title: lung, SCC_2

city: Guangzhou

first: Sicheng

last: Chen

state: Guangdong

address: NO.74 Zhongshan Road 2, Yuexiu District

institute: The First Affiliated Hospital, Sun Yat-sen University

description:
Library name: sample10
10x Genomics

data_processing:
For the same data subsets, their enrollment criteria must meet the following request: the number of genes that could be detected in each cell must be ≥ 200, and the number of cells in which each gene could be detected must be ≥ 3. The top 2000 highly variable genes were used for principal component analysis (PCA). The clusters were visualized and explored via UMAP and t-SNE. The R package DoubletFinder (v2.0.3) was employed to identify doublets via the same PCs as those used in the PCA above. Harmony methods were applied to integrate cells from different sequencing datasets. ScaleData and RunPCA were then performed on the integrated assay to compute 50 PCs. UMAP and t-SNE dimensionality reduction was carried out, and a shared nearest neighbor (SNN) graph was constructed using dimensions of 1:30 as input features and default PCA reduction. Clustering analysis was performed on the integrated assay at a resolution of 0.6.
Assembly: RGSC 6.0
Supplementary files format and content: Matrix table with raw counts for every gene and every cell

organism: Rattus norvegicus

source_name: lung

extract_protocol:
Fresh lung tissues from the rats were dissected and then dissociated via a tissue dissociation kit (Miltenyi Biotech, Germany). The tissue fragments were transferred to a C tube containing an enzyme mixture (including deoxyribonuclease I, dispase, collagenase D, and collagenase II) and incubated for 30 minutes at 37 °C on the MACSmix tube rotator. The C tube was subsequently inverted on the GentleMACS separator, and the GentleMACS program m_lung_01 was run twice. The cell suspension was filtered through a 70 µm filter. Dead cells and cell debris were further removed via Ficoll‒Paque PLUS (GE Healthcare, USA). Finally, the cells were stained with acridine orange (AO)/propyl iodide (PI), and the number and activity were detected on a fluorescent cell counter (Arthur, NanoEntek, Korea).
Single cells were captured via a Chromium Controller (10× Genomics) and processed to generate gel bead-in-emulsion (GEM) products. The libraries were established via the Chromium Single-cell 3' Library and Gel Bead Kit V2 (10x Genomics), with a target of 5,000 cells and 350 million reads. Each sample was processed on an independent Chromium single-cell A chip (10x Genomics). Libraries were pooled and sequenced on an Illumina HiSeq2500 platform.

value: lung

tag: Sex

value: female

value: Day 35

value: Squamous cell carcinoma, SCC


title: J3524_m

status: Public on Sep 03 2025

type: SRA

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

country: USA

institute: University of Pittsburgh

description: Library name: J3524_m

library_source: transcriptomic

data_processing:
Brain and muscle mRNA data were aligned with Rsubread (v 2.16.1), annotated with the org.Mm.eg.db package (v 3.19.1) and analyzed with edgeR (v 4.0.16). Gene ontology (GO) terms were generated in DAVID with a p-value cut-off of <0.05 followed by a fold-change cut-off of >0.5.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet containing normalized reads

molecule: total RNA

organism: Mus musculus

source_name: Muscle

growth_protocol: Animal studies were approved by the University of Pittsburgh Institutional Animal Care and Use Committee governed by regulatory standards from the Guide for the Care and Use of Laboratory Animals and the United States Department of Health and Human Services. Wild-type (WT) and KLOTHO HET (KlHET) mice were internally bred for this experiment and randomly assigned to either the control group or NMES treatment group. Mice were housed in a 75°C, 12:12 h light-dark cycled room with unrestricted access to standard food and water.

extract_protocol:
Brain: 30 mg brain sections were subjected to RLT buffer from RNeasy Mini Kit (Qiagen 74106) with 10% beta-mercaptoethanol added and passed through a 25G needle. Homogenate was transferred to QIAshredder (Qiagen 79656) for further dissociation. The remaining manufacturers protocol was followed to complete the RNA isolation. Quality and concentration were analyzed via RNA Nano 600 kit for Agilent 2100 Bioanalyzer (5067-1511). Muscle: 50 mg muscle sections were powdered by the addition of N2 and manually dissociated via mortar and pestle. QIAzol (Qiagen 5,346,994) was added to the powdered muscle and passed through a 25G needle. Homogenate was added to QIAshredder and the RNeasy Mini Kit protocol was followed for the duration of RNA isolation. Quality and concentration were analyzed via RNA Nano 600 kit for Agilent 2100 Bioanalyzer (5067-1511).
Brain and Muscle: Extracted RNA was sent to Novogene Co. located in Sacramento CA, for generation of total RNA libraries and sequencing on NovaSeq X Plus Series (PE150) machine. Data was received in .fq.gz formatting.

treatment_protocol: Electrical stimulation was performed with a Neuromuscular Stimulator (Empi 300 PV, Boston, USA) at 9 mA under 2.5% isoflurane anesthesia. Mice were shaved on both right and left hind legs along the sciatic nerve and exposed skin was coated in O.C.T. compound to ensure proper probe placement and to prevent dermal burns. The double-pronged pen attachment was placed at piriformis, causing leg extension. NMES was delivered in sets of 10 consecutive stimulations per side, oscillating between each leg after each set, for a total of 2 sets on each leg. NMES mice received treatment every other day for a total of 5 treatment sessions. Perfusions and sample collection occurred 24 hours after the final treatment session. Control mice received 15 minutes of 2.5% isoflurane anesthesia exposure each day the NMES treatment group received stimulation.

tag: tissue

value: Muscle

tag: genotype

value: KLOTHO HET

tag: treatment

value: NMES


title: Umbilical cord blood CD34+, IgG, WT, C&R, CB_2

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

description: Library name: C_R_IgG_CB_2

library_source: genomic

data_processing:
For RNA-seq, fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04. Surrogate Variable Analysis (SVA) was additionally applied to account for latent sources of variation.
For CITE-seq, raw sequencing data (FASTQ files) were processed using Cell Ranger (10x Genomics). The cellranger count pipeline was run with Feature Barcode support enabled to quantify both gene expression and cell surface protein tags (antibody-derived tags, ADTs). After processing individual samples, outputs were merged using the cellranger aggr function to generate a combined gene-barcode matrix for downstream analysis. The merged dataset was analyzed using the Seurat (v4) R package. Cells with a mitochondrial gene content greater than 5% were excluded to remove potentially stressed or dying cells. The expression data were normalized and scaled, followed by Principal Component Analysis (PCA). Both transcriptomic (RNA) and surface protein (ADT) data were respectively used for dimensionality reduction and clustering, including PCA and Uniform Manifold Approximation and Projection (UMAP) for visualization. TotalSeq B antibody (BioLegend) targets: CD201 (Cat. ID 351911, Clone RCR-401), barcode: GTTTCCTTGACCAAG, CD90 (Cat. ID 328147, Clone 5E10), barcode: GCATTGTACGATTCA, CD133 (Cat. ID 394017, Clone S16016B), barcode: GTAAGACGCCTATGC, CD34 (Cat. ID 343539, Clone 581), barcode: GCAGAAATCTCCCTT, CD45RA (Cat. ID 304161, Clone HI100), barcode: TCAATCCTTCCGCTT, CD38 (Cat. ID 356639, Clone HB-7), barcode: CCTATTCCGATTCCG, CD49f (Cat. ID 313639, Clone GoH3), barcode: TTCCGAGGATGATCT, CD135 (Cat. ID 313321, Clone BV10A4H2), barcode: CAGTAGATGGAGCAT, CD370 (Cat. ID 353811, Clone 8F9), barcode: CTGCATTTCAGTAAG, CD71 (Cat. ID 334127, Clone CY1G4), barcode: CCGTGTTCCTCATTA, CD41 (Cat. ID 303747, Clone HIP8), barcode: ACGTTGTGGCCTTGT, CD115 (Cat. ID 347327, Clone 9-4D2-1E4), barcode: AATCACGGTCCTTGT, CD15 (Cat. ID 323051, Clone W6D3), barcode: TCACCAGTACCTAGT
For scRNA-seq, Single-cell RNA-seq data were demultiplexed and aligned to the Genome Reference Consortium Human Genome, GRCh38. The aligned data were annotated and UMI-collapsed using Cell Ranger (v3.1.0, 10x Genomics). Cells with more than 10% mitochondrial gene expression or with the top 5% of unique feature counts were excluded from the analysis. Principal component analysis (PCA) was performed to reduce dimensionality using Seurat 4.0. Clusters were identified through dimensionality reduction techniques, including tSNE and UMAP, using the same package.
CUT&Run and CUT&Tag sequencing data were processed using the CUT&RUNTools 2.0 pipeline, which supports both assay types and provides integrated steps for alignment, peak calling, and quality control. Sequencing reads were aligned to the human genome (hg38) using Bowtie2, as implemented in the pipeline. Peak calling was performed within the pipeline using both MACS2 (for narrow and broad peaks) and SEACR (Sparse Enrichment Analysis for CUT&RUN).
Assembly: hg38
Supplementary files format and content: Bulk RNA-seq: Processed data were provided as gene count tables in plain text (.txt) format, with one file per sample. Each file contains gene-level expression counts across all detected transcripts. CITE-seq: Processed data were generated using 10x Genomics Cell Ranger with Feature Barcoding enabled. Each sample includes three files: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene and antibody-derived tag (ADT) identifiers matrix.mtx.gz: sparse matrix containing both transcriptome and ADT counts scRNA-seq: Processed with 10x Genomics Cell Ranger, resulting in the standard three-file output per sample: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene identifiers matrix.mtx.gz: sparse gene expression matrix Processed data were provided as signal tracks in bigWig (.bw) format. Each bigWig file represents genome-wide signal intensity for an individual sample, suitable for visualization in genome browsers and for quantitative peak analysis. In addition, pooled and normalized bigWig files are included for selected samples of interest, which can be directly used for high-resolution genome browser visualization.
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

source_name: Enriched hCD34+ from umbilical cord blood

growth_protocol: Enriched human cord blood CD34+ cells were cultured in SFEM II medium (StemCell Technologies, #09605) supplemented with Penicillin-Streptomycin (50 U/mL), human SCF (100 ng/mL), human TPO (100 ng/mL), and human FLT3L (100 ng/mL). Media were refreshed every other day.

extract_protocol:
All cell sorting was performed using a BD Aria Ilu SORP cell sorter. For scRNA-seq, 10,000 sorted CD34⁺ cells were used to prepare gene expression (GEX) libraries according to the 10x Genomics Chromium Single Cell 3′ Reagent Kits v3 User Guide. For CITE-seq, 10,000 sorted CD34⁺ cells were processed to generate GEX libraries using the 10x Chromium Single Cell 3' Reagent Kits User Guide, v3.1 Chemistry Dual Index, with Feature Barcoding Technology for Cell Surface Protein, User Guide CG000317. For RNA sequencing, approximately 5,000 CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻GFP⁺ cells were sorted, followed by RNA isolation using the NucleoSpin RNA XS kit (Macherey-Nagel #740902.250) and library preparation with the SMARTer Ultra Low RNA Kit (Clontech), according to the manufacturer's instructions. For CUT&Tag, 10,000–20,000 CD34⁺CD90⁺EPCR⁺CD49f⁻CD71⁻GFP⁺ cells or enriched human cord blood CD34⁺ cells were sorted and processed following the Bench-top CUT&Tag v3 protocol from Dr. Steven Henikoff's lab (DOI: dx.doi.org/10.17504/protocols.io.bcuhiwt6). For CUT&RUN, libraries were prepared using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher #14-1048) and the CUTANA™ CUT&RUN Library Prep Kit (Epicypher #14-1001).
scRNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3′ GEM Library and Gel Bead Kit v3 (PN-1000075), following the manufacturer's user guide. CITE-seq libraries were constructed using the 10x Genomics Chromium Single Cell 3′ Reagent Kits v3.1 (Dual Index Chemistry) along with Feature Barcoding Technology for Cell Surface Protein, according to the Feature Barcoding User Guide (CG000317). Bulk RNA-seq libraries were generated using the SMARTer Ultra Low RNA Kit (Clontech), following the manufacturer's instructions. CUT&Tag libraries were prepared using the Bench-top CUT&Tag v3 protocol from Dr. Steven Henikoff’s laboratory (DOI: 10.17504/protocols.io.bcuhiwt6). CUT&RUN libraries were prepared using the CUTANA™ ChIC/CUT&RUN Kit (Epicypher, #14-1048) and the CUTANA™ CUT&RUN Library Prep Kit (Epicypher, #14-1001), according to the manufacturer’s protocols.

treatment_protocol: We used an optimized microRNA lentiviral backbone to carry our shRNAs, as recommended by Fellmann et al. (2013). Lentiviral particles were produced by co-transfecting 293T cells with the packaging plasmids pMD.G, psPAX2, and pSFFV-eGFP-miR-E, in which the miR-E cassette was engineered to target Renilla, JARID2, EZH2, or STAT1. All plasmids were mixed at a 1:1:1 molar ratio. Enriched human cord blood CD34+ cells were transduced with constitutive lentiviral vectors carrying shRNAs, using LentiBOOST (1:100, SIRION Biotech, Cat No. SB-P-LV-101-12) and protamine sulfate (1:1000) to enhance transduction efficiency, as described by Schott et al. (2019).

tag: cell type

value: Umbilical cord blood CD34+

value: WT


title: Umbilical cord blood CD34+, IgG, WT, C&T, CB_1

description: Library name: C_T_IgG_CB_1

data_processing:
For RNA-seq, fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04. Surrogate Variable Analysis (SVA) was additionally applied to account for latent sources of variation.
For CITE-seq, raw sequencing data (FASTQ files) were processed using Cell Ranger (10x Genomics). The cellranger count pipeline was run with Feature Barcode support enabled to quantify both gene expression and cell surface protein tags (antibody-derived tags, ADTs). After processing individual samples, outputs were merged using the cellranger aggr function to generate a combined gene-barcode matrix for downstream analysis. The merged dataset was analyzed using the Seurat (v4) R package. Cells with a mitochondrial gene content greater than 5% were excluded to remove potentially stressed or dying cells. The expression data were normalized and scaled, followed by Principal Component Analysis (PCA). Both transcriptomic (RNA) and surface protein (ADT) data were respectively used for dimensionality reduction and clustering, including PCA and Uniform Manifold Approximation and Projection (UMAP) for visualization. TotalSeq B antibody (BioLegend) targets: CD201 (Cat. ID 351911, Clone RCR-401), barcode: GTTTCCTTGACCAAG, CD90 (Cat. ID 328147, Clone 5E10), barcode: GCATTGTACGATTCA, CD133 (Cat. ID 394017, Clone S16016B), barcode: GTAAGACGCCTATGC, CD34 (Cat. ID 343539, Clone 581), barcode: GCAGAAATCTCCCTT, CD45RA (Cat. ID 304161, Clone HI100), barcode: TCAATCCTTCCGCTT, CD38 (Cat. ID 356639, Clone HB-7), barcode: CCTATTCCGATTCCG, CD49f (Cat. ID 313639, Clone GoH3), barcode: TTCCGAGGATGATCT, CD135 (Cat. ID 313321, Clone BV10A4H2), barcode: CAGTAGATGGAGCAT, CD370 (Cat. ID 353811, Clone 8F9), barcode: CTGCATTTCAGTAAG, CD71 (Cat. ID 334127, Clone CY1G4), barcode: CCGTGTTCCTCATTA, CD41 (Cat. ID 303747, Clone HIP8), barcode: ACGTTGTGGCCTTGT, CD115 (Cat. ID 347327, Clone 9-4D2-1E4), barcode: AATCACGGTCCTTGT, CD15 (Cat. ID 323051, Clone W6D3), barcode: TCACCAGTACCTAGT
For scRNA-seq, Single-cell RNA-seq data were demultiplexed and aligned to the Genome Reference Consortium Human Genome, GRCh38. The aligned data were annotated and UMI-collapsed using Cell Ranger (v3.1.0, 10x Genomics). Cells with more than 10% mitochondrial gene expression or with the top 5% of unique feature counts were excluded from the analysis. Principal component analysis (PCA) was performed to reduce dimensionality using Seurat 4.0. Clusters were identified through dimensionality reduction techniques, including tSNE and UMAP, using the same package.
CUT&Run and CUT&Tag sequencing data were processed using the CUT&RUNTools 2.0 pipeline, which supports both assay types and provides integrated steps for alignment, peak calling, and quality control. Sequencing reads were aligned to the human genome (hg38) using Bowtie2, as implemented in the pipeline. Peak calling was performed within the pipeline using both MACS2 (for narrow and broad peaks) and SEACR (Sparse Enrichment Analysis for CUT&RUN).
Assembly: hg38
Supplementary files format and content: Bulk RNA-seq: Processed data were provided as gene count tables in plain text (.txt) format, with one file per sample. Each file contains gene-level expression counts across all detected transcripts. CITE-seq: Processed data were generated using 10x Genomics Cell Ranger with Feature Barcoding enabled. Each sample includes three files: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene and antibody-derived tag (ADT) identifiers matrix.mtx.gz: sparse matrix containing both transcriptome and ADT counts scRNA-seq: Processed with 10x Genomics Cell Ranger, resulting in the standard three-file output per sample: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene identifiers matrix.mtx.gz: sparse gene expression matrix Processed data were provided as signal tracks in bigWig (.bw) format. Each bigWig file represents genome-wide signal intensity for an individual sample, suitable for visualization in genome browsers and for quantitative peak analysis. In addition, pooled and normalized bigWig files are included for selected samples of interest, which can be directly used for high-resolution genome browser visualization.
Library strategy: CUT&Tag


title: lung, SCC_1

country: China

description:
Library name: sample9
10x Genomics

library_source: transcriptomic single cell

tag: time

tag: Stage


title: Umbilical cord blood CD34+, IgG, WT, C&R, CB_1

description: Library name: C_R_IgG_CB_1


title: J3519_m

description: Library name: J3519_m


title: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shREN, Day8, rep2

description: Library name: RNA-seq_shREN_CB2

data_processing:
For RNA-seq, fragments were sequenced on an Illumina NovaSeq X Plus using paired end reads extending 150 bases. Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04. Surrogate Variable Analysis (SVA) was additionally applied to account for latent sources of variation.
For CITE-seq, raw sequencing data (FASTQ files) were processed using Cell Ranger (10x Genomics). The cellranger count pipeline was run with Feature Barcode support enabled to quantify both gene expression and cell surface protein tags (antibody-derived tags, ADTs). After processing individual samples, outputs were merged using the cellranger aggr function to generate a combined gene-barcode matrix for downstream analysis. The merged dataset was analyzed using the Seurat (v4) R package. Cells with a mitochondrial gene content greater than 5% were excluded to remove potentially stressed or dying cells. The expression data were normalized and scaled, followed by Principal Component Analysis (PCA). Both transcriptomic (RNA) and surface protein (ADT) data were respectively used for dimensionality reduction and clustering, including PCA and Uniform Manifold Approximation and Projection (UMAP) for visualization. TotalSeq B antibody (BioLegend) targets: CD201 (Cat. ID 351911, Clone RCR-401), barcode: GTTTCCTTGACCAAG, CD90 (Cat. ID 328147, Clone 5E10), barcode: GCATTGTACGATTCA, CD133 (Cat. ID 394017, Clone S16016B), barcode: GTAAGACGCCTATGC, CD34 (Cat. ID 343539, Clone 581), barcode: GCAGAAATCTCCCTT, CD45RA (Cat. ID 304161, Clone HI100), barcode: TCAATCCTTCCGCTT, CD38 (Cat. ID 356639, Clone HB-7), barcode: CCTATTCCGATTCCG, CD49f (Cat. ID 313639, Clone GoH3), barcode: TTCCGAGGATGATCT, CD135 (Cat. ID 313321, Clone BV10A4H2), barcode: CAGTAGATGGAGCAT, CD370 (Cat. ID 353811, Clone 8F9), barcode: CTGCATTTCAGTAAG, CD71 (Cat. ID 334127, Clone CY1G4), barcode: CCGTGTTCCTCATTA, CD41 (Cat. ID 303747, Clone HIP8), barcode: ACGTTGTGGCCTTGT, CD115 (Cat. ID 347327, Clone 9-4D2-1E4), barcode: AATCACGGTCCTTGT, CD15 (Cat. ID 323051, Clone W6D3), barcode: TCACCAGTACCTAGT
For scRNA-seq, Single-cell RNA-seq data were demultiplexed and aligned to the Genome Reference Consortium Human Genome, GRCh38. The aligned data were annotated and UMI-collapsed using Cell Ranger (v3.1.0, 10x Genomics). Cells with more than 10% mitochondrial gene expression or with the top 5% of unique feature counts were excluded from the analysis. Principal component analysis (PCA) was performed to reduce dimensionality using Seurat 4.0. Clusters were identified through dimensionality reduction techniques, including tSNE and UMAP, using the same package.
CUT&Run and CUT&Tag sequencing data were processed using the CUT&RUNTools 2.0 pipeline, which supports both assay types and provides integrated steps for alignment, peak calling, and quality control. Sequencing reads were aligned to the human genome (hg38) using Bowtie2, as implemented in the pipeline. Peak calling was performed within the pipeline using both MACS2 (for narrow and broad peaks) and SEACR (Sparse Enrichment Analysis for CUT&RUN).
Assembly: hg38
Supplementary files format and content: Bulk RNA-seq: Processed data were provided as gene count tables in plain text (.txt) format, with one file per sample. Each file contains gene-level expression counts across all detected transcripts. CITE-seq: Processed data were generated using 10x Genomics Cell Ranger with Feature Barcoding enabled. Each sample includes three files: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene and antibody-derived tag (ADT) identifiers matrix.mtx.gz: sparse matrix containing both transcriptome and ADT counts scRNA-seq: Processed with 10x Genomics Cell Ranger, resulting in the standard three-file output per sample: barcodes.tsv.gz: cell barcodes features.tsv.gz: gene identifiers matrix.mtx.gz: sparse gene expression matrix Processed data were provided as signal tracks in bigWig (.bw) format. Each bigWig file represents genome-wide signal intensity for an individual sample, suitable for visualization in genome browsers and for quantitative peak analysis. In addition, pooled and normalized bigWig files are included for selected samples of interest, which can be directly used for high-resolution genome browser visualization.

source_name: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shREN, Day8 ex vivo culture

value: Lentivirus


title: lung, CIS_2

description:
Library name: sample8
10x Genomics

value: Day 28

value: Carcinoma in situ, CIS


title: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shREN, Day8, rep1

description: Library name: RNA-seq_shREN_CB1


title: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shREN, Day8, rep3

description: Library name: RNA-seq_shREN_CB3


title: lung, CIS_1

description:
Library name: sample7
10x Genomics


title: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shJARID2, Day8, rep2

description: Library name: RNA-seq_shJARID2_CB2

source_name: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shJARID2, Day8 ex vivo culture


title: lung, Dysplasia_1

description:
Library name: sample5
10x Genomics

value: Day 21

value: Dysplasia


title: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shEZH2, Day8, rep2

description: Library name: RNA-seq_shEZH2_CB2

source_name: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shEZH2, Day8 ex vivo culture


title: J3558_m

description: Library name: J3558_m

value: Control


title: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shJARID2, Day8, rep3

description: Library name: RNA-seq_shJARID2_CB3


title: J3512_m

description: Library name: J3512_m


title: J3508_m

description: Library name: J3508_m


title: J3557_m

description: Library name: J3557_m


title: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shEZH2, Day8, rep3

description: Library name: RNA-seq_shEZH2_CB3


title: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shEZH2, Day8, rep1

description: Library name: RNA-seq_shEZH2_CB1


title: lung, Metaplasia

description:
Library name: sample4
10x Genomics

value: Day 14

value: Metaplasia


title: lung, Dysplasia_2

description:
Library name: sample6
10x Genomics

value: lung


title: WT, Replicate 3, 6 Hours

city: Gainesville

first: Alejandro

last: Riveros Walker

state: Fl

address: 1395 Center Drive

department: Oral Biology

institute: University of Florida

description: Library name: WT36H

data_processing:
Quality control (FASTQC)
Quality based trimming (Cutadapt)
Mapping (bwa-mem) - mapping files handling (Samtools & Bedtools)
Gene counts (htseq-counts)
Assembly: Reference genomes: Homo sapiens assembly name GRCh38.p14 (Accession GCA_000001405.29) - Porphyromonas gingivalis strain ATCC_33277 (Genome assembly ASM1050v1 - NCBI RefSeq assembly GCF_000010505.1)
Supplementary files format and content: Text files

organism: Porphyromonas gingivalis

growth_protocol: Porphyromonas gingivalis ATCC 33277 wild type (WT) frozen stocks were streaked onto Blood Trypticase soy agar plates supplemented with 5µg/ml hemin and 1µg/ml menadione (BAPHK) and incubated anaerobically at 37°C for 5 days. Plate-grown P. gingivalis were collected and used to seed trypticase soy broths supplemented with 5µg/ml hemin and 1µg/ml menadione (TSBHK) and were incubated overnight anaerobically, centrifuged, and used in experiments as described below. For the growth and culture of the ∆cas7 mutant, BAPHK plates and TSBHK broths were supplemented with 10 µg/ml erythromycin. Human monocyte/macrophage cell line THP-1 (ATCC, Virginia, USA) were cultured at 37°C in a 5% CO2 incubator in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum, l-glutamine (2 mM), penicillin/streptomycin (100 U/100 μg/ml), HEPES (10 mM), sodium pyruvate (1 mM), glucose (4.5 mg/ml), sodium bicarbonate (1.5 mg/ml), and 2-mercaptoethanol (0.05 mM). For P. gingivalis infection assays, THP-1 cells were adjusted to 5 × 105 cells/ml and were treated with 100 ng/ml phorbol 12-myristate-13-acetate (PMA; Sigma-Aldrich, Missouri, USA) to induce differentiation into a macrophage-like state. These cells were added to each well of 24-well cell culture plates and allowed to differentiate into a macrophage-like state for 48 h.

extract_protocol:
Total RNA was extracted from THP-1 cells co-cultured with either P. gingivalis WT, ∆cas7 for 2h or 6h using a mirVana RNA isolation kit (Life Technologies, New York, USA). Briefly, after removing the media from the wells, cells were incubated with 1 mL of RNAlater (Thermofisher, Pittsburgh, USA) for 5 min. Followed by the addition of mirVana lysis buffer, cells were harvested from the bottom of the wells using a cell scraper and transferred to tubes for cell lysis by bead-beating for 20 seconds three times at maximum speed with diethyl pyrocarbonate (DEPC)-treated zirconia-silica beads (BioSpec Products, Oklahoma, USA). The extraction of RNA from the lysates was conducted as instructed by the manufacturer, following DNAse treatment with Invitrogen DNAse (RNAse free).
Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI)

tag: cell line

value: Wild type


title: J3578_m

description: Library name: J3578_m


title: WT, Replicate 2, 6 Hours

description: Library name: WT26H


title: WT, Replicate 1, 6 Hours

description: Library name: WT16H


title: lung, Normal_2

description:
Library name: sample2
10x Genomics

value: female

value: Day 0

value: Normal


title: WT, Replicate 3, 2 Hours

description: Library name: WT32H


title: WT, Replicate 2, 2 Hours

description: Library name: WT22H


title: J3577_m

description: Library name: J3577_m

value: Muscle

value: KLOTHO HET


title: J3576_m

description: Library name: J3576_m


title: WT, Replicate 1, 2 Hours

description: Library name: WT12H


title: lung, Normal_1

description:
Library name: sample1
10x Genomics


title: Sorted GFP+CD34+CD90+EPCR+CD49f-CD71-, shJARID2, Day8, rep1

description: Library name: RNA-seq_shJARID2_CB1


title: Cas 7, Replicate 3, 6 Hours

description: Library name: C736H


title: Cas 7, Replicate 2, 6 Hours

description: Library name: C726H


title: Cas 7, Replicate 1, 6 Hours

description: Library name: C716H


title: hzl-1 CLIP endo daf2 S1

city: Montreal

first: Sabih

last: Rashid

state: Quebec

address: 3611 Rue Sainte Famille, Unit 11

department: Biology

country: Canada

institute: McGill University

description:
Library name: Sample 9
endo_daf2_S1
endo_clip.tsv

data_processing:
Reference genome assembly and DESeq2. Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic version 0.35 and aligned to the reference C. elegans genome version WBcel235 (gene annotation from Ensembl version 104) using STAR version 2.7.1a. Gene expressions were obtained both as readcount directly from STAR as well as computed using RSEM in order to obtain gene and transcript level expression, either in TPM or FPKM values, for these stranded RNA libraries. DESeq2 version 1.30.1 was then used to normalize gene readcounts. Sample clustering based on normalized log readcounts produces the following hierarchy of samples
Assembly: WBcel235 (gene annotation from Ensembl version 104)
Supplementary files format and content: "clip_FC.tsv" contains read counts, fold change comparisons between aak and d2 samples in "clip_fpkmFC.tsv", endogenous clip data in "endo_clip.tsv"

organism: Caenorhabditis elegans

source_name: IP from whole animal

growth_protocol: Bleach-synchronized worms were put onto large NGM plates and grown at 25 °C. Dauer animals were collected after 96 hours (i.e. Day 2 in dauer) and washed with M9. Animals were fixed with formaldehyde and frozen until use.

extract_protocol:
Frozen worm samples were lysed via sonication and then immunoprecipitation using anit-GFP antibodies was carried out overnight. Subsequently, samples were subjected to standard Trizol RNA extraction directly with the beads. Sample concentration was measured using Nanodrop, and run on agarose gels to verify integrity of RNA. RNA was stored at -80 °C for up to 3 days before being sent for sequencing. Minimum of 100 ng/ul RNA was sent for sequencing.
mRNA-Seq with PolyA selection, 150 cycles Paired-End (maximum 2x80nt), 400M fragments, using KAPA mRNA Hyper Prep Hyperprep library per manufacturer instructions

treatment_protocol: IP then Trizol RNA extraction

value: whole animal

value: Hermaphrodite

value: daf-2; hzl-1; Ex(hzl-1p::hzl-1::GFP)

value: 96 hrs


title: J3549_m

description: Library name: J3549_m


title: J3528_m

description: Library name: J3528_m


title: hzl-1 CLIP GFP S1

description:
Library name: Sample 7
gfp_S1
clip_fkpm.tsv

value: daf-2; aak(0); Ex(nhx-2p::GFP)


title: hzl-1 CLIP endo aak S1

description:
Library name: Sample 8
endo_aak_S1
endo_clip.tsv

value: daf-2; aak(0); hzl-1; Ex(hzl-1p::hzl-1::GFP)


title: J3515_m

description: Library name: J3515_m


title: Cas 7, Replicate 1, 2 Hours

description: Library name: C712H


title: cow, Iso-seq, 4 cell embryo

city: Ithaca

first: Guangsheng

last: Li

state: NY

address: 507 Tower Rd.

department: Animal Science

institute: Cornell

description:
Library name: m84094_240524_151035
m84094_240524_151035

data_processing:
The adaptor removal and QC of the raw sequencing reads were performed using fastp (v 0.20.0) . Reads with a percentage of low-quality base (quality score <20) >40% were removed. Reads with length < 30 bp or with high N content (>5%) were also removed in this study. The cow reference genome (ARS-UCD 2.0) was downloaded from NCBI database, and clean reads were aligned to the reference genome using STAR (v 2.7.10b)  allowing no more than 3 mismatches. The raw read counts for each gene were extracted using featureCounts. Iso-seq long-read data was processed following the official protocol.
Assembly: ARS-UCD 2.0
Supplementary files format and content: tab-delimited text files include raw read count for each Sample

molecule: polyA RNA

organism: Bos taurus

source_name: 4 cell embryo

extract_protocol:
For RNA-seq samples, there was no separate extration step. For Iso-seq sample, RNA was extracted using PicoPure™ RNA isolation kit (KIT0204, Applied Biosytems™) with Dnase treatment (RNase-Free DNase Set, Qiagen).
For RNA-seq, libraries were constructed using SMART-Seq® HT PLUS Kit (R400748, Taraka), and 15 PCR cycle were applied  for cDNA synthesis and 13 PCR cycles for library amplification. For Iso-seq, ISO-Seq® express 2.0 kit for cDNA synthesis, SMRTbell® prep kit 3.0 for library preparation.

value: 4 cell embryo

value: Mixed sex


title: Cas 7, Replicate 2, 2 Hours

description: Library name: C722H


title: J3526_m

description: Library name: J3526_m

value: Control


title: J3523_m

description: Library name: J3523_m


title: hzl-1 CLIP daf2 S3

description:
Library name: Sample 6
daf2_S3
clip_fkpm.tsv

value: daf-2; hzl-1; Ex(nhx-2p::hzl-1::GFP)


title: lung, Hyperplasia

description:
Library name: sample3
10x Genomics

value: lung

value: Day 7

value: Hyperplasia


title: hzl-1 CLIP daf2 S2

description:
Library name: Sample 5
daf2_S2
clip_fkpm.tsv


title: J3531_s

description: Library name: J3531_s

data_processing:
Noncoding RNA library data were aligned and quality checked by STAR (v 2.5.3a) and analyzed with COMPSRA (v 1.0.3) and DESeq2 (v 1.42.1). Selected gene targets were analyzed using TargetScanMouse 8.0 at cumulative weighted context score cutoff<-0.25. Representative gene visualization was created utilizing STRING interaction network database.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet containing ncRNA overall reads generated from Compsra COMPSRA (v 1.0.3)

source_name: plasma-derived EVs

extract_protocol:
Total RNA was isolated from the 190 µl elution of EV solution with Norgen Biotek’s Exosomal RNA Isolation Kit (CAT# 58000), following manufacturer’s instructions. Quality and concentration were monitored by the RNA Pico 600 Assay Kit for the Agilent 2100 Bioanalyzer System (5067-1513).
Small non-coding libraries were produced by New England BioLabs’ NEBNext Multiplex Small RNA Library Prep Set (E7300S and E7580S). Library quality was assessed on samples by the High Sensitivity DNA Assay Kit for the Agilent 2100 Bioanalyzer System (5067-4626). Samples were sequenced by the UPMC Genome Center, Pittsburgh PA, on the NextSeq 2000 machine generating single-end reads. Data was received in .fastq.gz formatting.

value: plasma-derived EVs

value: NMES


title: J3527_s

description: Library name: J3527_s


title: J3514_s

description: Library name: J3514_s


title: mESCs grown with LIF and without LIF

city: Vilnius

first: Denis

last: Baronas

address: Saulėtekio al. 7

country: Lithuania

institute: Vilnius University

description:
Library name: mesc
CapSeq of mESCs grown with LIF or without LIF for 6 days

data_processing:
The STARsolo wrapper pipeline (https://github.com/jsimonas/solo-in-drops) was used to process the sequencing data and to obtain cell ⨉ gene count matrices. Shortly, barcode ligation linker sequences were removed from the read1 the and read1 was reassembled to have a structure of BC3[8nt]BC2[10nt]BC1[8nt] UMI[8nt]. Next, STAR(https://doi.org/10.1101/2021.05.05.442755) (version 2.7.10a) was run with the following parameters: --soloUMIdedup Exact, --soloFeatures GeneFull, --soloType CB_UMI_Complex, --soloCBposition 0_0_0_7 0_8_0_17 0_18_0_25, --soloUMIposition 0_26_0_33, --soloCBmatchWLtype EditDist_2. The reads were aligned to the mouse GRCm39 genome (GENCODE M30).
Assembly: GRCm39
Supplementary files format and content: Matrix files of gene expression raw count data in _matrix.mtx
Supplementary files format and content: Tab separated files of barcodes in _barcodes.tsv
Supplementary files format and content: Tab separated files of genes in _features.tsv
Supplementary files format and content: AnnData files in _adata.h5ad
Supplementary files format and content: Excel files of metadata containing barcode information linked to patient code or condition in _metadata.xlsx

source_name: mESC

extract_protocol:
Mouse embryonic stem (E14TG2a cell line) was obtained from the American Type Culture Collection of Authenticated Cell Cultures (ATCC, CRL-1821). Cells were cultivated on 0.15% gelatin-coated dishes in DMEM containing 15% FBS, 1× PS, 0.1 mM sodium pyruvate (Gibco), 0.1 mM β-mercaptoethanol (Gibco), 1 mM L-alanyl-L-glutamine (Gibco), 1× NEAA (Gibco), 3 μM CHIR99021 (Sigma), 1 μM PD0325901 (Sigma) and with 1×103 U/ml mouse leukemia inhibitory factor (mLIF; Millipore) or without mLIF. The cells were centrifuged for 7 min at 200g using a swinging-bucket rotor. Next, the media was removed, and the cell pellet was resuspended in 1 mL of 1X DPBS and transferred to a new 1.5 mL tube. The resuspended cells were then subjected to centrifugation for 7 min at 200g. Subsequently, the supernatant was discarded, and the cells were subjected to an identical wash procedure using 1 mL 1X DPBS. A 10 µL aliquot of the cell suspension was utilized to determine the cell concentration using a hemocytometer. Following removal of the supernatant, the cell pellet was resuspended to achieve a final volume corresponding to 4 million cells per milliliter.
Illumina sequencing libraries were prepared for each amplified cDNA aliquot with NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (NEB, cat. no. E7805S) according to the instructions in the manual, with minor changes. In particular, 5-10 ng of amplified cDNA was used for cDNA fragmentation and transferred to a PCR tube. Nuclease-free water was added to reach the final volume on 13 µL. Fragmentation reaction was assembled on ice by adding 3.5 µL of NEBNext® Ultra™ II FS Reaction Buffer followed by 1 µL of NEBNext® Ultra™ II FS Enzyme Mix. Reaction mix was vortexed and spun-down for 3-5 seconds. The fragmentation was performed for 8 minutes at 37 °C, followed by end-repair and dA tailing for 30 min at 65 °C (lid was set at 75 °C). Fragmented cDNA was purified with 0.6X-0.8X double-size selection using SPRIselect beads and eluted in 17.5 µL with nuclease-free water. Then, 1.5 µM ligation adapter was prepared in advance by mixing 1.5 µL of forward ligation primer (100 µM, /5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC; HPLC purification, IDT) and 1.5 µL of reverse ligation primer (/5AmMC6/GCTCTTCCGATCT; HPLC purification, IDT) with 97 µL of water. To anneal oligos, the solution was heated to 95 °C for 2 min (lid at 100 °C) and cooled at room temperature for 5 min. Next, purified fragmented cDNA was mixed with 15 µL of NEBNext® Ultra™ II Ligation Master Mix, 1.25 µL of ligation adapter and 0.5 µL of NEBNext® Ligation Enhancer. Reaction solution was well mixed by pipetting and incubated for 15 min at 20 °C (lid set at 37 °C). The ligation product was diluted to 100 µL with nuclease-free water, followed by a 0.8X SPRI size selection procedure and eluted in 40 µL with nuclease-free water. Finally, the ligation product was amplified by 12-cyles of PCR: 95 ºC for 3 min, 12-cycles [98 ºC for 20 s, 54 ºC for 30 s, 72 ºC for 20 s], and 72 ºC for 60 s. PCR mix was prepared by mixing 20 µL of ligation product, 2.5 µL of forward indexing primer (Table  S25), 2.5 µL of reverse indexing primer (Table S25) and 25 µL of 2X KAPA HiFi HotStart ReadyMix. Amplified sequencing libraries were purified with 0.6X-0.8X double-size selection using SPRIselect beads and eluted in 20 µL with nuclease-free water.

value: mESC


title: J3537_s

description: Library name: J3537_s

value: KLOTHO HET


title: J3510_m

description: Library name: J3510_m

value: Muscle


title: J3519_s

description: Library name: J3519_s


title: hzl-1 CLIP aak S3

description:
Library name: Sample 3
aak_S3
clip_fkpm.tsv

value: whole animal

value: Hermaphrodite

value: daf-2; aak(0); hzl-1; Ex(nhx-2p::hzl-1::GFP)


title: J3512_s

description: Library name: J3512_s


title: J3508_s

description: Library name: J3508_s


title: hzl-1 CLIP aak S2

description:
Library name: Sample 2
aak_S2
clip_fkpm.tsv

value: 96 hrs


title: hzl-1 CLIP aak S1

description:
Library name: Sample 1
aak_S1
clip_fkpm.tsv


title: J3549_s

description: Library name: J3549_s


title: J3528_s

description: Library name: J3528_s


title: A3207_m

description: Library name: A3207_m

value: WT


title: A3205_m

description: Library name: A3205_m


title: J3515_s

description: Library name: J3515_s


title: SCK_R_rep2

city: Chuncheon-si, Gangwon-do

first: Jueun

last: Kim

address: 1 Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

description: Library name: SCK_R_#2

data_processing:
Base calling through an integrated primary analysis software called RTA(Real Time Analysis. v1.18)
The BCL(base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq(v1.8.4)
Adapters are not trimmed away from the reads.
Assembly: Homo Sapians GRCh38
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: DESeq2-normalized counts for each sample

source_name: tumor samples from Korean patients with ICC

growth_protocol: SCK WT and SCK-R cells were maintained in DMEM supplemented with 10% FBS and 1% antibiotics in a 37°C, 5% CO2 incubator

extract_protocol:
Total cellular RNA was purified using TRIzol RNA Isolation Reagent (Qiagen, Germany; 79306) according to the manufacturer’s instructions
A strand-specific sequencing libraries were constructed using KAPA RNA Hyper kit according to the instruction manual.

treatment_protocol: 2 μg/ml cisplatin (cis-Diamineplatinum(II) dichloride, P4394, Sigma-Aldrich) was treated 12hr before harvest

value: SCK-R (Cisplatin-resistant SCK)

value: Human Intrahepatic cholangiocarcinoma (ICC) cells

value: Cisplatin resistant

value: cisplatin


title: J3578_s

description: Library name: J3578_s

value: Control


title: J3523_s

description: Library name: J3523_s


title: SCK_R_rep1

description: Library name: SCK_R_#1

value: tumor samples from Korean patients with ICC


title: J3526_s

description: Library name: J3526_s


title: A3203_m

description: Library name: A3203_m


title: J3517_m

description: Library name: J3517_m


title: J3517_s

description: Library name: J3517_s


title: SCK_WT_rep2

description: Library name: SCK_WT_#2

value: SCK


title: hzl-1 CLIP daf2 S1

description:
Library name: Sample 4
daf2_S1
clip_fkpm.tsv

value: daf-2; hzl-1; Ex(nhx-2p::hzl-1::GFP)


title: A3209_s

description: Library name: A3209_s

value: plasma-derived EVs

value: NMES


title: J3524_s

description: Library name: J3524_s

value: KLOTHO HET


title: J3510_s

description: Library name: J3510_s


title: A3209_m

description: Library name: A3209_m

value: Muscle


title: A3199_m

description: Library name: A3199_m


title: SCK_WT_rep1

description: Library name: SCK_WT_#1


title: Cas 7, Replicate 3, 2 Hours

description: Library name: C732H


title: A3203_s

description: Library name: A3203_s


title: A3207_s

description: Library name: A3207_s


title: A3208_m

description: Library name: A3208_m


title: A3201_s

description: Library name: A3201_s


title: BrM_IgG

city: beijing

first: wang

middle: xi

last: lin

address: 10 You’anmen Outer West 1st Street

institute: capital medical univercity

description: Library name: SAMPLE8

data_processing:
Upload fq.gz data to Galaxy version 23.2 rc1, Using FastQC to evaluate the quality of data, using cutadapt to de concatenate raw data
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

extract_protocol:
1 × 105 MDA-MB-231BrM cells were collected,for the CUT&Tag analysis, we utilized the Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD903, Vazyme)
For the CUT&Tag analysis, we utilized the Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD903, Vazyme). Briefly, 1 × 105 MDA-MB-231BrM cells were collected, resuspended in 100 μL wash buffer, transferred to an 8-tube strip containing activated ConA beads, and incubated for 10 min. Subsequently, 50 μL prechilled antibody buffer containing ADAMTS1 antibodies was added to cells and incubated at 4 °C overnight, followed by the addition of diluted secondary antibodies and incubation for 60 min. After washing thrice with DIG wash buffer, samples were incubated with diluted pA/G-Tnp transposase for 1 h. Next, 50 μL diluted TTBL was added, and samples were incubated at 37 °C in a PCR instrument for 60 min for fragmentation. Subsequently, DNA extraction was performed by adding 5 μL proteinase K, 100 μL buffer L/B, and 20 μL DNA extract beads on the fragmented samples and incubating at 55 °C for 10 min. Following washes with WA and WB buffers, samples were eluted using sterile ultrapure water. The extracted DNA underwent library amplification using the TruePrep Index Kit V2 for Illumina (TD202, Vazyme). PCR products were treated with VAHTS DNA clean beads (N411, Vazyme) for 5 min, the supernatant then was discarded, samples were washed with 80% ethanol, eluted using sterile ultrapure water, and the library was sequenced on the Illumina NovaSeq platform.

value: the MDA-MB-231 cell derivatives prone to brain


title: A3206_m

description: Library name: A3206_m


title: A3199_s

description: Library name: A3199_s


title: A3208_s

description: Library name: A3208_s


title: BrM_ADAMTS1

description: Library name: SAMPLE7


title: A3206_s

description: Library name: A3206_s


title: A3204_m

description: Library name: A3204_m


title: A3201_m

description: Library name: A3201_m


title: A3202_m

description: Library name: A3202_m


title: A3202_s

description: Library name: A3202_s


title: A3204_s

description: Library name: A3204_s


title: Patient 0031, 2 Years

city: Aurora

first: Austin

middle: E

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description: Library name: patient_0031_2Y

data_processing:
The raw sequencing reads were first trimmed with cutadapt (v2.1.0) to remove adapter sequences, short sequences, and low quality bases (-m20, -q10).
Trimmed reads were quantitated using Salmon (1.4.0) with a gencode v36 reference and -numBootstraps 50.
These Salmon assignments were imported into R and summarized by gene using tximport (v1.30.0).
Assembly: GRCh38
Supplementary files format and content: tsv file with gene-level counts from salmon/tximport

source_name: Nasal brush biopsy

extract_protocol:
Nasal brush biopsies were obtained serially from the same participant at baseline and at approximately 6 months and 2 years after initiating ETI therapy. Brushes from the right nostril were collected in Qiagen RLT Plus lysis buffer supplement with 40 mM DTT and stored at -80C. Total RNA and DNA were isolated simultaneously using the Qiagen AllPrep DNA/RNA Mini Kit (Qiagen).
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: Nasal brush biopsy

tag: individual

value: Patient 0031

tag: treatment timepoint

value: 2 Years


title: Patient 0031, Baseline

description: Library name: patient_0031_BL

value: Baseline


title: A3200_s

description: Library name: A3200_s

value: WT


title: A3205_s

description: Library name: A3205_s


title: A3200_m

description: Library name: A3200_m


title: Day12 EarlyfliTreg 2

city: Chicago

first: Qianli

last: Liu

state: IL

address: 303 E. Superior St. Simpson Querrey

institute: Northwestern Univesity

description:
Library name: Sample 11
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl-convert v3.10.5.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Assembly: GRCm38/mm10 or hg38
Supplementary files format and content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

source_name: iTreg cells (Foxp3-GFP+tdTomato+)

extract_protocol:
Genomic DNA was extracted from flow cytometry-sorted cells using the AllPrep DNA/RNA Micro Kit.
Genomic DNA was quantified with a Qubit 3.0 instrument. Genomic DNA was then digested with the restriction endonuclease MspI (New England BioLabs). Resulting fragments underwent size selection for fragments ~100-250-bp in length using SPRI beads (MagBio Genomics) and subsequent bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol.  Libraries for Illumina-based sequencing were prepared with the Pico Methyl-Seq Library Prep Kit (Zymo Research). Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and six pooled libraries per run were sequenced on an Illumina NextSeq 500 instrument using the NextSeq 500/550 V2 High Output reagent kit (1 x 75 cycles).

value: iTreg cells (Foxp3-GFP+tdTomato+)


title: Patient 0031, 6 Months

description: Library name: patient_0031_6M

value: 6 Months


title: A3198_s

description: Library name: A3198_s


title: Day12 EarlyfliTreg 3

description:
Library name: Sample 12
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Day12 EarlyfliTreg 1

description:
Library name: Sample 10
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Patient 0030, Baseline

description: Library name: patient_0030_BL

value: Patient 0030


title: Day12 DelfliTreg 2

description:
Library name: Sample 8
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: A3198_m

description: Library name: A3198_m

value: Control


title: J3568_b

description: Library name: J3568_b

source_name: Brain

value: Brain


title: Patient 0030, 6 Months

description: Library name: patient_0030_6M


title: Day12 DelfliTreg 1

description:
Library name: Sample 7
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: Day12 Early pos pos iTreg 3

description:
Library name: Sample 6
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Patient 0030, 2 Years

description: Library name: patient_0030_2Y


title: Day12 DelfliTreg 3

description:
Library name: Sample 9
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: J3562_b

description: Library name: J3562_b


title: Day12 Early pos pos iTreg 2

description:
Library name: Sample 5
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Day12 Early pos pos iTreg 1

description:
Library name: Sample 4
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Patient 0029, Baseline

description: Library name: patient_0029_BL

value: Patient 0029


title: Day12 Del pos pos iTreg 2

description:
Library name: Sample 2
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: Patient 0029, 6 Months

description: Library name: patient_0029_6M


title: J3531_b

description: Library name: J3531_b


title: Day12 Del pos pos iTreg 1

description:
Library name: Sample 1
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: Patient 0027, Baseline

description: Library name: patient_0027_BL

value: Patient 0027


title: Day12_EarlyfliTreg_4

description:
Library name: Sample 56
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12

data_processing:
Basecalls performed using Illumina RTA2 software.
bcl-convert/3.10.5 was used to convert bcl files to fastq files (default parameters).
Fastq files were aligned to the mm10 reference genome using Tophat v.2.1.0, and SeqMonk v1.45.4 was used to generate gene and transcript expression levels for protein-coding genes.
Assembly: GRCm38/mm10
Supplementary files format and content: csv files including raw counts values for each sample was generated for uniquely mapped reads over exons was obtained using SeqMonk v1.45.4.

extract_protocol:
RNA was extracted from FACSorted cells using the AllPrep DNA/RNA Micro Kit.
Next Ultra II RNA Kits (NEB)


title: Day12_EarlyfliTreg_6

description:
Library name: Sample 58
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Day12_EarlyfliTreg_3

description:
Library name: Sample 55
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Patient 0027, 6 Months

description: Library name: patient_0027_6M


title: J3527_b

description: Library name: J3527_b


title: J3537_b

description: Library name: J3537_b


title: J3514_b

description: Library name: J3514_b


title: Day12_EarlyfliTreg_1

description:
Library name: Sample 53
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Patient 0026, Baseline

description: Library name: patient_0026_BL

value: Patient 0026


title: Day5_EarlyfliTreg_6

description:
Library name: Sample 52
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Day12_EarlyfliTreg_5

description:
Library name: Sample 57
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: J3570_b

description: Library name: J3570_b

value: NMES


title: J3524_b

description: Library name: J3524_b

value: KLOTHO HET


title: Day5_EarlyfliTreg_4

description:
Library name: Sample 50
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Day12_EarlyfliTreg_2

description:
Library name: Sample 54
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Day5_EarlyfliTreg_3

description:
Library name: Sample 49
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Patient 0025, 6 Months

description: Library name: patient_0025_6M

value: Patient 0025


title: J3554_b

description: Library name: J3554_b


title: Day12 Del pos pos iTreg 3

description:
Library name: Sample 3
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: J3519_b

description: Library name: J3519_b


title: J3512_b

description: Library name: J3512_b


title: Patient 0028, Baseline

description: Library name: patient_0028_BL

value: Patient 0028


title: Day5_EarlyfliTreg_1

description:
Library name: Sample 47
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Patient 0025, 2 Years

description: Library name: patient_0025_2Y

value: Nasal brush biopsy


title: Day12_DelfliTreg_3

description:
Library name: Sample 46
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: J3508_b

description: Library name: J3508_b


title: Patient 0024, Baseline

description: Library name: patient_0024_BL

value: Patient 0024


title: Day5_DelfliTreg_2

description:
Library name: Sample 43
Uhrf1fl/fl iTreg cells sorted from culture on day 5


title: Day12_DelfliTreg_2

description:
Library name: Sample 45
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: Day5_DelfliTreg_1

description:
Library name: Sample 42
Uhrf1fl/fl iTreg cells sorted from culture on day 5


title: J3558_b

description: Library name: J3558_b


title: Day5_EarlyfliTreg_5

description:
Library name: Sample 51
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Patient 0024, 6 Months

description: Library name: patient_0024_6M


title: J3557_b

description: Library name: J3557_b


title: Patient 0025, Baseline

description: Library name: patient_0025_BL


title: Patient 0024, 2 Years

description: Library name: patient_0024_2Y

value: 2 Years


title: Day5_DelfliTreg_3

description:
Library name: Sample 44
Uhrf1fl/fl iTreg cells sorted from culture on day 5


title: Day12_Early_pos_pos_iTreg_4

description:
Library name: Sample 39
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Day5_EarlyfliTreg_2

description:
Library name: Sample 48
Uhrf1fl/fl iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Patient 0023, Baseline

description: Library name: patient_0023_BL

value: Patient 0023

value: Baseline


title: Day12_Early_pos_pos_iTreg_5

description:
Library name: Sample 40
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12

value: iTreg cells (Foxp3-GFP+tdTomato+)


title: Day12_Early_pos_pos_iTreg_2

description:
Library name: Sample 37
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Day12_Early_pos_pos_iTreg_6

description:
Library name: Sample 41
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Patient 0023, 6 Months

description: Library name: patient_0023_6M

value: 6 Months


title: Day5_Early_pos_pos_iTreg_6

description:
Library name: Sample 35
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: J3578_b

description: Library name: J3578_b


title: Patient 0023, 2 Years

description: Library name: patient_0023_2Y


title: J3576_b

description: Library name: J3576_b


title: J3577_b

description: Library name: J3577_b


title: Day12_Early_pos_pos_iTreg_1

description:
Library name: Sample 36
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Day12_Early_pos_pos_iTreg_3

description:
Library name: Sample 38
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Day5_Early_pos_pos_iTreg_5

description:
Library name: Sample 34
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: J3549_b

description: Library name: J3549_b


title: Day5_Early_pos_pos_iTreg_4

description:
Library name: Sample 33
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Patient 0022, Baseline

description: Library name: patient_0022_BL

value: Patient 0022


title: Day5_Early_pos_pos_iTreg_3

description:
Library name: Sample 32
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: J3528_b

description: Library name: J3528_b

value: Control


title: Day5_Early_pos_pos_iTreg_2

description:
Library name: Sample 31
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Day5_Early_pos_pos_iTreg_1

description:
Library name: Sample 30
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Patient 0022, 6 Months

description: Library name: patient_0022_6M


title: J3515_b

description: Library name: J3515_b

value: Brain


title: Day12_Del_pos_pos_iTreg_3

description:
Library name: Sample 29
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: Patient 0022, 2 Years

description: Library name: patient_0022_2Y


title: J3523_b

description: Library name: J3523_b


title: Day5_Del_pos_pos_iTreg_1

description:
Library name: Sample 24
Uhrf1+/+ iTreg cells sorted from culture on day 5


title: Patient 0021, Baseline

description: Library name: patient_0021_BL

value: Patient 0021


title: Day12_Del_pos_pos_iTreg_1

description:
Library name: Sample 27
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: J3517_b

description: Library name: J3517_b


title: Patient 0021, 6 Months

description: Library name: patient_0021_6M


title: Day5_Del_pos_pos_iTreg_2

description:
Library name: Sample 25
Uhrf1+/+ iTreg cells sorted from culture on day 5


title: J3526_b

description: Library name: J3526_b


title: Day12_EarlyflnTreg_3

description:
Library name: Sample 23
Uhrf1fl/fl nTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12

source_name: nTreg cells (Foxp3-GFP+tdTomato+)

value: nTreg cells (Foxp3-GFP+tdTomato+)


title: Day12_Del_pos_pos_iTreg_2

description:
Library name: Sample 28
Uhrf1+/+ iTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: Day5_Del_pos_pos_iTreg_3

description:
Library name: Sample 26
Uhrf1+/+ iTreg cells sorted from culture on day 5


title: A3209_b

description: Library name: A3209_b

value: WT


title: J3510_b

description: Library name: J3510_b


title: Patient 0019, 6 Months

description: Library name: patient_0019_6M

value: Patient 0019


title: Day12_EarlyflnTreg_2

description:
Library name: Sample 22
Uhrf1fl/fl nTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Day5_EarlyflnTreg_2

description:
Library name: Sample 19
Uhrf1fl/fl nTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Day12_EarlyflnTreg_1

description:
Library name: Sample 21
Uhrf1fl/fl nTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Day5_EarlyflnTreg_3

description:
Library name: Sample 20
Uhrf1fl/fl nTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: A3207_b

description: Library name: A3207_b

value: NMES


title: Patient 0019, Baseline

description: Library name: patient_0019_BL


title: Day5_EarlyflnTreg_1

description:
Library name: Sample 18
Uhrf1fl/fl nTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Day12_DelflnTreg_1

description:
Library name: Sample 15
Uhrf1fl/fl nTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: Day12_DelflnTreg_2

description:
Library name: Sample 16
Uhrf1fl/fl nTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: Patient 0018, Baseline

description: Library name: patient_0018_BL

value: Patient 0018


title: Patient 0021, 2 Years

description: Library name: patient_0021_2Y


title: A3205_b

description: Library name: A3205_b


title: Day5_DelflnTreg_3

description:
Library name: Sample 14
Uhrf1fl/fl nTreg cells sorted from culture on day 5


title: Patient 0019, 2 Years

description: Library name: patient_0019_2Y


title: Patient 0018, 6 Months

description: Library name: patient_0018_6M


title: Day12_Early_pos_pos_nTreg_2

description:
Library name: Sample 10
Uhrf1+/+ nTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Day5_DelflnTreg_2

description:
Library name: Sample 13
Uhrf1fl/fl nTreg cells sorted from culture on day 5


title: A3201_b

description: Library name: A3201_b


title: Day5_DelflnTreg_1

description:
Library name: Sample 12
Uhrf1fl/fl nTreg cells sorted from culture on day 5


title: Patient 0017, Baseline

description: Library name: patient_0017_BL

value: Patient 0017


title: A3199_b

description: Library name: A3199_b


title: Patient 0018, 2 Years

description: Library name: patient_0018_2Y

value: Nasal brush biopsy


title: Day12_Early_pos_pos_nTreg_3

description:
Library name: Sample 11
Uhrf1+/+ nTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: Day5_Early_pos_pos_nTreg_3

description:
Library name: Sample 8
Uhrf1+/+ nTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Day5_Early_pos_pos_nTreg_1

description:
Library name: Sample 6
Uhrf1+/+ nTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Day12_DelflnTreg_3

description:
Library name: Sample 17
Uhrf1fl/fl nTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: A3204_b

description: Library name: A3204_b


title: Day12_Del_pos_pos_nTreg_2

description:
Library name: Sample 4
Uhrf1+/+ nTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: A3206_b

description: Library name: A3206_b


title: Patient 0017, 2 Years

description: Library name: patient_0017_2Y


title: Patient 0017, 6 Months

description: Library name: patient_0017_6M


title: Day12_Del_pos_pos_nTreg_3

description:
Library name: Sample 5
Uhrf1+/+ nTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: Day12_Del_pos_pos_nTreg_1

description:
Library name: Sample 3
Uhrf1+/+ nTreg cells exposed to tamoxifen on day 5 sorted from culture on day 12


title: A3203_b

description: Library name: A3203_b


title: A3202_b

description: Library name: A3202_b


title: Day5_Del_pos_pos_nTreg_2

description:
Library name: Sample 2
Uhrf1+/+ nTreg cells sorted from culture on day 5


title: Patient 0016, Baseline

description: Library name: patient_0016_BL

value: Patient 0016


title: Day5_Del_pos_pos_nTreg_1

description:
Library name: Sample 1
Uhrf1+/+ nTreg cells sorted from culture on day 5


title: Patient 0016, 6 Months

description: Library name: patient_0016_6M


title: D24 Spleen Uhrf1fl/fl Ex-Foxp3-3

description:
Library name: Sample 46
Adoptively transferred Uhrf1fl/fl Ex-Foxp3 iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection

data_processing:
Basecalls performed using Illumina RTA2 software.
bcl-convert/3.10.5 was used to convert bcl files to fastq files (default parameters).
FASTQ files were processed using the nf-core/RNA-seq pipeline1 v3.18 implemented in Nextflow v24.04.4 with Northwestern University Quest HPC (Genomic Nodes) configuration
Assembly: GRCm38/mm10
Supplementary files format and content: csv files including raw counts values for each sample was generated by nf-core/RNA-seq pipeline1 v3.18 (--aligner star_salmon)

source_name: iTreg cells (Foxp3-GFP-tdTomato+)

extract_protocol:
RNA was extracted from FACSorted cells using the AllPrep DNA/RNA Micro Kit.
SMART-Seq v4 Ultra Low Input RNA Kit

value: iTreg cells (Foxp3-GFP-tdTomato+)


title: Day12_Early_pos_pos_nTreg_1

description:
Library name: Sample 9
Uhrf1+/+ nTreg cells exposed to tamoxifen on day 0 sorted from culture on day 12


title: A3200_b

description: Library name: A3200_b


title: A3208_b

description: Library name: A3208_b


title: Day5_Early_pos_pos_nTreg_2

description:
Library name: Sample 7
Uhrf1+/+ nTreg cells exposed to tamoxifen on day 0 sorted from culture on day 5


title: Patient 0016, 2 Years

description: Library name: patient_0016_2Y

value: 2 Years


title: D24 Spleen Uhrf1fl/fl Ex-Foxp3-2

description:
Library name: Sample 45
Adoptively transferred Uhrf1fl/fl Ex-Foxp3 iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection


title: D24 Spleen Uhrf1fl/fl Ex-Foxp3-1

description:
Library name: Sample 44
Adoptively transferred Uhrf1fl/fl Ex-Foxp3 iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection


title: D24 Spleen Uhrf1+/+ Ex-Foxp3-3

description:
Library name: Sample 42
Adoptively transferred Uhrf1+/+ Ex-Foxp3 iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection


title: A3198_b

description: Library name: A3198_b


title: D24 Spleen Uhrf1+/+ Ex-Foxp3-2

description:
Library name: Sample 41
Adoptively transferred Uhrf1+/+ Ex-Foxp3 iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection


title: D24 Spleen Uhrf1+/+ Ex-Foxp3-1

description:
Library name: Sample 40
Adoptively transferred Uhrf1+/+ Ex-Foxp3 iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection


title: Skin, UninjuredControl, biol rep 2

city: Ulm

first: Mahyar

last: Aghapour

address: Meyerhofstrasse 1

country: Germany

institute: Ulm University

description:
Library name: Sample 14
Column Name in Raw_counts_All_Samples.txt.: UN_0002

data_processing:
Quality control: Reads containing adapter, poly-N, and low quality reads were removed from raw reads using an in-inhouse perl script by Novogene. Q20, Q30, and GC contet of the clean data were calculated. All further data analyses were based on the clean data set.
Clean reads (paired-end) were aligned to the reference genome (Mus Musculus(GRCm38/mm10)) using Hisat2 v2.0.5.
For the quantification of gene espression levels, featureCounts v1.5.0-p3 was used. FPKM of each gene was calculated based on the length and reads count.
Differential expression analysis was performed using DESeq2 R package (1.20.0). The obtained p-values were adjusted using the Benjamini and Hochberg´s apporach for controlling the FDR. Genes were assigned as differentitally expressed when adjusted p-value reached <=0.05 (found by DESeq2).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: Skin

extract_protocol:
RNA was isolated using Rneasy mini plus kit (Qiagen). 1-5 µg of total RNA was used for the construction of RNA library.
Isolated RNA was sent to Novogene for library preparation. Libraries were prepared using mRNA Library preparation Poly A enrichment.

value: Skin

value: Uninjured

tag: time point


title: Skin, UninjuredControl, biol rep 3

description:
Library name: Sample 15
Column Name in Raw_counts_All_Samples.txt.: UN_0003


title: Patient 0015, Baseline

description: Library name: patient_0015_BL

value: Patient 0015

value: Baseline


title: D24 Spleen Uhrf1fl/flFoxp3+ 2

description:
Library name: Sample 38
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection

value: iTreg cells (Foxp3-GFP+tdTomato+)


title: D24 Spleen Uhrf1+/+Foxp3+ 4

description:
Library name: Sample 36
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection


title: D24 Spleen Uhrf1fl/flFoxp3+ 3

description:
Library name: Sample 39
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection


title: D24 Spleen Uhrf1fl/flFoxp3+ 1

description:
Library name: Sample 37
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection


title: Patient 0014, Baseline

description: Library name: patient_0014_BL

value: Patient 0014


title: Skin, UninjuredControl, biol rep 1

description:
Library name: Sample 13
Column Name in Raw_counts_All_Samples.txt.: UN_0001


title: Skin, TBI, Day 7, biol rep 3

description:
Library name: Sample 12
Column Name in Raw_counts_All_Samples.txt.: TB_0703

value: TBI

value: Day 7


title: Patient 0014, 6 Months

description: Library name: patient_0014_6M

value: 6 Months


title: D24 Spleen Uhrf1+/+Foxp3+ 2

description:
Library name: Sample 34
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection


title: Skin, TBI, Day 7, biol rep 2

description:
Library name: Sample 11
Column Name in Raw_counts_All_Samples.txt.: TB_0702

value: WT


title: D24 Spleen Uhrf1+/+Foxp3+ 1

description:
Library name: Sample 33
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection


title: Patient 0014, 2 Years

description: Library name: patient_0014_2Y


title: D24 Spleen Uhrf1+/+Foxp3+ 3

description:
Library name: Sample 35
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection


title: D11 lung UHRF1fl/fl iTreg 8

description:
Library name: Sample 32
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Patient 0015, 2 Years

description: Library name: patient_0015_2Y


title: D11 lung UHRF1fl/fl iTreg 7

description:
Library name: Sample 31
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Patient 0013, Baseline

description: Library name: patient_0013_BL

value: Patient 0013


title: D11 lung UHRF1fl/fl iTreg 6

description:
Library name: Sample 30
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: D24 Spleen Uhrf1+/+ Ex-Foxp3-4

description:
Library name: Sample 43
Adoptively transferred Uhrf1+/+ Ex-Foxp3 iTreg cells sorted from the spleens of recipient Foxp3DTR mice at day 24 post influenza infection


title: D11 lung UHRF1fl/fl iTreg 4

description:
Library name: Sample 28
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Patient 0013, 6 Months

description: Library name: patient_0013_6M


title: Skin, SHAM, Day 7, biol rep 2

description:
Library name: Sample 8
Column Name in Raw_counts_All_Samples.txt.:  SH_0702

value: Sham


title: Patient 0015, 6 Months

description: Library name: patient_0015_6M


title: D11 lung UHRF1fl/fl iTreg 3

description:
Library name: Sample 27
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: D11 lung UHRF1fl/fl iTreg 5

description:
Library name: Sample 29
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Skin, SHAM, Day 7, biol rep 1

description:
Library name: Sample 7
Column Name in Raw_counts_All_Samples.txt.:  SH_0701


title: Patient 0013, 2 Years

description: Library name: patient_0013_2Y


title: D11 lung UHRF1fl/fl iTreg 1

description:
Library name: Sample 25
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Patient 0012, 6 Months

description: Library name: patient_0012_6M

value: Patient 0012


title: D11 lung Uhrf1+/+ iTreg 7

description:
Library name: Sample 23
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Patient 0012, Baseline

description: Library name: patient_0012_BL

value: Nasal brush biopsy


title: D11 lung Uhrf1+/+ iTreg 8

description:
Library name: Sample 24
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: D11 lung Uhrf1+/+ iTreg 6

description:
Library name: Sample 22
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Skin, TBI, Day 1, biol rep 2

description:
Library name: Sample 5
Column Name in Raw_counts_All_Samples.txt.:  TB_0102

value: Day 1


title: D11 lung Uhrf1+/+ iTreg 5

description:
Library name: Sample 21
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Skin, TBI, Day 1, biol rep 1

description:
Library name: Sample 4
Column Name in Raw_counts_All_Samples.txt.:  TB_0101


title: Patient 0012, 2 Years

description: Library name: patient_0012_2Y


title: D11 lung Uhrf1+/+ iTreg 3

description:
Library name: Sample 19
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Patient 0011, Baseline

description: Library name: patient_0011_BL

value: Patient 0011


title: Skin, SHAM, Day 7, biol rep 3

description:
Library name: Sample 9
Column Name in Raw_counts_All_Samples.txt.:  SH_0703


title: D11 lung Uhrf1+/+ iTreg 2

description:
Library name: Sample 18
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Skin, SHAM, Day 1, biol rep 3

description:
Library name: Sample 3
Column Name in Raw_counts_All_Samples.txt.:  SH_0103


title: D11 lung Uhrf1+/+ iTreg 1

description:
Library name: Sample 17
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Patient 0011, 6 Months

description: Library name: patient_0011_6M


title: Skin, TBI, Day 7, biol rep 1

description:
Library name: Sample 10
Column Name in Raw_counts_All_Samples.txt.: TB_0701


title: D24 lung Uhrf1fl/fl iTreg 7

description:
Library name: Sample 16
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Patient 0011, 2 Years

description: Library name: patient_0011_2Y

value: 2 Years


title: D11 lung UHRF1fl/fl iTreg 2

description:
Library name: Sample 26
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: D24 lung Uhrf1fl/fl iTreg 5

description:
Library name: Sample 14
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Skin, SHAM, Day 1, biol rep 1

description:
Library name: Sample 1
Column Name in Raw_counts_All_Samples.txt.:  SH_0101

value: Skin


title: D24 lung Uhrf1fl/fl iTreg 6

description:
Library name: Sample 15
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: D24 lung Uhrf1fl/fl iTreg 4

description:
Library name: Sample 13
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Skin, TBI, Day 1, biol rep 3

description:
Library name: Sample 6
Column Name in Raw_counts_All_Samples.txt.:  TB_0103


title: D24 lung Uhrf1fl/fl iTreg 3

description:
Library name: Sample 12
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: D24 lung Uhrf1fl/fl iTreg 2

description:
Library name: Sample 11
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Patient 0010, Baseline

description: Library name: patient_0010_BL

value: Patient 0010


title: Patient 0010, 6 Months

description: Library name: patient_0010_6M


title: D24 lung Uhrf1fl/fl iTreg 1

description:
Library name: Sample 10
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: RNAseqseq of KPC cells with Cis treatment for 21h,rep2

city: Hangzhou

first: Yewei

last: Ji

address: Wenyixilu street

institute: Zhejiang Provincial Key Laboratory of Pancreatic Disease

description: Library name: Cis21h_RNAseq_rep2

data_processing:
Sequencing adaptors and low-quality reads were trimmed by Cutadapt. The clean reads were then aligned to the mouse genome using STAR.
Assembly: GRCm39
Supplementary files format and content: rpkm files containing rpkm for each transcripts,which are seperated by Tab.

source_name: KPC

extract_protocol:
Cells were washed twice with cold PBS. 500 μl lysis buffer (8 mM HEPES, pH 7.4, 80 mM KCl, 4 mM MgCl2, 2% Triton x-100, and 200 μg/ml cycloheximide) was then added, and the cells were quickly scraped and collected into RNase-free tubes. The sample were centrifuged at 12,000 rpm for 12 minutes at 4°C, and the supernatant was sent to Novogene (China) for RNA-seq library construction. Approximately 100 μl of supernatant were treated with RNase I (Thermo Fisher Scientific) for 3 hours, followed by RNA extraction using TRIzol™ LS.
The isolated RNA underwent denaturation at 65°C for 20 minutes and was then electrophoresed on a 15% TBE-Urea gel. The segment around 25-35 nucleotides was excised and eluted overnight in RNA elution buffer at 4°C. This was followed by precipitation of the RNA with an equivalent volume of isopropanol. The NEBNext Small RNA Library Prep Set for Illumina (E7330L, NEB, USA) was used for footprint library construction. The obtained DNA was then sent to Novogene for sequencing.

value: KPC


title: D11 lung Uhrf1+/+ iTreg 4

description:
Library name: Sample 20
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: D24 lung Uhrf1+/+ iTreg 9

description:
Library name: Sample 9
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: RNAseqseq of KPC cells with Cis treatment for 21h,rep1

description: Library name: Cis21h_RNAseq_rep1


title: D24 lung Uhrf1+/+ iTreg 8

description:
Library name: Sample 8
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: D24 lung Uhrf1+/+ iTreg 7

description:
Library name: Sample 7
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: RNAseqseq of KPC cells with Cis treatment for 6h,rep2

description: Library name: Cis6h_RNAseq_rep2


title: Patient 0009, Baseline

description: Library name: patient_0009_BL

value: Patient 0009

value: Baseline


title: D24 lung Uhrf1+/+ iTreg 6

description:
Library name: Sample 6
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection

value: iTreg cells (Foxp3-GFP+tdTomato+)


title: RNAseqseq of KPC cells with Cis treatment for 6h,rep1

description: Library name: Cis6h_RNAseq_rep1


title: D24 lung Uhrf1+/+ iTreg 5

description:
Library name: Sample 5
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Skin, SHAM, Day 1, biol rep 2

description:
Library name: Sample 2
Column Name in Raw_counts_All_Samples.txt.:  SH_0102


title: Patient 0009, 6 Months

description: Library name: patient_0009_6M


title: Patient 0010, 2 Years

description: Library name: patient_0010_2Y


title: D24 lung Uhrf1+/+ iTreg 4

description:
Library name: Sample 4
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: D24 lung Uhrf1+/+ iTreg 3

description:
Library name: Sample 3
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Patient 0009, 2 Years

description: Library name: patient_0009_2Y


title: Patient 0008, Baseline

description: Library name: patient_0008_BL

value: Patient 0008


title: D24 lung Uhrf1+/+ iTreg 1

description:
Library name: Sample 1
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Riboseq of KPC cells with Cis treatment for 21h,rep2

description: Library name: Cis21h_ribo_rep2

data_processing:
Sequencing adaptors and low-quality reads were trimmed by Cutadapt. The clean reads were then aligned to the mouse genome using STAR.
Assembly: GRCm39
Supplementary files format and content: rpkm files containing rpkm for each transcripts,which are seperated by Tab.
Library strategy: Ribo-Seq


title: RNAseqseq of KPC cells without treatment,rep1

description: Library name: WT_RNAseq_rep1


title: D11 UHRF1fl/fl iTreg 6

description:
Library name: Sample 24
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl-convert v3.10.5.
Reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences.
Sequence alignment to the GRCm38/mm10 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3.
Assembly: GRCm38/mm10 or hg38
Supplementary files format and content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Library strategy: EM-seq

extract_protocol:
Genomic DNA was extracted from flow cytometry-sorted cells using the AllPrep DNA/RNA Micro Kit.
Genomic DNA was quantified with a Qubit 3.0 instrument.  gDNA was fragmented with MspI (New England Biolabs) and then size-selected for 100- to 250-bp fragments using solid-phase reversible immobilization beads (MagBio Genomics). CG-enriched gDNA was then enzymatically converted using the NEBNext Enzymatic Methyl-seq Kit (New England BioLabs) per manufecture's instruction. Random priming, adaptor ligation, PCR product clean-up, and final library amplification were performed using the Pico Methyl-Seq Library Prep Kit (Zymo Research). Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and 4-6 pooled libraries per run were sequenced on an Illumina NextSeq 2000 instrument using the 100 cycles NextSeq 2000 P2 reagent kit.


title: D11 UHRF1fl/fl iTreg 5

description:
Library name: Sample 23
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Patient 0008, 6 Months

description: Library name: patient_0008_6M


title: D11 UHRF1fl/fl iTreg 4

description:
Library name: Sample 22
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: D11 UHRF1fl/fl iTreg 3

description:
Library name: Sample 21
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Patient 0008, 2 Years

description: Library name: patient_0008_2Y


title: Riboseq of KPC cells with Cis treatment for 21h,rep1

description: Library name: Cis21h_ribo_rep1


title: D11 UHRF1fl/fl iTreg 2

description:
Library name: Sample 20
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: D11 UHRF1fl/fl iTreg 1

description:
Library name: Sample 19
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Riboseq of KPC cells with Cis treatment for 6h,rep2

description: Library name: Cis6h_ribo_rep2


title: D11 Uhrf1+/+ iTreg 5

description:
Library name: Sample 17
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Patient 0007, Baseline

description: Library name: patient_0007_BL

value: Patient 0007


title: D11 Uhrf1+/+ iTreg 6

description:
Library name: Sample 18
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: RNAseqseq of KPC cells without treatment,rep2

description: Library name: WT_RNAseq_rep2


title: D11 Uhrf1+/+ iTreg 4

description:
Library name: Sample 16
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Riboseq of KPC cells with Cis treatment for 6h,rep1

description: Library name: Cis6h_ribo_rep1


title: D24 lung Uhrf1+/+ iTreg 2

description:
Library name: Sample 2
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Riboseq of KPC cells without treatment,rep1

description: Library name: WT_ribo_rep1


title: Riboseq of KPC cells without treatment,rep2

description: Library name: WT_ribo_rep2


title: D11 Uhrf1+/+ iTreg 3

description:
Library name: Sample 15
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: D11 Uhrf1+/+ iTreg 2

description:
Library name: Sample 14
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: Patient 0005, Baseline

description: Library name: patient_0005_BL

value: Patient 0005


title: D11 Uhrf1+/+ iTreg 1

description:
Library name: Sample 13
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 11 post influenza infection


title: D24 Uhrf1fl/fl iTreg 6

description:
Library name: Sample 12
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: D24 Uhrf1fl/fl iTreg 5

description:
Library name: Sample 11
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Patient 0005, 6 Months

description: Library name: patient_0005_6M

value: 6 Months


title: D24 Uhrf1fl/fl iTreg 4

description:
Library name: Sample 10
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Pool 2 - ADT

city: Oxford

first: Alexander

last: Clarke

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

country: United Kingdom

institute: University of Oxford

description: 10x Feature Barcode

library_source: other

data_processing:
Cellranger 7.1 was run in multi mode and filtered matrices generated.
Assembly: mm10
Supplementary files format and content: Filtered H5 format matrices

molecule: protein

source_name: Lymph node

extract_protocol:
Viable, TCRb+CD4+GFP+tdTomato+ Tregs were sorted and labelled with Biolegend TotalSeq C HTOs (TotalSeq™-C0301 anti-mouse Hashtag 1 Antibody = WT1; TotalSeq™-C0302 anti-mouse Hashtag 2 Antibody = WT2; TotalSeq™-C0303 anti-mouse Hashtag 3 Antibody = KO1; TotalSeq™-C0303 anti-mouse Hashtag 4 Antibody = KO2) and pooled (second pool has same format with WT3, WT4, KO3, KO4).
Approximately 10,000 cells per batch were loaded onto the 10X Genomics Chromium Controller (Chip K). Gene expression libraries were prepared using the 10x Genomics Single Cell 5' Reagent Kits v2 (Dual Index) following manufacturer user guide (CG000330 Rev B).

value: Lymph node

value: Tregs

value: Mixed (Foxp3-ERT2-cre x Gsk3a/b x tdTomato-Ai9 and Foxp3-ERT2-cre x tdTomato-Ai9)

tag: adt

value: TotalSeq-C0301 anti-mouse Hashtag 1 Antibody = Foxp3-ERT2-Cre x WT 3; TotalSeq-C0302 anti-mouse Hashtag 2 Antibody = Foxp3-ERT2-Cre x WT 4; TotalSeq-C0303 anti-mouse Hashtag 3 Antibody = Foxp3-ERT2-Cre x Gsk3a/b KO 3 TotalSeq-C0303 anti-mouse Hashtag 4 Antibody = Foxp3-ERT2-Cre x Gsk3a/b KO 4)

tag: library type

value: HTO


title: Patient 0005, 2 Years

description: Library name: patient_0005_2Y

value: Nasal brush biopsy


title: D24 Uhrf1fl/fl iTreg 3

description:
Library name: Sample 9
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Patient 0003, 2 Years

description: Library name: patient_0003_2Y

value: Patient 0003

value: 2 Years


title: D24 Uhrf1fl/fl iTreg 1

description:
Library name: Sample 7
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Patient 0004, Baseline

description: Library name: patient_0004_BL

value: Patient 0004


title: D24 Uhrf1fl/fl iTreg 2

description:
Library name: Sample 8
Adoptively transferred Uhrf1fl/fl iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Pool 1 - ADT

description: 10x Feature Barcode

value: TotalSeq-C0301 anti-mouse Hashtag 1 Antibody = Foxp3-ERT2-Cre x WT 1; TotalSeq-C0302 anti-mouse Hashtag 2 Antibody = Foxp3-ERT2-Cre x WT 2; TotalSeq-C0303 anti-mouse Hashtag 3 Antibody = Foxp3-ERT2-Cre x Gsk3a/b KO 1 TotalSeq-C0303 anti-mouse Hashtag 4 Antibody = Foxp3-ERT2-Cre x Gsk3a/b KO 2)


title: D24 Uhrf1+/+ iTreg 6

description:
Library name: Sample 6
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Patient 0007, 2 Years

description: Library name: patient_0007_2Y


title: Pool 1

description: 10x 5' Gex

value: mRNA


title: D24 Uhrf1+/+ iTreg 5

description:
Library name: Sample 5
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Pool 2

description: 10x 5' Gex


title: Patient 0002, Baseline

description: Library name: patient_0002_BL

value: Patient 0002

value: Baseline


title: D24 Uhrf1+/+ iTreg 3

description:
Library name: Sample 3
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection

value: iTreg cells (Foxp3-GFP+tdTomato+)


title: D24 Uhrf1+/+ iTreg 4

description:
Library name: Sample 4
Adoptively transferred Uhrf1+/+ iTreg cells sorted from the lungs of recipient Foxp3DTR mice at day 24 post influenza infection


title: Patient 0002, 6 Months

description: Library name: patient_0002_6M


title: D24 Uhrf1+/+ iTreg 2


title: Patient 0002, 2 Years

description: Library name: patient_0002_2Y


title: 46

city: New York

first: Yasmin

last: Hurd

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FASTQ files were aligned to the Rat Genome (mRatBN7.2) using STAR.
Aligned BAM files were counted against the Ensembly Rnor_6.0_ GTF reference file using featureCounts and assigned gene names using BioMart.
Differential expression analysis was completed with DESeq2
Assembly: mRatBN7.2
Supplementary files format and content: Comma-delimited file containing raw counts per sample.

extract_protocol:
RNA was extracted using the Zymo Clean and Concentrator Kit. Purified RNA was sent to Azenta Biosciences for quality control checking, library preparation, and sequencing.
Ilumina RNA with PolyA selection

value: Brain

value: WT