title: V3_Nil_HD_04

tag: treatment


title: Ctr Brain Perk Cre plus 04

status: Public on Nov 07 2025

type: SRA

city: Chicago

first: Brian

last: Popko

state: IL

address: 7601 Morton Medical Research Building, 320 East Superior Street

department: Neurology

country: USA

institute: Northwestern Feinberg School of Medicine

library_source: transcriptomic

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
The Aurum™ Total RNA Fatty and Fibrous Tissue Module kit (from Bio Rad #7326870) was used for RNA extractions.
Directional mRNA libraries were prepared using Illumina UDI Kits per the manufacturer’s instructions

tag: tissue

value: Brain

tag: genotype

value: WT Perk fl/fl Cre+

value: P19, olig2-Cre pos.


title: Gene expression of samples from IL-17A treated mice

city: Boston

first: Qiu Chang

last: Wu

state: MA

address: 220 Longwood Ave

department: Systems Biology

institute: Harvard University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The sequencing libraries were demultiplexed using Bcl2fastq (Illumina) and concatenated across multiple sequencing runs. The demultiplexed Fastq files were merged for the same libraries and individually processed using Cellranger (v6.1.2) Gene Expression Pipeline. Cellranger aggr function (see attached aggregation.csv file for input) was used for integrating multiple samples. Alignments were performed using M. musculus Ensembl release 84 mm10 v1.2.0 cDNA reference. The MULTI-seq library Fastq files were processed using CITE-seq-Count tool (v1.4.5) to determine sample identity of pooled cells. Sample barcode identity assignments to cells were performed using a custom python-based adaption inspired by the deMULTIplex R package.
Assembly: M. musculus Ensembl release 84 mm10
Supplementary files format and content: Gene expression output: gex_barcode.tsv.gz, gex_features.tsv.gz, gex_matrix.mtx.gz, gex_cell_metadata.tsv.gz
Supplementary files format and content: Hashtag  output: ht_barcode.tsv.gz, ht_features.tsv.gz, ht_matrix.mtx.gz

molecule: polyA RNA

source_name: spleen and bone marrow

extract_protocol:
Tissue Harvesting Femur, tibiae, and spleen were harvested following euthanasia and submerged in SB5 buffer (phosphate-buffered saline (PBS) supplemented with 0.2% (w/v) bovine serum albumin (BSA), 0.08% (w/v) glucose, and 5 mM of Ethylenediaminetetraacetic acid (EDTA)). Tissue harvest methods are described in detail in Swaminathan et al.3. In brief, for bone marrow samples, the ends of the bones were cut and flushed with SB5 using a 26-gauge needle and 5 mL syringe. Harvested bone marrow was filtered through a 100 µM cell strainer. For spleen samples, spleens were placed onto a staining buffer-wetted 100 µM cell strainer and macerated through using the rubber side of a syringe plunger. The samples were washed with more SB5 and pelleted at 2000rpm for 10 minutes. Bone marrow and spleen samples were then processed into single-cell suspensions by adding 2 mL of SB5 and triturating cell pellet using a P1000 pipette and a large orifice pipet tip.  Singe cell RNA sequencing (scRNAseq) of bone marrow and spleen cells CD117 positive cell enrichment Harvested tissue samples were first enriched for CD117+ cells. Bone marrow and spleen cell samples were washed using Easy Sep buffer (PBS, 2% fetal bovine serum (FBS), and 1 mM EDTA) and enriched for CD117 expressing cells using EasySepTM Mouse CD117 Positive Selection Kit. The enrichment was performed largely following the manufacturer’s protocol; however, all room temperature steps were instead performed at 4oC in a walk-in cold room.  Live cell enrichment using density centrifugation Following CD117 enrichment, dead cell and debris were removed using gradient centrifugation in OptiPrep. Solutions of 40%, 18%, 12%, and 5% OptiPrep were prepared using weight by volume (w/v) and pre-chilled. Cells were resuspended in 0.5 mL PBS and mixed with 1 mL of 40% OptiPrep in a 5 mL FACS tube. 18%, 12%, and 5% OptiPrep were sequentially and carefully overlay on-top of the cell sample. The samples were then spun at 800g for 15 minutes with the centrifuge break off to prevent disruption of gradient. The live cell layer, which formed between the 40% and 18% interface, was collected, and washed using cold PBS.  MULTIseq labeling of cell samples To reduce technical variability from sample processing, we performed MULTIseq labelling to multiplex samples for 10X Chromium-based encapsulation. Samples were labeled with MULTI-Seq Lipid-Modified Oligos and unique sample barcode oligos following the MULTI-Seq protocol (see "Sample_hashing_barcodes.csv" for MULTI-Seq barcodes per sample). Antibody-based hashing methods were tested for these cell samples but ultimately not used due to poor labeling of reticulocytes which lack of the hashing epitope.
Single cell encapsulation and library prep Following MULTI-seq sample labeling, samples were pooled in equal ratios and cells were resuspended in PBS and 0.04% BSA at 1000 cells/uL prior to cell encapsulation. To help with demultiplexing, single injection condition pools were run individually, and an all-sample pool was run in another, for a total of five unique pools (see "Library_barcodes.csv") and a target total cell number of 48,000 loaded separately onto a 10X Genomics Chromium Next GEM Chip G. Samples were encapsulated using a Chromium X Instrument based on manufacturer’s instructions.

treatment_protocol: Mice were injected with cytokines subcutaneously, in a total volume of 4 microliters/g body weight.  Recombinant IL-17A (made in Chinese Hamster Ovary (CHO) cells) was freshly resuspended in phosphate buffered saline (PBS) up to 12 hours prior to use and injected at 200 ng/g body weight every 12 hours. Epo (Procrit) was injected at 0.25 IU/g every 24 hours. Vehicle- treated mice were injected with an equal volume of PBS.

value: spleen and bone marrow

tag: cell type

value: Mixed

value: Wild type Balb/C

value: 200ng/g IL-17A injections

tag: library type

value: Gene Expression


title: Jimpy Brain Perk Cre minus 01

value: Jimpy Perk fl/fl Cre-

value: P19, olig2-Cre neg.


title: MQ130, Empty Vector, Day 1, Repeat 1

first: William

middle: B

last: Mair

address: 677 Huntington Avenue

department: Molecular Metabolism

institute: Harvard TH Chan School of Public Health

description:
Library name: 20180929_A7_MQ130_ev_SD6021-1_S7
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:clk1_ctrl_A7

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/). Raw reads were examined for quality issues using FastQC (v0.11.8) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing were suitable for further analysis. To perform additional quality checks of the data, all reads were aligned to Wormbase assembly WBcel235, release WS272 of the C. elegans genome (Project PRJNA13578 (N2 strain)) using STAR (v. 101 2.6.1d) (Dobin et al., 2013). Alignments were checked for evenness of coverage, rRNA content, genomic context of alignments (for example, alignments in known transcripts and introns), complexity and other quality checks using a combination of FastQC, Qualimap (García-Alcalde et al., 2012), (http://doi.org/10.1093/bioinformatics/bts503), MultiQC (https://github.com/ewels/MultiQC) and custom tools.
To quantitate the reads corresponding to each transcript, quasi alignment was performed using Salmon (v. 0.14.2) (Patro et al., 2017), outputting the transcripts Per Million (TPM) measurements per isoform. Differential expression at the gene level was called with DESeq2 (Love et al., 2014), using counts per gene estimated from the Salmon quasi alignments by tximport.
Assembly: Wormbase assembly WBcel235, release WS272 of the C. elegans genome (Project PRJNA13578 (N2 strain)) using STAR (v. 101 2.6.1d)
Supplementary files format and content: NormalizedCounts_REPO-1RNA-Seq.xlsx: Excel file that contains in each column each sample and the normalized count for each gene.

organism: Caenorhabditis elegans

source_name: Whole body

extract_protocol:
RNA was extracted using Qiagen miRNeasy kit. Submitted 300 ng of each sample for sequencing.
RNA libraries for RNA seq were prepared using Roche Kapa stranded mRNA HyperPrep, following manufacter's protocol.

value: Whole body

value: Empty vector

tag: batch


title: V3_Nil_HD_03

city: Washington, DC

first: Max

last: Stevenson

state: DC

address: 3970 Reservoir Rd. NW

institute: Georgetown University

data_processing:
miRNA expression profiles at the baseline and 3 months were quantified in UMI counts., Longitudinal differentially expressed miRNA (DEMs) were determined via DESeq2 with ratio of means normalization and followed by Wald test [65] to compute the longitudinal measurement at baseline and 3 months.
Assembly: hg38
Supplementary files format and content: Excel

organism: Homo sapiens

source_name: CSF

extract_protocol:
Cell-free total RNA was isolated from 200 μl of CSF using the Qiagen miRNAeasy extraction kit
Samples were normalized to an input volume of 5 μl RNA eluate to prepare miRNAseq libraries using Qiagen QiaSeq miRNA-seq library preparation kit

treatment_protocol: HD patients had CSF samples collected at baseline and after 3 months treatment with nilotinib, 150mg.

value: CSF

tag: disease

value: HD

tag: time point

value: Nilotinib


title: Ctr Brain Perk Cre plus 03


title: Jimpy Brain Perk Cre Plus 03

value: Jimpy Perk fl/fl Cre+


title: VC222, repo-1 RNAi, Day 1, Repeat 1

description:
Library name: 20180929_A6_VC222_repo-1_RNAi_SD6021-1_S6
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:raga1_repo1_A6

value: repo-1 RNAi


title: V3_Nil_HD_01


title: BL_Nil_HD_05

value: Baseline


title: Ctr Brain Perk Cre plus 02

value: Brain

value: WT Perk fl/fl Cre+


title: VC222, Empty Vector, Day 1, Repeat 1

description:
Library name: 20180929_A5_VC222_ev_SD6021-1_S5
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:raga1_ctrl_A5


title: BL_Nil_HD_04


title: BL_Nil_HD_03


title: Da1116, repo-1 RNAi, Day 1, Repeat 1

description:
Library name: 20180929_A4_DA1116_repo-1_RNAi_SD6021-1_S4
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:eat2_repo1_A4


title: Ctr Brain Perk Cre plus 01

value: P19, olig2-Cre pos.


title: BL_Nil_HD_01


title: DA1116, Empty Vector, Day 1, Repeat 1

description:
Library name: 20180929_A3_DA1116_ev_SD6021-1_S3
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:eat2_ctrl_A3


title: BL_Nil_HD_02


title: Ctr Brain Perk Cre minus 04

value: WT Perk fl/fl Cre-


title: Ctr Brian Perk Cre minus 03


title: SCC0002_2_Aguilar Multiseq

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
SCC0002_2_Aguilar_molecule_info.h5
CMO301_filtered_feature_bc_matrix.tar.gz
CMO302_filtered_feature_bc_matrix.tar.gz
CMO303_filtered_feature_bc_matrix.tar.gz
CMO304_filtered_feature_bc_matrix.tar.gz

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and feature barcode counts) was performed using the 10x genomics Cell Ranger pipeline with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.1.1 (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: other

source_name: 3D prostate organoid; prostate tissue

growth_protocol:
Organoids were split every 7 days at a ratio of 1:3/1:4 for 5 min at 37°C. Culture medium was replaced every 2-3 days. The organoid-derived monolayers were seeded from 7-day-old organoids.Single cells were counted and seeded in 48-well plate using culture medium. The seeded monolayers were grown for 6 days, reaching 90-100% confluency.
Organoids were split every 7 days at a ratio of 1:3/1:4 for 5 min at 37°C. Culture medium was replaced every 2-3 days. The organoid-derived monolayers were seeded from 7-day-old organoids.Single cells were counted and seeded in 48-well plate using culture medium. The seeded monolayers were grown for 6 days, reaching 90-100% confluency.

extract_protocol:
Prostates were minced into small pieces and digested in a two step protocol: with  5 mg mL-1 for 1 h at 37°C on a shaking platform; and then with TrypLE Express Enzyme for 15 min at 37°C  and mechanically disrupted every 5 min. Organoids and organoid-derived monolayers were harvested with TrypLE Express Enzyme for 15 min at 37°C  and mechanically disrupted every 5 min.  Cells were labelled with CMO tags (ex vivo units: CMO 1, 2; 3D organoids Ctrl: CMO 3; 3D organoids DHT: CMO 4; 2D organoids Ctrl : CMO 5, 6; 2D organoids DHT: CMO 7, 8). After labeling, cells were washed pooled in equal proportions in two different pools (ex vivo and 3D: 1300 cells/uL, 80% viability; 2D: 902 cells/uL; 86% viability). The pooled cells were subsequently loaded onto a Chromium Single Cell Controller (10x Genomics) to generate Gel Bead-In-Emulsions (GEMs). Post-GEM-RT cleanup was performed using Dynabeads MyOne Silane Beads (37002D, Thermo Fisher Scientific). cDNA was amplified by PCR and then fragmented, end-repaired, and A-tailed. Adapters were ligated, and the resulting constructs were enriched by PCR to generate the final libraries. Libraries were quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and their size distribution was assessed using an Agilent 2100 Bioanalyzer. Libraries were sequenced using Illumina NovaSeq6000 using a S2 flow cell with 100 cycles.
Single cells were encapsulated into droplets with the Chromium™ Controller (10x Genomics). Transcripts captured in all cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 12 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ reagents kit v3.1 (10x Genomics) including cell multiplexing via CellPlex kit Set A  following the detailed protocol provided by the manufacturer (CG000390 rev B, 000391 Rev B).
10x Gemoics library construction kit
Cell multiplexing via 10x Genomics CellPlex
Prostates were minced into small pieces and digested in a two step protocol: with  5 mg mL-1 for 1 h at 37°C on a shaking platform; and then with TrypLE Express Enzyme for 15 min at 37°C  and mechanically disrupted every 5 min. Organoids and organoid-derived monolayers were harvested with TrypLE Express Enzyme for 15 min at 37°C  and mechanically disrupted every 5 min.  Cells were labelled with CMO tags (ex vivo units: CMO 1, 2; 3D organoids Ctrl: CMO 3; 3D organoids DHT: CMO 4; 2D organoids Ctrl : CMO 5, 6; 2D organoids DHT: CMO 7, 8). After labeling, cells were washed pooled in equal proportions in two different pools (ex vivo and 3D: 1300 cells/uL, 80% viability; 2D: 902 cells/uL; 86% viability). The pooled cells were subsequently loaded onto a Chromium Single Cell Controller (10x Genomics) to generate Gel Bead-In-Emulsions (GEMs). Post-GEM-RT cleanup was performed using Dynabeads MyOne Silane Beads (37002D, Thermo Fisher Scientific). cDNA was amplified by PCR and then fragmented, end-repaired, and A-tailed. Adapters were ligated, and the resulting constructs were enriched by PCR to generate the final libraries. Libraries were quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and their size distribution was assessed using an Agilent 2100 Bioanalyzer. Libraries were sequenced using Illumina NovaSeq6000 using a S2 flow cell with 100 cycles.

treatment_protocol:
To induce the monolayers differentiation towards luminal cells, 10 nM (DiHydro)testosterone (5α-Androstan-17β-ol-3-one)was added to the medium on the day of splitting or seeding and kept throughout the experiment.
To induce the monolayers differentiation towards luminal cells, 10 nM (DiHydro)testosterone (5α-Androstan-17β-ol-3-one)was added to the medium on the day of splitting or seeding and kept throughout the experiment.

value: 3D prostate organoid; prostate tissue

value: Total viable cells

value: WT

value: Ctrl or DHT

value: Multiplexing Capture


title: SCC0002_2_Aguilar gene expression

value: mRNA


title: Wild type N2, repo-1 RNAi, Day 1, Repeat 1

description:
Library name: 20180929_A2_N2_repo-1_RNAi_SD6021-1_S2
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:WT_repo1_A2

value: Whole body

value: Wild type


title: Ctr Brain Perk Cre minus 02

value: P19, olig2-Cre neg.


title: SCC0002_1_Aguilar Multiseq

description:
SCC0002_1_Aguilar_molecule_info.h5
CMO305_filtered_feature_bc_matrix.tar.gz
CMO306_filtered_feature_bc_matrix.tar.gz
CMO307_filtered_feature_bc_matrix.tar.gz
CMO308_filtered_feature_bc_matrix.tar.gz

source_name: 2D prostate organoid

value: 2D prostate organoid


title: SCC0002_1_Aguilar gene expression


title: A549 cells, untreated, rep 4

city: Burnaby

first: Jonathan

last: Choy

state: BC

address: 8888 University Dr W

department: Molecular Biology and Biochemistry

country: Canada

institute: Simon Fraser University

data_processing:
Fastq files were aligned using STAR(ver 2.7.9a)  to GRCh38 release 110 obtained from Ensembl
Read counts were obtained using HTSeq(ver 2.0.2) to generate .txt files for analysis using DESeq2(ver1.44.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text files contain raw counts for each sample

growth_protocol: A549 human lung epithelial cells were cultured in Ham’s F-12K medium at 37 °C in a humidified atmosphere of 95% air and 5% CO2.

extract_protocol:
RNA from each sample was isolated using an AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Hilden, Germany)
RNA libraries made using the TruSeq Stranded mRNA kit (Illumina) and RNA-Seq (2x 50 bp paired-end reads) performed at the University of British Columbia Sequencing and Bioinformatics Consortium

treatment_protocol: Cells were untreated, treated with a selective iNOS inhibitor 1400W (50μM) alone, treated with cytokines (IL-1α 10ng/mL, TNFα 10ng/mL, IFNγ 100ng/mL) or treated with cytokines and 1400W in quadruplicates for 16 hours.

tag: cell line

value: human lung epithelial adenocarcinoma

value: untreated


title: Wild type N2, Empty Vector, Day 1, Repeat 1

description:
Library name: 20180929_A1_N2_ev_SD6021-1_S1
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:WT_ctrl_A1

value: Empty vector


title: H015_P3_3: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol, and 5 ng/ml tacrolimus in the media

city: Indianapolis

first: Michael

middle: T

last: Eadon

state: IN

address: 950 West Walnut Street Room 402 Room 402

institute: Indiana University School of Medicine

description:
Library name: H015_P3_3
10X Genomics

data_processing:
Alignment and quantification were accomplished with CellRanger (v. 7.1.0) using default options and reference genome GRCh38-2020-A.
The BPCells (v.0.2.0) package converted the matrices in the Hierarchical Data Format h5 to bitpacked compressed format stored as binary files on a hard drive. We used Seurat (v.5.1.0) to create a Seurat object for each sequencing sample.
Cells with mitochondria reads over 25% or fewer than 500 genes were removed.
All scRNA-seq samples were merged, and the cells were annotated by Azimuth (v.0.5.0) using the PBMC_ref_4546839 in Zenodo (https://zenodo.org/records/4546839).
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger (v. 7.1.0)
Supplementary files format and content: Tables and matrix files

source_name: peripheral blood

extract_protocol:
No extraction occurred prior to submission for single cell sequencing. Cells were in suspension in RPMI media supplemented with 10% FBS. Single cell capture and library preparation were carried out according to 10x Genomics Chromium Single Cell V3.1 NextGem platform. cDNA synthesis and amplification were performed according to the 10x Genomics protocols.
Paired-end reads were generated with a length of 100 base pairs (PE100), and sequencing depth was optimized according to experimental requirements

treatment_protocol: 1 - No CD3/CD28, No CBD, No Tacrolimus; 2 - CD3/CD28, No CBD; No Tacrolimus; 3 - CD3/CD28, No CBD, Tacrolimus; 4 - No CD3/CD28, CBD; No Tacrolimus; 5 - CD3/CD28, CBD; No Tacrolimus; 6 - CD3/CD28, CBD; Tacrolimus;

value: peripheral blood

tag: age

tag: Sex

value: Female

value: PBMC

value: CD3/CD28 +CBD +TAC


title: Ctr Brain Perk Cre minus 01

value: Brain

value: WT Perk fl/fl Cre-


title: A549 cells, untreated, rep 2


title: A549 cells, untreated, rep 3


title: A549 cells, cytokine+1400W treated, rep 3


title: V3_Nil_HD_02

value: CSF

value: HD

value: Nilotinib


title: A549 cells, cytokine treated, rep 4

value: cytokines


title: Human liver stellate cells LX-2 after NETs intervention, exp3

city: Nangjing

first: Jiajia

last: shen

address: No.300,guangzhou Road

country: China

institute: nanjing medical university

description:
Library name: exp3
exp3

data_processing:
The investigation of differentially expressed genes (DEGs) involved the use of Gene Ontology tools, specifically AMIGO and DAVID
Assembly: the Kyoto Encyclopedia of Genes and Genomes annotations was utilized to assess the enrichment levels of these DEGs.
Supplementary files format and content: fq files

source_name: Human liver

extract_protocol:
RNA was extracted and subsequently converted into cDNA for the creation of a sequenced library compatible with Illumina indices. The sequencing was conducted at the Beijing Genomics Institute in China, utilizing the BGISEQ-500 system.
A gene was considered to be significantly differentially expressed if it exhibited a more than twofold change in expression compared to the control, coupled with a p value below 0.05 after adjustment. Gene Ontology was employed to analyze the heat map, with the Cluster software for analysis and Java Treeview for visualization purposes.

value: Human liver

value: liver stellate cell

value: WT

value: NETs


title: Human liver stellate cells LX-2 after NETs intervention, exp2

description:
Library name: exp2
exp2


title: A549 cells, untreated, rep 1

value: human lung epithelial adenocarcinoma


title: H015_P3_2: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H015_P3_2
10X Genomics

value: CD3/CD28 +CBD -TAC


title: A549 cells, cytokine treated, rep 2


title: A549 cells, cytokine+1400W treated, rep 2


title: A549 cells, cytokine+1400W treated, rep 4


title: A549 cells, 1400W treated, rep 2

value: 1400W only


title: A549 cells, 1400W treated, rep 3


title: Human liver stellate cells LX-2 after NETs intervention, exp1

description:
Library name: exp1
exp1


title: A549 cells, cytokine+1400W treated, rep 1


title: A549 cells, 1400W treated, rep 1


title: H014_P2_3: PBMC, CD3/CD28 stimulation and 5 ng/ml tacrolimus in the media

description:
Library name: H014_P2_3
10X Genomics

value: peripheral blood

value: Male

value: CD3/CD28 -CBD +TAC


title: H015_P2_3: PBMC, CD3/CD28 stimulation and 5 ng/ml tacrolimus in the media

description:
Library name: H015_P2_3
10X Genomics

value: Female

value: PBMC


title: H015_P3_1: PBMC, No CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H015_P3_1
10X Genomics

value: No CD3/CD28 +CBD -TAC


title: H014_P2_2: PBMC, CD3/CD28 stimulation

description:
Library name: H014_P2_2
10X Genomics

value: CD3/CD28 -CBD-TAC


title: Human liver stellate cells LX-2 after neutrophil intervention, con3

description:
Library name: con3
con3

value: neutrophi


title: Adenoid3+4+5+6

city: Dallas

first: Samuel

last: Alvarez-Arguedas

state: Texas

address: 5323 Harry Hines Blvd

department: Internal Medicine

institute: University of Texas Southwestern Medical Center

description: Parse Biosciences (Evercode WT)

data_processing:
Sequencing data were processed, mapped to the human (GRCh38) genome, and demultiplexed using Parse pipeline v1.1.2. The resulting matrix was normalized and scaled using Seurat R package (version 4.3.0) standard pipeline in R version 4.2.3.
Samples 1 and 2 were sequenced in Sublibrary 1 while the samples 3 to 6 were in Sublibrary 2.
Assembly: GRCh38
Supplementary files format and content: Comma-separated values files and matrix files

molecule: nuclear RNA

source_name: Adenoid (pharyngeal tonsil)

extract_protocol:
Isolation of single nuclei from human adenoid tissue was carried out by adapting a  previously described protocol (Bhuiyan et al. 2023). Briefly, excised adenoids were immediately placed on ice after collection. Adenoid tissue was then placed in chilled homogenization buffer (0.25 M sucrose, 150 mM KCl, 5 mM MgCl2, 0.1 M Tris buffer pH 8.0, 0.1 mM DTT, 0.1 % Triton-X, and 0.2 U/l RNase inhibitor) and minced. Samples were individually transferred to a gentleMACS C tube and homogenized with a gentleMACS dissociator. The tissue homogenate was passed through a 70 m filter and diluted 1:1 with a chilled homogenization buffer. After centrifugation at 500g for 5 minutes at 4°C, nuclei were resuspended in wash buffer (1% BSA in DPBS with 0.2U/µl RNase inhibitor). Nuclear integrity was then assessed by microscopy, and the number of nuclei was counted using a BioRad TC20 automated counter. Only clump- and debris-free suspensions with at least 75-90% of nuclei with intact and smooth nuclear membranes were used for sequencing.
Nucleus suspension from each donor were fixed using the Parse Evercode Nuclei Fixation v1 (samples 1 – 4) or v2 (samples 5 – 6). Since not all the samples were collected on the same day, all samples were processed until fixation first. Two independent libraries were prepared using the Parse Evercode Whole Transcriptome kit (V1 or V2).

value: Adenoid (pharyngeal tonsil)


title: Adenoid1+2

description: Parse Biosciences (Evercode WT)


title: Human liver stellate cells LX-2 after neutrophil intervention, con2

description:
Library name: con2
con2


title: A549 cells, cytokine treated, rep 3

value: cytokines


title: H015_P2_2: PBMC, CD3/CD28 stimulation

description:
Library name: H015_P2_2
10X Genomics


title: H013_P2_3: PBMC, CD3/CD28 stimulation and 5 ng/ml tacrolimus in the media

description:
Library name: H013_P2_3
10X Genomics


title: AGS_Vehicle_3 (for BAY plus Uridine)

city: Guangzhou

first: Guodi

last: Cai

state: Guangdong Province

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-Sen university

data_processing:
Sequencing was performed on the BGISEQ platform at BGI Tech (Wuhan, China). The FASTQ-formatted sequence data were analyzed by using a standard BWA–Bowtie–Cufflinks workflow. Sequence reads were mapped to GRCh38/hg38 assembly with BWA and Biotie software. The Cufflinks package was used for transcript assembly, quantification of normalized gene and isoform expression, and analysis of different expression.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: AGS

growth_protocol: AGS cells were cultured in RPMI1640 supplemented with 10% FBS. Cells were grown at 37 °C in 5% CO2 incubators.

extract_protocol:
Total RNA was isolated using TRIzol reagent according to the manufacturer’s instruction (15596026, Invitrogen, USA).
RNA-seq libraries from 1 μg total RNA were prepared using Illumina Tru-Seq RNA Sample, according to the manufacturer’s instructions. Libraries were validated with an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA)

treatment_protocol: AGS cells were treated with vehicle or DHODH inhibitors BAY (5 nM) or Ach-A (0.75 μM), or the combination of BAY (5 nM) and uridine (100 μM), or NR4A1 agonists Csn-B (40 μM) for 48 h before RNA extraction.

value: AGS

value: gastric adenocarcinoma cells

value: Vehicle


title: A549 cells, 1400W treated, rep 4


title: A549 cells, cytokine treated, rep 1


title: Barcode03

city: Montpellier

first: Nadine

last: LAGUETTE

address: 1919 Rte de Mende

country: France

institute: Institut de Génétique Moléculaire de Montpellier

description:
Library name: Sample03
cyDNA, colum_name_in_minion_raw_ count: mock-3

data_processing:
MinION: MinKNOW24.02.8, Bream7.9.8, Configuration5.9.18, Dorado base-calling 7.3.11, MinKNOW Core5.9.12.
Illumina base-calling: RTA3 sofware
trimed sequence reads were mapped to gemone mm9  using minimap2 (v.2.28)
Read count extraction were performed using telescope (v.1.0.3)
Assembly: mm9
Supplementary files format and content: fastq file, RNA or DNA sequence

source_name: murine embryonic fibroblast

extract_protocol:
WT-RAW264.7 and RAW Mecp2 KO : extraction ARN kit RTN350. MEF cyDNA extraction: STAR Protocol, Isolation of endogenous cytosolic DNA from cultured cells
RNAseq: kit stranded mRNA Prep Ligation d’Illumina. CyDNAseq: MinION Barcoding Kit 24 V14 (SQK-NBD114.24)

value: murine embryonic fibroblast

value: WT

value: mock


title: H015_P2_1: PBMC, No CD3/CD28 stimulation

description:
Library name: H015_P2_1
10X Genomics

value: No CD3/CD28 -CBD -TAC


title: Human liver stellate cells LX-2 after neutrophil intervention, con1

description:
Library name: con1
con1

value: Human liver

value: liver stellate cell


title: AGS_CsnB

value: CsnB


title: Barcode01

description:
Library name: Sample01
cyDNA, colum_name_in_minion_raw_ count: mock-1


title: H013_P2_1: PBMC, No CD3/CD28 stimulation

description:
Library name: H013_P2_1
10X Genomics

value: peripheral blood

value: Male


title: AGS_AchA

value: AchA


title: AGS_Vehicle_2 (for AchA)


title: AGS_Vehicle_4 (for CsnB)


title: H012_P3_2: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H012_P3_2
10X Genomics

value: Female

value: PBMC

value: CD3/CD28 +CBD -TAC


title: AGS_Vehicle_1 (for BAY)


title: S341_J123_T6 [S341_S83_L004]

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

institute: Texas A&M University

data_processing:
Illumina RTA v3 software was used for basecalling.
Read quality was assessed in FastQC v0.11.9
Read trimming was performed with Trimmomatic v0.39 with parameters for a 4-base pair sliding window and removing read segments below a minimum base quality score of 20, read length of less than 28 bases, leading and trailing basepairs below a quality score of 3, and removal of all Illumina Universal adaptors.
Read mapping and indexing was performed with HISAT2 v2.1.1, using the bovine whole genome assembly ARS-UCD1.3; parameters -p 14 --dta -x GCF_002263795.2_ARS-UCD1.3
Read assembly and quantification was performed with StringTie v2.2.0 with parameters -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff, followed by stringtie --merge -p 14 -G GCF_002263795.2_ARS-UCD1.3_genomic.gff -o mergefile.gtf, and stringtie -e -p 14 -G mergefile.gtf -o. A read count matrix was generated with prepDE3.py with parameters python prepDE3.py  -l 150 -i mergelist.txt. ComBat-Seq within sva was used to account for lane bias. Differential expression analysis was performed with edgeR v3.36.0 and glmmSeq v0.2.0.
Assembly: GCF_002263795.2
Supplementary files format and content: Comma-delimited text file of raw gene counts for each sample

organism: Bos taurus

source_name: Whole blood

extract_protocol:
Total RNA was isolated via Tempus Spin RNA Isolation Kits (Applied Biosystems), per product instruction.
RNA libraries were prepared for sequencing using Illumina Stranded mRNA library preparation kits, using standard Illumina protocols.

treatment_protocol: All samples were collected into Tempus RNA Blood tubes (Applied Biosystems) and stored per product recommendation the same day of collection.

value: Whole blood

tag: ID

tag: timepoint

tag: vaccinated

value: no

tag: marketing

value: auction

tag: treated for_brd

value: yes

tag: sequencing lane


title: S340_J122_T6 [S340_S82_L004]

value: direct


title: Barcode05

description:
Library name: Sample05
cyDNA, colum_name_in_minion_raw_ count: dsDNA-2

value: murine embryonic fibroblast

value: WT

tag: treatment

value: dsDNA


title: S338_J117_T6 [S338_S80_L004]

tag: tissue


title: Barcode06

description:
Library name: Sample06
cyDNA, colum_name_in_minion_raw_ count_all: dsDNA-3

tag: genotype


title: AGS_BAY plus Uridine

value: AGS

tag: cell type

value: gastric adenocarcinoma cells

value: BAY plus Uridine


title: H014_P2_1: PBMC, No CD3/CD28 stimulation

description:
Library name: H014_P2_1
10X Genomics

value: peripheral blood

value: No CD3/CD28 -CBD -TAC


title: Barcode04

description:
Library name: Sample04
cyDNA, colum_name_in_minion_raw_ count: dsDNA-1


title: H013_P2_2: PBMC, CD3/CD28 stimulation

description:
Library name: H013_P2_2
10X Genomics

value: Male

value: CD3/CD28 -CBD-TAC


title: Barcode02

description:
Library name: Sample02
cyDNA, colum_name_in_minion_raw_ count: mock-2

value: mock


title: CR-sg-WT, rep1

city: Vancour

first: Xuesen

last: Dong

address: 276 - 2660 Oak Street

institute: Vancour Prostate Cancer

description:
Library name: sample 11
fpkm_CR_sg_mut1

data_processing:
The resulting BAM files are processed with HTSeq-count to quantify gene expression using the GENCODE v29lift37 annotation.
Assembly: hg19
Supplementary files format and content: Gene Count Files (e.g htseq-count.strandno.sorted.LN95-1.txt) - Each line represents a gene ID (GENCODE v29lift37) and its corresponding read count

source_name: cell line

growth_protocol: All cells were cultured in RPMI1640 media containing 10% charstripped serum. Cells were split when reached 90% confluency.

extract_protocol:
Total RNA was extracted from cells using the Purelink RNA mini kit (Invitrogen) following the manufacturer's standard protocol.
(1) Sample QC; (2) mRNA Isolation; (3) mRNA Fragmentation; (4) cDNA Synthesis; (5) End Repair, Add A and Adaptor Ligation; (6) PCR; (7) Library QC; (8) Circularization; (9) Sequencing

treatment_protocol: LN95(UGT2B17 KO) cells were transfected with UGT2B17WT UGT2B17Mut SRCK259M or SRCY530F

value: cell line

value: LN95-UGT2B15 knockout

value: prostate cancer cell

value: LN95-UGT2b15 cells transfected with UGT2B15 wild type plasmide for 72h


title: S344_J132 _T6 [S344_S86_L004]

value: Whole blood

value: yes

value: auction

value: no


title: S334_J111_T6 [S334_S76_L004]


title: H012_P2_1: PBMC, No CD3/CD28 stimulation

description:
Library name: H012_P2_1
10X Genomics

value: Female

value: PBMC


title: H012_P3_3: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol, and 5 ng/ml tacrolimus in the media

description:
Library name: H012_P3_3
10X Genomics

value: CD3/CD28 +CBD +TAC


title: S332_J109_T6 [S332_S74_L004]


title: CR-sg-mut, rep1

description:
Library name: sample 9
fpkm_CR_sg_WT1

value: LN95-UGT2b15 cells transfected with UGT2B15 mutantion plasmide for 72h


title: AGS_BAY

value: AGS

value: gastric adenocarcinoma cells

value: WT

value: BAY


title: S342_J128_T6 [S342_S84_L004]


title: S339_J121_T6 [S339_S81_L004]

value: direct


title: CR-sg-WT, rep2

description:
Library name: sample 12
fpkm_CR_sg_mut2

value: cell line


title: H012_P3_1: PBMC, No CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H012_P3_1
10X Genomics

value: peripheral blood

value: No CD3/CD28 +CBD -TAC


title: H012_P2_3: PBMC, CD3/CD28 stimulation and 5 ng/ml tacrolimus in the media

description:
Library name: H012_P2_3
10X Genomics

value: CD3/CD28 -CBD +TAC


title: S336_J113_T6 [S336_S78_L004]

value: Whole blood


title: S335_J112_T6 [S335_S77_L004]

value: yes


title: S337_J115_T6 [S337_S79_L004]


title: CR-sg-530, rep1

description:
Library name: sample 7
fpkm_CR_sg_530_1

value: LN95-UGT2B15 knockout

value: prostate cancer cell

value: LN95-UGT2b15 cells transfected with SRCY530 plasmide for 72h


title: H010_P3_2: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H010_P3_2
10X Genomics

value: Female

value: PBMC

value: CD3/CD28 +CBD -TAC


title: S328_J103_T6 [S328_S70_L004]


title: S343_J130_T6 [S343_S85_L004]


title: S326_J091_T6 [S326_S68_L004]

value: no


title: CR-sg-mut, rep2

description:
Library name: sample 10
fpkm_CR_sg_WT2

value: LN95-UGT2b15 cells transfected with UGT2B15 mutantion plasmide for 72h


title: H012_P2_2: PBMC, CD3/CD28 stimulation

description:
Library name: H012_P2_2
10X Genomics

value: CD3/CD28 -CBD-TAC


title: S331_J108_T6 [S331_S73_L004]


title: H010_P2_3: PBMC, CD3/CD28 stimulation and 5 ng/ml tacrolimus in the media

description:
Library name: H010_P2_3
10X Genomics


title: H010_P3_3: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol, and 5 ng/ml tacrolimus in the media

description:
Library name: H010_P3_3
10X Genomics

value: CD3/CD28 +CBD +TAC


title: CR-sg-530, rep2

description:
Library name: sample 8
fpkm_CR_sg_530_2


title: S330_J107_T6 [S330_S72_L004]

value: auction


title: S329_J104_T6 [S329_S71_L004]

value: direct


title: S323_J088_T6 [S323_S66_L004]


title: S333_J110_T6 [S333_S75_L004]


title: S327_J097_T6 [S327_S69_L004]


title: CR-sg-259, rep1

description:
Library name: sample 5
fpkm_CR_sg_259_1

value: cell line

value: LN95-UGT2b15 cells transfected with SRCY259 plasmide for 72h


title: S321_J086_T6 [S321_S64_L004]


title: H010_P3_1: PBMC, No CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H010_P3_1
10X Genomics

value: peripheral blood

value: No CD3/CD28 +CBD -TAC


title: S324_J089_T6 [S324_S67_L004]

value: Whole blood

value: yes


title: CR-sg-259, rep2

description:
Library name: sample 6
fpkm_CR_sg_259_2

value: LN95-UGT2B15 knockout

value: prostate cancer cell


title: S322_J087_T6 [S322_S65_L004]


title: S317_J081_T6 [S317_S60_L004]


title: CR, rep2

description:
Library name: sample 2
fpkm_CR_2


title: H009_P3_2: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H009_P3_2
10X Genomics

value: Male


title: CR-sg, rep2

description:
Library name: sample 4
fpkm_CR_sg_2


title: S320_J085_T6 [S320_S63_L004]


title: S319_J084_T6 [S319_S62_L004]


title: CR-sg, rep1

description:
Library name: sample 3
fpkm_CR_sg_1


title: H010_P2_2: PBMC, CD3/CD28 stimulation

description:
Library name: H010_P2_2
10X Genomics

value: Female

value: PBMC


title: H010_P2_1: PBMC, No CD3/CD28 stimulation

description:
Library name: H010_P2_1
10X Genomics

value: No CD3/CD28 -CBD -TAC


title: S312_J071_T6 [S312-2_S57_L004]

value: no


title: S318_J082_T6 [S318_S61_L004]


title: S311_J068_T6 [S311-2_S55_L004]


title: H009_P3_1: PBMC, No CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H009_P3_1
10X Genomics


title: H009_P3_3: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol, and 5 ng/ml tacrolimus in the media

description:
Library name: H009_P3_3
10X Genomics


title: S307_J055_T6 [S307_S50_L004]


title: S309_J061_T6 [S309_S52_L004]


title: H009_P2_2: PBMC, CD3/CD28 stimulation

description:
Library name: H009_P2_2
10X Genomics

value: CD3/CD28 -CBD-TAC


title: S316_J078_T6 [S316_S59_L004]


title: CR, rep1

description:
Library name: sample 1
fpkm_CR_1


title: S306_J053_T6 [S306_S49_L004]


title: S310_J062_T6 [S310_S53_L004]


title: H009_P2_3: PBMC, CD3/CD28 stimulation and 5 ng/ml tacrolimus in the media

description:
Library name: H009_P2_3
10X Genomics

value: CD3/CD28 -CBD +TAC


title: S308_J059_T6 [S308_S51_L004]

value: auction


title: Zebrafish head, osr2-/- , scRNA

city: Melbourne

first: Michelle

last: Meier

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: 30dpf head osr2 mutant, scRNA
10X Chromium (Single cell 3' V3)

data_processing:
Sequencing quality was assessed using FastQC v0.11.6 and MultiQC v1.7 viewer for aggregated reports. Cell Ranger count was used to generate count files and cellbender was used to remove ambient RNA. Doublets were identified from the filtered count files using Scrublet  in Python version 3.6. Sequence reads corresponding to ribosomal and global genes were removed, cells filtered according to library size and mitochondrial content, normalised, followed by UMAP dimension reduction, clustering (louvain) and cell-cycle analysis using Seurat for R statistical software. The quality of the dataset was evaluated before and after normalisation using both custom plots and built-in functions in Seurat and scater.  Cluster solutions were evaluated, and most appropriate resolution selected using ClusTree, and cluster identity was defined using key markers of phenotype
Assembly: GRCz11 (Ensembl 102)
Supplementary files format and content: cellranger output filtered_feature_bc_matrix: barcode, feature and count matrices
Supplementary files format and content: Seurat object of all cells after quality control filtering in RDS format

organism: Danio rerio

source_name: Head

extract_protocol:
Library preparation and sequencing was performed at the Molecular Genomics Core Facility (Peter MacCallum Cancer Centre). Single cell suspensions from FACS were spun down and a cell count was performed to determine post-sort viability and cell concentration. Single cell suspension was partitioned and barcoded using the 10X Genomics Chromium iX Controller (10X Genomics) and the Single Cell 3' Library and Gel Bead Kit (V3.1; 10X Genomics;  PN-1000121).  The cells were loaded onto the Chromium Single Cell Chip G (10X Genomics; PN-1000120) to target 10,000 cells.
GEM generation and barcoding, cDNA amplification, and library construction was performed according to the 10X Genomics Chromium User Guide. The resulting single cell transcriptome libraries contained unique sample indices for each sample. The libraries were quantified on the Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape and reagents (Agilent, 5067-5585, 5067-5584). Single cell transcriptome libraries were pooled in equimolar ratios before being sequenced on an Illumina NextSeq2000 using P4 100-cycle chemistry. Read1 supplies the cell barcode and UMI, i7 and i5 the sample indexes, and Read2 the 3’ sequence of the transcript. Sequencing read lengths were trimmed to 28bp (Read1), 10bp (i7 index), 10bp (i5 index), 91bp (Read2), ensuring compatibility with the 10X Genomics analysis software, Cell Ranger. After sequencing, fastq files were generated using bcl2fastq2 (v.2.20.0.422).

value: Head

tag: transgenic

tag: facs

value: fli1a (nEGFP) positive and lyve1b (dsRed2) positive

value: osr2 mutant

tag: internal id


title: Zebrafish head, wildtype sibling, scRNA

description:
Library name: 30dpf head wildtype, scRNA
10X Chromium (Single cell 3' V3)

value: WT


title: gWAT ND-fed Young Female

city: Ann Arbot

first: Raymond

last: Yung

state: Michigan

address: 109 Zina Pitcher Pl

institute: University of Michigan

description:
Library name: Sample_10436-AK-6
10X Genomics

data_processing:
Data were analyzed using Seurat v5.1.0. Cells were filtered to retain those with ≥500 UMIs, ≥250 genes, log10(genes per UMI) > 0.8, and mitochondrial gene content <15%. Genes expressed in fewer than 10 cells were excluded. Doublets were detected using scDblFinder v1.16.0  and further removed. Each dataset was normalized, and 4,000 variable features were identified using the “vst” method. Integration was performed using SelectIntegrationFeatures, FindIntegrationAnchors, and IntegrateData. Variables including gene count, mitochondrial ratio, and cell cycle scores (S and G2M) were regressed during scaling. PCA was performed using 60 principal components (PCs). UMAP was applied on the top 40 PCs, guided by elbow plot analysis. Clustering was performed at a resolution of 1.2. Cell clusters were annotated using SingleR v2.4.1, referencing the ImmGen and MouseRNAseq datasets from the cellDex v1.12.0 package. Annotations were finally refined manually based on top marker genes identified via FindAllMarkers.
Assembly: GRCm38 (10x Genomics mm10-2020-A)
Supplementary files format and content: The processed data files are HDF5 files generated by Cell Ranger  using the 10x Genomics.

source_name: gonadal white adipose tissue

extract_protocol:
Mice were euthanized using CO2 inhalation, and gonadal white adipose tissue (gWAT) was dissected. Tissue was finely minced and digested in 0.8 mg/ml Collagenase II (Worthington Biochemical) buffer containing 3% BSA, 1X penicillin/streptomycin, 1.2 mM CaCl₂, 1 mM MgCl₂, 0.8 mM ZnCl₂, and 15 mM HEPES for 40 minutes at 37°C with constant agitation. The digested suspension was centrifuged at 600g for 10 minutes at 4°C, and the SVF was filtered through 70 µm and 40 µm strainers. Red blood cell (RBC) lysis was performed as per manufacturer’s instructions (eBioscience), followed by washing and resuspension in RPMI1640 supplemented with 10% FBS and 1X penicillin/streptomycin. Fresh cells were stained with Zombie Aqua live/dead dye (Biolegend) for 10 minutes at room temperature. Cells were sorted using a Bigfoot Spectral Cell Sorter (Thermo Fisher Scientific).
Sorted cells were resuspended in RPMI medium with 10% FBS, equal number of cells from 3 mice per group were pooled and submitted to the University of Michigan Advanced Genomics Core for 3′ library preparation and sequencing. Briefly, cell counts were obtained using the Luna-FX7 Cell Counter (LogosBio). Libraries were prepared using the 10X Genomics Chromium Controller with 3′ v3.1 chemistry and Feature Barcoding technology for Cell Multiplexing, according to the manufacturer’s instructions (10X Genomics). Library quality was assessed on the LabChip GXII HT (PerkinElmer), and concentrations were determined using Qubit (Thermo Fisher). Pooled libraries were sequenced using paired-end 28×10×10×151 bp reads on the Illumina NovaSeq XPlus. Demultiplexed FASTQ files were generated using Bcl2fastq2 (Illumina), and count matrices were generated using the CellRanger pipeline (10X Genomics).

treatment_protocol: Young mice were fed a high-fat diet (HFD) (42% Kcal from fat, Inotiv; TD.88137) for 12 weeks starting from 4-6 weeks of age, while the remaining control young and aged mice were fed with normal diet.

value: gonadal white adipose tissue

tag: diet

value: Normal Diet

value: 4-5 months


title: gWAT ND-fed Young Male

description:
Library name: Sample_10436-AK-5
10X Genomics


title: H007_P2_3: PBMC, CD3/CD28 stimulation and 5 ng/ml tacrolimus in the media

description:
Library name: H007_P2_3
10X Genomics

value: peripheral blood

tag: cell line


title: S302_J047_T6 [S302_S45_L004]

value: Whole blood

value: yes


title: S314_J038_T6 [S314_S58_L004]


title: H009_P2_1: PBMC, No CD3/CD28 stimulation

description:
Library name: H009_P2_1
10X Genomics

tag: age

value: Male


title: H007_P2_2: PBMC, CD3/CD28 stimulation

description:
Library name: H007_P2_2
10X Genomics

tag: Sex

value: Female

value: PBMC


title: S303_J050_T6 [S303_S46_L004]

tag: ID

value: no

value: direct


title: S299_J041_T6 [S299_S42_L004]

tag: timepoint


title: gWAT ND-fed Aged Female

description:
Library name: Sample_10436-AK-2
10X Genomics

value: 21-24 months


title: gWAT HFD-fed Young Male

description:
Library name: Sample_10436-AK-3
10X Genomics

value: High Fat diet


title: S301_J045_T6 [S301_S44_L004]

tag: vaccinated


title: S297_J037_T6 [S297_S40_L004]

tag: marketing


title: H006_P3_3: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol, and 5 ng/ml tacrolimus in the media

description:
Library name: H006_P3_3
10X Genomics

value: CD3/CD28 +CBD +TAC


title: gWAT ND-fed Aged Male

description:
Library name: Sample_10436-AK-1
10X Genomics


title: S296_J036_T6 [S296_S39_L004]

tag: treated for_brd


title: H006_P3_2: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H006_P3_2
10X Genomics

value: CD3/CD28 +CBD -TAC


title: S294_J033_T6 [S294_S38_L004]

value: auction

tag: sequencing lane


title: S304_J051_T6 [S304_S47_L004]


title: S293_J032_T6 [S293_S37_L004]


title: H006_P3_1: PBMC, No CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H006_P3_1
10X Genomics

tag: treatment

value: No CD3/CD28 +CBD -TAC


title: S305_J052_T6 [S305_S48_L004]

tag: tissue


title: S292_J031_T6 [S292_S36_L004]


title: H007_P2_1: PBMC, No CD3/CD28 stimulation

description:
Library name: H007_P2_1
10X Genomics

value: No CD3/CD28 -CBD -TAC


title: H006_P2_3: PBMC, CD3/CD28 stimulation and 5 ng/ml tacrolimus in the media

description:
Library name: H006_P2_3
10X Genomics

value: CD3/CD28 -CBD +TAC


title: S291_J030_T6 [S291_S35_L004]


title: gWAT HFD-fed Young Female

description:
Library name: Sample_10436-AK-4
10X Genomics

value: gonadal white adipose tissue

value: 4-5 months


title: AIM_exp2_G4_S1_VDJ

city: La Jolla

first: Ester

last: Marina-Zarate

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description: Library name: AIM_exp2_G4_S1_VDJ

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v7.1.0
Assembly: Mmul10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca mulatta

source_name: Blood

extract_protocol:
Frozen PBMC and LN FNA samples were thawed in R10 media (RPMI + 10% FBS, 1x penicillin/streptomycin, 1x GlutaMAX), and counted. Cells were washed with FACS buffer (2% FBS in PBS) and stained first with fluorescent antigen probes. MD39 (MD39 WT) and MD39 epitope knock-out (MD39 KO) probes were prepared by mixing fluorophore-conjugated streptavidin (SA) with biotinylated antigen probes added in small increments every 15 minutes for a total of 1 hour in PBS at room temperature. MD39 KO probe was added for 15 min at 4 °C and then incubated with MD39 WT probes for an additional 15 min. Without washing, cells were stained with surface antibodies for an additional 30 min at 4 °C. For sorting, anti-human Total-Seq-C hashtag antibodies (Biolegend) were individually added to each sample at a concentration of 1 µg/5 million cells at the time of addition of the master mix. Cells were washed twice with FACS buffer. Cells were sorted on a FACSymphony S6 (BD Biosciences) or a FACSAria II (BD Biosciences).
Sorted AIM+ CD4 T cells from PBMCs and sorted LN FNA CD4 T cell populations were loaded onto a Chromium Next GEM Single Cell 5' v2 chip and processed using the Chromium Controller, following the manufacturer's protocol (10X Genomics).Indexed V(D)J, Feature Barcode, and Gene Expression (GEX) libraries were prepared using the Feature Barcoding Kit (10X Genomics) and sequenced on a NovaSeq 6000 (Illumina). Custom rhesus macaque primers for TCRβ and TCRα constant regions were used. Forward and reverse primers were used at a final concentration of 1 µM.

treatment_protocol: HIV Env trimer MD39 with adjuvant SMNP immunizations

value: Blood


title: S290_J029_T6 [S290_S34_L004]

value: Whole blood

value: yes


title: AIM_exp2_G3_S2_VDJ

description: Library name: AIM_exp2_G3_S2_VDJ


title: H006_P2_2: PBMC, CD3/CD28 stimulation

description:
Library name: H006_P2_2
10X Genomics

value: peripheral blood

value: Female

value: CD3/CD28 -CBD-TAC


title: S300_J043_T6 [S300_S43_L004]

value: no

value: direct


title: S289_J028_T6 [S289_S33_L004]


title: S298_J040_T6 [S298_S41_L004]


title: AIM_exp2_G3_S1_VDJ

description: Library name: AIM_exp2_G3_S1_VDJ


title: S287_J026_T6 [S287_S31_L004]


title: S285_J024_T6 [S285_S30_L004]


title: S288_J027_T6 [S288_S32_L004]


title: AIM_exp2_G2_S2_VDJ

description: Library name: AIM_exp2_G2_S2_VDJ


title: H006_P2_1: PBMC, No CD3/CD28 stimulation

description:
Library name: H006_P2_1
10X Genomics

value: PBMC


title: S284_J023_T6 [S284_S29_L004]


title: S283_J022_T6 [S283_S28_L004]


title: AIM_exp2_G2_S1_VDJ

description: Library name: AIM_exp2_G2_S1_VDJ


title: H005_P3_3: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol, and 5 ng/ml tacrolimus in the media

description:
Library name: H005_P3_3
10X Genomics

value: CD3/CD28 +CBD +TAC


title: H005_P3_2: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H005_P3_2
10X Genomics

value: CD3/CD28 +CBD -TAC


title: AIM_exp2_G1_S2_VDJ

description: Library name: AIM_exp2_G1_S2_VDJ


title: S281_J019_T6 [S281_S26_L004]


title: H005_P3_1: PBMC, No CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H005_P3_1
10X Genomics


title: AIM_exp2_G1_S1_VDJ

description: Library name: AIM_exp2_G1_S1_VDJ


title: S277_J015_T6 [S277_S22_L004]


title: AIM_exp1_G4_VDJ

description: Library name: AIM_exp1_G4_VDJ


title: H005_P2_2: PBMC, CD3/CD28 stimulation

description:
Library name: H005_P2_2
10X Genomics


title: S274_J011_T6 [S274_S19_L004]


title: AIM_exp1_G2_VDJ

description: Library name: AIM_exp1_G2_VDJ


title: AIM_exp1_G1G3_VDJ

description: Library name: AIM_exp1_G1G3_VDJ


title: S272_J132 _T5 [S272_S17_L004]

value: auction


title: H005_P2_1: PBMC, No CD3/CD28 stimulation

description:
Library name: H005_P2_1
10X Genomics


title: Wk59_TFH_S6_VDJ

description: Library name: Wk59_TFH_S6_VDJ

source_name: Lymph node

value: Lymph node


title: H002_P3_3: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol, and 5 ng/ml tacrolimus in the media

description:
Library name: H002_P3_3
10X Genomics


title: AIM_exp2_G4_S2_VDJ

description: Library name: AIM_exp2_G4_S2_VDJ


title: S273_J009_T6 [S273_S18_L004]


title: H002_P3_2: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H002_P3_2
10X Genomics


title: S279_J017_T6 [S279_S24_L004]


title: S268_J110_T5 [S268_S13_L004]


title: S269_J115_T5 [S269_S14_L004]


title: S280_J018_T6 [S280_S25_L004]


title: Wk59_TFH_Fusion_VDJ

description: Library name: Wk59_TFH_Fusion_VDJ


title: S271_J128_T5 [S271_S16_L004]


title: S282_J020_T6 [S282_S27_L004]


title: S267_J107_T5 [S267_S12_L004]


title: S278_J016_T6 [S278_S23_L004]


title: Wk59_NonTFH_Fusion_VDJ

description: Library name: Wk59_NonTFH_Fusion_VDJ


title: H005_P2_3: PBMC, CD3/CD28 stimulation and 5 ng/ml tacrolimus in the media

description:
Library name: H005_P2_3
10X Genomics


title: H002_P3_1: PBMC, No CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H002_P3_1
10X Genomics

value: No CD3/CD28 +CBD -TAC


title: S266_J104_T5 [S266_S11_L004]


title: S265_J089_T5 [S265_S10_L004]


title: H002_P2_3: PBMC, CD3/CD28 stimulation and 5 ng/ml tacrolimus in the media

description:
Library name: H002_P2_3
10X Genomics

value: CD3/CD28 -CBD +TAC


title: S276_J014_T6 [S276_S21_L004]


title: S275_J013_T6 [S275_S20_L004]


title: Wk55_TFH_S6_VDJ

description: Library name: Wk55_TFH_S6_VDJ


title: S263_J087_T5 [S263_S8_L004]


title: H002_P2_2: PBMC, CD3/CD28 stimulation

description:
Library name: H002_P2_2
10X Genomics


title: Wk55_TFH_Fusion_VDJ

description: Library name: Wk55_TFH_Fusion_VDJ


title: S270_J117_T5 [S270_S15_L004]


title: S262_J085_T5 [S262_S7_L004]


title: H002_P2_1: PBMC, No CD3/CD28 stimulation

description:
Library name: H002_P2_1
10X Genomics

value: No CD3/CD28 -CBD -TAC


title: S261_J084_T5 [S261_S6_L004]


title: S260_J082_T5 [S260_S5_L004]


title: H001_P3_3: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol, and 5 ng/ml tacrolimus in the media

description:
Library name: H001_P3_3
10X Genomics

value: Male


title: S259_J081_T5 [S259_S4_L004]


title: Wk55_NonTFH_Fusion_VDJ

description: Library name: Wk55_NonTFH_Fusion_VDJ


title: S257_J068_T5 [S257_S2_L004]


title: S256_J061_T5 [S256_S1_L004]


title: Wk48_TFH_Fusion_VDJ

description: Library name: Wk48_TFH_Fusion_VDJ


title: S254_J045_T5 [S254-2_S86_L003]


title: Wk48_TFH_S6_VDJ

description: Library name: Wk48_TFH_S6_VDJ


title: H001_P3_1: PBMC, No CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H001_P3_1
10X Genomics


title: H001_P3_2: PBMC, CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H001_P3_2
10X Genomics


title: S253_J037_T5 [S253-2_S84_L003]


title: Wk48_NonTFH_S6_VDJ

description: Library name: Wk48_NonTFH_S6_VDJ


title: S252_J036_T5 [S252_S82_L003]


title: H001_P2_3: PBMC, CD3/CD28 stimulation and 5 ng/ml tacrolimus in the media

description:
Library name: H001_P2_3
10X Genomics


title: S264_J088_T5 [S264_S9_L004]


title: Wk48_NonTFH_Fusion_VDJ

description: Library name: Wk48_NonTFH_Fusion_VDJ


title: H001_P2_2: PBMC, CD3/CD28 stimulation

description:
Library name: H001_P2_2
10X Genomics


title: S251_J034_T5 [S251_S81_L003]


title: S255_J051_T5 [S255_S87_L003]


title: S250_J030_T5 [S250_S80_L003]


title: S249_J029_T5 [S249_S79_L003]


title: H000_P2_3: PBMC, CD3/CD28 stimulation and 5 ng/ml tacrolimus in the media

description:
Library name: H000_P2_3
10X Genomics

value: not collected


title: H000_P2_2: PBMC, CD3/CD28 stimulation

description:
Library name: H000_P2_2
10X Genomics


title: Wk30_TFH_2_S6_VDJ

description: Library name: Wk30_TFH_2_S6_VDJ


title: S248_J028_T5 [S248_S78_L003]

value: Whole blood


title: S258_J075_T5 [S258_S3_L004]


title: S246_J020_T5 [S246_S76_L003]

value: yes


title: H000_P2_1: PBMC, No CD3/CD28 stimulation

description:
Library name: H000_P2_1
10X Genomics

value: peripheral blood


title: S245_J018_T5 [S245_S75_L003]


title: S244_J016 _T5 [S244_S74_L003]


title: Wk30_TFH_1_S6_VDJ

description: Library name: Wk30_TFH_1_S6_VDJ


title: S243_J132 _T4 [S243_S73_L003]


title: H021 PBMC, CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H021_P3_2
10X Genomics

data_processing:
Alignment and quantification were accomplished with CellRanger arc (v.2.0.2)  using default options and reference genome refdata-cellranger-arc-GRCh38-2020-A-2.0.0.
The BPCells (v.0.2.0) package converted the matrices in the Hierarchical Data Format h5 to bitpacked compressed format stored as binary files on a hard drive. We used Seurat (v.5.1.0) to create a Seurat object for each sequencing sample.
Cells with mitochondria reads over 25% or fewer than 500 genes were removed.
All snRNA-seq samples were merged, and the cells were annotated by Azimuth (v.0.5.0) using the PBMC_ref_4546839 in Zenodo (https://zenodo.org/records/4546839).
Assembly: refdata-cellranger-arc-GRCh38-2020-A-2.0.0
Supplementary files format and content: CellRanger arc (v.2.0.2)
Supplementary files format and content: Tables and matrix files

treatment_protocol: 1 - CD3/CD28, CBD; No Tacrolimus;

value: Female


title: Wk30_NonTFH_S6_VDJ

description: Library name: Wk30_NonTFH_S6_VDJ


title: Wk30_NonTFH_Fusion_VDJ

description: Library name: Wk30_NonTFH_Fusion_VDJ


title: S242_J130_T4 [S242_S72_L003]


title: S239_J122_T4 [S239_S69_L003]


title: S241_J128_T4 [S241_S71_L003]


title: HeLa_TurboID-only_rep2 PLAMseq

city: Sevilla

first: Román

last: González-Prieto

address: Americo Vespucio 24

country: Spain

institute: CABIMER

description:
Library name: HeLa_TurboID-only_rep2
Cell lines expressing untagged TurboID construction

library_source: genomic

data_processing:
Raw sequencing reads were aligned to the telomere-to-telomere (T2T-CHM13v2.0) reference genome with Rsubread, allowing multimapping but retaining only the best-mapped location for each read. Duplicate reads from BAM files were removed with samtools markdup, thus only properly paired and non-duplicated reads were retained for downstream analysis. Bigwig files were build with bamCoverage function from Deeptools2, using a bin size of 1 and CPM normalization.
Assembly: T2T-CHM13v2.0
Supplementary files format and content: Bigwig files

molecule: genomic DNA

source_name: HeLa

growth_protocol: DMEM (4,5g/L glucose, L-glutamine and sodium pyruvate), 10% Fetal Bovine Serum, 1x Penicillin/Streptomycin. Cells were culture at 37ºC at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
PLAMseq libraries of H1.4 and H1.0 samples were prepared using Tn5 transposase (tagmentation) 5 minutes 37ºC. Then, NEBNext® High-Fidelity 2X PCR Master Mix was used for PCR amplification and library indexing (Nextera DNA Indexes i5 and i7) according to the following program: 72°C for 5 minutes; 98°C for 30 seconds, 9-10 cycles of 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 30 seconds, final holding stage 72ºC 5 minutes. PCR product was double purified using 0.7 and 0.15 volumnes of Seramag Beads (Cytiva). PLAMseq libraries of CTCF, POL2RI and H1.2 samples were prepared using the ThruPLEX DNA-Seq kit of Takara (cat. N. R400675).

treatment_protocol: Biotin 50μM 10 minutes 37ºC

value: HeLa

value: Human cervical cancer

value: 1x Biotin 10min


title: S237_J117_T4 [S237_S67_L003]

value: no


title: S238_J121_T4 [S238_S68_L003]

value: direct


title: S240_J123_T4 [S240_S70_L003]


title: Wk27_TFH_S6_VDJ

description: Library name: Wk27_TFH_S6_VDJ


title: Wk30_TFH_Fusion_VDJ

description: Library name: Wk30_TFH_Fusion_VDJ


title: Wk55_NonTFH_S6_VDJ

description: Library name: Wk55_NonTFH_S6_VDJ


title: Wk27_TFH_Fusion_VDJ

description: Library name: Wk27_TFH_Fusion_VDJ


title: S235_J112_T4 [S235_S65_L003]


title: S247_J025_T5 [S247_S77_L003]


title: S236_J115_T4 [S236_S66_L003]


title: HeLa_TurboID-only_rep1 PLAMseq

description:
Library name: HeLa_TurboID-only_rep1
Cell lines expressing untagged TurboID construction


title: Wk27_NonTFH_S6_VDJ

description: Library name: Wk27_NonTFH_S6_VDJ


title: S232_J108_T4 [S232_S62_L003]


title: Wk27_NonTFH_Fusion_VDJ

description: Library name: Wk27_NonTFH_Fusion_VDJ


title: Macrophages_s3-13_786-O_Donor 3

city: Barcelona

first: Clara

last: Alsinet

address: Diagonal 615

institute: AstraZeneca

description:
Library name: 3-13
Column name in rawcounts file: s3-13

data_processing:
Illumina DRAGEN pipeline, software version 4.0 (07.021.645.4.0.3). Mapping to the human genome DRAGEN RNA-Seq spliced aligner (version of hash table dated 20231117, “sw_version”, ”01.003.044.4.0.3”, ”hash_table_version”: “8”) and quantification with enabled GC bias correction and automatic strand detection.
Assembly: GRCh38
Supplementary files format and content: Counts csv table with ENSEMBL IDs as rows and samples as columns

source_name: CD14+ monocytes from PBMCs

growth_protocol: All macrophages were differentiated from freshly isolated CD14+ monocytes over 6 days in the presence of 50ng/ml M-CSF supplemented at day 0 and day 3

extract_protocol:
Total RNA was extracted from frozen cell pellets using a column based kit
NovaSeq 600 2x150bp paired end

treatment_protocol: Monocytes were differentiated in a 1:1 ratio of cancer cell line media or ascites fluid and standard media supplemented with 50ng M-CSF

value: CD14+ monocytes from PBMCs

value: Macrophages

tag: genotype

tag: treatment name

tag: treatment source

value: 786-O cancer cell line media


title: S233_J110_T4 [S233_S63_L003]

value: auction


title: Macrophages_s3-12_DU145_Donor 3

description:
Library name: 3-12
Column name in rawcounts file: s3-12

tag: cell type

value: DU 145 cancer cell line media


title: H024 PBMC, CD3/CD28 stimulation with in vivo Cannabidiol

description:
Library name: H024_P3_2
10X Genomics

value: PBMC

value: CD3/CD28 +CBD -TAC


title: HeLa_TurboID-only_rep3 PLAMseq

description:
Library name: HeLa_TurboID-only_rep3
Cell lines expressing untagged TurboID construction


title: Wk24_TFH_2_Fusion_VDJ

description: Library name: Wk24_TFH_2_Fusion_VDJ

value: Lymph node


title: Macrophages_s3-9_JIMT1_Donor 3

description:
Library name: 3-9
Column name in rawcounts file: s3-9

value: JIMT-1 cancer cell line media


title: S230_J104_T4 [S230_S60_L003]

value: Whole blood

value: yes


title: S231_J107_T4 [S231_S61_L003]


title: Macrophages_s3-11_HEP3B_Donor 3

description:
Library name: 3-11
Column name in rawcounts file: s3-11

value: Hep 3B cancer cell line media


title: Wk24_TFH_1_S6_VDJ

description: Library name: Wk24_TFH_1_S6_VDJ


title: S226_J091_T4 [S226_S56_L003]


title: S227_J092_T4 [S227_S58_L003]


title: Wk24_TFH_Fusion_VDJ

description: Library name: Wk24_TFH_Fusion_VDJ


title: Wk24_NonTFH_S6_VDJ

description: Library name: Wk24_NonTFH_S6_VDJ


title: S234_J111_T4 [S234_S64_L003]


title: S224_J088_T4 [S224_S54_L003]


title: Macrophages_s3-7_M2_Donor 3

description:
Library name: 3-7
Column name in rawcounts file: s3-7


title: Macrophages_s3-8_MDA_Donor 3

description:
Library name: 3-8
Column name in rawcounts file: s3-8

value: MDA

value: MDA-MB.231 cancer cell line media


title: S222_J086_T4 [S222_S52_L003]


title: Wk24_NonTFH_Fusion_VDJ

description: Library name: Wk24_NonTFH_Fusion_VDJ


title: S223_J087_T4 [S223_S53_L003]


title: Macrophages_s3-6_MCSF_Donor 3

description:
Library name: 3-6
Column name in rawcounts file: s3-6

value: MCSF

value: control MCSF only


title: Wk24_leftLN_TFH_S6_VDJ

description: Library name: Wk24_leftLN_TFH_S6_VDJ


title: S220_J084_T4 [S220_S50_L003]

value: no


title: Macrophages_s3-5_Ascites 5_Donor 3

description:
Library name: 3-5
Column name in rawcounts file: s3-5

value: CD14+ monocytes from PBMCs

value: Ascites 5

value: ovarian cancer ascities fluid


title: S219_J082_T4 [S219_S49_L003]

value: auction


title: Wk24_leftLN_TFH_Fusion_VDJ

description: Library name: Wk24_leftLN_TFH_Fusion_VDJ


title: S221_J085_T4 [S221_S51_L003]


title: S228_J097_T4 [S228_S57_L003]

value: direct


title: S229_J103_T4 [S229_S59_L003]


title: Macrophages_s3-3_Ascites 3_Donor 3

description:
Library name: 3-3
Column name in rawcounts file: s3-3

value: Macrophages

value: Ascites 3


title: S218_J081_T4 [S218_S48_L003]


title: S217_J078_T4 [S217_S47_L003]


title: Macrophages_s2-12_DU145_Donor 2

description:
Library name: 2-12
Column name in rawcounts file: s2-12

value: DU 145 cancer cell line media


title: S215_J075_T4 [S215_S45_L003]


title: S216_J076_T4 [S216_S46_L003]


title: S211_J061_T4 [S211_S39_L003]


title: Wk24_leftLN_NonTFH_S6_VDJ

description: Library name: Wk24_leftLN_NonTFH_S6_VDJ

value: Lymph node


title: S212_J062_T4 [S212_S40_L003]

value: Whole blood


title: S225_J089_T4 [S225_S55_L003]

value: yes


title: Macrophages_s2-11_HEP3B_Donor 2

description:
Library name: 2-11
Column name in rawcounts file: s2-11

value: Hep 3B cancer cell line media


title: Wk24_leftLN_NonTFH_Fusion_VDJ

description: Library name: Wk24_leftLN_NonTFH_Fusion_VDJ


title: S213_J068_T4 [S213-2_S42_L003]


title: Macrophages_s2-13_786-O_Donor 2

description:
Library name: 2-13
Column name in rawcounts file: s2-13

value: 786-O cancer cell line media


title: S208_J052_T4 [S208_S36_L003]


title: S210_J059_T4 [S210_S38_L003]


title: Wk16_TFH_S6_VDJ

description: Library name: Wk16_TFH_S6_VDJ


title: S214_J071_T4 [S214-2_S44_L003]


title: S209_J055_T4 [S209_S37_L003]


title: Macrophages_s2-8_MDA_Donor 2

description:
Library name: 2-8
Column name in rawcounts file: s2-8

value: MDA

value: MDA-MB.231 cancer cell line media


title: S206_J050_T4 [S206_S34_L003]


title: S205_J047_T4 [S205_S33_L003]


title: Macrophages_s2-9_JIMT1_Donor 2

description:
Library name: 2-9
Column name in rawcounts file: s2-9

value: JIMT-1 cancer cell line media


title: Wk16_NonTFH_Fusion_VDJ

description: Library name: Wk16_NonTFH_Fusion_VDJ


title: Wk16_Intermediate_S6_VDJ

description: Library name: Wk16_Intermediate_S6_VDJ


title: Macrophages_s2-7_M2_Donor 2

description:
Library name: 2-7
Column name in rawcounts file: s2-7


title: Macrophages_s2-6_MCSF_Donor 2

description:
Library name: 2-6
Column name in rawcounts file: s2-6

value: MCSF

value: control MCSF only


title: S203_J043_T4 [S203_S31_L003]

value: no


title: S204_J045_T4 [S204_S32_L003]


title: S207_J051_T4 [S207_S35_L003]


title: Wk16_Intermediate_Fusion_VDJ

description: Library name: Wk16_Intermediate_Fusion_VDJ


title: Wk16_NonTFH_S6_VDJ

description: Library name: Wk16_NonTFH_S6_VDJ


title: Wk16_TFH_Fusion_VDJ

description: Library name: Wk16_TFH_Fusion_VDJ


title: S202_J041_T4 [S202_S30_L003]


title: Wk10_TFH_S6_VDJ

description: Library name: Wk10_TFH_S6_VDJ


title: Macrophages_s2-5_Ascites 5_Donor 2

description:
Library name: 2-5
Column name in rawcounts file: s2-5

value: CD14+ monocytes from PBMCs

value: Ascites 5

value: ovarian cancer ascities fluid


title: Macrophages_s2-3_Ascites 3_Donor 2

description:
Library name: 2-3
Column name in rawcounts file: s2-3

value: Macrophages


title: S199_J034_T4 [S199_S27_L003]

value: direct


title: Wk10_TFH_Fusion_VDJ

description: Library name: Wk10_TFH_Fusion_VDJ


title: S201_J037_T4 [S201_S29_L003]


title: S194_J028_T4 [S194_S22_L003]

value: auction


title: S195_J029_T4 [S195_S23_L003]


title: Macrophages_s1-9_JIMT1_Donor 1

description:
Library name: 1-9
Column name in rawcounts file: s1-9


title: S196_J030_T4 [S196_S24_L003]


title: S197_J031_T4 [S197_S25_L003]


title: Wk10_NonTFH_Fusion_VDJ

description: Library name: Wk10_NonTFH_Fusion_VDJ

value: Lymph node


title: Macrophages_s1-13_786-O_Donor 1

description:
Library name: 1-13
Column name in rawcounts file: s1-13


title: S193_J026_T4 [S193_S21_L003]

value: Whole blood


title: S198_J033_T4 [S198_S26_L003]

value: yes


title: Wk10_NonTFH_S6_VDJ

description: Library name: Wk10_NonTFH_S6_VDJ


title: Macrophages_s1-11_HEP3B_Donor 1

description:
Library name: 1-11
Column name in rawcounts file: s1-11

value: Hep 3B cancer cell line media


title: Macrophages_s1-8_MDA_Donor 1

description:
Library name: 1-8
Column name in rawcounts file: s1-8


title: S192_J025_T4 [S192_S20_L003]


title: Wk08_TFH_S6_VDJ

description: Library name: Wk08_TFH_S6_VDJ


title: S191_J024_T4 [S191_S19_L003]


title: Wk08_TFH_Fusion_VDJ

description: Library name: Wk08_TFH_Fusion_VDJ


title: S190_J020_T4 [S190_S18_L003]


title: S189_J019_T4 [S189_S17_L003]


title: S200_J036_T4 [S200_S28_L003]


title: S187_J017_T4 [S187_S15_L003]


title: Wk08_NonTFH_S6_VDJ

description: Library name: Wk08_NonTFH_S6_VDJ


title: Wk04_TFH_S6_VDJ

description: Library name: Wk04_TFH_S6_VDJ


title: S184_J013_T4 [S184_S12_L003]


title: Wk04_NonTFH_S6_VDJ

description: Library name: Wk04_NonTFH_S6_VDJ


title: S188_J018_T4 [S188_S16_L003]


title: S186_J016_T4 [S186_S14_L003]


title: Macrophages_s1-6_MCSF_Donor 1

description:
Library name: 1-6
Column name in rawcounts file: s1-6


title: Macrophages_s1-7_M2_Donor 1

description:
Library name: 1-7
Column name in rawcounts file: s1-7


title: ATAC, HEK293T cells, sgKMT2B, rep2

city: Shanghai

first: Tengjiao

last: Li

address: No.800, Dongchuan Road, Minhang District, Shanghai, China Address in Chinese

department: School of Pharmaceutical Sciences

institute: Shanghai Jiao Tong University

description: Library name: Sample 8

data_processing:
Paired-end sequencing reads were processed using Cutadapt (v4.9) to remove adapter sequences and bases with quality scores below 30. Read quality was assessed before and after trimming using FastQC (v0.7.2). Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.5.3). Resulting BAM files were filtered with BAMTools (v2.5.2) to remove alignments with mapping quality (MAPQ) scores below 30 and reads mapped to the mitochondrial genome. PCR duplicates were subsequently removed using Picard MarkDuplicates (v3.1.1.0). Filtered BAM files were converted to BED format, and peak calling was performed using MACS2 (v2.2.9.1, parameters --shift -100 --extend 200). For genomic annotation of ATAC-seq peaks, the ChIPseeker R package (v1.42.1) was applied, using the TxDb.Hsapiens.UCSC.hg38.knownGene database to associate peaks with proximal genes. BigWig files were generated from BAM files and normalized to counts per million reads for the visualization of ATAC-seq data.
Assembly: hg38
Supplementary files format and content: bigwig, narrow peak

extract_protocol:
50,000 cells were collected at 500 g for 5 min, which was followed by a wash using 50 µl of cold 1× PBS and centrifugation at 500 g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630), then centrifuged for 10 minutes at 500 g to collect nuclei.
Resuspend cell pellet in 50 ul of transposition mixture (25 ul 2× TD buffer, 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) by pipetting up and down 6 times. Incubate reaction at 37°C for 30 minutes in a HUXImixer (HUXI, shanghai) with 1000 RPM mixing. Transposition reactions were cleaned up with a UNIQ-10 Column MicroDNA Gel Extraction Kit (Songon Biotech, shanghai). Libraries were amplified with Illumina Nextera sequencing primers.

value: human embryonic kidney epithelial cell line

value: KMT2B knockout


title: S185_J014_T4 [S185_S13_L003]


title: Wk08_NonTFH_Fusion_VDJ

description: Library name: Wk08_NonTFH_Fusion_VDJ


title: S182_J132 _T3 [S182_S10_L003]


title: S183_J011_T4 [S183_S11_L003]


title: Macrophages_s1-12_DU145_Donor 1

description:
Library name: 1-12
Column name in rawcounts file: s1-12

value: DU 145 cancer cell line media


title: Wk04_NonTFH_Fusion_VDJ

description: Library name: Wk04_NonTFH_Fusion_VDJ


title: S177_J121_T3 [S177_S5_L003]


title: ATAC, HEK293T cells, sgKMT2B, rep1

description: Library name: Sample 7


title: Wk04_leftLN_TFH_S6_VDJ

description: Library name: Wk04_leftLN_TFH_S6_VDJ


title: Wk04_TFH_Fusion_VDJ

description: Library name: Wk04_TFH_Fusion_VDJ


title: S180_J128_T3 [S180_S8_L003]


title: S179_J123_T3 [S179_S7_L003]


title: Macrophages_s1-3_Ascites 3_Donor 1

description:
Library name: 1-3
Column name in rawcounts file: s1-3

value: Ascites 3


title: S181_J130_T3 [S181_S9_L003]


title: S178_J122_T3 [S178_S6_L003]


title: ATAC, HEK293T cells, sgKDM6A, rep2

description: Library name: Sample 6

value: KDM6A knockout


title: S175_J115_T3 [S175_S4_L003]


title: Wk04_leftLN_NonTFH_S6_VDJ

description: Library name: Wk04_leftLN_NonTFH_S6_VDJ


title: Wk04_leftLN_TFH_Fusion_VDJ

description: Library name: Wk04_leftLN_TFH_Fusion_VDJ


title: S170_J107_T3 [S170_S86_L002]


title: S174_J112_T3 [S174_S3_L003]


title: S169_J104_T3 [S169_S85_L002]


title: AIM_exp2_G4_S2_HT

description: Library name: AIM_exp2_G4_S2_HT

value: Blood


title: S173_J111_T3 [S173_S2_L003]


title: ATAC, HEK293T cells, sgKDM6A, rep1

description: Library name: Sample 5


title: S167_J097_T3 [S167_S83_L002]

value: no


title: S172_J110_T3 [S172_S1_L003]


title: ATAC, HEK293T cells, sgKDM5C, rep2

description: Library name: Sample 4

value: KDM5C knockout


title: Macrophages_s1-5_Ascites 5_Donor 1

description:
Library name: 1-5
Column name in rawcounts file: s1-5

value: CD14+ monocytes from PBMCs

value: Ascites 5


title: S168_J103_T3 [S168_S84_L002]


title: Wk04_leftLN_NonTFH_Fusion_VDJ

description: Library name: Wk04_leftLN_NonTFH_Fusion_VDJ


title: ATAC, HEK293T cells, sgKDM5C, rep1

description: Library name: Sample 3


title: S166_J092_T3 [S166_S82_L002]


title: AIM_exp2_G4_S1_HT

description: Library name: AIM_exp2_G4_S1_HT


title: ATAC, HEK293T cells, WT, rep1

description: Library name: Sample 1

value: WT


title: S164_J089_T3 [S164_S80_L002]

value: direct


title: S163_J088_T3 [S163_S79_L002]


title: AIM_exp2_G3_S1_HT

description: Library name: AIM_exp2_G3_S1_HT


title: AIM_exp2_G3_S2_HT

description: Library name: AIM_exp2_G3_S2_HT


title: S165_J091_T3 [S165_S81_L002]


title: S161_J086_T3 [S161_S77_L002]

value: auction


title: S160_J085_T3 [S160_S76_L002]


title: S159_J084_T3 [S159_S75_L002]


title: S171_J108_T3 [S171_S87_L002]


title: AIM_exp2_G2_S1_HT

description: Library name: AIM_exp2_G2_S1_HT


title: HEK293T cells, sgKMT2B, rep2

description:
Library name: Sample 8
Column name in Counts_All_Samples.txt: sgKMT2B_rep2

data_processing:
Raw FASTQ files were aligned to the GRCh38 (hg38) genome using STAR and raw counts were generated with HTSeq (v0.11.2).
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text files include read count for each sample.

growth_protocol: HEK293T cells were maintained in DMEM supplemented with10% fetal bovine serum (FBS) and antibiotics in humidified incubator containing 5% CO2 at 37 ℃.

extract_protocol:
RNA were harvested using EastepTM Super Total RNA Extraction Kit (Promega). 1.3 μg of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligoattached 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. After library quality control, quantified libraries will be pooled and sequenced on Illumina Novaseq 6000 PE150 platforms, according to effective library concentration and data amount.


title: HEK293T cells, sgKMT2B, rep1

description:
Library name: Sample 7
Column name in Counts_All_Samples.txt: sgKMT2B_rep1


title: S162_J087_T3 [S162_S78_L002]


title: AIM_exp2_G2_S2_HT

description: Library name: AIM_exp2_G2_S2_HT


title: S158_J082_T3 [S158_S74_L002]


title: HEK293T cells, sgKDM6A, rep1

description:
Library name: Sample 5
Column name in Counts_All_Samples.txt: sgKDM6A_rep1


title: ATAC, HEK293T cells, WT, rep2

description: Library name: Sample 2


title: S156_J078_T3 [S156-2_S71_L002]


title: HEK293T cells, sgKDM6A, rep2

description:
Library name: Sample 6
Column name in Counts_All_Samples.txt: sgKDM6A_rep2


title: S157_J081_T3 [S157-2_S73_L002]


title: AIM_exp2_G1_S2_HT

description: Library name: AIM_exp2_G1_S2_HT


title: HEK293T cells, sgKDM5C, rep2

description:
Library name: Sample 4
Column name in Counts_All_Samples.txt: sgKDM5C_rep2


title: S154_J075_T3 [S154_S68_L002]


title: S155_J076_T3 [S155_S69_L002]


title: HEK293T cells, sgKDM5C, rep1

description:
Library name: Sample 3
Column name in Counts_All_Samples.txt: sgKDM5C_rep1


title: S153_J071_T3 [S153_S67_L002]


title: AIM_exp2_G1_S1_HT

description: Library name: AIM_exp2_G1_S1_HT


title: S152_J068_T3 [S152_S66_L002]


title: AIM_exp1_G4_HT

description: Library name: AIM_exp1_G4_HT


title: S151_J062_T3 [S151_S65_L002]


title: HEK293T cells, WT, rep2

description:
Library name: Sample 2
Column name in Counts_All_Samples.txt: WT_rep2


title: S150_J061_T3 [S150_S64_L002]


title: HEK293T cells, WT, rep1

description:
Library name: Sample 1
Column name in Counts_All_Samples.txt: WT_rep1


title: S147_J052_T3 [S147_S62_L002]


title: S148_J055_T3 [S148_S63_L002]


title: AIM_exp1_G1G3_HT

description: Library name: AIM_exp1_G1G3_HT


title: S145_J050_T3 [S145_S60_L002]


title: Wk59_TFH_S6_HT

description: Library name: Wk59_TFH_S6_HT

value: Lymph node


title: S146_J051_T3 [S146_S61_L002]

value: Whole blood


title: S144_J047_T3 [S144_S59_L002]

value: yes


title: HeLa_SUMO2+H1.0_rep2  PLAMseq

description:
Library name: HeLa_SUMO2+H1.0_rep2
Cell lines expressing NTurboID-H1.0 + CTurboID-SUMO2 construction

value: HeLa

value: Human cervical cancer

value: 1x Biotin 10min


title: HeLa_SUMO2+H1.0_rep3  PLAMseq

description:
Library name: HeLa_SUMO2+H1.0_rep3
Cell lines expressing NTurboID-H1.0 + CTurboID-SUMO2 construction


title: Wk59_TFH_Fusion_HT

description: Library name: Wk59_TFH_Fusion_HT


title: S142_J043_T3 [S142_S57_L002]


title: S143_J045_T3 [S143_S58_L002]


title: Wk59_NonTFH_Fusion_HT

description: Library name: Wk59_NonTFH_Fusion_HT


title: S140_J037_T3 [S140_S55_L002]


title: HeLa_SUMO2+H1.0_rep1  PLAMseq

description:
Library name: HeLa_SUMO2+H1.0_rep1
Cell lines expressing NTurboID-H1.0 + CTurboID-SUMO2 construction


title: S139_J036_T3 [S139_S54_L002]


title: S138_J034_T3 [S138_S53_L002]


title: Wk55_TFH_S6_HT

description: Library name: Wk55_TFH_S6_HT


title: S137_J033_T3 [S137_S52_L002]


title: S141_J041_T3 [S141_S56_L002]


title: Wk55_TFH_Fusion_HT

description: Library name: Wk55_TFH_Fusion_HT


title: S136_J031_T3 [S136_S51_L002]


title: HeLa_SUMO1+H1.0_rep3  PLAMseq

description:
Library name: HeLa_SUMO1+H1.0_rep3
Cell lines expressing NTurboID-H1.0 + CTurboID-SUMO1 construction


title: HeLa_SUMO1+H1.0_rep1  PLAMseq

description:
Library name: HeLa_SUMO1+H1.0_rep1
Cell lines expressing NTurboID-H1.0 + CTurboID-SUMO1 construction


title: AIM_exp1_G2_HT

description: Library name: AIM_exp1_G2_HT


title: HeLa_SUMO1+H1.0_rep2  PLAMseq

description:
Library name: HeLa_SUMO1+H1.0_rep2
Cell lines expressing NTurboID-H1.0 + CTurboID-SUMO1 construction


title: S135_J030_T3 [S135_S50_L002]


title: Wk55_NonTFH_S6_HT

description: Library name: Wk55_NonTFH_S6_HT


title: Wk55_NonTFH_Fusion_HT

description: Library name: Wk55_NonTFH_Fusion_HT


title: S133_J028_T3 [S133_S48_L002]


title: S132_J026_T3 [S132_S47_L002]


title: HeLa_TurboID-H1.0_rep3  PLAMseq

description:
Library name: HeLa_TurboID-H1.0_rep3
Cell lines expressing TurboID-H1.0 construction


title: HeLa_TurboID-H1.0_rep2  PLAMseq

description:
Library name: HeLa_TurboID-H1.0_rep2
Cell lines expressing TurboID-H1.0 construction


title: Wk48_TFH_S6_HT

description: Library name: Wk48_TFH_S6_HT


title: S129_J020_T3 [S129_S45_L002]


title: HeLa_TurboID-H1.0_rep1  PLAMseq

description:
Library name: HeLa_TurboID-H1.0_rep1
Cell lines expressing TurboID-H1.0 construction


title: S126_J017_T3 [S126_S44_L002]


title: S125_J016_T3 [S125_S43_L002]


title: HeLa_SUMO2+H1.4_rep3  PLAMseq

description:
Library name: HeLa_SUMO2+H1.4_rep3
Cell lines expressing NTurboID-H1.4 + CTurboID-SUMO2 construction


title: S124_J014_T3 [S124_S42_L002]


title: Wk48_NonTFH_S6_HT

description: Library name: Wk48_NonTFH_S6_HT


title: S123_J013_T3 [S123_S41_L002]


title: Wk48_NonTFH_Fusion_HT

description: Library name: Wk48_NonTFH_Fusion_HT


title: S121_J132 _T2 [S121_S39_L002]


title: HeLa_SUMO2+H1.4_rep2  PLAMseq

description:
Library name: HeLa_SUMO2+H1.4_rep2
Cell lines expressing NTurboID-H1.4 + CTurboID-SUMO2 construction


title: S122_J011_T3 [S122_S40_L002]


title: HeLa_SUMO2+H1.4_rep1  PLAMseq

description:
Library name: HeLa_SUMO2+H1.4_rep1
Cell lines expressing NTurboID-H1.4 + CTurboID-SUMO2 construction


title: Wk30_TFH_Fusion_HT

description: Library name: Wk30_TFH_Fusion_HT


title: S120_J130_T2 [S120_S38_L002]


title: S119_J128_T2 [S119_S37_L002]


title: Wk30_TFH_2_S6_HT

description: Library name: Wk30_TFH_2_S6_HT


title: S118_J123_T2 [S118_S36_L002]


title: HeLa_SUMO1+H1.4_rep3  PLAMseq

description:
Library name: HeLa_SUMO1+H1.4_rep3
Cell lines expressing NTurboID-H1.4 + CTurboID-SUMO1 construction


title: S134_J029_T3 [S134_S49_L002]


title: S116_J121_T2 [S116_S34_L002]


title: HeLa_SUMO1+H1.4_rep2  PLAMseq

description:
Library name: HeLa_SUMO1+H1.4_rep2
Cell lines expressing NTurboID-H1.4 + CTurboID-SUMO1 construction


title: Wk30_TFH_1_S6_HT

description: Library name: Wk30_TFH_1_S6_HT


title: S115_J117_T2 [S115_S33_L002]


title: S130_J024_T3 [S130_S46_L002]


title: HeLa_SUMO1+H1.4_rep1  PLAMseq

description:
Library name: HeLa_SUMO1+H1.4_rep1
Cell lines expressing NTurboID-H1.4 + CTurboID-SUMO1 construction


title: S114_J115_T2 [S114_S32_L002]


title: S113_J112_T2 [S113-2_S31_L002]


title: HeLa_TurboID-H1.4_rep3  PLAMseq

description:
Library name: HeLa_TurboID-H1.4_rep3
Cell lines expressing TurboID-H1.4 construction


title: Wk30_NonTFH_S6_HT

description: Library name: Wk30_NonTFH_S6_HT


title: Wk48_TFH_Fusion_HT

description: Library name: Wk48_TFH_Fusion_HT


title: S112_J111_T2 [S112-2_S29_L002]


title: Wk27_TFH_S6_HT

description: Library name: Wk27_TFH_S6_HT


title: S110_J108_T2 [S110_S26_L002]


title: HeLa_TurboID-H1.4_rep1  PLAMseq

description:
Library name: HeLa_TurboID-H1.4_rep1
Cell lines expressing TurboID-H1.4 construction


title: S109_J107_T2 [S109_S25_L002]


title: Wk27_TFH_Fusion_HT

description: Library name: Wk27_TFH_Fusion_HT


title: S108_J104_T2 [S108_S24_L002]


title: S107_J103_T2 [S107_S23_L002]


title: S117_J122_T2 [S117_S35_L002]


title: S106_J097_T2 [S106_S22_L002]


title: Hela_SUMO2+H1.2_rep2  PLAMseq

description:
Library name: Hela_SUMO2+H1.2_rep2
Cell lines expressing NTurboID-H1.2 + CTurboID-SUMO2 construction


title: Wk27_NonTFH_Fusion_HT

description: Library name: Wk27_NonTFH_Fusion_HT


title: Hela_SUMO2+H1.2_rep1  PLAMseq

description:
Library name: Hela_SUMO2+H1.2_rep1
Cell lines expressing NTurboID-H1.2 + CTurboID-SUMO2 construction


title: S102_J088_T2 [S102_S18_L002]


title: Wk24_TFH_Fusion_HT

description: Library name: Wk24_TFH_Fusion_HT


title: S103_J089_T2 [S103_S19_L002]


title: S101_J087_T2 [S101_S17_L002]


title: S100_J086_T2 [S100_S16_L002]


title: Hela_SUMO1+H1.2_rep3  PLAMseq

description:
Library name: Hela_SUMO1+H1.2_rep3
Cell lines expressing NTurboID-H1.2 + CTurboID-SUMO1 construction


title: Wk30_NonTFH_Fusion_HT

description: Library name: Wk30_NonTFH_Fusion_HT


title: Wk24_TFH_2_Fusion_HT

description: Library name: Wk24_TFH_2_Fusion_HT


title: S111_J110_T2 [S111_S27_L002]


title: S98_J084_T2 [S98_S14_L002]


title: Hela_SUMO1+H1.2_rep2  PLAMseq

description:
Library name: Hela_SUMO1+H1.2_rep2
Cell lines expressing NTurboID-H1.2 + CTurboID-SUMO1 construction


title: HeLa_TurboID-H1.4_rep2  PLAMseq

description:
Library name: HeLa_TurboID-H1.4_rep2
Cell lines expressing TurboID-H1.4 construction


title: Wk24_TFH_1_S6_HT

description: Library name: Wk24_TFH_1_S6_HT


title: S97_J082_T2 [S97_S13_L002]


title: Hela_SUMO1+H1.2_rep1  PLAMseq

description:
Library name: Hela_SUMO1+H1.2_rep1
Cell lines expressing NTurboID-H1.2 + CTurboID-SUMO1 construction


title: Wk27_NonTFH_S6_HT

description: Library name: Wk27_NonTFH_S6_HT


title: Hela_SUMO2+H1.2_rep3  PLAMseq

description:
Library name: Hela_SUMO2+H1.2_rep3
Cell lines expressing NTurboID-H1.2 + CTurboID-SUMO2 construction


title: S95_J078_T2 [S95_S11_L002]


title: Wk24_NonTFH_S6_HT

description: Library name: Wk24_NonTFH_S6_HT


title: S93_J075_T2 [S93_S9_L002]


title: Wk24_NonTFH_Fusion_HT

description: Library name: Wk24_NonTFH_Fusion_HT


title: S105_J092_T2 [S105_S21_L002]


title: HeLa_TurboID-H1.2_rep3  PLAMseq

description:
Library name: HeLa_TurboID-H1.2_rep3
Cell lines expressing TurboID-H1.2 construction


title: S94_J076_T2 [S94_S10_L002]


title: S104_J091_T2 [S104_S20_L002]


title: HeLa_TurboID-H1.2_rep2  PLAMseq

description:
Library name: HeLa_TurboID-H1.2_rep2
Cell lines expressing TurboID-H1.2 construction


title: S92_J071_T2 [S92_S8_L002]


title: HeLa_POL2RI-TurboID_rep3  PLAMseq

description:
Library name: HeLa_POL2RI-TurboID_rep3
Cell lines expressing POL2RI-TurboID construction


title: Wk24_leftLN_TFH_Fusion_HT

description: Library name: Wk24_leftLN_TFH_Fusion_HT


title: S90_J062_T2 [S90_S6_L002]


title: S91_J068_T2 [S91_S7_L002]


title: S99_J085_T2 [S99_S15_L002]


title: Wk24_leftLN_NonTFH_S6_HT

description: Library name: Wk24_leftLN_NonTFH_S6_HT


title: HeLa_POL2RI-TurboID_rep2  PLAMseq

description:
Library name: HeLa_POL2RI-TurboID_rep2
Cell lines expressing POL2RI-TurboID construction


title: S88_J059_T2 [S88_S4_L002]


title: S89_J061_T2 [S89_S5_L002]


title: Wk24_leftLN_NonTFH_Fusion_HT

description: Library name: Wk24_leftLN_NonTFH_Fusion_HT


title: HeLa_POL2RI-TurboID_rep1  PLAMseq

description:
Library name: HeLa_POL2RI-TurboID_rep1
Cell lines expressing POL2RI-TurboID construction


title: S87_J055_T2 [S87_S3_L002]


title: S96_J081_T2 [S96_S12_L002]


title: S86_J052_T2 [S86_S2_L002]


title: HeLa_CTCF-TurboID_rep3  PLAMseq

description:
Library name: HeLa_CTCF-TurboID_rep3
Cell lines expressing CTCF-TurboID construction


title: S85_J051_T2 [S85_S1_L002]


title: S83_J047_T2 [S83_S86_L001]


title: Wk16_TFH_S6_HT

description: Library name: Wk16_TFH_S6_HT


title: S80_J041_T2 [S80_S83_L001]


title: S81_J043_T2 [S81_S84_L001]


title: Wk16_NonTFH_S6_HT

description: Library name: Wk16_NonTFH_S6_HT


title: Wk16_TFH_Fusion_HT

description: Library name: Wk16_TFH_Fusion_HT


title: TILs from NSG CD8ab CD4 and CD8 combo

city: Seattle

first: Aude

last: Chapuis

state: WA

address: 1100 Fairview Ave

institute: Fred Hutchinson Cancer Center

description:
Library name: NSG_WT
10X Genomics

data_processing:
Raw FASTAQ files were processed using the 10x Genomics Cell Ranger software (v7.1.0) with default parameters. The EmptyDrops8 method was applied to filter out cells with low RNA content. The “count” function was used for alignment, filtering, barcode counting, and UMI counting.
Assembly: Reads were aligned to the human reference genome (hg38, Ensembl) and the codon-optimized transgene sequence using Spliced Transcripts Alignment to a Reference (STAR).
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Dissected tumor from NSG models were digested with tumor dissociation kit(Miltenyi), washed and stained in FACS buffer, then sorted with BD Symphony S6 flow cytometry sorter. CD4+ and CD8+ T cells obtained were then proceeded with 10X library prep.
Cryopreserved tumor single-cell suspension from in vivo murine experiment were thawed, washed and processed using a 10x Chromium Controller following the 5’ Chromium Single Cell V(D)J Reagent Kit manual (10x Genomics). Library preparation was carried out according to the manufacturer’s protocol without modifications. Library quality was assessed using TapeStation High Sensitivity (Agilent) to evaluate library size, Qubit (Thermo Fisher) to measure dsDNA quantity, and KAPA qPCR analysis (KAPA Biosystems) to determine the quantity of amplifiable transcript. Samples were pooled in equimolar proportions and sequenced on an Illumina HiSeq 2500 in rapid run mode, following the standard 10x Genomics protocol. TCR target enrichment, 5’ gene expression library preparation, and TCR library construction were performed using to the 5’ Chromium Single Cell V(D)J Reagent Kit manual (10x Genomics).

value: Tumor

value: T cell


title: S82_J045_T2 [S82_S85_L001]


title: HeLa_CTCF-TurboID_rep1  PLAMseq

description:
Library name: HeLa_CTCF-TurboID_rep1
Cell lines expressing CTCF-TurboID construction


title: HeLa_CTCF-TurboID_rep2  PLAMseq

description:
Library name: HeLa_CTCF-TurboID_rep2
Cell lines expressing CTCF-TurboID construction


title: S79_J037_T2 [S79_S82_L001]


title: TILs from NSG CD8/28 CD4 and CD8 combo

description:
Library name: NSG_G_
10X Genomics


title: HeLa_WT_rep3  PLAMseq

description:
Library name: HeLa_WT_rep3
WT cell lines


title: Wk16_Intermediate_S6_HT

description: Library name: Wk16_Intermediate_S6_HT


title: Wk24_leftLN_TFH_S6_HT

description: Library name: Wk24_leftLN_TFH_S6_HT


title: S78_J036_T2 [S78_S81_L001]


title: Jimpy Brain 2BAct Diet P19 03

city: Chicago

first: Brian

last: Popko

address: 7601 Morton Medical Research Building, 320 East Superior Street

institute: Northwestern Feinberg School of Medicine

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: Brain

extract_protocol:
The Aurum™ Total RNA Fatty and Fibrous Tissue Module kit (from Bio Rad #7326870) was used for RNA extractions.
Directional mRNA libraries were prepared using Illumina UDI Kits per the manufacturer’s instructions

value: Brain

value: Jimpy

value: P19, 2BAct Diet


title: Jimpy Brain 2BAct Diet P19 02


title: HeLa_WT_rep2  PLAMseq

description:
Library name: HeLa_WT_rep2
WT cell lines


title: S84_J050_T2 [S84_S87_L001]

value: no


title: S77_J034_T2 [S77_S80_L001]


title: TILs from NSG CD8 and CD4 individual

description:
Library name: NSG_CD8_4
10X Genomics


title: Wk16_Intermediate_Fusion_HT

description: Library name: Wk16_Intermediate_Fusion_HT


title: MDMs, HIV+Daily, CBD+IL1B_3

first: Jerel

last: Fields

state: CA

address: 5320 La Jolla Hermosa Ave

department: Psychiatry

institute: University of California, San Diego

description:
Library name: HIV+Daily (C+I)3
D26-CPLUSI3_643215606

data_processing:
Using the Illumina NovaSeq 6000 platform, libraries were sequenced on a NovaSeq S4 flow cell, with initial quality control checks, including per-base sequence quality, GC content, and sequence duplication levels conducted using FastQC (v0.11.9).
Clean reads were aligned to the hg38 human reference genome using STAR aligner (v2.7.9a) with default parameters on the Illumina BaseSpace Sequence Hub platform.
Differential expression analysis was conducted using DESeq2 (v1.30.0) in R (v4.0.5), with genes displaying a false discovery rate (FDR) < 0.05 considered significantly differentially expressed.
Assembly: Human (hg38)
Supplementary files format and content: Comma Separated Spreadsheet (.csv) files include raw gene transcript counts

source_name: monocyte-derived macrophages

growth_protocol: Isolated monocytes were cultured in IMDM supplemented with 10% human serum plus 1% penicillin/streptomycin and maintained in a humidified incubator at 5% CO2 and 37°C. Media was renewed every 48-72 hours over the 7-day differentiation period.

extract_protocol:
RNA collection was performed using RNeasy Plus Mini Kits from Qiagen. Following NanoDrop quantification, a total of 80 ng of mRNA per sample was used for library construction.
Illumina Stranded mRNA Prep, according to manufacturer's instructions.

treatment_protocol: MDMs were treated with media containing IL1B (I; 20 ng/mL), CBD (C; 30 μM), or both C+I for 6 hours.

tag: disease state

value: HIV Positive

tag: condition

value: Daily

value: monocyte-derived macrophages

tag: donor

value: Donor 26 (D26)


title: MDMs, HIV+Daily, CBD+IL1B_2

description:
Library name: HIV+Daily (C+I)2
D26-CPLUSI2_643212591


title: S76_J033_T2 [S76_S79_L001]

value: auction


title: S75_J031_T2 [S75_S78_L001]

value: direct


title: Wk10_TFH_S6_HT

description: Library name: Wk10_TFH_S6_HT

value: Lymph node


title: Jimpy Brain 2BAct Diet P19 01


title: MDMs, HIV+Daily, CBD_3

description:
Library name: HIV+Daily (CBD)3
D26-C3_643224613

value: CBD


title: S74_J030_T2 [S74_S77_L001]

value: Whole blood

value: yes


title: Wk10_TFH_Fusion_HT

description: Library name: Wk10_TFH_Fusion_HT


title: MDMs, HIV+Daily, CBD+IL1B_1

description:
Library name: HIV+Daily (C+I)1
D26-CPLUSI1_643215605


title: Wk16_NonTFH_Fusion_HT

description: Library name: Wk16_NonTFH_Fusion_HT


title: MDMs, HIV+Daily, CBD_2

description:
Library name: HIV+Daily (CBD)2
D26-C2_643224583


title: Jimpy Brain Ctr Diet P19 04

value: P19, Control Diet


title: Jimpy Brain Ctr Diet P19 02


title: HeLa_WT_rep1 PLAMseq

description:
Library name: HeLa_WT_rep1
WT cell lines

tag: cell line

value: HeLa

value: Human cervical cancer

value: 1x Biotin 10min


title: Jimpy Brain Ctr Diet P19 03

value: Brain

value: Jimpy


title: MDMs, HIV+Daily, CBD_1

description:
Library name: HIV+Daily (CBD)1
D26-C1_643223582


title: Wk08_TFH_S6_HT

description: Library name: Wk08_TFH_S6_HT


title: Wk10_NonTFH_Fusion_HT

description: Library name: Wk10_NonTFH_Fusion_HT


title: S72_J028_T2 [S72_S75_L001]

value: no


title: Ctr Brain 2BAct Diet P19 03

value: WT

value: P19, 2BAct Diet


title: Wk08_TFH_Fusion_HT

description: Library name: Wk08_TFH_Fusion_HT


title: S71_J026_T2 [S71_S74_L001]


title: Wk08_NonTFH_Fusion_HT

description: Library name: Wk08_NonTFH_Fusion_HT


title: Wk08_NonTFH_S6_HT

description: Library name: Wk08_NonTFH_S6_HT


title: Wk10_NonTFH_S6_HT

description: Library name: Wk10_NonTFH_S6_HT


title: MDMs, HIV+Daily, IL1B_2

description:
Library name: HIV+Daily (IL1B)2
D26-I2_643226585

value: HIV Positive

value: Daily

value: monocyte-derived macrophages


title: S69_J024_T2 [S69_S72_L001]

value: auction


title: Ctr Brain 2BAct Diet P19 02


title: S73_J029_T2 [S73_S76_L001]

value: direct


title: Ctr Brain 2BAct Diet P19 01


title: Wk04_TFH_S6_HT

description: Library name: Wk04_TFH_S6_HT

value: Lymph node


title: S68_J020_T2 [S68_S71_L001]

value: Whole blood


title: Wk04_TFH_Fusion_HT

description: Library name: Wk04_TFH_Fusion_HT


title: MDMs, HIV+Daily, IL1B_1

description:
Library name: HIV+Daily (IL1B)1
D26-I1_643226584

value: Donor 26 (D26)


title: Ctr Brain Ctr Diet P19 03

value: P19, Control Diet


title: Jimpy Brain Ctr Diet P19 01


title: S67_J019_T2 [S67_S70_L001]

value: yes


title: S66_J018_T2 [S66_S69_L001]


title: MDMs, HIV+Daily, Vehicle_2

description:
Library name: HIV+Daily (Control)2
D26-V2_643226593

value: Vehicle


title: Ctr Brain Ctr Diet P19 02


title: Wk04_NonTFH_Fusion_HT

description: Library name: Wk04_NonTFH_Fusion_HT


title: Ctr Brain Ctr Diet P19 01


title: MDMs, HIV+Daily, Vehicle_1

description:
Library name: HIV+Daily (Control)1
D26-V1_643226592


title: Wk04_NonTFH_S6_HT

description: Library name: Wk04_NonTFH_S6_HT


title: MDMs, HIV+Daily, IL1B_3

description:
Library name: HIV+Daily (IL1B)3
D26-I3_643212592


title: MDMs, HIV+Moderate, CBD+IL1B_3

description:
Library name: HIV+Molderate (C+I)3
D10-CPLUSI3_643019395

value: Moderate

value: Donor 10 (D10)


title: S70_J025_T2 [S70_S73_L001]


title: S65_J017_T2 [S65_S68_L001]


title: Wk04_leftLN_TFH_S6_HT

description: Library name: Wk04_leftLN_TFH_S6_HT


title: S64_J016_T2 [S64_S67_L001]


title: Jimpy Brain 2BAct Diet P14 04

value: Brain

value: Jimpy

value: P14, 2BAct Diet


title: Jimpy Brain 2BAct Diet P14 03


title: MDMs, HIV+Moderate, CBD+IL1B_2

description:
Library name: HIV+Molderate (C+I)2
D10-CPLUSI2_643004380


title: Wk04_leftLN_TFH_Fusion_HT

description: Library name: Wk04_leftLN_TFH_Fusion_HT


title: MDMs, HIV+Daily, Vehicle_3

description:
Library name: HIV+Daily (Control)3
D26-V3_643226594


title: MDMs, HIV+Moderate, CBD+IL1B_1

description:
Library name: HIV+Molderate (C+I)1
D10-CPLUSI1_643019391


title: S62_J011_T2 [S62_S65_L001]

value: no


title: S61_J132 _T1 [S61_S64_L001]


title: Wk04_leftLN_NonTFH_S6_HT

description: Library name: Wk04_leftLN_NonTFH_S6_HT


title: MDMs, HIV+Moderate, CBD_2

description:
Library name: HIV+Moderate (CBD)2
D10-C2_643019383

value: HIV Positive

value: CBD


title: Wk04_leftLN_NonTFH_Fusion_HT

description: Library name: Wk04_leftLN_NonTFH_Fusion_HT


title: Jimpy Brain Ctr Diet P14 03

value: P14, Control Diet


title: Jimpy Brain 2BAct Diet P14 02


title: MDMs, HIV+Moderate, CBD_3

description:
Library name: HIV+Moderate (CBD)3
D10-C3_643019389

value: monocyte-derived macrophages


title: AIM_exp2_G4_S2_GEX

description:
Library name: AIM_exp2_G4_S2_GEX
totalSeqC_feature_ref_AIM_exp2.csv

value: Blood


title: MDMs, HIV+Moderate, CBD_1

description:
Library name: HIV+Moderate (CBD)1
D10-C1_643019380


title: S60_J130_T1 [S60_S63_L001]

value: direct


title: S59_J128_T1 [S59_S62_L001]

value: Whole blood

value: auction


title: MDMs, HIV+Moderate, IL1B_3

description:
Library name: HIV+Moderate (IL1B)3
D10-I3_643004389


title: Jimpy Brain Ctr Diet P14 02


title: Jimpy Brain Ctr Diet P14 01


title: AIM_exp2_G4_S1_GEX

description:
Library name: AIM_exp2_G4_S1_GEX
totalSeqC_feature_ref_AIM_exp2.csv