title: Patient 16, Week 24

description:
Library name: B33
B33: Patient 16, Week 24

value: No


title: Single-cell_Multiome_PLNH_Male_Donor77

status: Public on Jun 10 2025

type: SRA

city: Philadelphia

first: Golnaz

last: Vahedi

state: Pennsylvania

address: 421 Curie Boulevard

department: Genetics

country: USA

institute: University of Pennsylvania

library_source: transcriptomic single cell

data_processing:
Cell Ranger ARC, Seurat instructions
Assembly: Grch38
Supplementary files format and content: Cell Ranger ARC output

molecule: nuclear RNA

organism: Homo sapiens

source_name: PLNH

extract_protocol:
Both RNA and ATAC libraries were made based on the 10x single-cell multiome protocol.
Library was made based on manufaturer protocol.
Single Cell Multiome ATAC + Gene Expression

tag: tissue

value: PLNH

tag: Sex

value: Male

tag: donor


title: Single-cell_Multiome_PLNH_Female_Donor76

value: Female


title: Single-cell_Multiome_Spleen_Male_Donor75


title: Single-cell_Multiome_PLNB_Female_Donor87

library_source: genomic single cell

molecule: genomic DNA

source_name: PLNB

value: PLNB


title: f28m, scRNAseq

city: New Haven

first: Ruben

last: De Man

state: CT

address: 333 Cedar St

institute: Yale School of Medicine

description:
Library name: f28m
10x Genomics

data_processing:
Raw sequencing reads were demultiplexed based on sample index adaptors, which were added during the last step of cDNA library preparation.
Possible adaptor and/or primer contamination were removed using Cutadapt.
Using the scRNA-seq implementation of STAR (STARsolo), reads were mapped to the murine reference genome GRCm38 release M22 (GRCm38.p6), collapsed and counted, and summarized to a gene expression matrix.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Proximal pulmonary artery

extract_protocol:
Proximal pulmonary arteries were excised with surrounding tissue. The arteries were mechanically chopped and placed in 1mg/ml collagenase (Roche) and 3 U/ml elastase (Worthington).
Following cellular dissociation, we barcoded unique mRNA molecules of each cell using our 10x Genomics Chromium platform (3’ v3.1 kit) and a droplet-based microfluidic system, then performed reverse transcription, cDNA amplification, fragmentation, adaptor ligation, and sample index PCR according to the manufacturer’s protocol.

value: Proximal pulmonary artery


title: Patient 14, Week 24

city: Matsumoto

first: Keita

last: Hirai

state: Nagano

address: 3-1-1 Asahi

department: Graduate School of Medicine

country: Japan

institute: Shinshu University

description:
Library name: B31
B31: Patient 14, Week 24

library_source: transcriptomic

data_processing:
The sequence reads were trimmed for adapter sequences and low-quality reads using Trimmomatic (version 0.39), followed by quality verification using FastQC v0.11.9. Alignment of reads to the human reference genome (GRCh38 patch 13) was performed using the STAR alignment tool (version 2.7.5c) with gene annotation based on GENECODE release 39. Transcript counts were quantified using RSEM v1.3.1. The TCC R package (version 1.44.0) was utilized for count data normalization using the trimmed mean of M values (TMM) method, and differential gene expression analysis was conducted using edgeR (version 4.2.2).
Assembly: GRCh38
Supplementary files format and content: raw counts for each sample

source_name: Peripheral blood T cell

extract_protocol:
Total RNA was extracted from T cells using a miRNeasy kit (Qiagen)
Library preparation was conducted using the NEBNext Ultra II Directional RNA Library Prep Kit with NEBNext rRNA Depletion Kit (New England Biolabs), with 10 ng of total RNA used for each sample.

treatment_protocol: Following the collection of blood samples, T cells were immediately isolated by immunomagnetic negative selection using the EasySep Direct Human T Cell Isolation Kit (STEMCELL Technologies).

tag: cell type

value: Peripheral blood T cell

tag: responder

value: Yes

tag: time

value: Week 24


title: Single-cell_Multiome_Spleen_Female_Donor71

source_name: Spleen

value: Spleen


title: Single-cell_Multiome_PLNT_Male_Donor73

source_name: PLNT

value: PLNT


title: Single-cell_Multiome_PLNB_Male_Donor72


title: Patient 13, Week 24

description:
Library name: B30
B30: Patient 13, Week 24


title: 24m, scRNAseq

description:
Library name: 24m
10x Genomics


title: Single-cell_Multiome_Spleen_Male_Donor81


title: Single-cell_Multiome_Spleen_Male_Donor74


title: Patient 12, Week 24

description:
Library name: B29
B29: Patient 12, Week 24


title: 20m, scRNAseq

description:
Library name: 20m
10x Genomics


title: MOE, 5x21, OR1A1, rep3

city: Ar-Rayyan, Doha,

first: Melanie

last: Makhlouf

address: Al Gharrafa Street,

country: Qatar

institute: Sidra Medicine

data_processing:
Reads were mapped using TopHat/2.1.1 aligner.
HTSeq version 0.9.1 was used to generate the raw counts.
Assembly: Mouse genome GRCm38.p5 (GCA_000001635.7)
Supplementary files format and content: rawCounts.txt (tab-delimited text file includes raw count values for each Sample)

source_name: Mouse Olfactory Epithelium

extract_protocol:
Dissected MOE processed with miRNeasy Mini Kit (50) # 217004, QIAGEN.
mRNA was prepared for sequencing using the TruSeq® RNA Library Prep Kit ((NonStranded and Poly-A selection).
mRNA libraries were pooled and single-end 100-bp sequencing was performed on the Illumina HiSeq 4000 platform.

value: Mouse Olfactory Epithelium

tag: strain

tag: genotype

value: Hemizygous 5x21-OR1A1


title: Single-cell_Multiome_Spleen_Male_Donor68


title: Patient 11, Week 24

description:
Library name: B28
B28: Patient 11, Week 24


title: Single-cell_Multiome_PLNT_Male_Donor67


title: MOE, 5x21, OR1A1, rep2


title: Single-cell_Multiome_PLNH_Male_Donor66


title: Patient 10, Week 24

description:
Library name: B27
B27: Patient 10, Week 24


title: Single-cell_Multiome_PLNB_Male_Donor65


title: Patient 9, Week 24

description:
Library name: B26
B26: Patient 9, Week 24


title: MOE, 5x21, OR1A1, rep1


title: Patient 15, Week 24

description:
Library name: B32
B32: Patient 15, Week 24


title: Single-cell_TEA_Spleen_Male_Donor64


title: Single-cell_Multiome_PLNT_Male_Donor63


title: 3m, scRNAseq

description:
Library name: 3m
10x Genomics


title: MOE, Wt, rep3

value: wild-type


title: Patient 8, Week 24

description:
Library name: B25
B25: Patient 8, Week 24


title: Single-cell_Multiome_PLNH_Male_Donor62


title: Single-cell_Multiome_PLNB_Male_Donor61


title: MOE, Wt, rep2


title: Single-cell_Multiome_PLNH_Female_Donor70


title: Patient 7, Week 24

description:
Library name: B24
B24: Patient 7, Week 24


title: Single-cell_Multiome_Spleen_Female_Donor69


title: Single-cell_Multiome_Spleen_Male_Donor60


title: MOE, Wt, rep1


title: Single-cell_Multiome_Spleen_Male_Donor59


title: Single-cell_Multiome_PLNT_Male_Donor58


title: Patient 6, Week 24

description:
Library name: B23
B23: Patient 6, Week 24


title: larval trunk, 2dpi Needle Stick

city: St. Louis

first: Aaron

middle: N

last: Johnson

state: Missouri

address: 660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University in St.Louis

description:
Library name: 2days Post Local Injury
15 animals

data_processing:
After sequencing, the Illumina output was processed using the CellRanger (v8.0.1) pipeline to generate gene-barcode count matrices. A custom reference genome was made with the “cellranger mkref” command, using the fasta file of zebrafish reference genome GRCz11 constructed from the Ensemble genome build (https://useast.ensembl.org/Danio_rerio/Info/Index) and the sorted Gene Transfer Format file (v4.3.2) from the improved zebrafish transcriptome annotation (Lawson et al., 2020). Base call files for each sample from Illumina were demultiplexed into FASTQ reads. Then, the “cellranger count” pipeline was used to align sequencing reads in FASTQ files to the custom reference genome. Both exon and intron sequences were included during the alignment. The filtered gene-barcode count matrices generated by “cellranger count” was used for downstream analysis.
Datasets were integrated and analyzed using Seurat (v4.4.0) package with R (v4.4.2)(Stuart etal., 2019; Team, 2024). Each sample count matrix was filtered for genes that were expressed in at least 3 cells and cells expressing at least 200 genes, followed by cell quality assessment usingcommonly used QC matrixes (Ilicic et al., 2016). Cells having a unique number of genes between 200 and 6500, mitochondrial gene percentage <5 and total number of reads (UMIs) between 300and 35000 were used for downstream processing. Each dataset was independently normalizedand scaled using the “SCTransform” function, which is an improved method for normalization, that performs a variance-stabilizing transformation using negative binomial regression (Hafemeisterand Satija, 2019). Standard integration workflow of Seurat was used to identify shared sources of variation across experiments as well as mutual nearest neighbors (Butler et al., 2018; Haghverdiet al., 2018). Integration features were selected based on the top 6000 highly variable features using “SelectIntegrationFeatures” function (nfeatures = 6000), which was used as input for the“anchor.features” argument of the “FindIntegrationAnchors” function. PCA analysis was performed on the 6000 variable features and the top 50 principal components selected based on the elbow plot heuristic, which measures the contribution of variation in each component. These 50 principal components were used in “FindNeighbors” and “FindClusters” functions to perform graph-based clustering on a shared nearest neighbor graph (Levine et al., 2015; Xu and Su,2015). Louvain algorithm was used for modularity optimization in cell clustering using “FindClusters” function. The resolution parameter (res = 0.3) that determines the granularity of clusteringwas selected by visually inspecting clusters with resolutions ranging between 0.1 and 2.0 as well as clustree graph (Zappia and Oshlack, 2018). Uniform Manifold Approximation and Reduction (UMAP) was used for non-linear dimensional reduction of the first 50 principal components and visualize the data using “RunUMAP” function (Becht et al., 2018). Data was graphed using different plot functions, such as “DimPlot”, “VlnPlot”, “FeaturePlot”, “Dotplot” and “DoHeatmap”, to view the cell cluster identity and marker gene expression. Cell proportions were extracted using the “table” and “prop.table” functions. Differential gene expression for individual clusters was identified using Wilcoxon rank sum test in the “FindAllMarkers” function. Marker genes detected in at least 25% of the clustered cells and had a positive average log2(FC) were reported.
Muscle cells identified from the complete dataset were subclustered using the “subset” function for subcluster analysis. The muscle subset was again normalized and scaled using the “SCTransform” function with glmGamPoi method (Ahlmann-Eltze and Huber, 2021). Fifty principal components were used and the resolution parameter was set to 0.4. Downstream analysis was done as described above for the integrated analysis.
We used a zebrafish single atlas (Sur et al., 2023) to generate a database of markers for each tissue and cell type (Table S1). The differentially expressed markers of each cluster were crossreferenced with our compiled database using our “DE-Marker-Scoring” algorithm (Saraswathy et al., 2024). For every matching marker gene, one point was given to the respective cluster under the column name with matching cell identity. Iteration over every marker gene was performed to generate a scoring matrix with varying points for each cluster against the different cell identities compiled in the database (Table S2, sheet: scoring). The “phyper” function in R was then used to calculate one-tailed binomial probabilities using hypergeometric distribution for the total score obtained from each cluster against each cell identity in the database (Table S2, sheet: Binomial probability). −log10 of probability values were obtained for plotting the heatmap (Table S2, sheet:−log10P). The resulting values were scaled from 0 to 100 and plotted as a heatmap using GraphPad prism. Each cluster was given an identity based on the maximum −log10 p-score obtained in the heatmap. The top DE markers of clusters with ambiguous scores were manually annotated using the “ident genes” from the zebrafish single atlas (Sur et al., 2023) and literature search (McKellar et al., 2021). Top DE markers generated for each cluster is given in (Table S3, sheet:topDEmarkers.all.clusters) “RenameIdents” function was used to assign identity to each cluster. To confirm the assigned cluster identities, enrichment of classical markers of respective cell types were tested using Dot plot.
The R package CellChat (v2.1.2) was used to evaluate regenerative cell-cell interactions after local and systemic muscle injury (Jin et al., 2021). CellChat models the probability of cell-cell communication by integrating our gene expression data with a database of known interaction between signaling ligands, receptors, and their cofactors (CellChatDB). The RNA data was used to create CellChat object using “createCellChat” function, followed by the recommended preprocessing functions with default parameters for the analysis of individual datasets. Truncated mean method with 10% trimmed observation was used to compute average gene expression per cell group for the complete dataset. The default trimean method was used to compute average gene expression for the CellChat analysis. CellChatDB.zebrafish was used to infer cell-cell communication. All categories of ligand-receptor interactions in the database were used in the analysis. Communications involving less than 10 cells were excluded. The “netAnalysis_computeCentrality” function was used to calculate network centrality scores at each time point. Functions such as “netVisual_circle”, “netAnalysis_contribution”, “netVisual_aggregate”, “netVisual_bubble”, “netAnalysis_signalingRole_heatmap”, and “netAnalysis_signalingRole_scatter” were used to generate different plots used in this paper.
Assembly: zebrafish reference genome GRCz11 and the sorted Gene Transfer Format file (v4.3.2) from the improved zebrafish transcriptome annotation (Lawson et al., 2020).
Supplementary files format and content: Compressed Filtered Feature and Barcode files as .tsv file and count matrices in .mtx file format.

organism: Danio rerio

source_name: Trunk

growth_protocol: Larval zebrafish of 4 days post fertilization underwent drug treatments or needle stick injuries for muscle ablation

extract_protocol:
15 larvae per cohort were dissected to remove the head, caudal fin, and internal organs and then processed as described (Farnsworth DB 459 2020). For tissue lysis, 500μL of dissociation buffer (2ug/ul Collagenase P, 2mM CaCl2, 0.2 ul DNaseI, 0.25% Trypsin, in 1X PBS) was added to the samples and incubated at 28 °C until samples were visually dissociated (~15min). Dissociation was stopped with equal volume of stop buffer (10% FBS, 0.001mM EDTA, in 1X PBS). Samples were centrifuged at 750rcf for 7min at 4°C, the supernatant was discarded, and the pellet was resuspended in 100μL of resuspension buffer (1% FBS, 2mM CaCl2, 1X Penicillin/Streptomycin, in DMEM). The suspension was strained through 20μm cell strainer (Pluriselect USA, 43-10020- 40), centrifuged once (500rcf, 1 min, 4°C) to pass cells through the strainer, and centrifuged a second time (750rcf, 7 min, 4°C) to pellet the cells. The cells were resuspended in 100μL of resuspension buffer, centrifugated (750rcf, 7min, 4°C), and the pellet was resuspended in 50μL 0.04% BSA in PBS. 5μl of cells were then combined with 5μl of Hoechst (Invitrogen, H3570), incubated for 10min, and transferred to a hemocytometer (Bulldogbio, NC1731934) to determine cell concentration. An additional 5μl of cells were incubated with Trypan blue (Sigma, T8154) for 5min, transferred to a hemocytometer, and counted to assess cell viability. Samples with > 70% viability were then submitted for single cell sequencing.
For snRNA-seq, 30 µl of isolated nuclei at a concentration of ~1000 nuclei/µl was submitted to Genome Technology Access Center at McDonnel Genome Institute of Washington University. Two biological replicates of each genotype were used. cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  cDNA was amplified for 11-13 cycles then purified using SPRIselect beads. Purified cDNA samples were then run on a Bioanalyzer to determine the cDNA concentration. GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 3’ Reagent Kits User Guide (v3.1 Chemistry Dual Index) with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 3’ Kit v3.1, 16 rxns (PN-1000268), Chromium Next GEM Chip G Single Cell Kit, 48 rxns (PN-1000120), and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument. Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 50x10x16x150 sequencing recipe according to manufacturer protocol. A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression Library.

treatment_protocol: Fish were treated with 12 hours of metronidazole or were stuck locally with a needle

value: Trunk

tag: treatment

value: Needle Stick

tag: batch


title: Patient 5, Week 24

description:
Library name: B22
B22: Patient 5, Week 24


title: Patient 4, Week 24

description:
Library name: B21
B21: Patient 4, Week 24


title: larval trunk, 4dpi Negative Control

description:
Library name: 4days Uninjured
15 animals

value: Fish Water


title: Single-cell_TEA_Spleen_Female_Donor53


title: Single-cell_Multiome_PLNH_Female_Donor54


title: larval trunk, 4dpi mcherry MTZ

description:
Library name: 4days Post Systemic Injury
15 animals

value: Fish Water + MTZ


title: Single-cell_TEA_Spleen_Female_Donor55


title: Single-cell_TEA_Spleen_Male_Donor51


title: Patient 2, Week 24

description:
Library name: B19
B19: Patient 2, Week 24


title: Single-cell_Multiome_Spleen_Male_Donor50


title: larval trunk, 2dpi mcherry MTZ

description:
Library name: 2days Post Systemic Injury
15 animals


title: Single-cell_Multiome_PLNH_Female_Donor52

value: PLNH


title: Patient 3, Week 24

description:
Library name: B20
B20: Patient 3, Week 24


title: Single-cell_Multiome_PLNT_Male_Donor49

value: Male


title: Patient 1, Week 24

description:
Library name: B18
B18: Patient 1, Week 24

value: No


title: Single-cell_TEA_Spleen_Female_Donor47

value: Female


title: Single-cell_Multiome_PLNH_Male_Donor48


title: Single-cell_Multiome_PLNH_Male_Donor57


title: larval trunk, 2dpi Negative Control

description:
Library name: 2days Uninjured
15 animals


title: Single-cell_Multiome_PLNT_Female_Donor46


title: larval trunk, 1dpi mcherry MTZ

description:
Library name: 1day Post Systemic Injury
15 animals


title: Single-cell_Multiome_PLNH_Female_Donor45


title: Single-cell_Multiome_PLNB_Male_Donor56

value: PLNB


title: Patient 16, Week 0

description:
Library name: A16
A16: Patient 16, Week 0

value: Peripheral blood T cell

value: Week 0


title: larval trunk, 1dpi Negative Control

description:
Library name: 1day Uninjured
15 animals


title: TRIM33_LNCaP_24hR1881_r3

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

description: Library name: wz4473

library_source: genomic

data_processing:
Reads were aligned to the human genome build Hg38/GRCh38 using BWA 0.5.9-r26-dev
Duplicates have been marked using GATK markdupoplicates (UMI-aware)
Reads with a mapping quality (MAPQ) < 20 were removed from further analysis
bamCoverage (from deeptools) was used to generate RPGC normalized bigwigs
Assembly: Hg38/GRCh38
Supplementary files format and content: .narrowPeak
Supplementary files format and content: .bw

source_name: prostate cancer

growth_protocol: LNCaP prostate cancer cell line was cultured in RPMI-1640 (Gibco), supplemented with 10% Fetal Bovine Serum (FBS-12A, Capricorn Scientific) and penicillin/streptomycin (100μg/mL, Gibco).

extract_protocol:
Chromatin Immunoprecipitations of proteins of interest were performed as previously described (A.A. Singh, et al., Life Sci. Alliance; 2019) employing 1% formaldehyde to perform the crosslinking. At least 2 biological replicates are provided
Illumina kit, Paired-End 51bp, Novaseq6000 Illumina Kit, single-end, 65bp (trimmed), HiSeq4000

treatment_protocol: For hormone stimulation, cells were pre-cultured for 3 days in RPMI-1640 (Gibco) supplied with 5% dextran-coated charcoal (DCC) stripped FBS), and penicillin/streptomycin (100μg/mL, Gibco), then cells were stimulated with 10nM R1881 or DMSO for 4h or 24h hours.

value: prostate cancer

tag: cell line

value: LNCaP

tag: chip antibody

value: TRIM33 (90051S, Cell Signaling Technologies)

value: tumor


title: Single-cell_Multiome_PLNB_Female_Donor44


title: Patient 17, Week 0

description:
Library name: A17
A17: Patient 17, Week 0

value: Yes


title: Single-cell_Multiome_PLNT_Female_Donor41

value: PLNT


title: Patient 14, Week 0

description:
Library name: A14
A14: Patient 14, Week 0


title: Patient 15, Week 0

description:
Library name: A15
A15: Patient 15, Week 0


title: Single-cell_TEA_Spleen_Male_Donor39


title: Single-cell_Multiome_PLNH_Female_Donor40


title: TRIM33_LNCaP_24hR1881_r2

description: Library name: wz4472


title: Single-cell_TEA_Spleen_Female_Donor42


title: Patient 13, Week 0

description:
Library name: A13
A13: Patient 13, Week 0


title: Single-cell_Multiome_PLNT_Male_Donor37


title: Single-cell_Multiome_Spleen_Male_Donor38

value: Spleen


title: TRIM33_LNCaP_24hR1881_r1

description: Library name: wz4471


title: Single-cell_Multiome_PLNH_Male_Donor36


title: Patient 12, Week 0

description:
Library name: A12
A12: Patient 12, Week 0


title: TRIM33_LNCaP_4hR1881_r3

description: Library name: wz4470


title: Single-cell_Multiome_Spleen_Female_Donor35


title: TRIM33_LNCaP_4hR1881_r2

description: Library name: wz4469


title: Patient 11, Week 0

description:
Library name: A11
A11: Patient 11, Week 0


title: Single-cell_TEA_Spleen_Female_Donor43


title: Single-cell_Multiome_PLNs_Female_Donor34

source_name: PLNs

value: PLNs


title: Single-cell_Multiome_PLNH_Male_Donor32


title: TRIM33_LNCaP_4hR1881_r1

description: Library name: wz4468


title: Single-cell_Multiome_Spleen_Male_Donor33


title: Single-cell_Multiome_Spleen_Male_Donor31


title: Single-cell_Multiome_PLNT_Male_Donor30


title: TRIM33_LNCaP_4hDMSO_r3

description: Library name: wz4467

value: DMSO 4h


title: TRIM33_LNCaP_4hDMSO_r2

description: Library name: wz4466


title: Single-cell_Multiome_Spleen_Female_Donor29


title: Single-cell_Multiome_PLNH_Female_Donor28


title: TRIM33_LNCaP_4hDMSO_r1

description: Library name: wz4465


title: Patient 7, Week 0

description:
Library name: A7
A7: Patient 7, Week 0


title: Patient 8, Week 0

description:
Library name: A8
A8: Patient 8, Week 0


title: Pooled Bulk RNA-seq bat nasal organoids interferon

city: Vienna

first: Max

middle: J

last: Kellner

address: Dr Bohr Gasse 3

country: Austria

institute: IMBA

description:
Library name: Pooled_BulkRNASeq_RoNa_IFN
Pooled 3'-end Bulk RNA-seq

data_processing:
Raw FASTQ processing: For single-cell RNA-sequencing data, 10x Cellranger count (version 7.1) was run using a custom genome index of Rousettus aegyptiacus (Assembly mRouAeg1.p) or human (Assembly GRCh38.90), or a custom genome index of the Rousettus aegyptiacus (Assembly mRouAeg1.p) and human (Assembly GRCh38.90) reference genomes for mixed identity samples. For pooled 3'end bulk RNA-sequencing: Cutadapt was used to trim read1 to 25nt reads required for BRB-seq tools, read2 was aligned to the Rousettus aegyptiacus (Assembly mRouAeg1.p) or human (Assembly GRCh38.90) reference genomes, BRB-seq tools CreateDGEMatrix was used to create UMI count matrices from aligned read2 and trimmed read1 files. A sample sheet containing  barcodes for sample-demultiplexing is provided for each pooled sample. For further details, please see the associated manuscript.
For scRNA-Seq 10x data: To remove artefacts and noise, Cellbender remove-background was run with the raw_feature_bc_matrix.h5 file from Cellranger count (see methods in associated publication) to create a UMI count matrix.
For scRNA-Seq 10x data: For mixed samples (pooled cells form individual bats and human cultures), the souporcell pipeline (souporcell_pipeline.py) was further used to derive SNPs and assign individual sample identities to each cells (listed in barcodes.tsv file and further explained in the Processed_Data_Information_Readme.txt file) to samples from aligned reads (10x Cellranger count output: possorted_genome_bam.bam) using the following options (-k X, whereas X is the number of expected samples; -t 8 --skip_remap True --ignore True).
For scRNA-Seq 10x data: The output files from Cellbender (filtered UMI count matrix), Cellranger (gem_classification files containing species identity for mixed samples), Souporcell (Cluster information to separate individual bat samples) were then used for downstream analysis in R using Seuratv4 (version 4.2.1). Details to the full analysis can be found in the associated manuscript.
For 3'-end pooled bulk RNA-sequencing: CreateDGEMatrix was used to create a UMI count matrix with the trimmed read1 file containing UMI and sample-barcode information (-p BU -UMI 12), the STAR-aligned read2 bam file (STAR index made from Rousettus aegyptiacus (Assembly mRouAeg1.p) or human genomes (Assembly GRCh38.90) ), the sample barcode sheet for demultiplexing and a gtf annotation file from the the respective genome assembly for gene-level read  quantification.
Assembly: Rousettus aegyptiacus (Assembly mRouAeg1.p) and human (Assembly GRCh38.90)
Supplementary files format and content: *.h5 files contain single cell RNA-sequencing gene expression matrices from Cellbender
Supplementary files format and content: *gem_classification.csv files contain the Cellranger cell droplet species information for mixed samples
Supplementary files format and content: *_Souporcell_clusters.tsv contains the souporcell output that determines singlets or multiples based on SNP information and was used for separation of mixed identifiy single cell RNA-sequencing samples
Supplementary files format and content: *.rds contains Seurat R objects for analysed single cell RNA-sequencing data as presented in the associated publication
Supplementary files format and content: *_Demultiplex_Sample_Sheet.txt contains the sample-barcode information used in BRB-seq tools CreateDGEMatrix for Pooled 3'-end Bulk RNA-seq libraries
Supplementary files format and content: *_UMI_Counts.txt contains UMI count matrix output from BRB-seq tools CreateDGEMatrix for Pooled 3'-end Bulk RNA-seq libraries

organism: Rousettus aegyptiacus

source_name: Nasal epithelium

growth_protocol: Organoids were grown in expansion or differentiation medium (see methods of associated publication)

extract_protocol:
Single cell suspension were obtained by enzymatic digestion of tissue (collagenase from Clostridium histolyticum and Dispase) or organoids (TrypLE Express) followed by AnnexinV magnetic bead-based selection of viable cells (STEMCELL technologies). Cells were resuspended in DMEM/F12 and submitted to an on-campus facility for 10x library preparation. For bulk RNA sequencing, total RNA was extracted using a magnetic bead-based semi-automatic purification system (Kingfisher).
Single cell RNA-sequencing Libraries were generated according to the 10x Chromium Single Cell 3' Reagent Kit v3 and v4 kit manual instructions. Pooled 3'-end bulk RNA-sequencing libraries were prepared using an in-house protocol that adheres to the PLATE-seq (PMID: 28740083; modified to include UMIs and optimized steps for library generation) and BRB-seq (PMID: 30999927; for bioinformatic tools) methodologies (see methods of associated publication).

treatment_protocol: Untreated, virus infected and interferon stimulated organoids were analysed

value: Nasal epithelium

value: Nasal organoids

value: Epithelial cells


title: TRIM24_LNCaP_24hR1881_r3

description: Library name: wz4464

value: TRIM24 (NB100-2596, Novus Biologicals)


title: Single-cell_Multiome_Spleen_Female_Donor27

value: Female


title: Single-cell_Multiome_PLNs_Female_Donor26


title: Pooled Bulk RNA-seq bat nasal organoids Marburg virus

description:
Library name: Pooled_BulkRNASeq_RoNa_MARV
Pooled 3'-end Bulk RNA-seq

value: Nasal epithelial cell-derived ALI


title: TRIM24_LNCaP_24hR1881_r2

description: Library name: wz4463


title: Patient 6, Week 0

description:
Library name: A6
A6: Patient 6, Week 0

value: Peripheral blood T cell


title: Patient 5, Week 0

description:
Library name: A5
A5: Patient 5, Week 0

value: No

value: Week 0


title: Single-cell_Multiome_PLNH_Female_Donor24

value: PLNH


title: Single-cell_Multiome_Spleen_Female_Donor25


title: Pooled Bulk RNA-seq bat alveolar organoids

description:
Library name: Pooled_BulkRNASeq_RoAlv
Pooled 3'-end Bulk RNA-seq

source_name: Lung epithelium

value: Lung epithelium

value: Alveolar organoids


title: TRIM24_LNCaP_24hR1881_r1

description: Library name: wz4462

value: prostate cancer

value: LNCaP

value: tumor


title: Pooled Bulk RNA-seq bat small intestinal organoids

description:
Library name: Pooled_BulkRNASeq_RoSi
Pooled 3'-end Bulk RNA-seq

source_name: Small Intestine

value: Small Intestine

value: Small intestinal organoids


title: Patient 4, Week 0

description:
Library name: A4
A4: Patient 4, Week 0

value: Yes


title: Single-cell_Multiome_Spleen_Female_Donor23

value: Spleen


title: TRIM24_LNCaP_4hR1881_r3

description: Library name: wz4461


title: Single-cell_Multiome_PLNH_Female_Donor22


title: Patient 9, Week 0

description:
Library name: A9
A9: Patient 9, Week 0


title: 10x single-cell RNA-seq bat lung lib4

description:
Library name: ERB_Lung4_10xscRNA
10x genomics

source_name: Lung

value: Lung

value: tissue

value: Mixed cell types


title: Patient 10, Week 0

description:
Library name: A10
A10: Patient 10, Week 0


title: Patient 3, Week 0

description:
Library name: A3
A3: Patient 3, Week 0


title: Single-cell_Multiome_Spleen_Female_Donor21

value: Female


title: Patient 2, Week 0

description:
Library name: A2
A2: Patient 2, Week 0

value: Peripheral blood T cell


title: TRIM24_LNCaP_4hR1881_r1

description: Library name: wz4459

value: TRIM24 (NB100-2596, Novus Biologicals)


title: TRIM24_LNCaP_4hR1881_r2

description: Library name: wz4460


title: 10x single-cell RNA-seq bat trachea

description:
Library name: ERB_Trachea_10xscRNA
10x genomics

source_name: Trachea

value: Trachea


title: 10x single-cell RNA-seq bat lung lib3

description:
Library name: ERB_Lung3_10xscRNA
10x genomics


title: Single-cell_Multiome_PLNH_Female_Donor20

value: PLNH


title: TRIM24_LNCaP_4hDMSO_r3

description: Library name: wz4458

value: DMSO 4h


title: Patient 1, Week 0

description:
Library name: A1
A1: Patient 1, Week 0

value: No

value: Week 0


title: Single-cell_Multiome_Spleen_Male_Donor19

value: Male


title: 10x single-cell RNA-seq bat lung lib2

description:
Library name: ERB_Lung2_10xscRNA
10x genomics


title: 10x single-cell RNA-seq bat small intestine lib4

description:
Library name: ERB_Gut3_10xscRNA
10x genomics


title: TRIM24_LNCaP_4hDMSO_r1

description: Library name: wz4456

value: prostate cancer

value: LNCaP

value: tumor


title: Adult Midgut, Dredd mutant with PGRP-LE overexpression, rep5

city: Cologne

first: Gilles

last: Storelli

address: Joseph Stelzmannstrasse 26

department: CECAD Research Center

country: Germany

institute: University of Cologne

description: Dredd-; mex>PGRP-LE biol rep 5

data_processing:
The quality of the sequencing reads was checked using FastQC. Sequencing reads were trimmed using Trim Galore! Software.
D. melanogaster annotated transcripts (BDGP6.32) were downloaded from Ensembl.
Transcript abundance was estimated using Kallisto-Quant.
Read counts were normalised to ERCC spike-in controls and differential gene expression analysis was performed using RUVSeq and edgeR Bioconductor R packages.
Assembly: D. melanogaster annotated transcripts (BDGP6.32)
Supplementary files format and content: The excel file contains two spreadsheets. The “TPM” spreadsheet contains Transcripts Per Million (TPM) read counts for each transcript in each sample. The “results” spreadsheet contains log2 fold change (logFC) and p-value for transcripts in Dredd - ; mex>PGRP-LE intestines compared to control intestines (Dredd - ; mex>+). For each gene, the Flybase ID, official name and symbol are also given.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Midgut

growth_protocol: Animals were fed a yeast only diet until 7 days post ecolsion. Animals were maintained at 25°C with a 12h light/12h dark cycle.

extract_protocol:
Total RNA was extracted using the Promega Reliaprep RNA Tissue Miniprep System (#Z6112)
Libraries were prepared using the Illumina Stranded Truseq RNA sample Preparation Kit

value: Midgut

tag: Stage

value: Adult

value: Dredd D44; mex-GAL4/UAS-PGRP-LE

value: Yeast only diet


title: 10x single-cell RNA-seq bat lung lib1

description:
Library name: ERB_Lung1_10xscRNA
10x genomics

value: Lung

value: tissue

value: Mixed cell types


title: Adult Midgut, Dredd mutant with PGRP-LE overexpression, rep4

description: Dredd-; mex>PGRP-LE biol rep 4


title: TRIM24_LNCaP_4hDMSO_r2

description: Library name: wz4457

value: TRIM24 (NB100-2596, Novus Biologicals)


title: LNCaP_input_single_end

description: Library name: wz4455

value: Input


title: Single-cell_Multiome_PLNT_Male_Donor18

value: PLNT


title: Adult Midgut, Dredd mutant with PGRP-LE overexpression, rep3

description: Dredd-; mex>PGRP-LE biol rep 3


title: 10x single-cell RNA-seq bat small intestine lib3

description:
Library name: ERB_Gut2_10xscRNA
10x genomics

value: Small Intestine


title: Adult Midgut, Dredd mutant with PGRP-LE overexpression, rep2

description: Dredd-; mex>PGRP-LE biol rep 2


title: Single-cell_Multiome_PLNH_Male_Donor16

value: PLNH


title: Adult Midgut, Dredd mutant with PGRP-LE overexpression, rep1

description: Dredd-; mex>PGRP-LE biol rep 1


title: Feature_Barcode_CKDL220031167-1A

city: Pittsburgh

first: Min

last: Zhang

state: PA

address: Salk Hall, 3501 Terrace St

institute: University of Pittsburgh

description:
only processed data for human CD45+ cells were provided as used in the manuscript
HumanHTO3_exp_scale.csv: CD45+ cells, LNA-control + isotype control (IgG) antibody
HumanHTO6_exp_scale.csv: CD45+ cells, LNA-EPIC1 + isotype control (IgG) antibody
HumanHTO9_exp_scale.csv: CD45+ cells, LNA control + human anti-PD-1 antibody pembrolizumab
HumanHTO12_exp_scale.csv: CD45+ cells, LNA-EPIC1 + human anti-PD-1 antibody pembrolizumab
HumanHTO14_exp_scale.csv: CD45+ cells, LNA-EPIC1 + human anti-PD-1 antibody pembrolizumab

library_source: other

data_processing:
The Cell Ranger v 7.0.1 was used to process the FASTQ files using GRCh38 database as the human reference genome. The generated UMI count gene-by-cell matrix was then demultiplexed and analyzed using the “Seurat” R package (v 4.3.0). To filter the low-quality cells and cell doublets, cells with uniquely detected genes ranging from 200 and 2500 were selected. Low-quality/dying cells with more than 15% of reads that map to the mitochondrial genome were excluded. Gene expression was normalized and scaled using Seurat packages.
Assembly: GRCh38
Supplementary files format and content: csv files and expression matrix for each sample

molecule: other

source_name: Feature barcode sequencing data for the scRNAseq expression data

extract_protocol:
A total of five tumors from five individual humanized mice with four different treatments were used. Single-cell suspensions were prepared after tumor dissociation using tumor dissociation buffer (RPMI 1640 w/o serum supplemented with DNase I 0.3 mg/mL and Liberase TL 0.25 mg/mL). The cell suspensions were then dispersed through 70 μm cell strainers. After washing hCD45+ cells were isolated using human CD45 MicroBeads (Miltenyi Biotec, #130-045-801) according to the manufacturer’s instructions from tumor cells suspensions. Mouse cells were depleted from the hCD45- fractions using the Mouse Cell Depletion Kit (Miltenyi Biotec, #130-104-694) to isolate non-immune human cells according to the manufacturer’s instructions. The isolated human CD45+ and human tumor cells from each tumor were labeled using individual hashtag antibodies (cell hashing). TotalSeq anti-human hashtag antibodies #3, #6, #9, #12, #14 (BioLegend) used to label hCD45+ cells and anti-human hashtag antibodies #4, #7, #10, #13, #15 (BioLegend) used to label human tumor cells respectively.
Libraries were prepared according to the manufacturer’s instruction using 5PrimeV2 chemistry (10x Genomics, Chromium Next GEM Single Cell 5' Reagent Kits v2 - Dual Index). Briefly, pooled cells were resuspended in the master mix and loaded with portioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). Gene expression (GEX), TCR and BCR libraries dual indexed using the SI-TT indices from Dual Index Kit TT Set A, 96 rxns PN-1000215 (10x genomics) according to the manufacturer’s instruction. Antibody cell surface protein feature barcode containing hashtags dual indexed using SI-TT indices from Dual Index Kit TN Set A, 96 rxns PN-1000250 (10x genomics).

value: Human TNBC xenograft tumor

value: hCD45+ and hCD45- cells

value: HuCD34-NCG mouse

value: mixed group, non-demultiplexed


title: 10x single-cell RNA-seq bat small intestine lib1

description:
Library name: ERB_Gut1_10xscRNA
10x genomics


title: Single-cell_Multiome_Spleen_Male_Donor15

value: Spleen

value: Male


title: Adult Midgut, Dredd mutant control, rep5

description: Dredd-; mex>+ biol rep 5

value: Midgut

value: Adult

value: Dredd D44; mex-GAL4/+


title: Single-cell_Multiome_PLNH_Male_Donor14

source_name: PLNH


title: RNAseq of EPIC1 overexpressed MCF7

data_processing:
To quantify the ERVs in MCF7 cell lines after EPIC1 overexpression, whole transcriptome sequencing reads (pair-end) were mapped to human genome (build hg38) through bowtie2 (https://github.com/BenLangmead/bowtie2), followed by the quantification through RepEnrich2 (https://github.com/nerettilab/RepEnrich2) on uniquely mapping and multi-mapping reads separately.
The estimated count values per ERV for each sample were logarithmically transformed with a pseudo count of 1 being added.
To quantify gene expression in MCF7 cell lines after EPIC1 overexpression, whole transcriptome sequencing reads (pair-end) were mapped to human genome (build hg38) through STAR, followed by the quantification through RSEM on uniquely mapping and multi-mapping reads separately.
The gene expression (FPKM) for each sample were logarithmically transformed with a pseudo count of 1 being added.
Assembly: human genome (build hg38)
Supplementary files format and content: Gene expression matrix in CSV format
Supplementary files format and content: ERV expression matrix in CSV format

source_name: Mammary gland/Breast

extract_protocol:
Total RNA from cultured cells were isolated using TRIzol (ThermoFisher), purified using RNA purification kit (ZYMO) as per the manufacturer’s instructions and RNA libraries were prepared for sequencing.
RNA libraries for RNA-seq were prepared using KAPA RNA Hyper RiboErase HMR (96 rxn) KK8581/8098140702 according to manufacturer's protocols.

treatment_protocol: Full-length EPIC1 was identified and amplified from total RNAs of MCF-7 / T-47D cells by 5’RACE and 3’-RACE using FirstChoice RLM-RACE Kit (ThermoFisher, #AM1700). To construct retroviral EPIC1 expression plasmids, PCR products containing the CMVzsGreen1 portion of pLncEXP (Addgene plasmid # 64865) were inserted into a pBABE puro vector (Addgene, #1764), and the resulting construct was named as pBABE-lnc. To construct stable EPIC1-expressing cells, pBABE-lnc and lnc-EPIC1 plasmids were transfected into Phoenix cells to produce retrovirus, and viruses were collected 48 h post-transfection. MCF-7 cells were infected for 24 h with the retroviruses and selected with puromycin to establish stable EPIC1-expressing cells.

value: Mammary gland/Breast

value: Human epithelial cell

value: EPIC1 overexpression


title: 10x single-cell RNA-seq bat nasal ALI

description:
Library name: Nasal-ALI_10x_scRNA
10x genomics

value: Nasal epithelium

value: Bat and human nasal basel cell-derived ALI, pooled single cell (Processed_Data_Information_Readme.txt and associated publication)

value: Epithelial cells


title: 10x single-cell RNA-seq bat alveolar organoids

description:
Library name: Alv-Org_10x_scRNA
10x genomics

value: Lung epithelium

value: Bat alveolar organoids


title: Adult Midgut, Dredd mutant control, rep4

description: Dredd-; mex>+ biol rep 4

value: Yeast only diet


title: RNAseq of control MCF7

value: GFP vector


title: Single-cell_Multiome_Spleen_Male_Donor13


title: Adult Midgut, Dredd mutant control, rep3

description: Dredd-; mex>+ biol rep 3


title: Single-cell_Multiome_PLNH_Male_Donor12

value: PLNH


title: 10x single-cell RNA-seq bat lung ALI

description:
Library name: Lung-ALI_10x_scRNA
10x genomics

value: Bat and human lung basal cell-derived ALI, pooled single cell (Processed_Data_Information_Readme.txt and associated publication)


title: Single-cell_Multiome_PLNH_Female_Donor17

value: Female


title: 3367A, PD+MP

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

institute: University of Utah

data_processing:
The cellranger count command was employed for demultiplexing, barcode processing, and single-cell 3' gene counting, resulting in a filtered matrix of gene expression counts for individual cells.
Assembly: mm10
Supplementary files format and content: tsv and matrix files

source_name: Sys mouse tumor

extract_protocol:
different state of SS tumor of mice were harvested  at the point of morbidity. Half of the tissue was digested as described before using mouse tumor dissociation kit. (Miltenyi Biotec). The corresponding nearby tissue were embedded in OCT for H&E staining. After dissociation the cell suspension was filtered through 40 um strainer and then treat with red blood cell lysis solution (Miltenyi Biotec). At last, cells were resuspended in PBS+0.04%BSA at a concentration of ∼1,000 cells/μL ready for single-cell sequencing. 10,000 cells per samples were targeted. scRNA-seq library preparation processes were guided by Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide
scRNA-seq library preparation processes were guided by Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide (CG000204) followed by Illumina NovaSeq with paired-end dual-indexing (28 cycles Read 1, 10 cycles i7, 10 cycles i5, 90 cycles Read 2).

value: Sys mouse tumor

value: mouse  express SS18::SSX2 gene


title: Adult Midgut, Dredd mutant control, rep1

description: Dredd-; mex>+ biol rep 1

value: Midgut

value: Male

value: Adult


title: Single-cell_Multiome_PLNH_Male_Donor10


title: 10x single-cell RNA-seq bat small intestinal organoids

description:
Library name: Si-Org_10x_scRNA
10x genomics

value: Small Intestine

value: Bat and human small intestinal organoids, pooled single cell (Processed_Data_Information_Readme.txt and associated publication)


title: Single-cell_Multiome_Spleen_Male_Donor11

value: Spleen


title: 3372A, MP


title: B9642-Hindbrain

city: Cambridge

first: Michael

last: Tsabar

state: MA

address: 350 Water Street

institute: Sanofi

description:
Library name: S13
10x genomics library

data_processing:
Barcode processing, gene counting and aggregation were made using Cell Ranger software 7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mus_musculus.GRCm39 and gencode.vM30 annotation with GFP added
Supplementary files format and content: hierarchical data format file (.h5 files)

source_name: brain

extract_protocol:
Tissue samples were stored at -80°C. For tissue lysis and washing of nuclei, sample sections were added to 1 mL Nuclei PURE lysis buffer (Sigma, NUC-201) and thawed on ice. Samples were then Dounce homogenized with PestleAx20 and PestleBx20 before transfer to a new tube, with the addition of additional lysis buffer. Following incubation on ice for 15 minutes, samples were then filtered using a 30 mM MACS strainer (Fisher, NC0642012), centrifuged at 500xg for 5 minutes at 4°C using a swinging bucket rotor (Sorvall Legend RT, Thermo Fisher), and then pellets were washed with an additional 1 mL cold lysis buffer and incubated on ice for an additional 5 minutes. A 1.8M sucrose buffer was created and 1.8ml was mixed with 1ml of cell suspension. 1ml of sucrose buffer was deposited to ultra centrifuge tube (Fisher, NC9157569) then the cell suspension was layered on top (2.8ml). The suspension was then centrifuged at 30,000xg (17,800 rpm) for 45min at 4C, Rotor SW55ti. Supernatant was then aspirated off, and pellet was resuspended in 1ml of wash buffer (Nuclei Pure storage buffer, Sigma NUC-201) and spun at 500xg for 5 min at 4°C. Supernatant was aspirated and 0.5ml of wash buffer was added for resuspension
Library preparation and NovaSeq Sequencing: Libraries were prepared according to 10xGenomics protocol for Chromium Single Cell 3’ Gene Expression V3.1 kit. NovaSeq sequencing was performed according to illumine NovaSeq 6000 protocol.

value: brain


title: CD8+ T cells, Stub1 KO-3

city: Boston

first: Martin

middle: Wallace

last: LaFleur

address: 4 Blackfan Circle Room 140

institute: Harvard Medical School

description:
Library name: S6
Column name in rawcounts.csv and normalized_counts.csv = S6

data_processing:
Paired ends fastq files were aligned using Salmon version 1.8.0 to Mouse Gencode version M36 (GRCm39)
Transcript level abundance was generated using tximport version 1.32.0 package in R (version 4.4.1) with the following parameter: countsFromAbundance = lengthScaleTPM, type = Salmon
Count matrix was further filtered based on a minimum of 10 raw read count per sample prior to analysis by DESeq2 (version 1.44.0)
DESeq2 was performed on 5 samples (S1, S2, S3, S4, S6)
Assembly: Gencode Mouse Version M36
Supplementary files format and content: rawcounts.csv was generated using tximport in R, and contains transcript counts for S1, S2, S3, S4, S6
Supplementary files format and content: normalized_counts.csv was generated following normalization using DESeq2 package in R for S1, S2, S3, S4, S6
Supplementary files format and content: DESeq2_results.csv was generated following DESeq2 analysis in R for S1, S2, S3, S4, S6

source_name: Tumor

growth_protocol: Cells were extracted from C57BL6 mice (challenged with B16-OVA tumor subcutaneously).

extract_protocol:
Qiagen Rneasy kit
Takara SMARTseq v4 kit

value: Tumor

value: CD8+ T cells


title: Single-cell_Multiome_Spleen_Female_Donor9

source_name: Spleen


title: 3371C, BP


title: B9641-Hindbrain

description:
Library name: S11
10x genomics library


title: CD8+ T cells, Stub1 KO-2

description:
Library name: S5
Sample was excluded from analysis


title: Single-cell_Multiome_PLNH_Female_Donor8


title: B9638-Hindbrain

description:
Library name: S9
10x genomics library


title: Single-cell_Multiome_Spleen_Male_Donor7


title: 3371A, BP


title: GEX_CKDL220031167-1A

source_name: Single cell RNA sequencing expression data on the hCD45+ and tumor cells collected from four different treatment groups of hCD34+ humanized mice with human TNBC xenografic tumor model (mixed sample, non-demultiplexed)

value: Human TNBC xenograft tumor

value: hCD45+ and hCD45- cells

value: HuCD34-NCG mouse

value: mixed group, non-demultiplexed


title: CD8+ T cells, Stub1 KO-1

description:
Library name: S4
Column name in rawcounts.csv and normalized_counts.csv = S4


title: B9643-Forebrain

description:
Library name: S7
10x genomics library


title: CD8+ T cells, Control-3

description:
Library name: S3
Column name in rawcounts.csv and normalized_counts.csv = S3


title: Single-cell_Multiome_PLNH_Male_Donor6

value: PLNH


title: Adult Midgut, Dredd mutant control, rep2

description: Dredd-; mex>+ biol rep 2

value: Dredd D44; mex-GAL4/+

value: Yeast only diet


title: 1372, hSS1_PBRM1

data_processing:
Read alignment was accomplished with the STAR (2.7.11) against the mm10 version of the mouse genome [PMID: 23104886]. Generation of count matrices was carried out using featureCounts (version 1.6.3),
Assembly: mm10
Supplementary files format and content: Tab-delimited text, gene counts for each sample

extract_protocol:
Fresh frozen tumor tissue was disrupted using Tissue-Tearor (BioSpec) in 1ml of TRIzol™ reagent (ThermoFisher).  RNA was extracted with Zymo Direct-zolTM RNA Miniprep kit.
Total RNA samples (5-500 ng) were hybridized with NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat) (E7400) to substantially diminish rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L).  Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized and pooled in preparation for Illumina sequence analysis.

value: Sys mouse tumor

value: mouse  express SS18::SSX1 gene and conditional knockout PBRM1 gene


title: B9642–Forebrain

description:
Library name: S5
10x genomics library


title: B9643-Hindbrain

description:
Library name: S15
10x genomics library


title: B9641-Forebrain

description:
Library name: S3
10x genomics library


title: Single-cell_Multiome_Spleen_Male_Donor5

value: Male


title: CD8+ T cells, Control-2

description:
Library name: S2
Column name in rawcounts.csv and normalized_counts.csv = S2


title: CD8+ T cells, Control-1

description:
Library name: S1
Column name in rawcounts.csv and normalized_counts.csv = S1


title: 1569, hSS1_PBRM1


title: 3733A, MP+BP

value: mouse  express SS18::SSX2 gene


title: Single-cell_Multiome_PLNH_Male_Donor4


title: Single-cell_Multiome_PLNB_Female_Donor3

source_name: PLNB

value: PLNB

value: Female


title: B9638–Forebrain

description:
Library name: S1
10x genomics library


title: 1568, hSS1_PBRM1


title: KO_CD45_S2, scRNA

city: Beijing

first: Hang

middle: Hubert

last: Yin

address: Shuangqing Road

country: China

institute: Tsinghua University

description: Library name: KO_CD45_S2

data_processing:
Data were analyzed according to ENCODE guidelines.
Assembly: mm10
Supplementary files format and content: bigwig files of each sample, raw counts for each sample,matrix files.

extract_protocol:
Cells in  were fixed by 0.9 % formaldehyde (Sigma) for 10 min at room temperature followed by quenching with 125 mM glycine for 5 min and washed three times with PBS. Extracted nuclei were resuspended in ChIP dilution buffer and sonicated for 5 min using 4s on 11s off at 5% power using SCIENTZ-IID (Scientz Biotechnology) for ChIP-seq. RNA was extracted by Trizol for RNA-seq.
Library was constructed using DNA or RNA library construction kit (Vazyme).

value: CD48 immune cells

value: single cells

value: KO


title: PYMT

city: Palo Alto

first: Kevin

last: Brulois

state: CA

address: 3801 Miranda Ave

institute: Stanford University

description: 10x Genomics, chromium controller

data_processing:
Cell Ranger (v3.0, 10x Genomics) was used to align reads to the mm10 reference genome and perform quality control.
Assembly: mm10
Supplementary files format and content: tab-separated values  and .mtx files

source_name: PYMT tumor

extract_protocol:
Tumor tissues were manually minced and transferred to digestion buffer. Digestion buffer was prepared by adding collagenase D (Worthington Biochem) (400U/mL for PyMT tumors or 500U/mL for KPC tumors), 20 μg/mL DNase I (Sigma), and 2% fetal bovine serum (FBS), into Hanks Balanced Salt Solution (HBSS) (Thermo Fisher). Tumors were digested for 30 min at 37C with constant stirring, then quenched by ethylenediaminetetraacetic acid (EDTA), filtered through 40 μm Nylon mesh, pelleted by centrifugation (750 g for 5 min at 4C), and suspended in phosphate buffered saline (PBS) for staining.
Endothelial cells were sorted and processed for scRNAseq using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10x Genomics) according to manufacturer guidelines.

value: PYMT tumor

value: tumor endothelial cells

value: WT

value: orthotopic tumor


title: 1571, hSS1

value: mouse  express SS18::SSX1 gene


title: KO_CD45_S1, scRNA

description: Library name: KO_CD45_S1

value: Tumor

value: CD47 immune cells


title: Single-cell_Multiome_PLNH_Female_Donor1

value: PLNH


title: 1567, hSS1

value: Sys mouse tumor


title: Single-cell_Multiome_Spleen_Female_Donor2

value: Spleen


title: WT_CD45_S2, scRNA

description: Library name: WT_CD45_S2

value: CD46 immune cells


title: 1300, hSS1_PBRM1

value: mouse  express SS18::SSX1 gene and conditional knockout PBRM1 gene


title: KPC

description: 10x Genomics, chromium controller

source_name: KPC tumor

value: KPC tumor


title: 2950, hSS1


title: K24-Stem_rep2

city: Kansas City

first: Kaela

middle: Margaret

last: Varberg

state: MO

address: 2401 Gillham Road; CMRI 7902.19

department: Pediatrics

institute: Children's Mercy

description:
Stem_State_protocol: TS cells were cultured in tissue culture treated dishes pre-coated with type IV collagen in complete TS Cell Medium (Okae et al., 2018). Cell medium was replaced every two days of culture.
EVT_protocol_1_2018: EVT cell differentiation was induced by plating human TS cells onto 6-well plates pre-coated with 1 μg/mL collagen IV at a density of 80,000 cells per well. Cells were cultured in EVT Differentiation Medium and analyzed on day 8 of EVT cell differentiation (Okae et al., 2018).
EVT_protocol_2_2022: EVT cell differentiation was induced by plating human TS cells into 6 cm petri dishes at a density of 1x105 TS cells per dish and cultured for two days in Spheroid Medium. After two days spheroids collected and replated in EVT Differentiation Medium and Matrigel. Cells were analyzed on day 7 of EVT cell differentiation.
ST3D_protocol: Syncytiotrophoblast cell differentiation was induced by plating TS cells into 6 cm petri dishes at a density of 300,000 cells per dish in Three-dimensional (3D) Syncytiotrophoblast Differentiation Medium (Okae et al., 2018). Cells were analyzed on day 6 of syncytiotrophoblast cell differentiation.

data_processing:
Sequence data were converted from .bcl to FASTQ file format using bcl2fastq software and de-multiplexed.
Raw FASTQ files were trimmed using default parameters (-r 0.1 -d 0.03) in Skewer (Version 0.2.2), and reads shorter than 18 bp were discarded.
Transcripts were quantified using Kallisto (Version 0.46.2).
Differentially expressed genes at FDR of 0.05 were discovered using the Bioconductor package DESeq2 in R (Version 1.32.0)
Assembly: B38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: CVS

extract_protocol:
Total RNA was isolated using TRIzol/chloroform precipitation (15596018, Thermo Fisher Scientific) as previously reported (Varberg et al., 2021).
Stranded mRNA-sequencing was performed on the Illumina NovaSeq 6000 Sequencing System in the Genomics Core at the University of Kansas Medical Center. Quality control was completed with the RNA Screen Tape Assay kit (5067-5576, Agilent Technologies) on the Agilent TapeStation 4200. Total RNA (1 μg) was processed in the following steps: i) oligo dT bead capture of mRNA, ii) fragmentation, iii) reverse transcription, iv) cDNA end repair, v) Unique Dual Index (UDI) adaptor ligation, vi) strand selection, and vii) library amplification using the Universal Plus mRNA-Seq with NuQuant library preparation kit (0520-A01, Tecan Genomics). Library validation was performed with the D1000 Screen Tape Assay kit (5067-5582, Agilent) on the Agilent Tape Station 4200. Library concentrations were determined with the NuQuant module using a Qubit 4 Fluorometer (Thermo Fisher Scientific). Libraries were pooled based on equal molar amounts and the multiplexed pool was quantified, in triplicate, using the Roche Lightcycler96 with FastStart Essential DNA Green Master (06402712001, Roche) and KAPA Library Quant (Illumina) DNA Standards 1-6 (KK4903, KAPA Biosystems). Using the qPCR results, the RNA-Seq library pool was adjusted to 2.125 nM for multiplexed sequencing. Pooled libraries were denatured with 0.2 N NaOH (0.04N final concentration), neutralized with 400 mM Tris-HCl, pH 8.0, and diluted to 425 pM. Onboard clonal clustering of the patterned flow cell was performed using the NovaSeq 6000 S1 Reagent Kit (200 cycle, 20012864, Illumina). A 2x101 cycle sequencing profile with dual index reads was completed using the following sequence profile: Read 1 – 101 cycles x Index Read 1 – 8 cycles x Index Read 2 – 8 cycles x Read 2 – 101 cycles.

value: CVS

value: human trophoblast stem cells

tag: cell state

value: Stem

tag: passage

tag: protocol

tag: days of_differentiation


title: K24-Stem_rep3

tag: tissue


title: WT_CD45_S1, scRNA

description: Library name: WT_CD45_S1

value: CD45 immune cells

value: single cells


title: sample pool 18, run HGYVNCCX2

city: Charlottesville

first: Luke

last: Dillard

state: VA

institute: UVA

description: 10X Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation was performed using Cell Ranger toolkit (version 5.0.0)
Assembly: mm10
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: BMSC-OBs

extract_protocol:
Single cells were liberated from mineralizing cultures via incubations with 60 mM ethylenediaminetetraacetic acid pH 7.4 (EDTA [Thermo Fisher Scientific], made in DPBS), 8 mg/mL collagenase (Gibco) in HBSS/4 mM CaCl2 (Fisher), and 0.25% trypsin–EDTA (Gibco). After single-cell isolation, cells from mice were pooled into groups containing cells from five mice total and concentrated to 800 cells/μL in PBS supplemented with 0.1% BSA (bovine serum albumin).
Pooled single cells were prepared for sequencing using the 10× Chromium Controller (10× Genomics, Pleasanton, CA, USA) with the Single Cell 3’ v2 reagent kit, according to the manufacturer’s protocol. Libraries were sequenced on the NextSeq500 (Illumina, San Diego, CA, USA).

value: BMSC-OBs

tag: mouse id


title: 2245, hSS1


title: sample pool 18, run HHFFMCCX2

description: 10X Genomics


title: 812, SSM2

value: mouse  express SS18::SSX2 gene


title: K24-Stem_rep1


title: KO-TAM-2,RNA

description: Library name: TAM-KO-2-RNA

value: Tumor associated macrophages

value: macrophages

value: KO


title: K24-ST3D_rep3


title: 1909, hSS1

value: mouse  express SS18::SSX1 gene


title: sample pool 17, run HGYVNCCX2

description: 10X Genomics


title: KO-TAM-3,RNA

description: Library name: TAM-KO-3-RNA

value: Tumor


title: 762, SSM2

value: Sys mouse tumor


title: 5ECER4G20,fRIPA,Oct4,ChIP

city: Chuo-ku

first: Hitoshi

last: NIWA

state: Kumamoto

address: 2-2-1 Honjo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

description: Library name: d0_fRIPA_Oct4

data_processing:
Base calls were perfomed using bcl2fastq for Nextseq500 output.
ChIP-seq reads were trimmed from 3'end until the final base had a quuality score > 30, using Trime Galore!.
ChIP-seq reads were alighned to the UUCSC mm9 genome using Bowtie.
Assembly: mm9
Supplementary files format and content: bedGraph

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis in RIPA buffer, chromatin was sonicated using a E220 focused-ultrasonicator(Covaris).
ChIP-seq library was prepared using the KAPA Library Preparation Kit. 1ng of DNA was used as starting material for samples. Library was amplified on the thermocycle and size selected at 50-400bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA kit.

value: embryonic stem cells

value: OCT4(rabbit anti-Oct3/4 antisera, Niwa et al, Cell(2005))


title: KO-TAM-1,RNA

description: Library name: TAM-KO-1-RNA


title: K24-ST3D_rep2


title: sample pool 14, run HHFFMCCX2

description: 10X Genomics


title: 630, SSM2


title: WT-TAM-3,RNA

description: Library name: TAM-WT-3-RNA

value: WT


title: sample pool 14, run HGYVNCCX2

description: 10X Genomics


title: K24-ST3D_rep1


title: WT-TAM-2,RNA

description: Library name: TAM-WT-2-RNA


title: sample pool 13, run HHFFMCCX2

description: 10X Genomics


title: 534, SSM2


title: K24-EVT_rep3

value: EVT


title: 445, SSM2


title: sample pool 13, run HGYVNCCX2

description: 10X Genomics


title: 809, SSM2;ARID1A

value: mouse  express SS18::SSX2 gene and conditional knockout ARID1A gene


title: WT-TAM,EGR2,ChIP

description: Library name: CHIP-EGR2-WT


title: K24-EVT_rep1

value: CVS

value: human trophoblast stem cells


title: sample pool 12, run HHFFMCCX2

description: 10X Genomics


title: sample pool 17, run HHFFMCCX2

description: 10X Genomics


title: 808, SSM2;ARID1A


title: 768, SSM2;ARID1A


title: sample pool 12, run HGYVNCCX2

description: 10X Genomics


title: 636, SSM2;ARID1A


title: sample pool 11, run HHFFMCCX2

description: 10X Genomics


title: K23-Stem_rep2

value: Stem


title: K23-Stem_rep1


title: 533, SSM2;ARID1A


title: sample pool 10, run HHFFMCCX2

description: 10X Genomics


title: Duct Ligation, L-F127 day 7, replicate 2

city: South San Francisco

first: Russell

last: Fletcher

address: 171 Oyster Point Blvd, Suite 400

department: Discovery Biology

institute: Surrozen, Inc.

description:
Library name: RFSZ-10x--18F
10x Genomics v3.1 3'

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version 8.0.0
Data exploration, normalization, dimension reduction, clustering, DE, and GSEA analyses were done in R (version 4.3.2)
Assembly: GRCm39
Supplementary files format and content: aggregated cellular barcodes from Cellranger output
Supplementary files format and content: feature/genes from Cellranger output
Supplementary files format and content: aggregated UMI matrix from Cellranger output
Supplementary files format and content: scran normalized counts matrix as tab delimited text file
Supplementary files format and content: QC, batch, experimental condition, and cell type metadata in tab delimited text file

source_name: lacrimal gland

growth_protocol: Mice were obtained from Jackson Laboratories (Bar Harbor, ME, USA). All animal experimentation was in accordance with the ‘‘Guide for the Care and Use of Laboratory Animals’’ prepared by the National Academy of Sciences. Protocols for animal experimentation were approved by the Surrozen Institutional Animal Care and Use Committee. 7-week-old C57Bl/6J female mice were acclimatized 4-5 per cage a minimum of two days prior to the experiment. Mice were kept 12/12-hour light/dark cycle in a 30% to 70% humidity environment and room temperature ranging from 20°C to 26°C.

extract_protocol:
At the indictated timepoint, the lacrimal gland was extracted and dissociated with collagenase, hyaluronidase and DNase1 in Advanced DMEM/F12 solution, and live cells were then purified by FACS.
Standard 10x Genomics Chromium 3’ v3.1 scRNA-seq reagents were used. Approximately 2000-4000 cells were loaded per channel. Cells from one animal replicate were captured per channel. Standard 10x Genomics Chromium 3’ v3.1 scRNA-seq RT, cDNA amplification, and sequencing library preparation protocols were followed. Multiplexed sequencing libraries were sequenced on Illumina NovaSeq 6000, averaging about 50,000 reads per cell.

treatment_protocol: After duct ligation injury, the lacrimal gland was injected with 2 uL of solution containing either an Anti-GFP control antibody or L-F127 WNT mimetic and lacrimal glands were collected at day 0, day 1, day 5, day 7.

value: lacrimal gland

value: lacrimal gland cells

value: L-F127 WNT mimetic


title: Duct Ligation, AntiGFP day 7, replicate 3

description:
Library name: RFSZ-10x--18G
10x Genomics v3.1 3'

value: Anti-GFP antibody


title: Duct Ligation, AntiGFP day 7, replicate 2

description:
Library name: RFSZ-10x--18E
10x Genomics v3.1 3'


title: 535, SSM2;ARID1A


title: WT-TAM-1,RNA

description: Library name: TAM-WT-1-RNA

value: Tumor associated macrophages

value: macrophages


title: K23-ST3D_rep2


title: 446, SSM2;ARID1A


title: sample pool 10, run HGYVNCCX2

description: 10X Genomics

value: BMSC-OBs


title: Duct Ligation, AntiGFP day 7, replicate 1

description:
Library name: RFSZ-10x--18C
10x Genomics v3.1 3'


title: K24-EVT_rep2


title: Duct Ligation, L-F127 day 7, replicate 3

description:
Library name: RFSZ-10x--18H
10x Genomics v3.1 3'


title: 450, SSM2;ARID1A


title: sample pool 9, run HHFFMCCX2

description: 10X Genomics


title: K23-ST3D_rep1


title: K23-Stem_rep3


title: sample pool 9, run HGYVNCCX2

description: 10X Genomics


title: sample pool 11, run HGYVNCCX2

description: 10X Genomics


title: K23-EVT_rep3


title: Duct Ligation, L-F127 day 5, replicate 3

description:
Library name: RFSZ-10x--18A
10x Genomics v3.1 3'


title: K23-EVT_rep2


title: 1561, SSM2;ARID1B

value: mouse  express SS18::SSX2 gene and conditional knockout ARID1B gene


title: 1418, SSM2;ARID1B

value: Sys mouse tumor


title: sample pool 8, run HGYVNCCX2

description: 10X Genomics


title: K23-ST3D_rep3


title: Duct Ligation, AntiGFP day 5, replicate 3

description:
Library name: RFSZ-10x--17H
10x Genomics v3.1 3'


title: Duct Ligation, L-F127 day 5, replicate 2

description:
Library name: RFSZ-10x--17G
10x Genomics v3.1 3'


title: Duct Ligation, L-F127 day 7, replicate 1

description:
Library name: RFSZ-10x--18D
10x Genomics v3.1 3'


title: K23-EVT_rep1


title: Duct Ligation, AntiGFP day 5, replicate 2

description:
Library name: RFSZ-10x--17F
10x Genomics v3.1 3'


title: MBO, Day 14, BA patient No.4, scRNA-seq

city: Dallas

first: Jorge

middle: A.

last: Bezerra

state: Texas

address: 5323 Harry Hines Blvd.

department: Department of Pediatrics

institute: University of Texas Southwestern Medical Center

description: 10x Genomics

data_processing:
Demultiplexing and FASTQ generation using CellRanger version 6.0.0
Generate single-cell expression matrix using CellRanger version 6.0.0
Quality control and filtering using R 4.3.2
Create Seurat objects using Seurat version 4.0.3
Sample integration, normalization, clustering, and sub-clustering using Seurat version 4.0.3
Predict cell-cell interactions using CellPhoneDB and Seurat version 4.0.3
Assembly: NCBI Genome assembly GRCh38
Supplementary files format and content: Cell Ranger output files: tab-separated barcodes.tsv.gz, features.tsv.gz, and matrix.tsv.gz

source_name: Multilineage biliary organoid

growth_protocol: Epithelial organoid cells derived from human liver tissue were dissociated and co-cultured with HUVECs and human MSCs on basement membrane extract matrix for 5 days in expansion medium, followed by 9 days in differentiation medium.

extract_protocol:
MBOs were washed with DPBS and incubated with Accutase at 37 °C for 10 mins to dissociate into single cells. The dissociated cells were filtered thorough 30 µm cell strainer and resuspended in William’s E medium containing 0.01% BSA.
Libraries were constructed according to the the manufacter’s instructions (Chromium Single Cell 3' Reagent Kit v3.1 protocol with Chromium platform, 10× Genomics), aiming for 10,000 cells. The barcoded cDNA was cleaned with Silane DynaBeads and amplified using 14 PCR cycles. Full-length, barcoded cDNA was then enzymatically fragmented, sized-selected using SPRIselect Reagent, adapter-ligated, and amplified for library construction. During the library construction, Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and sample indexes were added.

value: Multilineage biliary organoid

value: Biliary epithelial, Mesenchymal, Endothelial cells

tag: diagnosis

value: Biliary atresia

value: Diagnosis

tag: culture period

value: day 14


title: 1809, SSM2;ARID1B


title: sample pool 7, run HHFFMCCX2

description: 10X Genomics

tag: cell type


title: 1549, SSM2;ARID1B


title: Duct Ligation, L-F127 day 5, replicate 1

description:
Library name: RFSZ-10x--17E
10x Genomics v3.1 3'


title: sample pool 7, run HGYVNCCX2

description: 10X Genomics


title: sample pool 6, run HHFFMCCX2

description: 10X Genomics


title: 1838, SSM2;ARID1B


title: MBO, Day 14, BA patient No.3, scRNA-seq

description: 10x Genomics

tag: time

value: Transplant


title: MBO, Day 14, BA patient No.2, scRNA-seq

description: 10x Genomics


title: UI_d7_1

description:
Library name: RFSZ-10x--18B
10x Genomics v3.1 3'

tag: strain


title: Duct Ligation, AntiGFP day 5, replicate 1

description:
Library name: RFSZ-10x--17D
10x Genomics v3.1 3'


title: sample pool 8, run HHFFMCCX2

description: 10X Genomics


title: MBO, Day 14, BA patient No.1, scRNA-seq

description: 10x Genomics


title: sample pool 6, run HGYVNCCX2

description: 10X Genomics


title: Uninjured, day 5, replicate 1

description:
Library name: RFSZ-10x--17C
10x Genomics v3.1 3'

value: Uninjured, day 5, replicate 1


title: 1400, SSM2;ARID1B

tag: genotype


title: MBO, Day 14, Control No.4, scRNA-seq

description: 10x Genomics

value: Healthy

value: Organ donation


title: sample pool 5, run HHFFMCCX2

description: 10X Genomics


title: 1398, SSM2;ARID1B


title: Duct Ligation, L-F127 day 1, replicate 3

description:
Library name: RFSZ-10x--16D
10x Genomics v3.1 3'

value: lacrimal gland

value: lacrimal gland cells

tag: treatment


title: 1296,  SSM2

value: mouse  express SS18::SSX2 gene


title: Duct Ligation, AntiGFP day 1, replicate 3

description:
Library name: RFSZ-10x--16C
10x Genomics v3.1 3'

value: Anti-GFP antibody

tag: batch


title: sample pool 4, run HHFFMCCX2

description: 10X Genomics


title: MBO, Day 14, Control No.2, scRNA-seq

description: 10x Genomics

value: Urea cycle defect


title: MBO, Day 14, Control No.1, scRNA-seq

description: 10x Genomics


title: 1403, SSM2


title: Duct Ligation, AntiGFP day 1, replicate 2

description:
Library name: RFSZ-10x--16A
10x Genomics v3.1 3'


title: 1831, SSM2;ARID1B


title: 1402, SSM2


title: Duct Ligation, L-F127 day 1, replicate 1

description:
Library name: RFSZ-10x--15H
10x Genomics v3.1 3'

value: L-F127 WNT mimetic


title: sample pool 3, run HHFFMCCX2

description: 10X Genomics

value: BMSC-OBs


title: sample pool 3, run HGYVNCCX2

description: 10X Genomics


title: MBO, Day 14, BA patient No.2, bulk RNA-seq

data_processing:
Quality assessment and pre-processing using FASTQC (version 0.11.2), Trim Galore (version 0.4.2) with Cutadapt (version 1.14), and SAMtools (version 1.10.0)
Alignmentofthe readsto hg38genomeusingBowtie2 (version 2.3.3.1)
Removing low-quality alignments and PCR duplicates using SAMtools (version 1.10.0) and Picard MarkDuplicates tool (version 2.18.22)
Gene expression count using htseq-count (version 0.6.1)
Differential expression analysis using Bioconductor DESeq2 package (version 1.34.0) in R  (version 4.1.2)
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample

extract_protocol:
RNA was extracted using miRNeasy Micro Kit (Qiagen) and verified for integrity by 2100 Bioanalyzer (Agilent).
Total RNA was poly A selected and reverse-transcribed using TruSeq RNA library preparation kit V2 (Illumina) to constuct the library. Each sample was fitted with one of the 24 adapters containing a different 6 base molecular barcode for high level multiplexing.


title: 2405, SSM2;PBRM1

value: Sys mouse tumor

value: mouse  express SS18::SSX2 gene and conditional knockout PBRM1 gene


title: sample pool 2, run HGYVNCCX2

description: 10X Genomics


title: MBO, Day 14, BA patient No.1, bulk RNA-seq

value: Multilineage biliary organoid

value: Biliary epithelial, Mesenchymal, Endothelial cells


title: Uninjured, day 1, replicate 1

description:
Library name: RFSZ-10x--15F
10x Genomics v3.1 3'

value: Uninjured, day 1, replicate 1


title: Duct Ligation, AntiGFP day 1, replicate 1

description:
Library name: RFSZ-10x--15G
10x Genomics v3.1 3'


title: MBO, Day 14, Control No.3, scRNA-seq

description: 10x Genomics

value: day 14


title: sample pool 5, run HGYVNCCX2

description: 10X Genomics


title: sample pool 2, run HHFFMCCX2

description: 10X Genomics


title: 2410, SSM2;PBRM1


title: Duct Ligation, L-F127 day 1, replicate 2

description:
Library name: RFSZ-10x--16B
10x Genomics v3.1 3'


title: MBO, Day 14, Control No.3, bulk RNA-seq


title: sample pool 1, run HHFFMCCX2

description: 10X Genomics


title: 2412, SSM2;PBRM1


title: 1806,  SSM2


title: MBO, Day 14, Control No.2, bulk RNA-seq

value: Transplant


title: Uninjured, day 0, replicate 2

description:
Library name: RFSZ-10x--15D
10x Genomics v3.1 3'

value: Uninjured, day 0, replicate 2


title: sample pool 4, run HGYVNCCX2

description: 10X Genomics


title: 2291, SSM2;PBRM1


title: sample pool 1, run HGYVNCCX2

description: 10X Genomics


title: MBO, Day 14, BA patient No.3, bulk RNA-seq

value: Biliary atresia

value: Diagnosis


title: Naïve-1

data_processing:
Paired ends fastq files were aligned using STAR version 2.7.0 to the mouse genome Gencode v.M24
FeatureCounts v2.0.1 were used to extract raw counts from STAR alignments
Assembly: Gencode Mouse Version 24
Supplementary files format and content: TPM values per sample

growth_protocol: Cells were extracted from C57BL6 mice (naïve or challenged with B16-OVA tumor subcutaneously).

treatment_protocol: Mice were treated with isotype or PD-1 blocking antibodies.

value: Spleen

value: CD8+ T cells


title: MBO, Day 14, Control No.1, bulk RNA-seq

value: Healthy

value: Organ donation


title: Duct Ligation, day 0, replicate 2

description:
Library name: RFSZ-10x--15C
10x Genomics v3.1 3'

value: lacrimal gland

value: lacrimal gland cells

value: Duct Ligation, day 0, replicate 2


title: 2279, SSM2;PBRM1

value: Sys mouse tumor


title: hiPSC+CCL19+CCR2B+haCD16+IL-15+NKG2D+DAP10

city: Kobe

first: Hironobu

last: Kimura

state: Hyogo

address: Kobe KIMEC Center Bldg. 3F, 1-5-2 Minatojima-Minamimachi, Chuo-ku

institute: HEALIOS K.K.

data_processing:
DRAGEN Bio-IT Platform 3.7.5
Sequence reads were mapped to GRCh38.p13 using the DRAGEN RNA-Seq spliced aligner.
Gene expression quantification was performed using a gene expression quantification module of the DRAGEN RNA pipeline.
Assembly: GRCh38.p13 (GENCODE release 35)
Supplementary files format and content: Microsoft Excel file includes TPM values and raw counts for each Sample

source_name: HGEC-0020 clone 18H5

growth_protocol: The hiPSC and gene-modified hiPSC cells were maintained in AK03N medium (Ajinomoto) on dishes coated with iMatrix511MG (Matrixome) at 37℃ and 5% CO2.

extract_protocol:
Total RNA was harvested using RNA Easy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA kit following manufacture's protocol

tag: cell line

value: HGEC-0020 clone 18H5

value: induced pluripotent stem cell

value: gene-modified iPS cells


title: Duct Ligation, day 0, replicate 1

description:
Library name: RFSZ-10x--15B
10x Genomics v3.1 3'

value: Duct Ligation, day 0, replicate 1


title: Tumor iso-1

value: Tumor

value: Isotype antibody


title: hiPSC

source_name: TC-1133HKK hiPSC 06E

value: TC-1133HKK hiPSC 06E

value: WT iPS cells


title: Uninjured, day 0, replicate 1

description:
Library name: RFSZ-10x--15A
10x Genomics v3.1 3'

value: Uninjured, day 0, replicate 1


title: CVS_K09_Stem_rep3

description:
Stem_State_protocol: TS cells were cultured in tissue culture treated dishes pre-coated with type IV collagen in complete TS Cell Medium (Okae et al., 2018). Cell medium was replaced every two days of culture.
EVT_protocol_1_2018: EVT cell differentiation was induced by plating human TS cells onto 6-well plates pre-coated with 1 μg/mL collagen IV at a density of 80,000 cells per well. Cells were cultured in EVT Differentiation Medium and analyzed on day 8 of EVT cell differentiation (Okae et al., 2018).
EVT_protocol_2_2022: EVT cell differentiation was induced by plating human TS cells into 6 cm petri dishes at a density of 1x105 TS cells per dish and cultured for two days in Spheroid Medium. After two days spheroids collected and replated in EVT Differentiation Medium and Matrigel. Cells were analyzed on day 7 of EVT cell differentiation.
ST3D_protocol: Syncytiotrophoblast cell differentiation was induced by plating TS cells into 6 cm petri dishes at a density of 300,000 cells per dish in Three-dimensional (3D) Syncytiotrophoblast Differentiation Medium (Okae et al., 2018). Cells were analyzed on day 6 of syncytiotrophoblast cell differentiation.

data_processing:
Sequence data were converted from .bcl to FASTQ file format using bcl2fastq software and de-multiplexed.
Raw FASTQ files were trimmed using default parameters (-r 0.1 -d 0.03) in Skewer (Version 0.2.2), and reads shorter than 18 bp were discarded.
Transcripts were quantified using Kallisto (Version 0.46.2).
Differentially expressed genes at FDR of 0.05 were discovered using the Bioconductor package DESeq2 in R (Version 1.32.0)

value: CVS

value: human trophoblast stem cells

value: Stem


title: Duct Ligation, day 0, replicate 3

description:
Library name: RFSZ-10x--15E
10x Genomics v3.1 3'

value: Duct Ligation, day 0, replicate 3


title: Tumor PD1-1

value: CD8+ T cells

value: PD-1 Blockade


title: Naïve-2

value: Spleen


title: CVS_K09_Stem_rep2


title: 2300, SSM2

value: Sys mouse tumor

value: mouse  express SS18::SSX2 gene


title: Hippocampus,CAPZA2+/-,rep1

first: Yong

last: Cheng

email: yongcheng@muc.edu.cn, guomei153@163.com

address: Zhongguancun South St, Haidian District

institute: College of Life & Environmental Science

description:
Library name: Het
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and  aggregation were made using the Cell Ranger software v7.1.0.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hippocampus

growth_protocol: The animals were raised at 23 ± 1 °C and 50 ± 1% relative humidity under a 12 h light/dark cycle (lights on from 8 a.m. to 8 p.m.) and provided ad libitum access to a standard diet and drinking water.

extract_protocol:
The frozen hippocampus tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM dithiothreitol, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% Nonidet P-40, and 0.04% bovine serum albumin). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in Dulbecco’s modified Eagle medium/F12 supplemented with 10% fetal bovine serum. All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin. The protocol was refered to Shun-Fat Lau, et al, 2020.
Library was performed according to the manufacter's instructions(single cell 3' v3 protocol, 10x Genomics).

treatment_protocol: Mice were euthanized, and hippocampal tissues were dissected and immediately frozen or processed for nuclei isolation. No additional in vitro treatments (e.g., drug exposure or fixation) were applied to tissues prior to extraction.

value: hippocampus

value: mixed neurons and glia

value: CAPZA2+/- (heterozygous knockout)


title: LN iso

source_name: Tumor-draining lymph node

value: Tumor-draining lymph node


title: 2285, SSM2;PBRM1

value: mouse  express SS18::SSX2 gene and conditional knockout PBRM1 gene


title: 2418, SSM2


title: CVS_K09_Stem_rep1


title: Tumor Iso-2

value: Tumor

value: Isotype antibody


title: E13.5 dermal SmoM2YFP mutant

city: New Haven

first: Ruiqi

address: 300 George St

institute: Yale University

description: 10x Genomics

data_processing:
Raw sequencing data was aligned using Cellranger (v.5.0.1).
Assembly: mm10
Supplementary files format and content: Gzipped text file which includes cell barcodes and gene names; Gzipped gene-by-cell count matrix

source_name: skin

extract_protocol:
Dorsolateral/flank skin was microdissected from E13.5 littermate control and mutant embryos and dissociated into a single-cell suspension using 0.25% trypsin (Gibco, Life Technologies) for 20 min at 37 °C. After genotyping, two to three embryos were pooled by condition. Single-cell suspensions were then stained with DAPI (Thermo Fisher Scientific, NBP2-31156) before fluorescence-activated cell sorting.
Chromium Single Cell 3’ GEM Library and Gel Bead Kit v3.1 (PN1000121) were used according to the manufacturer’s instructions in the Chromium Single Cell 3’ Reagents Kits V3.1 User Guide. After cDNA libraries were created, they were subjected to Novaseq 6000 (Illumina) sequencing. For each scRNA-seq experiment, control and littermate mutant samples were prepared in parallel at the same time, pooled and sequenced on the same lane.

value: skin

value: SmoM2 WT


title: CVS_K09_ST3D_rep3

value: CVS

value: human trophoblast stem cells


title: 2281, SSM2

source_name: Sys mouse tumor


title: E13.5 control (SmoM2YFP)

description: 10x Genomics

value: SmoM2 MUT


title: Tumor PD1-2

value: CD8+ T cells


title: CVS_K09_ST3D_rep2


title: 2409, SSM2


title: mSS_H3K27ac_HiChIP_rep2

data_processing:
Peaks were called from each of the aligned bam files against input reads using MACS2. ChIP input was used as the background for MACS2. MACS was used to produce normalized bedgraphs, which were subsequently converted to bigWig files
Chromatin loops were determined using the Hichipper pipeline 26 and those with an FDR value of less than 0.05 were selected as high-confidence loops for further investigation.
Generate BedGraph using macs2. then Convert BedGraph to BigWig using the bedGraphToBigWig. The scores in the BigWig file represent the normalized signal intensities or read coverage, reflecting the strength of the signal detected in the ChIP-Seq experiment
Assembly: mm10
Supplementary files format and content: bigwig, mango for loop information in HiChIP
Library strategy: Hi-ChIP

extract_protocol:
Zymo DNA clean up and concentration kit
Approximately 5-10 million cells were crosslinked and then H3K27ac antibodies were used for DNA fragment capture.
For ChIP-seq sequencing libraries were prepared from chromatin immunoprecipitated DNA samples (1 to 10 ng) using the New England Biolabs NEBNext Ultra II DNA Library Prep kit (cat#E7634L).  PCR-amplified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583) and the molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Libraries were normalized and pooled in preparation for Illumina sequencing.
HiChIP libraries were prepared using Illumina Tagment DNA Enzyme and Buffer Kit.

tag: chip antibody

value: H3K27ac (Abcam, # ab4729)


title: KO-TAM-2,EGR2,ATAC

description: mergedpeaks.bed

data_processing:
CUT&Tag-seq and ATAC-seq data were analyzed according to ENCODE guidelines.
Assembly: mm10
Supplementary files format and content: bed files containing merged peaks of each genotype or bigwig fils of each sample

extract_protocol:
Cells in  were fixed by 0.9 % formaldehyde (Sigma) for 10 min at room temperature followed by quenching with 125 mM glycine for 5 min and washed three times with PBS. Extracted nuclei were resuspended in ChIP dilution buffer and sonicated for 5 min using 4s on 11s off at 5% power using SCIENTZ-IID (Scientz Biotechnology).
Library was constructed using DNA library construction kit (Vazyme).

value: Tumor associated macrophages

value: macrophages

value: KO


title: CVS_K09_ST3D_rep1


title: 2298, SSM2;PBRM1

value: Sys mouse tumor


title: Kelly-shRUNX1T1_NT_LSD1_Rep1

city: Bologna

first: Giorgio

last: Milazzo

address: Via F.Selmi 3

department: FaBiT

country: Italy

institute: University of Bologna

data_processing:
ChIP-seq reads were aligned to the GRCh38 reference genome using BWA version 0.7.17.
Read density track for each ChIP library were generated using deepTools bamCoverage function with RPGC as scale unit.
Peak calling was performed using MACS2. Mapping artifacts were removed by excluding regions listed in ENCODE exclusion list (ENCFF356LFX) and MYCN amplified region.
Assembly: hg38
Supplementary files format and content: bigWig and tab-delimited text file includes (BED files) including coordinates of peaks after the exclusion of regions listed in ENCODE blacklist (ENCFF356LFX) and MYCN amplified region.

source_name: Kelly

growth_protocol: Kelly adrenergic neuroblastoma cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were fixes with 1% formaldehyde for 10 min. After quenching, chromaitin was fragmented through sonication. Chromatin samples were immunoprecipitated overnight at 4°C. The complexes were immunoprecipitated with antibodies specific for RCoR1 (#EPR13825-ABCAM), RCoR3 (#ab76921-ABCAM), FLAG (#F3165-Sigma Aldrich) and LSD1 (#ab129195-ABCAM). The antibody/protein complexes were collected by Sepharose rec-Protein A or G (#101042 Invitrogen) and washed several times. The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 6h and DNA was purified by phenol/chloroform extraction, ethanol precipitation, and resuspended in H2O.
DNA libraries for ChIP-seq were prepared using Kapa Hyper Prep Library Prep Kit following manufacturer's instructions.

value: Kelly

value: MYCN-amplified neuroblastoma

value: Non-treated

value: LSD1 Ab_ab129195-ABCAM


title: Kelly-shRUNX1T1_NT_LSD1_Rep2


title: 2009, SSM2;PBRM1

data_processing:
Read alignment was accomplished with the STAR (2.7.11) against the mm10 version of the mouse genome [PMID: 23104886]. Generation of count matrices was carried out using featureCounts (version 1.6.3),
Assembly: mm10
Supplementary files format and content: Tab-delimited text, gene counts for each sample

value: mouse  express SS18::SSX2 gene and conditional knockout PBRM1 gene


title: Hippocampus,WT,rep1

description:
Library name: WT
10x Genomics

value: hippocampus

value: mixed neurons and glia

value: wild-type


title: KO-TAM-1,EGR2,ATAC

description: mergedpeaks.bed

source_name: Tumor

value: Tumor


title: Mouse_SynSa_F1_N292_H3K27ac

value: mouse  express SS18::SSX2 gene


title: CVS_K09_EVT_prot2_rep2

value: CVS

value: human trophoblast stem cells

value: EVT


title: CVS_K09_EVT_prot2_rep3


title: mSS_H3K27ac_HiChIP_rep1

value: H3K27ac (Abcam, # ab4729)


title: Kelly_RCOR3_Rep2

value: RCOR3 Ab_ab76921-ABCAM


title: WT-TAM-3,EGR2,ATAC

description: mergedpeaks.bed

value: Tumor associated macrophages

value: macrophages

value: WT


title: WT-TAM-2,EGR2,ATAC

description: mergedpeaks.bed


title: Kelly_RCOR3_Rep1

value: Kelly

value: MYCN-amplified neuroblastoma


title: CVS_K09_EVT_prot2_rep1


title: Mouse_SynSa_G6_N292_input

value: Sys mouse tumor


title: Mouse_SynSa_F5_N292_H3K36me3


title: Kelly_RCOR1_Rep1

value: Non-treated

value: RCOR1 Ab_EPR13825-ABCAM


title: Kelly_RCOR1_Rep2


title: CVS_K09_EVT_prot1_rep2


title: WT-TAM-1,EGR2,ATAC

description: mergedpeaks.bed


title: KO-TAM-3,EGR2,ATAC

description: mergedpeaks.bed

value: KO


title: Mouse_SynSa_F4_N292_H3K27me3


title: WT-TAM-2,H3K4Me1,CUT-Tag

data_processing:
CUT&Tag-seq and ATAC-seq data were analyzed according to ENCODE guidelines.
Assembly: mm10
Supplementary files format and content: bed files containing merged peaks of each genotype or bigwig fils of each sample
Library strategy: CUT&Tag


title: Kelly_shCTRL_72h_rep2

data_processing:
RNA-seq reads were trimmed using TrimGalore (v. 0.6.7).
RNA-seq reads were aligned to the GRCh38 reference genome using HISAT2 version 2.2.1.
Transcript abundance was measured using StringTie (v2.1.7) using GENCODE (v36) gene reference.
Assembly: hg38
Supplementary files format and content: Stringtie output abudance files for each sample

extract_protocol:
RNA was harvested using Qiagen RNeasy Plus Mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA following manufacturer's instructions.

treatment_protocol: shRNA expression was induced by treating cells with 2 μg/mL doxycycline for 24 or 48h.

value: 2 μg/mL Doxycycline


title: CVS_K09_EVT_prot1_rep1


title: Mouse_SynSa_G5_N332_2_input


title: Kelly_shCTRL_72h_rep1


title: Kelly_shCTRL_NT_rep2


title: WT-TAM-1,H3K27Ac,CUT-Tag

value: Tumor


title: Kelly_shCTRL_NT_rep1


title: Mouse_SynSa_E1_N332_2_H3K27ac

value: mouse  express SS18::SSX2 gene


title: Mouse_SynSa_F3_N292_H3K4me1


title: CVS_K08_Stem_rep2

value: CVS

value: Stem


title: Kelly_shRCOR2_72h_rep2


title: Mouse_SynSa_E4_N332_2_H3K36me3


title: WT-TAM-1,H3K4Me1,CUT-Tag


title: KO-TAM-3,EGR2,CUT-Tag


title: CVS_K08_Stem_rep3

value: human trophoblast stem cells


title: CVS_K08_Stem_rep1


title: Kelly_shRCOR2_72h_rep1


title: Mouse_SynSa_E3_N332_2_H3K27me3


title: CVS_K08_ST3D_rep1


title: Kelly_shRCOR2_NT_rep2


title: WT-TAM-3,EGR2,CUT-Tag


title: CVS_K09_EVT_prot1_rep3

value: EVT


title: CVS_K08_ST3D_rep3


title: WT-TAM-2,H3K27Ac,CUT-Tag


title: Kelly_shRCOR2_NT_rep1


title: KO-TAM-2,EGR2,CUT-Tag


title: Mouse_SynSa_E2_N332_2_H3K4me1


title: Mouse_SynSa_D1_N332_1_H3K27ac

value: H3K27ac (Abcam, # ab4729)


title: WT-TAM-2,EGR2,CUT-Tag

value: Tumor associated macrophages


title: CVS_K08_ST3D_rep2


title: CVS_K08_EVT_prot2_rep3


title: KO-TAM-1,EGR2,CUT-Tag

value: macrophages


title: CVS_K08_EVT_prot2_rep2


title: Mouse_SynSa_D5_N332_1_H3K36me3


title: Mouse_SynSa_G4_N332_1_input


title: WT-TAM-1,EGR2,CUT-Tag

value: WT


title: Kelly_shRCOR1_72h_rep1

value: Kelly


title: CVS_K08_EVT_prot2_rep1


title: Kelly_shRCOR1_NT_rep2

value: MYCN-amplified neuroblastoma


title: m705RP

first: Heng

last: Du

address: 45 Francis St

institute: Brigham and Women's Hospital

data_processing:
Raw data (raw reads) of FASTQ format were firstly filterd and examed.
Burrows-Wheeler Aligner (BWA) was utilized to map the paired-end clean reads to the mouse reference genome
Single nucleotide polymorphisms (SNPs), also known as single nucleotide variants (SNVs), constitute the largest class of genome variants in genome.
Small insertions and deletions (InDels) that are less than 50bp in length constitute another class of genomic variants in reference genome.
muTect to detect somatic SNPs, and the tool Strelka to detect somatic InDels.
Assembly: mm10/hg38
Supplementary files format and content: VCF
Library strategy: whole exon sequencing

growth_protocol: Cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml of penicillin and streptomycin, and incubated at 37℃ in 5% CO2.

extract_protocol:
Genomic DNA was extracted using a QIAGEN kit
A total amount of 1.0μg genomic DNA per sample was used as input material for the DNA sample preparation.Sequencing libraries were generated using Agilent SureSelectXT Mouse All Exon kit (Agilent Technologies, CA, USA)

treatment_protocol: Cells were treated with DMSO, or 500 nM rapamycin for more than 3 months (duplicates or triplicates per condition).

value: rapamycin persistant Renal cell carcinoma

value: Tsc2 null

value: 500 nM Rapamycin


title: Mouse_SynSa_D4_N332_1_H3K27me3

value: Sys mouse tumor


title: Mouse_SynSa_D3_N332_1_H3K4me1


title: CVS_K08_EVT_prot1_rep3


title: m705

value: Renal cell carcinoma

value: DMSO


title: Kelly_shRCOR1_NT_rep1

value: Non-treated


title: Mouse_SynSa_C1_N308_MyF5_H3K27ac

value: mouse  express SS18::SSX2 gene


title: m105KRP


title: Kelly_shCTRL_NT


title: CVS_K08_EVT_prot1_rep1

value: CVS


title: CVS_K08_EVT_prot1_rep2

value: human trophoblast stem cells


title: Mouse_SynSa_C5_N308_MyF5_H3K36me3


title: Mouse_SynSa_C4_N308_MyF5_H3K27me3


title: Tsc2 MEFs RP

source_name: Tsc2-- MEFs RP

value: Tsc2-- MEFs RP

value: rapamycin persistant mouse embryonic fibroblasts


title: m105K


title: Kelly_shCTRL_48h

value: 2 μg/mL Doxycycline


title: CVS_K07_Stem_rep3

value: Stem


title: Kelly_shCTRL_24h


title: CVS_K07_Stem_rep1


title: Kelly_shRCOR2_NT


title: Tsc2 MEFs

source_name: Tsc2-- MEFs

value: Tsc2-- MEFs

value: mouse embryonic fibroblasts


title: Kelly_shRCOR1_72h_rep2

value: Kelly

value: MYCN-amplified neuroblastoma


title: CVS_K07_ST3D_rep3


title: Mouse_SynSa_C3_N308_MyF5_H3K4me1


title: Mouse_SynSa_G3_N308_MyF5_input


title: Mouse_SynSa_B1_N302_MyF5_H3K27ac

value: H3K27ac (Abcam, # ab4729)


title: CVS_K07_Stem_rep2


title: Kelly_shRCOR2_48h


title: Kelly_shRCOR2_24h


title: CVS_K07_ST3D_rep2


title: Tsc1 MEFs

source_name: Tsc1-- MEFs

value: Tsc1-- MEFs

value: Tsc1 null


title: Tsc1 MEFs RP

source_name: Tsc1-- MEFs RP

value: Tsc1-- MEFs RP

value: 500 nM Rapamycin


title: Mouse_SynSa_B5_N302_MyF5_H3K36me3

value: Sys mouse tumor


title: Kelly_shRCOR1_NT

value: Non-treated


title: CVS_K07_ST3D_rep1

value: CVS


title: m705RP_3

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp.
clean data (clean reads) were obtained by removing reads containing adapter and poly-N. Q20, Q30 and GC content of the clean data were calculated
sequences and reads with low quality from raw data
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene.
Assembly: mm10/hg38
Supplementary files format and content: tab-delimited text file including raw counts
Supplementary files format and content: tab-delimited text file including RPKM values

extract_protocol:
Total RNA was extracted using a RNeasy mini kit (Qiagen, #74104).
1 μg RNA per sample was used for cDNA library preparation using the NEBNextÒ UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: Cells were treated with DMSO, Rapamycin (10 nM), or RMC-6272 (3 nM) for 24h (triplicates per condition).

value: rapamycin persistant Renal cell carcinoma

value: Tsc2 null

value: Rapamycin

tag: concentration

value: > 3 months


title: Mouse_SynSa_B4_N302_MyF5_H3K27me3

value: mouse  express SS18::SSX2 gene


title: m705RP_2


title: Mouse_SynSa_B3_N302_MyF5_H3K4me1


title: Kelly_shRCOR1_48h

value: 2 μg/mL Doxycycline


title: CVS_K07_EVT_rep3

value: human trophoblast stem cells

tag: cell state

value: EVT


title: m705RP_1


title: CVS_K07_EVT_rep2

tag: passage


title: Kelly_shRCOR1_24h

value: Kelly

value: MYCN-amplified neuroblastoma


title: Mouse_SynSa_G2_N302_MyF5_input


title: CDXRP_2

source_name: 105K Xenograft after tumor regrowth

value: 105K Xenograft after tumor regrowth

value: rapamycin persistant Renal cell carcinoma xenograft

value: 3 mg/kg

value: 4 weeks


title: B01_EOS

city: Atlanta

first: Edwin

last: Horwitz

state: Georgia

address: 1570 Haygood Drive NE

institute: Emory University

description: 10x Genomics

data_processing:
Data were processed with Cell Ranger v7.1.0 (force_cells=10000 for EOS)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab delimited barcode and features, counts matrix

source_name: Blood

extract_protocol:
The Miltenyi Whole Blood Eosinophil Isolation Kit was used to quickly isolate untouched eosinophils without prior density gradient centrifugation. Following erythrocyte removal, non-eosinophils were gently removed by magnetic depletion
10x Chromium Next GEM Single Cell 3' kit was used to generate sequencing libraries

value: Blood

value: Eosinophil

tag: condition

value: Severe asthma