cells were resuspended in DMEM/F12 + 10% FBS + P/S, and filtered through a 40µm nylon cell strainer to remove aggregates. Cell counting and viability assessment using trypan blue revealed that all samples exhibited viability above 80%, so no sorting was performed. The cell concentration was then adjusted to approximately 1,000 cells/µL for library preparation.
Single-cell RNA sequencing libraries were generated using the 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v3.1, following the manufacturer's protocol. Specifically, 10,000 cells per sample were loaded onto a Chromium Controller to encapsulate individual cells into Gel Beads in Emulsion (GEMs). After cell lysis within the GEMs, mRNA was reverse transcribed to produce cDNA, which was then amplified by PCR. This cDNA was subsequently used for sequencing library preparation. The libraries were sequenced on an Illumina NextSeq 500 and NextSeq 2000 sequencers, targeting a depth of approximately 60,000 reads per cell. The library generation, validation, and sequencing were performed at the "Transcriptomique et Génomique Marseille Luminy (TGML)" platform.

value: mammary gland tumor

value: female

tag: recipient strain

value: 50% 129S2/SvPasOrlRj, 50% C57BL/6JRj


title: UVB-COL-MOCK1


title: BMDMs WT, Hepa1-6 CM-treated, R1

description:
Library name: WT_CM_R1
Column name in raw_counts.txt: WT_CM_R1


title: HFF_Fractionation_Uninfected_Cytosol_72hpi_C

description: Library name: Sample 24


title: BMDMs WT, control, R3

description:
Library name: WT_DMEM_R3
Column name in raw_counts.txt: WT_DMEM_R3


title: HFF_Fractionation_Uninfected_Cytosol_72hpi_B

description: Library name: Sample 23


title: BMDMs WT, control, R2

description:
Library name: WT_DMEM_R2
Column name in raw_counts.txt: WT_DMEM_R2


title: WL-COL-MOCK3

value: white light


title: Tim3 agonist1

description:
Library name: Sample_4
21079R-06-19_S15


title: HFF_Fractionation_Uninfected_Cytosol_72hpi_A

description: Library name: Sample 22


title: ISO3

description:
Library name: Sample_3
21079R-06-16_S14

value: isotype control


title: BMDMs WT, control, R1

description:
Library name: WT_DMEM_R1
Column name in raw_counts.txt: WT_DMEM_R1

value: Bone marrow-derived macrophage


title: ISO2

description:
Library name: Sample_2
21079R-06-15P1_S0