title: mouse neutrophil, 18h no-larvae ctrl, 01

description:
Library name: 13_18h_NoLarvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Ctrl


title: Thymus,Trp53-/-_mouse_1134,17_week-old

status: Public on Sep 10 2025

type: SRA

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

country: China

institute: Center for Stem Cell and Regenerative Medicine

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the BSTMatrixv software 1.9 (http://www.bmkmanu.com/wp-content/uploads/2022/10/BMKMANU-S1000-Library-Construction-Kit-User-Guide.pdf)
Assembly: Mus_musculus.GRCm38.88 genome
Supplementary files format and content: barcodes.tsv.gz: barcode name file, one barcode name per line, and each barcode represents a supSpot
Supplementary files format and content: barcodes_pos.tsv.gz: supSpot location file, tab split, the first column is the name of supSpot, and the second and third columns are the coordinates of supSpot on HE picture
Supplementary files format and content: barcodes_sequence.txt: barcode sequence file
Supplementary files format and content: features.tsv.gz: gene information file, tab division, the first column is gene ID, and the second column is gene name
Supplementary files format and content: matrix.mtx.gz:In the expression matrix file, the first column is the gene, the numerical value corresponds to the line number in features.tsv.gz file, the second column is supSpot, the numerical value corresponds to the line number in barcodes.tsv.gz file, and the third column is the umi number of the gene in this supSpot

molecule: polyA RNA

organism: Mus musculus

source_name: Thymus

extract_protocol:
The thymuses of Trp53-/- and Trp53+/+ mice were isolated and embedded in Optimal Cutting Temperature compound (OCT, Sakura Tissue-TEK) on dry ice.
Library preparations were performed with the BMKMANU S1000 protocol using Spatial transcriptomics Gene Expression Kit (BMKMANU, ST03002) and Tissue Optimization Kit (BMKMANU, ST03003)
stRNA-seq

treatment_protocol: After anaesthetization with 1% (i.p.) sodium pentobarbital, mice were weighed, shaved, and given transcardial perfusion with 20-30 ml cold PBS.

tag: tissue

value: Thymus

tag: strain

tag: genotype

tag: age

value: 17 weeks

tag: Sex

value: Female


title: Neutrophil, I2_R

city: Suzhou

first: Yixuan

last: Zhang

address: No.9 Chongwen Road

institute: Suzhou University

description: Library name: Sample 5

library_source: transcriptomic

data_processing:
Raw sequencing data were processed by Trim_galore (v0.6.4) to remove adapter sequences, low-quality reads, and short reads, yielding clean reads.
Bowtie2 (v2.4.2) was used to align reads to the corresponding rRNA database, and rRNA sequences were removed.
Read indexing and mapping to the human reference genome (GRCh38/hg38) were performed using Hisat2 (v2.0.0).
Followed by transcriptome assembly using StringTie (v2.1.4).
Gene expression levels were quantified using Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Assembly: GRCh38/hg38
Supplementary files format and content: The thresholds for determining DEGs are P < 0.05 and absolute fold change ≥ 2.

organism: Homo sapiens

source_name: blood

growth_protocol: Cells were grown to maximum confluency prior to treatment.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) following the manufacturer’s protocol.
RNA libraries were prepared using the VVAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605-0, Vazyme) and sequenced on the Illumina NovaSeq 6000 platform with a 150-bp paired-end sequencing strategy. Enrichment of mRNA, library construction, sequencing, and data analysis were performed on the Yunbios platform. Raw sequencing data were processed by Skewer (v0.2.2) and its quality was assessed with FastQC (v0.11.2). The sequencing reads had a length of 2×150 bp. Read indexing and mapping to the human reference genome (GRCh38/hg38) were performed using Hisat2 (v2.0.0), followed by transcriptome assembly using StringTie (v2.1.4). Gene expression levels were quantified using Fragments Per Kilobase of transcript per Million mapped reads (FPKM).

treatment_protocol: Neutrophils were collected from both the IFN-γ-stimulated group (experimental group) and the unstimulated group (control group).

value: blood

tag: cell line

value: primary

tag: cell type

value: Neutrophil

tag: treatment

value: Add IFN - γ to 1640 complete culture medium


title: Pancreas, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

library_source: genomic single cell

data_processing:
The original FASTQ files were converted to BAM format firstly. Then the cell barcodes were extracted and tagged with CB in the offered BAM files. Three 6bp barcodes and one 10bp Tn5 barcode ware combined to identify a single cell (a single cell barcode consists of four barcode fragments). Reads with the quality of cell barcodes less than 10 were tagged with XQ and removed afterwards. The processing above was based on Drop-seq_tools-2.5.1. Next, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each barcode fragments. Before alignment, the cell barcodes were added to the query names, the BAM files were converted to the FASTQ files and the 28bp barcodes at the 5’ end were trimmed simultaneously.
BWA (version 0.7.15), which is encapsulated in Snaptools, was used for reads alignment in single-end mode. The data were aligned to mm10 reference genome. Snaptools was again used to convert the aligned and shifted BAM files to SNAP files, which was then converted to Fragment files (BED format). The sorted and compressed Fragment files in BED format were required as inputs for subsequent analysis.
Assembly: Mus_musculus.GRCm38.88 genome
Supplementary files format and content: BED files recording coordinates of fragments captured by scATAC-seq

molecule: genomic DNA

source_name: Pancreas

extract_protocol:
Tissues were quickly transferred into cold DPBS, then washed and subjected to manual pulverization via grinded in liquid nitrogen. The pulverized tissues were aliquoted into pre-labelled and pre-chilled 1.5 ml nuclease-free tubes. After that, the powder in each tube was suspended in 1 ml Nuclear Permeabilization Buffer [1 × DPBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1 × Protease inhibitor], and followed by incubation for 3 minutes to isolate the nuclei. The suspension was transferred to a 15 ml centrifuge tubes pre-filled with 5 ml wash buffer, filtered through 40 μm strainers and centrifuged at 600 × g for 5 minutes at 4°C and re-suspended in 1 × DPBS.  For Bone marrow, cells were collected and centrifuged at 300 × g for 5 minutes at 4°C, then suspended in 1 ml Nuclear Permeabilization Buffer and followed by incubation for 6 minutes to isolate the nuclei. The suspension was transferred to 15 ml centrifuge tubes pre-filled with 5 ml wash buffer, centrifuged at 500 × g for 5 minutes at 4°C and re-suspended in 1 × DPBS.
Library preparations were performed with the Microwell ATAC-seq plus protocol

treatment_protocol: After anaesthetization with 1% (i.p.) sodium pentobarbital, mice were weighed, shaved, and given transcardial perfusion with 20-30 ml PBS.

value: Pancreas

value: 8 months

value: Male


title: Calu-3 treated with AdV1 (100 VP/mL), S-His, N-His (0.25 µg/mL) and incubated for 72 h at 34.5°C with 5% CO2. Rep 2

city: Warsaw

first: Monika

middle: Maria

last: Staniszewska

address: Poleczki 19

department: CEZAMAT

country: Poland

institute: Warsaw University of Technology

description:
Library name: Calu-3 AdV1+S+N rep2
“S14” column

data_processing:
Only reads that were longer than 35 nucleotides and properly paired were kept (cutadapt -m 35).
The reads were aligned to the human GRCh. 38 genome with GENCODE version 43 primary annotation, using the RSEM-1.3.3 pipeline coupled with STAR-2.7.10b (rsem-calculate-expression --star --star-path ~/STAR-2.7.10b --star-gzipped-read-file --paired-end --strandedness reverse -p 14 input.1.fastq.gz input.2.fastq.gz ./GRCH.38.gencode.v43.primary ./output/)
Assembly: human GRCh38
Supplementary files format and content: comma separated value text file with ENSEMBLE gene ID and RSEM estimated read count per gene for all samples

molecule: total RNA

growth_protocol: 3D alveoli-like co-culture consisting of Calu-3 cells and PBMCs onto Corning® Transwell® Inserts. The Calu-3 cell line (1 × 10^5 cells/mL) was seeded onto Corning Transwell Inserts (700 µL of cell growth medium under the insert, 300 µL of cell suspension on the insert) and incubated for 72 h at 37°C with 5% CO2. Then, the culture medium was discarded to create an air-liquid interface, allowing the Calu-3 cells to form microvilli, as monitored by SEM. The cells were cultured for 14 days, with the medium exchange every 72 hours to stimulate the cell growth. After 14 days, PBMCs in a total volume of 700 µL (2.5–3 × 10^6 cells/mL in Opti-MEM) were added to the liquid site of the culture. The model prepared in this way was immediately used for further experiments.

extract_protocol:
RNA was extracted from cell pellets using the Total RNA Mini Kit (A&A Bio technology, Gdansk, Poland).
Strand-specific,  read length of 100bp in a paired-end mode, with rRNA depletion

treatment_protocol: PBMCs were seeded into 24-well plates in triplicate to study all immunogenic factors and incubated overnight at 37°C with 5% CO2. Then, the cell growth medium was replaced by 1 mL/well of the OptiMEM medium with reduced FBS concentration (5% v/v), and the immunogenic factors were added in the concentrations as follows: AdV1 (100 VP/cell, [10],  Spike-S1-His (0.25 µg/mL, InvivoGen USA), Nucleocapsid-His (0.25 µg/mL, InvivoGen USA),  AdV1+Spike-S1-His+Nucleocapsid-His (100 VP/cell+0.25 µg/mL+0.25 µg/mL). Plates were incubated for 7 days at 34.5°C with 5% CO2, and then the cells were collected for the immunophenotyping and apoptosis assay. The cell growth medium was collected and stored at -80 °C for cryopreservation before cytokine profiling.

value: WT

value: Cellls treated with AdV1 (100 VP/mL), S-His, and N-His (0.25 µg/mL) and incubated for 72 h at 34.5°C with 5% CO2.

tag: batch


title: CUT&Tag of CDK9 in BRIP1 OE cells rep2.

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

description: Library name: BRIP1_CDK9_2

library_source: genomic

data_processing:
(CUT-tag)The data analysis workflow first involved adapter trimming and removal of low-quality bases from paired-end reads were conducted using Trim Galore software. Clean reads were then aligned to the hg38 reference genome using Bowtie2, followed by the removal of PCR duplicates with Picard. Genome browser tracks in bigWig format were produced from merged replicates using samtools, and peak calling was performed with MACS2 using the parameters -f BAMPE --broad -nomodel. The resulting bigWig data were visualized using the Integrative Genomics Viewer (IGV) software from the Broad Institute, while peak visualizations were prepared using Deeptools.
Assembly: hg38
Supplementary files format and content: bigwig for CUT&Tag
Library strategy: CUT&Tag

source_name: liver

extract_protocol:
CUT&Tag experiments, cell capture was achieved using ConA-coated magnetic beads for cell enrichment.
CUT&Tag libraries were prepared according to the protocol established by Steven Henikoff's laboratory.

value: liver

value: tumor cells

value: Early S Phase-Synchronized


title: LymphNodes, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

source_name: LymphNodes

value: LymphNodes


title: Lung, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

source_name: Lung

value: Lung


title: CUT&Tag of CDK9 in DHX36 OE cells rep2.

description: Library name: DHX_CDK9_2


title: CUT&Tag of CDK9 in BRIP1 OE cells rep1.

description: Library name: BRIP1_CDK9_1


title: Calu-3 treated with AdV1 (100 VP/mL), S-His, N-His (0.25 µg/mL) and incubated for 72 h at 34.5°C with 5% CO2. Rep 1

description:
Library name: Calu-3 AdV1+S+N rep1
“S13” column


title: mouse neutrophil, 18h larvae ctrl, 06

city: Philadelphia

first: Nathan

middle: M

last: Ryan

country: USA

institute: Thomas Jefferson University

description:
Library name: 12_18h_Larvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

data_processing:
Using a Linux computing cluster, sequencing reads were trimmed to remove low-quality or adapter-containing sequences using Trimmomatic v. 0.39, with the following settings LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Trimmed reads were mapped to the NCBI mm10 Mus musculus reference genome using STAR. Mapped reads were quantified using HTseq-count, with the following settings --mode union -a 1.
Mapped read count data were further analyzed in R, as follows: Counts were filtered to retain genes with count values greater than 0 for six or more samples, normalized and scaled to obtain counts per million (CPM) values using edgeR
Differentially expressed genes between immunized versus control groups were identified within each time point (18 hours or 36 hours), for diffusion chambers with or without larvae, using DESeq2
For each grouping (i.e., 18 h with larvae, 18 h without larvae, 36 h with larvae, 36 h without larvae), a DESeq2 model was fit using ~immunization as the model design parameter.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet (RNAseq_data-analyzed.xlsx) contains gene ID, mean read counts, log2FoldChange between control and immune mice, individual and FDR-adjusted p values, individual read counts for each sample, gene name, description, GO accession numbers and descriptions. The file is divided into 4 sheets based on time point and whether larvae were present in the diffusion chambers from which the neutrophils were collected.

source_name: Subcutaneous

extract_protocol:
The total RNA was isolated using the Qiagen RNAeasy Plus kit. RNA concentration was quantified using a Qubit fluorimeter, and integrity was determined by the TapeStation high-sensitivity RNA kit (Agilent Technologies, Santa Clara, CA, USA).
mRNA libraries were prepared by poly-A selection from 1 ng of each sample using the Takara SMART-seq HT kit (Takara, 634437).

treatment_protocol: Mice were either immunized with recombinant fusion protein vaccine plus adjuvant or adjuvant only controls

value: Subcutaneous

value: Primary cells

value: BALB/cByJ

value: Ctrl

tag: time

value: 18 hr


title: Calu-3 cells cultured for 72 h in cell growth medium. Rep 3

description:
Library name: Calu-3 control rep3
“S12” column

value: untreated


title: CUT&Tag of CDK9 in DHX36 OE cells rep1.

description: Library name: DHX_CDK9_1


title: mouse neutrophil, 18h larvae imm, 06

description:
Library name: 11_18h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Neutrophil

value: Imm


title: Calu-3 cells cultured for 72 h in cell growth medium. Rep 2

description:
Library name: Calu-3 control rep2
“S11” column


title: LargeIntestine, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

source_name: LargeIntestine

value: LargeIntestine

value: 8 months


title: mouse neutrophil, 18h larvae imm, 05

description:
Library name: 10_18h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: WT

value: Male


title: CUT&Tag of CDK9 in Ctrl cells rep2.

description: Library name: Ctrl_CDK9_2

value: liver


title: Kidney, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

source_name: Kidney

value: Kidney


title: Calu-3 cells cultured for 72 h in cell growth medium. Rep 1

description:
Library name: Calu-3 control rep1
“S10” column


title: mouse neutrophil, 18h larvae ctrl, 04

description:
Library name: 08_18h_Larvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description


title: CUT&Tag of CDK9 in Ctrl cells rep1.

description: Library name: Ctrl_CDK9_1

value: tumor cells

value: Early S Phase-Synchronized


title: PBMCs treated with AdV1 (100 VP/mL), S-His, and N-His (0.25 µg/mL) and incubated for 72 h at 34.5°C with 5% CO2. Rep 3

description:
Library name: PBMC AdV1+S+N rep3
“S9” column

source_name: PBMC

value: PBMC

value: Cellls treated with AdV1 (100 VP/mL), S-His, and N-His (0.25 µg/mL) and incubated for 72 h at 34.5°C with 5% CO2.


title: Heart, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

source_name: Heart

value: Heart


title: Liver, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

source_name: Liver

value: Liver


title: CUT&Tag of NELFB in BRIP1 OE cells treated with FB rep2.

description: Library name: BRIP1_FP_NELFB_2


title: mouse neutrophil, 18h larvae ctrl, 03

description:
Library name: 07_18h_Larvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Subcutaneous

value: Primary cells

value: BALB/cByJ

value: Ctrl


title: PBMCs treated with AdV1 (100 VP/mL), S-His, and N-His (0.25 µg/mL) and incubated for 72 h at 34.5°C with 5% CO2. Rep 2

description:
Library name: PBMC AdV1+S+N rep2
“S8” column


title: Gallbladder-BileDuct, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

source_name: Gallbladder-BileDuct

value: Gallbladder-BileDuct


title: mouse neutrophil, 18h larvae imm, 04

description:
Library name: 06_18h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Neutrophil

value: Imm

value: 18 hr


title: CUT&Tag of NELFB in BRIP1 OE cells treated with FB rep1.

description: Library name: BRIP1_FP_NELFB_1


title: PBMCs treated with AdV1 (100 VP/mL), S-His, and N-His (0.25 µg/mL) and incubated for 72 h at 34.5°C with 5% CO2. Rep 1

description:
Library name: PBMC AdV1+S+N rep1
“S7” column

value: WT


title: CUT&Tag of NELFA in BRIP1 OE cells treated with FB rep2.

description: Library name: BRIP1_FP_NELFA_2

value: liver


title: PBMCs cultured for 24 h at 37 deg. C and 5% CO2. Rep 3

description:
Library name: PBMC AdV1+rRBD rep3
“S6” column

value: treated AdV1 (100 VP/ml) and  rRBD (IC50 = 2.62 μg/ml)


title: mouse neutrophil, 18h larvae ctrl, 02

description:
Library name: 05_18h_Larvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Male


title: CUT&Tag of NELFA in BRIP1 OE cells treated with FB rep1.

description: Library name: BRIP1_FP_NELFA_1

value: tumor cells

value: Early S Phase-Synchronized


title: mouse neutrophil, 18h larvae imm, 03

description:
Library name: 04_18h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description


title: PBMCs cultured for 24 h at 37 deg. C and 5% CO2. Rep 2

description:
Library name: PBMC AdV1+rRBD rep2
“S5” column

value: PBMC


title: Bladder, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

source_name: Bladder

value: Bladder

value: 8 months


title: BoneMarrow, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

source_name: BoneMarrow

value: BoneMarrow


title: mouse neutrophil, 18h larvae imm, 02

description:
Library name: 03_18h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Subcutaneous

value: Primary cells


title: PBMCs cultured for 24 h at 37 deg. C and 5% CO2. Rep 1

description:
Library name: PBMC AdV1+rRBD rep1
“S4” column


title: mouse neutrophil, 18h larvae ctrl, 05

description:
Library name: 09_18h_Larvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: BALB/cByJ

value: Ctrl


title: CUT&Tag of NELFB in BRIP1 OE cells treated without FB rep1.

description: Library name: BRIP1_Ctrl_NELFB_1


title: mouse neutrophil, 18h larvae ctrl, 01

description:
Library name: 02_18h_Larvae_Ctrl
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: Neutrophil


title: PBMCs cultured for 72 h in a cell growth medium. Rep 3

description:
Library name: PBMC control rep3
“S3” column

value: untreated


title: Thymus, Trp53-/-_mouse_0011, 26.5_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

data_processing:
The original FASTQ files were converted to BAM format firstly with Drop-seq_tools-1.12, which was used for the subsequent processing except for barcode correction and alignment. The cell barcodes were extracted and tagged with XC in the offered BAM files, and the unique molecular identifiers (UMIs) were tagged with XM. Three 6bp barcodes ware combined to identify a single cell. Reads with the quality of cell barcodes or UMIs less than 10 were tagged with XQ and removed afterwards. Next, the PolyATrimmer was used to trim ployA. Before alignment, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each 6bp barcode.
STAR (version 2.5.2a) was used for reads alignment in single-end mode. The data were aligned to a GRCm38.88 reference genome. Then the aligned BAM files were sorted by query names and were merged with the unaligned BAM files, in order to recover the XC and XM tags that were lost after the alignment. Finally, the top 20,000 cell barcodes ranked by reads number were used to generate the digital expression matrices in each sample or each technical repeat.
Tab-delimited text files of digital expression matrix (DGE) based on raw UMIs counts, with genes as rows and cells as columns.
Assembly: Mus_musculus.GRCm38.88 genome
Supplementary files format and content: Tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq1.1 protocol

value: Thymus

value: 26.5 weeks

value: Female


title: Spleen, Trp53-/-_mouse_0011, 26.5_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Spleen

value: Spleen


title: mouse neutrophil, 18h larvae imm, 01

description:
Library name: 01_18h_Larvae_Imm
column names in RNAseq_data-analyzed.xlsx: gene_ID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,37_36h_NoLarvae_Ctrl,40_36h_NoLarvae_Ctrl,41_36h_NoLarvae_Ctrl,44_36h_NoLarvae_Ctrl,46_36h_NoLarvae_Ctrl,47_36h_NoLarvae_Ctrl,38_36h_NoLarvae_Imm,39_36h_NoLarvae_Imm,42_36h_NoLarvae_Imm,43_36h_NoLarvae_Imm,48_36h_NoLarvae_Imm,gene_name,description,GO_accession,GO_description

value: WT

value: Male

value: Imm

value: 18 hr


title: PBMCs cultured for 72 h in a cell growth medium. Rep 2

description:
Library name: PBMC control rep2
“S2” column

value: PBMC


title: CUT&Tag of NELFA in BRIP1 OE cells treated without FB rep2.

description: Library name: BRIP1_Ctrl_NELFA_2

value: liver

value: tumor cells

value: Early S Phase-Synchronized


title: CUT&Tag of NELFA in BRIP1 OE cells treated without FB rep1.

description: Library name: BRIP1_Ctrl_NELFA_1


title: LymphNodes, Trp53-/-_mouse_0011, 26.5_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: LymphNodes


title: Lung, Trp53-/-_mouse_0011, 26.5_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Lung


title: Brain, Trp53-/-_mouse_0515, 8_month-old

description: Microwell-based ATAC-seq

source_name: Brain

value: Brain

value: 8 months


title: PBMCs cultured for 72 h in a cell growth medium. Rep 1

description:
Library name: PBMC control rep1
“S1” column

value: untreated


title: CUT&Tag of NELFB in  DHX36 OE cells treated with FB rep2.

description: Library name: DHX_FP_NELFB_2


title: P635L mice injected with Tnpo3 virus, rep. 4

city: Heidelberg

first: Julia

last: Kornienko

state: Baden-Württemberg

address: Meyerhofstraße 1

country: Germany

institute: EMBL

description: Library name: P635L_Tnpo3_4

data_processing:
Reads were aligned to GRCm39.109 using STAR (2.7.9a). Read count files were generated with featureCounts v2.0.6 for each gene. Differential gene expression analysis was done using DeSeq2, and differential splicing analysis with rMATS.
Assembly: GRCm39.109
Supplementary files format and content: File FeatureCounts_read_counts_all.txt contains Feature Counts output for read counts in all samples. Files DeSeq2_WT.CTRvs….txt contain DeSeq2 output for differential gene expression analysis, pairwise comparisons to WT.CTR. Files rMATS_WT.CTRvs….txt contain rMATS output for differential splicing, pairwise comparisons to WT.CTR.

growth_protocol: All animal care and procedures performed in this study conformed to the EMBL Guidelines for the Use of Animals in Experiments and were reviewed and approved by the Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
LV tissues were homogenized and RNA was extracted using Direct-zol RNA Miniprep Plus Kit (Zymo Research), according to the manufacturer’s instructions
Barcoded stranded mRNA-seq libraries were prepared from 700 ng of high-quality total RNA samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA) implemented on the liquid handling robot Beckman i7. Obtained libraries that passed the QC step were pooled in equimolar amounts.

treatment_protocol: 1e12 v.g. of either AAV9-Ctr or -Tnpo3 were dissolved in PBS and injected in the tail vein of 4-weeks old mice (males and females)

value: Heart


title: P635L mice injected with Tnpo3 virus, rep. 3

description: Library name: P635L_Tnpo3_3


title: vascularized adipose organoid with Celastrol treatment-3

city: beijing

first: Sen

last: Li

state: beijing

address: No. 2 Yabao Road, Chaoyang District

institute: Capital Institute of Pediatrics

description:
Library name: SAMPLE_12
T02-3

data_processing:
Raw reads were filtered to remove adaptors using Cutadapt. Sequenced reads were single-end mapped to the human GRCh38 reference genome using NextGenMap and SAMtools. FeatureCounts was used to quantify the mapped sequences. Differential expression analysis was performed with DESeq2, and differentially expressed genes (DEGs) were defined as those with a fold change > 2 and a p-value < 0.05.
Assembly: human GRCh38
Supplementary files format and content: All.fpkm.anno.csv include FPKM values for all Samples

source_name: peripheral blood

extract_protocol:
RNA extraction from organoids was performed following the manufacturer's protocols (Isolation of RNA from organoids and spheroids, TFS-Assets/BID/Reference-Materials/isolation-rna-organoids-spheroids-white-paper.pdf). Briefly, samples processed with TRIzol Reagent (Invitrogen) were immediately flash-frozen in a mixture of dry ice and ethanol after cell lysis and stored at –80°C for RNA extraction at a later time. The purified total RNA was eluted in RNase-free water and stored at –20°C for subsequent analyses
DTT, dNTP, RNase Inhibitor, RT Enzyme, and 5x RT Buffer were added to synthesize single-stranded cDNA. Exonuclease I and 10x Exonuclease I Buffer were used to remove single-stranded DNA, followed by magnetic separation. Poly(A) RNA was removed using Elution Buffer, and magnetic separation was performed again. Random primers, 10x Reaction Buffer, enhancer, dNTP, and cDNA Extend Polymerase I were used for two-strand cDNA synthesis. After removing the supernatant, Elution Buffer was added, and DNA beads were used to recover fragments. PCR amplification was performed with 2x HIFI Amplification Mix and Index, followed by examination of DNA beads for library fragments.

value: peripheral blood

value: Primary Cells

value: peripheral blood mesenchymal stem cells(PBMSC)


title: Liver, Trp53-/-_mouse_0011, 26.5_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Liver

value: 26.5 weeks

value: Female


title: CUT&Tag of NELFB in BRIP1 OE cells treated without FB rep2.

description: Library name: BRIP1_Ctrl_NELFB_2


title: CUT&Tag of NELFB in  DHX36 OE cells treated with FB rep1.

description: Library name: DHX_FP_NELFB_1


title: Thymus, Trp53-/-_mouse_0011, 26.5_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Thymus

value: Thymus


title: CUT&Tag of NELFA in  DHX36 OE cells treated with FB rep2.

description: Library name: DHX_FP_NELFA_2


title: P635L mice injected with Tnpo3 virus, rep. 2

description: Library name: P635L_Tnpo3_2


title: P635L mice injected with Tnpo3 virus, rep. 1

description: Library name: P635L_Tnpo3_1


title: vascularized adipose organoid with Celastrol treatment-2

description:
Library name: SAMPLE_11
T02-2

value: WT


title: LymphNodes, Trp53-/-_mouse_0011, 26.5_week-old_plate1

description: Updated Microwell-seq_scRNA-seq


title: CUT&Tag of NELFB in  DHX36 OE cells treated without FB rep2.

description: Library name: DHX_Ctrl_NELFB_2

value: liver


title: Spleen, Trp53-/-_mouse_0011, 26.5_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Spleen


title: vascularized adipose organoid with Celastrol treatment-1

description:
Library name: SAMPLE_10
T02-1


title: vascularized adipose organoid-2-1

description:
Library name: SAMPLE_7
V01-1


title: CUT&Tag of NELFA in  DHX36 OE cells treated with FB rep1.

description: Library name: DHX_FP_NELFA_1

value: tumor cells

value: Early S Phase-Synchronized


title: CUT&Tag of NELFB in  DHX36 OE cells treated without FB rep1.

description: Library name: DHX_Ctrl_NELFB_1


title: P635L mice injected with Ctr virus, rep. 3

description: Library name: P635L_Ctr_3

value: Ctr


title: vascularized adipose organoid-2-3

description:
Library name: SAMPLE_9
V01-3


title: P635L mice injected with Ctr virus, rep. 4

description: Library name: P635L_Ctr_4


title: Liver, Trp53-/-_mouse_0011, 26.5_week-old_plate1

description: Updated Microwell-seq_scRNA-seq


title: WT mice injected with Tnpo3 virus, rep. 4

description: Library name: WT_Tnpo3_4


title: SubcutaneousMass, Trp53-/-_mouse_0018, 36_week-old_plate3

description: Updated Microwell-seq_scRNA-seq

source_name: SubcutaneousMass

value: SubcutaneousMass

value: 36 weeks


title: vascularized adipose organoid-1-3

description:
Library name: SAMPLE_6
VO3


title: CUT&Tag of NELFA in  DHX36 OE cells treated without FB rep1.

description: Library name: DHX_Ctrl_NELFA_1

source_name: liver


title: P635L mice injected with Ctr virus, rep. 1

description: Library name: P635L_Ctr_1


title: vascularized adipose organoid-1-1

description:
Library name: SAMPLE_4
VO1


title: vascularized adipose organoid-1-2

description:
Library name: SAMPLE_5
VO2


title: CUT&Tag of NELFB in Ctrl cells treated with FB rep2.

description: Library name: Ctrl_FP_NELFB_2


title: WT mice injected with Tnpo3 virus, rep. 3

description: Library name: WT_Tnpo3_3


title: WT mice injected with Tnpo3 virus, rep. 2

description: Library name: WT_Tnpo3_2


title: Stomach, Trp53-/-_mouse_0018, 36_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Stomach

value: Stomach


title: SubcutaneousMass, Trp53-/-_mouse_0018, 36_week-old_plate2

description: Updated Microwell-seq_scRNA-seq


title: CUT&Tag of NELFB in Ctrl cells treated with FB rep1.

description: Library name: Ctrl_FP_NELFB_1


title: Lung, Trp53-/-_mouse_0011, 26.5_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Lung

value: Lung


title: vascularized adipose organoid-2-2

description:
Library name: SAMPLE_8
V01-2

value: peripheral blood


title: P635L mice injected with Ctr virus, rep. 2

description: Library name: P635L_Ctr_2

value: Heart


title: WT mice injected with Tnpo3 virus, rep. 1

description: Library name: WT_Tnpo3_1


title: CUT&Tag of NELFA in Ctrl cells treated with FB rep2.

description: Library name: Ctrl_FP_NELFA_2


title: CUT&Tag of NELFA in  DHX36 OE cells treated without FB rep2.

description: Library name: DHX_Ctrl_NELFA_2


title: CUT&Tag of NELFA in Ctrl cells treated with FB rep1.

description: Library name: Ctrl_FP_NELFA_1


title: AbdominalMass, Trp53-/-_mouse_0018, 36_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: AbdominalMass


title: CUT&Tag of NELFB in Ctrl cells treated without FB rep2.

description: Library name: Ctrl_Ctrl_NELFB_2


title: WT mice injected with Ctr virus, rep. 4

description: Library name: WT_Ctr_4


title: standard adipose organoid-2

description:
Library name: SAMPLE_2
DO2

value: Primary Cells

value: peripheral blood mesenchymal stem cells(PBMSC)


title: AbdominalMass, Trp53-/-_mouse_0018, 36_week-old_plate3

description: Updated Microwell-seq_scRNA-seq

value: Female


title: Spleen, Trp53-/-_mouse_0018, 36_week-old_plate2

description: Updated Microwell-seq_scRNA-seq


title: SubcutaneousMass, Trp53-/-_mouse_0018, 36_week-old_plate1

description: Updated Microwell-seq_scRNA-seq


title: standard adipose organoid-1

description:
Library name: SAMPLE_1
DO1


title: WT mice injected with Ctr virus, rep. 3

description: Library name: WT_Ctr_3


title: Healthy Control  NO3

city: Nanjing

first: fang

last: lu

address: 300 Guangzhou Road

department: Department of Nephrology

institute: the First Affiliated Hospital of Nanjing Medical University

description:
Library name: NC sample 3
BD Rhapsody

data_processing:
Fastp and default parameters are used to filter the adapter sequence and delete low-quality reads to obtain clean data. With the application UMI-tools, the single cell transcriptome recognizes the whitelist of cell barcodes. Then the data were mapped to the human genome (Ensemble version 91) by STAR mapping. The UMI-tools standard pipeline was used to obtain the UMI counts for each sample. Cell with more than 200 expressed genes and mitochondria UMI rate below 20% passed the cell quality filtering and mitochondria genes.
Assembly: Human GRCh38
Supplementary files format and content: Tab-separated values files, matrix files,

source_name: PMBC

extract_protocol:
Peripheral blood were obtained and collected in heparin anticoagulant tubes. Fresh blood was separated to obtain peripheral blood mononuclear cells (PBMC) by using Histopaque-10771 (Sigma Aldrich, catalog No.10771-6 ×100 mL) according to the manufacturer’s protocol.
Single-cell transcriptome information was captured using the BD Rhapsody system. The single-cell suspension was randomly assigned to 200,000 micropores by a limited dilution method. The beads with oligonucleotide barcodes were added to the saturated state and paired with cells in the micropores. The cells were cleaved in micropores to hybridize mRNA molecules and the oligonucleotides on the beads were captured by bar code. After reverse transcription, ExoI digestion was performed in a test tube. During cDNA synthesis, a unique molecular identifier (UMI) was bound to each cDNA molecule at the 5’ end to indicate the origin of the cell. The BD Rhapsody single-cell full transcriptome workflow includes random primer and extension (RPE), RPE amplification PCR and WTA index PCR to prepare a full transcriptome library. The high-sensitivity DNA chip (Agilent) on the bioanalyzer 2200 and the qubit high-sensitivity DNA analysis (Thermo Fisher Scientific) were used to quantify the library. The sequencing was done on a 150-bp paired-end run by an Illumina sequencer (Illumina, San Diego, CA).

value: PMBC


title: CUT&Tag of NELFB in Ctrl cells treated without FB rep1.

description: Library name: Ctrl_Ctrl_NELFB_1


title: WT mice injected with Ctr virus, rep. 2

description: Library name: WT_Ctr_2

value: WT


title: Healthy Control  NO2

description:
Library name: NC sample 2
BD Rhapsody


title: WT mice injected with Ctr virus, rep. 1

description: Library name: WT_Ctr_1


title: keloid sample3

city: Dallas

first: Donald

last: Glass

state: TX

address: 5323 Harry Hines Blvd, Mail Code 9069

department: Dermatology

institute: UT Southwestern Medical Center

description:
Library name: DG305_1_keloid
gencode.v19_GENES_counts_normalized.counts.CPM.tab

data_processing:
Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4) and were quality trimmed using fastq-mcf (ea-utils/1.1.2–806).
Trimmed fastq files were mapped to hg19 (UCSC version from igenomes or genecode) using TopHat, duplicates were marked using picard-tools, read counts were generated using featureCounts and differential expression analysis was performed using edgeR.
Differential gene expression lists were generated using the following cut-offs: log2 counts per million (CPM) ≥ 0, log2 fold change (FC) ≥ 0.6 or ≤ − 0.6, false discovery rate (FDR) ≤ 0.05.
Assembly: hg19 (UCSC version from igenomes or genecode)
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: keloid

extract_protocol:
RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen, Germany). One microgram of total DNase treated RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared with the TruSeq Stranded mRNA Library Prep Kit from Illumina following manufacturer's instructions.

value: keloid


title: MN patient NO6

description:
Library name: MN sample 6
BD Rhapsody


title: standard adipose organoid-3

description:
Library name: SAMPLE_3
DO3


title: AbdominalMass, Trp53-/-_mouse_0018, 36_week-old_plate1

description: Updated Microwell-seq_scRNA-seq


title: CUT&Tag of RNAPS5P in BRIP1 OE cells rep2.

description: Library name: BRIP1_S5_2

value: liver


title: Stomach, Trp53-/-_mouse_0018, 36_week-old_plate1

description: Updated Microwell-seq_scRNA-seq


title: Spleen, Trp53-/-_mouse_0018, 36_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Spleen


title: MN patient NO5

description:
Library name: MN sample 5
BD Rhapsody


title: CUT&Tag of NELFA in Ctrl cells treated without FB rep1.

description: Library name: Ctrl_Ctrl_NELFA_1

value: tumor cells

value: Early S Phase-Synchronized


title: Healthy Control  NO1

description:
Library name: NC sample 1
BD Rhapsody


title: keloid sample2

description:
Library name: DG277_1_Keloid
gencode.v19_GENES_counts_normalized.counts.CPM.tab


title: MesentericMass2, Trp53-/-_mouse_0072, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: 27 weeks


title: keloid sample1

description:
Library name: DG233_1_Keloid
gencode.v19_GENES_counts_normalized.counts.CPM.tab


title: Spleen, Trp53-/-_mouse_0072, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq


title: MN patient NO4

description:
Library name: MN sample 4
BD Rhapsody


title: normal skin sample2

description:
Library name: DG277_1_Normal
gencode.v19_GENES_counts_normalized.counts.CPM.tab

source_name: normal skin

value: normal skin


title: CUT&Tag of RNAPS2P in BRIP1 OE cells rep2.

description: Library name: BRIP1_S2_2


title: normal skin sample3

description:
Library name: DG305_1_normal
gencode.v19_GENES_counts_normalized.counts.CPM.tab


title: LargeIntestine, Trp53-/-_mouse_0072, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: LargeIntestine


title: CUT&Tag of NELFA in Ctrl cells treated without FB rep2.

description: Library name: Ctrl_Ctrl_NELFA_2


title: MN patient NO3

description:
Library name: MN sample 3
BD Rhapsody


title: CUT&Tag of NELFB in BRIP1 OE cells rep2.

description: Library name: BRIP1_NELFB_2


title: CUT&Tag of NELFB in BRIP1 OE cells rep1.

description: Library name: BRIP1_NELFB_1


title: normal skin sample1

description:
Library name: DG233_1_Normal
gencode.v19_GENES_counts_normalized.counts.CPM.tab


title: MN patient NO1

description:
Library name: MN sample 1
BD Rhapsody


title: D8_TGFB _ALK5_072

city: Leiden

first: Eveline

last: Gart

state: Zuid Holland

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Homo_sapiens.GRCh38.gencode.v29
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).

source_name: primary cell line

growth_protocol: Cryopreserved primary human HSCs from 8 donors were thawed and plated for expansion in Poly-L-Lysine (PLL) (2 μg/cm2) (ScienceCell Research Laboratories) 75 cm2 coated flasks (Greiner, Cat#658175) to enhance cell attachment. Primary HSCs were seeded in Stellate cell medium (SteCM) containing 2% FBS 1%, penicillin/streptomycin (PS) and 1% Stellate cell growth supplement (SteCGS) (ScienceCell, SCC5301). Cells were incubated at 37°C and 5% CO2.  After 4h, when cells were attached to the bottom of the flask, they were refreshed with new SteCM medium. Cells were passaged after 7 days of culture by detaching them with 2.5 ml/flask accutase (Sigma, Cat#A6964). After 3-5 min incubation, accutase was inactivated with 7.5 ml/flask SteCM medium. Cells were counted with Scepter™ 3.0 Cell Counter with 60 μm counter sensors and seeded in 24-well cell culture plates (Costar Corning, Cat#3524) coated with fibronectin (Merck Life Science #10838039001) at a density of 3.69E+04 cells/well in a final volume of 500 μl/well.

extract_protocol:
Next generation sequencing (NGS) was performed in RNA samples extracted from the 8 conditions mentioned above in biological duplicates. RNA was isolated using the RNAqeus Microkit (Thermo Fisher Scientific, Cat#AM1931) and RNA concentrations were determined using NanoDrop 2000 (Unigen Life Sciences) and RNA integrity was assessed using RNA 6000 Nano LabChip 669 kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, the Netherlands). NGS (NovaSeq6000) was performed at GenomeScan (Leiden, the Netherlands).
Total RNA was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 sequencer with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~20-77 million read counts per sample.
Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: The following day (day 1), before trigger solutions were added, cells were washed with SteCM containing 1% FBS and 1% PS. Trigger solutions were prepared in complete SteCM containing 1% FBS, 1% PS, 1% insulin-transferrin-sodium selenite (ITS) (Sigma, Cat#I3146), 173 μM ascorbic acid (AA) (Sigma, Cat#A8960), 2.5 mM L-proline (Sigma, P5607), 2.5 mM lysine (Sigma, Cat#62840), and 2.5 mM glycine (Sigma, Cat#G5417). Trigger solutions included combinations of TGF-β1 (R&D Systems, Cat#240-B) at a concentration of 4 ng/ml, Alk5 inhibitor (Millipore #616459) at a concentration of 5 μM and IOX2 (Sigma, Cat#SML0652) at concentrations of 0.3 μM and 1 μM.  In total, 8 different trigger solutions (control, IOX2 0.3, IOX2 1, TGF-β1, TGF-β1 + Alk5, TGF-β1 + IOX2 0.3, TGF-β1 + IOX2 0.3 + Alk5 and TGF-β1 + IOX2 1) were added in a final volume of 300 μl/well and incubated for 4 days.

value: primary cell line

value: Healthy LiverStellate Cells

value: TA

tag: age donor

tag: causedeath donor

value: Trauma

tag: gender donor

value: Male

tag: ethnicity donor

value: Hispanic

tag: f-score donor_liver

tag: nas-score donor_liver

tag: bmi donor

tag: diagnosis donor_liver

value: Healthy


title: primary keloid fibroblasts sample3, siRUNX2

description: Library name: Sample_KD3

growth_protocol: keloid primary fibroblasts were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% Antibiotic-Antimycotic at 37°C in a humidified atmosphere with 5% CO₂

extract_protocol:
RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen, Germany). One microgram of total DNase treated RNA was used for the construction of sequencing libraries.
RNA libraries for RA-seq were prepared with the TruSeq Stranded mRNA Library Prep Kit from Illumina following manufacturer's instructions.

treatment_protocol: Fibroblasts were transfected using Amaxa P2 primary Cell 4D-Nucleofector X kit S (Lonza, Germany) and Lonza 4D-Nucleofector machine. After transfection, cells were incubated for 72 h before RNA extraction.

tag: tissue

value: primary keloid fibroblasts

value: RUNX2 knockdown


title: Spleen, Trp53-/-_mouse_0072, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

tag: strain

tag: genotype

value: Female


title: CUT&Tag of NELFA in BRIP1 OE cells rep2.

description: Library name: BRIP1_NELFA_2

value: liver


title: MesentericMass1, Trp53-/-_mouse_0072, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

tag: age

tag: Sex


title: CUT&Tag of RNAPS5P in BRIP1 OE cells rep1.

description: Library name: BRIP1_S5_1

tag: cell line

tag: cell type


title: MesentericMass2, Trp53-/-_mouse_0072, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq


title: CUT&Tag of NELFA in BRIP1 OE cells rep1.

description: Library name: BRIP1_NELFA_1

tag: treatment


title: D8_TGFB _ALK5_064


title: primary keloid fibroblasts sample1, siRUNX2

description: Library name: Sample_KD1

value: keloid


title: MesentericMass1, Trp53-/-_mouse_0072, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq


title: primary keloid fibroblasts sample2, siRUNX2

description: Library name: Sample_KD2


title: LargeIntestine, Trp53-/-_mouse_0072, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq


title: primary keloid fibroblasts sample3, siControl

description: Library name: Sample_CTRL3

value: WT


title: CUT&Tag of RNAPS2P in BRIP1 OE cells rep1.

description: Library name: BRIP1_S2_1

value: tumor cells

value: Early S Phase-Synchronized


title: CUT&Tag of cyclinT1 in BRIP1 OE cells rep2.

description: Library name: BRIP1_cyclinT1_2


title: D8_TGFB _ALK5_056


title: D8_TGFB_071

value: T


title: CUT&Tag of CTD in BRIP1 OE  cells rep2.

description: Library name: BRIP1_CTD_2


title: MN patient NO2

description:
Library name: MN sample 2
BD Rhapsody

value: PMBC


title: D8_TGFB_055

value: primary cell line


title: primary keloid fibroblasts sample2, siControl

description: Library name: Sample_CTRL2


title: Liver, Trp53-/-_mouse_0078, 24_week-old_plate4

description: Updated Microwell-seq_scRNA-seq

value: Liver

value: 24 weeks


title: Stomach, Trp53-/-_mouse_0078, 24_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Stomach


title: primary keloid fibroblasts sample1, siControl

description: Library name: Sample_CTRL1


title: Liver, Trp53-/-_mouse_0078, 24_week-old_plate3

description: Updated Microwell-seq_scRNA-seq


title: D8_TGFB_063

value: Healthy LiverStellate Cells

value: Trauma

value: Male


title: CUT&Tag of CTD in BRIP1 OE  cells rep1.

description: Library name: BRIP1_CTD_1


title: CUT&Tag of G4-DNA in BRIP1 OE cells rep2.

description: Library name: BRIP1_BG4_2


title: Liver, Trp53-/-_mouse_0078, 24_week-old_plate2

description: Updated Microwell-seq_scRNA-seq


title: D8_Control_070

value: C

value: Hispanic

value: Healthy


title: D7_TGFB _ALK5_069

value: TA

value: Anoxia

value: Caucasian


title: E_Foxf2-Flag_ChIP_r2

city: Planegg-Martinsried

first: Filippo M.

last: Cernilogar

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

data_processing:
The NGS pipeline (https://github.com/gscarnuntum/NGS.repeats.analysis) with default settings was used for primary analysis and quality controls. Briefly, after adapter trimming with Trimmomatic reads were mapped with Bowtie2 to the hg38 human genome (parameters: --very-sensitive -X 2000). Following alignment read deduplication was carried out using Picard MarkDuplicates (Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; parameters: --VALIDATION_STRINGENCY LENIENT). Signal tracks for visualization with IGV genome browser (https://doi.org/10.1038/nbt.1754) were generated with deepTools bamCoverage tool104 (parameters:  –bam --binSize 10 --normalizeUsing RPKM).
Assembly: hg38
Supplementary files format and content: Coverage  tracks (bigWig) for visualization  with IGV genome browser (https://doi.org/10.1038/nbt.1754) were generated with deepTools bamCoverage tool104 (parameters:  –bam --binSize 10 --normalizeUsing RPKM). The coverage is calculated as the number of normalized reads per bin, where bins are short consecutive counting windows of a defined size.
Supplementary files format and content: bigWig

growth_protocol: Cells grown in Endothelial cell medium (Promocell) until reaching 100% confluency

extract_protocol:
ChIPseq was done essentially as previously described (Cernilogar et al. Nucleic Acids Res, 2019  PMID 31350899). Briefly, two million cross-linked cells (1% formaldehyde, 10min RT) were lysed in 100 μl Buffer-B-0.3 (50mM Tris-HCl, pH 8.0, 10 mM EDTA, 0.3% SDS, 1x protease inhibitors, Roche) and sonicated in a microtube (Covaris, Cat# 520045) using a Covaris S220 device until most of the DNA fragments were 200-500 base pairs long (settings: temperature 4°C, duty cycle 2%, peak incident power 105 Watts, cycles per burst 200). After shearing, lysates were centrifuged (10min, 4°C, 12000g) and supernatant diluted with 1 volume of Dilution Buffer (1mM EGTA 300 mM NaCl, 2% Triton x-100, 0.2% sodium deoxycholate, 1x protease inhibitors, Roche). Sonicated chromatin was then incubated for 4 h at 4°C on a rotating wheel with 3 μg of anti-Flag antibody (Sigma Cat# F1804) conjugated to 30 µl of Protein-G Dynabeads (Thermofisher). Beads were washed five times with Buffer-A (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 0.5 mM EGTA,1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl, 1x protease inhibitors) and once with Buffer-C (10 mM Tris-HCl, pH 8.0, 10 mM EDTA). Beads were then incubated with 70 μl elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0) containing 2 μl of Proteinase K (20mg/ml) for 1 h at 55°C and 8 h at 65°C to revert formaldehyde crosslinking, and supernatant was transferred to a new tube. Another 30 μl of elution buffer was added to the beads for 1 minute and eluates were combined and incubated with another 1 μl of Proteinase K for 1 h at 55°C. Finally, DNA was purified with SPRI AMPure XP beads (Beckman Coulter) (sample-to-beads ratio 1:2).
Purified DNA was used as input for library preparation with Thruplex DNA-seq Kit (Takara, Cat# R400674) and processed according to the manufacturer´s instruction.

treatment_protocol: Doxycycline treatment 4ug/ml for 48h

value: IPS-derived endothelial cells

tag: chip antibody

value: Anti-Flag M2 Sigma F1804

tag: genetic modification

value: overexpressing FOXF2-FLAG-T2a-mCherry

value: doxycycline


title: CUT&Tag of CDK7 in BRIP1 OE cells rep2.

description: Library name: BRIP1_CDK7_2

value: liver

value: tumor cells

value: Early S Phase-Synchronized


title: CUT&Tag of G4-DNA in BRIP1 OE cells rep1.

description: Library name: BRIP1_BG4_1


title: D8_Control_062

value: primary cell line

tag: age donor

tag: causedeath donor


title: Pancreas, Trp53-/-_mouse_0078, 24_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Pancreas

value: Pancreas

value: 24 weeks

value: Female


title: Lung, Trp53-/-_mouse_0078, 24_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Lung


title: CUT&Tag of CDK7 in BRIP1 OE  cells rep1.

description: Library name: BRIP1_CDK7_1


title: D8_Control_054

value: Healthy LiverStellate Cells

value: C

value: Trauma

tag: gender donor

value: Male

tag: ethnicity donor

value: Hispanic


title: CUT&Tag of cyclinT1 in BRIP1 OE cells rep1.

description: Library name: BRIP1_cyclinT1_1


title: CUT&Tag of RNAPS5P in DHX36 OE cells rep2.

description: Library name: DHX_S5_2


title: Stomach, Trp53-/-_mouse_0078, 24_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Stomach


title: E_Foxf2-Flag_ChIP_r1

value: IPS-derived endothelial cells

value: Anti-Flag M2 Sigma F1804


title: 4T1_p24_4

type: RNA

city: Milan

first: Annamaria

last: Piva

address: via Amadeo, 42

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

description: Gene expresision data from a Triple Negative Breast Cancer (TNBC) cell line with low Sparc expression level

hyb_protocol: Hybridization was performed according to manufacturer's standard protocols

scan_protocol: Gene microarrays were scanned with the Gene Chip System 3000 Scanner

data_processing: The raw data were pre-processed using the SST-RMA algorithm provided in the Transcriptome Analysis Console software (Thermo Fisher).

label: biotin

label_protocol: RNA was labeled according to manufacturer's recommended protocols

extract_protocol: Total RNA was extracted using the Mirneasy mini kit (QIAGEN).

value: Triple Negative Breast Cancer (TNBC)


title: Pancreas, Trp53-/-_mouse_0078, 24_week-old_plate2

description: Updated Microwell-seq_scRNA-seq


title: Lung, Trp53-/-_mouse_0078, 24_week-old_plate1

description: Updated Microwell-seq_scRNA-seq


title: CUT&Tag of RNAPS5P in DHX36 OE cells rep1.

description: Library name: DHX_S5_1

value: liver


title: D7_TGFB _ALK5_053

value: TA

value: Anoxia

value: Caucasian

tag: f-score donor_liver

tag: nas-score donor_liver

value: Healthy


title: D7_TGFB_068

value: primary cell line

value: T

tag: bmi donor

tag: diagnosis donor_liver


title: Liver, Trp53-/-_mouse_0078, 24_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Liver

tag: tissue

value: Liver

tag: strain

value: 24 weeks

value: Female


title: D7_TGFB_060

value: Healthy LiverStellate Cells

tag: genotype


title: Uterus, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Uterus

value: Uterus

tag: age

value: 27 weeks

tag: Sex


title: D7_TGFB _ALK5_061

tag: cell line

tag: cell type

value: Male


title: CUT&Tag of NELFB in DHX36 OE cells rep2.

description: Library name: DHX_NELFB_2

value: tumor cells

tag: treatment

value: Early S Phase-Synchronized


title: CUT&Tag of RNAPS2P in DHX36 OE cells rep1.

description: Library name: DHX_S2_1


title: D7_TGFB_052


title: 4T1_p24_3

value: Triple Negative Breast Cancer (TNBC)


title: 4T1_p24_2


title: CUT&Tag of NELFB in DHX36 OE cells rep1.

description: Library name: DHX_NELFB_1

value: liver


title: Stomach, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Stomach


title: D7_Control_059

value: C

value: Anoxia


title: 4T1_p22_1


title: 4T1_cl5_sp548_p9_4


title: D7_Control_067

value: Caucasian

value: Healthy


title: Spleen, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Spleen


title: 4T1_cl5_sp548_p8_2


title: CUT&Tag of RNAPS2P in DHX36 OE cells rep2.

description: Library name: DHX_S2_2


title: D7_Control_051

value: primary cell line


title: D6_TGFB _ALK5_066

value: TA


title: CUT&Tag of NELFA in DHX36 OE cells rep2.

description: Library name: DHX_NELFA_2


title: SmallIntestine, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: SmallIntestine

value: SmallIntestine

value: Female


title: 4T1_cl5_sp548_p8_1


title: CUT&Tag of NELFA in DHX36 OE cells rep1.

description: Library name: DHX_NELFA_1


title: 4T1_Cl5_p21_4

description: Gene expresision data from a Triple Negative Breast Cancer (TNBC) cell line with high Sparc expression level

source_name: 4T1 cl 5

value: 4T1 cl 5


title: D6_TGFB _ALK5_058

value: Healthy LiverStellate Cells


title: Thymus, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Thymus

value: 27 weeks


title: MammaryGland, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: MammaryGland

value: MammaryGland


title: CUT&Tag of cyclinT1 in DHX36 OE cells rep2.

description: Library name: DHX_cyclinT1_2

value: tumor cells

value: Early S Phase-Synchronized


title: CUT&Tag of cyclinT1 in DHX36 OE cells rep1.

description: Library name: DHX_cyclinT1_1

value: liver


title: 4T1_cl5_sp548_p9_3

value: Triple Negative Breast Cancer (TNBC)


title: 4T1_Cl5_p21_3


title: D6_TGFB _ALK5_050

value: Anoxia


title: LymphNodes, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: LymphNodes

value: LymphNodes


title: CUT&Tag of CTD in DHX36 OE cells rep2.

description: Library name: DHX_CTD_2


title: Lung, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Lung


title: 4T1_Cl5_p19_1


title: Liver, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Liver


title: THP-1 derived macrophages, medium_control, bio_rep 3, tech_rep 2

city: Amsterdam

first: Selina

last: van Leeuwen

address: Science Park 904

department: MAD

institute: University of Amsterdam

description: Library name: S42

data_processing:
The raw sequencing data was subjected to quality control with FastQC v0.11.9 and MultiQC version 1.21. Subsequently, the reads were trimmed with Trimmomatic v0.39.
The reads were aligned (without softclipping) to the human reference genome (GRCh38.111) using HISAT2 version 2.2.1. HTSeq-count version 2.0.5 was used to count the amount of reads per gene and determine the gene expression values.
Assembly: GRCh38.111
Supplementary files format and content: tsv file includes raw counts for each sample

source_name: cell line

growth_protocol: THP-1 M0 macrophages, differentiated in 96 well plates, were incubated in RPMI-1640 at 37℃, 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74134) following manufacturer's protocols.
NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) was used to perform a poly-A enrichment, followed by the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and NEBNext Multiplex Oligos for Illumina (Unique Dual Index Primer Pairs) (New England BioLabs) following manufacturer's protocols.

treatment_protocol: RPMI-1640 was supplemented with various dilutions of the conditioned media (1:25, 1:50, 1:100, and 1:200, diluted in RPMI-1640) for 6 hours at 37℃, 5% CO2.

value: cell line

value: macrophages

tag: batch


title: CUT&Tag of CTD in DHX36 OE cells rep1.

description: Library name: DHX_CTD_1


title: CUT&Tag of CDK7 in DHX36 OE cells rep2.

description: Library name: DHX_CDK7_2


title: D6_TGFB_057

value: primary cell line

value: T

tag: age donor

value: Caucasian

value: Healthy


title: THP-1 derived macrophages, co-culture_mutant_exposure, bio_rep 1, tech_rep 1

description: Library name: S41


title: CUT&Tag of CDK7 in DHX36 OE cells rep1.

description: Library name: DHX_CDK7_1


title: D6_TGFB_049

value: Healthy LiverStellate Cells

tag: causedeath donor

value: Female


title: Kidney, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Kidney

value: Kidney

value: 27 weeks


title: Heart, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Heart

value: Heart


title: D6_Control_048

value: C

tag: gender donor


title: THP-1 derived macrophages, monocyte_control, bio_rep 2, tech_rep 2

description: Library name: S40


title: THP-1 derived macrophages, medium_control, bio_rep 1, tech_rep 1

description: Library name: S44


title: D6_Control_040

tag: ethnicity donor


title: CUT&Tag of G4-DNA in DHX36 OE cells rep1.

description: Library name: DHX_BG4_1

source_name: liver

value: liver

value: tumor cells

value: Early S Phase-Synchronized


title: D6_TGFB_065

value: Anoxia

tag: f-score donor_liver


title: Gallbladder-BileDuct, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Gallbladder-BileDuct

value: Gallbladder-BileDuct


title: 4T1_Cl5_p19_2

value: 4T1 cl 5

value: Triple Negative Breast Cancer (TNBC)


title: Brain, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Brain

value: Brain


title: THP-1 derived macrophages, medium_control, bio_rep 3, tech_rep 3

description: Library name: S38

value: cell line

value: macrophages


title: D6_Control_032

value: primary cell line

value: Caucasian

tag: nas-score donor_liver

value: Healthy


title: LargeIntestine, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: LargeIntestine

value: LargeIntestine

value: Female


title: THP-1 derived macrophages, co-culture_mutant_exposure, bio_rep 3, tech_rep 1

description: Library name: S43


title: THP-1 derived macrophages, medium_control, bio_rep 1, tech_rep 2

description: Library name: S37


title: CUT&Tag of RNAPS5P in Ctrl cells rep2.

description: Library name: Ctrl_S5_2


title: D5_TGFB _ALK5_047

value: Healthy LiverStellate Cells

value: TA

value: CVA/Stroke

value: Male

value: Hispanic

tag: bmi donor


title: BoneMarrow, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: BoneMarrow

value: BoneMarrow

value: 27 weeks


title: THP-1 derived macrophages, medium_control, bio_rep 2, tech_rep 1

description: Library name: S36


title: D5_TGFB _ALK5_039

tag: diagnosis donor_liver


title: Bladder, Trp53+/+_mouse_0704, 27_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Bladder

tag: tissue

value: Bladder


title: CUT&Tag of RNAPS5P in Ctrl cells rep1.

description: Library name: Ctrl_S5_1

value: liver

value: tumor cells

value: Early S Phase-Synchronized


title: CUT&Tag of RNAPS2P in Ctrl cells rep2.

description: Library name: Ctrl_S2_2


title: THP-1 derived macrophages, co-culture_mutant_exposure, bio_rep 1, tech_rep 3

description: Library name: S35

value: cell line

value: macrophages


title: CUT&Tag of G4-DNA in DHX36 OE cells rep2.

description: Library name: DHX_BG4_2


title: Uterus, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Uterus

tag: strain


title: D5_TGFB _ALK5_031

source_name: primary cell line

value: primary cell line

tag: genotype

value: Healthy


title: THP-1 derived macrophages, co-culture_mutant_exposure, bio_rep 2, tech_rep 3

description: Library name: S34


title: CUT&Tag of RNAPS2P in Ctrl cells rep1.

description: Library name: Ctrl_S2_1


title: THP-1 derived macrophages, co-culture_exposure, bio_rep 1, tech_rep 1

description: Library name: S39


title: Thymus, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Thymus

value: Thymus

tag: age

value: Female


title: D5_TGFB_046

value: Healthy LiverStellate Cells

value: T


title: CUT&Tag of NELFB in Ctrl cells rep2.

description: Library name: Ctrl_NELFB_2


title: THP-1 derived macrophages, monocyte_control, bio_rep 1, tech_rep 1

description: Library name: S33


title: Stomach, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Stomach

value: Stomach

tag: Sex


title: D5_TGFB_038

tag: cell line

value: CVA/Stroke

value: Male

value: Hispanic


title: CUT&Tag of NELFB in Ctrl cells rep1.

description: Library name: Ctrl_NELFB_1

tag: cell type


title: D5_TGFB_030

tag: treatment


title: THP-1 derived macrophages, c. albicans_exposure, bio_rep 1, tech_rep 1

description: Library name: S31

value: c. albicans_exposure

tag: batch


title: SmallIntestine, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: SmallIntestine

value: 27 weeks


title: CUT&Tag of NELFA in Ctrl cells rep1.

description: Library name: Ctrl_NELFA_1

value: liver

value: tumor cells

value: Early S Phase-Synchronized


title: Spleen, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Spleen

value: Spleen


title: D5_Control_037

value: primary cell line

value: C

tag: age donor


title: THP-1 derived macrophages, s. aureus_exposure, bio_rep 2, tech_rep 2

description: Library name: S30

value: cell line

value: macrophages

value: s. aureus_exposure


title: Pancreas, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Pancreas

value: Pancreas

value: Female


title: THP-1 derived macrophages, s. aureus_exposure, bio_rep 1, tech_rep 1

description: Library name: S29


title: CUT&Tag of NELFA in Ctrl cells rep2.

description: Library name: Ctrl_NELFA_2


title: CUT&Tag of cyclinT1 in Ctrl cells rep2.

description: Library name: Ctrl_cyclinT1_2


title: CUT&Tag of cyclinT1 in Ctrl cells rep1.

description: Library name: Ctrl_cyclinT1_1


title: MammaryGland, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: MammaryGland


title: D5_Control_045

value: Healthy LiverStellate Cells

tag: causedeath donor

value: CVA/Stroke

value: Male

value: Healthy


title: D5_Control_029

tag: gender donor

value: Hispanic


title: D4_TGFB _ALK5_044

value: Diseased LiverStellate Cells

value: TA

tag: ethnicity donor

value: Caucasian

value: Diseased


title: CUT&Tag of CTD in Ctrl cells rep2.

description: Library name: Ctrl_CTD_2

value: liver

value: tumor cells

value: Early S Phase-Synchronized


title: LymphNodes, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: LymphNodes

value: 27 weeks


title: D4_TGFB _ALK5_036

value: primary cell line

tag: f-score donor_liver


title: THP-1 derived macrophages, c. albicans_exposure, bio_rep 2, tech_rep 2

description: Library name: S32

value: cell line

value: macrophages

value: c. albicans_exposure


title: CUT&Tag of CTD in Ctrl cells rep1.

description: Library name: Ctrl_CTD_1


title: THP-1 derived macrophages, s. aureus_exposure, bio_rep 3, tech_rep 3

description: Library name: S26

value: s. aureus_exposure


title: Lung, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Lung

value: Lung

value: Female


title: D4_TGFB _ALK5_028

value: CVA/Stroke

value: Male

tag: nas-score donor_liver


title: Liver, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Liver

value: Liver


title: THP-1 derived macrophages, s. aureus_exposure, bio_rep 1, tech_rep 2

description: Library name: S25


title: D4_TGFB_043

value: Diseased LiverStellate Cells

value: T

value: Caucasian

tag: bmi donor


title: THP-1 derived macrophages, c. albicans_exposure, bio_rep 3, tech_rep 3

description: Library name: S24


title: CUT&Tag of CDK7 in  Ctrl cells rep1.

description: Library name: Ctrl_CDK7_1

value: liver

value: tumor cells


title: D4_TGFB_035

tag: diagnosis donor_liver

value: Diseased


title: LargeIntestine, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

tag: tissue

value: LargeIntestine

value: 27 weeks


title: THP-1 derived macrophages, co-culture_exposure, bio_rep 1, tech_rep 2

description: Library name: S23

value: cell line


title: CUT&Tag of RNAPS5P treated with PhpC rep2.

description: Library name: PhpC_S5_2

value: Early S Phase-Synchronized


title: Kidney, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Kidney

tag: strain


title: CUT&Tag of RNAPS5P treated with PhpC rep1.

description: Library name: PhpC_S5_1


title: THP-1 derived macrophages, c. albicans_exposure, bio_rep 3, tech_rep 1

description: Library name: S28

value: macrophages

value: c. albicans_exposure


title: THP-1 derived macrophages, co-culture_exposure, bio_rep 3, tech_rep 2

description: Library name: S22


title: D4_TGFB_027

value: primary cell line

tag: genotype


title: THP-1 derived macrophages, c. albicans_exposure, bio_rep 1, tech_rep 2

description: Library name: S27


title: D4_Control_042

value: C

value: CVA/Stroke


title: THP-1 derived macrophages, co-culture_mutant_exposure, bio_rep 1, tech_rep 2

description: Library name: S21


title: Gallbladder-BileDuct, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Gallbladder-BileDuct

tag: age

value: Female


title: CUT&Tag of RNAPS2P treated with PhpC rep2.

description: Library name: PhpC_S2_2


title: D4_Control_034

value: Diseased LiverStellate Cells

value: Male


title: THP-1 derived macrophages, co-culture_mutant_exposure, bio_rep 2, tech_rep 2

description: Library name: S20


title: CUT&Tag of RNAPS2P treated with PhpC rep1.

description: Library name: PhpC_S2_1

value: liver


title: Brain, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Brain

tag: Sex


title: CUT&Tag of CDK7 in Ctrl cells rep2.

description: Library name: Ctrl_CDK7_2

tag: cell line

value: tumor cells


title: CUT&Tag of G4-DNA treated with PhpC rep2.

description: Library name: PhpC_BG4_2

tag: cell type


title: BoneMarrow, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: BoneMarrow


title: D4_Control_026

tag: treatment

value: Caucasian

value: Diseased


title: THP-1 derived macrophages, medium_control, bio_rep 1, tech_rep 3

description: Library name: S19

value: cell line

tag: batch


title: D3_TGFB _ALK5_041

value: TA

tag: age donor

value: Anoxia


title: Bladder, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Bladder

value: 27 weeks


title: CUT&Tag of RNAPS5P in Ctrl cells  rep2.

description: Library name: without_PhpC_S2_2

value: Early S Phase-Synchronized


title: THP-1 derived macrophages, s. aureus_exposure, bio_rep 3, tech_rep 2

description: Library name: S18

value: macrophages

value: s. aureus_exposure


title: Uterus, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Uterus

value: Uterus

value: 20 weeks

value: Female


title: CUT&Tag of G4-DNA treated with PhpC rep1.

description: Library name: PhpC_BG4_1

value: liver


title: Thymus, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Thymus


title: D3_TGFB _ALK5_033

value: primary cell line

value: Diseased LiverStellate Cells

tag: causedeath donor

value: Male


title: THP-1 derived macrophages, s. aureus_exposure, bio_rep 2, tech_rep 3

description: Library name: S17

source_name: cell line


title: THP-1 derived macrophages, co-culture_exposure, bio_rep 2, tech_rep 3

description: Library name: S16


title: CUT&Tag of RNAPS2P in Ctrl cells  rep2.

description: Library name: without_PhpC_S5_2

value: tumor cells


title: THP-1 derived macrophages, monocyte_control, bio_rep 2, tech_rep 1

description: Library name: S15

value: cell line


title: Heart, Trp53+/+_mouse_0704, 27_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Heart


title: D3_TGFB _ALK5_025

value: TA

value: Anoxia

tag: gender donor

value: Caucasian

value: Diseased


title: CUT&Tag of RNAPS5P in Ctrl cells  rep1.

description: Library name: without_PhpC_S2_1

value: Early S Phase-Synchronized


title: Stomach, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Stomach


title: D3_TGFB_024

value: T

tag: ethnicity donor


title: CUT&Tag of RNAPS2P in Ctrl cells  rep1.

description: Library name: without_PhpC_S5_1


title: D3_TGFB_008

tag: f-score donor_liver


title: D3_TGFB_016

tag: nas-score donor_liver


title: THP-1 derived macrophages, co-culture_exposure, bio_rep 1, tech_rep 3

description: Library name: S14

value: macrophages


title: Spleen, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Spleen

value: 20 weeks

value: Female


title: THP-1 derived macrophages, co-culture_exposure, bio_rep 2, tech_rep 1

description: Library name: S13


title: Pancreas, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Pancreas


title: D3_Control_023

value: primary cell line

value: Diseased LiverStellate Cells

value: C

tag: bmi donor


title: CUT&Tag of G4-DNA  in Ctrl cells rep1.

description: Library name: ctrl_BG4_1

value: liver

value: tumor cells


title: CUT&Tag of G4-DNA in Ctrl cells rep2.

description: Library name: ctrl_BG4_2


title: THP-1 derived macrophages, c. albicans_exposure, bio_rep 2, tech_rep 1

description: Library name: S12

value: cell line

value: c. albicans_exposure


title: D3_Control_015

value: Anoxia

value: Male

value: Caucasian

tag: diagnosis donor_liver


title: MammaryGland, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: MammaryGland

tag: tissue

value: MammaryGland


title: THP-1 derived macrophages, c. albicans_exposure, bio_rep 1, tech_rep 3

description: Library name: S11


title: CUT&Tag of RNAPS5P in shRFC3 cells rep2.

description: Library name: shRFC3_S5_2

value: Early S Phase-Synchronized


title: D2_TGFB _ALK5_022

value: TA

value: Diseased


title: LymphNodes, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: LymphNodes

value: LymphNodes

tag: strain

value: 20 weeks


title: THP-1 derived macrophages, c. albicans_exposure, bio_rep 3, tech_rep 2

description: Library name: S10

value: macrophages


title: Lung, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Lung

tag: genotype

value: Female


title: D2_TGFB _ALK5_014

value: primary cell line

value: Diseased LiverStellate Cells


title: CUT&Tag of RNAPS5Pin shRFC3 cells rep1.

description: Library name: shRFC3_S5_1

source_name: liver

value: liver

value: tumor cells


title: THP-1 derived macrophages, co-culture_mutant_exposure, bio_rep 3, tech_rep 3

description: Library name: S09

value: cell line


title: CUT&Tag of RNAPS2P in shRFC3 cells rep2.

description: Library name: shRFC3_S2_2


title: Liver, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Liver

tag: age


title: D2_TGFB _ALK5_006

value: Anoxia


title: THP-1 derived macrophages, medium_control, bio_rep 2, tech_rep 2

description: Library name: S08


title: LargeIntestine, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: LargeIntestine

tag: Sex


title: CUT&Tag of NELFB in shRFC3 cells rep2.

description: Library name: shRFC3_NELFB_2

tag: cell line


title: D2_TGFB_021

tag: cell type

value: T

value: Caucasian


title: THP-1 derived macrophages, co-culture_exposure, bio_rep 3, tech_rep 3

description: Library name: S07

tag: treatment


title: Ovary, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Ovary

value: Ovary


title: Kidney, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Kidney

value: Kidney


title: THP-1 derived macrophages, co-culture_mutant_exposure, bio_rep 2, tech_rep 1

description: Library name: S06

tag: batch


title: CUT&Tag of NELFB in shRFC3 cells rep1.

description: Library name: shRFC3_NELFB_1

value: Early S Phase-Synchronized


title: CUT&Tag of NELFA in shRFC3 cells rep2.

description: Library name: shRFC3_NELFA_2


title: D2_Control_020

value: C

tag: age donor

value: Diseased


title: THP-1 derived macrophages, s. aureus_exposure, bio_rep 3, tech_rep 1

description: Library name: S05

value: macrophages

value: s. aureus_exposure


title: D2_Control_012

value: primary cell line

tag: causedeath donor

value: Female


title: D2_TGFB_013

value: Diseased LiverStellate Cells

tag: gender donor


title: D2_Control_004

tag: ethnicity donor


title: THP-1 derived macrophages, s. aureus_exposure, bio_rep 1, tech_rep 3

description: Library name: S04


title: CUT&Tag of DHX36 in shRFC3 cells rep2.

description: Library name: shRFC3_DHX_2

value: liver

value: tumor cells


title: Heart, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Heart

value: Heart

value: 20 weeks


title: BoneMarrow, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: BoneMarrow

value: BoneMarrow


title: CUT&Tag of NELFA in shRFC3 cells rep1.

description: Library name: shRFC3_NELFA_1


title: CUT&Tag of DHX36 in shRFC3 cells rep1.

description: Library name: shRFC3_DHX_1


title: Brain, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Brain

value: Brain


title: CUT&Tag of RNAPS2P in shRFC3 cells rep1.

description: Library name: shRFC3_S2_1


title: THP-1 derived macrophages, medium_control, bio_rep 3, tech_rep 1

description: Library name: S02

value: cell line


title: D1_TGFB _ALK5_019

source_name: primary cell line

value: TA

value: Anoxia

value: Caucasian

tag: f-score donor_liver


title: CUT&Tag of CyclinT1 in shRFC3 cells rep2.

description: Library name: shRFC3_cyclinT1_2

value: Early S Phase-Synchronized


title: THP-1 derived macrophages, co-culture_exposure, bio_rep 2, tech_rep 2

description: Library name: S01


title: THP-1 derived macrophages, monocyte_control, bio_rep 3, tech_rep 1

description: Library name: S03


title: Uterus, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Uterus


title: D1_TGFB _ALK5_003

tag: nas-score donor_liver

value: Diseased


title: D1_TGFB _ALK5_011

tag: bmi donor


title: CUT&Tag of CyclinT1 in shRFC3 cells rep1.

description: Library name: shRFC3_cyclinT1_1


title: Thymus, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Thymus

value: Thymus


title: D1_TGFB_018

value: primary cell line

value: T

tag: diagnosis donor_liver


title: CUT&Tag of CTD in shRFC3 cells rep2.

description: Library name: shRFC3_CTD_2

tag: tissue


title: Stomach, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Stomach

value: Stomach

tag: strain

value: Female


title: p381 T cells (day 0) scTCR-seq

city: New Haven

first: Meng

last: Wang

state: CT

address: 300 George St

institute: Yale University

description:
Library name: p381_T_d0_VDJ
10x Genomics

data_processing:
Cell Ranger 3.1.0 count subcommand was used to generate the count matrices, barcode assignments, and feature calls for gene expression data.
Cell Ranger 3.1.0 vdj subcommand was used to assemble TCR and BCR sequences.
Seurat v4 was used to filter out low quality cells and Azimuth was used to perform cell type annotations.
Assembly: GCRhg38
Supplementary files format and content: cell ranger count matrix in h5 file format, cell ranger vdj clonotype files, seurat object in RDS format

source_name: T cells

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated; B cells were positively selected (CD20 beads, Miltenyi). Single-cell suspensions of CD20⁺ B cells and CD4 T cells were prepared at 1,000 cells/µL in 0.04% PBS-BSA, with >90% viability by trypan blue. Samples were transferred to the Yale Center for Genomic Analysis (YCGA) for 10x Chromium processing and sequencing.
10x Genomics Chromium Single Cell 5′ chemistry was used to generate single-cell 5′ gene-expression libraries.

value: T cells


title: p381 T cells (day 0) scRNA-seq

description:
Library name: p381_T_d0_RNA
10x Genomics


title: D1_TGFB_010

value: Diseased LiverStellate Cells

tag: genotype


title: p381 T cells (7 months) scTCR-seq

description:
Library name: p381_T_7m_VDJ
10x Genomics


title: p381 T cells (7 months) scRNA-seq

description:
Library name: p381_T_7m_RNA
10x Genomics


title: Bladder, Trp53+/+_mouse_0107, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Bladder

value: Bladder

tag: age

value: 20 weeks


title: Pancreas, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Pancreas

value: Pancreas

tag: Sex


title: CUT&Tag of CDK9 in shRFC3 cells rep2.

description: Library name: shRFC3_CDK9_2

value: liver

tag: cell line

value: tumor cells


title: Ovary, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Ovary


title: CUT&Tag of CDK9 in shRFC3 cells rep1.

description: Library name: shRFC3_CDK9_1

tag: cell type


title: D1_Control_009

tag: treatment

value: C

value: Anoxia

value: Caucasian


title: D1_Control_017

value: Diseased


title: p381 T cells (week 6) scTCR-seq

description:
Library name: p381_T_6w_VDJ
10x Genomics


title: MammaryGland, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: MammaryGland


title: LymphNodes, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: LymphNodes


title: p381 T cells (week 6) scRNA-seq

description:
Library name: p381_T_6w_RNA
10x Genomics


title: p381 B cells (day 0) scBCR-seq

description:
Library name: p381_B_d0_VDJ
10x Genomics

source_name: B cells

value: B cells


title: QYLXD012

first: Guangjian

last: Jiang

address: Beijing University of Traditional Chinese Medicine, No. 11 North Third Ring East Road, Beijing City

institute: Beijing University of Chinese Medicine, Beijing

description: 99,expression matrix.xlsx

data_processing:
Screen cDNA fragments of approximately 370~420 bp using AMPure XP beads, amplify by PCR, and purify the PCR product again using AMPure XP beads to obtain the final library. Determine the quality of the library using the Agilent 2100 System (NanoDrop ND-1000) analyzer and accurately quantify it (library effective concentration higher than 2nM) through quantitative real-time polymerase chain reaction before data analysis.
Assembly: Remove ribosome RNA (rRNA) using the Epicentre Ribozero™ rRNA removal kit (Epicentre, USA) before data analysis. Remove linear RNA using RNase R (Epicentre, USA). Finally, merge libraries according to the requirements of effective concentration and data volume, and sequence them using the Illumina NovaSeq 6000.
Supplementary files format and content: The values in the expression matrix are FPKM values for gene expression in subjects

extract_protocol:
The total RNA was extracted from venous blood collected from people with T2DM using Trizol (Invitrogen, USA).  To further control quality, agarose gel electrophoresis was used to test samples' integrity and NanoDrop-1000 was used to quantify them.
To construct each library, 1-2 g of total RNA were selected. Total RNA was first subjected to mRNA enrichment with NEB Next@ Poly A (or rRNA removal using RiboZero Magnetic Gold Kit). In this study, stranded RNA-seq libraries were prepared with KAPA Stranded RNA-Seq Library Prep kit. The KAPA kit uses a dUTP-based method for the construction of chain-specific libraries, which included the following steps: 1) Fragmentation of mRNA enrichment products, 2) reverse transcription of the first strand of cRNA, 3) dUTP synthesis of double-stranded cDNA, 4) Rt-PCR amplification was used to repair double-stranded cDNA ends to create RNA sequencing libraries.

value: blood

tag: disease state


title: D1_Control_001

value: primary cell line

tag: age donor

value: Female


title: p381 B cells (day 0) scRNA-seq

description:
Library name: p381_B_d0_RNA
10x Genomics


title: Lung, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Lung

value: Lung


title: Spleen, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Spleen

value: Spleen


title: QYLXD013

description: 99,expression matrix.xlsx


title: CUT&Tag of BRIP1 in shRFC3 cells rep1.

description: Library name: shRFC3_BRIP1_1

value: Early S Phase-Synchronized


title: CUT&Tag of BRIP1 in shRFC3 cells rep2.

description: Library name: shRFC3_BRIP1_2


title: D1_TGFB_002

value: Diseased LiverStellate Cells

value: T

tag: causedeath donor


title: p381 B cells (7 months) scBCR-seq

description:
Library name: p381_B_7m_VDJ
10x Genomics


title: Liver, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Liver

value: Liver

value: 20 weeks


title: CUT&Tag of G4-DNA in shRFC3 cells rep2.

description: Library name: shRFC3_BG4_2

value: liver

value: tumor cells


title: CUT&Tag of CTD in shRFC3 cells rep1.

description: Library name: shRFC3_CTD_1


title: p381 B cells (7 months) scRNA-seq

description:
Library name: p381_B_7m_RNA
10x Genomics


title: CUT&Tag of CDK7 in shRFC3 cells rep2.

description: Library name: shRFC3_CDK7_2


title: QYLXD010

description: 99,expression matrix.xlsx


title: QYLXD011

description:
99,expression matrix.xlsx
12.expression matrix.xlsx


title: Kidney, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Kidney


title: QYLXD014

description: 99,expression matrix.xlsx


title: CUT&Tag of G4-DNA in shRFC3 cells rep1.

description: Library name: shRFC3_BG4_1


title: Brain, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Brain


title: p381 B cells (week 6) scBCR-seq

description:
Library name: p381_B_6w_VDJ
10x Genomics


title: CUT&Tag of RNAPS5Pin shCtrl cells rep1.

description: Library name: shCtrl_S5_1


title: p326 T cells (day 0) scTCR-seq

description:
Library name: p326_T_d0_VDJ
10x Genomics

value: T cells


title: QYD7

description: 99,expression matrix.xlsx


title: QYD4

description: 99,expression matrix.xlsx


title: Bladder, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Bladder


title: BoneMarrow, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: BoneMarrow


title: CUT&Tag of CDK7 in shRFC3 cells rep1.

description: Library name: shRFC3_CDK7_1


title: CUT&Tag of RNAPS5P in shCtrl cells rep2.

description: Library name: shCtrl_S5_2


title: Heart, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

value: Heart


title: p381 B cells (week 6) scRNA-seq

description:
Library name: p381_B_6w_RNA
10x Genomics

value: B cells


title: QYD6

description: 99,expression matrix.xlsx

value: blood


title: p326 T cells (7 months) scTCR-seq

description:
Library name: p326_T_7m_VDJ
10x Genomics


title: LargeIntestine, Trp53+/+_mouse_0107, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: LargeIntestine

value: LargeIntestine

value: Female


title: QYD5

description: 99,expression matrix.xlsx


title: SmallIntestine, Trp53+/+_mouse_0516, 20_week-old_plate3

description: Updated Microwell-seq_scRNA-seq

source_name: SmallIntestine

value: SmallIntestine


title: CUT&Tag of NELFB in shCtrl cells rep2.

description: Library name: shCtrl_NELFB_2

source_name: liver

value: Early S Phase-Synchronized


title: Stomach, Trp53+/+_mouse_0516, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Stomach


title: p326 T cells (week 6) scTCR-seq

description:
Library name: p326_T_6w_VDJ
10x Genomics


title: QYD1

description: 99,expression matrix.xlsx


title: CUT&Tag of RNAPS2P in shCtrl cells rep2.

description: Library name: shCtrl_S2_2


title: p326 T cells (day 0) scRNA-seq

description:
Library name: p326_T_d0_RNA
10x Genomics


title: p326 T cells (7 months) scRNA-seq

description:
Library name: p326_T_7m_RNA
10x Genomics


title: CUT&Tag of NELFB in shCtrl cells rep1.

description: Library name: shCtrl_NELFB_1


title: p326 T cells (week 6) scRNA-seq

description:
Library name: p326_T_6w_RNA
10x Genomics


title: T2DM


title: SRKPD013

description: 99,expression matrix.xlsx


title: CUT&Tag of NELFA in shCtrl cells rep2.

description: Library name: shCtrl_NELFA_2


title: p326 B cells (day 0) scBCR-seq

description:
Library name: p326_B_d0_VDJ
10x Genomics


title: CUT&Tag of RNAPS2P in shCtrl cells rep1.

description: Library name: shCtrl_S2_1


title: SmallIntestine, Trp53+/+_mouse_0516, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq


title: Bladder, Trp53+/+_mouse_0516, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq


title: CUT&Tag of NELFA in shCtrl cells rep1.

description: Library name: shCtrl_NELFA_1


title: CUT&Tag of DHX36 in shCtrl cells rep2.

description: Library name: shCtrl_DHX_2


title: p326 B cells (day 0) scRNA-seq

description:
Library name: p326_B_d0_RNA
10x Genomics


title: QYLXD005

description: 99,expression matrix.xlsx


title: QYLXD008


title: p326 B cells (7 months) scBCR-seq

description:
Library name: p326_B_7m_VDJ
10x Genomics


title: QYLXD007

description: 99,expression matrix.xlsx


title: QYLXD004


title: Stomach, Trp53+/+_mouse_0516, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq


title: CUT&Tag of DHX36 in shCtrl cells rep1.

description: Library name: shCtrl_DHX_1


title: CUT&Tag of CyclinT1 in shCtrl cells rep2.

description: Library name: shCtrl_cyclinT1_2


title: Ovary, Trp53+/+_mouse_0516, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Ovary

value: Ovary


title: CUT&Tag of CyclinT1 in shCtrl cells rep1.

description: Library name: shCtrl_cyclinT1_1


title: p326 B cells (7 months) scRNA-seq

description:
Library name: p326_B_7m_RNA
10x Genomics


title: QYLXD006

description: 99,expression matrix.xlsx


title: p326 B cells (week 6) scRNA-seq

description:
Library name: p326_B_6w_RNA
10x Genomics


title: Ovary, Trp53+/+_mouse_0516, 20_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: 20 weeks


title: CUT&Tag of CTD in shCtrl cells rep2.

description: Library name: shCtrl_CTD_2

value: liver


title: Bladder, Trp53+/+_mouse_0516, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq


title: QYLXD001


title: CUT&Tag of CTD in shCtrl cells rep1.

description: Library name: shCtrl_CTD_1

value: tumor cells


title: Thymus, Trp53-/-_mouse_0045, 29_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Thymus

value: 29 weeks


title: p196 T cells (day 0) scRNA-seq

description:
Library name: p196_T_d0_RNA
10x Genomics

value: T cells


title: SmallIntestine, Trp53+/+_mouse_0516, 20_week-old_plate1

description: Updated Microwell-seq_scRNA-seq


title: QYLXD002

description: 99,expression matrix.xlsx


title: CUT&Tag of CDK9 in shCtrl cells rep2.

description: Library name: shCtrl_CDK9_2


title: Spleen, Trp53-/-_mouse_0045, 29_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Spleen


title: p196 T cells (7 months) scTCR-seq

description:
Library name: p196_T_7m_VDJ
10x Genomics


title: CUT&Tag of CDK9 in shCtrl cells rep1.

description: Library name: shCtrl_CDK9_1


title: YXRSD001

description: 99,expression matrix.xlsx


title: YXRSD003

description: 99,expression matrix.xlsx


title: CUT&Tag of CDK7 in shCtrl cells rep2.

description: Library name: shCtrl_CDK7_2


title: Pancreas, Trp53-/-_mouse_0045, 29_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Pancreas


title: p196 T cells (7 months) scRNA-seq

description:
Library name: p196_T_7m_RNA
10x Genomics


title: MammaryGland, Trp53-/-_mouse_0045, 29_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: MammaryGland

value: MammaryGland


title: p326 B cells (week 6) scBCR-seq

description:
Library name: p326_B_6w_VDJ
10x Genomics

value: B cells


title: CUT&Tag of CDK7 in shCtrl cells rep1.

description: Library name: shCtrl_CDK7_1


title: p196 T cells (week 6) scTCR-seq

description:
Library name: p196_T_6w_VDJ
10x Genomics


title: CUT&Tag of BRIP1 in shCtrl cells rep2.

description: Library name: shCtrl_BRIP1_2


title: Uterus, Trp53-/-_mouse_0045, 29_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Uterus

value: Uterus


title: QYLXD003

description: 99,expression matrix.xlsx

value: blood


title: YXRSD004

description: 99,expression matrix.xlsx


title: p196 T cells (day 0) scTCR-seq

description:
Library name: p196_T_d0_VDJ
10x Genomics


title: Lung, Trp53-/-_mouse_0045, 29_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Lung

value: Female


title: CUT&Tag of BRIP1 in shCtrl cells rep1.

description: Library name: shCtrl_BRIP1_1

value: Early S Phase-Synchronized


title: p196 B cells (7 months) scBCR-seq

description:
Library name: p196_B_7m_VDJ
10x Genomics


title: p196 T cells (week 6) scRNA-seq

description:
Library name: p196_T_6w_RNA
10x Genomics


title: YXRSD007

description: 99,expression matrix.xlsx


title: CUT&Tag of G4-DNA in shCtrl cells rep2.

description: Library name: shCtrl_BG4_2


title: YXRSD006

description: 99,expression matrix.xlsx


title: Liver, Trp53-/-_mouse_0045, 29_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

value: Liver


title: p196 B cells (7 months) scRNA-seq

description:
Library name: p196_B_7m_RNA
10x Genomics


title: WSR003

description: 99,expression matrix.xlsx


title: Heart, Trp53-/-_mouse_0045, 29_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Heart

value: Heart


title: CUT&Tag of G4-DNA in shCtrl cells rep1.

description: Library name: shCtrl_BG4_1


title: CUT&Tag of RNAPS5P in Late_S cells rep2.

description: Library name: Late_RFC3_2

value: Late_S Phase-Synchronized


title: p196 B cells (week 6) scBCR-seq

description:
Library name: p196_B_6w_VDJ
10x Genomics


title: Kidney, Trp53-/-_mouse_0045, 29_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: Kidney

value: Kidney


title: CUT&Tag of RNAPS5P  in Late_S cells rep1.

description: Library name: Late_RFC3_1

value: liver

value: tumor cells


title: YXRSD005

description: 99,expression matrix.xlsx


title: BoneMarrow, Trp53-/-_mouse_0045, 29_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: BoneMarrow

value: BoneMarrow

value: 29 weeks


title: QYD2

description:
99,expression matrix.xlsx
12.expression matrix.xlsx


title: LymphNodes, Trp53-/-_mouse_0045, 29_week-old_plate2

description: Updated Microwell-seq_scRNA-seq

source_name: LymphNodes

value: LymphNodes


title: p196 B cells (week 6) scRNA-seq

description:
Library name: p196_B_6w_RNA
10x Genomics


title: p145 T cells (day 0) scTCR-seq

description:
Library name: p145_T_d0_VDJ
10x Genomics

source_name: T cells

value: T cells


title: p145 T cells (day 0) scRNA-seq

description:
Library name: p145_T_d0_RNA
10x Genomics


title: Thymus, Trp53-/-_mouse_0045, 29_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Thymus

value: Thymus


title: CUT&Tag of RNAPS2P  in Late_S cells rep2.

description: Library name: Late_S5_2


title: Uterus, Trp53-/-_mouse_0045, 29_week-old_plate1

description: Updated Microwell-seq_scRNA-seq