title: Breast Benign Disease [Patient 203_SH08L09_Cell2]


title: Breast Benign Disease [Patient 199_SH09X61_Cell4]

status: Public on Mar 01 2026

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Total RNA extracted from 0.3 mL of serum was labeled with the 3D-Gene® Labeling kit (Toray Industries Inc.). Labeled miRNAs were hybridized onto 3D-Gene® miRNA Oligo Chips at 42 °C for 17 hours.

hyb_protocol: Hybridized for 17 h at 42 C. Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

molecule: total RNA

organism: Homo sapiens

source_name: serum

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

extract_protocol: RNA samples were extracted from serum using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

treatment_protocol: The whole blood specimens were collected and processed at each institution using red/gray topped gel barrier tubes (Becton Dickinson Vacutainer® SST™ Tubes 367988, Franklin Lakes, NJ). The blood specimens were allowed to clot for 30 - 35 minutes at room temperature. The tubes were then centrifuged at either 4°C or room-temperature at 1,100 – 1,300 g for 10 minutes. After centrifugation, aliquots of 0.5 mL of serum were stored at or below -80 °C within 90 minutes of collection.

tag: Sex

value: female

tag: age

tag: category

value: Test


title: Breast Benign Disease [Patient 198_SH06F25_Cell2]


title: Patient 23-04_GEX timepoint T03 scRNAseq

type: SRA

city: San Francisco

first: Bridget

middle: P

last: Keenan

state: CA

address: 505 PARNASSUS AVE

country: USA

institute: University of California San Francisco

description:
Library name: 23-04_GEX
polyA RNA

library_source: transcriptomic

data_processing:
CellRanger version 3.1.0 (10x Genomics) was used to align the raw sequencing data and to generate count matrices (gene expression and ADT barcode counts). The ADT library sequences were aligned to a customized reference genome provided by BD containing the oligonucleotide sequences corresponding to each antibody.
Pre-processing of aligned sequencing data and identification of single nucleotide polymorphisms was performed using the Genome Analysis Toolkit (McKenna et al., 2010). We used demuxlet (Kang et al., 2018) (https://github.com/statgen/demuxlet) for sample deconvolution of multiplexed PBMC samples.
Further processing was done with Scanpy v1.4.6 (concatenation of samples, filtering for high quality cells, normalization, batch correction, clustering, annotation, and differential gene expression analysis). The .h5ad files are demultiplexed, concatenated, filtered, and annotated, but otherwise represent raw data prior to all processing steps.
Assembly: Genome Build: GRCh38 3.0.0
Supplementary files format and content: Cell Ranger output filtered matrix files for both scRNA-seq libraries and CITE-seq (feature barcoding) libraries: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz.
Library strategy: CITE-seq

molecule: polyA RNA

source_name: Biliary tract cancer (BTC)

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were obtained from patients with biliary tract cancer as part of a Phase II trial of pembrolizumab and GM-CSF. Blood samples were processed using ficoll; after centrifugation, the PBMC layer was isolated and cryopreserved in cell media with human serum and DMSO. Previously frozen PBMCs were thawed using media containing RPMI, heat-inactivated sterile filtered human serum, penicillin-streptomycin, non-essential amino acids, sodium pyruvate, and L-glutamine. Samples were then incubated for DNAse I before washing and counting. 1 x10>6 cells from 16 unique samples were combined and stained with one pooled cocktail containing 99 AbSeq antibody-oligonucleotide conjugates (BD Biosciences) per standard protocols (Olvera JG et al., 2018), following pre-incubation with TruStain FcX (Fc Receptor Blocking Solution). Samples from different individuals and timepoints were randomly mixed across experiments to minimize batch and confounding effects.
Droplet-based single cell RNA sequencing (scRNAseq) was performed using the 10x Genomics Chromium Single Cell 3ʹ Reagent Kits v3, according to manufacturer instructions. For preparation of ADT libraries, we followed the standard protocol available from Olvera JG et al., 2018 following pre-incubation with TruStain FcX (Fc Receptor Blocking Solution, Biolegend). Briefly, cell suspensions were combined with master mix and loaded into the chip with gel beads to generate the gel bead-in-emulsion (GEM), which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. Reverse transcription was performed on the poly-A RNA within each GEM. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads and amplified by PCR. To prepare libraries from cDNA, SPRIselect beads were used to isolate the correct size fragments. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added during library construction.

tag: tissue

value: Biliary tract cancer (BTC)

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)

tag: treatment

value: GM-CSF and pembrolizumab

tag: library type

value: mRNA

tag: time


title: Breast Benign Disease [Patient 197_SH06Y54_Cell4]


title: Patient 23-03_GEX timepoint T02 scRNAseq

description:
Library name: 23-03_GEX
polyA RNA


title: Breast Benign Disease [Patient 194_SH0ZE21_Cell3]


title: Breast Benign Disease [Patient 189_SH08L12_Cell2]


title: Patient 23-02_GEX timepoint T01 replicate 2 scRNAseq

description:
Library name: 23-02_GEX rep2
polyA RNA


title: Patient 22-05_GEX timepoint T04 scRNAseq

description:
Library name: 22-05_GEX
polyA RNA


title: Patient 23-02_GEX timepoint T01 replicate 1 scRNAseq

description:
Library name: 23-02_GEX rep1
polyA RNA


title: Breast Benign Disease [Patient 188_SH06901_Cell1]


title: Patient 22-04_GEX timepoint T03 scRNAseq

description:
Library name: 22-04_GEX
polyA RNA


title: Breast Benign Disease [Patient 187_SH11R09_Cell1]


title: Patient 22-02_GEX timepoint T01 replicate 1 scRNAseq

description:
Library name: 22-02_GEX rep1
polyA RNA


title: Patient 22-03_GEX timepoint T02 scRNAseq

description:
Library name: 22-03_GEX
polyA RNA


title: Patient 22-02_GEX timepoint T01 replicate 2 scRNAseq

description:
Library name: 22-02_GEX rep2
polyA RNA


title: Breast Benign Disease [Patient 185_SH0ZE28_Cell1]


title: Patient 21-02_GEX timepoint T01 scRNAseq

description:
Library name: 21-02_GEX
polyA RNA


title: Patient 21-04_GEX timepoint T03 scRNAseq

description:
Library name: 21-04_GEX
polyA RNA


title: Breast Benign Disease [Patient 190_SH11R15_Cell2]


title: Patient 20-02_GEX timepoint T01 replicate 1 scRNAseq

description:
Library name: 20-02_GEX rep1
polyA RNA


title: Breast Benign Disease [Patient 186_SH08L44_Cell4]


title: Patient 20-05_GEX timepoint T04 scRNAseq

description:
Library name: 20-05_GEX
polyA RNA


title: Breast Benign Disease [Patient 184_SH08L42_Cell2]


title: Patient 20-03_GEX timepoint T02 scRNAseq

description:
Library name: 20-03_GEX
polyA RNA


title: Breast Benign Disease [Patient 180_SH0ZE12_Cell3]


title: Patient 20-02_GEX timepoint T01 replicate 2 scRNAseq

description:
Library name: 20-02_GEX rep2
polyA RNA


title: Breast Benign Disease [Patient 183_SH08L22_Cell4]


title: Breast Benign Disease [Patient 181_SH0ZE08_Cell1]


title: Breast Benign Disease [Patient 179_SH05T45_Cell3]


title: Breast Benign Disease [Patient 182_SH11M34_Cell3]


title: Breast Benign Disease [Patient 177_SH08L37_Cell1]


title: Patient 19-05_GEX timepoint T04 replicate 1 scRNAseq

description:
Library name: 19-05_GEX rep1
polyA RNA


title: Breast Benign Disease [Patient 178_SH05T38_Cell2]


title: Breast Benign Disease [Patient 175_SH06909_Cell1]


title: Patient 19-04_GEX timepoint T03 scRNAseq

description:
Library name: 19-04_GEX
polyA RNA


title: Breast Benign Disease [Patient 176_SH08L13_Cell2]


title: Breast Cancer [Patient 173_SH0ZE33_Cell2]

value: Training


title: Patient 19-03_GEX timepoint T02 replicate 2 scRNAseq

description:
Library name: 19-03_GEX rep2
polyA RNA


title: Breast Cancer [Patient 174_SH0ZH01_Cell3]


title: Patient 19-03_GEX timepoint T02 replicate 1 scRNAseq

description:
Library name: 19-03_GEX rep1
polyA RNA


title: Patient 18-03_GEX timepoint T03 scRNAseq

description:
Library name: 18-03_GEX
polyA RNA


title: Patient 19-02_GEX timepoint T01 scRNAseq

description:
Library name: 19-02_GEX
polyA RNA


title: Patient 18-02_GEX timepoint T02 scRNAseq

description:
Library name: 18-02_GEX
polyA RNA


title: Patient 19-05_GEX timepoint T04 replicate 2 scRNAseq

description:
Library name: 19-05_GEX rep2
polyA RNA


title: Breast Cancer [Patient 169_SH0ZE28_Cell4]


title: Patient 18-01_GEX timepoint T01 scRNAseq

description:
Library name: 18-01_GEX
polyA RNA


title: Patient 17-04_GEX timepoint T04 replicate 1 scRNAseq

description:
Library name: 17-04_GEX rep1
polyA RNA


title: Patient 17-03_GEX timepoint T03 scRNAseq

description:
Library name: 17-03_GEX
polyA RNA


title: Patient 17-02_GEX timepoint T02 scRNAseq

description:
Library name: 17-02_GEX
polyA RNA


title: Breast Cancer [Patient 167_SH09X49_Cell1]


title: Breast Cancer [Patient 171_SH06F24_Cell3]


title: Breast Cancer [Patient 164_SH08L33_Cell4]


title: Breast Cancer [Patient 163_SH08L14_Cell1]


title: Breast Cancer [Patient 166_SH08L33_Cell3]


title: Breast Cancer [Patient 170_SH05T45_Cell2]


title: Breast Cancer [Patient 165_SH08L31_Cell1]


title: Breast Cancer [Patient 172_SH08L44_Cell2]


title: Patient 16-04_GEX timepoint T03 replicate 2 scRNAseq

description:
Library name: 16-04_GEX rep2
polyA RNA


title: Patient 16-04_GEX timepoint T03 replicate 1 scRNAseq

description:
Library name: 16-04_GEX rep1
polyA RNA


title: Patient 16-05_GEX timepoint T04 scRNAseq

description:
Library name: 16-05_GEX
polyA RNA


title: Breast Cancer [Patient 168_SH08L31_Cell4]


title: Breast Cancer [Patient 160_SH06F24_Cell4]


title: Breast Cancer [Patient 161_SH06Y49_Cell1]


title: Breast Cancer [Patient 162_SH0ZE26_Cell3]


title: Patient 16-03_GEX timepoint T02 scRNAseq

description:
Library name: 16-03_GEX
polyA RNA


title: Patient 16-02_GEX timepoint T01 scRNAseq

description:
Library name: 16-02_GEX
polyA RNA


title: Patient 15-04_GEX timepoint T03 replicate 2 scRNAseq

description:
Library name: 15-04_GEX rep2
polyA RNA


title: Breast Cancer [Patient 159_SH08L45_Cell3]


title: Patient 17-01_GEX timepoint T01 scRNAseq

description:
Library name: 17-01_GEX
polyA RNA


title: Patient 15-04_GEX timepoint T03 replicate 1 scRNAseq

description:
Library name: 15-04_GEX rep1
polyA RNA


title: Breast Cancer [Patient 158_SH08L32_Cell1]


title: Breast Cancer [Patient 157_SH08L20_Cell3]


title: Breast Cancer [Patient 156_SH08L19_Cell4]


title: Breast Cancer [Patient 154_SH09X60_Cell2]


title: Breast Cancer [Patient 155_SH0ZE34_Cell3]


title: Patient 15-05_GEX timepoint T04 scRNAseq

description:
Library name: 15-05_GEX
polyA RNA


title: Patient 17-04_GEX timepoint T04 replicate 2 scRNAseq

description:
Library name: 17-04_GEX rep2
polyA RNA


title: Patient 15-02_GEX timepoint T01 scRNAseq

description:
Library name: 15-02_GEX
polyA RNA


title: Breast Cancer [Patient 153_SH11R07_Cell2]


title: Patient 15-03_GEX timepoint T02 scRNAseq

description:
Library name: 15-03_GEX
polyA RNA


title: Breast Cancer [Patient 151_SH0ZE28_Cell3]


title: Breast Cancer [Patient 152_SH0ZE33_Cell3]


title: Patient 14-02_GEX timepoint T02 scRNAseq

description:
Library name: 14-02_GEX
polyA RNA


title: Patient 14-01_GEX timepoint T01 scRNAseq

description:
Library name: 14-01_GEX
polyA RNA


title: Patient 14-03_GEX timepoint T03 scRNAseq

description:
Library name: 14-03_GEX
polyA RNA


title: Breast Cancer [Patient 150_SH11R07_Cell4]


title: Patient 14-04_GEX timepoint T04 replicate 1 scRNAseq

description:
Library name: 14-04_GEX rep1
polyA RNA


title: Breast Cancer [Patient 149_SH0ZE20_Cell4]


title: Breast Cancer [Patient 147_SH09X52_Cell1]


title: Breast Cancer [Patient 146_SH06901_Cell2]


title: Patient 13-05_GEX timepoint T04 scRNAseq

description:
Library name: 13-05_GEX
polyA RNA


title: Breast Cancer [Patient 148_SH09X57_Cell2]


title: Breast Cancer [Patient 145_SH11R08_Cell1]


title: Patient 13-02_GEX timepoint T01 scRNAseq

description:
Library name: 13-02_GEX
polyA RNA


title: Patient 13-03_GEX timepoint T02 scRNAseq

description:
Library name: 13-03_GEX
polyA RNA


title: Patient 12-04_GEX timepoint T03 scRNAseq

description:
Library name: 12-04_GEX
polyA RNA


title: Patient 14-04_GEX timepoint T04 replicate 2 scRNAseq

description:
Library name: 14-04_GEX rep2
polyA RNA


title: Patient 12-02_GEX timepoint T02 scRNAseq

description:
Library name: 12-02_GEX
polyA RNA


title: Patient 12-05_GEX timepoint T04 scRNAseq

description:
Library name: 12-05_GEX
polyA RNA


title: Patient 12-01_GEX timepoint T01 scRNAseq

description:
Library name: 12-01_GEX
polyA RNA


title: Patient 13-04_GEX timepoint T03 scRNAseq

description:
Library name: 13-04_GEX
polyA RNA


title: Breast Benign Disease [Patient 138_SH11M32_Cell1]


title: Breast Cancer [Patient 143_SH08L14_Cell4]


title: Breast Benign Disease [Patient 140_SH08L42_Cell3]


title: Patient 11-06_GEX timepoint T04 replicate 2 scRNAseq

description:
Library name: 11-06_GEX rep2
polyA RNA


title: Breast Cancer [Patient 144_SH08L41_Cell1]


title: Patient 11-06_GEX timepoint T04 replicate 1 scRNAseq

description:
Library name: 11-06_GEX rep1
polyA RNA


title: Patient 11-03_GEX timepoint T02 scRNAseq

description:
Library name: 11-03_GEX
polyA RNA


title: Breast Cancer [Patient 141_SH06854_Cell4]


title: Patient 11-05_GEX timepoint T03 scRNAseq

description:
Library name: 11-05_GEX
polyA RNA


title: Patient 11-02_GEX timepoint T01 scRNAseq

description:
Library name: 11-02_GEX
polyA RNA


title: Breast Benign Disease [Patient 134_SH11R09_Cell4]


title: Breast Benign Disease [Patient 135_SH09X57_Cell1]


title: Patient 10-06_GEX timepoint T04 replicate 1 scRNAseq

description:
Library name: 10-06_GEX rep1
polyA RNA


title: Patient 10-06_GEX timepoint T04 replicate 2 scRNAseq

description:
Library name: 10-06_GEX rep2
polyA RNA


title: Breast Benign Disease [Patient 131_SH08L37_Cell3]


title: Breast Benign Disease [Patient 136_SH08L19_Cell2]


title: Breast Benign Disease [Patient 137_SH08L33_Cell1]


title: Breast Benign Disease [Patient 139_SH11M31_Cell3]


title: Breast Benign Disease [Patient 133_SH06F26_Cell1]


title: Breast Benign Disease [Patient 132_SH06902_Cell4]


title: Patient 10-03_GEX timepoint T02 replicate 2 scRNAseq

description:
Library name: 10-03_GEX_rep2
polyA RNA


title: Patient 10-03_GEX timepoint T02 replicate 1 scRNAseq

description:
Library name: 10-03_GEX_rep1
polyA RNA


title: Patient 10-05_GEX timepoint T03 scRNAseq

description:
Library name: 10-05_GEX
polyA RNA


title: Patient 10-02_GEX timepoint T01 scRNAseq

description:
Library name: 10-02_GEX
polyA RNA


title: Loffler syndrome 002

city: Tsukuba

first: Atsushi

last: Kawaguchi

address: 1-1-1 Tennodai

institute: University of Tsukuba

description:
Library name: Control case-1 002
FFPE Spatial transcriptome sequence

data_processing:
Sequencing data were processed using the GeoMx Analysis Suite, including quality control, read alignment, and normalization according to the manufacturer’s guidelines.
Assembly: GRch38
Supplementary files format and content: Processed data files include normalized gene expression matrices generated by the GeoMx Analysis Suite.
Library strategy: Spatial Transcriptomics

source_name: Heart

extract_protocol:
RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue sections following the GeoMx Digital Spatial Profiler workflow according to the manufacturer’s instructions.
Sequencing libraries were prepared from collected RNA using the GeoMx library preparation workflow according to the manufacturer’s protocol.

value: Heart

value: Female

value: 60 years


title: Loffler syndrome 003

description:
Library name: Control case-1 003
FFPE Spatial transcriptome sequence


title: Loffler syndrome 004

description:
Library name: Control case-1 004
FFPE Spatial transcriptome sequence


title: Breast Benign Disease [Patient 130_SH0ZE08_Cell3]


title: Breast Benign Disease [Patient 129_SH08L19_Cell3]


title: Breast Benign Disease [Patient 128_SH0ZE18_Cell3]


title: mRNA vaccine-associated myocarditis, severe 003

description:
Library name: Severe case-3 003
FFPE Spatial transcriptome sequence

value: Male

value: 15 years


title: Breast Benign Disease [Patient 126_SH11M34_Cell2]


title: Breast Benign Disease [Patient 127_SH11R06_Cell4]


title: Loffler syndrome 001

description:
Library name: Control case-1 001
FFPE Spatial transcriptome sequence


title: Breast Benign Disease [Patient 123_SH06Y37_Cell4]


title: mRNA vaccine-associated myocarditis, severe 002

description:
Library name: Severe case-3 002
FFPE Spatial transcriptome sequence


title: mRNA vaccine-associated myocarditis, severe 001

description:
Library name: Severe case-3 001
FFPE Spatial transcriptome sequence


title: mRNA vaccine-associated myocarditis, moderate 002

description:
Library name: Moderate case 002
FFPE Spatial transcriptome sequence

value: 26 years


title: Breast Benign Disease [Patient 120_SH06Y26_Cell1]


title: mRNA vaccine-associated myocarditis, mild 003

description:
Library name: Mild case-2 003
FFPE Spatial transcriptome sequence

value: 18 years


title: Breast Benign Disease [Patient 122_SH06F26_Cell4]


title: Breast Benign Disease [Patient 125_SH11M30_Cell3]


title: Breast Cancer [Patient 142_SH06Y52_Cell3]


title: mRNA vaccine-associated myocarditis, moderate 001

description:
Library name: Moderate case 001
FFPE Spatial transcriptome sequence


title: Breast Benign Disease [Patient 121_SH0ZE15_Cell3]


title: Breast Benign Disease [Patient 118_SH09X60_Cell1]


title: Breast Benign Disease [Patient 124_SH11R18_Cell4]


title: mRNA vaccine-associated myocarditis, mild 002

description:
Library name: Mild case-2 002
FFPE Spatial transcriptome sequence


title: Breast Benign Disease [Patient 116_SH11M32_Cell2]


title: Breast Benign Disease [Patient 117_SH06837_Cell1]


title: mRNA vaccine-associated myocarditis, mild 001

description:
Library name: Mild case-2 001
FFPE Spatial transcriptome sequence


title: Patient 44-pre biopsy Visium

description:
Library name: 44-pre
FFPE spatial transcriptomics

data_processing:
Raw data was then processed and transformed from h5ad files to a Seurat object (Seurat v4.1.1) in R, and then were merged into a large Seurat data object containing all samples. Cleaned sequencing data for each Visium sample were processed with Spaceranger (version 1.3.1) and mapped to Human GRCh38 reference genome to generate a raw gene expression matrix for each Visium sample, then RCTD (v2.0.0) were applied to conduct cell type deconvolution for all Visium samples with the merged single cell object as reference.
Assembly: Genome Build: GRCh38 3.0.0
Supplementary files format and content: barcodes, features, matrices, images
Library strategy: Spatial Transcriptomics

extract_protocol:
Tumor samples (FFPE) with adequate cellularity underwent spatial transcriptomics using the Spatial Gene Expression Slide & Reagent kit (10x Genomics). Tissue permeabilization was performed for 12-18 minutes for each sample, which was determined by the tissue optimization assay, and sequencing libraries were generated following standard protocols by Abiosciences. Samples were prepared by embedding in OCT and sectioning, then placing one 10um section of frozen tissues onto one 6.5 mm x 6.5 mm capture area of the 10x Genomics Visium spatial gene expression slide (v1), fixed, stained with H&E, imaged, followed by permeabilization, reverse transcription and spatial barcoding followed by denaturing to release the cDNA, and library construction.
For 10x Visium Spatial transcriptome library preparation, we followed the 10x user guides (G000238: Visium Spatial Tissue Optimization User Guide and CG000239: Visium Spatial Gene Expression Reagent Kits User Guide).  The libraries are then sequenced in an Illumina sequencer NovaSeq6000 with the specifications based on 10x Genomics user guide to obtain at least 50,000 read pairs per tissue-covered spot.

value: Tumor and immune cells

value: Pre-GM-CSF, post-pembrolizumab


title: Patient 43-post biopsy Visium

description:
Library name: 43-post
FFPE spatial transcriptomics

value: Post-GM-CSF, post-pembrolizumab


title: Breast Benign Disease [Patient 110_SH05T51_Cell2]

value: female


title: Patient 44-post biopsy Visium

description:
Library name: 44-post
FFPE spatial transcriptomics


title: Breast Benign Disease [Patient 114_SH08L19_Cell1]


title: Patient 42-pre biopsy Visium

description:
Library name: 42-pre
FFPE spatial transcriptomics


title: Breast Benign Disease [Patient 119_SH09X52_Cell3]

description: Total RNA extracted from 0.3 mL of serum was labeled with the 3D-Gene® Labeling kit (Toray Industries Inc.). Labeled miRNAs were hybridized onto 3D-Gene® miRNA Oligo Chips at 42 °C for 17 hours.


title: Patient 43-pre biopsy Visium

description:
Library name: 43-pre
FFPE spatial transcriptomics


title: Breast Benign Disease [Patient 109_SH05T39_Cell4]


title: Breast Benign Disease [Patient 115_SH08L09_Cell1]


title: Breast Benign Disease [Patient 113_SH05T39_Cell1]


title: Patient 41-post biopsy Visium

description:
Library name: 41-post
FFPE spatial transcriptomics


title: Breast Benign Disease [Patient 108_SH05T44_Cell3]


title: Breast Benign Disease [Patient 111_SH09X63_Cell2]


title: Patient 42-post biopsy Visium

description:
Library name: 42-post
FFPE spatial transcriptomics


title: Patient 38-pre biopsy Visium

description:
Library name: 38-pre
FFPE spatial transcriptomics


title: Breast Benign Disease [Patient 112_SH06Y53_Cell1]


title: Patient 41-pre biopsy Visium

description:
Library name: 41-pre
FFPE spatial transcriptomics


title: Patient 38-post biopsy Visium

description:
Library name: 38-post
FFPE spatial transcriptomics


title: Patient 30-post biopsy Visium

description:
Library name: 30-post
FFPE spatial transcriptomics


title: Breast Benign Disease [Patient 106_SH08L14_Cell2]


title: Breast Benign Disease [Patient 105_SH08L18_Cell2]


title: Breast Benign Disease [Patient 104_SH08L18_Cell1]


title: SKOV3 cells, shDDX18 3

city: Hefei

first: Hanyuan

last: Liu

address: 443 Huangshan Road Hefei, Anhui Province

country: China

institute: University of Science and Technology of China

description: Library name: Sample6

data_processing:
RNA-seq was performed on the Illumina platform using 150-bp paired-end reads. The reads were mapped to GRCh38 using hisat2 (v2.2.1) and converted the ENSG ID to Gene symbols.
Gene expression was analyzed, and p value < 0.05 in addition with absolute log2FC ≥1 was set as significant.
Assembly: hg38
Supplementary files format and content: csv files include reads for each RNA-seq Sample

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) according to the manufacturer’s instructions.

tag: cell line

value: ovarian cancer cell lines

tag: genotype

value: DDX18 knockdown


title: Breast Benign Disease [Patient 103_SH11M33_Cell3]


title: Patient 30-pre biopsy Visium

description:
Library name: 30-pre
FFPE spatial transcriptomics

value: Biliary tract cancer (BTC)


title: Breast Benign Disease [Patient 107_SH06Y53_Cell3]


title: SKOV3 cells, shDDX18 1

description: Library name: Sample4


title: SKOV5 cells, siControl 3

description: Library name: Sample3

value: WT


title: SKOV3 cells, shDDX18 2

description: Library name: Sample5


title: SKOV3 cells, siControl 2

description: Library name: Sample2


title: Breast Benign Disease [Patient 102_SH06Y52_Cell2]


title: Breast Benign Disease [Patient 100_SH08L23_Cell2]


title: Breast Benign Disease [Patient 099_SH08L11_Cell2]


title: Breast Benign Disease [Patient 101_SH11M31_Cell1]


title: mRNA vaccine-associated myocarditis, moderate 003

description:
Library name: Moderate case 003
FFPE Spatial transcriptome sequence


title: Breast Benign Disease [Patient 098_SH11R06_Cell2]


title: Batch6_Stimulated

city: Callao

first: George

middle: Dereck

last: Muñoz

state: Callao

address: Ca. Dalias 204-A, Bellavista - Callao

country: Peru

institute: Rockefeller University

description:
Library name: Sample 12
BRB-seq library generated from one 96-well plate of HEK293T cells cultured in DMEM + 10% FBS and seeded at 18,000 cells per well. Cells were transfected in quadruplicate with pEZY3-vTR plasmids (80 ng) or empty pEZY3 vector using Lipofectamine 3000. Twenty-four hours after transfection, cells were infected with Sendai virus at 4.0 × 10^6 CEID50/mL (VR-907, ATCC). RNA was harvested two days post-transfection. RNA-containing lysates from all wells in this plate were processed using the MERCURIUS DRUG-seq (BRB-seq) kit, pooled at the cDNA level, and prepared for sequencing on an Illumina NovaSeq platform. This library corresponds to a Sendai virus–stimulated plate (plate 12); individual well-level conditions (e.g. specific peptides or biological replicates) are detailed in the accompanying sample metadata table.

data_processing:
BRB-seq reads were aligned to a custom human reference based on GRCh38 (primary assembly) with Gencode v46 annotations,129 augmented by a concatenated FASTA of all VTR sequences and a merged GTF that combined genome and VTR features. Genome indices were built with STAR v2.7.9a130 using splice junctions (–-sjdbGTFfile Gencode+VTR, –-sjdbOverhang 79). Alignment and counting were performed with STARsolo in CB/UMI simple mode to recover per-barcode gene counts (–-soloType CB_UMI_Simple; –-soloFeatures Gene; –-soloStrand Forward; –-clipAdapterType CellRanger4; –-outSAMtype BAM SortedByCoordinate; –-outSAMunmapped Within; –-outReadsUnmapped Fastx). Barcodes and UMIs were parsed with a 14-nt cell barcode and 14-nt UMI (–-soloCBstart 1 –-soloCBlen 14; –-soloUMIstart 15 –-soloUMIlen 14), matched to a provided whitelist allowing one mismatch (–-soloCBmatchWLtype 1MM), and deduplicated with directional one-mismatch UMI collapsing (–-soloUMIdedup 1MM_Directional). STAR output included comprehensive SAM attributes (NH HI AS nM CR CY UR UY CB UB GX GN sS sQ sM). Scripts to process sequencing data are deposited in https://github.com/FuxmanBass-lab/vTRs.
Assembly: GENCODE v46 (GRCh38 primary assembly)
Supplementary files format and content: Processed data consist of STARsolo-generated gene-level UMI count matrices for each BRB-seq plate. Each processed dataset includes: (1) a sparse matrix file (matrix.mtx.gz) containing gene-by-barcode UMI counts; (2) a gene annotation file (genes.tsv.gz) reporting gene IDs and gene names; (3) a barcode file (barcodes.tsv.gz) listing barcoded wells; and (4) a metadata file (metadata_<batch>.tsv) linking each barcode to its corresponding well ID, vTR construct, and experimental condition. Files are gzip-compressed where applicable.

source_name: embryonic kidney

growth_protocol: HEK293T cells were cultured in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco) and maintained at 37°C and 5% CO₂. Cells were seeded at a density of 18,000 cells per well in 96-well plates one day prior to transfection.

extract_protocol:
RNA-containing lysates were generated directly from permeabilized HEK293T cells using the MERCURIUS DRUG-seq (BRB-seq) kit (Alithea Genomics). Cells were incubated on ice for 15 minutes in cell lysis buffer with periodic agitation, followed by centrifugation to clear debris. Lysates containing polyadenylated RNA were used immediately for barcoded reverse transcription.
BRB-seq libraries were prepared using the MERCURIUS DRUG-seq kit (Alithea Genomics) according to manufacturer’s instructions. Individual wells were reverse-transcribed using barcoded oligo-dT primers, enabling assignment of each sample to a unique 14 bp cell barcode and 14 bp UMI. cDNA from all wells on each plate (up to 95 barcoded samples) was pooled and purified using the Zymo Clean & Concentration Kit (Zymo Research). Residual primers were removed by exonuclease digestion, followed by second-strand synthesis. Twenty nanograms of double-stranded cDNA per plate were tagmented, indexed using Illumina-compatible adapters, and PCR-amplified. Final libraries were sequenced on an Illumina NovaSeq platform at approximately 5 million raw reads per well.

treatment_protocol: Cells were transfected in quadruplicate with 80 ng per well of pEZY3-vTR plasmids (84 distinct vTR constructs) or empty pEZY3 vector using Lipofectamine 3000 (Thermo Fisher Scientific) according to manufacturer’s instructions. Twenty-four hours after transfection, stimulated plates were infected with Sendai virus (VR-907, ATCC) at 4.0 × 10⁶ CEID50/mL, while unstimulated plates were left uninfected. Cells were incubated for an additional 48 hours prior to RNA harvesting.

value: embryonic kidney

value: epithelial cell line

value: HEK293T (wildtype)

value: Mixture of HEK293T wells transfected with 84 distinct pEZY3-vTR constructs or control/empty vector; Sendai virus infection at 4.0 × 10^6 CEID50/mL (VR-907, ATCC)

tag: batch


title: Breast Benign Disease [Patient 095_SH11M33_Cell2]

value: Training


title: Batch5_Stimulated

description:
Library name: Sample 11
BRB-seq library generated from one 96-well plate of HEK293T cells cultured in DMEM + 10% FBS and seeded at 18,000 cells per well. Cells were transfected in quadruplicate with pEZY3-vTR plasmids (80 ng) or empty pEZY3 vector using Lipofectamine 3000. Twenty-four hours after transfection, cells were infected with Sendai virus at 4.0 × 10^6 CEID50/mL (VR-907, ATCC). RNA was harvested two days post-transfection. RNA-containing lysates from all wells in this plate were processed using the MERCURIUS DRUG-seq (BRB-seq) kit, pooled at the cDNA level, and prepared for sequencing on an Illumina NovaSeq platform. This library corresponds to a Sendai virus–stimulated plate (plate 11); individual well-level conditions (e.g. specific peptides or biological replicates) are detailed in the accompanying sample metadata table.


title: Batch3_Stimulated

description:
Library name: Sample 9
BRB-seq library generated from one 96-well plate of HEK293T cells cultured in DMEM + 10% FBS and seeded at 18,000 cells per well. Cells were transfected in quadruplicate with pEZY3-vTR plasmids (80 ng) or empty pEZY3 vector using Lipofectamine 3000. Twenty-four hours after transfection, cells were infected with Sendai virus at 4.0 × 10^6 CEID50/mL (VR-907, ATCC). RNA was harvested two days post-transfection. RNA-containing lysates from all wells in this plate were processed using the MERCURIUS DRUG-seq (BRB-seq) kit, pooled at the cDNA level, and prepared for sequencing on an Illumina NovaSeq platform. This library corresponds to a Sendai virus–stimulated plate (plate 9); individual well-level conditions (e.g. specific peptides or biological replicates) are detailed in the accompanying sample metadata table.


title: Breast Benign Disease [Patient 097_SH08L39_Cell2]


title: SKOV3 cells, siControl 1

description: Library name: Sample1


title: Breast Benign Disease [Patient 096_SH11R10_Cell3]


title: Batch1_Stimulated

description:
Library name: Sample 7
BRB-seq library generated from one 96-well plate of HEK293T cells cultured in DMEM + 10% FBS and seeded at 18,000 cells per well. Cells were transfected in quadruplicate with pEZY3-vTR plasmids (80 ng) or empty pEZY3 vector using Lipofectamine 3000. Twenty-four hours after transfection, cells were infected with Sendai virus at 4.0 × 10^6 CEID50/mL (VR-907, ATCC). RNA was harvested two days post-transfection. RNA-containing lysates from all wells in this plate were processed using the MERCURIUS DRUG-seq (BRB-seq) kit, pooled at the cDNA level, and prepared for sequencing on an Illumina NovaSeq platform. This library corresponds to a Sendai virus–stimulated plate (plate 7); individual well-level conditions (e.g. specific peptides or biological replicates) are detailed in the accompanying sample metadata table.


title: Batch2_Stimulated

description:
Library name: Sample 8
BRB-seq library generated from one 96-well plate of HEK293T cells cultured in DMEM + 10% FBS and seeded at 18,000 cells per well. Cells were transfected in quadruplicate with pEZY3-vTR plasmids (80 ng) or empty pEZY3 vector using Lipofectamine 3000. Twenty-four hours after transfection, cells were infected with Sendai virus at 4.0 × 10^6 CEID50/mL (VR-907, ATCC). RNA was harvested two days post-transfection. RNA-containing lysates from all wells in this plate were processed using the MERCURIUS DRUG-seq (BRB-seq) kit, pooled at the cDNA level, and prepared for sequencing on an Illumina NovaSeq platform. This library corresponds to a Sendai virus–stimulated plate (plate 8); individual well-level conditions (e.g. specific peptides or biological replicates) are detailed in the accompanying sample metadata table.


title: Batch6_Unstimulated

description:
Library name: Sample 6
BRB-seq library generated from one 96-well plate of HEK293T cells cultured in DMEM + 10% FBS and seeded at 18,000 cells per well. Cells were transfected in quadruplicate with pEZY3-vTR plasmids (80 ng) or empty pEZY3 vector using Lipofectamine 3000. Twenty-four hours after transfection, cells were left uninfected (unstimulated). Two days post-transfection, RNA-containing lysates from all wells in this plate were processed using the MERCURIUS DRUG-seq (BRB-seq) kit, pooled at the cDNA level, and prepared for sequencing on an Illumina NovaSeq platform. This library corresponds to an unstimulated plate (Sendai virus–free control, plate 6); individual well-level conditions (e.g. specific peptides or biological replicates) are detailed in the accompanying sample metadata table.

value: Mixture of HEK293T wells transfected with 84 distinct pEZY3-vTR constructs or control/empty vector; no Sendai virus infection (unstimulated)


title: Breast Benign Disease [Patient 094_SH08L31_Cell2]


title: Breast Benign Disease [Patient 092_SH09X63_Cell3]


title: Breast Benign Disease [Patient 093_SH06839_Cell3]


title: Batch4_Unstimulated

description:
Library name: Sample 4
BRB-seq library generated from one 96-well plate of HEK293T cells cultured in DMEM + 10% FBS and seeded at 18,000 cells per well. Cells were transfected in quadruplicate with pEZY3-vTR plasmids (80 ng) or empty pEZY3 vector using Lipofectamine 3000. Twenty-four hours after transfection, cells were left uninfected (unstimulated). Two days post-transfection, RNA-containing lysates from all wells in this plate were processed using the MERCURIUS DRUG-seq (BRB-seq) kit, pooled at the cDNA level, and prepared for sequencing on an Illumina NovaSeq platform. This library corresponds to an unstimulated plate (Sendai virus–free control, plate 4); individual well-level conditions (e.g. specific peptides or biological replicates) are detailed in the accompanying sample metadata table.


title: Batch3_Unstimulated

description:
Library name: Sample 3
BRB-seq library generated from one 96-well plate of HEK293T cells cultured in DMEM + 10% FBS and seeded at 18,000 cells per well. Cells were transfected in quadruplicate with pEZY3-vTR plasmids (80 ng) or empty pEZY3 vector using Lipofectamine 3000. Twenty-four hours after transfection, cells were left uninfected (unstimulated). Two days post-transfection, RNA-containing lysates from all wells in this plate were processed using the MERCURIUS DRUG-seq (BRB-seq) kit, pooled at the cDNA level, and prepared for sequencing on an Illumina NovaSeq platform. This library corresponds to an unstimulated plate (Sendai virus–free control, plate 3); individual well-level conditions (e.g. specific peptides or biological replicates) are detailed in the accompanying sample metadata table.


title: Batch5_Unstimulated

description:
Library name: Sample 5
BRB-seq library generated from one 96-well plate of HEK293T cells cultured in DMEM + 10% FBS and seeded at 18,000 cells per well. Cells were transfected in quadruplicate with pEZY3-vTR plasmids (80 ng) or empty pEZY3 vector using Lipofectamine 3000. Twenty-four hours after transfection, cells were left uninfected (unstimulated). Two days post-transfection, RNA-containing lysates from all wells in this plate were processed using the MERCURIUS DRUG-seq (BRB-seq) kit, pooled at the cDNA level, and prepared for sequencing on an Illumina NovaSeq platform. This library corresponds to an unstimulated plate (Sendai virus–free control, plate 5); individual well-level conditions (e.g. specific peptides or biological replicates) are detailed in the accompanying sample metadata table.


title: Breast Benign Disease [Patient 090_SH08L42_Cell1]

description: Total RNA extracted from 0.3 mL of serum was labeled with the 3D-Gene® Labeling kit (Toray Industries Inc.). Labeled miRNAs were hybridized onto 3D-Gene® miRNA Oligo Chips at 42 °C for 17 hours.


title: Breast Benign Disease [Patient 089_SH11M29_Cell4]


title: Breast Benign Disease [Patient 091_SH11M30_Cell1]


title: Batch4_Stimulated

description:
Library name: Sample 10
BRB-seq library generated from one 96-well plate of HEK293T cells cultured in DMEM + 10% FBS and seeded at 18,000 cells per well. Cells were transfected in quadruplicate with pEZY3-vTR plasmids (80 ng) or empty pEZY3 vector using Lipofectamine 3000. Twenty-four hours after transfection, cells were infected with Sendai virus at 4.0 × 10^6 CEID50/mL (VR-907, ATCC). RNA was harvested two days post-transfection. RNA-containing lysates from all wells in this plate were processed using the MERCURIUS DRUG-seq (BRB-seq) kit, pooled at the cDNA level, and prepared for sequencing on an Illumina NovaSeq platform. This library corresponds to a Sendai virus–stimulated plate (plate 10); individual well-level conditions (e.g. specific peptides or biological replicates) are detailed in the accompanying sample metadata table.


title: Batch1_Unstimulated

description:
Library name: Sample 1
BRB-seq library generated from one 96-well plate of HEK293T cells cultured in DMEM + 10% FBS and seeded at 18,000 cells per well. Cells were transfected in quadruplicate with pEZY3-vTR plasmids (80 ng) or empty pEZY3 vector using Lipofectamine 3000. Twenty-four hours after transfection, cells were left uninfected (unstimulated). Two days post-transfection, RNA-containing lysates from all wells in this plate were processed using the MERCURIUS DRUG-seq (BRB-seq) kit, pooled at the cDNA level, and prepared for sequencing on an Illumina NovaSeq platform. This library corresponds to an unstimulated plate (Sendai virus–free control, plate 1); individual well-level conditions (e.g. specific peptides or biological replicates) are detailed in the accompanying sample metadata table.


title: Breast Benign Disease [Patient 088_SH0ZE12_Cell4]


title: Batch2_Unstimulated

description:
Library name: Sample 2
BRB-seq library generated from one 96-well plate of HEK293T cells cultured in DMEM + 10% FBS and seeded at 18,000 cells per well. Cells were transfected in quadruplicate with pEZY3-vTR plasmids (80 ng) or empty pEZY3 vector using Lipofectamine 3000. Twenty-four hours after transfection, cells were left uninfected (unstimulated). Two days post-transfection, RNA-containing lysates from all wells in this plate were processed using the MERCURIUS DRUG-seq (BRB-seq) kit, pooled at the cDNA level, and prepared for sequencing on an Illumina NovaSeq platform. This library corresponds to an unstimulated plate (Sendai virus–free control, plate 2); individual well-level conditions (e.g. specific peptides or biological replicates) are detailed in the accompanying sample metadata table.


title: Breast Benign Disease [Patient 087_SH11R17_Cell3]


title: replicate 1 of CTRL CK13 CUT&Tag in HCT116

city: Changsha

first: Kewei

last: Zheng

address: Lushan Road

department: School of Biomedical Sciences

institute: Hunan University

description: Library name: HCT116_CK13_CTRL_R1

library_source: genomic

data_processing:
The clean paired-end sequencing data were analyzed using the human genome (version hg38) as a reference. Reads were aligned with bowtie2 using --fast-local. Normalized (RPGC) coverage tracks were generated by deepTools bamCoverage using parameters --binSize 50 --normalize --extendReads --ignoreDuplicates.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: colon cancer tissue

growth_protocol: HeLa and HCT116 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. HCT116 cells were treated or untreated with 10 µM ZnTTAPc.

extract_protocol:
The G4-CUT&Tag method was constructed following the described protocol (Zheng et al., 2024) with some modifications. A total of 10^5 cells were washed twice with 100 µL wash buffer (20 mM HEPES–KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors). Next, 10 µL of pre-activated concanavalin A coated magnetic beads were added to the cells in 100 µL wash buffer and incubated on a rotator for 10 min at room temperature. The supernatant was removed, and the bead-bound cells were resuspended in 100 µL of dig-wash buffer (0.05% digitonin, 0.1% BSA, 20 mM HEPES–KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 2 mM EDTA, 1× protease inhibitors) containing 250 nM of G4P, 200 nM of CK13, 2 µL of anti-NCL antibody (ab70493, Abcam), or 1 µL of anti-Top1 antibody (ab109374, Abcam), respectively. After 2 hours rotation at room temperature, the cells incubated with G4P or CK13 were washed twice with 100 µL of dig-wash buffer and resuspended with 100 µL of dig-wash buffer containing 2 µL of anti-FLAG M2 antibody (Sigma-Aldrich), or 2 µL of anti-V5 tag antibody (ab15828, Abcam), incubated for another 1 hour at room temperature. The buffer containing primary antibodies was then removed from the cells, and 100 µL of dig-wash buffer containing 1 µL of Goat anti-mouse IgG (AP124, Sigma-Aldrich) or 1 µL of Goat anti-rabbit IgG (AP132, Sigma-Aldrich) was mixed with the cells and incubated for 1 hour at room temperature. After washing three times with dig-wash buffer, a 1:100 dilution of pAG-Tn5 adapter complex (~0.2 µM) was prepared in 100 µL of dig-wash buffer and added to the cells, which were then rotated for 1 hour at room temperature. After five washes with dig-wash buffer, the bead-bound cells were resuspended with 50 µL of tagmentation buffer (20 mM HEPES–KOH (pH 7.5), 150 mM KCl, 10 mM MgCl2, 0.5 mM spermidine, 1× protease inhibitors) and incubated at 37 ℃ for 1 hour. To terminate the tagmentation reaction, 2.5 µL of 0.5 M EDTA and 1 µL of 20 mg/mL proteinase K were added and incubated at 55 ℃ for 30 min. The DNA was then extracted using 120 µL of Ampure XP beads (Beckman Counter) for library preparation. DNA was eluted in 40 µL of 5 mM Tris−HCl (pH 8.0).
To amplify the libraries, 16 µL of DNA was mixed with a uniquely barcoded i5 and a uniquely barcoded i7 primer and amplified using Q5 high-fidelity 2 × master mix (New England Biolabs). The PCR cycles for G4P and CK13 groups were 16 to 18, and those for Top1, NCL, and IgG groups were 15, 17, and 22, respectively. The libraries were purified with 1.3 × volume of Ampure XP beads and eluted in 20 µL of 10 mM Tris−HCl (pH 8.0).

value: colon cancer tissue

value: untreated


title: Breast Benign Disease [Patient 086_SH11M30_Cell4]


title: Breast Benign Disease [Patient 085_SH08L16_Cell4]


title: replicate 1 of ZnTTAPc G4P CUT&Tag in HCT116

description: Library name: HCT116_G4P_ZnTTAPc_R1

value: 10 uM ZnTTAPc


title: replicate 2 of CTRL CK13 CUT&Tag in HCT116

description: Library name: HCT116_CK13_CTRL_R2


title: Breast Benign Disease [Patient 080_SH08L14_Cell3]


title: replicate 1 of ZnTTAPc CK13 CUT&Tag in HCT116

description: Library name: HCT116_CK13_ZnTTAPc_R1


title: replicate 2 of ZnTTAPc CK13 CUT&Tag in HCT116

description: Library name: HCT116_CK13_ZnTTAPc_R2


title: replicate 2 of ZnTTAPc G4P CUT&Tag in HCT116

description: Library name: HCT116_G4P_ZnTTAPc_R2


title: K3_3d

city: Xi'an

first: Lijun

last: Yang

state: Shaanxi

address: 127 Changle West Road

institute: Department of Urology, Xijing Hospital, Air Force Medical University,

description:
Library name: K3_3d
cellranger output matrix

library_source: transcriptomic single cell

data_processing:
Cell Ranger (v7.1.0, 10x Genomics) was used to align raw FASTQ files to the rat reference genome mRn7 (GCA_015227675.2). Seurat (v5.0.3) was employed for quality control, data preprocessing, and dimensionality reduction. Specimens at each time point (0, 1, 3, 7 days) were derived from transplanted kidneys of 3 rats per group. After obtaining the gene-cell matrices from transplanted and control groups, all matrices were merged. To filter low-quality cells, we applied the following criteria: Cells with >500 genes detected and <5,000 genes; Cells with mitochondrial gene percentage <5%; Genes detected in ≥5 cells with ≥1 feature count.
Assembly: mRatBN7.2
Supplementary files format and content: cellranger output matrix in h5 file

organism: Rattus norvegicus

source_name: kidney

extract_protocol:
kidneys were perfused via the abdominal aorta with ice-cold phosphate-buffered saline (PBS) for blood clearance. The three kidneys per group were pooled, minced into 1–2 mm³ fragments, and digested in collagenase (17018029/17104019, eBioscience™) at 37°C for 45 min. The digestate was filtered through a 40-μm cell strainer. Erythrocytes were lysed using 1 ml ice-cold RBC Lysis Buffer (C3702, Beyotime) for 5 min, followed by PBS washing to obtain a single-cell suspension. The prepared single-cell suspension was counted and examined by microscopy. Cells were incubated with anti-CD45-APC antibody (17-0461-82, eBioscience™) at 4°C for 30 min. During the last 5 min of incubation, DAPI (1:1000 dilution, 62248, eBioscience™) was added and mixed. After incubation, cells were washed once with RPMI-1640 medium (12633020, eBioscience™) via centrifugation (300 × g, 5 min), resuspended, and filtered through a 40-μm cell strainer. The final suspension was transferred to flow cytometry tubes and kept protected from light on ice. Pre-prepared collection tubes containing RPMI-1640 with 10% FBS were loaded into the sorting chamber for CD45⁺ cell sorting. After sorting, the fluidics system was flushed with sterile ultrapure water. A subset of sorted cells was re-analyzed for quality control, and flow cytometry data were recorded. The target cell suspension was transferred from flow tubes to 15-mL centrifuge tubes, pelleted by centrifugation, counted, examined microscopically, and processed for single-cell library preparation.
The cell suspension was loaded into Chromium microfluidic chips with 3’ (v2 or v3, depends on project) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina according to the manufacturer’s instructions (Illumina).

value: kidney

tag: donor strain

value: Wistar

tag: recipient strain

value: SD

tag: time point

value: 3 days post - transplantation

value: CD45+ immune cells


title: Breast Benign Disease [Patient 079_SH11R10_Cell1]

value: female


title: Breast Benign Disease [Patient 084_SH11R01_Cell3]


title: K3_7d

description:
Library name: K3_7d
cellranger output matrix

value: 7 days post - transplantation


title: Breast Benign Disease [Patient 082_SH11R02_Cell3]


title: replicate 1 of CK13 CUT&Tag in HEK293T

description: Library name: HEK293T_CK13_R1

source_name: human embryonic kidney

value: human embryonic kidney


title: replicate 2 of CK13 CUT&Tag in HEK293T

description: Library name: HEK293T_CK13_R2


title: NC_0d

description:
Library name: NC_0d
cellranger output matrix

value: NC; Untransplanted


title: Breast Benign Disease [Patient 081_SH06Y26_Cell2]


title: Breast Benign Disease [Patient 083_SH08L37_Cell2]


title: SP9

city: Orange

first: Patricia

middle: C

last: Lopes

address: 450 N Center St

department: Biological Sciences

institute: Chapman University

data_processing:
Base calls performed using Illumina Casava 1.8
Data filtering: reads containing adapters, reads containing N > 10% and low quality reads were filtered out
Mapping was done using HISAT2
HTSeq (v0.6.1) was used to count numbers of mapped reads.
Assembly: GCF_007115625.1_cibio_Scana_2019_genomic
Supplementary files format and content: tab-delimited text file includes raw (not normalized) readcount values for each sample

organism: Serinus canaria

source_name: spleen

extract_protocol:
Total RNA was isolated using the Zymo Quick-RNA kit following manufacturer’s instructions, including proteinase K digestion for 30 min and DNase I in-column treatment step.
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit, following standard protocols

value: spleen

value: MG


title: SP8


title: K3_1d

description:
Library name: K3_1d
cellranger output matrix

value: 1 day post - transplantation


title: Breast Benign Disease [Patient 075_SH09X49_Cell2]

value: Training


title: SP7


title: SP6

value: CONT


title: 2H6-neu-only

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

description: Library name: RS-04547499

data_processing:
Basecalls performed using bcl2fastq2 version 2.20
Sequenced reads were mapped to GRCh38 reference GENCODE (p13) annotation (r38) using STAR (v2.7.9a)
Reads counts are obtained using featureCounts from SubRead (v1.6.4) using –fracOverlap 0.95 parameter.
Assembly: GRCh38.p13 GENCODE r38
Supplementary files format and content: Raw counts. Comma-separated file.Includes GENCODE gene ids and gene symbols.

source_name: human bone marrow

growth_protocol: Human bone marrow neutrophils were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin-streptomycin

extract_protocol:
Total RNA (100 ng) was used to prepare sequencing libraries with the RNA HyperPrep Kit with RiboErase (HMR) (Roche Sequencing Solutions), following the manufacturer’s protocol.
Ribosomal RNA (rRNA) was first depleted, and the remaining RNA was treated with DNase to remove genomic DNA contamination. The RNA was then purified, fragmented, and primed for complementary DNA (cDNA) synthesis.First-strand cDNA synthesis was performed using random primers, followed by second-strand synthesis, during which dUTP was incorporated in place of dTTP to enable strand-specificity. The resulting double-stranded (ds) cDNA was purified using Pure Beads (KAPA Biosystems). To facilitate adapter ligation, an adenine (A) overhang was added to the 3’ ends of the blunt fragments, and indexing adapters with a complementary thymine (T) overhang were ligated. Adapter-ligated libraries were amplified by PCR, purified using Pure Beads, and assessed for fragment size distribution using the Agilent 4200 TapeStation D1000 ScreenTape (Agilent Technologies).Library quantification was performed using the KAPA qPCR kit (KAPA Biosystems), and libraries were pooled equimolarly based on the experimental design. The pooled libraries were denatured, diluted to 350 pM, and spiked with 1% PhiX control. Sequencing was conducted on an Illumina NovaSeq 6000 system using 100 bp paired-end reads, following the manufacturer’s protocol. On average, 50 million paired-end reads were generated per sample.

treatment_protocol: human bone marrow neutrophils were incubated for 6 hours in either control media (RPMI-1640 supplemented with 10% FBS and 100 U/mL penicillin-streptomycin), conditioned media, or control media supplemented with recombinant human IL-36γ/IL-1F9 protein.

value: human bone marrow

value: neutrophil

value: Untreated neutrophil


title: 3H6-neu-only

description: Library name: RS-04547500


title: Breast Benign Disease [Patient 076_SH08L16_Cell2]


title: SP5


title: 1H6-neu-only

description: Library name: RS-04547498


title: Breast Benign Disease [Patient 078_SH06Y37_Cell3]


title: Breast Benign Disease [Patient 074_SH11R16_Cell4]


title: SP4


title: SP2


title: SP3


title: Breast Benign Disease [Patient 077_SH06909_Cell3]


title: LIV9

source_name: liver

value: liver


title: Breast Benign Disease [Patient 073_SH06Y34_Cell4]


title: LIV8


title: LIV6


title: SP1


title: 2H6-unarm

description: Library name: RS-04547496

value: Unarmored CAR T


title: LIV7


title: Breast Benign Disease [Patient 072_SH09X63_Cell1]


title: LIV4


title: 1H6-unarm

description: Library name: RS-04547495


title: 3H6-unarm

description: Library name: RS-04547497


title: LIV5


title: 3H6-18

description: Library name: RS-04547494

value: IL-18 armored CAR T


title: Breast Benign Disease [Patient 071_SH06849_Cell1]


title: LIV3


title: LIV2


title: 1H6-18

description: Library name: RS-04547492


title: LIV1


title: 3H6-pro

description: Library name: RS-04547491

value: recombinant human IL-36γ protein


title: Breast Benign Disease [Patient 070_SH11R06_Cell1]


title: Siysl1-spikelet-biol rep 3

city: Wuhan

first: Shuo

last: Zhang

address: No. 3, Nanhu Avenue

institute: Food Crops Institute, Hubei Academy of Agricultural Sciences

description: Library name: Sample6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Assembly: Setaria_italica.JGI_v2.2

organism: Setaria italica

source_name: spikelet

growth_protocol: The materials are grown in a greenhouse with a 14-hour photoperiod at 30 °C.

extract_protocol:
The total RNA was extracted using the RNAprep Pure Plant Kit (Tiangen, Beijing, China ) in accordance with the instructions provided by the manufacturer. RNA concentration and purity were measured using a NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE). To assess the integrity of the RNA, an RNA Nano 6000 Assay Kit on the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) was used.
The Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina [Yeasen Biotechnology (Shanghai) Co., Ltd.] was used to generate the sequencing libraries in accordance with the manufacturer’s recommendations, and index codes were added to associate the sequences with each sample.

value: spikelet

value: SiYSL3 mutant


title: Siysl1-spikelet-biol rep 2

description: Library name: Sample5

value: SiYSL2 mutant


title: 2H6-18

description: Library name: RS-04547493


title: Breast Benign Disease [Patient 067_SH11M33_Cell4]

value: female


title: Siysl1-spikelet-biol rep 1

description: Library name: Sample4

value: SiYSL1 mutant


title: Yugu1-spikelet-biol rep 3

description: Library name: Sample3

value: WT


title: 2H6-pro

description: Library name: RS-04547490


title: 1H6-pro

description: Library name: RS-04547489


title: Breast Benign Disease [Patient 066_SH0ZE26_Cell1]


title: Breast Benign Disease [Patient 069_SH06839_Cell2]


title: Breast Benign Disease [Patient 065_SH06Y31_Cell4]


title: Yugu1-spikelet-biol rep 2

description: Library name: Sample2


title: Yugu1-spikelet-biol rep 1

description: Library name: Sample1


title: 3H6-36

description: Library name: RS-04547488

value: IL-36γ armored CAR T


title: 2_2_LM_DN

city: Freiburg

first: Maximilian

last: Fliegauf

address: Breisacherstraße 113

department: Institute for Neuropathology

country: Germany

institute: Uniklinikum Freiburg

description:
Library name: GEX2_2
Multiplexed samples from 12 mice CMO 1-12
2_2_LM_DN_raw_feature_bc_matrix.h5
1_2_LM_FB-IM_feature_reference.csv

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.10.30. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.
scRNA-seq data was aligned with Cellranger v7.1.0 to the mouse reference genome Gencode GRCm39.
Assembly: GRCm39
Supplementary files format and content: counts matrix files (h5 format)
Supplementary files format and content: reference.csv for CMOs

organism: Mus musculus

source_name: Leptomeninges

growth_protocol: SPF breeding facility

extract_protocol:
Samples were labeled with CMO1-12 and these samples were pooled for each tissue. Cells were FAC-sorted into 1.5 ml collection tubes containing 25 µl Sort Buffer (FACS Buffer supplemented with 1:200 RNAase inhibitor, New England Biolabs, M0314).
Up to 20,000 sorted cells per reaction were loaded on a Chromium controller (10x Genomics). Complementary DNA amplification and library preparation were performed according to the user guide for the Chromium Next GEM Single Cell 3′Reagent kits v.3.1 (CG000388 RevC). The libraries were sequenced on a NextSeq 1000/2000 machine (Illumina) with a sequencing depth appropriate to reach 20,000 reads per cell.

treatment_protocol: Mice were treated  for seven consectutive days with either Vehicle solution (CTL) or BLZ945. Cells were harvested 5d or  8 weeks after the end of the treatment on the same day from mice with the same age. 2 males and 2 females in both conditions.

value: Leptomeninges

value: living cells

value: remaining live cells

value: mRNA


title: 3_2_CTX_FB-IM

description:
Library name: GEX3_2
Multiplexed samples from 12 mice CMO 1-12
3_2_CTX_FB-IM_raw_feature_bc_matrix.h5
1_2_LM_FB-IM_feature_reference.csv

source_name: Cerebral cortex

value: Cerebral cortex

value: fibroblasts and immune cells

value: PDPN+ and CD45+CD11b+


title: Breast Benign Disease [Patient 064_SH06837_Cell4]

value: Training


title: 4_2_CTX_DN

description:
Library name: GEX4_2
Multiplexed samples from 12 mice CMO 1-12
4_2_CTX_DN_raw_feature_bc_matrix.h5
1_2_LM_FB-IM_feature_reference.csv


title: Breast Benign Disease [Patient 068_SH08L40_Cell2]


title: 1H6-36

description: Library name: RS-04547486

value: human bone marrow

value: neutrophil


title: 2_2_CMO_LM_DN

description:
Library name: CMO2_2
Multiplexed samples from 12 mice CMO 1-12
2_2_LM_DN_raw_feature_bc_matrix.h5
1_2_LM_FB-IM_feature_reference.csv

library_source: other

molecule: other

value: CMO


title: 3_2_CMO_CTX_FB-IM

description:
Library name: CMO3_2
Multiplexed samples from 12 mice CMO 1-12
3_2_CTX_FB-IM_raw_feature_bc_matrix.h5
1_2_LM_FB-IM_feature_reference.csv


title: CEP290_TTX3

city: Nijmegen

first: Sofia

last: Puvogel

address: Geert Grooteplein Zuid 10

country: Netherlands

institute: RadboudUMC

description: Library name: 106154-001-018

data_processing:
Quality Control: Fastp was used to eliminate PolyG artifacts and clip adapters, including a list of adapter sequences currently used by Illumina.
Human Reads Filtering: Human reads were separated from rat reads using Seal from BBTools, by aligning them to their respective reference genomes (Rnor_6.0 for rat and GRCh38 for human), with the ambig=first setting applied to resolve ambiguous mappings
Read Alignment: Reads were mapped to the GRCh38 human reference genome using HISAT2. The library was reversely stranded, and the parameter --rna-strandness = RF was used. Resulting SAM files were sorted and indexed using SAMtools.
UMI Deduplication: Deduplication was performed with UMI-tools to account for unique molecular identifiers.
Assembly: GRCh38
Supplementary files format and content: Processed data are provided as a .txt count matrix generated through feature counting.

source_name: iPSC-neuron

extract_protocol:
Total RNA was extracted using the Quick-RNA Microprep Kit (Zymo Research, #ZY-R1051), following the manufacturer's protocol.
cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit. Sequencing was performed using paired-end reads on an Illumina NovaSeq 6000 platform at GenomeScan B.V., Leiden.

value: iPSC-neuron

value: TTX

value: A


title: 1_2_CMO_LM_FB-IM

description:
Library name: CMO1_2
Multiplexed samples from 12 mice CMO 1-12
1_2_LM_FB-IM_raw_feature_bc_matrix.h5
1_2_LM_FB-IM_feature_reference.csv


title: 8_LM_EC-IM

description:
Library name: GEX8
Multiplexed samples from 12 mice CMO 1-12
8_LM_EC-IM_raw_feature_bc_matrix.h5
1_Dura_FB-DN_feature_reference.csv

value: endothelial and immune cells

value: CD31+ and CD45+CD11b+


title: Breast Benign Disease [Patient 062_SH06F30_Cell2]

value: female


title: CEP290_TTX2

description: Library name: 106154-001-017


title: Breast Benign Disease [Patient 061_SH11M33_Cell1]


title: 1_2_LM_FB-IM

description:
Library name: GEX1_2
Multiplexed samples from 12 mice CMO 1-12
1_2_LM_FB-IM_raw_feature_bc_matrix.h5
1_2_LM_FB-IM_feature_reference.csv

value: Leptomeninges


title: 2H6-36

description: Library name: RS-04547487

value: IL-36γ armored CAR T


title: Breast Benign Disease [Patient 063_SH11R16_Cell3]


title: 7_LM_FB-DN

description:
Library name: GEX7
Multiplexed samples from 12 mice CMO 1-12
7_LM_FB-DN_raw_feature_bc_matrix.h5
1_Dura_FB-DN_feature_reference.csv

value: fibroblasts and living cells

value: PDPN+ and remaining living cells


title: 2_Dura_EC-IM

description:
Library name: GEX2
Multiplexed samples from 12 mice CMO 1-12
2_Dura_EC-IM_raw_feature_bc_matrix.h5
1_Dura_FB-DN_feature_reference.csv

source_name: Dura mater

value: Dura mater

value: mRNA


title: CEP290_TTX1

description: Library name: 106154-001-016


title: 6_CTX_EC-IM

description:
Library name: GEX6
Multiplexed samples from 12 mice CMO 1-12
6_CTX_EC-IM_raw_feature_bc_matrix.h5
1_Dura_FB-DN_feature_reference.csv

value: Cerebral cortex


title: 5_CTX_FB-DN

description:
Library name: GEX5
Multiplexed samples from 12 mice CMO 1-12
5_CTX_FB-DN_raw_feature_bc_matrix.h5
1_Dura_FB-DN_feature_reference.csv


title: CEP290_veh3

description: Library name: 106154-001-015

value: ddH2O (veh)


title: Breast Benign Disease [Patient 059_SH0ZE18_Cell2]

description: Total RNA extracted from 0.3 mL of serum was labeled with the 3D-Gene® Labeling kit (Toray Industries Inc.). Labeled miRNAs were hybridized onto 3D-Gene® miRNA Oligo Chips at 42 °C for 17 hours.

value: Training


title: 4_2_CMO_CTX_DN

description:
Library name: CMO4_2
Multiplexed samples from 12 mice CMO 1-12
4_2_CTX_DN_raw_feature_bc_matrix.h5
1_2_LM_FB-IM_feature_reference.csv

value: living cells

value: remaining live cells


title: CEP290_veh2

description: Library name: 106154-001-014

value: iPSC-neuron


title: 1_Dura_FB-DN

description:
Library name: GEX1
Multiplexed samples from 12 mice CMO 1-12
1_Dura_FB-DN_raw_feature_bc_matrix.h5
1_Dura_FB-DN_feature_reference.csv


title: 8_CMO_LM_EC-IM

description:
Library name: CMO8
Multiplexed samples from 12 mice CMO 1-12
8_LM_EC-IM_raw_feature_bc_matrix.h5
1_Dura_FB-DN_feature_reference.csv

value: CMO


title: Breast Benign Disease [Patient 060_SH0ZE10_Cell2]


title: 7_CMO_LM_FB-DN

description:
Library name: CMO7
Multiplexed samples from 12 mice CMO 1-12
7_LM_FB-DN_raw_feature_bc_matrix.h5
1_Dura_FB-DN_feature_reference.csv


title: CEP290_veh1

description: Library name: 106154-001-013

value: A


title: Breast Benign Disease [Patient 058_SH09X51_Cell2]


title: 6_CMO_CTX_EC-IM

description:
Library name: CMO6
Multiplexed samples from 12 mice CMO 1-12
6_CTX_EC-IM_raw_feature_bc_matrix.h5
1_Dura_FB-DN_feature_reference.csv

value: endothelial and immune cells


title: 2_CMO_Dura_EC-IM

description:
Library name: CMO2
Multiplexed samples from 12 mice CMO 1-12
2_Dura_EC-IM_raw_feature_bc_matrix.h5
1_Dura_FB-DN_feature_reference.csv

value: CD31+ and CD45+CD11b+


title: 1_CMO_Dura_FB-DN

description:
Library name: CMO1
Multiplexed samples from 12 mice CMO 1-12
1_Dura_FB-DN_raw_feature_bc_matrix.h5
1_Dura_FB-DN_feature_reference.csv


title: Breast Benign Disease [Patient 056_SH06Y51_Cell2]

value: female


title: NPHP1_TTX3

description: Library name: 106154-001-012

value: NPHP1-/- -iPSC-neuron

value: TTX


title: NPHP1_TTX2

description: Library name: 106154-001-011


title: Breast Benign Disease [Patient 055_SH08L42_Cell4]


title: CamBLZ_tdT+

description:
Library name: Sample_25L008891
Subdural macrophages

library_source: genomic single cell

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.10.30. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.
Raw reads were processed using Cell Ranger ATAC v2.2.0 with alignment to the mm10 genome and generation of single-cell accessibility matrices.
Assembly: mm10
Supplementary files format and content: peaks matrix files (h5 format).
Supplementary files format and content: fragments files (tsv.gz)
Supplementary files format and content: fragments indeces (tsv.gz.tbi)
Supplementary files format and content: peak infos in singlecell.csv

source_name: Brain devoid of CP

extract_protocol:
Cells were sorted into 1.5 ml collection tubes containing 25 µl Sort Buffer (FACS Buffer with 2% BSA).
Nuclei were isolated following the 10x Genomics demonstrated protocol (CG000366, Rev A) with minor adaptations. Briefly, sorted cells were lysed in diluted lysis buffer for 3 min on ice, quenched with wash buffer, centrifuged, resuspended, and filtered through a 10-µm strainer. Nuclei integrity was assessed by DAPI staining and nuclei were counted using Trypan Blue on a Countess automated cell counter. Single-cell encapsulation and library preparation were performed using Chromium Next GEM Single Cell ATAC Reagent Kits v2. Library quality was assessed by Qubit and Bioanalyzer prior to sequencing. Raw reads were processed using Cell Ranger ATAC v2.2.0 with alignment to the mm10 genome and generation of single-cell accessibility matrices.

treatment_protocol: Mice were injected with Tamoxifen and treated four weeks later, either treated for seven consectutive days with either Vehicle solution (CTL) or BLZ945. Cells were harvested 8 weeks after the end of the treatment.

value: Brain devoid of CP

value: Mrc1CreERT2 R26tdT

value: CD45intCD11b+CD206+ tdT+

value: 8 weeks after the end of the treatment


title: 5_CMO_CTX_FB-DN

description:
Library name: CMO5
Multiplexed samples from 12 mice CMO 1-12
5_CTX_FB-DN_raw_feature_bc_matrix.h5
1_Dura_FB-DN_feature_reference.csv

value: Cerebral cortex

value: fibroblasts and living cells

value: PDPN+ and remaining living cells


title: Breast Benign Disease [Patient 057_SH06Y34_Cell1]

value: Training


title: CamV_tdT+

description:
Library name: Sample_25L008889
Subdural macrophages

value: CTL


title: NPHP1_TTX1

description: Library name: 106154-001-010

value: iPSC-neuron


title: CamBLZ_tdT-

description:
Library name: Sample_25L008890
Subdural macrophages

value: CD45intCD11b+CD206+ tdT-


title: NPHP1_veh3

description: Library name: 106154-001-009

value: ddH2O (veh)

value: A


title: DuraBLZ_tdT+

description:
Library name: Sample_25L008888
Dural macrophages

value: Dura mater

value: CD45intCD11b+CD206int-hi tdT+


title: Breast Benign Disease [Patient 053_SH05T45_Cell4]

value: female


title: Breast Benign Disease [Patient 054_SH11M31_Cell4]


title: DuraBLZ_tdT-

description:
Library name: Sample_25L008887
Dural macrophages

value: CD45intCD11b+CD206int-hi tdT-


title: NPHP1_veh2

description: Library name: 106154-001-008

value: NPHP1-/- -iPSC-neuron


title: BLZ_F1_F2_CML

description:
Library name: 4-CML
CMOs: F1 = 311; F2 = 312

data_processing:
Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.10.30. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.
scRNA-seq data was aligned with Cellranger v7.1.0 to the mouse reference genome Gencode GRCm39. The full length tdTomato mRNA was added as a chromosome to Cellranger.
Assembly: GRCm39
Supplementary files format and content: counts matrix files (h5 format).

source_name: Brain devoid of choroid plexuses

extract_protocol:
Cells were sorted into 1.5 ml collection tubes containing 25 µl Sort Buffer (FACS Buffer supplemented with 1:200 RNAase inhibitor, New England Biolabs, M0314).
Up to 20,000 sorted cells per reaction were loaded on a Chromium controller (10x Genomics). Complementary DNA amplification and library preparation were performed according to the user guide for the Chromium Next GEM Single Cell 3′Reagent kits v.3.1 (CG000388 RevC). The libraries were sequenced on a NextSeq 1000/2000 machine (Illumina) with a sequencing depth appropriate to reach 20,000 reads per cell.

treatment_protocol: Mice were injected with Tamoxifen and treated four weeks later either treated for seven consectutive days with either Vehicle solution (CTL) or BLZ945. Cells were harvested 8 weeks after the end of the treatment.

value: Brain devoid of choroid plexuses

value: CD45int-hi CD11b+ cells


title: MgBLZ_MonoBLZ

description:
Library name: Sample_25L008885
Microglia+Monocytes

source_name: Brain devoid of CP + Blood Monocytes

value: Brain devoid of CP + Blood Monocytes

value: Mrc1CreERT2 R26tdT

value: CD45intCD11b+CD206- and CD115+Ly6Chi cells

value: 8 weeks after the end of the treatment


title: Breast Benign Disease [Patient 050_SH08L20_Cell4]

source_name: serum

value: Training


title: Breast Benign Disease [Patient 051_SH11M29_Cell1]


title: BLZ_M1_M2_CML

description:
Library name: 3-CML
CMOs: M1 = 308; M2 = 309

value: CTL


title: Breast Benign Disease [Patient 052_SH05T56_Cell3]

description: Total RNA extracted from 0.3 mL of serum was labeled with the 3D-Gene® Labeling kit (Toray Industries Inc.). Labeled miRNAs were hybridized onto 3D-Gene® miRNA Oligo Chips at 42 °C for 17 hours.


title: CTL_M1_M2_CML

description:
Library name: 2-CML
CMOs: M1 = 306; M2 = 307


title: NPHP1_veh1

description: Library name: 106154-001-007

value: iPSC-neuron


title: Breast Benign Disease [Patient 049_SH06Y31_Cell1]


title: CTL_F1_F2_CML

description:
Library name: 1-CML
CMOs: F1 = 305; F2 = 310


title: BLZ_F1_F2_GEX

description:
Library name: 4-GEL
CMOs: F1 = 311; F2 = 312


title: DuraV_tdT+

description:
Library name: Sample_25L008886
Dural macrophages


title: WTC_TTX3

description: Library name: 106154-001-006

value: WT-iPSC-neuron

value: WT

value: TTX


title: Breast Benign Disease [Patient 048_SH09X49_Cell4]


title: MgV_MonoV

description:
Library name: Sample_25L008884
Microglia+Monocytes


title: CTL_M1_M2_GEX

description:
Library name: 2-GEL
CMOs: M1 = 306; M2 = 307


title: Dura, infected, replicates 1-5

first: Vitka

last: Gres

address: Breisacherstraße 115b

department: Institute for Infection Prevention and Control

institute: University of Freiburg

data_processing:
Fastq files were aligned using the CellRanger version 7.1. as well as demultiplexing and barcode processing.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Dura mater was peeled using forceps from calvaria and placed into a digestion solution (2.5 mg/ml collagenase IV in RPMI) and incubated for 20 min at 37°C shaking, after which the solution was filtered through 70 µm strainer (BD) and washed with FACS buffer.
Sorted samples were processed using the 10X Chromium Next GEM Single Cell 3’ Kit v3.1 (PN-1000269) and 3´ Feature Barcode Kit (PN-1000262). Single cell droplets were generated using Chromium Next GEM Chip G Single Cell Kit (PN-1000127) and Chromium Controller for 3’ gene expression and cell multiplexing libraries were generated according to the manufacturer’s specifications. Library quality was assessed using Agilent TapeStation 4150 Cell-free DNA ScreenTape assay (cat. no. 5067-5630) and NEBNext Library Quant Kit for Illumina (cat. no. E7630S).

treatment_protocol: A total of 50 µl (5 x 107 CFU) suspension of GBS or vehicle (PBS) was injected into the retro-orbital venous plexus. Mice were sacrificed 2 days post infection.

value: Dura mater

value: 8 weeks

value: 2 dpi

value: Wt

value: GBS


title: BLZ_M1_M2_GEX

description:
Library name: 3-GEL
CMOs: M1 = 308; M2 = 309

value: Brain devoid of choroid plexuses


title: WTC_TTX1

description: Library name: 106154-001-004

value: A


title: WTC_veh3

description: Library name: 106154-001-003

value: ddH2O (veh)


title: Dura, control, replicates 1-6

value: PBS


title: leg muscle, NT, rep3

city: Los Angeles

first: Jun

last: Chen

address: 420 Westwood Plaza 5121 Engineering V

department: Bioengineering

institute: University of California, Los Angeles

description:
Library name: LegmuscleNT3
Bulk RNA-seq from leg muscle; NT; biological replicate 3

data_processing:
Paired-end FASTQ files were aligned with STAR; gene-level counts were generated.
Counts were normalized and differential expression was performed with DESeq2 (MFIT vs NT within tissue/timepoint as applicable).
GO biological process enrichment / GSEA was performed to assess immune/inflammatory/fibrotic responses.
Assembly: GRCr8
Supplementary files format and content: Processed files include a tab-delimited gene count matrix (genes × samples)

source_name: leg muscle

extract_protocol:
Bulk RNA was extracted and purified from rat tissue using Direct-zol™ RNA Miniprep Kit (R2053, Zymo Research) following the manufacturer’s protocol. RNA was stored at −80°C prior to library preparation.
Total RNA from each sample was submitted to a commercial sequencing service for bulk RNA-seq library preparation and paired-end sequencing.

value: leg muscle

value: WT (Long-Evans)

value: NT


title: WTC_veh2

description: Library name: 106154-001-002


title: WTC_TTX2

description: Library name: 106154-001-005


title: Breast Benign Disease [Patient 047_SH08L34_Cell4]

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

extract_protocol: RNA samples were extracted from serum using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

value: female

value: Training


title: leg muscle, NT, rep2

description:
Library name: LegmuscleNT2
Bulk RNA-seq from leg muscle; NT; biological replicate 2


title: Breast Benign Disease [Patient 046_SH08L25_Cell3]


title: Breast Benign Disease [Patient 045_SH05T44_Cell2]


title: WTC_veh1

description: Library name: 106154-001-001

value: iPSC-neuron

value: WT-iPSC-neuron

value: Days in vitro 28


title: Breast Benign Disease [Patient 044_SH0ZE14_Cell2]


title: CTL_F1_F2_GEX

description:
Library name: 1-GEL
CMOs: F1 = 305; F2 = 310

value: CD45int-hi CD11b+ cells

value: CTL


title: leg muscle, MFIT, rep3

description:
Library name: LegmuscleMFIT3
Bulk RNA-seq from leg muscle; MFIT; biological replicate 3

value: MFIT


title: leg muscle, MFIT, rep2

description:
Library name: LegmuscleMFIT2
Bulk RNA-seq from leg muscle; MFIT; biological replicate 2


title: leg muscle, NT, rep1

description:
Library name: LegmuscleNT1
Bulk RNA-seq from leg muscle; NT; biological replicate 1


title: back muscle, NT, rep3

description:
Library name: backmuscleNT3
Bulk RNA-seq from back muscle; NT; biological replicate 3

source_name: back muscle

value: back muscle


title: Breast Benign Disease [Patient 043_SH08L48_Cell1]


title: PAF49delta1/2IDR-GFP

city: Gosselies

first: Denis

middle: LJ

last: Lafontaine

state: Hainaut

address: Av Profs Jeneer & Brachet, 12

country: Belgium

institute: Universite libre de Bruxelles

description: Library name: DLRMS00197

data_processing:
RMS was performed exactly as described (Marchand et al., 2016) . For each reaction, 150 ng of total RNA was used. The samples were sequenced at the ULB-BRIGHTcore facility (Brussels Interuniversity Genomics High-Throughput Core) on Illumina Novaseq 6000 as paired-end runs (100-nt read length). On average, 25 million reads were sequenced. Adapter sequences were removed using Trimmomatic (0.36; leading:30 trailing:30 slidingwindow:4:15 minlen:17 avgqual:30) and reads in forward direction were mapped to an artificial genome containing ribosomal RNA sequences using bowtie2 (2.3.3.1; sensitive). Mapped reads were analyzed using the R package version 1.2.0 RNAmodR. RiboMethSeq (https://bioconductor.org/packages/release/bioc/html/RNAmodR.RiboMethSeq.html) and the Score C/RiboMethScore was used as a measurement for 2′-O methylation. For the analysis of methylation levels on positions known to be methylated, data from the snoRNAdb (Lestrade and Weber, 2006) were used and updated to revised rRNA sequence coordinates based on NCBI accession NR_046235.3, which are available from the EpiTxDb R package version 1.0.0 (http://www.bioconductor.org/packages/release/bioc/html/EpiTxDb.html).
Assembly: The rRNA reference sequence used are 18S: NR_003286.4; 5.8S: NR_003285.2; and 28S: NR_003287.4
Supplementary files format and content: The processed data used to generate the Fig 4J are in the file "Meznad_et_al_Fig4J.xlsx".

extract_protocol:
Total RNA was extracted using the TRI Reagent (Life Technologies) according to the manufacturer’s protocol.
RNA was hydrolyzed in bicarbonate buffer and the reaction was stopped by ethanol precipitation. The resulting fragments were then end-repaired and converted into an Illumina library using the NEB Next Small RNA Library Prepkit (Bioke, E7300S), according to the manufacturer’s protocol.


title: back muscle, NT, rep1

description:
Library name: backmuscleNT1
Bulk RNA-seq from back muscle; NT; biological replicate 1


title: PAF49deltaIDR-GFP

description: Library name: DLRMS00198


title: leg muscle, MFIT, rep1

description:
Library name: LegmuscleMFIT1
Bulk RNA-seq from leg muscle; MFIT; biological replicate 1


title: Breast Benign Disease [Patient 042_SH06Y56_Cell3]

description: Total RNA extracted from 0.3 mL of serum was labeled with the 3D-Gene® Labeling kit (Toray Industries Inc.). Labeled miRNAs were hybridized onto 3D-Gene® miRNA Oligo Chips at 42 °C for 17 hours.


title: PAF49-GFP

description: Library name: DLRMS00196


title: back muscle, NT, rep2

description:
Library name: backmuscleNT2
Bulk RNA-seq from back muscle; NT; biological replicate 2


title: back muscle, MFIT, rep3

description:
Library name: backmuscleMFIT3
Bulk RNA-seq from back muscle; MFIT; biological replicate 3


title: back muscle, MFIT, rep2

description:
Library name: backmuscleMFIT2
Bulk RNA-seq from back muscle; MFIT; biological replicate 2


title: PAF49

description: Library name: DLRMS00195


title: back muscle, MFIT, rep1

description:
Library name: backmuscleMFIT1
Bulk RNA-seq from back muscle; MFIT; biological replicate 1


title: WT_R3

city: Villenave d'Ornon

first: martine

last: lemaire-chamley

address: 71 Avenue Edouard Bourlaux

department: FDFE

country: France

institute: INRAE

description: Library name: WT_R3

data_processing:
After FastQC control, read mapping was performed withSTAR aligner v2.7.5a (Dobin et al., 2013) against the tomato Heinz genome reference SL 4.00 (https://solgenomics.net/).
Aligned reads with a mapping quality above 10 were kept and counts of reads per genes were obtained using featureCounts program (Liao et al., 2014) based on iTAG4.0 gene models (https://solgenomics.net/).
Assembly: tomato Heinz genome reference SL 4.00
Supplementary files format and content: txt file, feature count for all samples

organism: Solanum lycopersicum

source_name: fruit locular tissue

growth_protocol: Tomato plants (Solanum lycopersicum) from the Micro-Tom cultivar were grown on subirrigation tables in a greenhouse under a long day photoperiod with a 23/18°C day/night temperature cycle. Flowers were pollinated by shaking and tagged at anthesis. Fruits were harvested at 6 days post anthesis.

extract_protocol:
LT was manually dissected from 6 DPA fruits into Invitrogen™ RNAlater™ Stabilization Solution, removing developing seeds, frozen in liquid nitrogen, and stored at −80 °C. After pooling LT samples from 6 fruits per replicate, total RNA was isolated using Arcturus™ PicoPure™ RNA Isolation Kit and RNA quality was checked on Agilent 2200 TapeStation system following the RNA ScreenTape Assay.
Total RNA was used for construction of libraries using the DNBSEQ stranded mRNA libraries kit on the DNBseq™ Hong Kong BGI platform
RNA-seq, 20M paired clean reads by sample, on PE150. sequencer DNBseq T7

value: Locular tissue

value: Micro-Tom


title: WT_R1

description: Library name: WT_R1


title: 2_5_R3

description: Library name: 2_5_R3


title: Breast Benign Disease [Patient 039_SH08L18_Cell3]


title: Breast Benign Disease [Patient 040_SH08L12_Cell3]


title: hfPSCs_single cell_2

city: Beijing

first: Qizhi

last: Wang

address: Chaoyang District

institute: Chinese Academy of Sciences

description: Library name: hfPSCs_single cell_2

data_processing:
For scRNA-seq data analysis, raw data based on 10XGenomics were processed by Cell Ranger software suite (version 3.0.2) with default parameters using the mm9 reference genome. The Seurat package (version 4) was used to analyze the data. Principal component analysis (PCA) was performed for dimension reduction and t-distributed stochastic neighbor embedding (t-SNE) was further used to project the cells into two dimensions.
Assembly: hg19
Supplementary files format and content: gz format; barcodes, features and matrix

source_name: hfPSCs

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension (300-600 living cells per microliter determined byCount Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cell will be recovered was estimated to be about 3,000 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs.Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°Cfor 5min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200(performed by CapitalBio Technology, Beijing).
Single-cell RNA-seq libraries wereconstructed using Single Cell 3 ’ Library andGel Bead Kit V3.1 The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) readingstrategy (performed by CapitalBio Technology, Beijing).

value: hfPSCs

value: hPSCs


title: 2_5_R2

description: Library name: 2_5_R2


title: Breast Benign Disease [Patient 037_SH06902_Cell3]

first: Satoshi

last: Kondo

address: Tebiro 6-10-1

institute: Toray Industries,Inc.


title: 2_11_R3

description: Library name: 2_11_R3


title: 2_5_R1

description: Library name: 2_5_R1


title: WT_R2

description: Library name: WT_R2


title: hfPSCs_single cell_1

description: Library name: hfPSCs_single cell_1


title: 2_11_R2

description: Library name: 2_11_R2


title: hfPSCs_single cell_4

description: Library name: hfPSCs_single cell_4


title: Breast Benign Disease [Patient 036_SH08L12_Cell4]


title: replicate 2 of CK13 CUT&Tag in HCT116

description: Library name: HCT116_CK13_R2

source_name: colon cancer tissue

growth_protocol: HeLa and HCT116 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
The CUT&Tag method was constructed following the described protocol (32) with some modifications. A total of 105 cells were washed twice with 100 µL wash buffer (20 mM HEPES–KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 1× protease inhibitors). Next, 10 µL of pre-activated concanavalin A coated magnetic beads were added to the cells in 100 µL wash buffer and incubated on a rotator for 10 min at room temperature. The supernatant was removed, and the bead-bound cells were resuspended in 100 µL of dig-wash buffer (0.05% digitonin, 0.1% BSA, 20 mM HEPES–KOH at pH 7.5, 150 mM KCl, 0.5 mM spermidine, 2 mM EDTA, 1× protease inhibitors) containing 250 nM of G4P, 200 nM of CK13, 2 µL of anti-NCL antibody (ab70493, Abcam), or 1 µL of anti-Top1 antibody (ab109374, Abcam), respectively. After 2 hours rotation at room temperature, the cells incubated with G4P or CK13 were washed twice with 100 µL of dig-wash buffer and resuspended with 100 µL of dig-wash buffer containing 2 µL of anti-FLAG M2 antibody (Sigma-Aldrich), or 2 µL of anti-V5 tag antibody (ab15828, Abcam), incubated for another 1 hour at room temperature. The buffer containing primary antibodies was then removed from the cells, and 100 µL of dig-wash buffer containing 1 µL of Goat anti-mouse IgG (AP124, Sigma-Aldrich) or 1 µL of Goat anti-rabbit IgG (AP132, Sigma-Aldrich) was mixed with the cells and incubated for 1 hour at room temperature. After washing three times with dig-wash buffer, a 1:100 dilution of pAG-Tn5 adapter complex (~0.2 µM) was prepared in 100 µL of dig-wash buffer and added to the cells, which were then rotated for 1 hour at room temperature. After five washes with dig-wash buffer, the bead-bound cells were resuspended with 50 µL of tagmentation buffer (20 mM HEPES–KOH (pH 7.5), 150 mM KCl, 10 mM MgCl2, 0.5 mM spermidine, 1× protease inhibitors) and incubated at 37 ℃ for 1 hour. To terminate the tagmentation reaction, 2.5 µL of 0.5 M EDTA and 1 µL of 20 mg/mL proteinase K were added and incubated at 55 ℃ for 30 min. The DNA was then extracted using 120 µL of Ampure XP beads (Beckman Counter) for library preparation. DNA was eluted in 40 µL of 5 mM Tris−HCl (pH 8.0).
To amplify the libraries, 16 µL of DNA was mixed with a uniquely barcoded i5 and a uniquely barcoded i7 primer and amplified using Q5 high-fidelity 2 × master mix (New England Biolabs). The PCR cycles for G4P and CK13 groups were 16 to 18, and those for Top1, NCL, and IgG groups were 15, 17, and 22, respectively. The libraries were purified with 1.3 × volume of Ampure XP beads and eluted in 20 µL of 10 mM Tris−HCl (pH 8.0).

value: colon cancer tissue


title: replicate 1 of CK13 CUT&Tag in HCT116

description: Library name: HCT116_CK13_R1


title: 2_11_R1

description: Library name: 2_11_R1


title: U937cells, oeBCL6B, replicate3

city: Kunming,Yunnan,CHina

first: Pan

last: Yuqing

address: 295 Xichang Road, Wuhua District, Kunming City, Yunnan Province, China

institute: the First Affiliated Hospital of Kunming Medical University

description: Library name: OE3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone Marrow

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

value: Bone Marrow

value: Acute Promyelocytic Leukemia Cell

value: phenotyping experiment


title: U937cells, control, replicate 2

description: Library name: NC2

value: NC


title: Breast Benign Disease [Patient 033_SH08L32_Cell4]

city: Kamakura

value: female

value: Training


title: U937cells, oeBCL6B, replicate 1

description: Library name: OE1


title: Breast Benign Disease [Patient 035_SH08L22_Cell1]


title: replicate 1 of G4P CUT&Tag in HCT116

description: Library name: HCT116_G4P_R1


title: U937cells, control, replicate 3

description: Library name: NC3


title: Breast Benign Disease [Patient 041_SH08L54_Cell3]


title: Breast Benign Disease [Patient 034_SH08L09_Cell3]


title: Breast Benign Disease [Patient 038_SH08L45_Cell1]


title: U937cells, control, replicate 1

description: Library name: NC1


title: hfPSCs_single cell_3

description: Library name: hfPSCs_single cell_3


title: Breast Benign Disease [Patient 032_SH0ZE11_Cell4]


title: CUTLL1 cells lentivirally transduced with miR-15b/16-2 and GFP vector. Sample 2

city: Madrid

first: María

middle: L

last: Toribio

state: Madrid

address: Calle Nicolás Cabrera, 1. Campus Cantoblanco

department: Interactions with the environment

country: Spain

institute: Centro de Biología Molecular Severo Ochoa (CSIC-UAM)

description: Library name: C2_MIRS

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. Reads were aligned with HISAT2 (2.2.1) to Human genome reference datasets (GRCh38).  FeatureCounts (2.0.6) was used to count the reads numbers mapped to each gene. Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between the two conditions/groups was performed using the DESeq2 R package (v1.42.0) on the NovoMagic platform (Novogene). Supplementary data are provided as an Excel (.xls) file containing FPKM values, p-values, adjusted p-values, gene names, and log2 fold changes for differential expression between CUTLL1_MIRS and CUTLL1_GFP.
Assembly: GRCh38 (Genome Reference Consortium Human Build 38)
Supplementary files format and content: FPKM

growth_protocol: CUTLL1 human T-ALL cell line was maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and was sent to Novogene Co., Ltd (GmbH, Germany) for library preparation and sequencing. RNA quality and quantity were assessed using the Agilent 5400 Bioanalyzer (Agilent Technologies, CA, USA) and Qubit® 2.0 Fluorometer (Life Technologies, CA, USA), respectively. 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene Co., Ltd (GmbH, Germany) using Novogene NGS RNA Library Prep Set (PT042)* following manufacturer´s protocols. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: CUTLL1 human T-ALL cells were transduced by spinoculation (1,800 rpm, room temperature) in the presence of 8 μg/mL polybrene. Twenty-four hours post-transduction, cells were washed and fresh RPMI medium supplemented with 10% FBS was added. After 72 hours, GFP-positive cells were quantified using a FACSCanto II flow cytometer. GFP-positive cells were subsequently sorted using a Cytek Aurora™ cell sorting system.

value: T-cell acute lymphoblastic leukemia

value: Lentiviral transduction with miR-15b/16- plus GFP vector


title: replicate 1 of NCL CUT&Tag in HCT116

description: Library name: HCT116_NCL_R1

data_processing:
The clean paired-end sequencing data were analyzed using the human genome (version hg38) as a reference. Reads were aligned with bowtie2 using --fast-local. Normalized (RPGC) coverage tracks were generated by deepTools bamCoverage using parameters --binSize 50 --normalize --extendReads --ignoreDuplicates.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag


title: replicate 2 of G4P CUT&Tag in HCT116

description: Library name: HCT116_G4P_R2


title: CUTLL1 cells lentivirally transduced with a mock GFP control vector. Sample 3

description: Library name: C3_GFP

value: Lentiviral transduction with mock GFP control vector


title: Breast Benign Disease [Patient 031_SH05T50_Cell4]


title: CUTLL1 cells lentivirally transduced with miR-15b/16-2 and GFP vector. Sample 1

description: Library name: C1_MIRS


title: replicate 2 of NCL CUT&Tag in HCT116

description: Library name: HCT116_NCL_R2


title: CUTLL1 cells lentivirally transduced with a mock GFP control vector. Sample 2

description: Library name: C2_GFP


title: CUTLL1 cells lentivirally transduced with a mock GFP control vector. Sample 1

description: Library name: C1_GFP


title: U937cells, oeBCL6B, replicate 2

description: Library name: OE2


title: CUTLL1 cells lentivirally transduced with miR-15b/16-2 and GFP vector. Sample 3

description: Library name: C3_MIRS


title: 293T-shRK-ERCC

first: Ruikun

last: Wu

state: Anhui

address: No.443 Huangshan Road

institute: University of Science and Technology of China

description:
Library name: sample2
293T-mRNA-ERCC-NC-RK.txt

data_processing:
For data processing, raw reads were first processed with fastp to obtain clean reads. Clean Reads were then aligned to the reference genome (Human: hg19; C. elegans: ce10)Bowtie2. For linear RNA, read counts were generated using BEDTools. For poly(A)-selected RNA-seq with ERCC spike-in, clean reads were aligned to a combined reference consisting of the human/C. elegans genome and ERCC spike-in sequences. Read counts for endogenous genes and ERCC transcripts were obtained using standard counting procedures. ERCC read counts were modeled using a negative binomial distribution to estimate sample-specific scaling factors, which were subsequently applied to normalize endogenous gene expression levels for assessment of global mRNA abundance.
Assembly: hg19(human), ce11(C. elegans)
Supplementary files format and content: tab-delimited text files include count values for each Sample

extract_protocol:
Total RNA from cells or C. elegans strains was extracted by TRIzol Reagent or TRIzol LS Reagent according to the manufacturer’s procedures.
The concentration of isolated RNAs was verified by Nanodrop, and RNA quality was checked with gel electrophoresis. For poly(A)-selected RNA-seq, external RNA Control Consortium (ERCC) spike-in RNA controls (Invitrogen, 4456740) were diluted and added according to the manufacturer’s instructions. Specifically, 1 μL of 1:100 diluted ERCC spike-in RNA mix was added to 5 μg total RNAs prior to enrichment using oligo(dT) magnetic beads and library preparation.


title: replicate 1 of IgG CUT&Tag in HCT116

description: Library name: HCT116_IgG_R1


title: Breast Benign Disease [Patient 030_SH08L25_Cell2]


title: replicate 2 of IgG CUT&Tag in HCT116

description: Library name: HCT116_IgG_R2


title: Breast Benign Disease [Patient 029_SH08L20_Cell2]