title: Xeno 2.2

city: oxford

first: Thomas

last: Jackson

address: weatherall institute of molecular medicine

department: paediatrics

institute: University of Oxford

description: Library name: Xeno 2.2

data_processing:
SeqNado pipeline (https://github.com/alsmith151/SeqNado)
Assess read quality with the fastQC package
Perform trimming using Trim Galore
Map trimmed reads to the human genome assembly(hg38) using STAR
Assembly: hg38

source_name: Xenograft

growth_protocol: NSG Xeno tail vein injection

extract_protocol:
RNA extraction was performed using a RNeasy Micro Kit (Qiagen).
RNA extraction Library preparation and sequencing were performed using using the Ultra II Directional RNA Library Prep Kit (NEB, E7765). RNA libraries were sequenced by paired-end sequencing using a 150-cycle high output kit on a Nextseq 500 (Illumina). Adult bone marrow library preparation using small cell number modified SMARTseq 2 protocol.

treatment_protocol: Transfromed FL cells via CRISPR induced MLL_AF4 translocation

value: Xenograft

tag: cell type

value: Human fetal liver


title: mouse_NS_10X

status: Public on Jun 26 2025

type: SRA

city: Cambridge

first: Helle

last: Jorgensen

address: Papworth Road

department: Cardiorespiratory section

country: United Kingdom

institute: University of Cambridge

description: Single-cell RNA seq, 10X Chromium

library_source: transcriptomic single cell

data_processing:
Sample 1 and 2: Cell Ranger pipeline v.3.1.0 was used to align raw sequencing reads to a custom genome (based on the GRCm38 mouse genome, including the open reading frame encoding EYPF (Srinivas et al., 2001). Quality control (QC), normalization and gene expression analysis was performed using the CRAN R package Seurat v.3.1.2 (Butler et al., 2018; Stuart et al., 2019) in R v.3.6.2. Cells with <5,000 UMI counts (healthy) or <3500 UMI counts (injury), <2,000 genes detected (healthy) or <1500 genes detected (injury) and >5% mitochondrial reads (both) were excluded. Normalization was performed using SCTransform (Hafemeister and Satija, 2019) v.0.2.1 implemented in Seurat.
Sample 3-6: Sequencing data was aligned to a 10X-supplied human reference genome (GRCh38-3.0.0) using Space Ranger (v.1.0). Downstream analysis was performed with R (v.4.0.3). The Spaniel R package (v.1.2.0) was used to import the data into SingleCellExperiment objects and was also used to create spot images. Any spots with fewer than 200 UMIs were removed. The SingleCellExperiment objects were then converted into SeuratObjects for downstream analysis using Seurat (v.3.1.3). Individual replicates were normalised using the “NormaliseData” function followed by the identification of the top 200 highly variable genes using the “FindVariableFeatures” function.
Assembly: Sample 1 and 2: Custom genome based on the GRCm38 mouse genome, including the open reading frame encoding EYFP (Srinivas et al., 2001)
Assembly: Sample 3-6: 10X-supplied human reference genome (GRCh38-3.0.0)
Supplementary files format and content: barcodes.tsv.gz: barcodes of detected cells (single-cell RNA-seq) or capture spots (spatial RNA-seq)
Supplementary files format and content: features.tsv.gsz: IDs of detected genes
Supplementary files format and content: mtx files containing matrix of raw count values
Supplementary files format and content: scalefactors_json.json:scale factors
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the image
Supplementary files format and content: tissue_positions_list.csv: list of capture spot barcodes and coordinates
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and capture spots
Supplementary files format and content: tissue_hires_image.png: hi-res image of the tissues
Supplementary files format and content: tissue_lowres_image.png: low-res image of the tissue

molecule: total RNA

organism: Mus musculus

source_name: Carotid artery

extract_protocol:
Sample 1 and 2: Datasets of lineage-labelled VSMCs from healthy and injured mouse carotid arteries were generated as described (Worssam et al. 2023) after pooling cells from 5 Myh11eYFP animals 11 days post-ligation (D11) or 2 control Myh11eYFP animals that did not undergo surgery (NS). After carotid artery harvest and dissection, arteries were incubated for 6 minutes in collagenase type IV (1 mg/mL, Life Technologies) and porcine pancreatic elastase (1 U/mL, Worthington) in DMEM. After removing the adventitia, the medial samples from each animal cohort were pooled and digested in collagenase type IV (2.5 mg/mL, Life Technologies) and porcine pancreatic elastase (2.5 U/mL, Worthington) in DMEM for 90 minutes. Medial cell suspensions were filtered through a 40 µm filter and singlet cells expressing eYFP isolated by fluorescence-activated cell sorting (FACS, Aria-Fusion flow cytometer, BD Bioscience) into PBS with 0.05% BSA and 5 µL/mL recombinant RNAse inhibitor (Sigma). Isolation of single cells was verified with a haemocytometer. Sorted cells (10,000) were pelleted, resuspended in 47 µL of PBS with 0.05% BSA and loaded for Drop-Seq using the 10X Chromium system. Amplified cDNA libraries were sequenced on a HiSeq 4000 system.
Sample 3-6: A plaque-containing aortic sample from a 54 year old male organ donor was snap-frozen by fully submerging in an isopentane bath cooled by dry ice until frozen, embedded in OCT (2-8°C), sectioned and analysed using VISIUM technology (cat 1000184) according to manufacturer's instructions (10X).
Sample 1 and 2: A total of 10,000 EYFP+ cells were loaded onto a Chromium system (10x Genomics) and amplified cDNA libraries generated using the 3’ Gene Expression v3.0 kit (10x Genomics) were sequenced using 150 cycle paired end protocol (NovaSeq, Illumina).
Sample 3-6: Frozen sections were processed using the Visium Spatial Gene Expression protocol (10x Genomics), and spatially resolved transcriptomic libraries were constructed and sequenced using a 150-cycle paired-end protocol (NovaSeq, Illumina).

tag: tissue

value: Carotid artery

tag: genotype

tag: background


title: Dog_9_TMS_3

city: Davis

first: Stephanie

last: Goldschmidt

state: CA

address: one shields ave

department: VSR

country: USA

institute: UC-Davis

description: Library name: DSP-1001660022199-E-B12

library_source: transcriptomic

data_processing:
Raw FASTQ sequence reads were processed through the GeoMx NGS Pipeline Software for conversion to digital counts (DCC files) and subsequent downstream analyses with the GeoMx DSP Data Analysis Suite.
Assembly: Canine Cancer Atlas probe
Supplementary files format and content: Cf_R_NGS_CA_v1.0.pkc contains information about the probes and barcodes used in GeoMx assays (allows to map probe barcode to gene name)
Supplementary files format and content: dcc files contain raw counts of the probe barcodes detected in a ROI.
Library strategy: Spatial Transcriptomics

organism: Canis lupus familiaris

source_name: Rostral maxilla

growth_protocol: This study consisted of 9 formalin-fixed paraffin embedded (FFPE) samples from dogs with spontaneously occurring canine oral squamous cell carcinoma (COSCC)

extract_protocol:
GeoMx DSP analysis was performed according to NanoString’s standard procedures for NGS readout. Briefly, semi-automated slide preparation was conducted on a Leica BOND RX stainer for deparaffinization, epitope retrieval, and proteinase K treatment to expose RNA targets. The GeoMx Canine Cancer Atlas probe set was hybridized in situ to the tissue sections by overnight incubation at 37C. Subsequently, tissue sections were stained with fluor-conjugated morphology marker antibodies specific for pan-cytokeratin (PanCK; Alexa 532, Cy3/568nm channel), CD45 (Alexa 594, Texas Red/615nm channel), CD3 (Alexa 647,  Cy5/666 nm channel), and the SYTO-13 nucleic acid stain (FITC/525nm channel, for instrument focus).  Morphology markers facilitated selection of regions of interest (ROIs) containing approximately 300 cells, as defined by the nuclear stain. Four ROIs were selected for each phenotype (5 phenotypes: surface normal, surface tumor, surface peri-tumoral dysplasia, deep invasive tumor, tumor microenvironment), leading to a total of approximately 20 ROIs per patient.
indexed libraries were prepared from the DSP DNA oligonucleotides using high-fidelity PCR with GeoMx Seq Code Illumina-compatible primers.
Validated libraries (i.e., expected amplicon size of 162 bp) were sequenced on an Illumina NovaSeq X Plus Sequencing System

treatment_protocol: Within this study the pathologic specimens were serially sectioned every 5 millimeters (mm). Thus, selecting these patients allowed us to select slides that had surface of the tumor, its deep invasive front, the TMS, peritumoral dysplasia, and normal on a single block. Spatial transcriptomic analysis of COSCC and non-malignant tissues was performed on the NanoString GeoMx Digital Spatial Profiler (DSP) platform utilizing the GeoMx Canine Cancer Atlas.

value: Rostral maxilla

tag: tumor variant

value: Conventional

tag: tumor size


title: Xeno 2.1

description: Library name: Xeno 2.1

molecule: polyA RNA

organism: Homo sapiens

tag: treatment


title: DoxACY Hippocamus

city: Houston

first: Rajasekaran

last: Mahalingam

state: TX

address: 6565 MD Anderson Blvd

department: Symptom Research

institute: University of Texas MD Anderson Cancer Center

description: 10x Genomics

data_processing:
The demultplexing, barcoded processing, gene counting and aggregation wee made using the Cell Ranger v6.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hippocampus

extract_protocol:
Bilateral hippocampi from 4 mice/group was flash-frozen and combined. Tissue was then homogenized and lysed with Triton X-100 in RNase-free water for nuclei isolation
Library was performed according to the manufacture's instruction (single cell 3' v3 protocol, 10x Genomics)

value: Hippocampus

value: Brain cells

value: Doxorubcin and ACY-1083


title: Dog_9_TMS_2

description: Library name: DSP-1001660022199-E-B11


title: Xeno 1.A

description: Library name: Xeno 1.A

value: WT


title: Dox Hippocamus

description: 10x Genomics

value: Doxorubicin


title: Xeno 3.4.1

description: Library name: Xeno 3.4.1


title: Dog_9_TMS_1

description: Library name: DSP-1001660022199-E-B10


title: 6/B

city: Balice

first: Anna

middle: Dominika

last: Steg

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

description: Library name: Sample 6

data_processing:
Quality control (fastQC)
Processing fastq files with the QuantSeq Data Analysis Pipeline on BlueBee® Genomics
Filtration of low raw reads number samples. Minimal counts of reads set to 10 mln, and only samples that reach that condition are submitted.
Assembly: Sus Scrofa 11.1
Supplementary files format and content: Processed data files are in txt format providing read counts

organism: Sus scrofa

source_name: liver

extract_protocol:
RNA was isolated with A&A Biotechnology Total RNA Mini kit
Libraries were prepared using  QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) according to the manufacturer recommendations.

value: liver

value: Polish Large White sows covered with a Landrace boars

value: B (5000 U vit. D3/kg of feed)


title: Control Hippocamus

description: 10x Genomics

value: Control (no treatment)


title: Dog_9_deep_4

description: Library name: DSP-1001660022199-E-B09


title: 13/C

description: Library name: Sample 13

value: C (10000 U vit. D3/kg of feed)


title: TRF2_HFD_10X

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

institute: The Babraham Institute

description: Single-cell RNA seq, 10X Chromium

data_processing:
Alignment of raw sequence reads to the GRCm38 mouse genome was performed using the 10X Genomics Cell Ranger pipeline v.7.0.0. scRNA-seq datasets were analysed using Seurat v.4.3.0 in R v.4.2.2. Cells with < 1,500 genes detected, > 8% mitochondrial reads for the control and < 1,000 genes detected, > 8% mitochondrial reads for Sm22a-Trf2T188A/ApoE-/- mice were excluded from analysis.
Assembly: GRCm38

source_name: Aorta and carotid artery

extract_protocol:
Plaques were micro-dissected from the aorta (root, arch) and carotid arteries of Trf2T188A/ApoE-/- and  ApoE-/- mice before enzymatic digestion and single cell suspensions were analyzed using the 10X Genomics Chromium system as described (Dobnikar et al).
Cells were loaded onto a Chromium system (10x Genomics) and amplified cDNA libraries generated using Single Cell 3' v3 kit (10x Genomics) were sequenced using NovaSeq (Illumina).


title: 5/B

description: Library name: Sample 5


title: Xeno 3.4.1.1

description: Library name: Xeno 3.4.1.1


title: Xeno 3.3.1

description: Library name: Xeno 3.3.1


title: 4/A

description: Library name: Sample 4

value: A (control)


title: Dog_9_deep_2

description: Library name: DSP-1001660022199-E-B07


title: WT_HFD_10X

description: Single-cell RNA seq, 10X Chromium


title: Xeno 3.2.1

description: Library name: Xeno 3.2.1


title: 10/A

description: Library name: Sample 10


title: Dog_9_deep_1

description: Library name: DSP-1001660022199-E-B06


title: 2/C

description: Library name: Sample 2


title: Xeno 3.2.1.1

description: Library name: Xeno 3.2.1.1


title: TRF2_TA_10X

description: Single-cell RNA seq, 10X Chromium

data_processing:
Raw sequencing reads were aligned to GRCm38 mouse genome by using 10X Genomics Cell Ranger pipeline v.6.1.2. Dataset analysis was performed using Seurat v.3.2.1 15,20 in R v.3.6.2. Cells with < 1,200 genes detected, > 6% mitochondrial reads, or >40% reads from the most highly expressed genes were excluded from analysis.
Assembly: GRCm38
10X matrix file: CellRanger h5 file of raw counts of all genes in all valid cells
10X normalized count file: Gzipped text files containing normalized and filtered count values with genes in rows and cells in columns.

extract_protocol:
sc-RNA-seq profiles from SM22α-TRF2T188A or wild-type littermate control mice were generated 28d after carotid ligation. The adventitia and non-remodelled sections were removed from carotid arteries before enzymatic digestion to single cell suspensions that were analysed using a Chromium system (10X Genomics).
Cells were loaded onto a Chromium system (10x Genomics) and amplified cDNA libraries generated using Single Cell 3' v3 kit (10x Genomics) were sequenced using NovaSeq (Illumina).

tag: strain background


title: Dog_1_normal_4

description: Library name: DSP-1001660022199-E-B05

source_name: Rostral mandible

value: Rostral mandible

value: Papillary


title: WT_10X

description: Single-cell RNA seq, 10X Chromium

value: wild type control


title: 8/C

description: Library name: Sample 8


title: Xeno 3.1.1

description: Library name: Xeno 3.1.1

value: Xenograft

value: Human fetal liver


title: 1/C

description: Library name: Sample 1


title: Dog_1_normal_3

description: Library name: DSP-1001660022199-E-B04


title: PanT24-Tumor

city: ShangHai

first: Da

last: Lin

address: No. 650 Songjiang Road

country: China

institute: Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China

description:
Library name: PanT24-Tumor
Uni-C library

library_source: genomic

data_processing:
SNP and INDEL calling from Uni-C datasets: For SNP and INDEL detection, raw read pairs are initially processed using FASTP (version: 0.23.2) to remove residual sequencing adapter sequences. To mitigate background noise associated with Hi-C ligation junctions, we filter out all read pairs that contain the MboI restriction site ligation junction "GATCGATC". Subsequently, these filtered read pairs are aligned to the reference genome GRCh37 or GRCm38 using BWA (version: 0.7.17). The aligned BAM files are sorted with SAMTOOLS (version: 1.15.1), and duplicate reads are removed via SAMBAMBA (version: 0.6.6). Next, base quality scores are recalibrated using the BaseRecalibrator (from GATK, version 4.2.2), followed by the detection of SNPs and indels using HaplotypeCaller (from GATK, version 4.2.2). We then conduct a statistical analysis of the variant data in each single-cell VCF. Variants present in two or more VCF files will be considered genuine and retained, whereas variants that only appear in one VCF file will be filtered out. The statistics for base substitution types, mutation spectrum, 96 mutational profiles, and types of Indels are implemented using the R package MutationalPatterns (version 3.12.0).
Construction of single-cell genome-wide chromatin interaction matrix: Uni-C raw read pairs are initially processed using FASTP (version: 0.23.2) to remove residual sequencing adapter sequences. After filtering, the read pairs are aligned to the reference genome using “mem” module of BWA (version: 0.7.17) with parameters “-5SP -T0”. After alignment, we use the “parse” module of PAIRTOOLS (Version: 0.3.0) to convert the generated SAM files into PAIRSAM format, with specific parameters set to “--min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30”. The pairsam files are then sorted and deduplicated using the “sort” and “dedup” modules of PAIRTOOLS, respectively. Following deduplication, the “split” module of PAIRTOOS is used to convert the deduplicated PAIRSAM files into PAIRS format. These final pairs files are utilized to generate the chromatin interaction matrices using tools such as JUICERTOOLS (Version: 1.9.9) or COOLER (Version: 0.9.3).
Assembly: GRCh37 or GRCm38
Supplementary files format and content: The Hi-C pairs files used to generate the genome-wide chromatin interaction matrix
Supplementary files format and content: These VCF files were generated using the HaplotypeCaller module of GATK (version 4.2.2) and contain information on both SNPs and INDELs.

molecule: genomic DNA

source_name: Pancreas

growth_protocol: PanT24 and COLO320-DM  were cultured in complete medium (RPMI1640, 10% FBS, 1% Pen/Strep/glutamate) at 37 ℃ and 5% CO2.

extract_protocol:
The PCR products were performed size sellection using VAHTS DNA Clean Beads (Vazyme, N411). Briefly, to obtain PCR products with a fragment size of 300 bp - 400 bp, 70 μl of DNA Clean Beads were added to 100 μl of the sample to adsorb DNA fragments larger than 400 bp. After collecting the supernatant, 20 μl of beads were added to adsorb DNA fragments ranging from 300 bp to 400 bp, and the supernatant was removed. After washing twice with 80% ethanol (Sigma-Aldrich, E7023), 20 μl of ddH2O was added to recover the magnetic bead-bound DNA fragments.
Cell fixation and permeabilization: Cells were fixed directly with 1% formaldehyde (Sigma-Aldrich, 47608-250ML-F) for 10 min with rotation at room temperature. The reaction was terminated by 0.2% BSA (Sigma-Aldrich, V900933) for 5 min. After washing twice with PBS (Hyclone, SH30256.FS), cells were crosslinked with freshly made 3 mM EGS (Thermo Fisher Scientific, 21565) for 20 min with rotation at room temperature. Then, 0.25 M glycine (Sigma-Aldrich, 410225) was add to quench the reaction. Subsequently, the cells were washed twice with ice-cold Wash Buffer (10 mM Tris-HCl pH 8.0 (Sango Biotech, B548127), 10 mM NaCl (Sigma-Aldrich, S9888) and 0.1 mg/ml BSA). Fixed cells were then resuspended in ice-cold Hi-C Lysis Buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% NP40 (Sigma-Aldrich, 127087-87-0)) containing a protease inhibitor (Roche, 11836170001) and incubated on ice for 15 min. After centrifugation, cells were further permeabilized with 40 ml of 0.5% SDS (Sigma-Aldrich, 05030) at 65 °C for 10 min and then immediately placed on ice for 3 min.   In situ digestion: Add 20 ml of 10% Triton X-100 (Sigma-Aldrich, T8787) to the reaction and incubated for 5 min to quench the SDS. Subsequently, the digestion mix (100 μl of ddH2O, 20 μl of 10× NEB buffer 2, 20 μl of MboI (NEB, R0147S, 20 units/μl)) was added to the reaction and incubated at 37 °C for 4 h.  End repairing and in situ proximity ligation: The reaction was incubated at 65 °C for 20 min to terminate digestion, then cool to room temperature. Add 81 μl of ddH2O, 10 μl of 10× NEB buffer 2, 3 μl of dNTPs (NEB, N0447S), and 6 μl of DNA polymerase I Klenow fragment (NEB, M0210) to the reaction system, and incubated the sample at 37 °C for 1 h. Ligation was performed by the addition of 270 μl of H2O, 50 μl of T4 Ligase Buffer, 50 μl of 10% Triton X-100, 5 μl of 2% BSA and 25 μl of T4 DNA ligase (Thermo Fisher Scientific, EL0011), and incubated at room temperature for 2 h.  Single cell isolation and amplification: Individual Nuclei were transferred with a glass micropipette into a 0.2 ml low-bind PCR tube (Axygen, PCR-02-L-C) with 2 μl of Buffer L (200 mM NaOH (Sigma-Aldrich, 72068) and 50 mM DTT (Sigma-Aldrich, D9779)) and incubated at 72 °C for 10 min. Then 2 μl of Buffer N (200 mM HCl) was added and incubated in thermomixer (Eppendorf) with rotation at 1000 rpm for 3 min to terminate lysis and neutralize the reaction. Added 6.8 μl of ddH2O, 0.5 μl of dNTPs (10 mM each), 1 μl of Alpha Thiol-modified ddNTPs (10 mM each, Trilink), 2 μl of Exo-Resistant Random Primer (500 μM), 2 μl of EquiPhi29™ DNA Polymerase Reaction Buffer (10×), 2 μl of 20 mM MnCl2 (Sigma-Aldrich, 63535), 0.2 μl of DTT (0.1 M) and 1 μl of EquiPhi29™ DNA Polymerase (Thermo Fisher Scientific, A39390) to the reaction and mixed thoroughly, followed by incubation at 45 °C for 2 h. Subsequently, the reaction was terminated by incubating at 65 °C for 10 min.   DNA size selection: The PCR products were performed size sellection using VAHTS DNA Clean Beads (Vazyme, N411). Briefly, to obtain PCR products with a fragment size of 300 bp - 400 bp, 70 μl of DNA Clean Beads were added to 100 μl of the sample to adsorb DNA fragments larger than 400 bp. After collecting the supernatant, 20 μl of beads were added to adsorb DNA fragments ranging from 300 bp to 400 bp, and the supernatant was removed. After washing twice with 80% ethanol (Sigma-Aldrich, E7023), 20 μl of ddH2O was added to recover the magnetic bead-bound DNA fragments.  Sequencing library construction: DNA sequencing libraries were prepared using the VAHTS Universal Plus DNA Library Prep Kit (Vazyme, NDM627) according to the manufacturer’s protocol.

value: Pancreas

value: tissue


title: 7/C

description: Library name: Sample 7


title: Xeno 3.1.1.1

description: Library name: Xeno 3.1.1.1


title: snRNA-seq SPF ImP Hypothalamus Baseline D3

city: Los Angeles

first: Xia

last: Yang

state: California

address: 610 Charles E. Young Drive East

department: Integrative Biology and Physiology

institute: University of California, Los Angeles

description: Library name: 111CM3

data_processing:
Single-nucleus RNA-seq data were processed using Cell Ranger v8.0.1 with the --include-introns=true option to retain unspliced reads. Reads were aligned to the GRCm39-2024-A mouse reference genome. Denoising was performed using CellBender v0.3.0. Seurat (v5.0.0) was used for downstream analysis: nuclei expressing 200–5,000 genes and <10% mitochondrial content were retained (total: 169,960 nuclei). Data were normalized using SCTransform, batch-corrected using HarmonyIntegration, and clustered using FindClusters at resolution 0.5. Cell identities were assigned using mapscvi with the HypoMap reference.
Assembly: Reads were aligned to the GRCm39-2024-A mouse reference transcriptome from 10x Genomics.
Supplementary files format and content: Gene-barcode expression matrices

source_name: Hypothalamus

growth_protocol: Does not apply

extract_protocol:
Mice were deeply anesthetized with isoflurane then were transcardially perfused with ice-cold PBS. Brains were extracted, and the hypothalamus was microdissected, snap-frozen and stored at –80°C until processing
Hypothalamic nuclei were isolated using the Chromium Nuclei Isolation Kit (10x Genomics). Approximately 10,000 nuclei per sample were loaded onto the Chromium Controller and processed using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Complementary DNA (cDNA) amplification and library construction were performed following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq X Plus platform, targeting a minimum depth of 40,000 read pairs per nucleus.

treatment_protocol: ImP was prepared by dilution in sterile distilled water containing 1% DMSO to aid solubilization.  For chronic administration, Alzet osmotic pumps (models 1002 and 1004; Alzet) were used to deliver ImP continuously. The concentration of ImP was calculated to achieve a delivery rate of 350 µg per 24-hour period based on the manufacturer’s specifications for each pump model. To implant the pumps, mice were anesthetized with isoflurane, and preoperative analgesia was provided by a subcutaneous injection of 100 µL of an analgesic solution containing lidocaine and buprenorphine. A small (~1 cm) midline incision was made in the lower abdominal region, and the osmotic pump was carefully placed into the peritoneal cavity. The incision was then sutured, and mice were allowed to recover in a clean cage placed over a heating pad to maintain body temperature during the immediate postoperative period. All procedures were performed under sterile conditions and in accordance with approved animal care protocols.

value: Hypothalamus

value: Brain cells

value: Wild type

value: ImP


title: PanT24-Cell7

description: Uni-C library

source_name: Blood

extract_protocol:
The PCR products were performed size sellection using VAHTS DNA Clean Beads (Vazyme, N411). Briefly, to obtain PCR products with a fragment size of 300 bp - 400 bp, 70 μl of DNA Clean Beads were added to 100 μl of the sample to adsorb DNA fragments larger than 400 bp. After collecting the supernatant, 20 μl of beads were added to adsorb DNA fragments ranging from 300 bp to 400 bp, and the supernatant was removed. After washing twice with 80% ethanol (Sigma-Aldrich, E7023), 20 μl of ddH2O was added to recover the magnetic bead-bound DNA fragments.
Cell fixation and permeabilization: Cells were fixed directly with 1% formaldehyde (Sigma-Aldrich, 47608-250ML-F) for 10 min with rotation at room temperature. The reaction was terminated by 0.2% BSA (Sigma-Aldrich, V900933) for 5 min. After washing twice with PBS (Hyclone, SH30256.FS), cells were crosslinked with freshly made 3 mM EGS (Thermo Fisher Scientific, 21565) for 20 min with rotation at room temperature. Then, 0.25 M glycine (Sigma-Aldrich, 410225) was add to quench the reaction. Subsequently, the cells were washed twice with ice-cold Wash Buffer (10 mM Tris-HCl pH 8.0 (Sango Biotech, B548127), 10 mM NaCl (Sigma-Aldrich, S9888) and 0.1 mg/ml BSA). Fixed cells were then resuspended in ice-cold Hi-C Lysis Buffer (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% NP40 (Sigma-Aldrich, 127087-87-0)) containing a protease inhibitor (Roche, 11836170001) and incubated on ice for 15 min. After centrifugation, cells were further permeabilized with 40 ml of 0.5% SDS (Sigma-Aldrich, 05030) at 65 °C for 10 min and then immediately placed on ice for 3 min.    In situ digestion: Add 20 ml of 10% Triton X-100 (Sigma-Aldrich, T8787) to the reaction and incubated for 5 min to quench the SDS. Subsequently, the digestion mix (100 μl of ddH2O, 20 μl of 10× NEB buffer 2, 20 μl of MboI (NEB, R0147S, 20 units/μl)) was added to the reaction and incubated at 37 °C for 4 h.   End repairing and in situ proximity ligation: The reaction was incubated at 65 °C for 20 min to terminate digestion, then cool to room temperature. Add 81 μl of ddH2O, 10 μl of 10× NEB buffer 2, 3 μl of dNTPs (NEB, N0447S), and 6 μl of DNA polymerase I Klenow fragment (NEB, M0210) to the reaction system, and incubated the sample at 37 °C for 1 h. Ligation was performed by the addition of 270 μl of H2O, 50 μl of T4 Ligase Buffer, 50 μl of 10% Triton X-100, 5 μl of 2% BSA and 25 μl of T4 DNA ligase (Thermo Fisher Scientific, EL0011), and incubated at room temperature for 2 h.  Single cell isolation and amplification: Individual Nuclei were transferred with a glass micropipette into a 0.2 ml low-bind PCR tube (Axygen, PCR-02-L-C) with 2 μl of Buffer L (200 mM NaOH (Sigma-Aldrich, 72068) and 50 mM DTT (Sigma-Aldrich, D9779)) and incubated at 72 °C for 10 min. Then 2 μl of Buffer N (200 mM HCl) was added and incubated in thermomixer (Eppendorf) with rotation at 1000 rpm for 3 min to terminate lysis and neutralize the reaction. Added 6.8 μl of ddH2O, 0.5 μl of dNTPs (10 mM each), 1 μl of Alpha Thiol-modified ddNTPs (10 mM each, Trilink), 2 μl of Exo-Resistant Random Primer (500 μM), 2 μl of EquiPhi29™ DNA Polymerase Reaction Buffer (10×), 2 μl of 20 mM MnCl2 (Sigma-Aldrich, 63535), 0.2 μl of DTT (0.1 M) and 1 μl of EquiPhi29™ DNA Polymerase (Thermo Fisher Scientific, A39390) to the reaction and mixed thoroughly, followed by incubation at 45 °C for 2 h. Subsequently, the reaction was terminated by incubating at 65 °C for 10 min.    DNA size selection: The PCR products were performed size sellection using VAHTS DNA Clean Beads (Vazyme, N411). Briefly, to obtain PCR products with a fragment size of 300 bp - 400 bp, 70 μl of DNA Clean Beads were added to 100 μl of the sample to adsorb DNA fragments larger than 400 bp. After collecting the supernatant, 20 μl of beads were added to adsorb DNA fragments ranging from 300 bp to 400 bp, and the supernatant was removed. After washing twice with 80% ethanol (Sigma-Aldrich, E7023), 20 μl of ddH2O was added to recover the magnetic bead-bound DNA fragments.   Sequencing library construction: DNA sequencing libraries were prepared using the VAHTS Universal Plus DNA Library Prep Kit (Vazyme, NDM627) according to the manufacturer’s protocol.

value: Blood


title: Xeno 28.A

description: Library name: Xeno 28.A


title: Dog_9_deep_3

description: Library name: DSP-1001660022199-E-B08

value: Rostral maxilla

value: Conventional


title: Dog_1_normal_1

description: Library name: DSP-1001660022199-E-B02


title: Xeno 28.3

description: Library name: Xeno 28.3


title: Xeno 2.1.9

description: Library name: Xeno 2.1.9


title: snRNA-seq SPF ImP Hypothalamus Baseline D4

description: Library name: 113CM4


title: snRNA-seq SPF Vehicle Hypothalamus Baseline D2

description: Library name: 113CM2

value: Vehicle


title: PanT24-Cell4

description: Uni-C library


title: PanT24-Cell6

description: Uni-C library


title: snRNA-seq SPF Vehicle Hypothalamus Baseline D1

description: Library name: 111CM1


title: PanT24-Cell5

description: Uni-C library


title: PanT24-Cell3

description: Uni-C library


title: Dog_1_surface_4

description: Library name: DSP-1001660022199-E-B01


title: Treg, aIL2/IL2+5-Ph-IAA #8, Foxp3AIDTIR1(F74G), Spl+LNs

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description: Library name: 316248

data_processing:
Reads were trimmed using Cutadapt and filtered using standard illumina quality metrics.
Reads from ribosomal DNA were were removed using Bowtie 2.
Remaining reads were aligned to the mm10 genome version of December 2011 (GRCm38) using STAR version 2.4.2a.
To quantify reads aligning to exons and introns, we used a custom-curated and extended version of mm10 RefSeq (downloaded on December 6, 2018) in which intron annotations were created by extrapolating from the annotated exons of each transcript.
Read quantification was performed separately for exons and introns over the whole gene body using subread featureCounts version 2.0.2.
Reads were separated into two groups: those entirely overlapping with exons (exonic reads) and those overlapping entirely with introns or with intron-exon junctions (intronic reads).
Assembly: mm10
Supplementary files format and content: txt = raw count values, in ASCII text format tab delimited.

source_name: Spleen + Lymph nodes

extract_protocol:
RNA was extracted using an in-house kit. Sorted cells were lysed with a buffer containing guanidine thiocyanate, Triton X-100 and 𝛽-mercapthoethanol. RNA was captured using magnetic beads. Following a series of wash steps, the beads were incubated with a DNAse I-containing buffer (NEB, cat #M0303) for 15 minutes at 37°C to degrade genomic DNA. After washing, the RNA was eluted in 20uL nuclease-free water for 5 mins at 60°C from pre-dried beads. RNA quality and concentration were assessed using the Agilent DNF-471 RNA kit and Agilent Fragment Analyzer.
SMARTer Stranded Total Pico Input RNA Kit v3 (Takara, cat. #634487) was used according to manufactor protocol.

treatment_protocol: Samples 284087 - 284116: For resting Treg cells, mice were injected with either PBS or 0.30mg 5-Ph-IAA per mouse (intraperitoneally), 6 hours prior to harvest. To induce Treg cell activation, mice were injected with diphtheria toxin (40ug/kg per dose) on 2 consecutive days, 11 days before harvesting the mice. Then, they were injected with either PBS or 0.3mg 5-Ph-IAA per mouse (intraperitoneally), 6 hours prior harvest. Samples 316222- 316249: 1μg recombinant IL-2 (Pepro Tech, 212-12-250UG) was pre-incubated with 5μg JES6-1 antibody (BioXcell, BE0043) for 30 min at 37°C and intraperitoneally injected into mice on three consecutive days before harvest on day 5. On day 5, mice were injected with PBS, aIL2/IL2, or aIL2/IL2 + 0.3mg 5-Ph-IAA per mouse (intraperitoneally), 6 hours prior harvest.

value: Spleen + Lymph nodes

value: Treg cell

value: Foxp3AID-V5-DTR-GFP Rs26Tir1(F74G)

value: aIL2/IL2 + 5-Ph-IAA


title: Treg, aIL2/IL2+5-Ph-IAA #9, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316249


title: Dog_9_dysplasia_3

description: Library name: DSP-1001660022199-E-C04


title: Dog_1_surface_2

description: Library name: DSP-1001660022199-E-A11

value: Rostral mandible

value: Papillary


title: Xeno 2.1.1

description: Library name: Xeno 2.1.1

value: Xenograft

value: Human fetal liver


title: PanT24-Cell2

description: Uni-C library


title: Xeno 2.1.6

description: Library name: Xeno 2.1.6


title: Dog_1_surface_1

description: Library name: DSP-1001660022199-E-A10


title: Treg, aIL2/IL2+5-Ph-IAA #7, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316247


title: Dog_1_normal_2

description: Library name: DSP-1001660022199-E-B03


title: Treg, aIL2/IL2 #11, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316246


title: Xeno 3.C

description: Library name: Xeno 3.C

value: WT


title: Xeno 3.A

description: Library name: Xeno 3.A


title: Dog_1_TMS_4

description: Library name: DSP-1001660022199-E-A09


title: PanT24-Cell1

description: Uni-C library


title: Dog_1_TMS_3

description: Library name: DSP-1001660022199-E-A08


title: Xeno 3.4

description: Library name: Xeno 3.4


title: Treg, aIL2/IL2 #10, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316245


title: Xeno 3.3

description: Library name: Xeno 3.3


title: Treg, PBS #8, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316243

value: PBS


title: COLO320DM-Cell6

description: Uni-C library

source_name: cell line

value: cell line

tag: cell line


title: Dog_1_surface_3

description: Library name: DSP-1001660022199-E-A12


title: Xeno 3.2

description: Library name: Xeno 3.2


title: COLO320DM-Cell5

description: Uni-C library


title: Xeno 3.1

description: Library name: Xeno 3.1


title: COLO320DM-Cell4

description: Uni-C library


title: Treg, PBS #7, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316242


title: COLO320DM-Cell3

description: Uni-C library


title: Dog_1_deep_3

description: Library name: DSP-1001660022199-E-A04


title: C17_RAD21AID_SC6,mCherry_IAA,Input,rep2

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Reads were mapped and processed using the 4DN ChIP-seq data processing pipeline (https://github.com/4dn-dcic/chip-seq-pipeline2)
Assembly: hg38
Supplementary files format and content: pval bigWig and IDR narrowPeaks

growth_protocol: eHap1 cells were cultured in Iscove's Modified Dulbecco's Medium (IMDM) medium supplemented with Glutamax (Thermofisher), 25mM Hepes, 10% FBS, and 1% Penicillin-Streptomycin following standard procedures. Cells were routinely checked and sorted for haploidy.

extract_protocol:
100 million cells were crosslinked with 1% formaldehyde for 10min. Cells were subsequently quenched with 125mM glycine for 10min and washed twice with cold PBS. Cells were scraped from culture dishes and cell pellets were subsequently lysed in LB1 buffer (50mM Hepes, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100), washed in LB2 buffer (10mM Tris, 200mM NaCl, 1mM EDTA, 0.5mM EGTA), and resuspended in LB3 buffer (10mM Tris, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine) prior sonication. Chromatin was sonicated using Bioruptor Pico (Diagnode) with a setting of 30s on, 30s off for 8 cycles. Fragmented chromatin was then incubated with 6ug of antibodies pre-coupled to Dynabeads protein G beads (Thermofisher) overnight at 4oC. Beads-bound chromatin was then washed 10x with RIPA buffer (50mM Hepes, 500mM LiCl, 1mM EDTA, 1% NP40, 0.7% sodium deoxycholate), once with TBS buffer, and decrosslinked in elution buffer (50mM Tris, 10mM EDTA, 1% SDS) at 65oC for 18h. Eluted DNA was then treated with protease K and RNAse A, and subsequently purified with phenol/chloroform/isoamyl alcohol 25:24:1.
Purified DNA was either assessed with qPCR or continued with ChIP-seq NGS sequencing library preparation. Sequencing libraries was constructed using NEBnext Ultra II DNA library prep kit (NEB) following the manufacture’s protocol. Briefly, DNA was end-repaired and poly-A tailed, ligated to NEBnext adapters, and digested with USER enzyme. Annealed libraries were then purified with AMPure XP beads (Beckman Coulter) and PCR amplified with indexing primers for 4-12 cycles. Sequencing libraries were checked with Bioanalyzer HS DNA chip (Agilent).

treatment_protocol: To release TetR from the TetO platform, cells were treated with doxycycline for 1h.To deplete factors, cells were treated with auxin (5-Ph-IAA, BioAcademia)for 2 (RAD21) or 3h (STAG2, WAPL, CTCF, PDS5A).

tag: protein

value: Input

tag: replicate

tag: antibody


title: Treg, PBS #6, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316241


title: COLO320DM-Cell2

description: Uni-C library


title: Dog_1_deep_2

description: Library name: DSP-1001660022199-E-A03


title: Treg, aIL2/IL2+5-Ph-IAA #6, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316240


title: Dog_1_deep_4

description: Library name: DSP-1001660022199-E-A05


title: C17_RAD21AID_SC6,mCherry,SMC1,rep2

description: C17_RAD21AID_SC6_mCherry_SMC1_rep1_rep2.pval.bigwig

value: mCherry

value: Anti-SMC1 (A300-055A, Bethyl)


title: Treg, aIL2/IL2+5-Ph-IAA #5, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316239


title: C17_RAD21AID_SC6,mCherry,Input,rep3


title: COLO320DM-Cell1

description: Uni-C library


title: Dog_1_deep_1

description: Library name: DSP-1001660022199-E-A02


title: GM12878-BULK

description: Uni-C library


title: Dog_1_TMS_2

description: Library name: DSP-1001660022199-E-A07


title: Treg, aIL2/IL2 #9, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316244


title: NTC-plate1

description: Library name: DSP-1001660022199-E-A01


title: COLO320DM-BULK

description: Uni-C library


title: C17_RAD21AID_SC6,mCherry,Input,rep2


title: Dog_1_TMS_1

description: Library name: DSP-1001660022199-E-A06


title: Treg, aIL2/IL2+5-Ph-IAA #4, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316238


title: C17_RAD21AID_SC1,TACL-ON_IAA,SMC3,rep1

value: anti-SMC3 (A300-060A, Bethyl)


title: GM12878-Cell10

description: Uni-C library


title: KOLF2.2J cells, OsTIR1(F74G+S210A), RBBP4_mAID, biol rep2

city: Chicago

first: De

last: Xing

state: IL

address: 264 E Huron St., Suite: 4-121

department: Feinberg School of Medicine, Obstetrics and Gynecology

institute: Northwestern University

description:
Library name: Ocp210A_RBBP4_C19_rep2
Ocp210A_RBBP4_C19_rep2_S14

data_processing:
The quality of sequencing FastQ files were checked using FastQC.
The reads were aligned to the GENCODE human genome V46 ( GRCh38.p14) by the STAR aligner (v2.7.9a) with default parameters.
Differential expression analysis was performed using the R package DESeq2 (V1.44.0) with Benjamini-Hochberg correction for multiple testing.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file inludes raw counts for each Sample
Supplementary files format and content: tsv files include statistic values for each Sample

source_name: iPSC

extract_protocol:
Total RNA was isolated using the Quick RNA miniprep kit (Zymo Research, R1057) with DNase I treatment by following the manufacturer's instructions. The integrity of total RNA was assessed through 1% TAE agarose gel electrophoresis. mRNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490L).
RNA-Seq libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, E7760L) and NEBNext Multiplex Oligos (NEB, E7500L) with index primers according to the manufacturer's instructions.

value: iPSC


title: Treg, aIL2/IL2 #8, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316237


title: GM12878-Cell9

description: Uni-C library


title: KOLF2.2J cells, OsTIR1(F74G+S210A), RBBP4_mAID, biol rep1

description:
Library name: Ocp210A_RBBP4_C19_rep1
Ocp210A_RBBP4_C19_rep1_S13


title: GM12878-Cell8

description: Uni-C library


title: C17_RAD21AID_SC1,TACL-ON_IAA,SMC1,rep2

description: C17_RAD21AID_SC1_TACL-ON_IAA_SMC1_rep1_rep2.pval.bigwig


title: KOLF2.2J cells, OsTIR1(F74G), RBBP4_mAID, biol rep2

description:
Library name: Ocp74G_RBBP4_C2_rep2
Ocp74G_RBBP4_C2_rep2_S12


title: Treg, aIL2/IL2 #6, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316235


title: C17_RAD21AID_SC1,TACL-ON_IAA,SMC1,rep1


title: GM12878-Cell7

description: Uni-C library


title: Treg, aIL2/IL2 #5, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316234


title: C17_RAD21AID_SC1,TACL-ON_IAA,NIPBL,rep1

value: NIPBL

value: anti-NIPBL (A301-779A, Bethyl)


title: KOLF2.2J cells, OsTIR1(F74G), RBBP4_mAID, biol rep1

description:
Library name: Ocp74G_RBBP4_C2_rep1
Ocp74G_RBBP4_C2_rep1_S11


title: KOLF2.2J cells, OsTIR1(F74G+S210A), parent, biol rep2

description:
Library name: Ocp210A_Parent_rep2
Ocp210A_Parent_rep2_S8


title: Treg, PBS #5, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316233

value: Spleen + Lymph nodes

value: Treg cell


title: GM12878-Cell5

description: Uni-C library


title: GM12878-Cell6

description: Uni-C library


title: KOLF2.2J cells, OsTIR1(F74G+S210A), parent, biol rep1

description:
Library name: Ocp210A_Parent_rep1
Ocp210A_Parent_rep1_S7


title: Treg, PBS #3, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316231

value: Foxp3AID-V5-DTR-GFP Rs26Tir1(F74G)


title: GM12878-Cell4

description: Uni-C library


title: KOLF2.2J cells, OsTIR1(F74G), parent, biol rep2

description:
Library name: Ocp74G_Parent_rep2
Ocp74G_Parent_rep2_S6


title: Treg, aIL2/IL2 #7, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316236


title: GM12878-Cell3

description: Uni-C library


title: Treg, aIL2/IL2+5-Ph-IAA #3, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316230

value: aIL2/IL2 + 5-Ph-IAA


title: C17_RAD21AID_SC1,TACL-ON_IAA,Input,rep1


title: C17_RAD21AID_SC1,TACL-ON_IAA,FLAG,rep1

value: FLAG

value: anti-FLAG (F1804, Merck)


title: Treg, PBS #4, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316232


title: KOLF2.2J cells, OsTIR1(F74G), parent, biol rep1

description:
Library name: Ocp74G_Parent_rep1
Ocp74G_Parent_rep1_S5


title: Treg, aIL2/IL2+5-Ph-IAA #2, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316229


title: C17_RAD21AID_SC1,TACL-ON_IAA,Input,rep2


title: HUVEC, Dox treatment protocol, Dox 2

city: Kansas City

first: Eugene

last: Konorev

state: MO

address: 1750 Independence Ave

institute: Kansas City University

description: Library name: Sample 4

data_processing:
PartekFLOW  12.4.3
Pre-alignment QC/QA was performed to assess raw sequencing read quality, and low-quality reads were trimmed using a Phred quality score threshold of >30 with a minimum read length of 25 bp (algorithm is built in PartekFLOW).
Alignment was performed using the STAR 2.7.8a aligner against the human hg38 reference genome and Ensembl transcripts (release 109) index. After alignment, low-quality reads (mapping quality < 20), singletons, and unaligned reads were filtered out.
TGFbeta2 treatment study: Transcripts per kilobase million (TPM) normalization was applied followed by a Poisson regression model with the Wald statistic for p-value calculation. Dox treatment and Dox washout study: protein coding genes were analyzed after median ratio normalization using the DESeq2 method.
Genes meeting the significance threshold of p<0.05 (after Bonferroni correction for multiple testing) with a ≥2-fold change between groups were selected for further analysis.
Assembly: hg 38
Supplementary files format and content: tab delimited text files include raw counts for each sample

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVEC) and human cardiac microvascular endothelial cells (HCMVEC) were grown in EGM2 and EGM2-MV, respectively, in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using mirVana RNA isolation kit and used for construction of the sequencing libraries.
Doxorubicin project: Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. TGF-beta2 project: cDNA library was constructed using the Illumina TruSeq RNA sample preparation kit.

treatment_protocol: Doxorubicin project: Cells were treated with 16 nM doxorubicin for 48 hours before total RNA extraction (treatment protocol). Additionally, doxorubicin was removed from media to culture cell in doxorubicin free media for 48 hours before total RNA extraction (washout protocol). For the TGF-beta2 study, cells were starved and treated with 0.3 ng/ml TGF-beta2 for 16 hours.

value: HUVEC

value: endothelial cells

value: Doxorubicin 16 nM


title: C17_RAD21AID_SC1,TACL-ON,SMC1,rep2

description: C17_RAD21AID_SC1_TACL-ON_SMC1_rep1_rep2.pval.bigwig

value: TACL-ON


title: Treg, aIL2/IL2+5-Ph-IAA #1, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316228


title: HUVEC, Dox treatment protocol, Dox 1

description: Library name: Sample 3

value: WT


title: Treg, aIL2/IL2 #4, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316227


title: MC38-Uni-C-Cell8

description:
Library name: MC38-Uni-C-Cell8
Uni-C library

value: cell line


title: C17_RAD21AID_SC1,TACL-ON,SMC1,rep1

value: Anti-SMC1 (A300-055A, Bethyl)


title: HUVEC, Dox treatment protocol, control 2

description: Library name: Sample 2

value: No treatment


title: MC38-Uni-C-Cell7

description:
Library name: MC38-Uni-C-Cell7
Uni-C library


title: C17_RAD21AID_SC1,TACL-ON,NIPBL,rep1


title: Treg, aIL2/IL2 #3, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316226


title: HUVEC, Dox treatment protocol, control 1

description: Library name: Sample 1


title: C17_RAD21AID_SC1,TACL-ON,SMC3,rep1

value: anti-SMC3 (A300-060A, Bethyl)


title: C17_RAD21AID_SC1,TACL-ON,Input,rep2

value: Input


title: pHSC5_P3

city: Brussels

first: Stefaan

last: Verhulst

address: Laarbeeklaan 103, D022

department: BMWE

country: Belgium

institute: Vrije Universiteit Brussel

description: Library name: pHSC5_P3

data_processing:
Quality control of sequencing reads was conducted using FastQC, followed by adapter trimming and error correction with BBDuk.
The processed reads were aligned to the reference genome (Homo Sapiens_GRCm38.p6) using the STAR aligner.
Transcript assembly was carried out with HTSeq.
Raw count matrices were generated and normalized with the DESeq2 package in R.
Assembly: GRCm38.p6
Supplementary files format and content: CSV file containing raw count matrix with gene symbols and counts for all samples
Supplementary files format and content: CSV file containing normalized count matrix processed by DESeq2 with all samples

source_name: pHSC

extract_protocol:
RNA was harvested using ReliaPrep RNA Cell Miniprep System (Promega)
Library prep for RNA sequencing was performed using QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI 12 nt set B1 (Lexogen).

value: pHSC

tag: batch


title: pHSC4_P3

description: Library name: pHSC4_P3


title: Treg, aIL2/IL2 #1, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316224

value: Spleen + Lymph nodes


title: Treg, aIL2/IL2 #2, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316225

value: Treg cell


title: GM12878-Cell2

description: Uni-C library


title: MC38-Uni-C-Cell6

description:
Library name: MC38-Uni-C-Cell6
Uni-C library


title: C17_RAD21AID_SC1,TACL-ON,Input,rep1


title: MC38-Uni-C-Cell4

description:
Library name: MC38-Uni-C-Cell4
Uni-C library


title: pHSC3_P4

description: Library name: pHSC3_P4


title: MC38-Uni-C-Cell5

description:
Library name: MC38-Uni-C-Cell5
Uni-C library


title: C17_RAD21AID_SC1,TACL-ON,FLAG,rep1


title: MC38-Uni-C-Cell3

description:
Library name: MC38-Uni-C-Cell3
Uni-C library


title: C17_RAD21AID_SC1,TACL-ON,Input,rep3


title: Treg, PBS #1, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316222

value: Foxp3AID-V5-DTR-GFP Rs26Tir1(F74G)

value: PBS


title: GM12878-Cell1

description: Uni-C library


title: pHSC2_P4

description: Library name: pHSC2_P4


title: C17,mCherry,NIPBL,rep1

value: mCherry

value: NIPBL

value: anti-NIPBL (A301-779A, Bethyl)


title: C17,mCherry,Input,rep6


title: MC38-Uni-C-Cell2

description:
Library name: MC38-Uni-C-Cell2
Uni-C library


title: aTreg, 5-Ph-IAA#8, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284116

value: activated Treg cell


title: aTreg, 5-Ph-IAA#7, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284115


title: MC38-PTA-Cell4

description:
Library name: MC38-PTA-Cell4
Uni-C library


title: C17,mCherry,Input,rep5


title: MC38-Uni-C-Cell1

description:
Library name: MC38-Uni-C-Cell1
Uni-C library


title: aTreg, 5-Ph-IAA#6, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284111


title: MC38-PTA-Cell3

description:
Library name: MC38-PTA-Cell3
Uni-C library


title: iHEP2_P2

description: Library name: iHEP2_P2

source_name: iHEP

value: iHEP


title: Treg, PBS #2, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 316223


title: C17,mCherry,Input,rep3


title: aTreg, 5-Ph-IAA#5, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284110


title: MC38-PTA-Cell2

description:
Library name: MC38-PTA-Cell2
Uni-C library


title: HepaRG3

description: Library name: HepaRG3

source_name: HepaRG

value: HepaRG


title: iHEP1_P2

description: Library name: iHEP1_P2


title: C17,mCherry,Input,rep2


title: MC38-PTA-Cell1

description:
Library name: MC38-PTA-Cell1
Uni-C library


title: C17,mCherry,Input,rep1


title: MC38-BULK-2

description:
Library name: MC38-BULK-2
Uni-C library


title: aTreg, 5-Ph-IAA#3, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284105


title: HepaRG2

description: Library name: HepaRG2


title: aTreg, 5-Ph-IAA#2, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284104


title: HepaRG1

description: Library name: HepaRG1


title: pHSC1_P3

description: Library name: pHSC1_P3


title: aTreg, 5-Ph-IAA#4, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284106


title: MC38-BULK-1

description:
Library name: MC38-BULK-1
Uni-C library


title: C17,TACL-OFF,Input,rep3

value: TACL-OFF


title: C17,mCherry,FLAG,rep1

value: FLAG

value: anti-FLAG (F1804, Merck)


title: iHEP3_P2

description: Library name: iHEP3_P2


title: aTreg, 5-Ph-IAA#1, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284103


title: C17,TACL-ON,Input,rep7

value: TACL-ON


title: C57-WT-WGS

description: WGS library

data_processing:
SNP and INDEL calling from Uni-C datasets: For SNP and INDEL detection, raw read pairs are initially processed using FASTP (version: 0.23.2) to remove residual sequencing adapter sequences. To mitigate background noise associated with Hi-C ligation junctions, we filter out all read pairs that contain the MboI restriction site ligation junction "GATCGATC". Subsequently, these filtered read pairs are aligned to the reference genome GRCh37 or GRCm38 using BWA (version: 0.7.17). The aligned BAM files are sorted with SAMTOOLS (version: 1.15.1), and duplicate reads are removed via SAMBAMBA (version: 0.6.6). Next, base quality scores are recalibrated using the BaseRecalibrator (from GATK, version 4.2.2), followed by the detection of SNPs and indels using HaplotypeCaller (from GATK, version 4.2.2). We then conduct a statistical analysis of the variant data in each single-cell VCF. Variants present in two or more VCF files will be considered genuine and retained, whereas variants that only appear in one VCF file will be filtered out. The statistics for base substitution types, mutation spectrum, 96 mutational profiles, and types of Indels are implemented using the R package MutationalPatterns (version 3.12.0).
Construction of single-cell genome-wide chromatin interaction matrix: Uni-C raw read pairs are initially processed using FASTP (version: 0.23.2) to remove residual sequencing adapter sequences. After filtering, the read pairs are aligned to the reference genome using “mem” module of BWA (version: 0.7.17) with parameters “-5SP -T0”. After alignment, we use the “parse” module of PAIRTOOLS (Version: 0.3.0) to convert the generated SAM files into PAIRSAM format, with specific parameters set to “--min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30”. The pairsam files are then sorted and deduplicated using the “sort” and “dedup” modules of PAIRTOOLS, respectively. Following deduplication, the “split” module of PAIRTOOS is used to convert the deduplicated PAIRSAM files into PAIRS format. These final pairs files are utilized to generate the chromatin interaction matrices using tools such as JUICERTOOLS (Version: 1.9.9) or COOLER (Version: 0.9.3).
Assembly: GRCh37 or GRCm38
Supplementary files format and content: The Hi-C pairs files used to generate the genome-wide chromatin interaction matrix
Supplementary files format and content: These VCF files were generated using the HaplotypeCaller module of GATK (version 4.2.2) and contain information on both SNPs and INDELs.
Library strategy: WGS

value: Blood


title: aTreg, PBS#10, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284114


title: C17,TACL-ON,Input,rep3

value: Input


title: KPC0403-Cell6

description: Uni-C library


title: HEP_iHSC2

description: Library name: pHEP2

source_name: pHEP

value: pHEP


title: aTreg, PBS#9, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284113

value: Spleen + Lymph nodes


title: C17,TACL-ON,Input,rep2


title: aTreg, PBS#8, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284112


title: KPC0403-Cell5

description: Uni-C library


title: HEP_iHSC1

description: Library name: pHEP1


title: C17,TACL-ON,Input,rep1


title: KPC0403-Cell4

description: Uni-C library


title: aTreg, PBS#7, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284109


title: C17,TACL-ON,FLAG,rep1

description:
C17_TACL-ON_FLAG_rep1_rep2.pval.bigwig
C17_TACL-ON_FLAG_rep1_rep2.idr.optimal_peak.regionPeak.bb


title: iHSC6_D21_9CRA

description: Library name: iHSC6_D21_9CRA

source_name: iHSC

value: iHSC


title: aTreg, PBS#6, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284108

value: Foxp3AID-V5-DTR-GFP Rs26Tir1(F74G)


title: KPC0403-Cell3

description: Uni-C library


title: iHSC6_D21

description: Library name: iHSC6_D21


title: HEP_iHSC4

description: Library name: pHEP4


title: YCU_EZH2

city: Yokohama

first: Hiroyoshi

last: Kunimoto

address: 3-9 Fukuura, Kanazawa

department: Department of Stem Cell and Immune Regulation

country: Japan

institute: Yokohama City University Graduate School of Medicine

data_processing:
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: xls file includes raw counts for each sample

source_name: hematopoietic tissue

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA LP Kit after mRNA capture.

value: hematopoietic tissue

value: YCU-AML1 cell line

value: leukemia cells

value: valemetostat


title: YCU_Ve3

value: vehicle


title: aTreg, PBS#5, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284107

value: activated Treg cell

value: PBS


title: KPC0403-Cell2

description: Uni-C library


title: KPC0403-Cell1

description: Uni-C library


title: iHSC5_D21_9CRA

description: Library name: iHSC5_D21_9CRA


title: aTreg, PBS#4, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284102


title: KPC0402-Cell6

description: Uni-C library


title: HEP_iHSC3

description: Library name: pHEP3


title: aTreg, PBS#3, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284101


title: YCU_Ve2


title: YCU_Ve1


title: aTreg, PBS#2, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284100


title: KPC0402-Cell5

description: Uni-C library


title: Krox20-positive cells

city: Dallas

first: Elnaz

last: Ghotbi

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v5.0.1(https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Skin

extract_protocol:
PMID: 28745643, PMID: 30788828
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)
The sample was run on the Illumina NextSeq 500 on a single 150 cycle High Output flowcell. We targeted 20K reads per cell.

value: Skin

value: Keratinocytes


title: iHSC5_D0

description: Library name: iHSC5_D0

value: iPSC


title: aTreg, PBS#1, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284099


title: iHSC4_D21_9CRA

description: Library name: iHSC4_D21_9CRA


title: KPC0402-Cell4

description: Uni-C library


title: rTreg, 5-Ph-IAA#6, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284098

value: resting Treg cell


title: KPC0402-Cell3

description: Uni-C library

value: Blood


title: iHSC4_D21

description: Library name: iHSC4_D21


title: iHSC6_D0

description: Library name: iHSC6_D0


title: ChAT-eGFP_in_vitro_plate5

first: Hugo

last: Snippert

state: Utrecht

address: Universiteitsweg 100

department: Center for Molecular Medicine

institute: University Medical Center Utrecht

data_processing:
Raw FASTQ files were processed with an adopted version of the nf-core scrnaseq pipeline (2.4.0) [https://github.com/gowanaka/nf-core-scrnaseq]. In brief, STARsolo (2.7.10b) was used to align reads to a custom mm10 transcriptome including eGFP and P2A-mScarlet-I-P2A-DTR transgenes and ERCC spike-ins. Following mapping, count matrices were generated with STARsolo (2.7.10b).
Assembly: mm10
Supplementary files format and content: Tab-seperated values files

source_name: Small intestinal organoids

growth_protocol: Organoids were seeded in medium containing EGF, Noggin and Rspondin (ENR) 3 to 4 days prior to treatment with differentiation medium and harvested on the 7th day after seeding.

extract_protocol:
Trypsinization to make single cell suspensions, followed by FACS
CEL-Seq2 (SORT-seq)

treatment_protocol: Mouse small intestinal organoids were cultured in Matrigel and treated with ENR, ENR+IL4+IL13 or IL4+IL13+BMP2+BMP4+WNT5a+IL25+NRG1+Acetylcholine

value: Small intestinal organoids

value: FACS-enriched fluorescent cell populations

value: ENR or ENR+IL4+IL13


title: rTreg, 5-Ph-IAA#5, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284097

value: Spleen + Lymph nodes


title: KPC0402-Cell2

description: Uni-C library


title: iHSC4_D0

description: Library name: iHSC4_D0


title: KPC0402-Cell1

description: Uni-C library


title: iHSC3_P1

description: Library name: iHSC3_P1

value: iHSC


title: ChAT-eGFP_in_vitro_plate3


title: ChAT-eGFP_in_vitro_plate2

value: ENR


title: Implant with S. aureus 3

city: Newark

first: Dane

last: Parker

state: NJ

address: 205 South Organge Ave, G-1208

department: Pathology, Immunology and Laboratory Medicine

institute: Rutgers New Jersey Medical School

description: Library name: SAhu3

data_processing:
Sequencing files were processed in Partek Flow
Assembly: STAR 2.7.8a with hg38 for human
Assembly: STAR 2.7.8a with SA-000013465 for S. aureus
Supplementary files format and content: xls file with normalized counts and expression differences

organism:
Staphylococcus aureus
Homo sapiens

source_name: Staphylococcus aureus

extract_protocol:
Direct-zol micro RNA extraction kit (Zyzmo)
Ribozero plus (Illumina)

value: human lung

value: Staphylococcus aureus JE2

value: Growth in vivo


title: rTreg, 5-Ph-IAA#4, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284096

value: Foxp3AID-V5-DTR-GFP Rs26Tir1(F74G)


title: iHSC5_D21

description: Library name: iHSC5_D21


title: iHSC3_D10

description: Library name: iHSC3_D10


title: rTreg, 5-Ph-IAA#3, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284095


title: iHSC3_D0

description: Library name: iHSC3_D0


title: rTreg, 5-Ph-IAA#2, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284094


title: Implant with S. aureus 2

description: Library name: SAhu2


title: ChAT-eGFP_ex_vivo_plate3

source_name: Small intestine

value: Small intestine

value: GFP+ epithelial cells

value: ChAT-eGFP


title: Implant with S. aureus 1

description: Library name: SAhu1


title: iHSC2_P1

description: Library name: iHSC2_P1


title: rTreg, 5-Ph-IAA#1, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284093


title: ChAT-eGFP_ex_vivo_plate2


title: ChAT-eGFP_in_vitro_plate4

value: ChAT-eGFP;Nrep-mScarlet


title: iHSC2_D10

description: Library name: iHSC2_D10


title: rTreg, PBS#6, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284092

value: PBS


title: iHSC2_D0

description: Library name: iHSC2_D0

value: iPSC


title: ChAT-eGFP_ex_vivo_plate1


title: rTreg, PBS#4, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284090

value: resting Treg cell


title: DCs_RT-iPSC_HDR_CASS

city: Isehara-shi

first: Atsushi

last: Fukuda

institute: Tokai University

data_processing:
Single cell RNA-seq library were prepared using 10x Genomics Chromium (human, ~3000 cells target, v3.1).
Sequencing were performed on the DNBSEQ System, in a 2x150bp paired-end (PE) configuration Read 1 (28bp) + i7 index (8bp) + i5 index (0bp) + Read2 (91bp) per lane, with ~350M paired-read per lane, 0.5 lane(s) per sample.
Interactive differential gene expression were analysed through the 10X Genomics Cell Ranger (human, --force-cell=FALSE, aggregation).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cortical brain organoid

growth_protocol: Cortical organoids were generated from hPSCs using the STEMdiff Cerebral Organoid Kit (#08570; StemCell Technologies).

extract_protocol:
RNA extract and libraries were prepared for sequencing using standard protocols of HiSeq X Ten by Genewiz.
ScRNA-seq libraries were generated using the 10X Genomics Chromium Single Cell 3’ Kit v2 and the 10x Chromium Controller (10x Genomics) according to the 10X Single Cell 3’ v2 protocol. Single cells, reagents and single gel beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized droplets and subjected to reverse transcription. Droplets were broken and the barcoded cDNAs were purified with DynaBeads and amplified by 12 cycles of PCR. The amplified cDNA was fragmented, end-repaired, ligated with index adaptors, and size-selected with clean-ups between each step using the SPRIselect Reagent Kit. Quality control of the resulting barcoded libraries was performed with the Agilent TapeStation and by PCR with primers specific to the P5 and P7 sequence.

value: cortical brain organoid

value: rescue XIST_HDR_CASS

tag: gender

value: female


title: rTreg, PBS#5, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284091

value: Spleen + Lymph nodes


title: A2780GPT2si2

city: Hefei

first: Yifan

last: Feng

state: Anhui

address: Jixi Road 218

institute: The Anhui Medical University

description:
Library name: Sanple 5
si_2

data_processing:
Bridge amplification. Bridge PCR amplification was performed on the cBot instrument to generate clusters.
The Illumina sequencing platform uses a 2*150 sequencing mode for Sequencing by Synthesis. Four fluorescently labeled dNTPs, DNA polymerase, and adapter primers are added to the flow cell for amplification. During the extension of the complementary strand in each sequencing cluster, the addition of each fluorescently labeled dNTP releases a corresponding fluorescence. The sequencer captures the fluorescence signals, and computer software converts the light signals into sequencing peaks, thereby obtaining the sequence information of the target fragments.
The image data of sequencing fragments obtained by the high-throughput sequencer are converted into sequence data (reads) through CASAVA base calling, and the files are in fastq format, which mainly contains the sequence information of the sequencing fragments and their corresponding sequencing quality information. The raw data are in fastq format files, which include the base sequences of the reads and their sequencing quality values. Each read is represented by four lines of information: the first line is the unique identifier of the read in Illumina sequencing, the second line is the base sequence, the third line is a + sign followed by the omitted read identifier, and the fourth line is the base quality value.
Assembly: For each sample, the results of reads aligned to the reference genome were used by the StringTie software to assemble transcripts in the sample based on the known transcript location information file as a guide. Transcripts with expression levels equal to 0 were filtered out, and the StringTie-assembled transcripts from all samples were reassembled.
Supplementary files format and content: xls file includes raw counts for each sample

extract_protocol:
Total RNA was extracted from cell samples, and a total of 1 μg of RNA was required for mRNA sequencing library construction.
1.mRNA Enrichment  For eukaryotic mRNA, enrichment was performed using Oligo (dT) magnetic beads to isolate poly(A)-tailed mRNA.  2.mRNA Fragmentation  The enriched mRNA was randomly fragmented into short fragments of approximately 200 bp using chemical or enzymatic methods.  3.Strand-Specific cDNA Synthesis  First-strand cDNA was synthesized using fragmented mRNA as a template and random primers for reverse transcription.  During second-strand cDNA synthesis, dTTP in the dNTP mix was replaced with dUTP to enable strand specificity.  4.Adapter Ligation  Double-stranded cDNA was purified using AMPure XP beads.  The cDNA ends were repaired and A-tailed using an End Repair Mix.  Sequencing adapters were ligated to the A-tailed cDNA.  5.Second-Strand cDNA Digestion  USER enzyme was used to digest the second-strand cDNA (containing dUTP), ensuring the final library contained only first-strand cDNA.  6.PCR Enrichment  The cDNA library was amplified by PCR for approximately 15 cycles using primers complementary to the sequencing adapters to enrich the final library.  7.Library Quality Control and Quantification  The quality of the library was assessed using an Agilent Bioanalyzer or similar instrument to confirm the expected fragment size distribution (~200-500 bp).  The library concentration was quantified using qPCR or a fluorometric method (e.g., Qubit) to ensure optimal concentration for sequencing.

value: Ovarian cancer


title: iHSC1_P1

description: Library name: iHSC1_P1

value: iHSC


title: A2780GPT2sinc3

description:
Library name: Sanple 3
nc_3


title: rTreg, PBS#3, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284089


title: DCs_RT-iPSC_NHEJ

value: rescue XIST_NHEJ


title: A2780GPT2sinc2

description:
Library name: Sanple 2
nc_2


title: A2780GPT2si1

description:
Library name: Sanple 4
si_1


title: iHSC1_D0

description: Library name: iHSC1_D0


title: iHSC1_D10

description: Library name: iHSC1_D10


title: A2780GPT2sinc1

description:
Library name: Sanple 1
nc_1


title: DCs_adsc_iPSCs

value: WT


title: ChAT-eGFP_in_vitro_plate1

value: Small intestinal organoids

value: FACS-enriched fluorescent cell populations


title: A2780GPT2si3

description:
Library name: Sanple 6
si_3


title: HIV Positive Fibrosis, LHCC423

status: Public on Jun 25 2025

type: genomic

first: Yinan

last: Zheng

state: Illinois

address: 680 N Lake Shore Drive, Suite 1400

department: Department of Preventive Medicine

description: HIV Positive Fibrosis

hyb_protocol: Bisulphite converted DNA was samplified, fragmented and hybridized to human infinium MethylationEPIC BeadChip (illumina) using standard illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended illumina scanner setting

data_processing:
ENmix package in R environment (v4.4.0)
processed value definition: Average Beta (processed_data.txt is linked as a Supplementary file on the Series record)

label: Cy3 and Cy5

source_name: Plasma

label_protocol: Standard illumina Protocol

extract_protocol: Circulating cell-free DNA was extracted and concentrated using the QIAamp MinElute ccfDNA Kit (QIAGEN) in batches within three days of blood sample collection.

tag: participant id

tag: Sex

value: Female

tag: cancer stage

tag: group

value: Plasma

tag: age

tag: bmi

tag: site

value: LUTH


title: HIV Positive Fibrosis, LHCC417

description: HIV Positive Fibrosis

tag: tissue


title: HIV Positive Cirrhosis, LHCC425

description: HIV Positive Cirrhosis

value: Male


title: HIV Positive Hepatocellular Carcinoma, LHCC410

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Cirrhosis, LHCC405

description: HIV Positive Cirrhosis


title: rTreg, PBS#2, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284088

tag: cell type

tag: genotype

value: Foxp3AID-V5-DTR-GFP Rs26Tir1(F74G)

value: PBS


title: HIV Positive Cirrhosis, LHCC392

description: HIV Positive Cirrhosis


title: HIV Positive Fibrosis, LHCC391

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC389

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC386

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC385

description: HIV Positive Fibrosis


title: HIV Positive Cirrhosis, LHCC384

description: HIV Positive Cirrhosis


title: DCs_SE1_5a_NHEJ


title: HIV Positive Fibrosis, LHCC388

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC383

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC374

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC373

description: HIV Positive Fibrosis


title: rTreg, PBS#1, Foxp3AIDTIR1(F74G), Spl+LNs

description: Library name: 284087

value: resting Treg cell

tag: treatment


title: HIV Positive Hepatocellular Carcinoma, LHCC370

description: HIV Positive Hepatocellular Carcinoma

value: D


title: HIV Positive Cirrhosis, LHCC372

description: HIV Positive Cirrhosis


title: HIV Positive Fibrosis, LHCC366

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC365

description: HIV Positive Fibrosis


title: HIV Positive Cirrhosis, LHCC362

description: HIV Positive Cirrhosis


title: HIV Positive Fibrosis, LHCC399

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC359

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC369

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC349

description: HIV Positive Fibrosis


title: HIV Positive Hepatocellular Carcinoma, LHCC361

description: HIV Positive Hepatocellular Carcinoma

value: C


title: HIV Positive Fibrosis, LHCC358

description: HIV Positive Fibrosis


title: HIV Positive Cirrhosis, LHCC377

description: HIV Positive Cirrhosis


title: HIV Positive Hepatocellular Carcinoma, LHCC343

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Fibrosis, LHCC340

description: HIV Positive Fibrosis


title: HIV Positive Cirrhosis, LHCC346

description: HIV Positive Cirrhosis


title: HIV Positive Fibrosis, LHCC337

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC357

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC336

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC353

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC387

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC331

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC329

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC339

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC325

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC324

description: HIV Positive Fibrosis


title: HIV Positive Hepatocellular Carcinoma, LHCC323

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Cirrhosis, LHCC319

description: HIV Positive Cirrhosis


title: HIV Positive Cirrhosis, LHCC320

description: HIV Positive Cirrhosis


title: HIV Positive Cirrhosis, LHCC317

description: HIV Positive Cirrhosis


title: HIV Positive Fibrosis, LHCC314

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC311

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC300


title: HIV Positive without Hepatocellular Carcinoma, LHCC301


title: HIV Positive Fibrosis, LHCC304

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC299


title: HIV Positive without Hepatocellular Carcinoma, LHCC296


title: HIV Positive without Hepatocellular Carcinoma, LHCC297


title: HIV Positive Fibrosis, LHCC294

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC298


title: HIV Positive without Hepatocellular Carcinoma, LHCC295


title: HIV Positive without Hepatocellular Carcinoma, LHCC292


title: HIV Positive without Hepatocellular Carcinoma, LHCC286


title: HIV Positive Cirrhosis, LHCC293

description: HIV Positive Cirrhosis


title: HIV Positive Cirrhosis, LHCC278

description: HIV Positive Cirrhosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC290


title: HIV Positive without Hepatocellular Carcinoma, LHCC280


title: HIV Positive without Hepatocellular Carcinoma, LHCC266


title: HIV Positive Fibrosis, LHCC288

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC265


title: HIV Positive without Hepatocellular Carcinoma, LHCC263


title: HIV Positive without Hepatocellular Carcinoma, LHCC261


title: HIV Positive Hepatocellular Carcinoma, LHCC312

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive without Hepatocellular Carcinoma, LHCC262


title: HIV Positive without Hepatocellular Carcinoma, LHCC264


title: HIV Positive Fibrosis, LHCC306

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, LHCC302

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC258


title: HIV Positive without Hepatocellular Carcinoma, LHCC257


title: HIV Positive without Hepatocellular Carcinoma, LHCC289


title: HIV Positive Fibrosis, LHCC255

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC251


title: HIV Positive Fibrosis, LHCC277

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC254


title: HIV Positive without Hepatocellular Carcinoma, LHCC276


title: HIV Positive without Hepatocellular Carcinoma, LHCC246


title: HIV Positive without Hepatocellular Carcinoma, LHCC245


title: HIV Positive Fibrosis, LHCC241

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC235


title: HIV Positive without Hepatocellular Carcinoma, LHCC234


title: HIV Positive without Hepatocellular Carcinoma, LHCC233


title: HIV Positive without Hepatocellular Carcinoma, LHCC228


title: HIV Positive without Hepatocellular Carcinoma, LHCC238


title: HIV Positive without Hepatocellular Carcinoma, LHCC223


title: HIV Positive without Hepatocellular Carcinoma, LHCC218


title: HIV Positive without Hepatocellular Carcinoma, LHCC215


title: HIV Positive without Hepatocellular Carcinoma, LHCC221


title: HIV Positive without Hepatocellular Carcinoma, LHCC232


title: HIV Positive without Hepatocellular Carcinoma, LHCC211


title: HIV Positive without Hepatocellular Carcinoma, LHCC214


title: HIV Positive without Hepatocellular Carcinoma, LHCC199


title: HIV Positive without Hepatocellular Carcinoma, LHCC217


title: HIV Positive without Hepatocellular Carcinoma, LHCC204


title: HIV Positive without Hepatocellular Carcinoma, LHCC203


title: HIV Positive without Hepatocellular Carcinoma, LHCC219


title: HIV Positive Cirrhosis, LHCC090

description: HIV Positive Cirrhosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC206


title: HIV Positive without Hepatocellular Carcinoma, LHCC054


title: HIV Positive without Hepatocellular Carcinoma, LHCC033


title: HIV Positive without Hepatocellular Carcinoma, LAF008


title: HIV Positive without Hepatocellular Carcinoma, LAF007


title: HIV Positive Fibrosis, LAF002

description: HIV Positive Fibrosis


title: HIV Positive Hepatocellular Carcinoma, JHCC538

description: HIV Positive Hepatocellular Carcinoma

value: JUTH


title: HIV Positive Fibrosis, JHCC522

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC510

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC506

description: HIV Positive Fibrosis


title: HIV Positive Cirrhosis, JHCC499

description: HIV Positive Cirrhosis


title: HIV Positive Fibrosis, JHCC504

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC508

description: HIV Positive Fibrosis


title: HIV Positive Cirrhosis, JHCC494

description: HIV Positive Cirrhosis


title: HIV Positive Hepatocellular Carcinoma, JHCC501

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Fibrosis, JHCC498

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC488

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC490

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC207


title: HIV Positive without Hepatocellular Carcinoma, LHCC202


title: HIV Positive Fibrosis, JHCC509

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC220


title: HIV Positive without Hepatocellular Carcinoma, LHCC224


title: HIV Positive Cirrhosis, JHCC484

description: HIV Positive Cirrhosis


title: HIV Positive Cirrhosis, JHCC480

description: HIV Positive Cirrhosis


title: HIV Positive Hepatocellular Carcinoma, JHCC478

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Fibrosis, JHCC474

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC530

description: HIV Positive Fibrosis


title: HIV Positive Hepatocellular Carcinoma, JHCC533

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Fibrosis, JHCC466

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC507

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC461

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC491

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC487

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC222


title: HIV Positive Fibrosis, JHCC451

description: HIV Positive Fibrosis


title: HIV Positive Hepatocellular Carcinoma, JHCC453

description: HIV Positive Hepatocellular Carcinoma

value: A


title: HIV Positive Fibrosis, JHCC456

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC454

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC448

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC446

description: HIV Positive Fibrosis


title: HIV Positive Hepatocellular Carcinoma, JHCC442

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Hepatocellular Carcinoma, JHCC439

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Hepatocellular Carcinoma, JHCC438

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Hepatocellular Carcinoma, JHCC437

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Hepatocellular Carcinoma, JHCC435

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive without Hepatocellular Carcinoma, JHCC430


title: HIV Positive without Hepatocellular Carcinoma, JHCC429


title: HIV Positive Hepatocellular Carcinoma, JHCC433

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Hepatocellular Carcinoma, JHCC436

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Fibrosis, JHCC460

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, JHCC428


title: HIV Positive without Hepatocellular Carcinoma, JHCC426


title: HIV Positive Cirrhosis, JHCC425

description: HIV Positive Cirrhosis


title: HIV Positive Fibrosis, LHCC227

description: HIV Positive Fibrosis


title: HIV Positive Fibrosis, JHCC424

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, LHCC249


title: HIV Positive without Hepatocellular Carcinoma, JHCC423


title: HIV Positive without Hepatocellular Carcinoma, JHCC421


title: HIV Positive Hepatocellular Carcinoma, JHCC432

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive without Hepatocellular Carcinoma, JHCC419


title: HIV Positive without Hepatocellular Carcinoma, JHCC413


title: HIV Positive without Hepatocellular Carcinoma, JHCC417


title: HIV Positive Hepatocellular Carcinoma, JHCC418

description: HIV Positive Hepatocellular Carcinoma

value: B


title: HIV Positive without Hepatocellular Carcinoma, JHCC420


title: HIV Positive Cirrhosis, JHCC398

description: HIV Positive Cirrhosis


title: HIV Positive Hepatocellular Carcinoma, JHCC401

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Hepatocellular Carcinoma, JHCC397

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive without Hepatocellular Carcinoma, JHCC404


title: HIV Positive Fibrosis, JHCC415

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, JHCC412


title: HIV Positive without Hepatocellular Carcinoma, JHCC406


title: HIV Positive without Hepatocellular Carcinoma, JHCC403


title: HIV Positive without Hepatocellular Carcinoma, JHCC416


title: HIV Positive without Hepatocellular Carcinoma, JHCC411


title: HIV Positive Cirrhosis, JHCC391

description: HIV Positive Cirrhosis


title: HIV Positive Hepatocellular Carcinoma, JHCC402

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive without Hepatocellular Carcinoma, JHCC392


title: HIV Positive without Hepatocellular Carcinoma, JHCC427


title: HIV Positive without Hepatocellular Carcinoma, JHCC405


title: HIV Positive Fibrosis, JHCC393

description: HIV Positive Fibrosis


title: HIV Positive Cirrhosis, JHCC396

description: HIV Positive Cirrhosis


title: HIV Positive without Hepatocellular Carcinoma, JHCC414


title: HIV Positive Cirrhosis, JHCC389

description: HIV Positive Cirrhosis


title: HIV Positive Hepatocellular Carcinoma, JHCC388

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Hepatocellular Carcinoma, JHCC422

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Hepatocellular Carcinoma, JHCC387

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Cirrhosis, JHCC386

description: HIV Positive Cirrhosis


title: HIV Positive without Hepatocellular Carcinoma, JHCC384


title: HIV Positive without Hepatocellular Carcinoma, JHCC383


title: HIV Positive without Hepatocellular Carcinoma, JHCC385


title: HIV Positive without Hepatocellular Carcinoma, JHCC382


title: HIV Positive without Hepatocellular Carcinoma, JHCC367


title: HIV Positive without Hepatocellular Carcinoma, JHCC373


title: HIV Positive without Hepatocellular Carcinoma, JHCC372


title: HIV Positive without Hepatocellular Carcinoma, JHCC366


title: HIV Positive without Hepatocellular Carcinoma, JHCC377


title: HIV Positive without Hepatocellular Carcinoma, JHCC369


title: HIV Positive Hepatocellular Carcinoma, JHCC359

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive Fibrosis, JHCC357

description: HIV Positive Fibrosis


title: HIV Positive Cirrhosis, JHCC360

description: HIV Positive Cirrhosis


title: HIV Positive without Hepatocellular Carcinoma, JHCC328


title: HIV Positive without Hepatocellular Carcinoma, JHCC345


title: HIV Positive without Hepatocellular Carcinoma, JHCC358


title: HIV Positive without Hepatocellular Carcinoma, JHCC314


title: HIV Positive without Hepatocellular Carcinoma, JHCC313


title: HIV Positive without Hepatocellular Carcinoma, JHCC312


title: HIV Positive Cirrhosis, JHCC300

description: HIV Positive Cirrhosis


title: HIV Positive Fibrosis, JHCC283

description: HIV Positive Fibrosis


title: HIV Positive Hepatocellular Carcinoma, JHCC297

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive without Hepatocellular Carcinoma, JHCC361


title: HIV Positive Cirrhosis, JHCC363

description: HIV Positive Cirrhosis


title: HIV Positive Hepatocellular Carcinoma, JHCC381

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive without Hepatocellular Carcinoma, JHCC365


title: HIV Positive without Hepatocellular Carcinoma, LHCC242


title: HIV Positive Cirrhosis, JHCC324

description: HIV Positive Cirrhosis


title: HIV Positive without Hepatocellular Carcinoma, JHCC242


title: HIV Positive without Hepatocellular Carcinoma, JHCC243


title: HIV Positive Hepatocellular Carcinoma, JHCC239

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive without Hepatocellular Carcinoma, JHCC248


title: HIV Positive without Hepatocellular Carcinoma, JHCC238


title: HIV Positive Cirrhosis, JHCC320

description: HIV Positive Cirrhosis


title: HIV Positive without Hepatocellular Carcinoma, JHCC235


title: HIV Positive without Hepatocellular Carcinoma, JHCC236


title: HIV Positive without Hepatocellular Carcinoma, JHCC234


title: HIV Positive without Hepatocellular Carcinoma, JHCC237


title: HIV Positive without Hepatocellular Carcinoma, JHCC232


title: HIV Positive Cirrhosis, JHCC219

description: HIV Positive Cirrhosis


title: HIV Positive Fibrosis, JHCC227

description: HIV Positive Fibrosis


title: HIV Positive without Hepatocellular Carcinoma, JHCC202


title: HIV Positive without Hepatocellular Carcinoma, JHCC218


title: HIV Positive Cirrhosis, JHCC216

description: HIV Positive Cirrhosis


title: HIV Positive without Hepatocellular Carcinoma, JHCC228


title: HIV Positive without Hepatocellular Carcinoma, JHCC200


title: HIV Positive without Hepatocellular Carcinoma, JHCC205


title: HIV Positive without Hepatocellular Carcinoma, JHCC199


title: HIV Positive without Hepatocellular Carcinoma, JHCC185


title: HIV Positive Hepatocellular Carcinoma, JHCC189

description: HIV Positive Hepatocellular Carcinoma


title: HIV Positive without Hepatocellular Carcinoma, JHCC183


title: HIV Positive without Hepatocellular Carcinoma, JHCC175


title: HIV Positive without Hepatocellular Carcinoma, JHCC169


title: B Stage I [HIV_b_a_3]

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

institute: Pomeranian Medical University

description: peripheral blood from HIV-1 patient

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Data were processed in R using ChAMP package, normalized using BMIQ method
Normalized beta values (before cell fraction correction)

label: Cy5 and Cy3

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from peripheral blood samples using QIAamp DNA Mini Kit (QIAGEN GmbH, Hilden, Germany)

value: Whole blood

tag: Stage

value: B Stage I


title: B Stage IV [HIV_b_c_1]

description: peripheral blood from HIV-1 patient

value: B Stage IV


title: B Stage I [HIV_b_a_4]

description: peripheral blood from HIV-1 patient


title: A6 Stage I [HIV_a6_a_2]

description: peripheral blood from HIV-1 patient

value: A6 Stage I


title: HIV Positive without Hepatocellular Carcinoma, JHCC176


title: HIV Positive without Hepatocellular Carcinoma, JHCC177


title: HIV Positive without Hepatocellular Carcinoma, JHCC225


title: A6 Stage I [HIV_a6_a_1]

description: peripheral blood from HIV-1 patient


title: A6 Stage IV [HIV_a6_c_4]

description: peripheral blood from HIV-1 patient

value: A6 Stage IV


title: B Stage IV [HIV_b_c_4]

description: peripheral blood from HIV-1 patient


title: A6 Stage I [HIV_a6_a_4]

description: peripheral blood from HIV-1 patient


title: B Stage IV [HIV_b_c_2]

description: peripheral blood from HIV-1 patient


title: A6 Stage IV [HIV_a6_c_1]

description: peripheral blood from HIV-1 patient


title: B Stage I [HIV_b_a_6]

description: peripheral blood from HIV-1 patient


title: A6 Stage I [HIV_a6_a_5]

description: peripheral blood from HIV-1 patient


title: B Stage IV [HIV_b_c_6]

description: peripheral blood from HIV-1 patient


title: B Stage I [HIV_b_a_1]

description: peripheral blood from HIV-1 patient


title: A6 Stage IV [HIV_a6_c_5]

description: peripheral blood from HIV-1 patient


title: B Stage IV [HIV_b_c_3]

description: peripheral blood from HIV-1 patient


title: A6 Stage I [HIV_a6_a_3]

description: peripheral blood from HIV-1 patient


title: B Stage I [HIV_b_a_2]

description: peripheral blood from HIV-1 patient


title: B Stage IV [HIV_b_c_5]

description: peripheral blood from HIV-1 patient


title: A6 Stage IV [HIV_a6_c_6]

description: peripheral blood from HIV-1 patient


title: A6 Stage IV [HIV_a6_c_2]

description: peripheral blood from HIV-1 patient


title: A6 Stage I [HIV_a6_a_6]

description: peripheral blood from HIV-1 patient


title: A6 Stage IV [HIV_a6_c_3]

description: peripheral blood from HIV-1 patient


title: PA#14, PBMC, scTCR-seq

city: shenzhen

first: Minmin

last: Chen

state: GuangDong

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

institute: Shenzhen bay lab

description:
Library name: PA#14-PBMC-VDJ
10x Genomics V(D)J

data_processing:
Raw BCL files were processed using Cell Ranger (version 7.1.0) pipeline. Raw read sequences were aligned to the 10X reference genome based on Ensembl GRCh38. Raw data from each sample from the ‘‘filtered_contig_annotations.csv’’ output was further filtered by only including TCR alpha (TRA) or TCR beta (TRB) calls that was reported as ‘‘productive’’. TCR clonotypes were defined as the combination of Vα, Vβ, Jα, Jβ, CDR3α, and CDR3β segments, together with the CDR3α and CDR3β amino acid sequences. In total, 6,503 distinct TCR clonotypes were identified across all samples and categorized into three groups: unique (n = 1), duplicated (n = 2), and clonal (n ≥ 3).
Assembly: GRCh38
Supplementary files format and content: clonotypes.csv: Tab-delimited file containing clonotype-level summary data including clonotype IDs, frequencies, CDR3 sequences, and clonal expansion metrics from 10x Genomics V(D)J analysis.
Supplementary files format and content: filtered_contig_annotations.csv: Tab-delimited file containing cell-level TCR contig annotations including cell barcodes, V(D)J gene assignments, CDR3 sequences, chain types, and quality metrics from 10x Genomics V(D)J pipeline.
Library strategy: TCR-seq

source_name: PBMC

extract_protocol:
Tumors and adjacent normal tissues were cut into approximately 1 mm3 pieces and enzymatically digested with MACS Tumour Dissociation Kit (Miltenyi Biotec,130-095-929) for 40 minutes (for normal tissues) or 1 hour (for tumor tissues) on the gentleMACS™ Octo Dissociator with Heaters, following the manufacturer’s instruction. The dissociated cells were subsequently passed through a 70-μm cell-strainer (BD Bioscience, 352350) to remove debris and centrifuged at 450g for 10 min. Pelleted cells were resuspended in sorting buffer (Miltenyi Biotec, 130-091-221) and stained with FITC Mouse Anti-Human CD45 (BD Bioscience,555482) and APC anti-human CD235a (Biolegend,349114). DAPI (BD Bioscience,564907) was added to the cell suspension immediately before FACS. CD235-DAPI- live cells were FACS-sorted for single-cell RNA-sequencing.
The sorted cells were stained with Typan Blue for viability counting. Single-cell suspensions with >80% viability were processed to scRNA-seq. Libraries were generated using the Chromium Controller and the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (10xGenomics, 1000244) following the manufacturer’s instructions. Briefly, cells were loaded onto the Single Cell Chip K for encapsulation into droplets, aiming to capture 10,000 cells. cDNA was amplified by 13 PCR cycles and a total of 50ng cDNA was used for library preparation. Qualitative and quantitative assessments of the final libraries were performed on a Bioanalyzer 2200 with the High Sensitivitiy DNA kit (Agilent, 5067-4626), and the Qubit 3.0 Fluorometer with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854), respectively. Libraries were then normalized, pooled and sequenced on the NovaSeq 6000 (Illumina) with a 150 bp paired-end run. For TCR sequencing, we performed V(D)J amplification from the cDNA pool with the T cell mix 1&2 included in the 5’ Reagent Kits.

value: PBMC


title: PA#13, PBMC, scTCR-seq

description:
Library name: PA#13-PBMC-VDJ
10x Genomics V(D)J


title: PA#14, Tumor, scTCR-seq

description:
Library name: PA#14-Tumor-VDJ
10x Genomics V(D)J

source_name: Tumor

value: Tumor


title: PA#15, PBMC, scTCR-seq

description:
Library name: PA#15-PBMC-VDJ
10x Genomics V(D)J


title: PA#12, Tumor, scTCR-seq

description:
Library name: PA#12-Tumor-VDJ
10x Genomics V(D)J