title: Ctrl-ADAR

city: Houston

first: Ge

last: Deng

state: Texas

address: 6670 Bertner Avenue, R7-217

institute: Houston Methodist Hospital and Houston Methodist Research Institute

description: Library name: X9

data_processing:
Trimmomatic (0.38) was adapted to paired-end sequencing model for additional inferior read filtering and then the filtered data were aligned to the mouse genome (mm10) using STAR aligner (2.7.11b). PCR duplicates were identified and removed by Picard (2.8.2) if needed. Uniquely mapped alignments in SAM format were loaded into a MySQL table with genomic coordinates. The edited events were identified using the wtRNA-RNA approach, in which the nucleotides at each position in the test RNA library (Reg1-D141N-ADAR, Ctrl-ADAR) were compared with those of the control RNA library (wt RNA: Ctrl-GFP). Only those edited events with a minimum of 20 read coverage and 5% editing were considered for further analysis. The resulting editing events from Reg1-D141N-ADAR and Ctrl-ADAR were compared against each other to determine the editing sites that were unique to Reg1-D141N-ADAR. Finally, a list of transcripts was created by tabulating all transcript that contain edited sites
Assembly: mm10
Supplementary files format and content: tab-delimited BedGraph with edit sites and frequencies

source_name: Mouse primary lymphocytes

growth_protocol: CD4+ T cells were purified using Dynabeads Untouched Mouse CD4 Cells Kit from the spleen of WT B6 mice and cultured in RPMI1640 medium with 10% FBS, 1% pen-strep.

extract_protocol:
Total RNA were prepared using the Direct-zol RNA Microprep Kit. At least 1.0 ug RNA per sameple were sent to sequence.
RNA libraries were prepared by firstly depleting ribosomal RNA using DNBSEQ rRNA Depletion Kit (MGI Tech, 1000005953), the libraires were sequenced by BGI Genomics using the DNBSEQ platform. After filtering low-quality reads using BGI Genomics in house protocols, the data were further processed following the recommended HyperTRIBE pipeline  with some modifications.

treatment_protocol: CD4+ T cells were activated, transduced with indicated vector using retroviral-mediated gene transfer method and grown for 24 hours. Then cells were FACS-sorted based on the GFP expression and used for RNA sequence.

value: Mouse primary lymphocytes

value: CD4+ T cells

value: ADAR alone


title: A549 cells, TGFβ1, bio rep 1

status: Public on Mar 19 2026

type: SRA

city: Guangzhou

first: Xingyu

last: Lv

address: No. 107, West Jiangxi Road

department: Sun Yat-Sen Memorial Hospital

country: China

institute: Sun Yat-sen University

description: Library name: Sample 4

library_source: transcriptomic

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: cell line

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: alveolar epithelial cells

tag: genotype

value: WT

tag: treatment

value: TGFβ1 10ng/mL for 48 hours


title: WT-NAC, bio rep 1

city: Little Rock

first: Rami

middle: Ahmad Nawaf

last: Shahror

state: AR

address: APT 277, 11800 Pleasent Ridge Rd.

country: USA

institute: University of Arkansas for Medical Sciences

description: Library name: Sample 4

data_processing:
sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCm38
Supplementary files format and content: tab-delimited file includes raw counts for each sample

organism: Mus musculus

source_name: Macrophages

growth_protocol: Bone marrow was obtained from femurs and differentiated in vitro into macrophages as we previously described.11 Briefly,  bone marrow cells were isolated in cold PBS, filtered, and resuspended in a DMEM high glucose medium containing 20% FBS with 20% L929 conditioned media and 1% penicillin-streptomycin to induce macrophage differentiation. Cells were seeded in  100 mm dishes and allowed to adhere. After 4 days, the media was replaced with fresh differentiation media.

extract_protocol:
Machrophages were homogenized in TRIzol reagent
NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions

treatment_protocol: the suspended  K562 cells were subjected to UV-B irradiation for 15 minutes using a UV crosslinker ). then the cells were resuspended in fresh DMEM media with 10% FBS  and incubated them in a 5% CO2 incubator at 37°C for two hours. Macrophages were co-cultured with apoptotic K562 cells for 45 minutes at 37°C. Non-apoptotic cells were used in control groups. After incubation, the suspended K562 cells were removed and washed with PBS. The BMDMs were maintained for 5 hours for total RNA isolation

value: Macrophages

value: Non apototic cells


city: Shenzhen

first: Yongzhou

last: Bao

address: BuxinRoad NO. 97, Dapeng District

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

description: Library name: Nicotiana benthamiana, plasmid  replicate 1

library_source: genomic

data_processing:
follow the bioinformatic pipeline of ATAC-STARR-seq
Assembly: Niben261
Supplementary files format and content: bed

molecule: genomic DNA

organism: Nicotiana benthamiana

source_name: 4-weeks old leaves

extract_protocol:
We spun 500g Nicotiana benthamiana leaf to prepare nuclei.
First，assay for transposase-accessible chromatin (ATAC) was conducted.Then，adapter-ligated DNA was then amplified using PCR, incorporating homologous arms for cloning. The purified PCR products, now containing homologous arms, were inserted into the linearized vector backbone. After recombination, all products were pooled, and DNA constructs were subsequently transformed into MegaX DH10B™ T1R electrocompetent cells. All transformed Escherichia coli cultures were pooled and grown in LB medium. The input plasmid library was extracted. The input plasmid library was introduced into Agrobacterium tumefaciens strain GV3101 carrying the helper plasmid pSoup via electroporation. The transformed Agrobacterium culture was grown in YEP medium. The bacteria were harvested and resuspended in infiltration buffer. The suspension was then infiltrated into the leaves of Nicotiana benthamiana plants. The plants were maintained under normal growth conditions for 72 hours. Total RNA was extracted from the transformed Nicotiana benthamiana leaves. Polyadenylated  mRNA was then isolated. The mRNA was treated. First-strand cDNA was synthesized using SuperScript III. Target-specific reverse transcription (RT) was performed. After RT, the reaction was treated with RNase A and H, followed by pooling. In the final PCR amplification, cDNA reaction was used as a template for PCR reaction. Each index PCR was performed. The PCR products were size-selected (450–500 bp) and submitted for Illumina sequencing.The input library for sequencing was generated using a similar PCR setup.

value: 4-weeks old leaves


title: Reg1-D141N-ADAR

description: Library name: X8

value: CD4+ T cells were activated, transduced with indicated vector using retroviral-mediated gene transfer method and grown for 24 hours


title: Overexpressing rocR (low cdGMP), rep1

city: Southampton

first: Rubén

last: de Dios

state: Hampshire

address: University Road

department: School of Biological Sciences

country: United Kingdom

institute: University of Southampton

description: Library name: 57R1

data_processing:
Demultiplexing, quality control, and adapter trimming was performed with bcl-convert (v4.2.4)
Read mapping was performed with HISAT2. Read quantification was performed using Subread’s featureCounts functionality.
Read counts loaded into R4 were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm. Subsequent values were then converted to counts per million (CPM). Differential expression analysis was performed using edgeR’s glmQLFTest.
Assembly: NC_011586.2
Supplementary files format and content: raw_counts.tsv includes a tab-delimited matrix with headers with the raw read values for each gene in each sample and condition
Supplementary files format and content: normalised_counts.tsv includes a tab-delimited matrix with headers with the normalised read values for each gene in each sample and condition

organism: Acinetobacter baumannii AB0057

source_name: bacterial cell

growth_protocol: A. baumannii AB0057 derivatives carrying either rocR or pleD* inserted in a miniTn7 transposon  were grown in LB supplemented with IPTG 1 mM (3 biological replicates per strain) until reaching mid-exponential phase (approx. OD600 0.6).

extract_protocol:
Cultures were harvested by centrifugation (or direct resuspension for desiccated cells) in RNAlater to preserve RNA integrity. RNA was isolated using athe Qiagen RNAeasy Kit with on-column DNAase digestion (Qiagen). RNA quality was assessed using a Bioanalyzer.
Library preparation was performed using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp IDT for Illumina indices.

treatment_protocol: Induction pof the expression of either rocR of pleD* by addition of IPTG 1 mM.

tag: strain

value: bacterial cell


title: HaCaT cells DNA, minP plasmid candidate enhancer library, biol rep 2

city: Biberach

first: Martin

last: Oti

address: Birkendorfer Str. 65

country: Germany

institute: Boehringer Ingelheim

description: Library name: DNA_Cell_HaCaT_minP_Transfection_2

data_processing:
The NGS paired-end reads were mapped to the human genome (assembly hg38) using bowtie2 (v2.2.9). Mapped reads were filtered for those mapping to a single genomic location using samtools (v1.2), and those mapping to the capture library target regions were quantified using the ‘featureCounts’ tool of the Subread NGS alignment suite (v1.6.2)
For fragment-level analyses, the fragments were processed using the BEDTools suite v2.26.0. First, they were extracted from the name-sorted paired-end BAM files (sorted with ‘samtools sort -n’) using the ‘bedtools bamtobed’ command with the ‘-bedpe’ flag, and their overall start and end coordinates were stored in the normal BED file format, with the mapping quality (MAPQ) placed in the score field and the read name in the name field. They were then filtered for MAPQ >= 30 using the Linux ‘awk’ command, their coordinates were rounded to the nearest 10 bp to account for reads with slightly trimmed ends, they were quantified using ‘bedtools groupby –c 4 –o count’, and finally they were intersected with the capture library target regions using ‘bedtools intersect’.
Assembly: hg38
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited text file with normalized counts for each cellular DNA & RNA sample

source_name: HaCaT

growth_protocol: HepG2 and HaCaT cells were cultured at 37°C in a humidified atmosphere containing 5% CO2. Growth medium consisted of Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen Life Technology, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific, Waltham, USA).

extract_protocol:
DNA and RNA were extracted using the ALLprep 96 DNA/RNA kit (QIAGEN, Hilden, Germany).
2 µg of total RNA were used for mRNA enrichment utilizing the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, USA) followed by cDNA synthesis and amplicon PCR using enhancer cassette-specific primers. 20 ng of PCR product as well as 20 ng of DNA were used for index PCR with UDI primers (New England Biolabs, Ipswich, USA), which bind inside the enhancer cassette. Additionally, 5 ng and 10 ng of plasmid and viral input DNA were used for index PCR, respectively.

treatment_protocol: HepG2 and HaCaT cells were grown to 80% confluency in 12 well plates. Cells were transduced with the STARR-CRAAVT AAV libraries using a multiplicity of infection (MOI) of 100,000 viral genomes per cell. The minP plasmid library was also transfected using 1 ug of DNA and Lipofectamine 3000. Cells were harvested after 72h.

value: HaCaT

value: keratinocyte

value: minP enhancer candidate plasmid library


title: WT-NO Treatment, bio rep 1

description: Library name: Sample 1

value: No treatment


title: A549 cells, TGFβ1, bio rep 2

description: Library name: Sample 5


title: HaCaT cells DNA, minP plasmid candidate enhancer library, biol rep 3

description: Library name: DNA_Cell_HaCaT_minP_Transfection_3


title: wtRNA

description: Library name: X11

value: empty vector


title: Single cells from islets, WT2 GlcN

city: Jerusalem

first: Yael

last: Riahi

address: Kyriat Hadassah

country: Israel

institute: The Hebrew University

description: Library name: Sample 5

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version v2.1.1
Assembly: mm39
Supplementary files format and content: The processed data is provided as an RDS file containing a Seurat object including all quality-controlled cells, scaled data, and UMAP coordinates.

source_name: primary pancreatic endocrine cells

growth_protocol: Mouse islets were isolated and maintained for 24 hours in complete RPMI-1640 medium containing 11 mmol/l glucose supplemented with 10% heat-inactivated FBS, 100 IU/mL Pen/Strep. solution, 10 mmol/l HEPES, 2 mmol/l l-glutamine, 1 mmol/l sodium pyruvate and 0.05 mmol/l 2-mercaptoethanol with or without 0.5mM glucosamine in a humidified 37°C, 5% CO2 incubator.

extract_protocol:
Following treatment, pancreatic islets were dissociated into single-cell suspension using Accutase. Nuclei were subsequently isolated according to the 10x Genomics Demonstrated Protocol ("Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing”, CG000365"). During the lysis buffer incubation, manual dissociation was performed by passing the suspension through a 30G needle with a 1-mL syringe to facilitate nuclear release and isolation
The scRNA libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC and Gene expression reagent Kit (10x Genomics). Nuclei were diluted in 5 ul and proceed to the transposition mix and incubated for one hour at 37⁰C and according to the company manufacture (10x Genomics). Then the mix was separated into droplet emulsion using a Chromium X machine (10x Genomics) and libraries were prepare according to the manufacturer’s protocol. The scRNA-seq libraries were sequenced on the Illumina Novaseq6000 sequencing system (Illumina) as a 28-bp and 90-bp paired-ended.

treatment_protocol: 0.5mM Glucosamine into the media or vehicle for 24 hours

value: Pancreatic islets of Langerhans

value: pancreatic endocrine cells

value: WT- C57BL

value: islets treated with 0.5mM GlcN,24h


title: HaCaT cells DNA, minP AAV candidate enhancer library, biol rep 2

description: Library name: DNA_Cell_HaCaT_minP_Transduction_2

value: minP enhancer candidate AAV library


title: A549 cells, Control, bio rep 1

description: Library name: Sample 1

value: cell line

value: alveolar epithelial cells

value: WT


title: A549 cells, Control, bio rep 3

description: Library name: Sample 3


title: HaCaT cells DNA, AFP AAV candidate enhancer library, biol rep 1

description: Library name: DNA_Cell_HaCaT_AFP_Transduction_1

value: AFP enhancer candidate AAV library


title: Single cells from islets, WT1 GlcN

description: Library name: Sample 4


title: WT CD4+ T cells, sample2

description:
Library name: WT_sample2
FPKM_WT_2

data_processing:
After filtering sequencing adaptors and low-quality bases, the clean data were aligned to the mouse genome (mm10) using Bowtie2 (2.4.4), and gene expression level was calculated by RSEM (v1.2.28).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM for each samples

molecule: polyA RNA

growth_protocol: CD4+ T cells were purified using Dynabeads Untouched Mouse CD4 Cells Kit from the spleen of WT B6 or Cd4CreERT2LSL-R111Afl/fl mice with tamoxifen administration (75 mg/kg, i.p. for 5 days, Sigma-Aldrich, T5648-5G) and maintained in RPMI1640 medium with 10% FBS, 1% pen-strep. Then cells were used for FACS.

extract_protocol:
Total RNA were prepared using the Direct-zol RNA Microprep Kit. At least 1.0 ug RNA per sameple were sent to sequence.
PolyA+ RNA was isolated and RNA sequencing was performed by BGI Genomics.

treatment_protocol: FACS sorted WT and R111A CD4+ T cells were stimulated with anti-CD3 plus CD28 (5 µg/mL + 1 µg/mL) for 12 hrs.

value: Mouse primary lymphocytes

value: CD4+ T cells

value: wild type

value: anti CD3+CD28 activation for 12 hours


title: A549 cells, Control, bio rep 2

description: Library name: Sample 2


title: HaCaT cells DNA, minP AAV candidate enhancer library, biol rep 3

description: Library name: DNA_Cell_HaCaT_minP_Transduction_3

value: HaCaT

value: keratinocyte


title: Overexpressing rocR (low cdGMP), rep2

description: Library name: 57R2

value: bacterial cell


title: HaCaT cells DNA, minP AAV candidate enhancer library, biol rep 1

description: Library name: DNA_Cell_HaCaT_minP_Transduction_1


title: Single cells from islets, WT3 Control

description: Library name: Sample 3

value: untreated islets


title: Human femoral head, osteoarthritis, donor13

city: New Orleans

first: Hong-Wen

state: LA

address: 1440 Canal St, suite 1619G

institute: Tulane University

description:
Library name: Osteo74
10x Genomics

data_processing:
Raw sequencing data were demultiplexed and converted to FASTQ files using Illumina bcl2fastq.
FASTQ files were processed using Cell Ranger (10x Genomics) for read alignment, barcode processing, and gene counting.
Reads were aligned to the human reference genome using the Cell Ranger pipeline.
Assembly: GRCh38
Supplementary files format and content: Matrix Market format (matrix.mtx), gene annotations (features.tsv), and cell barcodes (barcodes.tsv).

source_name: femoral head

growth_protocol: Human femoral head bone tissues were obtained from patients undergoing hip arthroplasty surgery. Samples were collected immediately after surgery and processed for single-cell dissociation.

extract_protocol:
Femoral head bone tissues were mechanically minced and enzymatically digested to generate single-cell suspensions. Cells were filtered through a 40 μm cell strainer and washed with PBS containing 0.04% BSA before library preparation.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3′ platform according to the manufacturer's protocol. Single cells were encapsulated into droplets with barcoded gel beads, followed by reverse transcription, cDNA amplification, and library construction.

treatment_protocol: No experimental treatment was applied prior to RNA extraction.

value: femoral head

tag: diagnosis

value: Osteoarthritis

tag: batch


title: R111A CD4+ T cells, sample2

description:
Library name: R111A_sample2
FPKM_R111A_2

value: R111A overexpression


title: Single cells from islets, WT2 Control

description: Library name: Sample 2

value: Pancreatic islets of Langerhans

value: pancreatic endocrine cells

value: WT- C57BL


title: HEK293T cells, rep3

city: Kyoto

first: Masanori

last: Yoshinaga

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku

department: Graduate School of Medicine

country: Japan

institute: Kyoto University

library_source: other

data_processing:
Raw sequencing reads were trimmed using cutadapt (v2.3). Then UMI sequences (17 nt, N14D3) attached to 5' end of tRNA sequences were removed and recorded as UMI tag by fastp (v0.20.1). The reads were quality-filtered using trimmomatic (v0.39), and then aligned to the human tRNA sequences obtained from GtRNAdb (http://gtrnadb.ucsc.edu/) using bowtie (v2.3.4.3) with very sensitive local mode and -L 10. PCR duplicates were removed using the UMI tag by UMICollapse (v1.0.0). The mapped read numbers on each tRNA gene were counted by samtools (v1.5).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: other

source_name: HEK293T cells

extract_protocol:
Total RNA was harvested using TRIzol (ThermoFisher Scientific).
Total RNA was deacylated in 100 mM CHES-NaOH (pH 9.0) at 37 °C for 30 min and purified by ethanol precipitation. Then deacylated RNAs were incubated with the recombinant AlkB WT (1.5 μM) and L118V D135S (0.1 μM) in the presence of 1 mM α-ketoglutarate, 2 mM L-ascorbic acid, 50 μM (NH4)2Fe(SO4)2 in 50 mM HEPES-KOH (pH 8.1) at 37 °C for 1 h, followed by phenol/chloroform extraction and ethanol precipitation. RNAs were further incubated with 10 U of T4 polynucleotide kinase (New England BioLabs) at 37 °C for 1 h, and purified using RNA Clean & Concentrator-5. Then samples were separated using 10% 7M urea gel and the bands corresponding to tRNAs were excised and subjected to gel-extraction. tRNA samples were ligated with adenylated adaptors using T4 RNA Ligase 2, truncated KQ (New England BioLabs), followed by gel-purification. Then samples were reverse-transcribed using TGIRT-III (InGex) and subjected to alkaline hydrolysis. Then samples were circularized using CircLigase II (Lucigen) and purified, followed by the PCR amplification using Phusion Polymerase (ThermoFisher Scientific). Sequencing was performed using NextSeq 500 Sequencer and NextSeq 500/550 Mid-Output v2 Kit (Illumina).

value: HEK293T cells

value: Wild-type


title: K7M2col3D_rep3

city: Washington

first: Aykut

last: Uren

state: DC

address: 3970 Reservoir Road, N.W.

department: Department of Oncology

institute: Georgetown University

description:
Library name: Sample 22
Ezrin-T567D transfected Ezrin -/- K7M2 cells

data_processing:
After sequencing, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. The quality of data was examined after filtering.
CLC Genomcs Workbench 20.0.4 was used for mapping the reads to mouse genome.
Assembly: GRCm38
Supplementary files format and content: CSV files include raw counts for each sample
Supplementary files format and content: CSV files include RPKM values for each sample

source_name: Bone

growth_protocol: Mouse OS cell line K7M2 and its derivatives were cultured in DMEM (Gibco, #11875) supplemented with 10% FBS (Sigma-Aldrich #F0926). Cells were maintained at 37C in a humidified atmosphere with 5% CO2 and regularly tested for mycoplasma with MycoAlertTM Mycoplasma Detection kit (Lonza, #75860). K7M2 cell line was fingerprinted with a CellCheck 19 mouse panel by IDEXX BioAnalytics Inc and its STR profile was authenticated by comparing them to the available profile of K7M2 wt (ATCC, Inc., #CRL-2836).

extract_protocol:
Total RNA was isolated from the cells by using RNeasy Mini Kit (Qiagen, #74106).
1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail for DNBSEQ Eukaryotic Strand-specific mRNA library; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB); 10. Sequencing on DNBSEQ (DNBSEQ Technology) platform.

treatment_protocol: No treatment was performed.

value: Bone

value: Mouse Osteoblast Osteosarcoma

value: Ezrin-T567D transfected Ezrin -/-


title: HEK293T cells, rep2


title: K7M2col3D_rep1

description:
Library name: Sample 21
Ezrin-T567D transfected Ezrin -/- K7M2 cells


title: Single cells from islets, WT1 Control

description: Library name: Sample 1


title: HaCaT cells DNA, minP plasmid candidate enhancer library, biol rep 1

description: Library name: DNA_Cell_HaCaT_minP_Transfection_1

value: minP enhancer candidate plasmid library


title: Human femoral head, osteoarthritis, donor11

description:
Library name: Osteo71
10x Genomics


title: Human femoral head, osteoarthritis, donor14

description:
Library name: Osteo77
10x Genomics


title: HiC DuxR70A OE 24h rep2

city: Shaanxi

first: Qifeng

last: Gao

state: Shaanxi

address: No.3 Taicheng Road, Yangling, Shaanxi, China

institute: Northwest A&F University

description:
Library name: HiC DuxR70A OE 24h rep2
MUT1_10000_iced.matrix
MUT1_10000_abs.bed
MUT1.allValidPairs.hic

data_processing:
Data processing step: Reads were aligned and processed using HiCPro (v3.1.0) with the mm10 genome and MboI restriction site (^GATC). The pipeline was run with default parameters for iterative alignment, filtering of valid pairs, and generation of contact matrices at multiple resolutions.
Valid interaction pairs were then converted to the .hic format using Juicer Tools (v1.22.01) for visualization in Juicebox. Normalization and further analysis were performed within the Juicebox environment.
Assembly: mm10
Supplementary files format and content: .hic;Hic 10k iced matrix and raw_abs.bed

growth_protocol: Mouse embryonic stem cells were maintained in standard mESC culture medium supplemented with leukemia inhibitory factor (LIF) on gelatin-coated plates under 37°C and 5% CO2 conditions.

extract_protocol:
For Hi‑C library preparation, cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, and the reaction was quenched with 0.125 M glycine. Crosslinked cells were lysed, and chromatin was digested overnight with 5 U of MboI restriction enzyme at 37°C. The digested ends were filled in with biotin‑14‑dATP, followed by blunt‑end ligation of the proximal fragments.
After reversal of crosslinks and proteinase K treatment, DNA was purified and sonicated to a size range of 200–600 bp. Biotin‑containing fragments were pulled down with streptavidin beads, and sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB) according to the manufacturer’s instructions. Libraries were amplified by 12–14 cycles of PCR and purified with AMPure XP beads.

treatment_protocol: Cells were treated with doxycycline (4 μg/mL) for 24 hours to induce DUX or DUXR70A expression. Untreated controls were maintained in parallel.

value: mESCs

value: WT

value: dox

tag: group

value: DuxR70A OE


title: Human femoral head, osteoarthritis, donor12

description:
Library name: Osteo73
10x Genomics


title: WT CD4+ T cells, sample1

description:
Library name: WT_sample1
FPKM_WT_1

value: Mouse primary lymphocytes

value: CD4+ T cells

value: wild type

value: anti CD3+CD28 activation for 12 hours


title: HEK293T cells, rep1


title: K7M2 col3A_rep3

description:
Library name: Sample 20
Ezrin-T567A transfected Ezrin -/- K7M2 cells

value: Ezrin-T567A transfected Ezrin -/-


title: R111A CD4+ T cells, sample1

description:
Library name: R111A_sample1
FPKM_R111A_1

value: R111A overexpression


title: HiC mESC rep2

description:
Library name: HiC mESC rep2
ctrl_10000_iced.matrix
Ctl_2_10000_abs.bed
Ctl_2.allValidPairs.hic

value: no

value: control


title: HEK293T cells, Input, rep3

data_processing:
Reads were trimmed and quality filtered using fastp (v0.21.0 4), and the UMI and barcode sequences were extracted using fastx-split. Then reads were mapped to the list of noncoding RNAs and then the unmapped reads were mapped to the human genome using STAR (v2.7.0a), followed by the duplicate removal using UMItools (v1.1.2).
Assembly: hg38
Supplementary files format and content: comma-delimited text file includes raw counts for each sample
Library strategy: Thor-Ribo-Seq

extract_protocol:
Cells were transfected with the pFLAG-DHX29-WT vector, and the transfected cells were subjected to in vivo DSP crosslinking. After that, the lysates were treated with RNase I, followed by the treatment of SUPERase•In RNase inhibitor. Some of the lysates were taken out and used for input. The lysates were then layered on the sucrose cushion and subjected to ultracentrifugation. The supernatants were discarded, and the pellets were resuspended in the Lysis buffer. The samples were pre-cleared with Dynabeads Protein G, followed by the incubation with Dynabeads Protein G pre-incubated with the anti-FLAG antibody. Then, the beads were washed and mixed with TRIzol (ThermoFisher Scientific).
Thor-Ribo-Seq was performed as described previously (Mito et al., bioRxiv. 2023).

value: HEK293T cells


title: Human femoral head, osteoarthritis, donor8

description:
Library name: Osteo52
10x Genomics

value: femoral head

value: Osteoarthritis


title: Human femoral head, osteoarthritis, donor10

description:
Library name: Osteo65
10x Genomics


title: K7M2col3E_rep3

description:
Library name: Sample 16
Mock transfected Ezrin -/- K7M2 cells

value: Bone

value: Mouse Osteoblast Osteosarcoma

value: Mock transfected Ezrin -/-


title: HiC Dux OE 24h rep2

description:
Library name: HiC Dux OE 24h rep2
WT1_10000_iced.matrix
WT1_10000_abs.bed
WT1.allValidPairs.hic

value: mESCs

value: WT

value: Dux OE


title: HEK293T cells, Input, rep2


title: HEK293T cells, DHX29-IP, rep2


title: K7M2_col3A_rep2

description:
Library name: Sample 19
Ezrin-T567A transfected Ezrin -/- K7M2 cells


title: K7M2col3E_rep2

description:
Library name: Sample 15
Mock transfected Ezrin -/- K7M2 cells


title: HEK293T cells, DHX29-IP, rep3


title: HEK293T cells, DHX29-IP, rep1


title: HiC mESC rep1

description:
Library name: HiC mESC rep1
ctrl_10000_iced.matrix
Ctl_2_10000_abs.bed
Ctl_2.allValidPairs.hic


title: Human femoral head, osteoarthritis, donor4

description:
Library name: Osteo30
10x Genomics


title: HiC Dux OE 24h rep1

description:
Library name: HiC Dux OE 24h rep1
WT1_10000_iced.matrix
WT1_10000_abs.bed
WT1.allValidPairs.hic

value: dox


title: Human femoral head, osteoarthritis, donor9

description:
Library name: Osteo63
10x Genomics


title: K7M2col3WT_rep1

description:
Library name: Sample 17
Ezrin-WT transfected Ezrin -/- K7M2 cells

value: Ezrin-WT transfected Ezrin -/-


title: HiC DuxR70A OE 24h rep1

description:
Library name: HiC DuxR70A OE 24h rep1
MUT1_10000_iced.matrix
MUT1_10000_abs.bed
MUT1.allValidPairs.hic

value: DuxR70A OE


title: K7M2_rep3

description:
Library name: Sample 12
parental K7M2 cells


title: Single cells from islets, WT3 GlcN

description: Library name: Sample 6

value: Pancreatic islets of Langerhans

value: pancreatic endocrine cells

value: WT- C57BL

value: islets treated with 0.5mM GlcN,24h


title: K7M2_rep1

description:
Library name: Sample 11
parental K7M2 cells


title: E6.5 Epi,Sp1 ko,Ser2p,ChIP,rep2

city: chongqing,china

first: xipeng

last: shen

address: yixueyuan road NO.1

department: basic medicine

institute: CQMU

description: Library name: E65Epi_Sp1ko_Ser2p_rep2

data_processing:
After removal of reads with poor quality calls and adapters with Trim Galore (v. 0.4.2) using default parameters, reads from ChIP-seq datasets were mapped to the mouse mm9 reference genome (or human hg19 for datasets generated from Hela cell) using Bowtie2 with the parameters: --t --q --N 1 --L 25. Multiple mapped reads and PCR duplicates were further removed with a javascript (MarkDuplicates.jar). The monoclonal reads were then normalized by calculating the number of RPKM. After validation of the reproducibility, replicates were pooled for downstream analysis.
Assembly: mm9
Supplementary files format and content: All attached processed data were in .bed format.

source_name: Epi

growth_protocol: PWK&PhJ male mouses (6-8weeks) were mated with C57BL/6N female mouses (6-8weeks) and the time when the vaginal plug was observed the next day was considered E0.5. The embyos were disserted at E6.5 and E7.5, respectively. Germ layers were seperated using enzyme digestion coupled with mechanical separation.

extract_protocol:
ChIP-seq was performed with minor adjustments to the STAR ChIP-seq protocol. Samples were lysed in a buffer containing 0.5% Tween-20, 0.5% NP-40, and 0.1% SDS, and gently pipetted to release genomic DNA. The mixture was then digested with MNase (Sigma) at 37°C for 5 minutes. Primary antibodies—anti-Pol II RBP1 (BioLegend), anti-Phospho-POLR2A CTD-S2 (Abclonal), anti-SP1(Proteintech), anti-H3K4me3 (Millipore) or anti-H3K27me3 (Abclonal)—were added, followed by incubation at 4°C overnight. Protein A Dynabeads (Thermo Fisher Scientific) were added to the solution and incubated for 3-4 hours. Beads were washed five times with RIPA buffer containing 0.1% protease inhibitor and once with LiCl wash buffer. Elution of DNA fragments was achieved with proteinase K treatment.
The library was constructed using NEB Next® UltraTM II DNA Library Prep Kit according to the operation instruction.

treatment_protocol: C57BL/6N female mouses(5 weeks) were superovulated with PMSG following hCG 48h later. After mating with PWK mouses, PN3 zygotes were colleted in M2 medium the next day. The CRISPR-ZEN methods were used to deliver Cas9-sgRNA complex into zygotes for gene editing. Zygotes were cultured to 2-cell stage in vitro and transferred to E0.5 pseudopregnancy foster mice. Germ layers were seperated as described above. The ExVE of embryos was collected for genotyping.

value: Epi


title: Human femoral head, osteoarthritis, donor5

description:
Library name: Osteo32
10x Genomics


title: Human femoral head, osteoarthritis, donor7

description:
Library name: Osteo43
10x Genomics


title: HEK293T cells, DHX29-KO, 6 h, rep2

data_processing:
Reads were trimmed and filtered using cutadapt according to the manufacturer’s instructions (Lexogen). Then reads were mapped and the mutation rates were calculated using the SlamDunk pipeline (v0.4.3).
Assembly: hg38
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

extract_protocol:
Control and DHX29-deficient HEK293T cells were plated and maintained in the culture media supplemented with 25 μM 4-thiouridine (s4U, Sigma Aldrich) for 24 h. Then cells were washed with DPBS and the culture media were replaced with fresh ones that contained 2.5 mM uridine (Sigma Aldrich). After 0, 3, and 6 h of incubation, cells were lysed in TRIzol, and total RNA was isolated according to the manufacturer’s protocol under reducing conditions (supplemented with 0.1 mM DTT). Samples were protected from light whenever possible. Then 10 µg of total RNA was incubated in the reaction mix containing 10 mM iodoacetamide (Sigma Aldrich), 50% DMSO, and 50 mM NaPO4 (pH 8). Samples were incubated at 50 °C for 15 min, followed by the addition of DTT (20 mM). The alkylated RNA samples were purified using RNA Clean & Concentrator-5 (Zymo Research).
RNA sequencing libraries were generated using QuantSeq 3' mRNA-Seq V2 Library Prep Kit (FWD) with Unique Dual Indices (12nt, Lexogen) according to the manufacturer’s protocol. Sequencing was performed using NextSeq 500 Sequencer and NextSeq 500/550 High-Output v2 Kit (Illumina).

value: HEK293T cells


title: HEK293T cells, DHX29-KO, 6 h, rep3


title: HEK293T cells, Input, rep1


title: HEK293T cells, DHX29-KO, 6 h, rep1


title: BT474_KO_Ner_Rep_3

city: Madison

first: Huy

last: Dinh

state: WI

address: 1111 Highland Avenue

institute: University of Wisconsin-Madison

description: BT474 parental and BRD8 KO cells were treated with neratinib (200nM) for 4h, then total RNA was extracted using E.Z.N.A total RNA kit (Omega Bio-tek). RNA sequencing libraries were prepared using the Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer’s instructions. Each library was sequenced in single read mode, 1 × 50 bp, using the HiSeq4000 platform.

data_processing:
Read quality was QC using FastQC 0.11.7
Read mapping was done by STAR 2.7.9
Read count was calculated using Rsubread 2.10.5 and edgeR 3.40.2
Assembly: GRCh38 (hg38)
Supplementary files format and content: BT474_Bulk_ReadCountsMatrix.csv: comma-delimited text file includes read count for each samples (Column names: Samples, Row names: Genes)

source_name: Cell line

growth_protocol: BT474 cells were maintained in RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (VWR) and 1% Penicillin-Streptomycin (P/S) (Gibco).

extract_protocol:
For RNA extraction, total RNA was extracted using E.Z.N.A total RNA kit (Omega Bio-tek)
RNA sequencing libraries were prepared using the Illumina TruSeq RNA Library Prep Kit v2 following the manufacturer’s instructions.
Each library was sequenced in single read mode, 1 × 50 bp, using the HiSeq4000 platform.

treatment_protocol: BT474 parental and BRD8 KO cells were treated with neratinib (200nM) for 4h.

value: BRD8 KO

value: neratinib (200nM) for 4h


title: Human femoral head, osteoarthritis, donor3

description:
Library name: Osteo29
10x Genomics

value: femoral head

value: Osteoarthritis


title: HEK293T cells, DHX29-KO, 3 h, rep3


title: Human femoral head, osteoarthritis, donor1

description:
Library name: Osteo24
10x Genomics


title: E6.5 Epi,Sp1 ko,Ser2p,ChIP,rep1

description: Library name: E65Epi_Sp1ko_Ser2p_rep1


title: BT474_KO_Ner_Rep_1


title: K7M2col3WT_rep3

description:
Library name: Sample 18
Ezrin-WT transfected Ezrin -/- K7M2 cells

value: Bone

value: Mouse Osteoblast Osteosarcoma


title: E6.5 Epi,Sp1 ko,Pol2,ChIP,rep2

description: Library name: E65Epi_Sp1ko_Pol2_rep2


title: Human femoral head, osteoarthritis, donor2

description:
Library name: Osteo25
10x Genomics


title: HEK 293, T4A_52x_2rep

city: Austin

first: Qian

last: Zhang

state: TX

address: 2515 Speedway

institute: The Unibersity of Texas at Austin

description: Library name: T4A2

data_processing:
Quality of raw reads was assessed using FastQC read quality reports。
Adapter Illumina sequences (--illumina) were trimmed off by cutadapt 4.6 with cutadapt --trim-n -m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT parameters.
Reads were aligned to human reference genome (GRCh38) or yeast reference genome (S. cerevisiae) using STAR aligner 2.7.11b with default.
Marked duplicates by picard MarkDuplicates.
Generate forward and reverse bigwig files for all samples with bamCoverage in deeptools 3.5.6.
computeMatrix for forward and reverse bigwig files on plus and minus PCGs strands in deeptools 3.5.6.
Assembly: GRCh38 (Homo sapiens) and Saccharomyces cerevisiae reference genome (for spike-in normalization).
Supplementary files format and content: Processed data include strand-specific genome coverage tracks (bigWig format) generated using deepTools bamCoverage. Forward and reverse strand bigWig files were generated for each sample.  Gene-level count matrices and normalized signal matrices are provided as tab-delimited text files. Signal matrices across protein-coding genes were generated using deepTools computeMatrix.

growth_protocol: Cells were routinely cultured in Dulbecco’s modified Eagle’s media, supplemented with 10% fetal bovine serum at 37 °C in humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was isolated using TRIzol/chloroform/isopropanol method. 50 ng RNA per sample was used for library construction.
Newly synthesized RNA was labeled with 4-thiouridine (4-SU) and co-extracted with total RNA. The RNA was fragmented, and 4-SU labeled RNA was biotinylated and purified using streptavidin pull-down. First-strand cDNA synthesis was performed using random hexamer primers, followed by second-strand cDNA synthesis incorporating dUTP to generate strand-specific libraries.

treatment_protocol: We transfected RPB1 constructs containing either the 52× wild-type CTD or a T4A mutation plasmids in RPB1 degron HEK293 cells separately, after 48 h of transfection, auxin was added in the culture media for extra 48 h.

value: embryonic kidney cells

value: RPB1 degron

value: Auxin


title: E6.5 Epi,Sp1 Ctr,Ser2p,ChIP,rep2

description: Library name: E65Epi_Sp1Ctr_Ser2p_rep2


title: E6.5 Epi,Sp1 ko,Pol2,ChIP,rep1

description: Library name: E65Epi_Sp1ko_Pol2_rep1


title: Human femoral head, osteoarthritis, donor6

description:
Library name: Osteo36
10x Genomics


title: E6.5 Epi,Sp1 Ctr,Ser2p,ChIP,rep1

description: Library name: E65Epi_Sp1Ctr_Ser2p_rep1


title: HEK293T cells, DHX29-KO, 3 h, rep2


title: BT474_KO_Ner_Rep_2


title: HEK 293, T4A_52x_1rep

description: Library name: T4A1


title: E6.5 Epi,Eed ko,Pol2,ChIP

description: Library name: E65Epi_Eedko_Pol2_spikein


title: HEK293T cells, DHX29-KO, 3 h, rep1


title: BT474_Ner_Rep_1

value: Parental


title: HEK 293, WT_52x_2rep

description: Library name: WT2


title: BT474_Ner_Rep_2


title: E6.5 Epi,Eed Ctr,Pol2,ChIP

description: Library name: E65Epi_EedCtr_Pol2_spikein


title: KPM tumor

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description:
Library name: KPM
3’ mRNA (v4 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

data_processing:
10X datasets: Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
BD Rhapsody platform: the raw FASTQ files were mapped  to the mouse genome using the BD Rhapsody Sequence Analysis Pipeline
Assembly: mm10/GRCm38
Supplementary files format and content: Compressed .h5/tar.gz files containing UMI RNA/ADT counts in Cellranger output format, seurat R .rds objects contatining cell annotations and dimensionality reduction embeddings and text .csv files, containing the VDJ contig annotations of the BCR-seq datasets

source_name: tumor

extract_protocol: All methods listed in Caro et al. Pan-cancer single-cell atlas of mouse and human tumor-associated dendritic cells.

value: tumor

value: No sorting

value: KrasLSL-G12D/+;p53fl/fl;Msh2fl/fl in a C57BL/6 background.

value: PBS treated (control)


title: HEK 293, WT_52x_1rep

description: Library name: WT1


title: HEK293T cells, Control, 6 h, rep3

value: Control


title: BT474_KO_DMSO_Rep_3

value: DMSO


title: KP early stage tumor,ADT

description:
Library name: KP_early_ADT
5’ mRNA (v1.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

data_processing:
10X datasets: Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
BD Rhapsody platform: the raw FASTQ files were mapped  to the mouse genome using the BD Rhapsody Sequence Analysis Pipeline
Assembly: mm10/GRCm38
Supplementary files format and content: Compressed .h5/tar.gz files containing UMI RNA/ADT counts in Cellranger output format, seurat R .rds objects contatining cell annotations and dimensionality reduction embeddings and text .csv files, containing the VDJ contig annotations of the BCR-seq datasets
Library strategy: CITE-seq

molecule: protein

value: KrasLSL-G12D/+; Trp53fl/fl


title: HEK293T cells, DHX29-KO, 0 h, rep3

value: HEK293T cells


title: HEK293T cells, DHX29-KO, 0 h, rep1


title: 5637 cells, sh-RAD51C2

city: Shanghai

first: Ying

last: Xiao

address: 197 Ruijin 2nd Road, Huangpu District, Shanghai, China

institute: Ruijin Hospital

description: Library name: Sample 5

data_processing:
The sequencing was conducted using the Illumina NovaSeq 6000 platform, a system known for its high throughput and flexibility, capable of delivering up to 200 billion reads and 6 Tb of data within 2 days, as per industry standards. Gene expression levels were quantified in terms of FPKM values. PCA was performed using R software (v3.2.0). Differential expression analysis was performed using DESeq2. Genes with q-value < 0.05 and fold change > 2 or < -2 were screened as differentially expressed genes. Differentially expressed genes were functionally enriched for GO terms, KEGG pathways, and Reactome pathways. GSEA was conducted by ranking genes based on differential expression.
Assembly: hg38
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted from transfected bladder cancer cells using TRIzol reagent.
The sequencing libraries were prepared using the VAHTS Universal V6 RNA-seq Library Prep Kit.

value: bladder cancer cells

value: RAD51C knockdown


title: BT474_Ner_Rep_3

value: neratinib (200nM) for 4h


title: BT474_DMSO_Rep_3


title: 5637 cells, sh-RAD51C1

description: Library name: Sample 4


title: BT474_KO_DMSO_Rep_1

value: BRD8 KO


title: 5637 cells, sh-RAD51C3

description: Library name: Sample 6


title: KP early stage tumor, cDNA

description:
Library name: KP_early_cDNA
5’ mRNA (v1.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: BT474_DMSO_Rep_2


title: BT474_KO_DMSO_Rep_2


title: 5637 cells, NC3

description: Library name: Sample 3

value: WT


title: HEK293T cells, DHX29-KO, 0 h, rep2


title: HEK293T cells, Control, 3 h, rep3


title: 5637 cells, NC2

description: Library name: Sample 2


title: KP late stage tumor, cDNA

description:
Library name: KP_late_cDNA
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: HEK293T cells, Control, 6 h, rep1


title: HEK293T cells, Control, 6 h, rep2


title: Spleen LLC-OVA tumor-bearing mice, BCR

description:
Library name: LLCOVA_spleen_BCR
5’ V(D)J B contigs : read1 contains cell barcode and UMI; read2 contains BCR contig sequence

data_processing:
10X datasets: Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
BD Rhapsody platform: the raw FASTQ files were mapped  to the mouse genome using the BD Rhapsody Sequence Analysis Pipeline
Assembly: mm10/GRCm38
Supplementary files format and content: Compressed .h5/tar.gz files containing UMI RNA/ADT counts in Cellranger output format, seurat R .rds objects contatining cell annotations and dimensionality reduction embeddings and text .csv files, containing the VDJ contig annotations of the BCR-seq datasets
Library strategy: BCR-Seq

source_name: spleen

value: spleen


title: KP late stage tumor, ADT

description:
Library name: KP_late_ADT
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: HEK293T cells, Control, 3 h, rep1


title: Spleen LLC-OVA tumor-bearing mice, cDNA

description:
Library name: LLCOVA_spleen_cDNA
5’ mRNA (v1.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: 5637 cells, NC1

description: Library name: Sample 1


title: Spleen naive mice, BCR

description:
Library name: Naive_spleen_BCR
5’ V(D)J B contigs : read1 contains cell barcode and UMI; read2 contains BCR contig sequence


title: BT474_DMSO_Rep_1


title: HEK293T cells, Control, 3 h, rep2


title: Male, Astrocyte, 7 weeks post-Fx, Trap Sample 2

city: Palo Alto

first: Vivianne

middle: L

last: Tawfik

state: CA

address: 3174 Porter Drive

department: Anesthesiology, Perioperative and Pain Medicine

institute: Stanford University

description:
Library name: Male_7wpFx_Trap_2
Column Y

data_processing:
FASTQ files were passed through the nf-core RNAseq (v3.12.0) pipeline which performed quality control (FastQC), trimming (Trim Galore), alignment to genome reference (STAR; GRCm38), and transcript quantification (RSEM). Genes with ≥ 25 counts in at least 90% of samples were included for analysis.
Assembly: GENCODE GRCm38
Supplementary files format and content: comma-separated values files report raw gene counts for each sample

source_name: Homogenized lumbar spinal cord

extract_protocol:
RNA was isolated by Azenta Life Sciences (formerly GeneWiz) using a routine protocol.
RNA libraries for RNA-seq were prepared by Azenta Life Sciences (formerly GeneWiz) using a standard poly-A selection protocol for mRNA species (eukaryotic).

value: Homogenized lumbar spinal cord

value: Spinal cord astrocytes

value: Fracture


title: HEK293T cells, Control, 0 h, rep3


title: SKMEL5 BRAFi 8 day treated bulk ATAC-seq

city: Nashville

first: Blake

last: Baleami

state: TN

address: 1161 21st Ave S

department: Human Genetic PhD Program

institute: Vanderbilt University

description:
Library name: SKMEL5_idling_ATAC
SKMEL5 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 8 days prior to ATAC-seq analysis of chromatin accessibility.

data_processing:
For bulk RNA-seq, reads were aligned to the hg38 human reference genome using HISAT2 and gene counts were generated using featureCounts. For scRNA-seq, reads were processed using Cell Ranger v3.0.2 with the GRCh38 reference transcriptome to generate gene expression count matrices. For bulk ATAC-seq, reads were trimmed with cutadapt, aligned to hg38 using bwa-mem, deduplicated, and peaks were called using MACS2. Processed files deposited in GEO include gene expression matrices and chromatin accessibility peak files used for downstream analyses.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data files include RNA-seq gene expression matrices, ATAC-seq peak files, and single-cell RNA-seq count matrices.
Supplementary files format and content: Bulk RNA-seq: Gene-level expression counts generated using featureCounts. The file is a comma-separated values (CSV) matrix where rows correspond to genes and columns correspond to samples. Entries represent raw read counts assigned to each gene.
Supplementary files format and content: ATAC-seq: Chromatin accessibility peaks identified from aligned reads. Peak regions are provided in BED/narrowPeak format with genomic coordinates and associated peak scores.
Supplementary files format and content: scRNA-seq: Processed count matrices generated from single-cell RNA-seq data. Each dataset contains the standard three files used by common single-cell analysis pipelines (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz). The matrix.mtx file contains the sparse gene-by-cell count matrix, features.tsv.gz lists gene identifiers, and barcodes.tsv.gz lists cell barcodes.

source_name: skin

growth_protocol: SKMEL5 melanoma cells were obtained from ATCC and maintained in a 1:1 mixture of Dulbecco’s Modified Eagle Medium (DMEM) and Ham’s F-12 medium supplemented with 10% fetal bovine serum at 37°C in 5% CO2. Cells were passaged twice weekly using TrypLE and confirmed to be mycoplasma-free. Single cell-derived SKMEL5 subclones were generated by limiting dilution as described previously.

extract_protocol:
For bulk RNA-seq, total RNA was isolated using the TRIzol extraction method according to the manufacturer’s instructions. For scRNA-seq, cells were washed and resuspended in 0.04% BSA in PBS prior to single-cell capture. For ATAC-seq, cells were lysed and nuclei prepared using Omni-ATAC lysis and resuspension buffers prior to transposition.
Bulk RNA-seq libraries were prepared following mRNA enrichment and cDNA library construction using the Illumina TruSeq stranded mRNA sample preparation kit. Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium 3′ gene expression protocol (version 2 chemistry). Bulk ATAC-seq libraries were generated using the Omni-ATAC protocol with Tn5 transposition followed by PCR amplification.

treatment_protocol: Cells were treated with the BRAF inhibitor PLX4720 at a final concentration of 8 µM for the indicated durations. For drug-treated samples, media and drug were replaced every 3 days. Cells treated with PLX4720 for 8 days are referred to as idling cells.

value: skin

value: SKMEL5 melanoma cells

value: melanoma cell line


title: Male, Astrocyte, 7 weeks post-Fx, Trap Sample 3

description:
Library name: Male_7wpFx_Trap_3
Column AG


title: HEK293T cells, Control, 0 h, rep1


title: Spleen naive mice, cDNA

description:
Library name: Naive_spleen_cDNA
5’ mRNA (v1.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

value: No sorting


title: Male, Astrocyte, 5 weeks post-Fx, Trap Sample 3

description:
Library name: Male_5wpFx_Trap_3
Column AF


title: scRNA-seq_CTD-ILD02

city: Beijing

first: Qingya

last: Shi

address: 30 Shuangqing Road, Haidian District

department: Tsinghua Medicine

institute: Tsinghua University

description: Library name: CTD-ILD02

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to produce FASTQ files.
The sequences were mapped to the hg38 genome for gene expression counting using Space Ranger's default parameters.
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format

source_name: Peripheral blood mononuclear cells

extract_protocol:
Ten milliliters of peripheral venous blood were collected from two clinically stable CTD-ILD patients after lung transplantation. PBMCs were immediately isolated using Ficoll–Hypaque density gradient centrifugation, and cell viability exceeded 90%.
Chromium 5’ Library Construction: Fresh cells (300–600 viable cells/µL) were loaded into the Chromium system to form single-cell GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (53°C for 45 min, then 85°C for 5 min), and cDNA was amplified and quality-checked using an Agilent 4200. Libraries were constructed with a Single Cell 5′ Library and Gel Bead kit, sequenced with paired-end 150-bp reads on an Illumina NovaSeq6000.

value: Peripheral blood mononuclear cells

tag: disease state

value: Stable Connective Tissue Disease-associated Interstitial Lung Disease (CTD-ILD)


title: Male, Astrocyte, 5 weeks post-Fx, Trap Sample 2

description:
Library name: Male_5wpFx_Trap_2
Column X


title: LLC-OVA tumor

description:
Library name: LLCOVA_tumor
3’ mRNA (v3 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

value: tumor

value: HBSS treated (control)


title: Male, Astrocyte, 7 weeks post-Fx, Trap Sample 1

description:
Library name: Male_7wpFx_Trap_1
Column R


title: Male, Astrocyte, 3 weeks post-Fx, Trap Sample 3

description:
Library name: Male_3wpFx_Trap_3
Column AE


title: Lymph node naive mice

description:
Library name: Naive_LN
3’ mRNA (v3 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

source_name: lymph node

value: lymph node


title: Male, Astrocyte, 5 weeks post-Fx, Trap Sample 1

description:
Library name: Male_5wpFx_Trap_1
Column P


title: B16-F10 tumor

description:
Library name: B16_F10
3’ mRNA (BD Biosciences): read1 contains cell barcode and UMI; read2 contains transcript sequence

value: Treated with isotype control antibody for anti-CD40


title: Lymph node LLC-OVA tumor-bearing mice

description:
Library name: LLCOVA_LN
3’ mRNA (v3 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: SKMEL5 untreated bulk ATAC-seq

description:
Library name: SKMEL5_untreated_ATAC
Untreated SKMEL5 cells used for ATAC-seq analysis of chromatin accessibility.

value: untreated


title: TREM2-KD-rep2

city: DUARTE

first: Naseeb

middle: Kaur

last: Malhi

email: naseebmalhi@gmail.com, nmalhi@coh.org

address: 1500 E Duarte Road

department: DMRI

institute: City of Hope

description: Library name: TREM2-KD-rep2

data_processing:
Adaptors were timmed by Trimmomatic-0.39
Trimmed data was aligned to hg38 with STAR(2.7.10a)
reads map to genomic features were counted by FeatureCounts
Assembly: hg38
Supplementary files format and content: The processed counts.txt files are tab-delimited tables which includes annotation columns (‘Geneid’) and data columns (i.e. read counts for genes) for each library.

growth_protocol: THP-1 monocytes were cultured according to manufacturer's protocol and differentiated to macrophages using PMA at 20 ng/mL 3 days prior to treatment

extract_protocol:
Approximately 1 million cells were used for total RNA extraction and construction of strand-specific mRNA-seq library
The libraries were constructed using the KAPA mRNA stranded Hyper kit following the user manual

treatment_protocol: THP-1 derived macrophages transfected with scrambled or silencing RNA against (100nM) and then treated with HT and then harvested 3 days later

value: THP-1 derived macrophages

value: transfected with TREM2 siRNA (100nM) and then treated with HT and then harvested 3 days later


title: HEK293T cells, Control, rep2

data_processing:
Raw reads were trimmed by trim_galore (v0.6.10), aligned to the hg38 human reference genome by HISAT2 (v2.2.1), and then counted by the featureCounts function in subread (v2.0.1).
Assembly: hg38
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was harvested using TRIzol LS (ThermoFisher Scientific) and RNeasy Mini Kit (QIAGEN).
RNA-seq libraries were prepared using TruSeq Stranded Total RNA Kit (Illumina) according to the manufacturer’s protocol. Sequencing was performed using NextSeq 500 Sequencer and NextSeq 500/550 High-Output v2 Kit (150 cycles, Illumina).

value: HEK293T cells

value: Control


title: scRNA-seq_CTD-ILD01

description: Library name: CTD-ILD01


title: Male, Astrocyte, 3 weeks post-Fx, Trap Sample 1

description:
Library name: Male_3wpFx_Trap_1
Column N

value: Homogenized lumbar spinal cord

value: Spinal cord astrocytes


title: SKMEL5 BRAFi 8 day treated scRNA-seq, 10x Genomics Chromium 3' v2

description:
Library name: SKMEL5_idling_scRNA
SKMEL5 cells treated with 8 µM BRAF inhibitor (PLX 4720) for 8 days prior to single-cell RNA sequencing.

value: skin


title: HEK293T cells, DHX29-KO, rep2


title: TREM2-KD-rep3

description: Library name: TREM2-KD-rep3


title: HEK293T cells, Control, 0 h, rep2


title: Male, Astrocyte, 3 weeks post-Fx, Trap Sample 2

description:
Library name: Male_3wpFx_Trap_2
Column W

value: Fracture


title: SKMEL5 untreated scRNA-seq, 10x Genomics Chromium 3' v2

description:
Library name: SKMEL5_untreated_scRNA
Untreated SKMEL5 cells used for single-cell RNA sequencing.

value: SKMEL5 melanoma cells

value: melanoma cell line


title: E0771 tumor day 9

description:
Library name: E0771_D9
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Male, Astrocyte, Uninjured, Trap Sample 3

description:
Library name: Male_Uninjured_ Trap_3
Column AH

value: No fracture


title: U937 cells, Control, rep2

source_name: U937 cells

extract_protocol:
Total RNA was harvested using TRIzol (ThermoFisher Scientific) and RNeasy Mini Kit (QIAGEN). Poly(A)+ mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer’s protocol. Sequencing was performed using NextSeq 500 Sequencer and NextSeq 500/550 High-Output v2 Kit (75 cycles, Illumina).

value: U937 cells


title: U937 cells, DHX29-KO, rep1


title: E0771 tumor day 20

description:
Library name: E0771_D20
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence

value: tumor


title: Male, Astrocyte, Uninjured, Trap Sample 1

description:
Library name: Male_Uninjured_ Trap_1
Column L


title: Treg-enriched lung lymphocytes from chimeric mice 15 days following PR8 infection, VDJ

city: Chapel Hill

first: Jason

middle: Robert

last: Mock

state: NC

address: 125 Mason Farm Road

institute: University of North Carolina

description:
Library name: Day15_vdj
VDJ, RNA
day15_features.tsv.gz
day15_matrix.mtx.gz

data_processing:
The 10X Genomics cellranger mkfastq command was used to convert raw data into fastq files. the mkfastq command was also used to de-multiplex raw data. The cellranger multi command and human GRCh38 reference files were used to integrate gene expression, V(D)J, and feature barcoding.
Assembly: GRCm39_gcM36_CR8
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-Seq

source_name: lung

growth_protocol: Briefly, wild-type CD45.1+CD45.2+ mice were irradiated and reconstituted with a mixture of wild-type (B6) CD45.2+ and CNS1-deficient CD45.1+ bone marrow and splenocytes.

extract_protocol:
Lungs were harvested and digested in RPMI 1640 medium containing 5mg/mL collagenase type 1 and 0.25mg/mL DNaseI for 20 minutes at 37 ⁰C, 5% CO2. Lungs were then dissociated mechanically and passed through a 100uM filter, then multiple lungs were combined and enriched for lymphocytes using a 33% Percoll gradient (Cytiva). Samples were then enriched for regulatory T cells using the mouse CD4+CD25+ Regulatory T Cell Isolation Kit (Miltenyi Biotec) and stored in Cryostor (Sigma) in liquid nitrogen prior to analysis.
Cell viability was determined, then cells were stained with TotalSeq C anti-mouse antibodies (BioLegend, San Diego, CA) per manufacturer's protocol. Sample loading resulted in ~10,000 cells for analysis. Chromium X was used to process samples. RNA libraries were created with the Chromium Next GEM Single Cell 5' Kit with Feature Barcoding. Chromium Single Cell Human BCR Amplification Kit was used for V(D)J library construction. Agilent Tapestation (Agilent Technologies, Palo Alto, CA) was used to confirm sequencing library integrity, and the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA), as well as qPCR (Applied Biosystems, Carslbad, CA), was used to quantify libraries. The Illumina sequencing platform was used to sequence libraries as recommended by 10X Genomics.

treatment_protocol: Following reconstitution, mice were infected with PR8 H1N1. Mice were analyzed at naive state, day 10 following PR8 infection, and day 15 following PR8 infection.

value: lung

value: Treg-enriched lymphocytes

value: Jaxboy (The Jackson Laboratory # 033076) x B6 wild-type mice (The Jackson Laboratory # 000664); irridiated and reconstituted with bone marrow from B6 and CNS1-deficient (Zheng et al., 2010. Nature) mice

value: Day 15 post-PR8

tag: library type

value: mRNA VDJ

tag: Sex

value: pooled male and female


title: U937 cells, Control, rep1


title: Scr_rep1

description: Library name: Scr_rep1

value: THP-1 derived macrophages

value: transfected with scrambled RNA (100nM) and then treated with HT and then harvested 3 days later


title: HEK293T cells, Control, rep1

value: HEK293T cells

value: Control


title: U937 cells, DHX29-KO, rep2


title: Treg-enriched lung lymphocytes from chimeric mice 15 days following PR8 infection, GEX

description:
Library name: Day15_GEX
RNA
day15_features.tsv.gz
day15_matrix.mtx.gz

data_processing:
The 10X Genomics cellranger mkfastq command was used to convert raw data into fastq files. the mkfastq command was also used to de-multiplex raw data. The cellranger multi command and human GRCh38 reference files were used to integrate gene expression, V(D)J, and feature barcoding.
Assembly: GRCm39_gcM36_CR8
Supplementary files format and content: Tab-separated values files and matrix files

value: naïve

value: mRNA


title: Scr_rep2

description: Library name: Scr_rep2


title: E0771 tumor day 14

description:
Library name: E0771_D14
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Female, Astrocyte, 7 weeks post-Fx, Trap Sample 3

description:
Library name: Female_7wpFx_ Trap_3
Column AC

value: Homogenized lumbar spinal cord

value: Spinal cord astrocytes

value: Fracture


title: Male, Astrocyte, Uninjured, Trap Sample 2

description:
Library name: Male_Uninjured_ Trap_2
Column Z

value: No fracture


title: Treg-enriched lung lymphocytes from chimeric mice 15 days following PR8 infection, Feature

description:
Library name: Day15_feature
Adntibody-derived oligonucleotide (ADT)
day15_features.tsv.gz
day15_matrix.mtx.gz

data_processing:
The 10X Genomics cellranger mkfastq command was used to convert raw data into fastq files. the mkfastq command was also used to de-multiplex raw data. The cellranger multi command and human GRCh38 reference files were used to integrate gene expression, V(D)J, and feature barcoding.
Assembly: GRCm39_gcM36_CR8
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

value: Day 10 post-PR8

value: ADT

tag: adt

value: TotalSeq- C0178 anti-mouse CD45.1 Antibody,  TotalSeq-C0157 anti-mouse CD45.2 Antibody


title: Treg-enriched lung lymphocytes from chimeric mice 10 days following PR8 infection, VDJ

description:
Library name: Day10_vdj
VDJ, RNA
day10_features.tsv.gz
day10_matrix.mtx.gz

value: lung

value: Treg-enriched lymphocytes

value: Jaxboy (The Jackson Laboratory # 033076) x B6 wild-type mice (The Jackson Laboratory # 000664); irridiated and reconstituted with bone marrow from B6 and CNS1-deficient (Zheng et al., 2010. Nature) mice


title: HEK293T cells, DHX29-KO, rep1


title: BE2C, HPLM

city: Chicago

first: Zongjie

last: Wang

state: Illinois

address: 400 N Aberdeen St., STE800

department: Biohub Chicago

institute: Biohub

description: Library name: Sample 2

data_processing:
Sequence reads were trimmed using Trimmomatic (0.36) and mapped to the Homo sapiens GRCh38 using STAR aligner (2.5.2b). Unique gene hit counts were calculated by the Subread package (1.5.2) and the differentially expressed genes (DEGs) were generated by DESeq2 using the following cutoff: an adjusted p-value < 0.05 and absolute log2 fold change (FC) >1.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: csv files include TPM and DEG

growth_protocol: Grow in HPLM or EMEM/F12 supplied with 10% FBS and 1% P/S.

extract_protocol:
Qiagen QIAcube Connect with RNeasy Mini Kits and QIAshredder columns
Illumina TruSeq RNA Library Prep Kit v2

value: Neuroblastoma

value: WT

value: Culture in HPLM


title: TREM2-KD-rep1

description: Library name: TREM2-KD-rep1

value: THP-1 derived macrophages

value: transfected with TREM2 siRNA (100nM) and then treated with HT and then harvested 3 days later


title: K562 cells, DHX29-KO, rep2

source_name: K562 cells

value: K562 cells


title: Female, Astrocyte, 7 weeks post-Fx, Trap Sample 1

description:
Library name: Female_7wpFx_ Trap_1
Column J


title: BE2C, EMEM/F12

description: Library name: Sample 1

value: Culture in EMEM/F12


title: K562 cells, CTR, rep2

value: Control


title: Primitive macrophage EVs, Mac-EVs, rep 4

city: Toronto

first: Milica

last: Radisic

state: Ontario

address: 160 College St

country: Canada

institute: University of Toronto

description: Library name: MacEV4

data_processing:
CM-, CF-, HCMVEC-EVs: Libraries were sequenced using a NextSeq500 (Illumina) at 1x 75 (bp) and an average depth of 30 million reads. Mac-EVs: Libraries were sequenced using a NovaSeq 6000 S4 (Illumina) at  2× 150 (bp) and an average depth of 12 million reads.
For Mac-EVs, R1 reads were trimmed to 75 bp before analysis and these were the files used for further analyses consistent with CM-, CF-, and HCMVEC-EVs.
CM-, CF-, HCMVEC-EVs: The Bio-Rad SeqSense pipeline employing STARaligner (v2.7.0 f) was used to aligned reads to the human genome (GRCh38.p12) and generate miRNA count files. Mac-EVs: The Qiagen RNA-seq Analysis Portal 3.0 (workflow version 1.2) was used to align trimmed R1 sequencing data to the human genome (GRCh38.103) via the miRbase v22 database and generate raw miRNA count files for each sample. Count file format was harmonized between the alignment pipelines for compatibility with downstream analyses; miRNAs absent in one pipeline with non-zero counts in the other were manually added as entries with zero counts as needed, while miRNAs missing -3p/-5p delineation in the BioRad pipeline were determined based on the solely expressed form in the Qiagen pipeline as well as the provided chromosome location.
Assembly: hg38, miRbase v22
Supplementary files format and content: CardiacEVs_rawcounts.txt: tab-delimited text file including raw counts for each sample

source_name: H1 hESC

growth_protocol: To produce primitive macrophages, the H1 hESC line was first differentiated into CD43+ primitive hematopoietic progenitors according to a previously published protocol1, which were isolated via magnetic-activated cell sorting and frozen. To complete primitive macrophage differentiation, cells were thawed then cultured in suspension for 3 days in poly-HEMA coated 6 well plates at a density of approximately 500,000 cells per well. Cells were cultured in supplemented StemPro-34 base medium (2ml per well, containing transferrin (ROCHE 10652202001, 150µg/ml), ascorbic acid (Sigma Aldrich A4544, 50µg/ml), L-glutamine (ThermoFisher 25040081, 2mM), and monothioglycerol (Sigma Aldrich M6145, 50µg/ml)) with the addition of MCSF (R&D Systems 216-MC, 30ng/mL), IL3 (R&D Systems 203IL, 50ng/mL) and SCF (R&D Systems 255SC, 100ng/mL). Then, for 18+ days, cells were cultured in the same supplemented StemPro-34 base medium with the addition of MCSF (30ng/mL) alone and medium was changed weekly.  CMs were differentiated from BJ1D human iPSCs as described previously.2 Briefly, iPSCs cultured in mTeSR Plus medium (STEMCELL Technologies) were passaged at 0.75 million cells per well onto 12-well Matrigel (Corning) coated plates. When confluent, medium was changed to RPMI supplemented with B27 minus insulin (Gibco), 1% Pen-Strep, and 8 µM CHIR99021 (Cayman Chemical) for 24 h. On day 3, medium was changed to the same RPMI based medium (without CHIR) plus 5µM IWP4 (Stemgent) for 48 h. After this, cells were cultured in RPMI with B27 minus insulin until day 7 then RPMI with B27 supplement (Gibco) thereafter. After at least day 14, CMs were harvested by 30 min treatment with 10x TrypLE Express (Gibco) at 37°C, media was added to neutralize TrypLE and rinse wells, then cells were centrifuged for 5 min at 300 g, resuspended in medium, and live cells counted with the addition of trypan blue.  Human ventricular cardiac fibroblasts (CFs) (Lonza, CC-2904) were cultured in Fibroblast Growth Medium 3 (FGM3; PromoCell, C-23025) with 1% 10,000 U/ml penicillin/streptomycin in T75 or T175 flasks.  Human cardiac microvascular endothelial cells (HCMVECs) (Applied Biological Materials Inc, T0514) were cultured in Endothelial Cell Growth Medium 2 (EGM2; PromoCell, C-22011) with 1 % 10,000 U/ml penicillin/streptomycin in T75 or T175 flasks. 1. Atkins MH, Scarfò R, McGrath KE, Yang D, Palis J, Ditadi A, Keller GM. Modeling human yolk sac hematopoiesis with pluripotent stem cells. J Exp Med. 2021;219(3). doi:10.1084/jem.20211924 2. Lian X, Zhang J, Azarin SM, Zhu K, Hazeltine LB, Bao X, Hsiao C, Kamp TJ, Palecek SP. Directed cardiomyocyte differentiation from human pluripotent stem cells by modulating Wnt/β-catenin signaling under fully defined conditions. Nat Protoc. 2013;8(1):162-175. doi:10.1038/nprot.2012.150

extract_protocol:
miRNA was isolated from lysed EV pellets using the miRNeasy Micro Kit (Qiagen, 217084) according to the manufaturer's protocol. Samples were treated with DNase.
CM-, CF-, HCMVEC-EVs: SEQuoia Complete Stranded RNA Library Prep Kit and Dual Indexed Primers (Bio-Rad 17005726 and 12011928) Mac-EVs: Library preparation was performed using the QIAseq miRNA Library Kit (Qiagen, catalog no. 331502).

treatment_protocol: Following macrophage differentiation as outlined above, supplemented StemPro-34 base medium with the addition of MCSF (30ng/mL) was prepared as before then depleted of background particles via ultrafiltration: media was centrifuged in Amicon Ultra-15 100kDa centrifugal filters (MilliporeSigma, UFC910024) at 4000g for 30 min at room temperature. Macrophage cells in suspension were pelleted via centrifugation at 200g for 5 minutes, supernatant was removed, and cells were resuspended in 1ml of medium for counting in the presence of trypan blue. Cells were then centrifuged and resuspended in 4ml ultrafiltered medium per well of cells collected from 6 well plate. After 48h of culture, conditioned media was collected and centrifuged to pellet cells. Supernatant was collected and frozen at -20°C until EV isolation.  Following CM differentiation, between days 14-22, conditioned media (RPMI with B27 supplement) was collected from culture plates after 72h of culture (in accordance with the regular media change timeline for CM differentiation protocol) until the timepoint where CMs were dissociated and counted. Conditioned media was frozen at -20°C until EV isolation.  For CFs, when cells reached 80% confluence, flasks were washed briefly with PBS then media was changed to un-supplemented basal FGM3 medium with the addition of 10% exosome-depleted FBS (ThermoFisher Scientific, A2720803) and 1% 10,000 U/ml penicillin/streptomycin. 15ml of media was used in T75 flasks and 35ml in T175 flasks. After 48h of culture, conditioned media was collected and frozen at -20°C until EV isolation. Cells were detached from flasks with trypsin, centrifuged, and resuspended for counting in the presence of trypan blue. HCMVEC conditioned media was collected using the exact same protocol as CFs except that un-supplemented basal EGM2 with the addition of 2% exosome-depleted FBS and 1% 10,000 U/ml penicillin/streptomycin was employed. Thawed conditioned media was centrifuged at 3200g for 10min to pellet cell debris. Supernatant was collected. The PEG-based miRCURY exosome isolation kit (Qiagen, 76743) was utilized for EV isolation. PEG-media solutions were rotated overnight at 4°C then centrifuged for 30min at 3200g and 21°C to pellet EVs. Pellets were rinsed superficially with PBS without resuspension. EV pellets were resuspended directly in Qiazol lysis buffer for total RNA extraction.

value: H1 hESC

value: macrophage


title: Treg-enriched lung lymphocytes from chimeric mice 10 days following PR8 infection, Feature

description:
Library name: Day10_feature
Adntibody-derived oligonucleotide (ADT)
day10_features.tsv.gz
day10_matrix.mtx.gz

value: pooled male and female


title: K562 cells, DHX29-KO, rep1


title: Primitive macrophage EVs, Mac-EVs, rep 3

description: Library name: MacEV3


title: Treg-enriched lung lymphocytes from uninfected chimeric mice, VDJ

description:
Library name: T-Reg-Naive-resub_vdj
VDJ, RNA
T-Reg-Naive-resub_features.tsv.gz
T-Reg-Naive-resub_matrix.mtx.gz

value: Day 15 post-PR8

value: mRNA VDJ


title: Female, Astrocyte, 3 weeks post-Fx, Trap Sample 3

description:
Library name: Female_3wpFx_ Trap_3
Column AA

value: Homogenized lumbar spinal cord

value: Spinal cord astrocytes

value: Fracture


title: Primitive macrophage EVs, Mac-EVs, rep 2

description: Library name: MacEV2


title: Female, Astrocyte, 7 weeks post-Fx, Trap Sample 2

description:
Library name: Female_7wpFx_ Trap_2
Column U


title: Scr_rep3

description: Library name: Scr_rep3

value: transfected with scrambled RNA (100nM) and then treated with HT and then harvested 3 days later


title: Female, Astrocyte, 5 weeks post-Fx, Trap Sample 3

description:
Library name: Female_5wpFx_ Trap_3
Column AB


title: K562 cells, DHX29/4EHP-knockdown, rep2


title: Female, Astrocyte, 3 weeks post-Fx, Trap Sample 2

description:
Library name: Female_3wpFx_ Trap_2
Column S


title: Primitive macrophage EVs, Mac-EVs, rep 1

description: Library name: MacEV1


title: Female, Astrocyte, 5 weeks post-Fx, Trap Sample 2

description:
Library name: Female_5wpFx_ Trap_2
Column T


title: DMSO_3

first: Haruhisa

last: Inoue

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

description:
Library name: TV0260_T0009-791-UDP0270_H1
T0009-799

data_processing:
The pooled libraries were sequenced on the NovaSeq 6000 system with the NovaSeq 6000 S4 Reagent Kit v1.5 (Illumina Inc.), generating 2 × 150 bp paired-end reads. The raw sequencing data were converted to FASTQ format using dedicated software (bcl2fastq Conversion Software, Illumina). All procedures were performed following the manufacturer’s manuals.
Assembly: The sequencing reads were mapped to the GRCh38 reference genome.

source_name: iPSCs

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (QIAGEN) following the manufacturer’s protocol, and RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
Employing the Switching Mechanism at 5' End of RNA Template (SMART) technology to add adapter sequences to both ends of the first-strand cDNA, full-length cDNA was synthesized using the SMART-Seq mRNA Kit (Takara Bio USA, Inc.), followed by PCR amplification using primers recognizing the adapter sequences. Subsequently, the double-stranded cDNA was fragmented and tagged at both ends through a tagmentation reaction using the Nextera XT DNA Library Prep Kit (Illumina Inc.), which applies transposon-mediated fragmentation and adapter insertion.Amplified libraries were generated using index primers (IDT for Illumina - DNA/RNA UD Indexes, Integrated DNA Technologies, Inc.).

value: iPSCs

value: Neural cells

value: healthy

value: DMSO


title: Treg-enriched lung lymphocytes from chimeric mice 10 days following PR8 infection, GEX

description:
Library name: Day10_GEX
RNA
day10_features.tsv.gz
day10_matrix.mtx.gz

value: lung

value: Treg-enriched lymphocytes

value: Jaxboy (The Jackson Laboratory # 033076) x B6 wild-type mice (The Jackson Laboratory # 000664); irridiated and reconstituted with bone marrow from B6 and CNS1-deficient (Zheng et al., 2010. Nature) mice

value: naïve

value: mRNA


title: Female, Astrocyte, 5 weeks post-Fx, Trap Sample 1

description:
Library name: Female_5wpFx_ Trap_1
Column H


title: K562 cells, CTR, rep1

value: K562 cells

value: Control


title: Treg-enriched lung lymphocytes from uninfected chimeric mice, Feature

description:
Library name: T-Reg-Naive-resub_feature
Adntibody-derived oligonucleotide (ADT)
T-Reg-Naive-resub_features.tsv.gz
T-Reg-Naive-resub_matrix.mtx.gz

value: Day 10 post-PR8

value: ADT

value: TotalSeq- C0178 anti-mouse CD45.1 Antibody,  TotalSeq-C0157 anti-mouse CD45.2 Antibody

value: pooled male and female


title: K562 cells, DHX29/4EHP-knockdown, rep1


title: Treg-enriched lung lymphocytes from uninfected chimeric mice, GEX

description:
Library name: T-Reg-Naive-resub_GEX
RNA
T-Reg-Naive-resub_features.tsv.gz
T-Reg-Naive-resub_matrix.mtx.gz


title: K562 cells, 4EHP-knockdown, rep2


title: K562 cells, 4EHP-knockdown, rep3


title: WT5-STAT

city: Evry

first: Eric

last: Bonnet

address: 2 rue Gaston Crémieux

country: France

institute: CNRGH

description: Library name: C002MAC

data_processing:
Quality control of sequencing data was performed with FastQC (v0.11.9). Reads were mapped on the GRCm39 (mm39) mouse genome assembly with STAR (v2.7.9a) and quantified with RSEM (v1.3.3). We selected samples that passed quality control filters based on the number of detected genes (> 15% expressed coding genes; threshold at 1 transcript per million, TPM) and the number of uniquely mapped reads (> 60%). This excluded nine samples, probably due to the small number of input cells. The final number of samples per group was N=5, 2, 2 for STAT3+, NF-kB+ and STAT3+/NF-kB+ astrocytes in APP and N=4, 2, 3 in WT mice. Differential gene expression analysis was performed with DESeq2 (v1.32.0) Bioconductor (v3.13) package on R (v4.1.1). Only genes with a raw count number greater than or equal to 10, in at least one sample in each of the two compared groups were analyzed. Results were considered statistically significant for an adjusted p value smaller than or equal to 0.05 and a |log2(fold-change)| greater than or equal to 1.
Assembly: GRCm39
Supplementary files format and content: tab-delimited file with raw counts for each sample

source_name: Prefrontal cortex

extract_protocol:
Twelve-month-old WT and APP mice were killed and their PFC rapidly collected in Hank's Balanced Salt Solution without Ca2+ and Mg2+ (HBSS; Sigma). The PFC of three mice were pooled, resulting in N=5 independent PFC samples from APP mice. Cells were mechanically and enzymatically dissociated with fire-polished Pasteur pipettes and the neural tissue dissociation kit with papain (Miltenyi Biotec), following manufacturer's instructions. Myelin removal beads II (Miltenyi Biotec) were used to deplete myelin from cell suspensions using MS columns. Cells were centrifuged at 300 g for 5 min at 4°C, resuspended in 400 µl HBSS with Ca2+ and Mg2+ and sorted on a BD Influx cell sorter. GFP was detected at 530/40 nm (488 nm excitation), CFP at 450/50 nm (408 nm excitation).
The complete protocol is described in Ceyzériat et al. 2018 (PMID 30322407). Sorted cells were placed 5 min at RT and chloroform was added to TRIzol for 3 min. Samples were centrifuged at 12,000 g for 15 min at RT. Aqueous phase was collected and 1 volume of 70% ethanol was added. Samples were transferred onto an RNeasyMin Elute spin column and RNA was purified according to manufacturer’s instructions, with on-column DNAse treatment (RNeasy micro kit, Qiagen, Hilden, Germany). RNA was eluted with 14 µl of RNAse-free deionized water and stored at - 80 °C until transcriptomic analysis. The lower number of astrocytes sorted per sample was not compatible with RNA quality assessment, and full length double strand cDNA libraries were amplified with 18 LD-PCR cycles.

treatment_protocol: Astrocyte-specific lentiviral reporters (LV) were generated to monitor the activity of the transcription factors STAT3 and NF-kB (p65). Six copies of the cis-acting enhancer element recognized by STAT3 or NF-kB were placed upstream of a minimal TA promoter with the TATA box from the Herpes simplex virus thymidine kinase promoter. The STAT3-responsive promoter (P-STAT3) controls the expression of the fluorescent protein eGFP, while the NF-kB-responsive promoter (P-NF-kB) drives the expression of eCerulean with a nuclear localization sequence (CFPnuc).

value: Prefrontal cortex

value: Astrocytes

tag: subpopulation

value: STAT


title: WT4-DOUBLE

description: Library name: C002MAA

value: DOUBLE


title: K562 cells, DHX29/4EHP-knockdown, rep3

first: Masanori

last: Yoshinaga

address: Yoshida-konoe-cho, Sakyo-ku


title: DMSO_1

description:
Library name: TV0260_T0009-791-UDP0268_H1
T0009-797

value: iPSCs

value: Neural cells

value: healthy


title: DMSO_2

description:
Library name: TV0260_T0009-791-UDP0269_H1
T0009-798

value: DMSO


title: WT5-DOUBLE

description: Library name: C002MAE


title: WT4-NFKB

description: Library name: C002MA9

value: NFKB


title: Female, Astrocyte, 3 weeks post-Fx, Trap Sample 1

description:
Library name: Female_3wpFx_ Trap_1
Column F

value: Homogenized lumbar spinal cord

value: Spinal cord astrocytes

value: Fracture


title: Female, Astrocyte, Uninjured, Trap Sample 2

description:
Library name: Female_Uninjured_ Trap_2
Column V

value: No fracture


title: WT4-STAT

description: Library name: C002MA8


title: K562 cells, GIGYF2-knockdown, rep2

value: K562 cells


title: Female, Astrocyte, Uninjured, Trap Sample 3

description:
Library name: Female_Uninjured_ Trap_3
Column AD


title: K562 cells, GIGYF2-knockdown, rep3


title: TR033_3

description:
Library name: TV0260_T0009-791-UDP0267_H1
T0009-796


title: TR033_2

description:
Library name: TV0260_T0009-791-UDP0266_H1
T0009-795


title: K562 cells, 4EHP-knockdown, rep1


title: K562 cells, GIGYF2-knockdown, rep1


title: Male, Astrocyte, 7 weeks post-Fx, Input Sample 1

description:
Library name: Male_7wpFx_Input_1
Column Q

value: All spinal cord cell types


title: TR033_1

description:
Library name: TV0260_T0009-791-UDP0265_H1
T0009-794


title: Male, Astrocyte, 5 weeks post-Fx, Input Sample 1

description:
Library name: Male_5wpFx_Input_1
Column O


title: TR065_1

description:
Library name: TV0260_T0009-791-UDP0262_H1
T0009-791


title: WT2-NFKB

description: Library name: C002MA1


title: WT2-DOUBLE

description: Library name: C002MA2


title: TR065_2

description:
Library name: TV0260_T0009-791-UDP0263_H1
T0009-792


title: K562 cells, DHX29-knockdown, rep3


title: Male, Astrocyte, 3 weeks post-Fx, Input Sample 1

description:
Library name: Male_3wpFx_Input_1
Column M


title: K562 cells, DHX29-knockdown, rep1


title: 201B7_Air_ALI_day62

city: Kyoto city

first: Shimpei

last: Gotoh

state: Kyoto prefecture

department: Department of clinical application

institute: Kyoto University CiRA

description: Library name: Sample 1

data_processing:
Seurat objects were constructed by filtering for cells with ≥200 genes and genes expressed in ≥3 cells. Cells with >15% mitochondrial RNA content, <200 or >10,000 detected genes were excluded. Mitochondrial reads were quantified using PercentageFeatureSet() with the pattern "^MT-". Gene expression data were normalized using LogNormalize (scaling factor = 10,000), and highly variable features (top 2,000) were identified via the “vst” method. All genes were scaled prior to dimensionality reduction using principal component analysis (PCA). Clustering was performed using FindNeighbors() and FindClusters() based on the top 15 principal components. Dimensionality reduction for visualization was conducted using UMAP via RunUMAP.Initial clusters were annotated manually based on the expression of canonical marker genes for each cell lineage. A subset of epithelial clusters (denoted epi.sub) was extracted for refined analysis. Reclustering was performed using PCA, FindNeighbors(), and FindClusters(). UMAPs were regenerated with adjusted parameters.Differential gene expression was evaluated using FindAllMarkers() with a log₂ fold change cutoff >0.25 and expression in >25% of cells. Top marker genes for each cluster were visualized using DoHeatmap(). Additional expression visualization was conducted using VlnPlot(), DotPlot(), and FeaturePlot().Pseudotime trajectory analysis was performed using Monocle 3 (Cao et al., 2019). Selected clusters (e.g., deuterosomal and multiciliated cells) were converted from Seurat objects to Monocle cell_data_set objects via as.cell_data_set(). UMAP embeddings were transferred, and trajectories were inferred using learn_graph() and order_cells(), with the root node set in the deuterosomal population. Pseudotime dynamics were visualized using plot_cells() with viridis color gradients.All analyses were performed in R (v4.3.1) using the following packages: Seurat, monocle3, SoupX, DoubletFinder, sctransform, patchwork, ggplot2, tidyverse, and ROCR.
Assembly: hg38
Supplementary files format and content: Format: H5. Content: filtered_feature_bc_matrix

source_name: airway epithelium

growth_protocol: Single-cell RNA sequencing (scRNA-seq) was performed on airway epithelial cells (AECs) derived from human iPSCs.The 201B7 line was processed according to a previously published protocol (Konishi et al., 2016), in which airway organoids were first generated in 3D culture and subsequently replated into a ALI system on day 42. Single-cell suspensions were collected on day 62.

extract_protocol:
Single-cell suspensions were prepared by enzymatic dissociation. Cells cultured on Transwell inserts were rinsed with pre-warmed PBS, treated with 0.5 mM EDTA in PBS at 37 °C for 10 minutes, and then incubated with Accutase at 37 °C for 20 minutes. Gentle pipetting was applied to facilitate dissociation.
Single-cell libraries were constructed using the Chromium platform (10X Genomics) and the Single Cell 3′ Reagent Kits v3.1 (for 201B7), according to the manufacturer’s protocols. Sequencing data were processed using Cell Ranger (v7.1.0) for demultiplexing, alignment to the GRCh38 reference genome (refdata-gex-GRCh38-2020-A, including reporter sequences), and generation of gene count matrices.

value: airway epithelium

value: iPSC-derived airway epithelial cells

value: no


title: Female, Astrocyte, 7 weeks post-Fx, Input Sample 1

description:
Library name: Female_7wpFx_Input_1
Column I


title: AD4-DOUBLE

description: Library name: C002M9R

value: Prefrontal cortex

value: Astrocytes


title: WT1-STAT

description: Library name: C002M9W

value: STAT


title: K562 cells, Control, rep3

city: Kyoto

institute: Kyoto University

value: Control


title: TR065_3

description:
Library name: TV0260_T0009-791-UDP0264_H1
T0009-793

value: iPSCs

value: Neural cells


title: WT2-STAT

description: Library name: C002MA0


title: Female, Astrocyte, 5 weeks post-Fx, Input Sample 1

description:
Library name: Female_5wpFx_Input_1
Column G


title: K562 cells, DHX29-knockdown, rep2


title: Diabetic mesenteric artery

description:
Library name: T2D-8
Single-cell RNA sequencing assay

data_processing:
10X Genomics cellranger (v6.1.1) was used to process sequencing data produced from Chromium Single Cell Gene Expression
Assembly: GRCh38-2020-A
Supplementary files format and content: Three processed data files per each sample: a matrix file (.mtx format) with UMI counts per each gene (rows) and single cell (columns); genes list (.tsv format) with the list of genes (features) detected; cell barcodes list (.tsv format) with the list of barcodes of the single cells in the sample.

source_name: Blood Vessel

extract_protocol:
Single-cell suspension was prepared by using the 10XGenomics Chromium Controller
10X Genomics Single Cell 3' v3.0 gene expression

treatment_protocol: Primary endothelial cells were freshly isolated from human mesenteric arteries

value: Blood Vessel

value: Artery cells isolated from human mesenteric arteries


title: AD5-STAT

description: Library name: C002M9S


title: AD4-NFKB

description: Library name: C002M9Q

value: NFKB


title: Male, Astrocyte, Uninjured, Input Sample 1

description:
Library name: Male_Uninjured_Input_1
Column K

value: Homogenized lumbar spinal cord


title: K562 cells, Control, rep1


title: K562 cells, Control, rep2


title: Female, Astrocyte, Uninjured, Input Sample 1

description:
Library name: Female_Uninjured_Input_1
Column C


title: Diabetic mesenteric artery intima 5

description:
Library name: T2D-5
Single-cell RNA sequencing assay

value: Intima cells isolated from human mesenteric arteries


title: Female, Astrocyte, 3 weeks post-Fx, Input Sample 1

description:
Library name: Female_3wpFx_Input_1
Column E

value: Fracture


title: Non-Diabetic mesenteric artery 2

description:
Library name: ND-9
Single-cell RNA sequencing assay


title: Diabetic mesenteric artery intima 4 replicate 3

description:
Library name: T2D-4_3
Single-cell RNA sequencing assay