title: P102, HCC, tumour and background liver tissues, Tconv, VDJ

description:
Library name: Patient P102_Tconv_vdj
polyA RNA

data_processing:
Sequence reads from all samples were processed and aggregated using Cell Ranger (10X Genomics, v7.2).
Assembly: hg38  (GRCh38 )
Supplementary files format and content: CellRanger output files: Liver_and_PBMC_cellranger_aggr.gz containing:  aggregation.csv, all_contig_annotations_aggr.csv.gz, filtered_feature_bc_matrix/barcodes.tsv.gz, filtered_feature_bc_matrix/features.tsv.gz, filtered_feature_bc_matrix/matrix.mtx.gz, raw_feature_bc_matrix/barcodes.tsv.gz, raw_feature_bc_matrix/features.tsv.gz, raw_feature_bc_matrix/matrix.mtx.gz
Supplementary files format and content: CellRanger output files: HCC_tumour_and_background_cellranger_aggr.gz containing:  aggregation.csv, all_contig_annotations_aggr.csv.gz, filtered_feature_bc_matrix/barcodes.tsv.gz, filtered_feature_bc_matrix/features.tsv.gz, filtered_feature_bc_matrix/matrix.mtx.gz, raw_feature_bc_matrix/barcodes.tsv.gz, raw_feature_bc_matrix/features.tsv.gz, raw_feature_bc_matrix/matrix.mtx.gz
Library strategy: TCR-Seq


title: P108, HCC, tumour and background liver tissues, Tconv, ADT

status: Public on Feb 25 2026

type: SRA

city: London

first: Alberto

last: Sanchez-Fueyo

address: Denmark Hill

department: James Black Centre

country: United Kingdom

institute: Kings College London University

description:
Library name: Patient P108_Tconv_adt
Antibody-derived oligonucleotide (ADT)

library_source: other

data_processing:
Sequence reads from all samples were processed and aggregated using Cell Ranger (10X Genomics, v7.2).
Assembly: hg38  (GRCh38 )
Supplementary files format and content: CellRanger output files: Liver_and_PBMC_cellranger_aggr.gz containing:  aggregation.csv, all_contig_annotations_aggr.csv.gz, filtered_feature_bc_matrix/barcodes.tsv.gz, filtered_feature_bc_matrix/features.tsv.gz, filtered_feature_bc_matrix/matrix.mtx.gz, raw_feature_bc_matrix/barcodes.tsv.gz, raw_feature_bc_matrix/features.tsv.gz, raw_feature_bc_matrix/matrix.mtx.gz
Supplementary files format and content: CellRanger output files: HCC_tumour_and_background_cellranger_aggr.gz containing:  aggregation.csv, all_contig_annotations_aggr.csv.gz, filtered_feature_bc_matrix/barcodes.tsv.gz, filtered_feature_bc_matrix/features.tsv.gz, filtered_feature_bc_matrix/matrix.mtx.gz, raw_feature_bc_matrix/barcodes.tsv.gz, raw_feature_bc_matrix/features.tsv.gz, raw_feature_bc_matrix/matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

organism: Homo sapiens

source_name: HCC and background liver

extract_protocol:
PBMCs were isolated from heparinised blood by density centrifugation using Ficoll-Paque PLUS (Sigma-Aldrich). Tissue samples obtained from different surgical liver resections (HCC and paired non-tumoral background tissues from HCC resections; and histologically healthy liver tissue from liver metastasis resections) were collected in cold DMEM medium (Life Technologies) and processed within 2 hours. Tumour and tissue single cell suspensions were obtained by enzymatic digestion with the BD HorizonTM Dri Tumour & Tissue Dissociation Reagent (TTDR) (BD Biosciences) as per manufacturer instructions.
scRNAseq libraries (5´ gene expression library GEX, T cell receptor enriched library VDJ, and surface protein library containing the TotalSeq-C CITE-seq antibodies) were prepared using the Chromium Single Cell Immune Profiling kit (10x Genomics, v1.1) according to the manufacturer’s instructions. The generated scRNAseq libraries were sequenced using a total of 100 cycles (paired end reads) with a NovaSeq 6000 S2 flow cell (Illumina).

tag: tissue

value: HCC and background liver

tag: cell type

value: CD4+ T cells

tag: library type

value: ADT


title: P102, HCC, tumour and background liver tissues, Tconv, GEX

description:
Library name: Patient P102_Tconv_mrna
polyA RNA

library_source: transcriptomic

molecule: polyA RNA

value: mRNA


title: P102, HCC, tumour and background liver tissues, Tconv, ADT

description:
Library name: Patient P102_Tconv_adt
Antibody-derived oligonucleotide (ADT)


title: P102, HCC, tumour and background liver tissues, Treg, VDJ

description:
Library name: Patient P102_Treg_vdj
polyA RNA

value: TCR


title: N2(wt), E. coli OP50 diet, rep1

city: Cologne

first: Jonathan

last: Kölschbach

address: Joseph-Stelzmann-Straße 9B

department: Antebi

country: Germany

institute: Max Planck Institute for Biology of Ageing

description: Library name: wt_OP50.Rep_1

data_processing:
rRNA transcripts were removed from the annotation file (Ensembl C. elegans release 105/ce11) by depleting all lines with 'rrna' tag.
cDNA fasta was generated using cufflinks (v2.2.1). cDNA index was build using kallisto (v0.46.1).
Strandness was determined by pseudoalignment of 4 million reads to reference transcriptome using kallisto (v0.46.1). Mapping strand was identified via RSeQC (v4.0).
Reads were pseudoaligned to reference transcriptome (WBcel235_89) and quantified using kallisto (v0.46.1).
Normalized read counts were created by standard median-ratio for estimation of size factors using DESeq2 (v1.24)
Assembly: ce11
Supplementary files format and content: fpkm csv file includes fpkm-normalized counts for all samples
Supplementary files format and content: median-of-ratios csv file includes median-of-ratios-normalized counts for all samples

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans strains were maintained at 20°C on nematode growth medium (NGM) 10 cm plates seeded with standard E. coli OP50.

extract_protocol:
C. elegans samples were lysed using QIAzol lysis reagent (Quiagen). RNA was isolated by chloroform extraction and samples were purified using Rneasy mini plus kit (Quiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
The Illumina Tru-Seq stranded RiboZero protocol was used for RNA preparation. After purification and validation via TapeStation (Agilent Technologies), libraries were pooled for quantification using the KAPA Library Quantification kit (Peqlab) and the 7900HT Sequence Detection System (Applied Biosystems).

treatment_protocol: C. elegans strains were synchronized by egg-laying and grown on NGM 10 cm plates seeded with E. coli OP50 or BW25113. After 3 days of growth, D1 adult worms were harvested for subsequent RNA extraction.

value: whole animal

tag: genotype

tag: treatment

value: E. coli OP50 diet


title: CTRL URO QKO 1

type: RNA

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

hyb_protocol: Following fragmentation, 5.5 ug of fragmented and labeled ss-cDNA were hybridized for 16 hr at 45ºC at 60 rpm on Hybridization Oven 640 de Affymetrix. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 7G de Affymetrix

data_processing: RMA

label: Biotin

organism: Mus musculus

source_name: Urothelial cells harvested from the bladder of QKO mice

label_protocol: cRNA is converted to biotinylated single-stranded cDNA prepared according to the standard Affymetrix protocol from 12 ngs total RNA (GeneChip Whole Trasncript WT Expression Arrays, Affymetrix).

extract_protocol: Total RNA was extracted from FFPE tissue sections using the miRNeasy FFPE kit (Qiagen), or from fresh tissue/cells using the RNeasy Mini kit (Qiagen) following the manufacturer’s instructions.

tag: mouse tissue

value: Control urothelium

tag: type of sample

value: Fresh

tag: mouse strain

value: QKO

tag: targeted cell (adenovirus)


title: P102, HCC, tumour and background liver tissues, Treg, ADT

description:
Library name: Patient P102_Treg_adt
Antibody-derived oligonucleotide (ADT)


title: P108, HCC, tumour and background liver tissues, Treg, ADT

description:
Library name: Patient P108_Treg_adt
Antibody-derived oligonucleotide (ADT)


title: N2(wt), E. coli BW25113 diet, rep3

description: Library name: wt_BW.Rep_3

value: E. coli BW25113 diet


title: P097, HCC, tumour and background liver tissues, Tconv, VDJ

description:
Library name: Patient P097_Tconv_vdj
polyA RNA


title: P097, HCC, tumour and background liver tissues, Tconv, ADT

description:
Library name: Patient P097_Tconv_adt
Antibody-derived oligonucleotide (ADT)


title: P097, HCC, tumour and background liver tissues, Treg, VDJ

description:
Library name: Patient P097_Treg_vdj
polyA RNA


title: P097, HCC, tumour and background liver tissues, Tconv, GEX

description:
Library name: Patient P097_Tconv_mrna
polyA RNA


title: P091, HCC, tumour and background liver tissues, Tconv, VDJ

description:
Library name: Patient P091__Tconv_vdj
polyA RNA


title: P097, HCC, tumour and background liver tissues, Treg, GEX

description:
Library name: Patient P097_Treg_mrna
polyA RNA


title: P091, HCC, tumour and background liver tissues, Treg, ADT

description:
Library name: Patient P091_Treg_adt
Antibody-derived oligonucleotide (ADT)


title: P091, HCC, tumour and background liver tissues, Treg, GEX

description:
Library name: Patient P091_Treg_mrna
polyA RNA


title: P091, HCC, tumour and background liver tissues, Treg, VDJ

description:
Library name: Patient P091_Treg_vdj
polyA RNA


title: P069, HCC, tumour and background liver tissues, Treg, ADT

description:
Library name: Patient P069_Treg_adt
Antibody-derived oligonucleotide (ADT)


title: P069, HCC, tumour and background liver tissues, Tconv, GEX

description:
Library name: Patient P069_Tconv_mrna
polyA RNA


title: P069, HCC, tumour and background liver tissues, Treg, VDJ

description:
Library name: Patient P069_Treg_vdj
polyA RNA


title: P097, HCC, tumour and background liver tissues, Treg, ADT

description:
Library name: Patient P097_Treg_adt
Antibody-derived oligonucleotide (ADT)


title: epi22_B

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

data_processing:
Trimmomatic (Bolger et al., 2014) was used to remove adapters and discard low-quality reads.
The cleaned reads were mapped to Arabidopsis reference genome (TAIR10 version) by TopHat2 (Kim et al., 2013).
Picard tools (available from http://broadinstitute.github.io/picard/) was used to discard duplicated reads.
Mapped reads from TopHat2 analysis were subsequently counted using htseq-count (Anders et al., 2015), and the raw count per gene was used to determine differentially expressed genes between control and Tenofovir-treated samples using DESeq (Anders and Huber, 2010) and default parameters. Genes with a significance p-value below 0.05 after Benjamini and Hochberg correction were considered to be differentially expressed
Assembly: TAIR 10
Supplementary files format and content: For each genotype, the rawcount file is provided, generated with htseq-count (Anders et al., 2015).

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seedlings were grown in plates on ½ MS media (1% sucrose and 0.8% agar, pH5.7) at 20°C under 12h light conditions (12h light/12h dark)

extract_protocol:
Total RNA was isolated from seedlings using the RNeasy Plant Mini Kit (Qiagen), following the manufacturer's instructions. The RNA quality and integrity were assessed on the Agilent 2200 Tape Station.
Libraries for RNA expression analysis were prepared in tripicate from 1 µg of  high-integrity total RNA (RIN>8) using the TrueSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA)  following the manufacturer’s instructions. Libraries quality and fragment sizes were checked with a TapeStation 2200 (Agilent technologies, Santa Clara, CA) instrument.

value: seedlings

tag: ecotype


title: P091, HCC, tumour and background liver tissues, Tconv, ADT

description:
Library name: Patient P091_Tconv_adt
Antibody-derived oligonucleotide (ADT)


title: P069, HCC, tumour and background liver tissues, Tconv, ADT

description:
Library name: Patient P069_Tconv_adt
Antibody-derived oligonucleotide (ADT)


title: P080, Liver metastasis, PBMC and healthy liver, Tconv, ADT

description:
Library name: Patient P080_Tconv_adt
Antibody-derived oligonucleotide (ADT)

source_name: PBMC and liver resection

value: PBMC and liver resection


title: P080, Liver metastasis, PBMC and healthy liver, Treg, VDJ

description:
Library name: Patient P080_Treg_vdj
polyA RNA


title: P080, Liver metastasis, PBMC and healthy liver, Tconv, GEX

description:
Library name: Patient P080_Tconv_mrna
polyA RNA


title: P080, Liver metastasis, PBMC and healthy liver, Tconv, VDJ

description:
Library name: Patient P080_Tconv_vdj
polyA RNA


title: P091, HCC, tumour and background liver tissues, Tconv, GEX

description:
Library name: Patient P091_Tconv_mrna
polyA RNA


title: P066, Liver metastasis, PBMC and healthy liver, Tconv, VDJ

description:
Library name: Patient P066_Tconv_vdj
polyA RNA


title: P066, Liver metastasis, PBMC and healthy liver, Tconv, GEX

description:
Library name: Patient P066_Tconv_mrna
polyA RNA


title: P066, Liver metastasis, PBMC and healthy liver, Tconv, ADT

description:
Library name: Patient P066_Tconv_adt
Antibody-derived oligonucleotide (ADT)


title: P080, Liver metastasis, PBMC and healthy liver, Treg, GEX

description:
Library name: Patient P080_Treg_mrna
polyA RNA


title: P102, HCC, tumour and background liver tissues, Treg, GEX

description:
Library name: Patient P102_Treg_mrna
polyA RNA


title: P069, HCC, tumour and background liver tissues, Tconv, VDJ

description:
Library name: Patient P069_Tconv_vdj
polyA RNA


title: P069, HCC, tumour and background liver tissues, Treg, GEX

description:
Library name: Patient P069_Treg_mrna
polyA RNA


title: P066, Liver metastasis, PBMC and healthy liver, Treg, ADT

description:
Library name: Patient P066_Treg_adt
Antibody-derived oligonucleotide (ADT)


title: P080, Liver metastasis, PBMC and healthy liver, Treg, ADT

description:
Library name: Patient P080_Treg_adt
Antibody-derived oligonucleotide (ADT)


title: P066, Liver metastasis, PBMC and healthy liver, Treg, GEX

description:
Library name: Patient P066_Treg_mrna
polyA RNA


title: P066, Liver metastasis, PBMC and healthy liver, Treg, VDJ

description:
Library name: Patient P066_Treg_vdj
polyA RNA


title: P064, Liver metastasis, PBMC and healthy liver, Tconv, VDJ

description:
Library name: Patient P064_Tconv_vdj
polyA RNA


title: P064, Liver metastasis, PBMC and healthy liver, Tconv, ADT

description:
Library name: Patient P064_Tconv_adt
Antibody-derived oligonucleotide (ADT)


title: P064, Liver metastasis, PBMC and healthy liver, Treg, VDJ

description:
Library name: Patient P064_Treg_vdj
polyA RNA


title: P064, Liver metastasis, PBMC and healthy liver, Treg, ADT

description:
Library name: Patient P064_Treg_adt
Antibody-derived oligonucleotide (ADT)


title: P064, Liver metastasis, PBMC and healthy liver, Treg, GEX

description:
Library name: Patient P064_Treg_mrna
polyA RNA


title: P064, Liver metastasis, PBMC and healthy liver, Tconv, GEX

description:
Library name: Patient P064_Tconv_mrna
polyA RNA


title: P063, Liver metastasis, PBMC and healthy liver, Treg, ADT

description:
Library name: Patient P063_Treg_adt
Antibody-derived oligonucleotide (ADT)


title: P061, Liver metastasis, PBMC and healthy liver, Tconv, ADT

description:
Library name: Patient_P061_Tconv_adt
Antibody-derived oligonucleotide (ADT)


title: P061, Liver metastasis, PBMC and healthy liver, Tconv, VDJ

description:
Library name: Patient_P061_Tconv_vdj
polyA RNA


title: Scar, PR2-M6, scRNAseq

first: Yung-Yi

last: Chen

address: Vincent Drive

institute: University of birmingham

description:
Library name: PR2M6
10x Genomics

library_source: transcriptomic single cell

data_processing:
Cellranger v7.0.0 used to generate count matricies and aggregate samples.
Assembly: hg38
Supplementary files format and content: Barcode (.tsv), matrix (.mtx) and feature (.tsv) files

source_name: skin

extract_protocol:
Skin biopsy samples (n=16) were thawed and washed with Dulbecco's Phosphate-Buffered Saline (DPBS) supplemented with 5% foetal calf serum (FCS) once before incubating with 1mg/ml collagenase P (Sigma Aldrich, UK) and 100mg/ml DNase I (Sigma Aldrich, UK) for 3.5 hours at 37°C in a humidified CO2 incubator. Cell suspensions were filtered through a 70mm cell strainer. Dissociated cells were then labelled with live and dead dye before live cell sorting using a BD LSR FORTESSAÔ X-20 Cell Analyzer (BD Biosciences, USA). Single cells were captured and barcoded using 10x Chromium platform and the sequencing libraries were prepared following manufacturer’s instructions using dual index Chromium Next GEM G Single Cell 3’ kit v3.1 (10xGemonics, California, USA)
Single cells were captured and barcoded using 10x Chromium platform and the sequencing libraries were prepared following manufacturer’s instructions using dual index Chromium Next GEM G Single Cell 3’ kit v3.1 (10xGemonics, California, USA). Libraries were quantified using an Agilent Bioanalyzer High Sensitivity DNA chip and pooled together to get similar numbers of reads from each single cell before sequencing. Overall, approximately 50,000 cells per sample were used for construction libraries and sequenced using Novogene single cell RNA sequencing services.

value: skin

tag: cell line

value: All primary isolated skin cells

value: total RNA

value: 6 Month post treatment

tag: batch


title: Scar, PR2-D0, scRNAseq

description:
Library name: PR2D0
10x Genomics

value: Baseline- before treatment


title: Scar, PR2-Y1, scRNAseq

description:
Library name: PR2Y1
10x Genomics

value: Y1 end point


title: P063, Liver metastasis, PBMC and healthy liver, Tconv, ADT

description:
Library name: Patient P063_Tconv_adt
Antibody-derived oligonucleotide (ADT)

value: CD4+ T cells

value: ADT


title: P063, Liver metastasis, PBMC and healthy liver, Treg, VDJ

description:
Library name: Patient P063_Treg_vdj
polyA RNA

value: TCR


title: P063, Liver metastasis, PBMC and healthy liver, Tconv, GEX

description:
Library name: Patient P063_Tconv_mrna
polyA RNA

value: mRNA


title: P061, Liver metastasis, PBMC and healthy liver, Treg, ADT

description:
Library name: Patient_P061_Treg_adt
Antibody-derived oligonucleotide (ADT)


title: Scar, PR2-W3, scRNAseq

description:
Library name: PR2W3
10x Genomics

value: 3 Weeks post treatment


title: Scar, GR2-D0, scRNAseq

description:
Library name: GR2D0
10x Genomics


title: P063, Liver metastasis, PBMC and healthy liver, Tconv, VDJ

description:
Library name: Patient P063_Tconv_vdj
polyA RNA


title: normal, replicate 3

city: Shanghai

first: Zhang

last: Jun

address: Second Ruijin Road

department: Department of Oncology

country: China

institute: Ruijin Hospital

description: Library name: Sample_N4

data_processing:
Basecalls performed using CASAVA version 1.8
Raw reads were processed using fastp version 0.20.0. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference  N. coloratarep genome using hisat2(v2.1.0) with parameters -p 8 --fr --dta-cufflinks
FPKM value of each gene was calculated using cufflinks(v2.2.1) with parameters --no-update-check -u -p 8 --library-type fr-firststrand, and the read counts of each gene were obtained by htseq-count(version 0.7.2) with parameters -i gene_id -f bam -s reverse -r name.
DEGs were identified using the Deseq library . P value < 0.05 and absolute value of foldchange >=2 was set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Normal Adjacent Tissue

extract_protocol:
A total amount of 1 µg RNA per sample was used as initial material for the RNA sample preparations. Ribosomal RNA was removed using Ribo-off™ rRNA Depletion Kit (Human/Mouse/Rat)(Vazyme, China). Subsequently, the sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, USA).
RNA-seq

treatment_protocol: Total RNA of fresh tumor and adjacent normal tissue samples was extracted using the TRIzol (Thermo Scientific, USA)  reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: Normal Adjacent Tissue


title: normal, replicate 2

description: Library name: Sample_N3


title: cervical cancer, replicate 3

description: Library name: Sample_C3

source_name: cervical cancer

value: cervical cancer


title: cervical cancer, replicate 1

description: Library name: Sample_C1


title: normal, replicate 1

description: Library name: Sample_N1


title: P063, Liver metastasis, PBMC and healthy liver, Treg, GEX

description:
Library name: Patient P063_Treg_mrna
polyA RNA


title: Scar, GR2-Y1, scRNAseq

description:
Library name: GR2Y1
10x Genomics


title: P061, Liver metastasis, PBMC and healthy liver, Tconv, GEX

description:
Library name: Patient_P061_Tconv_mrna
polyA RNA


title: P061, Liver metastasis, PBMC and healthy liver, Treg, GEX

description:
Library name: Patient_P061_Treg_mrna
polyA RNA


title: Scar, GR2-W3, scRNAseq

description:
Library name: GR2W3
10x Genomics


title: cervical cancer, replicate 4

description: Library name: Sample_C4


title: Scar, GR2-M6, scRNAseq

description:
Library name: GR2M6
10x Genomics


title: normal, replicate 4

description: Library name: Sample_N5


title: cervical cancer, replicate 2

description: Library name: Sample_C2


title: Single cell RNAseq of SafeCell AlloAccept tissue

city: Hong Kong

first: Vivian

last: Tam

address: L3-13, Laboratory Block, 21 Sassoon Rd, Pokfulam

country: Hong Kong

institute: The University of Hong Kong

description: Library name: CFS65-9tumour

data_processing:
The libraries were then sequenced using paired-end sequencing (151 bp) using the Illumina NovaSeq 6000, resulting in 1,040,732, raw reads in total giving a total throughput of 157.2Gb, with raw sequencing data processed with Cell Ranger 6.1.2.
Raw sequencing data were processed with Cell Ranger 6.1.2 to generate FASTQ files. These files were then aligned to the human and mouse reference genome (refdata-gex GRCh38_and_GRCm39-2024-A to dirferentiate between mouse and  human cells), followed by filtering, barcode and UMI counting.
Assembly: refdata-gex GRCh38_and_GRCm39-2024-A
Supplementary files format and content: filtered feature matrix in h5 format

source_name: Teratoma

growth_protocol: SC-AlloAccept cells were injected subcutaneously into a humanised mouse and allowed to grow for 108 days

extract_protocol:
One teratoma derived from SC-AlloAccept cells was isolated and the tissue cut to small pieces and enzymatically digested to single cells. 20,000 cells were prepared for single-cell RNA sequencing using the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 and Chromium Next GEM Chip G Single Cell Kit (10X Genomics) at the Centre for PanorOmic Sciences at The University of Hong Kong.
Single cells were encapsulated into Gel Beads-in-emulsion (GEM) by 10X Chromium iX. Single Cell 3’ Reagent Kit v3.1 was used to perform reverse transcription, cDNA cleanup and amplification. The double-stranded cDNA underwent enzymatic fragmentation, adapter ligation, index PCR and SPRIselect  size selection as per manufacturer’s protocol. The library size and concentration were determined by Qubit and Bioanalyser assays.

value: Teratoma

value: H1 embyronic stem cell

value: ESC differentiated to mesoderm, endoderm and ectoderm cells

value: Safe-cell AlloAccept

value: in vivo teratoma formation for 108 days


title: P061, Liver metastasis, PBMC and healthy liver, Treg, VDJ

description:
Library name: Patient_P061_Treg_vdj
polyA RNA

value: PBMC and liver resection


title: siNegative Control treated hTERT 2105 - 3

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

country: USA

institute: Stanford University

description: Library name: T6_serum

data_processing:
After fastqc, read trimming with cutadapt, fastq files were mapped to hg38/GRCh37 genome with STAR (2.7.10b).
Feature counts matrix from bam files are generated using subread package and table read into R for further processing
Using DESeq2, count matrix is read in, followed by trimming genes with less than 10 reads and subsequent differential expression analysis.
Assembly: hg38
Supplementary files format and content: bam files are generated as the final processed file for downstream analysis

source_name: coronary artery

extract_protocol:
RNA extraction was performed using RNAEasy Mini kits (Qiagen 74106).
Library construction was performed by a commercial third party (Novogene)

value: coronary artery

value: 2105 hTERT

value: smooth muscle

value: siCtrl


title: ECEV_RNA1

city: Chicago

first: Heidi

last: Yuan

address: 801 S Paulina St

institute: University of Illinois Chicago

description: Library name: Sample 1

data_processing:
1) Quality control: Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean data (clean reads) were obtained by removing reads containing poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing poly A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw data were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
2) Reads mapping to the reference sequence: The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch or with only one mismatch to analyze their expression and distribution on the reference.
3)  Known miRNA alignment: Mapped small RNA tags were used to looking for known miRNA. miRBase22.0 was used as reference, modified software mirdeep2 (Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.
4) Remove tags from these sources: To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of data from the specified species itself.
5) Novel miRNA prediction: The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvo (Wen et al., 2012) and mirdeep2 (Friedlander et al., 2011) were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps. At the same time, custom scripts were used to obtain the identified miRNA counts as well as base bias on the first position with certain length and on each position of all identified miRNA respectively.
6) Small RNA annotation summary: Summarizing all alignments and annotations obtained before. In the alignment and annotation before, some small RNA tags may be mapped to more than one category. To make every unique small RNA mapped to only one annotation, we follow the following priority rule: known miRNA > rRNA > tRNA > snRNA > snoRNA > repeat > gene > NAT-siRNA > gene > novel miRNA > ta-siRNA. The total rRNA proportion was used a marker as sample quality indicator. Usually it should be less than 60% in plant samples and 40% in animal samples as high quality.
7) miRNA editing analysis: Position 2~8 of a mature miRNA were called seed region which were highly conserved. The target of a miRNA might be different with the changing of nucleotides in this region. In our analysis pipeline, miRNA which might have base edit could be detected by aligning all the sRNA tags to mature miRNA, allowing one mismatch.
8) miRNA family analysis: Exploring the occurrence of miRNA families identified from the samples in other species. In our analysis pipeline, known miRNA used miFam.dat (http://www.mirbase.org/ftp.shtml) to look for families; novel miRNA precursor was submitted to Rfam (http://rfam.sanger.ac.uk/search/) to look for Rfam families.
9) Quantification of miRNA: miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Assembly: hg38
Supplementary files format and content: CSV file includes readcounts and normalized TPM counts for each sample.

source_name: Skin

growth_protocol: Primary human dermal microvascular endothelial cells were grown to confluency in normal growth media, followed by exosome-depleted media for 48h.

extract_protocol:
RNA was harvested using Trizol and purified with an RNA Clean & Concentrator-25 kit (Zymo, Tustin, CA, USA). RNA samples were submitted to Novogene (Novogene Corporation Ince., Sacramento, CA, USA) for quality control, library preparation, sequencing, and quantitation as per the in-house standard.
The library preparation, genome mapping, and raw gene counts for mRNA-sequencing analysis were performed by Novogene (Novogene America). The following methods were those provided by Novogene. Briefly, 3’ and 5’ adaptors were ligated to 3’ and 5’ end of small RNA, respectively. Then the first strand cDNA was synthesized after hybridazition with reverse transcription primer. The double-stranded cDNA library was generated through PCR enrichment. After purification and size selection, libraries with insertions between 18~40 bp were ready for sequencing on Illumina sequencing with SE50. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

treatment_protocol: Culture media was then collected and ECEVs were isolated using a 4x PEG-based isolation protocol. Collected ECEVs were then subjected to RNA extraction.

value: Skin

value: primary dermal microvascular endothelial cells

tag: molecule type

value: extracellular vesicle/exosomal RNA


title: ECEV_RNA2

description: Library name: Sample 2


title: ECEV_RNA3

description: Library name: Sample 3


title: OCI-AML3 StAMP Resistant BioRep1 Sample 2 Sequencing Batch 2

city: Boston

first: Michael

middle: James

last: Schmidt

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description:
Library name: OCI-AML3-R_R1_2
column name in STAR_Gene_Counts_run2: OCI-AML3-R_R1_2

data_processing:
Sequencing reads were aligned to the hg38 human genome, and gene expression counts were obtained. Differential expression analysis was conducted using DESeq2 v1.22.1 (Love et al., 2014). The entire RNA-seq data analysis workflow was executed using the VIPER Snakemake pipeline (Cornwell et al., 2018).
Assembly: hg38

growth_protocol: see manuscript

extract_protocol:
total RNA was isolated using the Qiagen RNeasy Mini Kit, following the manufacturer’s protocol
Libraries were generated from 200 ng of total RNA using the Roche Kapa mRNA HyperPrep strand-specific kit according to the manufacturer’s guidelines, automated on a Beckman Coulter Biomek i7
Double-stranded DNA libraries were quantified using a Qubit fluorometer and Agilent TapeStation 4200. Dual-indexed libraries were pooled in equimolar amounts and initially shallow-sequenced on an Illumina MiSeq to assess library concentration and pooling accuracy. The final library pool was sequenced on an Illumina NovaSeq6000 with a target of 40 million 100 bp paired-end reads per sample

treatment_protocol: see manuscript

value: myeloid

value: Res

value: StAMP


title: siTEAD1 treated hTERT 2105 - 2

description: Library name: T2_serum


title: OCI-AML3 StAMP Resistant BioRep1 Sample 3 Sequencing Batch 2

description:
Library name: OCI-AML3-R_R1_3
column name in STAR_Gene_Counts_run2: OCI-AML3-R_R1_3


title: OCI-AML3 StAMP Resistant BioRep2 Sample 1 Sequencing Batch 2

description:
Library name: OCI-AML3-R_R2_1
column name in STAR_Gene_Counts_run2: OCI-AML3-R_R2_1


title: TEAD1 ChIPseq

description: Library name: CHIP_TEAD1

library_source: genomic

data_processing:
Fastq files were mapped to hg38/GRCh37 genome with Bowtie2 (1.2.3). ChIP-seq peaks were then called with MACS2 (2.2.7.1) using default parameters. From this output, ‘robust’ peaks were selected by specifying a minimum fold-enrichment of 5.
Assembly: hg38
Supplementary files format and content: bw files are generated as the final processed file for data visualization

molecule: genomic DNA

extract_protocol:
1,000,000 HCASMCs were cross linked in 1% formaldehyde for 10 minutes and washed with PBS and replaced with hypotonic buffer (20 mM Hepes (pH 7.9), 10 mM KCl, 1 mM EDTA (pH 8) and 10% glycerol) and incubated on ice for 6 minutes. Cells were then sonicated using a Branson 250 Sonifier (using power setting 5, constant duty for 10 rounds of 30-second pulses) with confirmation of chromatin fragments at 250-400 babse pairs. Lysates were then incubated overnight with 5 µg of anti-CEBPB (Santa Cruz sc-150), TEAD(Cell Signaling 12292S), or H3K27ac(Abcam 4729). Protein-DNA complexes were captured with Protein G agarose beads (Sigma 8104) and eluted in 1% SDS TE buffer at 65 °C. After reverse cross-linking followed by RNase A and proteinase K digestion, chromatin was purified using a QIAquick PCR purification kit (Qiagen 28706).
ChIP DNA sequencing libraries were prepared using the Kappa HyperPrep (Roche 07962347001)


title: OCI-AML3 Vehcile Sample 2 Sequencing Batch 2

description:
Library name: OCI-AML3-R_V_2
column name in STAR_Gene_Counts_run2: OCI-AML3-R_V_2

value: WT

value: DMSO


title: OCI-AML3 StAMP Resistant BioRep1 Sample 1 Sequencing Batch 2

description:
Library name: OCI-AML3-R_R1_1
column name in STAR_Gene_Counts_run2: OCI-AML3-R_R1_1


title: OCI-AML3 StAMP Resistant BioRep2 Sample 3 Sequencing Batch 2

description:
Library name: OCI-AML3-R_R2_3
column name in STAR_Gene_Counts_run2: OCI-AML3-R_R2_3


title: K562 Parental Sample 1

description:
Library name: K562Naive1
column name in STAR_Gene_Counts_run1: K562Naive1

value: erythroleukemia


title: K562 Parental Sample 2

description:
Library name: K562Naive2
column name in STAR_Gene_Counts_run1: K562Naive2


title: OCI-AML3 Parental Sample 3

description:
Library name: OCIAML3Naive3
column name in STAR_Gene_Counts_run1: OCIAML3Naive3


title: siNegative Control treated hTERT 2105 - 2

description: Library name: T5_serum


title: siTEAD1 treated hTERT 2105 - 3

description: Library name: T3_serum


title: siTEAD1 treated hTERT 2105 - 1

description: Library name: T1_serum


title: OCI-AML3 Parental Sample 2

description:
Library name: OCIAML3Naive2
column name in STAR_Gene_Counts_run1: OCIAML3Naive2


title: siNegative Control treated hTERT 2105 - 1

description: Library name: T4_serum


title: OCI-AML3 Vehicle Sample 31Sequencing Batch 2

description:
Library name: OCI-AML3-R_V_1
column name in STAR_Gene_Counts_run2: OCI-AML3-R_V_1


title: OCI-AML3 StAMP Resistant BioRep1 Sample 3 Sequencing Batch 1

description:
Library name: OCIAML3StAMPRes3
column name in STAR_Gene_Counts_run1: OCIAML3StAMPRes3


title: OCI-AML3 StAMP Resistant BioRep1 Sample 1 Sequencing Batch 1

description:
Library name: OCIAML3StAMPRes1
column name in STAR_Gene_Counts_run1: OCIAML3StAMPRes1


title: OCI-AML3 Parental Sample 1

description:
Library name: OCIAML3Naive1
column name in STAR_Gene_Counts_run1: OCIAML3Naive1


title: OCI-AML3 Vehcile Sample 2 Sequencing Batch 1

description:
Library name: OCIAML3DMSO2
column name in STAR_Gene_Counts_run1: OCIAML3DMSO2


title: OCI-AML3 StAMP Resistant BioRep2 Sample 2 Sequencing Batch 2

description:
Library name: OCI-AML3-R_R2_2
column name in STAR_Gene_Counts_run2: OCI-AML3-R_R2_2


title: OCI-AML3 Vehcile Sample 1 Sequencing Batch 1

description:
Library name: OCIAML3DMSO1
column name in STAR_Gene_Counts_run1: OCIAML3DMSO1


title: OCI-AML3 Vehicle Sample 3 Sequencing Batch 1

description:
Library name: OCIAML3DMSO3
column name in STAR_Gene_Counts_run1: OCIAML3DMSO3


title: KrasG12D-transduced organoids S22

city: New York

first: Joo-Hyeon

last: Lee

address: 430 East 67th Street, New York, NY 10065, US

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: SIGAF12_S22
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: lung

extract_protocol:
Single cells were isolated from alveolar lung organoids derived from human normal donors using Dispase/TrypLE treatment.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, organoids were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: lung


title: OCI-AML3 Vehicle Sample 3 Sequencing Batch 2

description:
Library name: OCI-AML3-R_V_3
column name in STAR_Gene_Counts_run2: OCI-AML3-R_V_3


title: KrasG12D-transduced organoids S23

description:
Library name: SIGAF12_S23
10x Genomics


title: K562 Parental Sample 3

description:
Library name: K562Naive3
column name in STAR_Gene_Counts_run1: K562Naive3


title: KrasG12D-transduced organoids S24

description:
Library name: SIGAF12_S24
10x Genomics


title: KrasG12D-transduced organoids S21

description:
Library name: SIGAF12_S21
10x Genomics


title: H3K27 acetylation ChIPseq

description: Library name: CHIP_H3K27


title: KrasG12D-transduced organoids S56

description:
Library name: SIGAF11_S56
10x Genomics


title: KrasG12D-transduced organoids S54

description:
Library name: SIGAF11_S54
10x Genomics


title: Control organoids S18

description:
Library name: SIGAE12_S18
10x Genomics


title: OCI-AML3 StAMP Resistant BioRep1 Sample 2 Sequencing Batch 1

description:
Library name: OCIAML3StAMPRes2
column name in STAR_Gene_Counts_run1: OCIAML3StAMPRes2


title: Control organoids S52

description:
Library name: SIGAE11_S52
10x Genomics


title: KrasG12D-transduced organoids S55

description:
Library name: SIGAF11_S55
10x Genomics


title: Control organoids S17

description:
Library name: SIGAE12_S17
10x Genomics


title: KrasG12D-transduced organoids S53

description:
Library name: SIGAF11_S53
10x Genomics


title: Control organoids S20

description:
Library name: SIGAE12_S20
10x Genomics


title: Control organoids S19

description:
Library name: SIGAE12_S19
10x Genomics


title: Control organoids S50

description:
Library name: SIGAE11_S50
10x Genomics


title: Control organoids S51

description:
Library name: SIGAE11_S51
10x Genomics


title: Control organoids S49

description:
Library name: SIGAE11_S49
10x Genomics


title: K562 SF3B1-K700E mut 3

city: Jerusalem

first: Maayan

last: Salton

address: Ein-Kerem Canpus

country: Israel

institute: Hebrew University

description: Library name: MUT-3

data_processing:
Raw reads were processed for quality trimming and adaptors removal using fastx_toolkit v0.0.14 and cutadapt v2.10. The processed reads were aligned to the human transcriptome and genome version GRCh37 using TopHat v2.1. Reads were counted with featureCounts version 2.0.1 using GENCODE v47. DESeq2 (PMID: 25516281) was used to identify differentially expressed genes using FDR threshold of 0.1. rMATS (version 4.1.2) (PMID: 25480548) was used to identify differential alternative splicing events. For each alternative splicing event, we used the calculation on both the reads mapped to the splice junctions and the reads mapped to the exon body [Junction Counts and Exon Counts (JCEC)] and filtered events by FDR threshold of 0.1. Gene set enrichment analysis was performed using the GeneAnalytics (PMID: 26983021) online tool. FDR was controlled by the Benjamini-Hochberg procedure.
Assembly: Hg19
Supplementary files format and content: Gene level counts (TPM)

extract_protocol:
RNA was extracted with Qiuck-RNA MagBead (Zymo, R2132) according to the manufacturer’s instructions.
Sequencing Libraries were prepared using INCPM mRNA Seq.


title: K562 SF3B1-K700E mut 1

description: Library name: MUT-1


title: K562 SF3B1-WT 2

description: Library name: WT-2


title: K562 SF3B1-K700E mut 2

description: Library name: MUT-2


title: K562 SF3B1-WT 3

description: Library name: WT-3


title: MDM, MafB3, Rep2

city: Liège

last: Marichal

address: Avenue de l'Hopital 11

department: GIGA Institute

country: Belgium

institute: University of Liege

description: Library name: MDM_MafB3_R2-NGS25-K155

data_processing:
Raw reads were processed using the nf-core/cutandrun pipeline for adapter trimming, alignment to the mouse reference genome (GRCm38/mm10), and quality control. For MafB CUT&RUN, peaks were called using SEACR (Sparse Enrichment Analysis for CUT&RUN) in stringent mode.
Normalized tag counts were calculated with the annotatePeaks.pl function from HOMER. MafB binding sites were defined as peaks with higher normalized tag counts in wild-type compared with Mafb-deficient cells. MafB binding sites were assigned to target genes based on proximity to transcription start sites (±2 kb) using HOMER. CUT&RUN signal tracks were visualized with the Integrative Genomics Viewer (IGV).
Assembly: GRCm38
Supplementary files format and content: bedGraph
Library strategy: CUT&Run

source_name: Lung

extract_protocol:
Bone marrow derived macrophages BMMos were isolated from BM using Monocyte Isolation Kit (BM) (Miltenyi Biotec, 130100629) and were seeded in tissue culture-treated plates and cultured for 4 days in RPMI supplemented with 10% FBS, 1 mM Sodium Pyruvate (Thermo Fisher Scientific, 11360070), 1X Minimum Essential Medium Non-Essential Amino Acids (MEM NEAA; Thermo Fisher Scientific, 11140050), 50 µM β-mercaptoethanol (Thermo Fisher Scientific, 31350010) and 40 ng/ml Csf-1 (Peprotech, 31502) to differentiate them into BMDMs.  Large peritoneal macrophages Lyz2CreMafbfl/fl mice and Mafbfl/fl littermate controls were terminally anesthetized and peritoneal lavage was obtained by injecting 10 ml PBS (Thermo Fisher Scientific, 14190094) containing 10 mM EDTA into the peritoneal cavity and collecting the washout. LPMs were FACS sorted from the peritoneal lavage as CD45+Lin−Ly6C−CD11b+CD115+F4/80+MHC-II− live cells.  Human monocyte-derived macrophages Buffy coats from healthy volunteers were obtained through the Belgian Red Cross. Peripheral blood mononuclear cells were isolated by density gradient centrifugation on Lymphoprep (1.077 g/ml; StemCell Technologies). Classical monocytes were negatively selected using the Classical Monocyte Isolation Kit (Miltenyi Biotec, 130117337) according to the manufacturer’s instructions. Monocytes were seeded in Petri dishes (10 × 106 cells/dish) in RPMI supplemented with 10% FBS, 1× MEM NEAA (Thermo Fisher Scientific, 11140050), 50 µM β-mercaptoethanol, and 50 ng/ml recombinant human CSF-1 (Immunotools, 11343115). Fresh differentiation medium was added on day 3. On day 7, monocyte-derived macrophages (MDMs) were detached using cold PBS containing 0.25 mM EDTA.
CUT&RUN was performed using the CUTANA ChIC/CUT&RUN Kit (EpiCypher, 141048) according to the manufacturer’s instructions, with minor modifications. BMDMs or LPMs from Mafbfl/fl or Lyz2CreMafbfl/fl mice, as well as human MDMs from healthy donors, were washed with ice-cold PBS and fixed with 0.1% formaldehyde in PBS for 2 min at room temperature. Fixation was quenched with 0.125 M glycine (Merck, 104691000). For each CUT&RUN sample, 0.5 × 106 fixed cells were incubated with 0.5 µg antibody. The following antibodies were used: IgG (EpiCypher, 13-0042) MafB1 (Sigma, HPA005653) MafB2 (Cell Signaling Technology, 41019) MafB3 (Proteintech, 20189-1-AP)
CUT&RUN libraries were prepared using the CUTANA CUT&RUN Library Prep Kit  (EpiCypher, 141001) following the manufacturer’s instructions and sequenced on a NovaSeq 6000 (Illumina) with an S4 flow cell at a depth of 10 million reads per sample.

value: Lung

value: Mono-derived Macrophage

tag: cut&run antibody

value: MafB3 (Proteintech, 20189-1-AP)


title: K562 SF3B1-WT 1

description: Library name: WT-1


title: MDM, MafB2, Rep1

description: Library name: MDM_MafB2_R1-NGS25-K152

value: MafB2 (Cell Signaling Technology, 41019)


title: MDM, MafB3, Rep1

description: Library name: MDM_MafB3_R1-NGS25-K154


title: MDM, MafB1, Rep1

description: Library name: MDM_MafB1_R1-NGS25-K150

value: MafB1 (Sigma, HPA005653)


title: Patient189

city: Kyoto

first: Kohei

last: Hamada

address: 54 Shogoin Kawahara, Sakyo, Kyoto

department: Gynecology and Obstetrics

country: Japan

institute: Kyoto University Graduate School of Medicine

description: Library name: 189B9393

data_processing:
Raw fastq files were trimmed using Trim-Galore, then mapped to the human reference genome (GRCh38) with the gene annotation of Ensemble GRCh38.v99 using STAR (v2.7.8a). Subsequently, gene expression levels were normalised as TPM or FPKM values using RSEM (v1.3.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes gene TPM values for each sample

source_name: Tumor

extract_protocol:
Tumor specimens were snap-frozen (frozen tumor samples) and total RNA was extracted
Libraries were prepared using the SMART-Seq kit following the manufacturer’s instructions.

value: Tumor

tag: age

tag: residual tumor

tag: figo stage


title: Patient186

description: Library name: 186B9696

tag: tissue


title: MDM, MafB1, Rep2

description: Library name: MDM_MafB1_R2-NGS25-K151

tag: cell type


title: MDM, MafB2, Rep2

description: Library name: MDM_MafB2_R2-NGS25-K153


title: MDM, IgG

description: Library name: MDM_IgG-NGS25-K148

value: IgG (EpiCypher, 13-0042)


title: Patient187

description: Library name: 187B5353


title: Patient183

description: Library name: 183B9090


title: Patient180

description: Library name: 180B9494


title: Patient178

description: Library name: 178B9292


title: Patient185

description: Library name: 185B5252


title: Patient177

description: Library name: 177B9191


title: Patient181

description: Library name: 181B5151


title: Patient184

description: Library name: 184B9191


title: Patient179

description: Library name: 179B9393


title: Patient182

description: Library name: 182B9595


title: Patient174

description: Library name: 174B8989


title: Patient173

description: Library name: 173B8888


title: Patient176

description: Library name: 176B9090


title: Patient175

description: Library name: 175B5050


title: Patient172

description: Library name: 172B4949


title: Patient188

description: Library name: 188B9292


title: Patient169

description: Library name: 169B8989


title: Patient170

description: Library name: 170B8787


title: Patient171

description: Library name: 171B4848


title: Patient168

description: Library name: 168B4747


title: Patient165

description: Library name: 165B8484


title: Patient161

description: Library name: 161B8888


title: Patient166

description: Library name: 166B8585


title: Patient160

description: Library name: 160B8787


title: Patient159

description: Library name: 159B4444


title: Patient158

description: Library name: 158B8282


title: Patient163

description: Library name: 163B4646


title: Patient157

description: Library name: 157B8181


title: Patient156

description: Library name: 156B8080


title: Patient167

description: Library name: 167B8686


title: Patient151

description: Library name: 151B8484


title: Patient154

description: Library name: 154B4343


title: Patient152

description: Library name: 152B8585


title: Patient155

description: Library name: 155B8686


title: Patient148

description: Library name: 148B4141


title: Patient162

description: Library name: 162B4545


title: Patient150

description: Library name: 150B8383


title: Patient149

description: Library name: 149B7979


title: Patient147

description: Library name: 147B4040


title: Patient146

description: Library name: 146B3939


title: Patient164

description: Library name: 164B8383


title: Patient144

description: Library name: 144B7777


title: Patient142

description: Library name: 142B8181


title: Patient139

description: Library name: 139B3838


title: Patient143

description: Library name: 143B8282


title: Patient141

description: Library name: 141B7676


title: Patient140

description: Library name: 140B7575


title: Patient153

description: Library name: 153B4242


title: Patient145

description: Library name: 145B7878


title: Patient132

description: Library name: 132B3636


title: Patient134

description: Library name: 134B7171


title: Patient136

description: Library name: 136B7272


title: Patient137

description: Library name: 137B7373


title: Patient135

description: Library name: 135B3737


title: Patient130

description: Library name: 130B3434


title: Patient131

description: Library name: 131B3535


title: Patient133

description: Library name: 133B7070


title: Patient129

description: Library name: 129B8080


title: Patient125

description: Library name: 125B3333


title: Patient122

description: Library name: 122B6565


title: Patient128

description: Library name: 128B6969


title: Patient127

description: Library name: 127B6868


title: Patient120

description: Library name: 120B6363


title: Patient121

description: Library name: 121B6464


title: Patient138

description: Library name: 138B7474


title: Patient123

description: Library name: 123B6666


title: Patient124

description: Library name: 124B3232


title: Patient116

description: Library name: 116B3030


title: Patient117

description: Library name: 117B6161


title: Patient118

description: Library name: 118B3131


title: Patient115

description: Library name: 115B6060


title: Patient114

description: Library name: 114D0101


title: Patient113

description: Library name: 113B7979


title: Patient112

description: Library name: 112B7878


title: Patient111

description: Library name: 111B7777


title: Patient110

description: Library name: 110B2929


title: Patient126

description: Library name: 126B6767


title: Patient119

description: Library name: 119B6262


title: Patient106

description: Library name: 106B5757


title: Patient109

description: Library name: 109B7676


title: Patient105

description: Library name: 105B5656


title: Patient108

description: Library name: 108B5959


title: Patient107

description: Library name: 107B5858


title: Patient102

description: Library name: 102B7474


title: Patient103

description: Library name: 103B5454


title: Patient100

description: Library name: 100B5353


title: Patient098

description: Library name: 098B5151


title: Patient094

description: Library name: 094B7171


title: Patient099

description: Library name: 099B5252


title: Patient092

description: Library name: 092B4848


title: Patient096

description: Library name: 096B5050


title: Patient097

description: Library name: 097B7272


title: Patient093

description: Library name: 093B4949


title: Patient101

description: Library name: 101B7373


title: Patient091

description: Library name: 091B7070


title: Patient095

description: Library name: 095B2828


title: Patient089

description: Library name: 089B4747


title: Patient090

description: Library name: 090B2727


title: Patient087

description: Library name: 087B2525


title: Patient085

description: Library name: 085B2424


title: Patient083

description: Library name: 083B4646


title: Patient104

description: Library name: 104B7575


title: Patient086

description: Library name: 086B6969


title: Patient084

description: Library name: 084B6868


title: Patient081

description: Library name: 081B2323


title: Patient082

description: Library name: 082B4545


title: Patient088

description: Library name: 088B2626


title: Patient079

description: Library name: 079B2222


title: Patient080

description: Library name: 080B4444


title: Patient078

description: Library name: 078B2121


title: Patient076

description: Library name: 076B6767


title: Patient075

description: Library name: 075B2020


title: Patient077

description: Library name: 077B4343


title: Patient074

description: Library name: 074B6666


title: Patient072

description: Library name: 072B1919


title: Patient071

description: Library name: 071B4141


title: Patient069

description: Library name: 069B4040


title: Patient064

description: Library name: 064B3636


title: Patient068

description: Library name: 068B1717


title: Patient066

description: Library name: 066B3838


title: Patient067

description: Library name: 067B3939


title: Patient065

description: Library name: 065B3737


title: Patient063

description: Library name: 063B3535


title: Patient073

description: Library name: 073B4242


title: Patient061

description: Library name: 061B1515


title: Patient055

description: Library name: 055B3030


title: Patient053

description: Library name: 053B1313


title: Patient059

description: Library name: 059B3434


title: Patient070

description: Library name: 070B1818


title: Patient057

description: Library name: 057B3232


title: Patient054

description: Library name: 054B2929


title: Patient060

description: Library name: 060B1414


title: Patient050

description: Library name: 050B2727


title: Patient051

description: Library name: 051B2828


title: Patient049

description: Library name: 049B2626


title: Patient045

description: Library name: 045B2424


title: Patient046

description: Library name: 046B1111


title: Patient056

description: Library name: 056B3131


title: Patient062

description: Library name: 062B1616


title: Patient058

description: Library name: 058B3333


title: Patient048

description: Library name: 048B2525


title: Patient047

description: Library name: 047B6565


title: Patient044

description: Library name: 044B6464


title: Patient052

description: Library name: 052B1212


title: Patient042

description: Library name: 042B0909


title: Patient040

description: Library name: 040B2323


title: Patient038

description: Library name: 038B2121


title: Patient039

description: Library name: 039B2222


title: Patient037

description: Library name: 037B0808


title: Patient041

description: Library name: 041B6363


title: Patient036

description: Library name: 036B2020


title: Patient043

description: Library name: 043B1010


title: Patient035

description: Library name: 035B0707


title: Patient034

description: Library name: 034B1919


title: Patient033

description: Library name: 033B1818


title: Patient031

description: Library name: 031B1717


title: Patient030

description: Library name: 030B1616


title: Patient029

description: Library name: 029D0303


title: Patient028

description: Library name: 028B1515


title: Patient027

description: Library name: 027B6262


title: Patient032

description: Library name: 032B0606


title: Patient026

description: Library name: 026B1414


title: Patient023

description: Library name: 023B1212


title: Patient022

description: Library name: 022B1111


title: Patient019

description: Library name: 019B6161


title: Patient020

description: Library name: 020B0404


title: Patient018

description: Library name: 018B0909


title: Patient016

description: Library name: 016B0808


title: Patient021

description: Library name: 021B1010


title: Patient015

description: Library name: 015B6060


title: Patient025

description: Library name: 025B1313


title: Patient011

description: Library name: 011B5858


title: Patient024

description: Library name: 024B0505


title: Patient017

description: Library name: 017B0303


title: Patient013

description: Library name: 013B0707


title: Patient014

description: Library name: 014B5959


title: Patient010

description: Library name: 010B0505


title: Patient012

description: Library name: 012B0606


title: Patient008

description: Library name: 008B0202


title: Patient006

description: Library name: 006B0404


title: Patient005

description: Library name: 005B0303


title: Patient004

description: Library name: 004B0202


title: Patient003

description: Library name: 003B0101


title: Patient009

description: Library name: 009D0202


title: Patient007

description: Library name: 007B5757


title: Patient002

description: Library name: 002B5656


title: Patient001

description: Library name: 001B0101


title: J0644 CD3T rep2

city: Beijing

first: Ruoqi

last: Cheng

state: Beijing

address: NO.5, Yiheyuan Road, Haidian District

department: School of Life Sciences

institute: Peking University

description:
Library name: J0644 CD3T rep2
column name in counts.csv: J0644-T-2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low quality data by Trimmomatic v0.39, then mapped to hg38 whole genome using STAR v2.7.10b and annotated using gencode v47 gtf file.
sam file generated by STAR was converted to bam and counts were generated using featureCounts v2.0.6.
Assembly: hg38
Supplementary files format and content: csv file with raw gene counts for every gene and every sample.

extract_protocol:
Total RNA was extracted utilizing the TGuide S32 Blood/Cell/Tissue RNA kit in conjunction with the TGuide S32 nucleic acid extractor.
For the preparation of RNA-seq libraries, the NEBNext Ultra RNA Library Prep Kit for Illumina (provided by New England BioLabs, catalog number E7775) was used. The resultant libraries, comprising fragmented and randomly primed RNA molecules, were sequenced as paired-end reads of 2 x 150 base pairs


title: J0644 CD3T rep1

description:
Library name: J0644 CD3T rep1
column name in counts.csv: J0644-T-1


title: J0644 CD3T S1 rep1

description:
Library name: J0644 CD3T S1 rep1
column name in counts.csv: J0644-T-S1-1

value: induced from CD3T


title: J0644 CD3T S1 rep2

description:
Library name: J0644 CD3T S1 rep2
column name in counts.csv: J0644-T-S1-2


title: AT2_pbs3

city: Minato-ku

first: Yuta

last: Hirano

state: Tokyo

address: 3-25-8 Nishi-shimbashi

department: Internal Medicine

institute: The Jikei University School of Medicine

description: Library name: AT2_pbs3

data_processing:
Pair-end sequenced reads were checked by FastQC.
Estimation of transcripts was performed using Kallisto.
The expression matrix was constructed and normlized by Tximport in R
Assembly: GRCh38 (Ensembl Release 114)
Supplementary files format and content: CSV files (genes as rows, samples as columns) containing gene level counts summarized from Kallisto via tximport and rounded to the nearest integer.

source_name: alveolar cell

growth_protocol: Primary lung fibroblasts were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere containing 5% CO₂. Alveolar type II cells were isolated, washed with advanced DMEM/F12, counted, and seeded in growth factor–reduced Matrigel. After Matrigel solidification, organoids were cultured in serum- and feeder-free medium at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted from cultured cells using QIAzol and the miRNeasy Mini Kit (Qiagen, 217004)
mRNA libraries were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme International LLC, NR605-01)

treatment_protocol: Lung fibroblasts were serum-starved for 24 hours and subsequently treated with 100 μM Rosiglitazone (Tokyo Chemical Industry, R0106) for 72 hours before RNA extraction. AT2 organoids were treated with either PBS or LipoFB-EVs every other day for 14 days, after which organoids were harvested for RNA extraction.

value: alveolar cell

value: AT2 organoids treated with PBS


title: AT2_LipoEV2

description: Library name: AT2_LipoEV2

value: AT2 organoids treated with Rosiglitazone-induced Lipofibroblast derived EVs


title: AT2_pbs1

description: Library name: AT2_pbs1


title: LF2213rosi

description: Library name: LF2213rosi

source_name: lung fibroblast

value: lung fibroblast

value: 100μM Rosiglitazone


title: AT2_pbs2

description: Library name: AT2_pbs2


title: LF2178rosi

description: Library name: LF2178rosi


title: LF2213ctrl

description: Library name: LF2213ctrl

value: Vehicle


title: LF216ctrl

description: Library name: LF216ctrl


title: LF216rosi

description: Library name: LF216rosi


title: LF2178ctrl

description: Library name: LF2178ctrl


title: hTCiPSCs Z0684 16 rep2

description:
Library name: hTCiPSCs Z0684 16 rep2
column name in counts.csv: Z0684-T-IPSC-16#-2

value: CD3T derived hCiPSC

value: WT


title: hTCiPSCs Z0684 16 rep1

description:
Library name: hTCiPSCs Z0684 16 rep1
column name in counts.csv: Z0684-T-IPSC-16#-1


title: AT2_LipoEV1

description: Library name: AT2_LipoEV1


title: hTCiPSCs 250114 25 rep2

description:
Library name: hTCiPSCs 250114 25 rep2
column name in counts.csv: 250114-CD8T-IPSC-25#-2

value: CD8T derived hCiPSC


title: hTCiPSCs Z0684 14 rep2

description:
Library name: hTCiPSCs Z0684 14 rep2
column name in counts.csv: Z0684-T-IPSC-14#-2


title: hTCiPSCs Z0684 13 rep1

description:
Library name: hTCiPSCs Z0684 13 rep1
column name in counts.csv: Z0684-T-IPSC-13#-1


title: hTCiPSCs Z0684 12 rep2

description:
Library name: hTCiPSCs Z0684 12 rep2
column name in counts.csv: Z0684-T-IPSC-12#-2


title: hTCiPSCs Z0684 14 rep1

description:
Library name: hTCiPSCs Z0684 14 rep1
column name in counts.csv: Z0684-T-IPSC-14#-1


title: AT2_LipoEV3

description: Library name: AT2_LipoEV3


title: hTCiPSCs YB3271 2 rep2

description:
Library name: hTCiPSCs YB3271 2 rep2
column name in counts.csv: YB3271T-IPSC-2#-2


title: hTCiPSCs Z0684 12 rep1

description:
Library name: hTCiPSCs Z0684 12 rep1
column name in counts.csv: Z0684-T-IPSC-12#-1


title: 250114 CD8T rep2

description:
Library name: 250114 CD8T rep2
column name in counts.csv: 250114-CD8T-2


title: hTCiPSCs YB3271 2 rep1

description:
Library name: hTCiPSCs YB3271 2 rep1
column name in counts.csv: YB3271T-IPSC-2#-1


title: hTCiPSCs Z0684 13 rep2

description:
Library name: hTCiPSCs Z0684 13 rep2
column name in counts.csv: Z0684-T-IPSC-13#-2


title: hTCiPSCs 250114 25 rep1

description:
Library name: hTCiPSCs 250114 25 rep1
column name in counts.csv: 250114-CD8T-IPSC-25#-1


title: Z0684 CD3T rep1

description:
Library name: Z0684 CD3T rep1
column name in counts.csv: Z0684-T-1


title: H1703 cells, Control, Repeat3

city: guangzhou

first: Fei

last: Wang

address: jinsuilu 9

institute: Guangzhou Medical University

description: Library name: Sample9

data_processing:
Raw read QC – FastQC v0.11.9 assessed base-quality and nucleotide composition for each FASTQ file.
Filtering / trimming – fastp removed adapter sequences, trimmed bases with Q < 20 from the 3′ ends, discarded reads < 25 nt, and optionally flagged rRNA reads.
Read alignment – clean paired-end reads were aligned to the reference genome with HISAT2 v2.1.0 (spliced alignment, default tolerant parameters).
Transcript assembly & quantification – per-sample BAM files were assembled and quantified with StringTie v1.3.3b; raw fragment counts were exported.
Normalization & differential expression – gene-level counts were imported into edgeR v3.30.3; TMM normalization was applied and differential expression was tested with the exact negative-binomial model (FDR < 0.05, |log₂FC| ≥ 1).
Functional annotation – DE gene lists were annotated and enriched with GO and KEGG terms using custom R scripts (ggplot2 for graphics).
Assembly: Organism: Homo sapiens，GRCh38, Ensembl release 91
Supplementary files format and content: xls files include raw counts and FPKM values for each Sample

growth_protocol: Cells were cultured in RPMI-1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in a 5% CO₂ humidified incubator at 37°C.

extract_protocol:
Total RNA was extracted from cells grown in 6-well plates (2 × 105 cells per well, ~70 % confluence at harvest) using TRIzol reagent (Invitrogen) and purified with the RNeasy Mini Kit (Qiagen), including an on-column DNase I digestion. RNA purity (A260/280 ratio = 2.05 ± 0.04, A260/230 ratio = 1.98 ± 0.03) was measured using NanoDrop 2000, and RNA integrity (RIN ≥ 9.6) was confirmed by an Agilent 2100 Bioanalyzer. High-quality RNA (500 ng per sample) was used to generate strand-specific poly(A) libraries with the NEBNext Ultra II Directional RNA Library Prep Kit.
Poly-(A)-tailed mRNA was isolated from total RNA extracted from human cell lines and converted to cDNA with random hexamer priming. A non-directional (un-stranded) Illumina library was prepared according to the manufacturer’s standard protocol (comparable to TruSeq RNA v2), without rRNA depletion. Adapters with unique dual indices were ligated, fragments were size-selected (~300 bp insert), PCR-amplified, quantified, pooled, and sequenced on an Illumina NovaSeq 6000 (PE150) platform.

treatment_protocol: Cells were treated for 24 h with 0, 2.5, 10 or 40 µM SAHA; 0.1 % DMSO served as vehicle control.

value: Lung

value: Epithelial

value: DMSO


title: H1703 cells, SAHA, Repeat3

description: Library name: Sample12

value: SAHA


title: YB3271 CD3T rep1

description:
Library name: YB3271 CD3T rep1
column name in counts.csv: YB3271-CD3T-1


title: H1703 cells, SAHA, Repeat1

description: Library name: Sample10


title: 250114 CD8T rep1

description:
Library name: 250114 CD8T rep1
column name in counts.csv: 250114-CD8T-1


title: H1703 cells, Control, Repeat1

description: Library name: Sample7


title: Z0684 CD3T rep2

description:
Library name: Z0684 CD3T rep2
column name in counts.csv: Z0684-T-2


title: H1299 cells, SAHA, Repeat2

description: Library name: Sample5


title: YB3271 CD3T rep2

description:
Library name: YB3271 CD3T rep2
column name in counts.csv: YB3271-CD3T-2


title: H1299 cells, SAHA, Repeat1

description: Library name: Sample4


title: H1703 cells, Control, Repeat2

description: Library name: Sample8


title: H1299 cells, SAHA, Repeat3

description: Library name: Sample6


title: H1299 cells, Control, Repeat3

description: Library name: Sample3


title: H1703 cells, SAHA, Repeat2

description: Library name: Sample11


title: Day25: mature γδT cell, rep2

city: 深圳市

first: 张

last: 雪燕

state: 广东省深圳市南山区

address: 南山区

institute: 华南理工大学

description:
Library name: Sample 11
Day25-2

data_processing:
When the N> content of any read exceeded 10% of the base number of the read, the paired reads were removed. paired reads were excluded when the number of low quality (Q<=5) bases in any read exceeded 50% of the number of bases in the read. When any sequencing read contained a splice sequence > column, the paired reads were removed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: in vitro differentiated cells

growth_protocol: The hESCs, H9 cells (WA09) cultured and passaged on the feeder cells of mouse embryonic fibroblasts (MEF).   The culture medium was DMEM-F12 (Gibco) basal medium supplemented with 20% knockout ™ Gibco), 4 ng/ml fibroblast growth factor bFGF (Peprotech), 100 mM L-glutamine (Gibco), 1% MEM non-essential amino acids solution (ThermoFisher), 0.0007% b Mercaptoethanol.   The medium was changed daily.

extract_protocol:
RNA was harvested using Trizol reagent (AKARA, 9109).   100 ng of total RNA was used for the construction of sequencing libraries.
100 ng of total RNAs was used to prepare sequencing libraries using Ligation Mediated Sequencing (LM-Seq) protocol (21) and quantified with Qubit 2.0 fluorometer (ThermoFisher). Final cDNA libraries were quantitated with Agilent 2100 bioanalyzer, multiplexed and loaded at final concentration of 2.5 nM, and sequenced as single reads on the Illumina NovaSeq 6000 (Illumina).

treatment_protocol:
Cell aggregates of hESCs were obtained by treating hESC cultures at 70%−80% confluency with Gentle Cell Dissociation Reagent (STEMCELL, 07174). At day 0, the medium was completely replaced by STEMdiff™ APEL™2 Medium (STEMCELL, 05275) supplemented with 3 μM CHIR99021 (Selleckchem, S1263), 10 ng/mL BMP4 (Peprotech, 120-05), 2 ng/mL Activin A (Peprotech, 120-14) and 10 μM Rock inhibitor (Y-27632, Selleckchem, S1049). At day 2, the medium was replaced by STEMdiff™ APEL™2 supplemented with 40 ng/mL VEGF (Peprotech, 100-20). At day 3, the medium was replaced by STEMdiff™ APEL™2 supplemented with 40 ng/mL VEGF and 20 ng/mL bFGF (Peprotech, 100-18B). At day 6, the medium was replaced by STEMdiff™ APEL™2 supplemented with 50 ng/mL VEGF, 20 ng/mL bFGF, 10 ng/mL Flt3L (Peprotech, 300-19), 10 ng/mL IL-7 (Peprotech, 200-07), 20 ng/mL SCF (Peprotech, 300-07) and 4 μM SB431542 (Selleckchem，S1067).
At day 10, the medium was replaced by MEM-α (Gibco, 12561049) supplemented with 20% FBS (Excell Bio, FND500), 1% GlutaMAX (Thermo Fisher, 35050061), 30 μM MAP (Sigma, A8960-5G), 10 ng/mL SCF, 5 ng/mL IL-7, 5 ng/mL Flt3L and 10 ng/mL DLL4 (Peprotech, 140-07). Then, half of the medium was changed every other day.

value: in vitro differentiated cells

value: mature gamma-delta T cell

value: wild-type

value: cytokine-induced


title: Day20: T progenitor cells, rep3

description:
Library name: Sample 9
Day20-3

value: T progenitor cells


title: H1299 cells, Control, Repeat2

description: Library name: Sample2


title: Day25: mature γδT cell, rep3

description:
Library name: Sample 12
Day25-3


title: Day20: T progenitor cells, rep2

description:
Library name: Sample 8
Day20-2


title: H1299 cells, Control, Repeat1

description: Library name: Sample1


title: Day15: T progenitor cells, rep3

description:
Library name: Sample 6
Day15-3


title: Day15: T progenitor cells, rep1

description:
Library name: Sample 4
Day15-1


title: Day25: mature γδT cell, rep1

description:
Library name: Sample 10
Day25-1


title: Day10: Hematopoietic progenitor cells, rep3

description:
Library name: Sample 3
Day10-3

value: Hematopoietic progenitor cells


title: Day15: T progenitor cells, rep2

description:
Library name: Sample 5
Day15-2


title: CTRL URO QKO 4

data_processing: RMA

extract_protocol: Total RNA was extracted from FFPE tissue sections using the miRNeasy FFPE kit (Qiagen), or from fresh tissue/cells using the RNeasy Mini kit (Qiagen) following the manufacturer’s instructions.

value: Control urothelium

value: Fresh

value: QKO


title: Day20: T progenitor cells, rep1

description:
Library name: Sample 7
Day20-1


title: Day10: Hematopoietic progenitor cells, rep1

description:
Library name: Sample 1
Day10-1


title: PBMC low PRS pair 6

city: Philadelphia

first: Jelte

last: Kelchtermans

state: PA

address: 3401 Civic Center Blvd

institute: Children's Hospital of Philadelphia

description:
Library name: JelteKelchtermans-20241216-GEX-6-L6
PBMCs collected from a pediatric asthma patient with low PM2.5 sPRS

data_processing:
Raw sequencing reads were processed using Cell Ranger (10x Genomics) for alignment, filtering, and UMI counting.
Reads were aligned to the human reference genome using STAR within Cell Ranger.
Quality control filtering was applied to remove low-quality cells and doublets.
Cell-type annotation was performed using SingleR with the celldex::DatabaseImmuneCellExpressionData() reference.
Pseudobulk gene expression matrices were generated by aggregating counts per cell type per individual. Differential expression was assessed using the Wilcoxon rank-sum test, with Benjamini-Hochberg FDR correction.
Assembly: GRCh38/hg38
Supplementary files format and content: For each sample, processed data include Cell Ranger-generated output files: barcodes.tsv.gz: contains the list of cell barcodes; features.tsv.gz: lists gene identifiers and annotations; matrix.mtx.gz: sparse matrix of UMI counts for each gene-cell pair
Supplementary files format and content: These files represent the filtered gene expression matrix for each individual sample in 10x Genomics format.

source_name: blood

growth_protocol: Not applicable. PBMCs were isolated directly from peripheral blood of pediatric asthma patients; no in vitro culture was performed.

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using density gradient centrifugation. Single-cell suspensions were prepared and viability was assessed before library preparation. RNA was extracted as part of the single-cell 10x Genomics workflow.
Single-cell RNA libraries were constructed using the 10x Genomics Chromium Single Cell 3' v3.1 kit, following the manufacturer's protocol. Libraries were barcoded, amplified, and pooled for sequencing.

treatment_protocol: Subjects were environmentally exposed to ambient PM2.5. No in vitro treatment was administered. Matching was based on high vs. low PM2.5 sensitivity polygenic risk scores (sPRS) and real-world air pollution exposure.

value: blood

value: mixed immune cells

value: low PRS

value: PM2.5 exposure

value: same batch


title: PBMC high PRS pair 5

description:
Library name: JelteKelchtermans-20241216-GEX-5-H5
PBMCs collected from a pediatric asthma patient with high PM2.5 sPRS

value: high PRS


title: PBMC low PRS pair 4

description:
Library name: JelteKelchtermans-20241217-GEX-4-L4
PBMCs collected from a pediatric asthma patient with low PM2.5 sPRS


title: PBMC low PRS pair 5

description:
Library name: JelteKelchtermans-20241216-GEX-5-L5
PBMCs collected from a pediatric asthma patient with low PM2.5 sPRS


title: Day10: Hematopoietic progenitor cells, rep2

description:
Library name: Sample 2
Day10-2


title: PBMC high PRS pair 8

description:
Library name: JelteKelchtermans-20241217-GEX-8-H9
PBMCs collected from a pediatric asthma patient with high PM2.5 sPRS


title: PBMC high PRS pair 7

description:
Library name: JelteKelchtermans-20241217-GEX-7-H8
PBMCs collected from a pediatric asthma patient with high PM2.5 sPRS


title: PBMC high PRS pair 3

description:
Library name: JelteKelchtermans-20241216-GEX-3-H3
PBMCs collected from a pediatric asthma patient with high PM2.5 sPRS


title: PBMC low PRS pair 7

description:
Library name: JelteKelchtermans-20241217-GEX-7-L8
PBMCs collected from a pediatric asthma patient with low PM2.5 sPRS


title: PBMC low PRS pair 8

description:
Library name: JelteKelchtermans-20241217-GEX-8-L9
PBMCs collected from a pediatric asthma patient with low PM2.5 sPRS


title: Naevi and adjacent skin, sample ID: 111CM_21_L

city: WOOLLOONGABBA

first: Mitchell

middle: S

last: Stark

state: QLD

address: 37 Kent St

department: Frazer Institute

country: Australia

institute: The University of Queensland

description: Library name: 111CM_21_L

data_processing:
The deep sequencing reads were mapped to the human genome (GRCh37) using the STAR RNA-seq aligner. Expression values (read counts) were obtained with the program FeatureCounts from the Subread software package. FeatureCounts was run with gene annotations from Gencode version 33.
Assembly: GRCh37
Supplementary files format and content: Deep sequencing read counts in the csv format

extract_protocol:
Samples were micro-dissected using a sterile scalpel to isolate naevi from adjacent perilesional skin prior to being flash frozen at −80 °C  or preserved in RNAlater before storage at −80 °C
Sequencing libraries were prepared from total RNA using the Illumina TruSeq Stranded Total RNA library preparation kit and 2x101bp paired-end reads were sequenced on an Illumina NovaSeq 6000 machine.

value: skin

tag: gender

value: M

tag: sample type

value: Naevus

tag: histopathology

value: Intradermal

tag: benign/dysplastic

value: Benign

tag: dermoscopic pattern

value: Globular


title: PBMC low PRS pair 2

description:
Library name: JelteKelchtermans-20241216-GEX-2-L2
PBMCs collected from a pediatric asthma patient with low PM2.5 sPRS

tag: genotype

tag: treatment


title: Naevi and adjacent skin, sample ID: 970HH_75_P

description: Library name: 970HH_75_P

value: F

value: Skin


title: PBMC low PRS pair 1

description:
Library name: JelteKelchtermans-20241217-GEX-1-L1
PBMCs collected from a pediatric asthma patient with low PM2.5 sPRS


title: Naevi and adjacent skin, sample ID: 822MT_RLA_P

description: Library name: 822MT_RLA_P


title: PBMC high PRS pair 4

description:
Library name: JelteKelchtermans-20241217-GEX-4-H4
PBMCs collected from a pediatric asthma patient with high PM2.5 sPRS


title: Naevi and adjacent skin, sample ID: 510AN_2_P

description: Library name: 510AN_2_P


title: Naevi and adjacent skin, sample ID: 822MT_10_P

description: Library name: 822MT_10_P


title: Naevi and adjacent skin, sample ID: 61JB_115_P

description: Library name: 61JB_115_P


title: Naevi and adjacent skin, sample ID: 1294HS_20_L

description: Library name: 1294HS_20_L

value: Junctional

value: Non-specific (PRG)


title: PBMC high PRS pair 1

description:
Library name: JelteKelchtermans-20241217-GEX-1-H1
PBMCs collected from a pediatric asthma patient with high PM2.5 sPRS


title: Naevi and adjacent skin, sample ID: 61JB_133_P

description: Library name: 61JB_133_P


title: Naevi and adjacent skin, sample ID: 111CM_3_L

description: Library name: 111CM_3_L

value: Compound


title: Naevi and adjacent skin, sample ID: 52JH_40_P

description: Library name: 52JH_40_P


title: PBMC high PRS pair 2

description:
Library name: JelteKelchtermans-20241216-GEX-2-H2
PBMCs collected from a pediatric asthma patient with high PM2.5 sPRS

value: blood


title: Naevi and adjacent skin, sample ID: 673PS_1_P

description: Library name: 673PS_1_P


title: Naevi and adjacent skin, sample ID: 28RH_135_P

description: Library name: 28RH_135_P


title: PBMC high PRS pair 6

description:
Library name: JelteKelchtermans-20241216-GEX-6-H6
PBMCs collected from a pediatric asthma patient with high PM2.5 sPRS

value: mixed immune cells


title: Naevi and adjacent skin, sample ID: 1546CC_19_P

description: Library name: 1546CC_19_P


title: Naevi and adjacent skin, sample ID: 1078JG_47_L

description: Library name: 1078JG_47_L

value: Dysplastic


title: Naevi and adjacent skin, sample ID: 158RP_4_P

description: Library name: 158RP_4_P


title: PBMC low PRS pair 3

description:
Library name: JelteKelchtermans-20241216-GEX-3-L3
PBMCs collected from a pediatric asthma patient with low PM2.5 sPRS

value: low PRS

value: PM2.5 exposure


title: Naevi and adjacent skin, sample ID: 1564MV_34_P

description: Library name: 1564MV_34_P


title: Naevi and adjacent skin, sample ID: 1557LO_3_P

description: Library name: 1557LO_3_P


title: Naevi and adjacent skin, sample ID: 1325DB_9_P

description: Library name: 1325DB_9_P


title: Naevi and adjacent skin, sample ID: 1078JG_100_L

description: Library name: 1078JG_100_L


title: Naevi and adjacent skin, sample ID: 1294HS_20_P

description: Library name: 1294HS_20_P


title: Naevi and adjacent skin, sample ID: 1062DM_76_L

description: Library name: 1062DM_76_L


title: Naevi and adjacent skin, sample ID: 1546CC_2_P

description: Library name: 1546CC_2_P


title: Naevi and adjacent skin, sample ID: 1511AC_2_P

description: Library name: 1511AC_2_P


title: Naevi and adjacent skin, sample ID: 1510SW_3_P

description: Library name: 1510SW_3_P


title: Naevi and adjacent skin, sample ID: 007LW_152_P

description: Library name: 007LW_152_P


title: Naevi and adjacent skin, sample ID: 1501GA_1_P

description: Library name: 1501GA_1_P


title: Naevi and adjacent skin, sample ID: 1062DM_76_P

description: Library name: 1062DM_76_P


title: Naevi and adjacent skin, sample ID: 1504EG_3_P

description: Library name: 1504EG_3_P


title: Naevi and adjacent skin, sample ID: 39RB_6_P

description: Library name: 39RB_6_P


title: Naevi and adjacent skin, sample ID: 1427RB_RC_P

description: Library name: 1427RB_RC_P


title: Naevi and adjacent skin, sample ID: 1048KP_RA_L

description: Library name: 1048KP_RA_L


title: Naevi and adjacent skin, sample ID: 1427RB_RA_P

description: Library name: 1427RB_RA_P


title: Naevi and adjacent skin, sample ID: 510AN_23_P

description: Library name: 510AN_23_P


title: Naevi and adjacent skin, sample ID: 61JB_133_L

description: Library name: 61JB_133_L


title: Naevi and adjacent skin, sample ID: 111CM_21_P

description: Library name: 111CM_21_P


title: Naevi and adjacent skin, sample ID: 111CM_3_P

description: Library name: 111CM_3_P


title: Naevi and adjacent skin, sample ID: 1078JG_47_P

description: Library name: 1078JG_47_P


title: Naevi and adjacent skin, sample ID: 1078JG_100_P

description: Library name: 1078JG_100_P


title: Naevi and adjacent skin, sample ID: 510AN_2_L

description: Library name: 510AN_2_L


title: Naevi and adjacent skin, sample ID: 970HH_75_L

description: Library name: 970HH_75_L


title: Naevi and adjacent skin, sample ID: 28RH_135_L

description: Library name: 28RH_135_L


title: Naevi and adjacent skin, sample ID: 007LW_155_P

description: Library name: 007LW_155_P


title: Naevi and adjacent skin, sample ID: 510AN_23_L

description: Library name: 510AN_23_L

value: Reticular


title: Naevi and adjacent skin, sample ID: 1048KP_RA_P

description: Library name: 1048KP_RA_P

value: skin


title: Naevi and adjacent skin, sample ID: 52JH_40_L

description: Library name: 52JH_40_L


title: Naevi and adjacent skin, sample ID: 158RP_4_L

description: Library name: 158RP_4_L

value: M


title: Naevi and adjacent skin, sample ID: 822MT_RLA_L

description: Library name: 822MT_RLA_L

value: Naevus


title: Naevi and adjacent skin, sample ID: 822MT_10_L

description: Library name: 822MT_10_L


title: Naevi and adjacent skin, sample ID: 673PS_1_L

description: Library name: 673PS_1_L


title: Naevi and adjacent skin, sample ID: 1427RB_RA_L

description: Library name: 1427RB_RA_L


title: Naevi and adjacent skin, sample ID: 1501GA_1_L

description: Library name: 1501GA_1_L

value: Non-specific (other)


title: Naevi and adjacent skin, sample ID: 1427RB_RC_L

description: Library name: 1427RB_RC_L

value: Benign


title: Naevi and adjacent skin, sample ID: 61JB_115_L

description: Library name: 61JB_115_L

value: Globular


title: Naevi and adjacent skin, sample ID: 007LW_152_L

description: Library name: 007LW_152_L


title: Naevi and adjacent skin, sample ID: 1564MV_34_L

description: Library name: 1564MV_34_L


title: Naevi and adjacent skin, sample ID: 39RB_6_L

description: Library name: 39RB_6_L

value: Intradermal


title: Naevi and adjacent skin, sample ID: 1557LO_3_L

description: Library name: 1557LO_3_L

value: F


title: Naevi and adjacent skin, sample ID: 007LW_155_L

description: Library name: 007LW_155_L

value: Junctional


title: Naevi and adjacent skin, sample ID: 1546CC_19_L

description: Library name: 1546CC_19_L


title: Naevi and adjacent skin, sample ID: 1546CC_2_L

description: Library name: 1546CC_2_L


title: Naevi and adjacent skin, sample ID: 1511AC_2_L

description: Library name: 1511AC_2_L


title: Naevi and adjacent skin, sample ID: 1510SW_3_L

description: Library name: 1510SW_3_L


title: Naevi and adjacent skin, sample ID: 1325DB_9_L

description: Library name: 1325DB_9_L


title: Naevi and adjacent skin, sample ID: 1504EG_3_L

description: Library name: 1504EG_3_L


title: HCT116 subcutaneous xenograft in nude mice supplied by 7.5% PAD, replicate1

city: Hangzhou

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

institute: College of Pharmaceutical Sciences

description: Library name: SAMPLE 24

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCm38/GRCh38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm38/GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Paired-end libraries were synthesized by using the TruSeq® RNA sample preparation kit (Illumina, USA) following TruSeq® RNA sample preparation guide.

treatment_protocol: For colonic tissue, Male C57BL/6 mice at 8 weeks old were administrated with 1.5% DSS diluted in drinking water for 7 days following 7 days of untreated drinking water.  This treatment cycle was repeated three times and followed by 7 days of 1.5% DSS solution. The entire experimental period is 50 days in total. Meanwhile, mice were randomly subjected to 4 groups fed with different diets: 7.5% PAD (7.5% PAD contains 7.5% (w/w) palmitic acid with 26.6% Kcal fat), 15% PAD (15% PAD contains 15% (w/w) palmitic acid with 45% Kcal fat), HFD (HFD contains 19.5% (w/w) lard with 45% Kcal fat) and ND as control (Normal diet contains 12.5 % Kcal fat supplemented with soybean oil). For HCT116 xenografts, Female nude mice at 4-5 weeks old were supplied with ND or 7.5% PAD for two weeks in advance (and supplied throughout the whole experimental period). Then 1×106 HCT116 cells were injected subcutaneously into these nude mice. The HCT116 xenografts were harvested after 15 days.

value: Colon cancer cells

value: WT

value: HCT116-xenografted mice fed with 7.5% PAD


title: HCT116 subcutaneous xenograft in nude mice supplied by 7.5% PAD, replicate3

description: Library name: SAMPLE 26


title: HCT116 subcutaneous xenograft in nude mice supplied by 7.5% PAD, replicate2

description: Library name: SAMPLE 25


title: SVF scRNA OA - 127

city: Atlanta

first: Krishnendu

last: Roy

state: Georgia

address: 345 ferst drive NW, marcus nanotechnology building, room no 3102B, 3rd floor

department: IBB

institute: Georgia tech

description: Library name: SVF_05_029

data_processing:
R, Cellranger, Linux server commndline, Bash, Python
Assembly: grch38
Supplementary files format and content: tab delimited barcode, feature and count matrices

source_name: knee - OA

extract_protocol:
3' mRNA was barcoded using 10x Genomics Chromium instrument
10x Genomics 3' GEX kitwas used as per manufacturer's manual

value: Adipose Tissue

value: SVF


title: SVF scRNA OA - 125

description: Library name: SVF_05_014


title: SVF scRNA OA - 124

description: Library name: SVF_05_008


title: HCT116 subcutaneous xenograft in nude mice supplied by ND, replicate3

description: Library name: SAMPLE 23

value: HCT116-xenografted mice fed with ND


title: HCT116 subcutaneous xenograft in nude mice supplied by ND, replicate2

description: Library name: SAMPLE 22


title: SVF scRNA OA - 133

description: Library name: SVF_05_065


title: SVF scRNA OA - 123

description: Library name: SVF_05_006


title: HCT116 subcutaneous xenograft in nude mice supplied by ND, replicate1

description: Library name: SAMPLE 21


title: SVF scRNA OA - 119

description: Library name: SVF_04_050


title: SVF scRNA OA - 131

description: Library name: SVF_05_053


title: SVF scRNA OA - 132

description: Library name: SVF_05_060


title: SVF scRNA OA - 126

description: Library name: SVF_05_025


title: SVF scRNA OA - 117

description: Library name: SVF_04_046


title: SVF scRNA OA - 130

description: Library name: SVF_05_047


title: SVF scRNA OA - 128

description: Library name: SVF_05_036


title: SVF scRNA OA - 129

description: Library name: SVF_05_038


title: SVF scRNA OA - 112

description: Library name: SVF_04_026


title: SVF scRNA OA - 120

description: Library name: SVF_04_052


title: SVF scRNA OA - 121

description: Library name: SVF_04_055


title: SVF scRNA OA - 118

description: Library name: SVF_04_049


title: SVF scRNA OA - 113

description: Library name: SVF_04_027


title: SVF scRNA OA - 111

description: Library name: SVF_04_021


title: SVF scRNA OA - 109

description: Library name: SVF_04_011


title: SVF scRNA OA - 116

description: Library name: SVF_04_042


title: SVF scRNA OA - 122

description: Library name: SVF_05_005


title: SVF scRNA OA - 114

description: Library name: SVF_04_032


title: SVF scRNA OA - 110

description: Library name: SVF_04_014


title: SVF scRNA OA - 101

description: Library name: SVF_03_101


title: SVF scRNA OA - 105

description: Library name: SVF_03_112


title: SVF scRNA OA - 99

description: Library name: SVF_03_094


title: SVF scRNA OA - 107

description: Library name: SVF_04_002


title: SVF scRNA OA - 106

description: Library name: SVF_03_115


title: SVF scRNA OA - 115

description: Library name: SVF_04_040


title: SVF scRNA OA - 96

description: Library name: SVF_03_084


title: SVF scRNA OA - 102

description: Library name: SVF_03_102


title: SVF scRNA OA - 93

description: Library name: SVF_03_076


title: SVF scRNA OA - 104

description: Library name: SVF_03_111


title: SVF scRNA OA - 100

description: Library name: SVF_03_099


title: SVF scRNA OA - 95

description: Library name: SVF_03_083


title: SVF scRNA OA - 103

description: Library name: SVF_03_109


title: SVF scRNA OA - 108

description: Library name: SVF_04_008


title: SVF scRNA OA - 94

description: Library name: SVF_03_079


title: SVF scRNA OA - 89

description: Library name: SVF_03_060


title: SVF scRNA OA - 98

description: Library name: SVF_03_090


title: SVF scRNA OA - 97

description: Library name: SVF_03_086


title: SVF scRNA OA - 86

description: Library name: SVF_03_049


title: SVF scRNA OA - 87

description: Library name: SVF_03_055


title: SVF scRNA OA - 90

description: Library name: SVF_03_063


title: SVF scRNA OA - 92

description: Library name: SVF_03_072


title: SVF scRNA OA - 85

description: Library name: SVF_03_044


title: SVF scRNA OA - 91

description: Library name: SVF_03_066


title: SVF scRNA OA - 80

description: Library name: SVF_03_026


title: SVF scRNA OA - 78

description: Library name: SVF_03_016


title: SVF scRNA OA - 83

description: Library name: SVF_03_038


title: SVF scRNA OA - 77

description: Library name: SVF_03_015


title: SVF scRNA OA - 82

description: Library name: SVF_03_036


title: SVF scRNA OA - 81

description: Library name: SVF_03_030


title: SVF scRNA OA - 66

description: Library name: SVF_02_120


title: SVF scRNA OA - 79

description: Library name: SVF_03_021


title: SVF scRNA OA - 88

description: Library name: SVF_03_059


title: SVF scRNA OA - 84

description: Library name: SVF_03_040


title: SVF scRNA OA - 74

description: Library name: SVF_02_162


title: SVF scRNA OA - 76

description: Library name: SVF_03_013


title: SVF scRNA OA - 73

description: Library name: SVF_02_154


title: SVF scRNA OA - 69

description: Library name: SVF_02_128


title: SVF scRNA OA - 64

description: Library name: SVF_02_113


title: SVF scRNA OA - 68

description: Library name: SVF_02_125


title: SVF scRNA OA - 72

description: Library name: SVF_02_151


title: SVF scRNA OA - 65

description: Library name: SVF_02_115


title: SVF scRNA OA - 60

description: Library name: SVF_02_096


title: SVF scRNA OA - 58

description: Library name: SVF_02_082


title: SVF scRNA OA - 62

description: Library name: SVF_02_101


title: SVF scRNA OA - 71

description: Library name: SVF_02_150


title: SVF scRNA OA - 55

description: Library name: SVF_02_070


title: SVF scRNA OA - 63

description: Library name: SVF_02_106


title: SVF scRNA OA - 56

description: Library name: SVF_02_080


title: SVF scRNA OA - 61

description: Library name: SVF_02_099


title: SVF scRNA OA - 59

description: Library name: SVF_02_091


title: SVF scRNA OA - 57

description: Library name: SVF_02_081


title: SVF scRNA OA - 67

description: Library name: SVF_02_123


title: SVF scRNA OA - 54

description: Library name: SVF_02_063


title: SVF scRNA OA - 75

description: Library name: SVF_02_164


title: SVF scRNA OA - 44

description: Library name: SVF_02_003


title: SVF scRNA OA - 53

description: Library name: SVF_02_060


title: SVF scRNA OA - 70

description: Library name: SVF_02_131


title: SVF scRNA OA - 43

description: Library name: SVF_02_002


title: SVF scRNA OA - 51

description: Library name: SVF_02_046


title: SVF scRNA OA - 41

description: Library name: SVF_01_163


title: SVF scRNA OA - 50

description: Library name: SVF_02_044


title: SVF scRNA OA - 48

description: Library name: SVF_02_033


title: SVF scRNA OA - 39

description: Library name: SVF_01_153


title: SVF scRNA OA - 47

description: Library name: SVF_02_030


title: SVF scRNA OA - 49

description: Library name: SVF_02_041


title: SVF scRNA OA - 38

description: Library name: SVF_01_150


title: SVF scRNA OA - 32

description: Library name: SVF_01_130


title: SVF scRNA OA - 46

description: Library name: SVF_02_024


title: SVF scRNA OA - 36

description: Library name: SVF_01_146


title: SVF scRNA OA - 45

description: Library name: SVF_02_010


title: SVF scRNA OA - 52

description: Library name: SVF_02_053


title: SVF scRNA OA - 42

description: Library name: SVF_01_165


title: SVF scRNA OA - 26

description: Library name: SVF_01_107


title: SVF scRNA OA - 30

description: Library name: SVF_01_125


title: SVF scRNA OA - 27

description: Library name: SVF_01_108


title: SVF scRNA OA - 40

description: Library name: SVF_01_162


title: SVF scRNA OA - 37

description: Library name: SVF_01_149


title: SVF scRNA OA - 28

description: Library name: SVF_01_113


title: SVF scRNA OA - 33

description: Library name: SVF_01_132


title: SVF scRNA OA - 25

description: Library name: SVF_01_105


title: SVF scRNA OA - 35

description: Library name: SVF_01_140


title: SVF scRNA OA - 31

description: Library name: SVF_01_127


title: SVF scRNA OA - 29

description: Library name: SVF_01_121


title: SVF scRNA OA - 21

description: Library name: SVF_01_089


title: SVF scRNA OA - 16

description: Library name: SVF_01_066


title: SVF scRNA OA - 18

description: Library name: SVF_01_072


title: SVF scRNA OA - 20

description: Library name: SVF_01_087


title: SVF scRNA OA - 22

description: Library name: SVF_01_096


title: SVF scRNA OA - 17

description: Library name: SVF_01_069


title: SVF scRNA OA - 24

description: Library name: SVF_01_103


title: SVF scRNA OA - 13

description: Library name: SVF_01_052


title: SVF scRNA OA - 8

description: Library name: SVF_01_036


title: SVF scRNA OA - 11

description: Library name: SVF_01_050


title: SVF scRNA OA - 9

description: Library name: SVF_01_043


title: SVF scRNA OA - 15

description: Library name: SVF_01_065


title: SVF scRNA OA - 19

description: Library name: SVF_01_086


title: SVF scRNA OA - 34

description: Library name: SVF_01_138


title: SVF scRNA OA - 12

description: Library name: SVF_01_051


title: SVF scRNA OA - 10

description: Library name: SVF_01_048


title: SVF scRNA OA - 7

description: Library name: SVF_01_035


title: SVF scRNA OA - 5

description: Library name: SVF_01_028


title: SVF scRNA OA - 1

description: Library name: SVF_01_011


title: SVF scRNA OA - 6

description: Library name: SVF_01_033


title: SVF scRNA OA - 4

description: Library name: SVF_01_021


title: SVF scRNA OA - 3

description: Library name: SVF_01_018


title: BMAC scRNA OA - 134

description: Library name: BMAC_05_049

value: Bone Marrow

value: BMAC


title: BMAC scRNA OA - 130

description: Library name: BMAC_05_032


title: BMAC scRNA OA - 133

description: Library name: BMAC_05_043


title: BMAC scRNA OA - 129

description: Library name: BMAC_05_031


title: BMAC scRNA OA - 127

description: Library name: BMAC_05_018


title: BMAC scRNA OA - 131

description: Library name: BMAC_05_035


title: BMAC scRNA OA - 125

description: Library name: BMAC_04_057


title: BMAC scRNA OA - 128

description: Library name: BMAC_05_019


title: SVF scRNA OA - 2

description: Library name: SVF_01_014


title: BMAC scRNA OA - 132

description: Library name: BMAC_05_037


title: BMAC scRNA OA - 123

description: Library name: BMAC_04_048


title: BMAC scRNA OA - 126

description: Library name: BMAC_05_012


title: BMAC scRNA OA - 119

description: Library name: BMAC_04_019


title: BMAC scRNA OA - 116

description: Library name: BMAC_04_004


title: BMAC scRNA OA - 124

description: Library name: BMAC_04_053


title: BMAC scRNA OA - 120

description: Library name: BMAC_04_028


title: BMAC scRNA OA - 114

description: Library name: BMAC_03_110


title: BMAC scRNA OA - 121

description: Library name: BMAC_04_029


title: SVF scRNA OA - 14

description: Library name: SVF_01_057


title: BMAC scRNA OA - 122

description: Library name: BMAC_04_039


title: BMAC scRNA OA - 117

description: Library name: BMAC_04_005


title: BMAC scRNA OA - 118

description: Library name: BMAC_04_015


title: SVF scRNA OA - 23

description: Library name: SVF_01_097


title: BMAC scRNA OA - 113

description: Library name: BMAC_03_108


title: BMAC scRNA OA - 112

description: Library name: BMAC_03_105


title: BMAC scRNA OA - 109

description: Library name: BMAC_03_096


title: BMAC scRNA OA - 111

description: Library name: BMAC_03_100


title: BMAC scRNA OA - 110

description: Library name: BMAC_03_097


title: BMAC scRNA OA - 105

description: Library name: BMAC_03_087


title: BMAC scRNA OA - 115

description: Library name: BMAC_04_003


title: BMAC scRNA OA - 106

description: Library name: BMAC_03_088


title: BMAC scRNA OA - 104

description: Library name: BMAC_03_077


title: BMAC scRNA OA - 102

description: Library name: BMAC_03_073


title: BMAC scRNA OA - 107

description: Library name: BMAC_03_089


title: BMAC scRNA OA - 103

description: Library name: BMAC_03_074


title: BMAC scRNA OA - 99

description: Library name: BMAC_03_061


title: BMAC scRNA OA - 101

description: Library name: BMAC_03_069


title: BMAC scRNA OA - 108

description: Library name: BMAC_03_091


title: BMAC scRNA OA - 100

description: Library name: BMAC_03_065


title: BMAC scRNA OA - 97

description: Library name: BMAC_03_051


title: BMAC scRNA OA - 96

description: Library name: BMAC_03_047


title: BMAC scRNA OA - 98

description: Library name: BMAC_03_058


title: BMAC scRNA OA - 92

description: Library name: BMAC_03_039


title: BMAC scRNA OA - 94

description: Library name: BMAC_03_045


title: BMAC scRNA OA - 95

description: Library name: BMAC_03_046


title: BMAC scRNA OA - 93

description: Library name: BMAC_03_042