title: RNA Sequencing of  mouse Follicle nac-1

description: Library name: nac-1


title: IORT_Sample_05

status: Public on Apr 07 2026

type: SRA

city: Neuherberg

first: Benedek

last: Dankó

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Munich

description: Library name: IORT_Quantseq_05

library_source: transcriptomic

data_processing:
trimming of adapter sequences using BBDUK  k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCh38.93 --runThreadN 6 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
indexing BAM files using samtools: samtools index Aligned.sortedByCoord.out.bam
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using  Homo_sapiens.GRCh38.93.gtf
Assembly: hg38
Supplementary files format and content: tab-delimited text file with raw counts

molecule: total RNA

organism: Homo sapiens

source_name: Wound fluid obtained from the surgical cavity (breast tissue), collected via surgical drainage on postoperative day 2.

growth_protocol: Primary patient-derived immune cells from wound fluid were used without in vitro expansion.

extract_protocol:
Cryopreserved immune cell samples were thawed, washed with PBS, and processed using the NucleoSpin miRNA kit (Macherey & Nagel, Cat. No. 740971) following the manufacturer’s instructions for total RNA extraction (cell lysis in buffer ML, no DNA/protein isolation). RNA was eluted in 50 µL nuclease-free water and quantified via NanoDrop.
RNA libraries were constructed using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), following the manufacturer’s instructions. Sequencing was performed by Novogene (Cambridge, UK).

treatment_protocol: Patients either received intraoperative radiotherapy (IORT, single dose during tumor resection) or underwent surgery alone (control). Wound fluid was collected on postoperative day 2 using Redon drains.

tag: tissue

tag: cell line

value: tissue

tag: cell type

value: Mononuclear immune cells isolated from wound fluid via density gradient centrifugation (Biocoll; 1.077 g/ml); includes a mix of myeloid and lymphoid cell populations.

tag: group


title: UCSD-RT4 lineage tracing

city: Shenzhen

first: Zeqin

last: Yan

address: No. 1, Fuxin Road, Pinghu Street, Longgang District, Shenzhen, Guangdong Province, China

country: China

institute: Shenzhen University

description: Library name: UCSD-RT4-lineage

library_source: genomic

data_processing:
Raw sequencing reads were demultiplexed using bcl2fastq. Barcode sequences were extracted and aligned to the reference barcode library using custom scripts. Character matrices were generated by counting barcode variants across different tumor regions or time points.
Phylogenetic trees were reconstructed using maximum parsimony methods. Clonal dynamics were analyzed using custom R and Python scripts.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Character matrix in tab-delimited text format containing barcode mutation counts across different tumor regions/time points. Each file contains merged data from multiple tumors/time points for a given sample.

molecule: genomic DNA

source_name: Bladder

extract_protocol:
Genomic DNA was extracted from tumor tissues using the DNeasy Blood & Tissue Kit (Qiagen) following manufacturer's instructions. DNA quality and concentration were assessed using Qubit and Bioanalyzer.
Lineage tracing barcodes were amplified using PCR with indexing primers. PCR products were purified using AMPure XP beads and quantified using Qubit. Libraries were prepared using the Illumina DNA Prep Kit.

value: Bladder


title: Pleural mesothelioma, tumor, sample 180154

city: Durham

first: David

last: Severson

state: North Carolina

address: 2301 Erwin Road

department: Department of Surgery

country: USA

institute: Duke University Health System

description:
Library name: 180154
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 180154

library_source: transcriptomic single cell

data_processing:
Reads were processed using the Drop-seq tools pipeline aligned to the hg38 transcriptome using standard parameters.
Raw sequencing data are available through controlled access in dbGaP under accession phs004285.
Processed files provided here include per-library count matrices and corresponding cell-level metadata files.
Assembly: hg38
Supplementary files format and content: Sparse counts matrices (initial and stringently filtered cells) with associated column and row name files are formatted in tab-delmited compressed text files. Metadata for cells is formatted as a compressed tab delimited text file.

source_name: Tumor

extract_protocol:
Single-cell suspensions were generated from surgical pleural specimens after tissue dissociation. Seq-Well arrays containing RNA capture beads were loaded with approximately 10,000-20,000 cells per array. For selected specimens, technical replicates were created by splitting cell suspensions across multiple arrays processed in parallel.
Single-cell RNA sequencing libraries were generated using the Seq-Well platform. Cells were loaded onto bead-containing arrays, sealed with a membrane, lysed, and RNA was captured on beads. Reverse transcription, second-strand synthesis, whole transcriptome amplification, and Nextera XT library construction were performed prior to sequencing on Illumina NextSeq 500/550 or NovaSeq 6000 instruments.

value: Tumor

tag: diagnosis

value: Pleural Mesothelioma

tag: histology

value: B

tag: age at_surgery

tag: tumor status

value: Yes

tag: subject id


title: CTR-MGH-U3 scATAC-seq

description:
Library name: CTR-MGH-U3-scATAC
Control MGHU3 bladder cancer cells

library_source: genomic single cell

data_processing:
Cell Ranger ATAC (v2.1.0) was used for initial alignment and peak calling. Further analysis including fragment file generation, peak matrix construction, and TF motif analysis was performed using Signac and ArchR packages in R.
Assembly: GRCh38 (hg38)
Supplementary files format and content: scATAC_fragments.tar.gz: ATAC-seq fragment files for all samples (TSV.gz format). scATAC_peak_bc_matrices.tar.gz: Peak-by-cell count matrices in 10X H5 format. scATAC_tf_bc_matrices.tar.gz: Transcription factor motif matrices in 10X H5 format. scATAC_peaks_annotations.tar.gz: Peak coordinates (BED format) and peak annotations (TSV format). All files use SRA standard sample names (CTR-MGH-U3, MP-MGH-U3, UCSD-MGH-U3).
Illumina NovaSeq 6000
Gene expression matrices were generated using Cell Ranger (10x Genomics) with default parameters. Data was filtered to include high-quality cells.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Gene expression matrix in h5 format (filtered_feature_bc_matrix.h5) containing UMI-counted gene expression data. Compatible with Scanpy/Seurat for analysis.

source_name: bladder tumor

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent following manufacturer's instructions. RNA quality was assessed using Bioanalyzer.
scRNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3' v3.1 Kit according to manufacturer's protocol. Libraries were quantified using Qubit.

value: bladder tumor

value: basal carcinoma

tag: genotype

value: Control

tag: treatment

value: Vehicle

tag: batch

value: genomic DNA


title: Pleural mesothelioma, tumor, sample 179506

description:
Library name: 179506
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 179506


title: IORT_Sample_03

description: Library name: IORT_Quantseq_03

value: Wound fluid obtained from the surgical cavity (breast tissue), collected via surgical drainage on postoperative day 2.


title: CTR-RT4 lineage tracing

description: Library name: CTR-RT4-lineage


title: IORT_Sample_06

description: Library name: IORT_Quantseq_06


title: IORT_Sample_08

description: Library name: IORT_Quantseq_08


title: Pleural mesothelioma, tumor, sample 179872, tech rep 1

description:
Library name: 179872.1
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 179872; replicate: 1.0; replicate_type: Technical

value: NM


title: IORT_Sample_02

description: Library name: IORT_Quantseq_02


title: RNA Sequencing of  mouse Follicle nac-2

city: Chengdu

first: Xue

last: Zhao

state: SiChuan

address: Sichuan Agricultural University, Chendu, Sichuan province

institute: Sichuan Agricultural University

description: Library name: nac-2

data_processing:
Raw sequencing data generated form Illumina sequencer are used to the following analysis. Trimmed reads (trimmed 5ÿ , 3ÿ -adaptor bases by cutadapt [9] ) are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software [6] . The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2 [7] . Based on alignment statistical analysis (mapping ratio, read length, fragment sequence bias), we determine whether the results can be used for subsequent data analysis. If so, the expression profiling and differentially expressed tRFs & tiRNAs and miRNAs are calculated. Principal Component Analysis (PCA), Correlation Analysis, Pie plots, Venn plots, Hierarchical clustering, Scatter plots and Volcano plots are performed for the expressed tRF & tiRNA in R or perl environment for statistical computing and graphics.
Assembly: Genomic tRNA Database or tRNAscan-SE
Supplementary files format and content: Differential expression analysis of tRF & tiRNA and miRNA
Supplementary files format and content: count and CPM for each sample

organism: Mus musculus

source_name: Follicle

extract_protocol:
Total RNA was extracted by the chloroform method
Total RNA of each sample was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was then synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer

value: Follicle

tag: strain

value: mGC

tag: Sex

value: female


title: RNA Sequencing of  mouse Follicle EC-4

description: Library name: EC-4


title: IORT_Sample_01

description: Library name: IORT_Quantseq_01

value: tissue


title: RNA Sequencing of  mouse Follicle EC-2

description: Library name: EC-2


title: Pleural mesothelioma, tumor, sample 175512

description:
Library name: 175512
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 175512


title: RNA Sequencing of  mouse Follicle Con4

description: Library name: Con-4


title: MP-MGH-U3 lineage tracing

description: Library name: MP-MGH-U3-lineage


title: patient_22_day10

city: Lausanne

first: Nicolas

last: Rayroux

address: Rue du Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre Hospitalier Universitaire Vaudois

description:
Library name: 22d10
patient_22_colon_treatment_1

data_processing:
The scRNA-seq reads were aligned to the GRCh38 reference genome and quantified using Cell Ranger count (10X Genomics, version 4.0.0). We only retained gene-code matrices with unique molecular identifier (UMI) counts who passed the cell detection threshold. Further processing and analysis of the data was performed using the R package Seurat (version 4.3.0).
Quality control (QC) was applied to the immune-specific datasets. Filtering was performed using mitochondrial and ribosomal RNA as QC metric with cells having expression levels below/above 20 and 60 percent, respectively, being deemed of low quality and filtered out
Assembly: GRCh38
Supplementary files format and content: Processed gene expression raw count with Gene Symbol mapping for filtered non-apoptotic cells in comma-separted format

extract_protocol:
The day of the assay, frozen tissues were thawed in 10ml of R10 before cutting and fresh biopsies were chopped upon reception. Some biopsies were processed fresh. Tissues were cut with scalpels in a Petri dish containing few microliters of R10 medium. Fragments were transferred in a 2ml Eppendorf tube with 1ml of digestion mix (RPMI + 2% Gelatin + 50 IU/mL Collagenase I + 50 IU/mL Collagenase IV + 30 IU/mL Deoxyribonuclease I + 0.1% RNasin and incubated 15-20 minutes at 37°C under agitation at 130 rpm. Digestion reaction was stopped by adding 500ul of R10 to the mix. Digested fragments were filtered on a 70um strainer placed on the top of a 50ml Falcon tube. 1ml of R10 was added to the filter before filtering the cell suspension. The remaining pieces were smashed against the filter using the plunger of a 2ml syringe and washed with 10-15ml of R10. Suspension was centrifuged 5min at 400g and supernatant discarded. For counting and estimation of viability with Trypan blue, cells were resuspended in an appropriate volume (300 to 500ul) of PBS + 1%Gelatin + 0.1%RNasin according to the pellet size.
When cell number was sufficient, a maximum of 15’000 live cells per sample was loaded into the Chromium machine for encapsulation and barcoding using the Next GEM Single Cell 5’ Library and Gel beads kit v1.1. Resulting cDNA was amplified with 15 PCR cycles then 5GEX libraries were constructed according to 10XGenomics protocol (CG000208). Quality controls were performed on a Fragment Analyzer (Agilent) and quantification of libraries was done with the Qubit HS dsDNA assay kit (InVitrogen).

tag: cancer type

value: Colon

tag: patient

tag: time

value: Treatment

tag: biopsy site

value: Liver


title: UCSD-MGH-U3 lineage tracing

description: Library name: UCSD-MGH-U3-lineage

tag: tissue

value: Bladder

tag: cell line


title: Pleural mesothelioma, tumor, sample 174957

description:
Library name: 174957
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 174957

value: Tumor

value: Pleural Mesothelioma

value: B


title: CTR-MGH-U3 lineage tracing

description: Library name: CTR-MGH-U3-lineage


title: RNA Sequencing of  mouse Follicle Con3

description: Library name: Con-3

tag: cell type


title: RNA Sequencing of  mouse Follicle Con2

description: Library name: Con-2


title: patient_22_baseline

description:
Library name: 22b
patient_22_colon_baseline_1

value: Baseline


title: patient_20_baseline

description:
Library name: 20b
patient_20_prostate_baseline_1

value: Prostate

value: Lymphnode


title: Pleural mesothelioma, tumor, sample 173264

description:
Library name: 173264
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 173264

tag: diagnosis

value: E

value: Yes


title: RNA Sequencing of  mouse Follicle EC-1

description: Library name: EC-1


title: patient_20_day10

description:
Library name: 20d10
patient_20_prostate_treatment_1


title: Pleural mesothelioma, tumor, sample 175421

description:
Library name: 175421
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 175421

tag: histology


title: UCSD-RT4 tumor scRNA

description: Library name: UCSD-RT4-tumor-scRNA

data_processing:
Illumina NovaSeq 6000
Gene expression matrices were generated using Cell Ranger (10x Genomics) with default parameters. Data was filtered to include high-quality cells.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Gene expression matrix in h5 format (filtered_feature_bc_matrix.h5) containing UMI-counted gene expression data. Compatible with Scanpy/Seurat for analysis.

value: Tumor epithelial cell


title: Pleural mesothelioma, tumor, sample 175227

description:
Library name: 175227
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 175227

tag: age at_surgery


title: RNA Sequencing of  mouse Follicle Con1

description: Library name: Con-1

value: Follicle


title: patient_19_day10

description:
Library name: 19d10
patient_19_ovarian_treatment_2

value: Ovarian


title: Pleural mesothelioma, tumor, sample 172907

description:
Library name: 172907
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 172907

tag: tumor status


title: CTR-RT4 scRNA-seq

description: Library name: CTR-RT4-scRNA-seq

value: Epithelial cell


title: Pleural mesothelioma, tumor, sample 172444

description:
Library name: 172444
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 172444

tag: subject id


title: lung, WT, naive, rep3

city: Chapel Hill

first: Hong

last: Dang

address: 125 Mason Farm Rd, Cb#7248

institute: University of North Carolina at Chapel Hill

description:
Library name: WT_12022021
10x Genomics

data_processing:
Gene counts were generated with cellranger pipeline v6 from 10x Genomics, with default parameters (include_introns=false)
Assembly: GRCm39
Assembly: GENCODE vM26 gene annotation
Supplementary files format and content: Tab-delimited value files and matrix files
Supplementary files format and content: Integrated data analysis using Seurat, exported as .RDS file

source_name: Lung

extract_protocol:
Following sacrifice, the lungs were perfused with cold saline using a 25-gauge needle and a 10 mL syringe via the right ventricle to clear the lung of circulating blood. The lungs were inflated through the trachea with 1mL of digestion mix, consisting of Collagenase Type I (catalog #17100–017, 450 U/mL; Gibco), Dispase (catalog #354235, 5 U/mL; BD Biosciences) and DNase I (catalog #10104159001, 1 mg/ml; Roche) in DMEM/F12. Lungs were dissected out of the thoracic cavity and extraneous tissues removed. Lungs were minced manually with scissors in 1.5 mL Eppendorf tube and then incubated in 4 mL of digestion mix for 25 min at 37 °C with constant agitation. The homogenate was pipetted using 1,000 µl pipette using a wide orifice pipette. This was then centrifuged at 400 g (1,500 rpm) for 7 min. The supernatant was removed, and the pellet resuspended in 5 ml Accutase + 5 mM EDTA for 10 min at 37 °C with constant agitation. This was then filtered using a 70 µm filter, followed by centrifugation of the flowthrough at 400 g for 5-8 min at 4 oC. The supernatant was removed and 2 mL of red blood cell lysis buffer was added, for 2 min at RT. 5 ml of DMEM/F12 +10% FBS was added to stop RBC lysis. Further centrifugation at 400 g for 5-8 minute at 4oC. The pellet was resuspended in 1 ml of FACS buffer (PBS, 1.5% BSA, 2mM EDTA) and filtered through a 40 µm filter (H13680-0040 from Bel-Art). Cells were counted and viability checked using a hemocytometer by Trypan blue exclusion. The concentration was adjusted to 1 x107 cells in 100 ml of FACS buffer for flow cytometry staining and sorting.
Library construction was performed as per the manufacturer's instructions.

value: Lung

tag: age

value: 10-12 weeks

value: female

tag: genotype

value: WT


title: Pleural mesothelioma, tumor, sample 168748

description:
Library name: 168748
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 168748


title: patient_19_baseline

description:
Library name: 19b
patient_19_ovarian_baseline_2

tag: batch


title: patient_18_baseline

description:
Library name: 18b
patient_18_breast_baseline_1

value: Breast

value: Liver


title: lung, WT, naive, rep2

description:
Library name: WT_07082021
10x Genomics

tag: strain


title: MP-MGH-U3 scRNA-seq

description: Library name: MP-MGH-U3-scRNA-seq

value: Bladder


title: Mets-MGH-U3 scRNA-seq

description: Library name: Mets-MGH-U3-scRNA-seq

value: Metastatic tumor epithelial cell


title: patient_18_day10

description:
Library name: 18d10
patient_18_breast_treatment_1

value: Tumor

value: Treatment


title: UCSD-MGH-U3 scRNA-seq

description: Library name: UCSD-MGH-U3-scRNA-seq


title: patient_17_day10

description:
Library name: 17d10
patient_17_pancreatic_treatment_1

value: Pancreatic


title: MGHU3_sgScr_control_replicate_3

description: Library name: MP-MGHU3-LT-3

data_processing:
Raw reads were quantified using Salmon with reference genome. Gene-level counts were summarized using tximport. TPM normalization was applied.
Assembly: Human: GRCh38/hg38; Mouse: GRCm38/mm10
Supplementary files format and content: Tab-delimited/CSV files contain gene/transcript expression quantification. MP_count.tsv: human transcript-level raw counts; MP_tpm.tsv: human TPM values; CUUC-G_counts.csv: mouse gene-level raw counts; CUUC-G_tmp.csv: mouse TPM values; GEMM_mus_counts.exp.tsv: GEMM gene-level raw counts; GEMM_mus_tpm.exp.tsv: GEMM TPM values.

molecule: polyA RNA

growth_protocol: Bladder cancer cell lines (MGHU3) and GEMM models were grown under standard conditions. Tumors were harvested at appropriate time points for RNA extraction.

extract_protocol:
Total RNA was extracted using TRIzol reagent following manufacturer's protocol.
RNA libraries were constructed using polyA selection and Illumina TruSeq Stranded mRNA library preparation kit. Libraries were sequenced on Illumina platform.

treatment_protocol: Cells/mice were treated with vehicle control, sgIGFBP5 (IGFBP5 knockdown), or chemotherapy (cisplatin + gemcitabine).

tag: treatment


title: Pleural mesothelioma, tumor, sample 167165

description:
Library name: 167165
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 167165

value: Pleural Mesothelioma

value: E


title: lung, WT, naive, rep1

description:
Library name: WT_02102022
10x Genomics

tag: Sex


title: lung, Scnn1b, naive, rep2

description:
Library name: BENaC_07082021
10x Genomics


title: patient_11_day10

description:
Library name: 11d10
patient_11_ovarian_treatment_2

tag: cancer type

tag: patient

value: Subcutaneous


title: lung, Scnn1b, naive, rep1

description:
Library name: BENAC_02102022
10x Genomics


title: patient_11_baseline

description:
Library name: 11b
patient_11_ovarian_baseline_2

tag: time

value: Baseline

tag: biopsy site


title: Pleural mesothelioma, tumor, sample 164161

description:
Library name: 164161
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 164161

tag: tissue

value: B

value: Yes


title: Pleural mesothelioma, tumor, sample 167915

description:
Library name: 167915
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 167915


title: CTR-MGH-U3 scRNA-seq

description: Library name: CTR-MGH-U3-scRNA-seq

tag: cell type

value: Tumor epithelial cell


title: Mets-MGH-U3 lineage tracing

description: Library name: Mets-MGH-U3-lineage

tag: cell line


title: Pleural mesothelioma, tumor, sample 162703

description:
Library name: 162703
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 162703

tag: diagnosis

tag: histology

value: S


title: Pleural mesothelioma, tumor, sample 163323

description:
Library name: 163323
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 163323

tag: age at_surgery

tag: tumor status


title: MGHU3_sgScr_control_replicate_2

description: Library name: MP-MGHU3-LT-2


title: MGHU3_sgScr_control_replicate_1

description: Library name: MP-MGHU3-LT-1


title: Mesenteric arteries, normotensive Sphk1 flox/flox  4

city: Kraków

first: Mateusz

last: Siedliński

address: Skarbowa 1

country: Poland

institute: Jagiellonian University Medical College

description: Library name: Mesenteric12

data_processing:
Bioinformatic analysis included trimming of adapters using Cutadapt. RNASeq reads were mapped to the reference genome Mus musculus M28 (GRCm39) (https://www.gencodegenes.org/mouse/) using Hisat2 software. Reads were counted with HTseq.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files contain raw counts for each sample

source_name: mesenteric arteries

growth_protocol: To obtain mice lacking Sphk1 in SMCs, Sphk1f/f mice were crossed with transgenic mice harboring Cre recombinase gene under control of the mouse smooth muscle protein 22-alpha/transgelin (SM22α/Tagln) promoter. Subsequently, resulting Sphk1f/-Tagln-cre+ offsprings were mated to Sphk1f/f mice to generate mice lacking Sphk1 specifically in SMCs (Sphk1f/fTagln-cre+, later referred to as SMC KO-Sphk1) and control mice (Sphk1f/fTagln-cre-, hereafter referred to as wild type (WTf/f) mice).

extract_protocol:
Total RNA from mesenteric arteries and aortas of WTf/f control (WTf/f Sham, n=4), AngII-infused WTf/f (WTf/f AngII, n=4), and AngII-infused SMC KO-Sphk1 (SMC KO-Sphk1 AngII, n=5) mice was isolated using PureLink™ RNA Micro Kit (Thermo Fisher, USA) and treated with DNase.
The mRNA libraries were prepared using NEBNextUltra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA), and samples were sequenced on the Illumina NovaSeq 6000 System using a 2x150bp paired-end configuration.

treatment_protocol: At the age of 12-14 weeks hypertension (HTN) was induced in male SMC KO-Sphk1 mice, as well as in appropriate control strain, by a chronic, 14-day infusion of angiotensin II (AngII, 490 ng/kg/min.) with osmotic minipump (Alzet, USA) implanted subcutaneously under anesthesia

value: mesenteric arteries

value: C57BL6J Sphk1 flox/flox

value: Sham


title: MGHU3_hIGFBP5_knockdown_replicate_3

description: Library name: MP-MGHU3-LT-hI-3-1


title: Mesenteric arteries, hypertensive Sphk1 SMC KO  5

description: Library name: Mesenteric13

value: C57BL6J SMC KO-Sphk1

value: Angiotensin II


title: patient_10_baseline

description:
Library name: 10b
patient_10_colon_baseline_2

value: Colon

value: Lung


title: patient_8_baseline

description:
Library name: 8b
patient_8_colon_baseline_2

value: Tumor

value: Lymphnode


title: Mesenteric arteries, normotensive Sphk1 flox/flox  2

description: Library name: Mesenteric10


title: MGHU3_hIGFBP5_knockdown_replicate_2

description: Library name: MP-MGHU3-LT-hI-2-1


title: patient_6_day10

description:
Library name: 6d10
patient_6_prostate_treatment_2

value: Prostate

value: Treatment

value: Abdominal


title: Pleural mesothelioma, tumor, sample 158520

description:
Library name: 158520
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 158520

value: Pleural Mesothelioma

value: E

tag: subject id


title: Pleural mesothelioma, tumor, sample 158986

description:
Library name: 158986
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 158986

value: B

value: Yes


title: Mesenteric arteries, normotensive Sphk1 flox/flox  3

description: Library name: Mesenteric11

tag: genotype


title: Peripheral nerve sheath tumor, tumor, sample 160580

description:
Library name: 160580
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 160580

value: Peripheral Nerve Sheath Tumor

value: PNS


title: Mesenteric arteries, normotensive Sphk1 flox/flox  1

description: Library name: Mesenteric9

value: mesenteric arteries

value: C57BL6J Sphk1 flox/flox


title: patient_6_baseline

description:
Library name: 6b
patient_6_prostate_baseline_2

value: Baseline

tag: batch


title: MGHU3_hIGFBP5_knockdown_replicate_1

description: Library name: MP-MGHU3-LT-hI-1


title: Mesenteric arteries, hypertensive Sphk1 flox/flox  4

description: Library name: Mesenteric8

value: Angiotensin II


title: patient_3_baseline

description:
Library name: 3b
patient_3_ovarian_baseline_1

value: Ovarian

value: Vaginal


title: MR-3

city: Nanjing

first: Shuya

last: Sun

state: Jiangsu

address: No.12 Jiangwangmiao Street, Xuanwu District, Nanjing, Jiangsu Province, China

institute: Hospital for Skin Diseases, Institute of Dermatology, PUMC

description:
Library name: sample12
MR-3

data_processing:
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
HISAT2
Supplementary files format and content: FPKM
Supplementary files format and content: count

source_name: HaCaT

extract_protocol:
Total RNA from mouse epidermises was extracted using the TRIzol reagent (Invitrogen) according to the manufacturer’s protocol.
RNA libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: HaCaT

value: Keratinocytes

value: WT

value: same


title: MR-2

description:
Library name: sample11
MR-2


title: patient_1_day10

description:
Library name: 1d10
patient_1_ovarian_treatment_1

value: Tumor

value: Treatment

value: Liver


title: Pleural mesothelioma, tumor, sample 155040

description:
Library name: 155040
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 155040

value: Pleural Mesothelioma

value: E


title: patient_1_baseline

description:
Library name: 1b
patient_1_ovarian_baseline_1


title: Mesenteric arteries, hypertensive Sphk1 flox/flox  3

description: Library name: Mesenteric7


title: Pleural mesothelioma, tumor, sample 155528

description:
Library name: 155528
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 155528

value: Yes


title: Mesenteric arteries, hypertensive Sphk1 flox/flox  2

description: Library name: Mesenteric6


title: Pleural mesothelioma, tumor, sample 155007

description:
Library name: 155007
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 155007


title: Mesenteric arteries, hypertensive Sphk1 flox/flox  1

description: Library name: Mesenteric5


title: ML-3

description:
Library name: sample9
ML-3


title: patient_23_baseline

description:
Library name: 23b
patient_23_baseline

data_processing:
Illumina single-end sequencing reads were aligned to the human reference GRCh37.75 genome using STAR aligner and the two-pass method as briefly followed: the reads were aligned in a first round using the –runMode alignReads parameter, then a sample-specific splice-junction index was created using the –runMode genomeGenerate parameter. Finally, the reads were aligned using this newly created index as a reference. The number of counts was summarized at the gene level using htseq-count.
Illumina paired-end sequencing reads were aligned to the human reference GRCh37.75 genome using STAR aligner (version 2.6.0c) and the 2-pass method as briefly follows: the reads were aligned in a first round using the --runMode alignReads parameter, then a sample-specific splice-junction index was created using the --runMode genomeGenerate parameter. Finally, the reads were aligned using this newly created index as a reference. The number of counts was summarized at the gene level using htseq-count (version 0.9.1). The Ensembl ID were converted into gene symbols using the biomaRt package and only protein-coding, immunoglobulin.
Assembly: GRCh37
Supplementary files format and content: Processed coding gene expression raw count with Gene Symbol mapping

extract_protocol:
Total RNA was extracted from snap frozen biopsies, two time points were analyzed (baseline and day 10). Directly after the thawing, samples were mechanically lyzed with a metallic bead in TRIzol solution using the Tissue Lyzer (InVitrogen). After a phase separation with chloroform, RNA purification was done with the RNeasy mini or RNeasy micro kit (Qiagen) depending of the size of input material. The quality of resulting RNA was evaluated by a Nanodrop spectrophotometer (Thermofisher) and a Fragment Analyzer (Agilent). Quantification with Qubit HS RNA assay kit (InVitrogen) was also done. Sequencing libraries were constructed according to Illumina protocol using the Illumina TruSeq Stranded Total RNA kit and sequenced on a Novaseq sequencer (Lausanne Genomic Technologies Facility) according to manufacturer recommendations.
RNA quality was assessed on a Fragment Analyzer (Agilent Technologies) and the RNAs had RQNs from 6.1 - 9.9. RNA-seq libraries were prepared from 100 ng of total RNA with the Illumina Stranded Total RNA Prep with Ribo-Zero Plus reagents (Illumina) using a unique dual indexing strategy and following the official protocol. Libraries were quantified by a fluorimetric method (QubIT, Life Technologies) and their quality assessed on a Fragment Analyzer (Agilent Technologies). Sequencing was performed on an Illumina NovaSeq 6000 for 300 cycles (paired-end 150 reads). Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (version 2.20, Illumina). Two samples had low RNA quantity and were sequenced separately. RNA-seq libraries were prepared by first generating double-stranded cDNA with the Ovation RNA-Seq System V2 (TECAN). 100 ng of the resulting double-stranded cDNA were used for sequencing library preparation with the Illumina DNA Prep kit (Illumina) according to the protocol supplied by the manufacturer. Sequencing was performed on an Illumina NovaSeq 6000 for 300 cycles (paired-end 150 reads). Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (version 2.20, Illumina).

value: Colon

tag: sequencing batch


title: patient_24_baseline

description:
Library name: 24b
patient_24_baseline

value: Peritoneum


title: MR-1

description:
Library name: sample10
MR-1

tag: treatment


title: Pleural mesothelioma, tumor, sample 153021

description:
Library name: 153021
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 153021

value: B


title: Pleural mesothelioma, tumor, sample 153707

description:
Library name: 153707
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 153707


title: Mesenteric arteries, hypertensive Sphk1 SMC KO  2

description: Library name: Mesenteric2

value: mesenteric arteries

value: C57BL6J SMC KO-Sphk1


title: Mesenteric arteries, hypertensive Sphk1 SMC KO  3

description: Library name: Mesenteric3

value: Angiotensin II


title: M5-3

description:
Library name: sample6
M5-3


title: patient_22_baseline

description:
Library name: 22b
patient_22_baseline

value: Baseline


title: ML-2

description:
Library name: sample8
ML-2

value: HaCaT


title: Mesenteric arteries, hypertensive Sphk1 SMC KO  4

description: Library name: Mesenteric4


title: patient_22_day10

description:
Library name: 22d10
patient_22_day10


title: Mesenteric arteries, hypertensive Sphk1 SMC KO  1

description: Library name: Mesenteric1


title: Pleural mesothelioma, tumor, sample 151311, tech rep 1

description:
Library name: 151311.1
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 151311; replicate: 1.0; replicate_type: Technical


title: Pleural mesothelioma, tumor, sample 151311, tech rep 3

description:
Library name: 151311.3
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 151311; replicate: 3.0; replicate_type: Technical


title: M5-1

description:
Library name: sample4
M5-1

value: Keratinocytes


title: ML-1

description:
Library name: sample7
ML-1

value: WT


title: patient_21_baseline

description:
Library name: 21b
patient_21_baseline


title: patient_20_day10

description:
Library name: 20d10
patient_20_day10

value: Prostate

value: Lymphnode


title: Pleural mesothelioma, tumor, sample 151311, tech rep 2

description:
Library name: 151311.2
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 151311; replicate: 2.0; replicate_type: Technical

value: Tumor


title: Pleural mesothelioma, tumor, sample 151213

description:
Library name: 151213
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 151213


title: Pleural mesothelioma, tumor, sample 151208

description:
Library name: 151208
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 151208


title: Breast Metastasis, pleura, sample 149713

description:
Library name: 149713
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 149713

source_name: Pleura

value: Pleura

value: Breast Metastasis

value: NP

value: No


title: M5-2

description:
Library name: sample5
M5-2

value: same


title: patient_20_baseline

description:
Library name: 20b
patient_20_baseline


title: patient_21_day10

description:
Library name: 21d10
patient_21_day10

value: Colon

value: Treatment

value: Liver


title: Aorta, normotensive Sphk1 flox/flox  2

description: Library name: Aorta10

source_name: aorta

value: aorta

value: C57BL6J Sphk1 flox/flox

value: Sham


title: Pleural mesothelioma, tumor, sample 147026

description:
Library name: 147026
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 147026

value: Pleural Mesothelioma

value: B

value: Yes


title: WT-3

description:
Library name: sample3
WT-3

value: HaCaT

value: Keratinocytes

value: WT


title: Aorta, hypertensive Sphk1 SMC KO  5

description: Library name: Aorta13

value: C57BL6J SMC KO-Sphk1

value: Angiotensin II


title: WT-2

description:
Library name: sample2
WT-2


title: Aorta, normotensive Sphk1 flox/flox  1

description: Library name: Aorta9


title: WT-1

description:
Library name: sample1
WT-1


title: Aorta, normotensive Sphk1 flox/flox  3

description: Library name: Aorta11


title: Bortezomib resistant K562 cell line 2, sample 2, geldanamycin treated, replicates 1 and 2

city: Hyderabad

first: Rama Krishna

last: Kancha

state: Telangana

address: Centre for Plant Molecular Biology, Osmania University Campus

department: CPMB

country: India

institute: Osmania University

description: Library name: K562-BR2-Geldanamycin-2

data_processing:
Differential expression analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: excel files include the list of differentially expressed genes (DEGs) along with their fold change and associated statistics

source_name: Blood

extract_protocol:
RNA was isolated using Trizol and quantified using RNA HS assay kit (Thermofisher) on Qubit flurometer (Thermofisher).
The library preparation was carried out using NEBNext Ultra II Directional RNA Library Prep Kit (NEB #E7760S/L). Final libraries were quantified using Qubit 4.0 fluorometer (Thermofisher #Q33238) using DNA HS assay kit (Thermofisher #Q32851) following manufacturer’s protocol.

value: Blood

value: Myeloid

value: Not genetically modified

value: Geldanamycin treated

value: 22nd August, 2023


title: patient_18_baseline

description:
Library name: 18b
patient_18_baseline

value: Tumor

value: Breast

value: Baseline

value: Liver


title: Pleural mesothelioma, tumor, sample 146334

description:
Library name: 146334
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 146334

value: Pleural Mesothelioma

value: E


title: Bortezomib resistant K562 cell line 2, sample 1, geldanamycin treated, replicates 1 and 2

description: Library name: K562-BR2-Geldanamycin-1


title: Aorta, hypertensive Sphk1 flox/flox  4

description: Library name: Aorta8

value: aorta

value: C57BL6J Sphk1 flox/flox


title: Pleural mesothelioma, tumor, sample 145511

description:
Library name: 145511
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 145511

value: Yes


title: NSCLC-Adenocarcinoma, pleura, sample 144255, tech rep 1

description:
Library name: 144255.1
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 144255; replicate: 1.0; replicate_type: Technical

value: Pleura

value: NSCLC-Adenocarcinoma

value: NP

value: No


title: patient_18_day10

description:
Library name: 18d10
patient_18_day10

value: Treatment


title: Aorta, hypertensive Sphk1 flox/flox  3

description: Library name: Aorta7

value: Angiotensin II


title: Bortezomib resistant K562 cell line 1, sample 1, geldanamycin treated, replicates 1 and 2

description: Library name: K562-BR1-Geldanamycin-1

value: Blood

value: Myeloid

value: Not genetically modified

value: Geldanamycin treated


title: patient_16_baseline

description:
Library name: 16b
patient_16_baseline

value: Tumor

value: Neck

value: Baseline

value: Lung


title: patient_17_baseline

description:
Library name: 17b
patient_17_baseline

value: Pancreatic

value: Liver


title: Aorta, hypertensive Sphk1 SMC KO  4

description: Library name: Aorta4

value: aorta

value: C57BL6J SMC KO-Sphk1


title: NSCLC-Adenocarcinoma, pleura, sample 144255, tech rep 3

description:
Library name: 144255.3
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 144255; replicate: 3.0; replicate_type: Technical

value: Pleura

value: NSCLC-Adenocarcinoma


title: Bortezomib resistant K562 cell line 1, sample 2, geldanamycin treated, replicates 1 and 2

description: Library name: K562-BR1-Geldanamycin-2

value: 22nd August, 2023


title: Wildtype K562, sample 2, geldanamycin treated, replicates 1 and 2

description: Library name: K562-WT-Geldanamycin-2


title: Wildtype K562, sample 1, geldanamycin treated, replicates 1 and 2

description: Library name: K562-WT-Geldanamycin-1


title: Aorta, normotensive Sphk1 flox/flox  4

description: Library name: Aorta12

value: C57BL6J Sphk1 flox/flox

value: Sham


title: Pleural mesothelioma, tumor, sample 141635

description:
Library name: 141635
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 141635

value: Pleural Mesothelioma

value: B

value: Yes


title: Aorta, hypertensive Sphk1 SMC KO  3

description: Library name: Aorta3

value: Angiotensin II


title: patient_17_day10

description:
Library name: 17d10
patient_17_day10

value: Tumor

value: Treatment


title: patient_15_day10

description:
Library name: 15d10
patient_15_day10

value: Colon


title: Pleural mesothelioma, tumor, sample 144197

description:
Library name: 144197
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 144197

value: E


title: patient_15_baseline

description:
Library name: 15b
patient_15_baseline

value: Baseline


title: Aorta, hypertensive Sphk1 SMC KO  2

description: Library name: Aorta2


title: Aorta, hypertensive Sphk1 flox/flox  1

description: Library name: Aorta5


title: Aorta, hypertensive Sphk1 flox/flox  2

description: Library name: Aorta6


title: Bortezomib resistant K562 cell line 2, sample 2, untreated, replicates 1 and 2

description: Library name: K562-BR2-2

value: Blood

value: Myeloid

value: Not genetically modified

value: Untreated


title: Pleural mesothelioma, tumor, sample 131952

description:
Library name: 131952
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 131952


title: patient_14_baseline

description:
Library name: 14b
patient_14_baseline

value: Cervical

value: Pleura


title: patient_14_day10

description:
Library name: 14d10
patient_14_day10


title: Pleural mesothelioma, tumor, sample 131560

description:
Library name: 131560
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 131560


title: Pleural mesothelioma, tumor, sample 131180

description:
Library name: 131180
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 131180


title: Aorta, hypertensive Sphk1 SMC KO  1

description: Library name: Aorta1

value: aorta

value: C57BL6J SMC KO-Sphk1


title: Bortezomib resistant K562 cell line 1, sample 2, untreated, replicates 1 and 2

description: Library name: K562-BR1-2

value: 22nd August, 2023


title: Bortezomib resistant K562 cell line 1, sample 1, untreated, replicates 1 and 2

description: Library name: K562-BR1-1


title: wt_s_2

city: Jinan

first: zheng

last: yi

address: 07 Wenhua xi road, Jinan, Shandong

institute: Shandong  University

description: Library name: Sample 6

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome mm10 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: cell line

growth_protocol: RAW264.7 cells with or without CSDE1 were grown in DMEM with 10% FBS

extract_protocol:
Total RNA was extracted with an RNA extraction kit (Fastagen Biotech Co., RNAfast200)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RAW264.7 cells were mock treated or stimulated with in vitro transcribed S RNA (2 μg/ml) for 6 hour

value: WT

value: WT RAW264.7 cell with SARS CoV-2 S RNA stimulation


title: patient_12_day10

description:
Library name: 12d10
patient_12_day10

value: Rectal

value: Liver


title: Bortezomib resistant K562 cell line 2, sample 1, untreated, replicates 1 and 2

description: Library name: K562-BR2-1


title: patient_12_baseline

description:
Library name: 12b
patient_12_baseline

value: Tumor


title: Pleural mesothelioma, tumor, sample 131427

description:
Library name: 131427
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 131427

value: Pleural Mesothelioma

value: B

value: Yes


title: Pleural mesothelioma, tumor, sample 130099

description:
Library name: 130099
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 130099

value: S


title: wt_s_1

description: Library name: Sample 5


title: Wildtype K562, sample 2, untreated, replicates 1 and 2

description: Library name: K562-WT-2

value: Blood

value: Myeloid


title: wt_mock

description: Library name: Sample 4

value: WT RAW264.7 cell without SARS CoV-2 S RNA stimulation


title: Wildtype K562, sample 1, untreated, replicates 1 and 2

description: Library name: K562-WT-1

value: Not genetically modified

value: Untreated


title: patient_11_day10

description:
Library name: 11d10
patient_11_day10

value: Ovarian

value: Treatment

value: Subcutaneous


title: ko_s_2

description: Library name: Sample 3

value: Csde1 KO

value: Csde1 KO RAW264.7 cell with SARS CoV-2 S RNA stimulation


title: Peripheral nerve sheath tumor, tumor, sample 128083

description:
Library name: 128083
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 128083

value: Peripheral Nerve Sheath Tumor

value: PNS


title: patient_13_baseline

description:
Library name: 13b
patient_13_baseline

value: Tumor

value: Colon

value: Baseline

value: Liver


title: patient_11_baseline

description:
Library name: 11b
patient_11_baseline


title: Pleural mesothelioma, tumor, sample 125117

description:
Library name: 125117
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 125117

value: Pleural Mesothelioma

value: B

value: Yes


title: patient_7_day10

description:
Library name: 7d10
patient_7_day10

value: Prostate

value: Bone


title: Pleural mesothelioma, tumor, sample 125811

description:
Library name: 125811
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 125811


title: ko_s_1

description: Library name: Sample 2


title: Pleural mesothelioma, tumor, sample 123895

description:
Library name: 123895
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 123895

value: E


title: patient_4_day10

description:
Library name: 4d10
patient_4_day10


title: ko_mock

description: Library name: Sample 1

value: Csde1 KO RAW264.7 cell without SARS CoV-2 S RNA stimulation


title: patient_4_baseline

description:
Library name: 4b
patient_4_baseline


title: Pleural mesothelioma, tumor, sample 120329

description:
Library name: 120329
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 120329


title: T cells treated with a Cas9 targeting TRAC, B2M and TET2 (Triple-KO), rep2

city: Milano

first: Sara

last: Valsoni

state: MI

address: via Olgettina 60

department: TIGET

country: Italy

institute: SR-TIGET

description: Library name: TRAC-sample-4

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the CAST-Seq pipeline with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: hg38
Supplementary files format and content: matrix table of translocation sites detected with CAST-Seq pipeline. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.

growth_protocol: Activated T cells were cultured in RPMI supplemented with 1% penicillin/streptomyci, 2% L-glutamine, 10% FBS, and 5 ng/ml of each IL-7 and IL-15. Cells were cultured at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
4 days post-nucleofection, genomic DNA was extracted using the DNeasy Blood and Tissue DNA Isolation Kit (Qiagen)
customized library prep, locus specific, CAST-Seq

treatment_protocol: Activated T cells, post-Dynabeads removal, were nucleofected with poly-editor or Cas9 mRNA and gene-specific gRNAs. Immediately after nucleofection cells were plated in complete RPMI supplemented with 1mM Alt-R HDR Enhancer V2, IDT.

value: Blood

value: T lymphocytes

value: Triple-KO


title: T cells treated with a poly-functional editor targeting TRAC, epi-silencing B2M and TET2, rep2

description: Library name: TRAC-sample-8

value: Poly-editing


title: MMDTR, colon LP cell, Day9

city: Boston

first: Xi

last: Lin

state: MA

address: 77 Avenue Louis Pasteur, Rm641

institute: Brigham and Women's Hospital

description: Library name: D9MMDTR_scRNAseq

data_processing:
For scRNA-seq, raw data reads were aligned to the mouse transcriptome (mm10) using the Cell Ranger toolkit (version 6.1.1), which was also used for cell selection, filtering, and unique molecular identifier (UMI) counting. For bulk RNA-seq, FASTQ raw data were uploaded to Partek Flow (Partek, building version: 10.0.21.0201) and analyzed with the default setting. Briefly, trimmed reads were aligned to the mouse genome (GRCm38/mm10) using STAR 2.5.3a, and gene expression was quantified using the Partek E/M annotation model with a default setting.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colon

extract_protocol:
For scRNA-seq, and sorted cell bulk RNA-seq,  the entire colon from postnatal mice was collected, opened longitudinally, washed with ice-cold PBS to remove fecal content, and cut into 2–3 cm segments. Tissue segments were placed in a 50 mL Falcon tube containing 10 mL HBSS with 2mM EDTA and shaken at 250 rpm for 45 min at 37°C. The supernatant containing epithelial cells was discarded, and the remaining LP tissue was digested in 10 mL RPMI medium containing 10% FBS, 1.5% HEPES, 1 mg/mL Collagenase VIII, and 10 µg/mL DNase I. Digestion was performed at 250 rpm for 45 min at 37°C. Enzymatic activity was stopped by adding 10 mL ice-cold FACS buffer (PBS with 2% FBS and 1mM EDTA). The cell suspension was filtered through a 70 µm cell strainer, centrifuged at 1500 rpm for 5 min, and resuspended for FACS sorting. For whole tissue bulk RNA-seq, Total RNA from whole colon tissue of CT and MMDTR mice was extracted using the RNeasy Plus Mini Kit (QIAGEN, 74134) and used as input material.
For scRNA-seq, live cells were FACS-sorted for single-cell RNA sequencing, which was performed by the Brigham and Women’s Hospital Single Cell Genomics Core. Briefly, sorted live cells were separated into a single droplet using the Chromium Single Cell 3' v3 kit (10x Genomics) according to the manufacturer’s protocol. For whole tissue bulk RNA-seq, Library preparation and transcriptome sequencing were performed by Novogene Bioinformatics Technology Co., Ltd. For FACS sorted cell bulk RNA-seq, library preparation (Illumina Nextera XT) and sequencing were performed at the Biopolymers Facility at Harvard Medical School.

value: colon

value: whole colon lamina propria cell

value: MMDTR


title: CT, colon LP cell, Day9

description: Library name: D9CT_scRNAseq

value: CT


title: TRAC_Mock-treated T cells

description: Library name: TRAC-sample-9-unedited

value: Mock-treated


title: T cells treated with a Cas9 targeting TRAC, B2M and TET2 (Triple-KO), rep1

description: Library name: TRAC-sample-2


title: Pleural mesothelioma, tumor, sample 120271

description:
Library name: 120271
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 120271

value: Tumor


title: patient_3_day10

description:
Library name: 3d10
patient_3_day10

value: Ovarian

value: Treatment

value: Subcutaneous


title: NM1 KO spleen 04

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: abu dhabi

address: NYUAD Saadiyat Island

country: United Arab Emirates

institute: Biology

description: Library name: Sample12

data_processing:
Subsequent analysis, including quality trimming, was executed using the BioSAILs workflow execution system. Trimmomatic (version 0.36) was used for quality trimming of the raw reads to get rid of low-quality bases, systematic base-calling errors and sequencing adapter contamination(Bolger et al., 2014). The quality of the sequenced reads pre/post quality trimming was assessed by FastQC and only the reads that passed quality trimming in pairs were selected for downstream analysis (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The quality-trimmed RNA-Seq reads were aligned to the Mus musculus GRCm38 (mm10) genome using HISAT2 (version 2.0.4)(Kim et al., 2015). The conversion and sorting of SAM alignment files for each sequenced sample to BAM format were done by using SAMtools (version 0.1.19)(Li et al., 2009). The BAM alignment files were processed using HTseq-count, using the reference annotation file to produce raw counts for each sample.
Assembly: GRCm38 (mm10)
Supplementary files format and content: txt files (.txt)

source_name: Spleen

growth_protocol: Wild type and NM1 KO C57/Bl6 mice (8 months old; 25-35 g in weight) were used for the analysis(Venit et al., 2013). The mice were housed in a pathogen-free sterile ventilation system supplied with sterile woodchip and ad libitum feed and water supply. Mice were kept in a room maintained at a temperature of 21-24 °C on a schedule of 12 h light/dark cycle. All animal experiments were performed after approval by the NYUAD-IACUC (Protocol 20-0004).

extract_protocol:
Spleen was isolated from euthanized mice and cleaned from surrounding fat and connective tissue. Approximately 5mm3 of tissue from the tip of the spleen was merged in RNAzol and homogenized in bead mill homogenizer followed by standard RNA isolation protocol. Blood samples were collected by submandibular vein bleeding according to a previously published protocol (Golde et al, 2005). Collected blood was immediately mixed with the double amount of RNAzol and samples were thoroughly mixed and stored on dry ice before RNA isolation by standard protocol. The final RNA concentration was measured by the Qubit RNA BR Assay Kit.
Three replicates were prepared for each genotype. 500ng of total RNA was used for the RNA-Seq library preparation by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) and sequenced with the NextSeq 500/550 sequencing platform (performed at the NYUAD Sequencing Center).

value: Spleen

value: NM1 KO


title: patient_3_baseline

description:
Library name: 3b
patient_3_baseline

value: Baseline

value: Vaginal


title: T cells treated with a poly-functional editor targeting TRAC, epi-silencing B2M and TET2, rep1

description: Library name: TRAC-sample-6

value: Blood


title: Pleural mesothelioma, tumor, sample 118014, bio rep 2

description:
Library name: 118014.2
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 118014; replicate: 2.0; replicate_type: Biologic

value: Pleural Mesothelioma

value: S

value: Yes


title: NM1 KO spleen 03

description: Library name: Sample11


title: patient_1_day10

description:
Library name: 1d10
patient_1_day10

value: Liver


title: T cells treated with a Cas9 targeting B2M, CD3D and TGFBR2 (Triple-KO), rep2

description: Library name: B2M-sample-13

value: T lymphocytes

value: Triple-KO


title: Pleural mesothelioma, tumor, sample 118014, bio rep 1

description:
Library name: 118014.1
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 118014; replicate: 1.0; replicate_type: Biologic


title: Pleural mesothelioma, tumor, sample 115261

description:
Library name: 115261
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 115261

value: E


title: Pleural mesothelioma, tumor, sample 114626, tech rep 3

description:
Library name: 114626.3
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 114626; replicate: 3.0; replicate_type: Technical

value: B


title: NM1 WT spleen 01

description: Library name: Sample7

value: WT


title: NM1 WT spleen 04

description: Library name: Sample9


title: T cells treated with a poly-functional editor targeting B2M, epi-silencing CD3D and TGFBR2, rep2

description: Library name: B2M-sample-17

value: Poly-editing


title: T cells treated with a Cas9 targeting B2M, CD3D and TGFBR2 (Triple-KO), rep1

description: Library name: B2M-sample-11


title: NM1 KO spleen 01

description: Library name: Sample10


title: B2M_Mock-treated T cells

description: Library name: B2M-sample-9-unedited

value: Mock-treated


title: patient_1_baseline

description:
Library name: 1b
patient_1_baseline

value: Tumor

value: Ovarian


title: Pleural mesothelioma, tumor, sample 114626, tech rep 2

description:
Library name: 114626.2
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 114626; replicate: 2.0; replicate_type: Technical


title: NM1 WT spleen 02

description: Library name: Sample8

value: Spleen


title: Pleural mesothelioma, tumor, sample 114626, tech rep 1

description:
Library name: 114626.1
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 114626; replicate: 1.0; replicate_type: Technical


title: NM1 KO blood 04

description: Library name: Sample6

value: NM1 KO


title: P121

city: Vienna

first: Katharina

last: Rindler

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

description: Single Cell 5' PE

data_processing:
Raw data files were demultiplexed using the 10X Genomics Cell ranger (v6.1.2) pipeline with the command “mkfastq”, assembled, and aligned to the human reference genome using the “count” pipeline
Assembly: GRCh38-2020-A
Supplementary files format and content: tsv file containing barcode information for each cell of the sample
Supplementary files format and content: tsv file containing feature information for the sample
Supplementary files format and content: mtx file containing matrix information for the sample

source_name: skin

extract_protocol:
Skin punch biopsies were acquired after written informed consent, and samples were dissociated into single cell suspensions using the Skin Dissociation Kit by Miltenyi Biotech (Bergisch Gladbach, Germany).
Isolated skin cells were prepared for scRNA-seq using the Chromium Single Cell Controller and Single Cell 5’ Library & Gel Bead Kits (10X Genomics, Pleasanton, CA), according to the manufacturer’s protocol.

value: skin

value: Healthy control


title: NM1 KO blood 03

description: Library name: Sample5

value: Blood


title: LPS-induced BV-2 cells, rep3, SUP

type: RNA

city: Qingdao

first: Shuixian

last: Du

state: Shandong

address: No. 5, Donghai Middle Road

institute: Qingdao Municipal Hospital

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10 Blocking Agent and 1 μL of 25 Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2 Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in a certain proportion were retained for further “m6A quantity” analyses. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. Differentially m6A-methylated RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds. Hierarchical Clustering was performed using the R software. GO analysis was performed using topGO package in R environment for statistical computing and graphics, and Pathway analysis was calculated by fisher's exact test.
IP(Cy5 normalized intensity)=log2(IP(Cy5 raw) )-Average[log2(IP(spike-in_Cy5 raw) )]
Sup(Cy3 normalized intensity)=log2(Sup(Cy3 raw) )-Average[log2(Sup(spike-in_Cy3 raw) )]

source_name: LPS-stimulated (1 µg/mL, 6 h)

label_protocol: The “IP” RNAs and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labeling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific actitity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000.

growth_protocol: BV-2 cells were maintained in high glucose-DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin (100 units/mL)/streptomycin (100 μg/mL) at 37°C in a humidified 5% CO2-containing atmosphere.

extract_protocol: RNA was harvested using Trizol reagent.RNA quality and quantity was measured by using NanoDrop and RNA Integrity was determined by Agilent 2100 bioanalyzer. Total RNAs were immunoprecipitated with anti-N6-methyladenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs.

treatment_protocol: BV-2 cells were pre-incubated with hUC-MSC-EXO (10 μl, 1 μg/mL) in six-well plates for 24 hours, then washed twice with PBS, and subsequently exposed to LPS (1 μg/mL) for 6 hours to establish a microglial activation model.

tag: cell ine

value: LPS

tag: fraction

value: supernatant unmodified RNAs


title: T cells treated with a poly-functional editor targeting B2M, epi-silencing CD3D and TGFBR2, rep1

description: Library name: B2M-sample-15


title: P220

description:
Library name: Sample 1
Single Cell 5' PE

value: Lymphomatoid Papulosis


title: Pleural mesothelioma, tumor, sample 110926

description:
Library name: 110926
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 110926

data_processing:
Reads were processed using the Drop-seq tools pipeline aligned to the hg38 transcriptome using standard parameters.
Raw sequencing data are available through controlled access in dbGaP under accession phs004285.
Processed files provided here include per-library count matrices and corresponding cell-level metadata files.
Assembly: hg38
Supplementary files format and content: Sparse counts matrices (initial and stringently filtered cells) with associated column and row name files are formatted in tab-delmited compressed text files. Metadata for cells is formatted as a compressed tab delimited text file.

value: Pleural Mesothelioma

value: Yes


title: LPS-induced BV-2 cells following hUC-MSC-EXO treatment, rep1, SUP

source_name: hUC-MSC-EXO pre-incubation (24 h) + LPS-stimulated (6 h)

value: EXO


title: P116

description: Single Cell 5' PE


title: LPS-induced BV-2 cells following hUC-MSC-EXO treatment, rep3, SUP


title: Pleural mesothelioma, tumor, sample 112946

description:
Library name: 112946
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 112946

value: B


title: NM1 KO blood 02

description: Library name: Sample4


title: Pleural mesothelioma, tumor, sample 108021

description:
Library name: 108021
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 108021


title: Pleural mesothelioma, tumor, sample 107957

description:
Library name: 107957
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 107957

value: E


title: LPS-induced BV-2 cells following hUC-MSC-EXO treatment, rep2, SUP


title: NM1 WT blood 03

description: Library name: Sample2

value: WT


title: P112

description: Single Cell 5' PE


title: P95

description: Single Cell 5' PE

value: Mycosis fungoides


title: Pleural mesothelioma, tumor, sample 107932

description:
Library name: 107932
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 107932

value: Tumor


title: A. fumigatus, Day 7

city: Columbus

first: Jose

middle: P

last: Guirao-Abad

state: OH

address: 2255 Kenny Rd

department: Emergency Medicine

institute: Ohio State University

description:
Library name: Sample 4
10x Genomics

data_processing:
The 10x scRNA-seq data were preprocessed using Cell Ranger software (7.0.0).
We used the ‘mkfastq.gz’, ‘count’ and ‘aggr’ commands to process the 10x scRNA-seq output into one cell by gene expression count matrix using default parameters. scRNA-seq data analysis was performed with the Scanpy (1.9.0) package in Python (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1382-0). Genes expressed in fewer than three cells were removed from further analysis. Cells expressing less than 100 and more than 7,000 genes were also removed from further analysis.
Cells with a high (≥ 10%) mitochondrial genome transcript ratio were removed
Assembly: Mouse mm39
Supplementary files format and content: For downstream analysis, we used count per million (CPM) normalization to control for library size differences in cells and transformed those into log (CPM + 1) values. After normalization, the data were then z-score normalized for each gene across all cells. We then used the following commands, tl.pca’, ‘pp.neighbors’ and ‘tl.leiden, in Scanpy to partition the single cells into clusters.
Supplementary files format and content: h5 files
Supplementary files format and content: Differential expression analysis was done using the Wilcoxon rank sum test at the single cell level.

growth_protocol: The stromal cell population was then isolated from total lung cells on days 1 and 7 post-inoculation by flow cytometry, excluding the non-stromal population based on expression of CD31, CD45 and EpCAM

extract_protocol:
Sorted pulmonary stromal cells (negative for CD45, CD31 and EpCAM) were collected in a tube containing DMEM (Corning, 10013CV) with 10% FBS at a concentration of 100 cells/μL.
The single-cell RNA-Seq assay was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index), 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate a gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every GEM was reverse transcribed into cDNA, adding an Illumina TruSeq R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The cell barcoded molecules were then cleaned up with Silane DynaBeads and amplified using 14 PCR cycles.  Next, full-length, barcoded cDNA was then enzymatically fragmented, sized-selected, adapter-ligated, and amplified for library construction. During the library construction, P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 were added. Samples were pooled and run on the NovaSeq 6000 sequencer with a S4 flow cell using the following sequencing parameters: R1: 28 cycles, i7: 10 cycles, i5: 10 cycles, R2: 90 cycles.

treatment_protocol: Immunocompetent mice were exposed to either a single inoculum of conidia or a mock inoculation with saline.

value: Lung

tag: cell type_1

value: Stromal cells

tag: cell type_2

value: Fibroblast

value: A. fumigatus

tag: day post-inoculation

value: Day 7

tag: group

value: Experimental


title: P115

description: Single Cell 5' PE

tag: tissue

value: skin

value: Healthy control


title: NM1 WT blood 01

description: Library name: Sample1

value: Blood


title: P72

description: Single Cell 5' PE


title: PGS

description: Single Cell 5' PE


title: NM1 WT blood 04

description: Library name: Sample3


title: Pleural mesothelioma, tumor, sample 106649

description:
Library name: 106649
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 106649

extract_protocol:
Single-cell suspensions were generated from surgical pleural specimens after tissue dissociation. Seq-Well arrays containing RNA capture beads were loaded with approximately 10,000-20,000 cells per array. For selected specimens, technical replicates were created by splitting cell suspensions across multiple arrays processed in parallel.
Single-cell RNA sequencing libraries were generated using the Seq-Well platform. Cells were loaded onto bead-containing arrays, sealed with a membrane, lysed, and RNA was captured on beads. Reverse transcription, second-strand synthesis, whole transcriptome amplification, and Nextera XT library construction were performed prior to sequencing on Illumina NextSeq 500/550 or NovaSeq 6000 instruments.

value: Pleural Mesothelioma


title: Untreated normal BV-2 cells, rep1, SUP

source_name: Untreated, no LPS, no EXO

value: Con

value: supernatant unmodified RNAs


title: Pleural mesothelioma, tumor, sample 108535

description:
Library name: 108535
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 108535

value: Yes


title: Saline, Day 7

description:
Library name: Sample 3
10x Genomics

value: Saline

value: Mock


title: LPS-induced BV-2 cells, rep2, SUP

value: LPS


title: P71

description: Single Cell 5' PE

value: Mycosis fungoides


title: LPS-induced BV-2 cells following hUC-MSC-EXO treatment, rep3, IP

value: EXO

value: IP enriched m6A methylated RNAs


title: Untreated normal BV-2 cells, rep3, SUP


title: Pleural mesothelioma, tumor, sample 106083

description:
Library name: 106083
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 106083

value: Tumor

value: B


title: A. fumigatus, Day 1

description:
Library name: Sample 2
10x Genomics

value: Lung

value: Stromal cells

value: Fibroblast

value: A. fumigatus

value: Day 1


title: Untreated normal BV-2 cells, rep2, SUP


title: PEN

description: Single Cell 5' PE

value: skin

value: Lymphomatoid Papulosis


title: Pleural mesothelioma, tumor, sample 105944

description:
Library name: 105944
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 105944

value: Pleural Mesothelioma

value: S


title: Saline, Day 1

description:
Library name: Sample 1
10x Genomics

value: Saline


title: LPS-induced BV-2 cells, rep1, SUP

value: supernatant unmodified RNAs


title: Pleural mesothelioma, tumor, sample 104538

description:
Library name: 104538
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 104538

value: Yes


title: Pleural mesothelioma, tumor, sample 106064

description:
Library name: 106064
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 106064

value: E


title: P217

description: Single Cell 5' PE


title: LPS-induced BV-2 cells following hUC-MSC-EXO treatment, rep2, IP

value: EXO


title: T1, PostnLin cells, A. fumigatus, Day7

description:
Library name: Sample 8
Column name in Expression Browser.xlsx: T1

data_processing:
CLC Genomics Workbench (Qiagen)
Fastq ﬁles from each sample were merged, and quality control of the sequencing reads was conducted.
Adapters sequences were trimmed before further analysis.
Gene expression analysis was carried out using the Mus musculus reference genome GRCm39 (mm39) in CLC Genomics Workbench (Qiagen).
Differential expression was assessed between PostnLin cells treated with A. fumigatus and Pdgfrα-GFP cells treated with saline.
Assembly: Mouse mm39
Supplementary files format and content: Expression values were reported as total counts or Reads Per Kilobase per Million mapped reads (RPKM)
Supplementary files format and content: Statistical cutoff of a Bonferroni-adjusted P-value ≤ 0.05 and a fold change greater than +/- 1.5

growth_protocol: PostnLin or Pdgfrα-GFP cells were sorted

extract_protocol:
RNA was isolated using an RNeasy Plus Micro Kit (Qiagen, 74034) according to the manufacturer’s instructions. . The cDNA was amplified with the Ovation RNA-Seq System v2 (Tecan Genomics)
Libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: PostnLin mice were administered a single inoculum of A. fumigatus conidia to induce fibroblast activation and Pdgfrα-GFP mice were given a mock inoculation with saline. Cells were isolated on day 7 post-inoculation.

tag: cell line

value: Primary cells

tag: cell type

value: PostnLin

value: Experimental


title: Pleural mesothelioma, tumor, sample 104124, tech rep 3

description:
Library name: 104124.3
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 104124; replicate: 3.0; replicate_type: Technical

value: Tumor

tag: diagnosis

tag: histology

value: B


title: P101

description: Single Cell 5' PE


title: P213

description: Single Cell 5' PE


title: T479, PostnLin cells, A. fumigatus, Day7

description:
Library name: Sample 7
Column name in Expression Browser.xlsx: T479

value: Lung

value: Fibroblast


title: Pleural mesothelioma, tumor, sample 104124, tech rep 2

description:
Library name: 104124.2
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 104124; replicate: 2.0; replicate_type: Technical

tag: age at_surgery

tag: tumor status


title: T462, PostnLin cells, A. fumigatus, Day7

description:
Library name: Sample 6
Column name in Expression Browser.xlsx: T462

tag: genotype

value: A. fumigatus


title: P193

description: Single Cell 5' PE

value: skin


title: T182, PostnLin cells, A. fumigatus, Day7

description:
Library name: Sample 5
Column name in Expression Browser.xlsx: T182


title: LPS-induced BV-2 cells, rep2, IP

value: LPS

value: IP enriched m6A methylated RNAs


title: LPS-induced BV-2 cells, rep3, IP


title: Pleural mesothelioma, tumor, sample 104124, tech rep 1

description:
Library name: 104124.1
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 104124; replicate: 1.0; replicate_type: Technical

value: Pleural Mesothelioma

tag: subject id


title: Pleural mesothelioma, tumor, sample 103805

description:
Library name: 103805
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 103805

value: S


title: P118

description: Single Cell 5' PE

value: Lymphomatoid Papulosis


title: A2780, cPVP, biol rep 2

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
Reads contain Ad1 adapters were discarded by cutadapt (version 3.5).
Reads were aligned to GRCh38 genome using bowtie1 (version 1.3.1).
PCR duplicates were removed using Picard MarkDuplicates 58 (version 2.26.10; http://broadinstitute.github.io/picard)
Then, unique reads in BED format were further filtered with Bedtools (version v2.27.1) and custom BASH scripts
To plot average Damage-seq signal at ATAC-Seq peaks, these steps were done: The gene’s annotation file was downloaded from Ensembl, assembly GRCh38, release 96. Only peaks that don’t overlap genes were obtained using custom scripts and Bedtools (version 2.27.1) slop and merge commands. Damage-Seq reads intersecting peak list were obtained using Bedtools intersect command and profiles flanking ATAC-seq peaks were created using the R (version 4.1.3) Bioconductor genomation package (version 1.26.0).
Assembly: GRCh38
Supplementary files format and content: No quantified processed data provided for this study.
Library strategy: Damage-seq

source_name: ovarian carcinoma

growth_protocol: A2780 cells (93112519 , Sigma-Aldrich) were cultured in RPMI 1640 Medium, supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U/mL penicillin and 0.1 mg/mL streptomycin. Culturse were maintained in a humidified 5% CO2 incubator at 37 °C. Cells were sub-cultured every 3–4 days to maintain logarithmic growth.

extract_protocol:
Cells were harvested by scraping into ice-cold PBS. DNA was extracted by using DNeasy® Blood & Tissue kit (69504, Qiagen), and quantified by the QuantiFluor® dsDNA System (E2670, Promega). 2 µg of each DNA sample were taken for library preparation.
Damage-seq was performed as previously described by Hu et al. (PNAS, 2017) without biotin purification after the primer extension step (Jiang et al., ACS Central Science, 2023). Briefly, Genomic DNA was sheared by sonication with Biotuptor Pico sonicator (Diagenode Inc) to generate fragments averaging 300 bp in length. Damaged DNA immunoprecipitation was performed as described previously, with anti-cisplatin modified DNA antibody (ab103261, Abcam).

treatment_protocol: Cells were grown to ~80% confluence in 100 mm dishes, culture medium was replaced with media containing either 200 µM cisplatin or 30 µM cPVP, incubated for 2h.

value: ovarian carcinoma

value: cancerous

tag: ip antibody

value: cPVP, 30 uM

tag: time


title: G244, Pdgfra-GFP cells, Saline, Day7

description:
Library name: Sample 4
Column name in Expression Browser.xlsx: G244

value: Primary cells

value: Pdgfra-GFP

tag: treatment

value: Saline

value: Mock


title: Untreated normal BV-2 cells, rep1, IP

tag: cell ine

value: Con

tag: fraction


title: A2780, cPVP, biol rep 1

value: anti-cisplatin modified DNA antibody (ab103261, Abcam)


title: G231, Pdgfra-GFP cells, Saline, Day7

description:
Library name: Sample 3
Column name in Expression Browser.xlsx: G231

value: Lung

value: Fibroblast


title: DR-PBMCs-scATAC-seq_rep2

city: Yangzhou

first: Cui

address: NO.88 University South Road

institute: Yangzhou University

data_processing:
(scRNA-Seq data)Cell Ranger v3.1.0 was used to align reads
(scRNA-Seq data)doublets were identified using Scrublet v0.2.3 (Wolock et al., 2019) ,the data were filtered using Seurat v4.0.1 (Stuart et al., 2019) to remove low-quality cells and genes.
(scATAC-Seq data)Cell Ranger ATAC (v1.2.0) was used to align scATAC-Seq reads
(scATAC-Seq data)Seurat v4.0.1 and Signac v1.1.1 (Stuart et al., 2019) are used for downstream analysis of scATAC-Seq data analysis, including quality control, pre-processing, gene activity quantification and data visualization.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each gene in  each cell
Supplementary_files_format_and_content: h5 files include peak information for each cell

organism: Sus scrofa

source_name: PBMCs

growth_protocol: Modern intensive breeding conditions, unified management

extract_protocol:
The PBMCs were isolated from venous blood of healthy pigs using a Ficoll-Hypaque density solution according to standard density gradient centrifugation methods.
scRNA-seq: The single-cell suspensions not cryopreserved of scRNA-seq samples were converted to barcoded scRNA-seq libraries using the Chromium Single Cell Library Kit v3, Gel Bead and Multiplex Kit, and Chip B Kit (10X Genomics). The poly-adenylated transcripts were reverse-transcribed later. Libraries were prepared by the Chromium Single Cell 5′ Reagent kit according to the manufacturer’s protocol (10x Genomics, CA, USA). And then all libraries were sequenced on an Illmina Novaseq 6000 with a read length of 150 bp paired-end reads.  scATAC-seq: Part of the prepared PBMCs is separated for ATAC sequencing. All protocols to generate scATAC-seq data on the 10x Chromium platform, including sample preparation, library preparation and instrument and sequencing settings.

treatment_protocol: untreated

tag: breed

value: Duroc

value: venous blood

value: Peripheral Blood Mononuclear Cells

value: untreated


title: G212, Pdgfra-GFP cells, Saline, Day7

description:
Library name: Sample 2
Column name in Expression Browser.xlsx: G212


title: LPS-induced BV-2 cells, rep1, IP

value: LPS

value: IP enriched m6A methylated RNAs


title: Pleural mesothelioma, tumor, sample 101941

description:
Library name: 101941
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 101941

source_name: Tumor

value: Tumor

value: Pleural Mesothelioma

value: B

value: Yes


title: G207, Pdgfra-GFP cells, Saline, Day7

description:
Library name: Sample 1
Column name in Expression Browser.xlsx: G207

value: Primary cells

value: Pdgfra-GFP


title: A2780, cisplatin, biol rep 2

value: ovarian carcinoma

value: cancerous

value: cisplatin, 200 uM


title: Peripheral nerve sheath tumor, tumor, sample 100724

description:
Library name: 100724
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 100724

value: Peripheral Nerve Sheath Tumor

value: PNS


title: MS-PBMCs-scRNA-seq_rep2

value: Meishan


title: Peripheral nerve sheath tumor, tumor, sample 102833

description:
Library name: 102833
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 102833


title: Salmonella 24h post-infection, GFP+, Batch 1, Replicate 1

first: Matan

last: Hofree

address: The Edmond J. Safra, Givat Ram Campus

department: School of Computer Science and Engineering | The Lautenberg Center for Immunology and Cancer Research

institute: The Hebrew University of Jerusalem

data_processing:
STARsolo v2.7.10 was used to align reads and collect cell barcode transcript quantification, using multi-mapping EM mode.
Cellranger  barcodes from 3M-february-2018.txt were used a cell barcode whitelist.
EmptyDrops (DropletUtils v1.7.1) were used to exclude likely empty cells from analysis.
Cellbender (v3) was used to remove ambient contamination from analysis.
Assembly: GRCm39, genecode M32
Supplementary files format and content: STARsolo output: *_features.tsv.gz, *_barcodes.tsv.gz, *_UniqueAndMult-EM.mtx.gz

source_name: Small intestine

extract_protocol:
Small intestine was extracted and rinsed in cold Phosphate buffered saline (PBS). The tissue was opened longitudinally and sliced into small fragments roughly 2 mm long followed by incubation with 20mM EDTA-PBS on ice for 75 min. Then, the tissue was shaken vigorously, and the supernatant was collected as fraction 1 in a new conical tube. The tissue was incubated in fresh PBS, and a new fraction was collected every 5 min. Fractions were collected until the supernatant consisted almost entirely of crypts. The fractions 3-4 (enriched for crypts) were filtered through a 70 µm filter, centrifuged at 400g for 5 min, and dissociated with TrypLE Express (Gibco) for 1 min and 30 seconds at 37°C. The single-cell suspension was then passed through a 40μm filter. Cells for each condition or mouse were stained with the Dapi-NucBlue (ThermoFisher, cat no. R37605), CD45 (Biolegend, 30-F11), Biotin anti-mouse CD326 (EpCAM) antibody (cat #118204) followed by staining using TotalSeq™ PE Streptavidin (B0951 - B0955). Isolated IEC were sorted into a cooled 15 mL tube with 0.04% BSA in PBS using a Sony SH800 cell sorter. 20,000 cells EpCAM+ CD45- (IEC), EpCAM+ CD45- GFP+ (Invaded IEC) were sorted for each mouse or condition and pooled following manufacturer’s instructions. 30,000 single-cell suspension was loaded onto Next GEM Chip G targeting 15,000 cells and then ran on a Chromium Controller instrument to generate GEM emulsion. Single-cell 3’ RNA-seq libraries and cell surface protein libraries were generated according to the manufacturer’s protocol (Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index). Final libraries were quantified using NEBNext Library Quant Kit for Illumina (NEB) and high sensitivity D5000/D1000 TapeStation (Agilent). Libraries were pooled according to targeted cell number, aiming for ~20,000 reads per cell for gene expression libraries and ~5,000 reads per cell for cell surface protein libraries. Pooled libraries were sequenced on a NovaSeq 6000 instrument using an S1 100 cycles reagent kit (Illumina).
A total of 8000 cells were loaded into each well of a Chromium Next GEM Chip G and run on the Chromium Controller (10X Genomics) for Gel Bead-in-emulsion (GEM) generation. The samples were processed according to the CG000317 Chromium Next GEM Single Cell 3’ v3.1 (Dual Index) Rev. D protocol (10X Genomics) for RNA library construction.

value: Small intestine

value: Epithelial cells

value: Salmonella+


title: MS-PBMCs-scRNA-seq_rep1

value: venous blood

value: Peripheral Blood Mononuclear Cells

value: untreated


title: DR-PBMCs-scATAC-seq_rep1

value: Duroc


title: Pleural mesothelioma, tumor, sample 100620

first: David

address: 2301 Erwin Road

institute: Duke University Health System

description:
Library name: 100620
Seq-Well single-cell RNA-seq; collection event: Surgery; manuscript_id: 100620

value: Tumor

value: Pleural Mesothelioma

value: B


title: A2780, cisplatin, biol rep 1

value: anti-cisplatin modified DNA antibody (ab103261, Abcam)


title: Untreated normal BV-2 cells, rep2, IP

value: Con

value: IP enriched m6A methylated RNAs


title: Salmonella 24h post-infection, Batch 1, Replicate 1


title: DR-PBMCs-scRNA-seq_rep2


title: Untreated normal BV-2 cells, rep3, IP


title: A2780, cPVP, biol rep 2

data_processing:
Adapter sequence was trimmed from each read using Cutadapt version 1.15 with the command options: -m 10.
Reads were aligned to the genome using Bowtie2 version 2.4.1 with the command options: --very-sensitive  -k 10.
Reads mapped to chromosome Y or mitochondrial chromosome were filtered.
PCR duplicates were removed using PicardCommandLine MarkDuplicates version 2.26.10 (http://broadinstitute.github.io/ picard/).
All bam files of replicates from condition were merged to create a pooled bam file.
Peaks were called separately for each replicate and pooled bam files using macs2 callpeak command version 2.2.7.1.
Peak files from replicates of the same condition were merged with the pooled bam peak file using bedtools intersect to create one set of peaks per condition.
Per base read counts were calculated using bedtools genomecov and normalized per billion mapped reads per chromosome. Read counts were converted to bigwig using the bedGraphToBigWig command to create signal maps in bigwig file format.
Assembly: GRCh38
Supplementary files format and content: bigwig files of the data normalized to mapped reads per chromosome counts.
Supplementary files format and content: narrowpeak files

extract_protocol:
Cells were washed with PBS and incubated in the 37°C incubator with media containing 200 units/mL DNase (LS002006, Worthington) in 1.2 mM MgCl2 and 0.5 mM CaCl2 for 30 min.
ATAC-seq was performed using an ATAC-seq kit (Active motif, 53150) according to manufacturer’s protocol. 100,000 cells were taken per reaction. ATAC-seq libraries were purified and size selected with HighPrep PCR beads (AC-60005, MagBio). Two rounds of size selection were performed. In the first, 0.6X beads were added, and the supernatant recovered. In the second, 0.6X beads were added to the supernatant and DNA was eluted from the beads in 10 mM Tris-HCl.

treatment_protocol: 100,000 cells were treated with medium containing either 200 µM cisplatin or 30 µM cPVP, incubated for 2h.

value: ovarian carcinoma

value: cancerous

value: cPVP, 30 uM


title: Salmonella 12h post-infection, Batch 1, Replicate 1


title: iALI-Control-_scRNA

city: Montpellier

first: Said

last: Assou

state: Languedoc-Roussillon

address: 80 av Augustin fliche, IRMB

country: France

institute: IRMB, Hôpital Saint Eloi

description: 10x Genomics

data_processing:
Image analyses and base calling were performed using the NovaSeq Control Software and Real-Time Analysis component (Illumina).
Demultiplexing was performed using cellranger mkfastq v6.1.2. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
cellranger count v6.1.2 was used to align reads to the reference genome (refdata-gex-GRCh38-2020-A) and generate the raw and filtered gene-barcodes matrices.
cellranger aggr v6.1.2 was used to combine the results of the two samples.
Assembly: GRCh38
Supplementary files format and content: MEX file format: the matrix.mtx file contains the filtered gene-barcode matrix (total UMI count per cell and gene combination); the .tsv files contain all annotated genes and cell barcodes represented in the mtx file.

source_name: Lung

growth_protocol: Bronchial epithelium was generated as previously described (Ahmed et al 2022). Cells were cultured in air liquid interface on Transwell®, in PneumaCult™-ALI Medium. The medium was changed dialy, included the one of exposed condition. Cells were collected after 48 days of culture.

extract_protocol:
Cells were dissociated from Transwells by using Trypsin (15 minutes, 37°C). Then, cells were passed into a  40 μm Corning filter and centrifuged at 1200 rpm for 5 min. All cells were maintained in PneumaCult™-ALI Medium and separated in 2 ependorfs to perform isotype-PE and CD326 antibody labelling (30 min at 4°C). At last, after several washes with media complemented with BSA (0,01%), cells were sorted on BD FACSAria™, with MRI platform. At last, 10 000 cells were captured for single cell RNA sequencing in each condition.
Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell 3' v3.1 Reagent Kits and a Chromium instrument.

treatment_protocol: Pollution exposure was performed on basal side of iALI, From day 33 to day 48 of culture. It was changed everydays. The pollution PM2.5 from NIST was used, diluted in PneumaCultTM-ALI Medium at the concentration of 50 µg/mL.

value: Lung

value: iPS-derived bronchial mesenchymal cells


title: LPS-induced BV-2 cells following hUC-MSC-EXO treatment, rep1, IP

value: EXO


title: DR-PBMCs-scRNA-seq_rep1


title: A2780, cPVP, biol rep 1


title: iALI-Pollution-_scRNA

description: 10x Genomics

value: iPS-derived bronchial mesenchymal cells under pollution

value: Pollution PM2.5


title: 129_MN_1

status: Public on Apr 06 2026

city: Berkeley

first: Rachel

middle: B

last: Brem

state: CA

address: 321 Koshland Hall

department: Plant and Microbial Biology

institute: UC Berkeley

data_processing:
Reads were mapped to either the GRCm38, CAST_EiJ, 129S1, or a concatenated CAST+129 genome using STAR
Gene counts were generated using STAR's built in quantification (--quantMode GeneCounts)
Assembly: mm10
Supplementary files format and content: tab-delimited including raw read counts for each sample

organism: Mus musculus domesticus

source_name: motor neuron

extract_protocol:
motor neurons were processed using RNAqueous™-Micro Total RNA Isolation Kit (Thermo Fisher Scientific); PSCs were processed using RNAeasy-Micro Total RNA Isolation Kit (Thermo Fisher Scientific); for both cell types samples were treated on-column with RNase-Free DNase Set (QIAGEN, Hilden, Germany)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: motor neuron


title: 129_MN_1

description: Library name: 129_MN_1

data_processing:
Reads were mapped to either the CAST_EiJ, 129S1, or a concatenated CAST+129 genome using STAR
Assembly: mm10
Supplementary files format and content: tab-delimited including raw read counts for each sample

extract_protocol:
motor neurons were processed using Rneasy Micro Kit (Qiagen); samples were treated on-column with RNase-Free DNase Set (QIAGEN, Hilden, Germany)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

tag: strain


title: 129_MN_2


title: 129_MN_3

description: Library name: 129_MN_3


title: 129_MN_2

description: Library name: 129_MN_2


title: Uninfected control 12h, Batch 1, Replicate 1

value: Small intestine

value: Epithelial cells

value: Control


title: iALI-Pollution+_scRNA

description: 10x Genomics

value: iPS-derived airway epithelium under pollution


title: BL6_MN_4


title: BL6_MN_2


title: BL6_PSC_1

source_name: pluripotent stem cell

value: pluripotent stem cell


title: BL6_PSC_2


title: BL6_MN_3


title: BL6_MN_5


title: BL6_MN_7


title: C57BL6_neuron_rep3

data_processing:
Reads were re-mapped to either the GRCm38 or CAST_EiJ genome using TopHat v 2.1.1 (parameters: -N 0 --library-type fr-unstranded)
Aligned reads were sorted with Samtools sort (parameters: -o)
Gene counts were generated using the htseq-count Python script (parameters: -s no -r pos)
Assembly: mm10
Supplementary files format and content: tab-delimited including raw read counts for each sample

tag: batch info


title: BL6_MN_6


title: BL6_MN_1


title: C57BL6_neuron_rep4


title: C57BL6_neuron_rep2


title: C57BL6_neuron_rep1


title: sci-RNA-seq3_Arabidopsis_HA_Stress_Biological_Replicate_6_and_7

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: Arabidopsis_HA_Stress_Biological_Replicate_6_and_7
sci-RNA-seq3

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed as described in https://github.com/JunyueC/sci-RNA-seq3_pipeline
Assembly: Arabidopsis TAIR10
Supplementary files format and content: Seurat object

molecule: nuclear RNA

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were grown on hard agar (HA) stress at different stress levels

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter.
Library construction was performed following the sci-RNA-seq3 workflow

tag: tissue

value: leaf

tag: age

value: seedlings


title: 6 Weeks, ovaries

city: San Francisco

first: Todd

last: Nystul

address: 513 Parnassus Ave, Box 0412

institute: UCSF

description:
Library name: 6_week
10x Genomics

data_processing:
The sequencing, barcode processing, and demultiplexing was perfomed by UCSF Center for Advanced Technologies (CAT).
Alignment to the Drosophila genome and gene counting was performed using CellRanger-9.0.0, through 10x Genomics Cloud CLI.
Assembly: Drosophila.melanogaster_genome (BDGP6.28)
Supplementary files format and content: Tab-separated values and matrix files

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: Female and male Drosophila collected at eclosion and maintained in vials and flipped regularly until timepoint for dissection and sequencing.

extract_protocol:
Dissections and dissociation were performed following the protocol outlined in Meyer et al, 2023 (DOI: 10.1007/978-1-0716-2970-3_17). The only deviation was that we did not enrich for anterior structures because the 6 week ovaries were too fragile.
Library construction was performed by UCSF CoLabs using 10x Genomics Single Cell 3’ kit (v4).

value: Ovary

value: 6 weeks post-eclosion

tag: Sex

value: female


title: C57BL6_stem_cell_rep2

tag: cell type


city: Stanford

first: Lay Teng

last: Ang

address: Institute for Stem Cell Biology & Regenerative Medicine, Lokey Stem Cell Bldg, 265 Campus Drive

department: Urology

institute: Stanford University

description:
Library name: day 4 hPSC-derived vein endothelial cells bulkrnaseq, replicate 2
trim

data_processing:
Assembly: Human reference genome Hg38 (GRCh38)
Supplementary files format and content: Processed data files abundance files generated using Kallisto (https://github.com/pachterlab/kallisto)

source_name: H1 hPSC-derived

growth_protocol: hPSCs were maintained in mTesR Plus media before differentiation.

extract_protocol:
For bulk RNA-seq, Zymo RNA extraction was performed on cell lysates as per manufacturer's protocol.
Poly(A) mRNAs were converted into cDNA libraries during library construction by Novogene

treatment_protocol: Differentiation of hPSCs into artery and vein ECs. All differentiation was conducted in defined, serum-free CDM2 basal media. Detailed instructions to how to prepare CDM2 are available.  Seeding hPSCs for differentiation (Step 0).   Step 1: Mid primitive streak induction, 24 hours.   Step 2: Lateral mesoderm induction, 24 hours.   Step 3A: Artery EC induction, 24 hours.   Step 3B: Primed EC induction, 24 hours.   Step 4B: Vein EC induction, 24 hours.

tag: cell line

value: H1 hPSC-derived

value: vein EC

value: XY, wild-type

value: CD144+ FACS sorted


description:
Library name: day 4 hPSC-derived vein endothelial cells bulkrnaseq, replicate 1
trim


title: 1 Week, ovaries

description:
Library name: 1_week
10x Genomics

value: 1 week post-eclosion


description:
Library name: day 3 hPSC-derived primed endothelial cells bulkrnaseq, replicate 1
trim

value: primed EC


description:
Library name: day 3 hPSC-derived primed endothelial cells bulkrnaseq, replicate 2
trim


title: C57BL6_stem_cell_rep1


description:
Library name: day 3 hPSC-derived artery endothelial cells  bulkrnaseq, replicate 2
trim

value: artery EC


description:
Library name: day 2 hPSC-derived lateral mesoderm  bulkrnaseq, replicate 2
trim

value: lateral mesoderm

value: Unsorted


description:
Library name: day 3 hPSC-derived artery endothelial cells  bulkrnaseq, replicate 1
trim


description:
Library name: day 1 hPSC-derived primitive streak  bulkrnaseq, replicate 3
trim

value: primitive streak


description:
Library name: day 1 hPSC-derived primitive streak bulkrnaseq, replicate 1
trim


title: H1 hPSC bulkrnaseq, replicate 3

description:
Library name: H1 hPSC bulkrnaseq, replicate 3
trim

source_name: H1 hPSC

value: H1 hPSC

value: hPSC