title: GN015 3+8

city: London

first: Philip

last: East

address: Midland Road

institute: The Francis Crick Institute

data_processing:
bcl2fastq2 v2.2.0
reads trimmed with cutadapt
aligned and quantified with STAR and RSEM
Assembly: GRCh38
Supplementary files format and content: tab delimited RSEM gene-level count matrix

source_name: Colon

growth_protocol: Primary gut lymphocytes were obtained using an adaptation of the method of Kupper and Clarke (Clark et al., 2006) 9mm x 9mm x 1.5mm Cellfoam matrices (Cytomatrix PTY Ltd), were autoclaved and incubated in 100mg/mL rat tail collagen I (BD Biosciences) in PBS for 30min at 37 C, and washed twice in PBS. In compliance with local ethical approval, 12 endoscopic biopsies were taken from the ascending colon of donors. Biopsies were washed for 20min in 5mL wash medium (RPMI 1640 10% FCS, b-mercaptoethanol, penicillin [500U/ml], streptomycin [500 mg/ml], metronidazole [5 mg/ml, Pharmacy department, Guy’s Hospital], gentamicin [100 mg/ml, Sigma-Aldrich] and amphotericin 12.5 mg/ml [Thermo Fisher Scientific]). One endoscopic biopsy was placed on top of each matrix, which was inverted, and pressure applied, to crush the biopsy into the matrix. The matrices were placed into a 24-well plate (1 per well) and covered with 2mL RPMI 1640 (supplemented with 10% FCS, b-mercaptoethanol, penicillin [100U/ml], streptomycin [100 mg/ml], metronidazole [1 mg/ml], gentamicin [20 mg/ml], amphotericin [2.5 mg/ml]), IL-2 (100U/mL, Novartis Pharmaceutical UK) and IL-15 (10ng/mL, Biolegend). 1ml of medium was aspirated every second day and replaced with complete medium containing 2x concentrated cytokines. Cells were harvested and residual biopsy and empty wells were washed with PBS 0.02mM HEPES. The cell suspension was passed through a 70 mm nylon cell strainer, centrifuged at 400 g for 5min and resuspended in complete medium without additional cytokine and placed into co-culture immediately. Lymphocytes were used after 5-7 days of culture.

extract_protocol:
After overnight co-culture cells were labelled sorted and RNA was extracted using the RNeasy Micro Plus Kit (Qiagen)
cDNA was prepared with Ovation RNA-Seq System V2 (NuGEN) and libraries were constructed with Ultralow Library System V2 (NuGEN). Resulting libraries were pooled and sequenced on an Illumina HiSeq 2500 platform with single ended 75 bp reads.

treatment_protocol: 5x105 HEK293T cells, transduced with either empty vector (EV) or BTNL3+8 (transduction is described in Di Marco Barros et al Cell 2016; 167: 203-218)  and 2x105 freshly harvested primary human lymphocytes were co-cultured in 96-well plates with complete medium without supplementary cytokine and incubated at 37C at 5% CO2 for 16hrs

value: Colon

value: Co-culture over 16hrs with 293T cells expressing BTNL3 and BTNL8


title: AC16 cells, Control_12h

status: Public on Oct 03 2023

type: genomic

city: Rochester

first: Hangchuan

last: Shi

state: NY

address: 601 Elmwood Avenue

country: USA

institute: University of Rochester

description: SAMPLE 1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: Illumina's GenomeStudio methylation module (v1.9.0)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: AC16 control 12h

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from AC16 cells using Quick-DNA Isolation Kit according to standard instructions

tag: cell line

tag: treatment

value: Control

tag: time


title: AC16 cells, IGF1_12h_3

description: SAMPLE 7


title: LN-Negative-3

type: RNA

city: Kanazawa

first: Naohiro

last: Wakisaka

state: Ishikawa

country: Japan

institute: National Hospital Organization Kanazawa Medical Center

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LN3

hyb_protocol: Hybridization was performed using GeneChip Hybridization Oven 645. GeneChips were washed and stained in the  GeneChip Fluidics Station 450.

scan_protocol: The array was scanned using GeneChip Scanner 3000 7G, Affymetrix,.

data_processing: The data were analyzed with Transcriptome Analysis Console T hermo Fisher Scientific Inc.using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

source_name: Lymph Node

label_protocol: cDNA synthesis, amplification and labeling were performed with WT Pico Reagent, and according to the standard Affymetrix protocol using Veriti 200, Life Technologies, Inc.

extract_protocol: Total RNA from FFPE block was isolated using RNeasyⓇ FFPE Kit.

tag: disease state

value: lymph node of oropharyngeal cancer


title: AC16 cells, AngII_12h_3

description: SAMPLE 4

source_name: AC16 AngII 12h 3

value: AngII


title: GN016 3+8

type: SRA

country: United Kingdom

library_source: transcriptomic

tag: tissue

tag: cell type


title: RNA_Mutres_3

city: New York

first: Rajal

last: Sharma

address: 1425 Madison Ave., Room 16-52

institute: ISMMS

data_processing:
Basecalls performed using CASAVA version 1.4
Read sequences were filtered by Trimmomatic 0.36
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie v1.0.1
Peaks were called using MACS with Input as control with the following setting: pvalue cutoff (1.00e-05), model fold (10, 30).
For RNA-Seq: Tophat (v2.1.0) alignment was performed using the mm9 reference genome. HT-seq was used to find read counts across genes. DESeq2 was used to find differentially expressed genes with FDR < 0.1 and Fold-change > 1.5.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files generated by computing feature density over a 5 bp window across the genome. http://genome.ucsc.edu/goldenPath/help/wiggle.html For RNA-Seq: Tab-delimited text file of normalized counts for all samples.

source_name: HCT116 cells

growth_protocol: WT HCT116 p53+/+ cells were cultured in RPMI-1640 (Gibco) contained 10% fetal calf serum (Gibco), 100 units of penicillin (Gibco) and 100 µg/ml streptomycin (Gibco). Cells were treated with 500 nM Doxorubicin or DMSO as noted prior to collection for further analysis.

extract_protocol:
For ChIP-Seq: Whole cell lysates were sonicated and protein-DNA complexes were isolated with antibodies. For RNA-Seq: Compound treated cells were collected and RNA was extracted using TRIzol.
ChIP-sequencing for GAS41, c-Myc, H3K27cr and H3K27ac and RNA-sequencing in HCT116 cells with and without Dox treatment were performed on the Illumina HiSeq 2500v4 platform with 100bp read length under rapid run mode. Two to three biological replicates were prepared for each treatment condition. Specifically, for these genomic sequencing samples, ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar. Adaptor-modified fragments were enriched by 16 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size. Additionally, RNA-sequencing for HCT116 GAS41 wt and GAS41 KO cells, or GAS41 KO cells stably expressing GFP-Flag-GAS41 wt (wt rescue), or GFP-Flag-GAS41 Y74A/W93A (mutant rescue), was performed using an BGISEQ-500 platform at BGI. Three biological replicates were prepared for each treatment. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and single-end read of 50 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA. nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method

tag: replicate

tag: genotype

value: GAS41-KO (mut rescue)


title: AC16 cells, IGF1_12h_1

description: SAMPLE 5


title: GN016 EV

value: Co-culture over 16hrs with 293T cells expressing EV


title: AC16 cells, IGF1_12h_2

description: SAMPLE 6


title: RNA_Mutres_2


title: 2-week LNAME/HFD - 2524

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

data_processing:
Partek Flow platform used for data processing
Tophat 2 was used to align reads to the mm10 genome build
Reads were quantified to mm10 using the Partek E/M annotation model
Reads were normalized to counts per million (CPM) with 0.0001 added to the result.
Assembly: mm10
Supplementary files format and content: Text file including CPM for each sample (in columns) and gene (in rows)

organism: Mus musculus

source_name: Whole Lung

extract_protocol:
After sacrifice, lungs were immediately taken and flash frozen. RNA was isolated using Rneasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice underwent treatment with either L-NAME (0.5 g/L) in the water and high fat diet (60% lipid content) for 2 and 5 weeks, compared to 0 week controls.

value: Whole Lung

value: L-NAME/HFD for 2 weeks


title: RNA_WTres_1

value: GAS41-KO (wt rescue)


title: GN015 EV


title: 2-week LNAME/HFD - 2529


title: IP_cancerous-peritoneum1

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

data_processing:
CLC Genomics Workbench version 9.5.3 program
Sequence reads were trimmed and mapped to the miRbase 21 database allowing up to two mismatches
Reads per million mapped reads (RPM) method was used for normalization.
Assembly: miRbase 21

source_name: ascites

growth_protocol: Murine epithelial ovarian cancer cell line (ID8) were used. Then, we established the subclone of ID8 (ID8-T6), which has high metastatic ability in the peritoneal cavity. The cells were cultured in Dulbecco's modified Eagle medium (DMEM)-high glucose (Nacalai Tesque) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% antibiotics

extract_protocol:
The EV sheet was fabricated from cellulose nanofibers. The EV capture process from moistened organs using the EV sheet consists of the following steps: EV capture by absorption of ascites on organs, EV storage by drying, washing, and EV release. Then, total RNA was extracted using RNA purification kit (Norgen Biotek Corp, Thorold,  Canada). To obtain tissue RNA, tissues were shredded using the gentleMACS Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany) and total RNAs was extracted by using the miRNeasy Plus Mini Kit (QIAGEN, Hilden, Germany).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA). Then, PCR products were separated by electrophoresis (120 V, 60 min), and DNA fragments corresponding to 140–160 bp (the length of small non-coding RNA plus the adaptors) were recovered.

treatment_protocol: Eight-week-old female BALB/cSlc-nu/nu mice were used. ID8-T6 cells were intraperitoneally (IP) or orthotopically (OT) transplanted into the left ovarian bursa.

tag: type

value: EV

value: pelvis

value: intraperitoneal transplantation


title: LN-Positive-8

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LP8


title: RNA_Mutres_1


title: G080 3+8


title: 2-week LNAME/HFD - 2528


title: RNA_WTres_3


title: G078 3+8


title: G078 EV


title: 2-week LNAME/HFD - 2526


title: RNA_KO_2


title: RNA_KO_1


title: LN-Positive-7

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LP7


title: LN-Positive-9

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LP9


title: wingPupal-OsaGFP-deGrad-FAIRE-rep2

city: Chapel Hill

first: Matthew

last: Niederhuber

state: NC

address: 250 Bell Tower Dr.

institute: UNC-Chapel Hill

library_source: genomic

data_processing:
Adapters were trimmed from paired-end reads using Bbmap BBduk (v38.71)
Trimmed reads were aligned to the dm6 reference genome with Bowtie2 (v2.3.4.1) with the settings: "--very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700"
Aligned reads were filtered against the modENCODE dm6 exclusion list and quality filtered (q > 5) with Samtools (v1.9)
Duplicate reads were removed with Picard (v2.2.4)
Coverage files were generated with deepTools (v2.4.1) and normalized to 1x genomic coverage (RPGC)
Peaks were called with MACS2 (v2.1.2) and default settings and a sheared genomic DNA control
Z-normalized coverage files were generated with a custom Rscript from RPGC-normalized files
Assembly: dm6
Supplementary files format and content: MACS2 narrowPeak files from individual replicates
Supplementary files format and content: Z-normalized bigwig files from individual replicates

organism: Drosophila melanogaster

source_name: wing

growth_protocol: Animals were raised at 23C until larval stage. Third larval wandering animals were moved to 29C to induce GFP-deGrad. The following morning prepupae (0-12h APF) were staged at 29C and then dissected 24h later for FAIRE.

extract_protocol:
40 wings from homozygous osaGFP female pupae aged 24-36h APF were dissected per replicate
Libraries were prepared using the Takara ThruPLEX DNA-seq kit with dual-indexes following the manufacturer's instructions.

value: wing

tag: developmental stage

value: 24-36h APF Pupae

tag: Sex

value: female

value: nub-GAL4, UAS-Nslmb-vhhGFP ; osa-GFP


title: LN-Positive-6

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LP6


title: RNA_WT_3

value: WT


title: RNA_KO_3


title: H9_EOS_rep1

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description: PBAT

data_processing:
nf-core/methylseq v1.4 pipeline used to process the data
Bismark genomePrep v0.22.2 used for bisulfite genome preparation
FastQC v0.11.8 used for quality control
TrimGalore v0.6.4 used for trimming low quality bases + adapter sequences
Bismark v0.22.2 with HISAT2 v2.1.0 used for read mapping
Bismark Deduplication v0.22.2 used to remove alignments with identical mapping position
Bismark methXtract v0.22.2 used to generate the cytosine methylation calls
Assembly: hg38
Supplementary files format and content: Bismark CpG coverage report files tab-delimited with 1-based genomic coordinates for every covered cytosine position in the experiment and are in the following format: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count non-methylated>

source_name: H9-EOS (parental line for cR-H9-EOS)

extract_protocol:
Genomic DNA was isolated from the samples using the Beckman Coulter's Agencourt RNAdvance Cell v2 kit following the manufacture’s instructions.
Post-bisulfite adaptor-tagging libraries for whole-genome DNA methylation analysis were prepared from purified genomic DNA as previously described (von Meyenn et al., 2016; Miura et al., 2012; Smallwood et al., 2014). PBAT libraries were prepared by bisulfite converting Proteinase K digested cell lysates using the EZ DNA Methylation-Direct Kit (Zymo). After cleanup, 1st strand synthesis was performed using 6N-forward oligos at 37°C for 90 minutes. Subsequently, samples were treated with Exonuclease I for 1 hour at 37°C, and DNA was purified using AMPure XP beads (Agencourt). Samples were eluted in 2nd strand synthesis mix with 6N-reverse oligos and incubated at 37°C for 90 minutes. DNA was purified and amplified with KAPA HiFi HotStart DNA Polymerase (KAPA Biosystems). All amplified libraries were purified and assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer. Paired-end sequencing was carried out on HiSeq 2500 instruments (Illumina).

value: H9-EOS (parental line for cR-H9-EOS)

value: conventional hPSC

tag: day of_formative_transition

tag: biological replicate

tag: culture condition


title: G080 EV

value: Colon


title: wingPupal-OsaGFP-control-FAIRE-rep2

value: UAS-Nslmb-vhhGFP ; osa-GFP


title: wingPupal-OsaGFP-control-FAIRE-rep1


title: RNA_WT_1


title: H9_EOS_rep3

description: PBAT


title: wingPupal-OsaGFP-deGrad-FAIRE-rep1


title: RNA_Dox_3

value: Dox 500 nM


title: cR_H9_EOS_d20X_rep2

description: PBAT

source_name: chemically reset cR-H9-EOS

value: chemically reset cR-H9-EOS

value: chemically reset hPSC

value: N2B27 + 2uM XAV939 + 3ng/ml Activin A + 10ng/ml FGF2 (XAF)


title: Bulk RNA-seq of sorted CD8 T cells from CSF of  a third person living with FBSS

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

institute: King's College London

description:
X013_FBSS_CD8T
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx

data_processing:
Bulk sequencing reads were pseudo-aligned with kallisto version 0.48.0 to the human genome: Homo Sapiens GCRh38, kallisto index version 10 (Bray et al., 2016).
Differential expression analyses were performed using DESeq2 (Love et al., 2014) or limma (Ritchie et al., 2015) in R.
CITE-sequencing reads were aligned using 10X Genomics CellRanger.
CITE-seq data were further processed using the R package Seurat (Hao et al., 2021).
Other packages we used were: SingleR (Aran et al., 2019) and SingleCellExperiment  (Amezquita et al., 2020).
Assembly: Homo Sapiens GCRh38
Supplementary files format and content: Seurat objects are provided for single cell data. Please see manuscript for detailed descriptions.
Supplementary files format and content: Excel files are provided for bulk sequencing data. Please see manuscript for detailed descriptions.

molecule: polyA RNA

source_name: Cerebrospinal Fluid

extract_protocol:
For bulk sequencing,lysed cells were directly amplified into double stranded cDNA using the SMARTer protocol as described elsewhere (Picelli et al., 2014). All three cell types (CD4+ T cells, CD8+ T cells and monocytes) derived from one individual would be amplified at once. For single cell sequencing, we used a 10X Chromium Platform following manufacturer's protocols.
For bulk sequencing, library preparation from cDNA and sequencing were performed by an external company (Genewiz). For CITE-sequencing, the King's BRC Genomics facility followed the workflow recommended by 10X.

value: Cerebrospinal Fluid


title: Tonsil-Positive-6

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PP6

source_name: Tonsil

value: peritumoral tonsillar tissue


title: RNA_Dox_2


title: RNA_WT_2


title: cR_H9_EOS_d20X_rep3

description: PBAT


title: RNA_Dox_1


title: Bulk RNA-seq of sorted monocytes from CSF of a third person living with FBSS

description:
X013_FBSS_monocytes
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: cR_H9_EOS_d20X_rep1

description: PBAT


title: LN-Positive-2

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LP2

value: lymph node of oropharyngeal cancer


title: Tonsil-Negative-4

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PN4


title: H9_EOS_rep4

description: PBAT


title: RNA_DMSO_3

value: DMSO


title: cR_H9_EOS_d20E_rep3

description: PBAT


title: RNA_WTres_2

value: GAS41-KO (wt rescue)


title: LN-Positive-4

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LP4


title: LN-Positive-3

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LP3


title: Tonsil-Positive-9

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PP9


title: Tonsil-Positive-7

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PP7


title: RNA_DMSO_2


title: Bulk RNA-seq of sorted CD8 T cells from CSF of another person living with FBSS

description:
X07_FBSS_CD8T
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: HNES1_d10_rep4

description: PBAT

source_name: embryo-derived HNES1

value: embryo-derived HNES1

value: embryo-derived naive hPSC

value: N2B27 and 2uM XAV939


title: Bulk RNA-seq of sorted CD4 T cells from CSF of  a third person living with FBSS

description:
X013_FBSS_CD4T
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: RNA_DMSO_1


title: Tonsil-Positive-2

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PP2


title: Tonsil-Positive-8

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PP8


title: LN-Positive-1

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LP1


title: Tonsil-Positive-5

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PP5


title: Bulk RNA-seq of sorted monocytes from CSF of another person living with FBSS

description:
X07_FBSS_monocytes
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: cR_H9_EOS_d20E_rep1

description: PBAT


title: Bulk RNA-seq of sorted CD4 T cells from CSF of another person living with FBSS

description:
X07_FBSS_CD4T
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: HNES1_d10_rep1

description: PBAT


title: Mouse HFpEF Lung

first: Vineet

last: Agrawal

address: 1310 24th Ave South

institute: Veterans Affairs Hospital in Nashville, TN

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Alignment and demultiplexing were performed using CellRanger v7.0.1. Ambient RNA filtering was performed using CellBender v0.2.2.7 ScRNA-seq analysis was performed using Seurat8 v5 adapted from our previous work9-11 with additional data visualization using scCustomize (https://doi.org/10.5281/zenodo.7534950). Demultiplexing was performed using the HTOdemux function, and singlet cells were carried forward for downstream analysis. Following quality-control filtering (excluding cells with <500 or >5000 genes, and cells with >10% mitochondrial reads), data were normalized and scaled using the SCTransform function, including mitochondrial and ribosomal percentages as regression variables, followed by principal components analysis, neighborhood graph calculation and UMAP embedding using 45 dimensions, and recursive louvain-clustering/subclustering. Heterotypic doublet clusters were identified by coexpression of lineage-specific marker genes, and cell annotation was performed manually, informed by published reference datasets.12,13 Cell-type specific differential expression was performed on SCT-transformed counts using wilcoxon test. Gene ontology enrichment analysis was performed using PANTHER.
Supplementary files format and content: Processed and filtered h5 files

extract_protocol:
Mouse lungs were cleared of red-blood cells by cardiac perfusion with 3mL of sterile saline, then were excised and placed in a C-Tube (Miltenyi) (one C-tube/mouse) containing 5mL lung digest solution (5mL phenol free DMEM (Gibco), Dispase (Roche 04942078001), collagenase (Sigma-Aldrich C0130-1G), and 5uL DNAse (10,000iU). Lungs were dissociated using a gentleMacs dissociator for 17 minutes at 37 degrees Celsius. Cell suspensions were passed through 100mm then 70mm cell strainers and washed 3-times in 5mL cell buffer (phenol free DMEM, 0.2mM EDTA, and 0.5% FBS). Cells were centrifuged at 500g for 10 minutes. Red blood cells were removed by lysing with 2mL ACK buffer (KD Medical RGC-3015) for 5 minutes. Cells were then washed, centrifuged, passed through a 40mm cell strainer and resuspended for counting.Cell-hashing was performed by incubating 1X106 cells with Total-SeqB (B0301-B0304) cell-hashing antibodies (Biolegend) for 30 minutes. Cells were then washed x3 times in cell buffer, and equal numbers of cells from each of the 4 mice per condition were pooled into a single reaction for scRNA-seq library generation using the 10X Genomics Chromium 3’v3 kit.
Library sequencing was performed on an Illumina Novaseq6000 targeting 50,000 reads per cell and following manufacturer's recommendations for 10X Genomics Chromium 3'v3 kit

value: Whole Lung

tag: strain

value: L-NAME in water and high fat diet


title: HNES1_d10_rep2

description: PBAT


title: Brown adipose tissue KO

city: ALBUQUERQUE

first: Xing

last: Zhang

state: NEW MEXICO

address: 915 Camino de Salud NE

institute: University of New Mexico

description: 10x Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger Pipeline (version 2.0) to generate FASTQ files and aligned to mm10 genome sequence file in gene expression count.
Assembly: mm10
Supplementary files format and content: Filtered feature matrix files

molecule: nuclear RNA

source_name: Brown adipose tissue

extract_protocol:
Fresh Brown fat depots nuclei were collected from 10-week-old JunB FKO and control mice. Tissue samples were minced into 1 mm3, homogenized in Nuclei EZ Lysis Buffer (NUC101, Sigma-Aldrich) with pre-chilled Dounce homogenizer. The homogenate was filtered using a 40-μm cell strainer (VWR#76327-098). After centrifugation, the pellet was washed, re-suspended, and stained with DAPI, the single and health nuclei were isolated using sorting. Reconstitute nuclei with concentration of 700-1,200 nuclei/μl was used for the sequencing.
Single-nuclei RNA libraries were prepared according to the Chromium™ Single Cell 3' Reagent Kits v2 User Guide (10x Genomics). Approximately 10,000 cells were loaded on a Chromium single Cell Controller Instrument (10x Genomics) to generate single cell gel beads in emulsion (GEMs). The barcoded sequencing libraries were constructed using the Chromium Single-Cell 3’Library Kit (10x Genomics) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup. Libraries were sequenced with NovaSeq System with a depth of 50,000to 100,000 reads per targeted cell.

value: Brown adipose tissue

value: Primary brown adipocytes

value: Adipocyte

value: JunB KO

value: Normal chow


title: Mouse Control Lung

description: 10X Genomics

value: Low fat diet and regular water


title: LN-Negative-1

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LN1


title: Bulk RNA-seq of sorted monocytes from CSF of someone living with FBSS

description:
X04_FBSS_monocytes
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: Bulk RNA-seq of sorted CD8 T cells from CSF of someone living with FBSS

description:
X04_FBSS_CD8T
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: LN-Positive-5

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LP5


title: Brown adipose tissue Control

description: 10x Genomics

value: Control


title: Bulk RNA-seq of sorted CD4 T cells from CSF of someone living with FBSS

description:
X04_FBSS_CD4T
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx

value: Cerebrospinal Fluid


title: cR_H9_EOS_d10_rep1

description: PBAT

value: chemically reset cR-H9-EOS

value: chemically reset hPSC


title: Bulk RNA-seq of sorted CD8 T cells from CSF of another person living with CRPS

description:
X08_CRPS_CD8T
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: cR_H9_EOS_d10_rep4

description: PBAT


title: Bulk RNA-seq of sorted CD4 T cells from CSF of another person living with CRPS

description:
X08_CRPS_CD4T
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: Y20

city: Baltimore

first: ATSUSHI

last: KAMIYA

state: MD

address: 600 North Wolfe St, Meyer 3-162A

department: Psychiatry

institute: Johns Hopkins University

description: TableCPM

data_processing:
The software package “rsem-1.3.0” was used for running the alignments as well as generating gene and isoform expression levels.
The ‘rsem-calculate-expression’ module was used with the following options:--star, --calc-ci, --star-output-genome-bam, --forward-prob 0.5. The data were then aligned to GRCm38/mm10 mouse reference genome.
The outputs of this pipeline include count data and TPM and FPFM data, in addition to BAM formatted files of read alignments in genomic and transcript coordinates.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes sample information and CPM value for each sample

extract_protocol:
Total RNA was isolated from cells using the Qiagen Allprep DNA/RNA kit (Cat. No./ID: 80284) according to the manufacturer's specifications.
RNA libraries construction was completed with the low input Nugen ovation RNA-seq V2 according to the manufacture's specifications.

treatment_protocol: The mice were treated daily with a single subcutaneous injection (s.c.) of THC (8mg/kg) or vehicle during adolescence (Postnatal day 30 [P30]-P51)

tag: strain background

value: 16p11.2 duplication

value: THC

tag: brain region

value: mPFC

value: microglia (CD45/CD11b/P2ry12)


title: Y21

description: TableCPM


title: Y18

description: TableCPM


title: Bulk RNA-seq of sorted monocytes from CSF of another person living with CRPS

description:
X08_CRPS_monocytes
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: cR_H9_EOS_d10_rep2

description: PBAT

tag: cell line

value: N2B27 and 2uM XAV939


title: cR_H9_EOS_d10_rep3

description: PBAT


title: Tonsil-Positive-4

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PP4

value: peritumoral tonsillar tissue


title: HNES1_d10_rep3

description: PBAT

value: embryo-derived HNES1

value: embryo-derived naive hPSC


title: Tonsil-Negative-2

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PN2


title: Y17

description: TableCPM

tag: treatment


title: HNES1_d0_rep4

description: PBAT


title: Tonsil-Negative-1

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PN1


title: Tonsil-Positive-3

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PP3


title: Bulk RNA-seq of sorted CD4 T cells from CSF of someone living with CRPS

description:
X06_CRPS_CD4T
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: HNES1_d0_rep2

description: PBAT


title: Tonsillitis-4

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
C4

value: chronic tonsillitis


title: Y16

description: TableCPM

value: Vehicle


title: Bulk RNA-seq of sorted monocytes from CSF of someone living with CRPS

description:
X06_CRPS_monocytes
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: Tonsil-Negative-3

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PN3


title: Y14

description: TableCPM


title: Tonsil-Positive-1

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
PP1


title: Y13

description: TableCPM


title: Y12

description: TableCPM


title: cR_H9_EOS_d0_rep2

description: PBAT


title: Pt6_ascites3

description:
ICA001-07329A-001-E24-C01-NGS001_S24_L001_R1_001
Pt6_data file(RPM).xlsx

value: EV

value: pre-operation


title: Bulk RNA-seq of sorted CD8 T cells from CSF of someone living with CRPS

description:
X06_CRPS_CD8T
Data_File_1.xlsx
Data_File_2.xlsx
Data_File_3.xlsx


title: Wildtype Control 2

city: Pittsburgh

first: Corrine

last: Kliment

state: PA

address: 200 Lothrop street

institute: University of Pittsburgh

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 andreads were aligned to the reference genome using Hisat2 v2.0.5.  paired-end clean
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.

growth_protocol: CRISPR knockout (KO) clones were generated for SLC25A4 (ANT1). To induce senescence, Beas2b cells were treated with 10 mg/ml bleomycin over 2 days.

extract_protocol:
Trizol
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: Bronchial epithelial cell

value: Wildtype


title: cR_H9_EOS_d0_rep4

description: PBAT


title: Wildtype Control 1

value: Control


title: Y9

description: TableCPM

source_name: WT-THC

value: WT


title: Tonsillitis-2

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
C2


title: Y11

description: TableCPM


title: HNES1_d0_rep3

description: PBAT


title: Tonsillitis-1

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
C1


title: Wildtype Bleomycin 3

value: Bleomycin


title: Pt6_ascites1

description:
ICA001-07329A-001-E22-C01-NGS001_S22_L001_R1_001
Pt6_data file(RPM).xlsx


title: Tonsillitis-3

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
C3


title: Pt6_liver-surface3

description:
ICA001-07329A-001-E18-C01-NGS001_S18_L001_R1_001
Pt6_data file(RPM).xlsx

source_name: liver

tag: location

value: surface


title: Y8

description: TableCPM

value: THC


title: HNES1_d0_rep1

description: PBAT


title: Y7

description: TableCPM

value: mPFC


title: HNES1_d10_rep1, H3K27me3

description:
HNES1_d10_R1.mLb.clN_H3K27me3.bigWig
HNES1_d10_R2.mLb.clN_H3K27me3.bigWig
HNES1_d10_R1_peaks_H3K27me3.xls
HNES1_d10_R2_peaks_H3K27me3.xls

data_processing:
nf-core/chipseq v1.1.0 pipeline used to process the data
FastQC v0.11.8 used for quality control
TrimGalore v0.5.0 used for trimming low quality bases + adapter sequences
BWA  BWA v0.7.17-r1188 used for read mapping
Samtools v1.9 used for sorting bam files
BEDTools v2.27.1 used for converting sorted bam files into bedgraph files
MACS2 v2.1.2 used for calling peaks
Assembly: hg38
Supplementary files format and content: bigWig, txt files with MACS2 peaks, included in tar archives on the series record

extract_protocol:
500.000 to 1.000.000 cells were used for ChIP per sample. Cross-linking was done with 1% formaldehyde in DMEM added directly to cells in culture dishes for 8 min at room temperature. Quenching was performed using 0.1M glycine (final concentration). The cells were washed with ice-cold PBS and scrapped with PBS with protease inhibitor cocktail (Cat. 11697498001, Roche). Lysis was performed in LB1 buffer (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% Igepal CA-630, 0.25% Triton X100, protease inhibitors) by rotating for 10 min at +4C, followed by centrifugation at 2000g for 5 min. The pellet was incubated in LB2 buffer (10mM Tris-HCl pH8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, protease inhibitors) by rotating for 5 min at +4C, followed by centrifugation at 2000g for 5 min. The pellet was resuspended in a buffer containing 50mM Tris-HCl pH8.0, 10mM EDTA, 1% SDS, the sonication was performed for 45 cycles, 30-sec intervals on/off. Debris was removed by centrifugation, and 10% from the sonicated material was saved as input. Prior to immunoprecipitation, 5ug antibody and 100ul Protein A beads were pre-incubated overnight at +4C in a total volume of 250ul, adjusted with PBS with 5mg/ml BSA, followed by three washes using the same solution. Immunoprecipitation was done by combining the sonicated material with the bead-antibody complexes, in a total volume of 400ul adjusted with ChIP dilution buffer (10mM Tris-HCl pH8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X100, protease inhibitors), by rotating overnight at +4C. After the incubation, the beads were washed 6 times with RIPA buffer (50mM HEPES-KOH pH7.5, 500mM LiCl, 1mM EDTA, 1% Igepal CA-630, 0.7% sodium deoxycholate) followed by one wash in TE (10mM Tris-HCl pH8.0, 1mM EDTA). Reverse-crosslinking was done in elution buffer containing 1% SDS, 100mM sodium bicarbonate, and 200mM NaCl at 65C for 9-15 hours. The input sample was also reverse-crosslinked. After this step, the beads were removed from the mixture, and the remaining DNA in the solution was treated with 8 ug RNAse A for 1h at 37C, followed by 80ug proteinase K for 2 hours at 55C.
DNA was purified using MinElute columns and then used for ChIP-Seq library preparation using the NEXTflex Rapid DNA-Seq Kit (NOVA-5144-02) according to the manufacturer's protocol with some minor modifications. Briefly, we amplified the final libraries with 4 cycles of PCR, then performed an AMPure XP-based size selection (0.5x to eliminate larger fragments followed by 1.8x to extract the smaller fragments), and then continued with 8 more PCR cycles on the size selected material.  The final libraries were then cleaned up with 0.8x vol AMPure XP beads.

tag: histone modification


title: H9_EOS_rep2

description: PBAT

value: H9-EOS (parental line for cR-H9-EOS)

value: conventional hPSC


title: Wildtype Bleomycin 1


title: Pt6_liver-surface2

description:
ICA001-07329A-001-E17-C01-NGS001_S17_L001_R1_001
Pt6_data file(RPM).xlsx


title: cR_H9_EOS_d0_rep3

description: PBAT

value: chemically reset cR-H9-EOS

value: chemically reset hPSC

value: N2B27 and 2uM XAV939


title: Pt6_ascites2

description:
ICA001-07329A-001-E23-C01-NGS001_S23_L001_R1_001
Pt6_data file(RPM).xlsx


title: Y6

description: TableCPM

source_name: WT-Veh

value: microglia (CD45/CD11b/P2ry12)


title: Pt6_liver-surface1

description:
ICA001-07329A-001-E16-C01-NGS001_S16_L001_R1_001
Pt6_data file(RPM).xlsx


title: HNES1_d0_rep2, H3K27me3

description:
HNES1_d0_R1.mLb.clN_H3K27me3.bigWig
HNES1_d0_R2.mLb.clN_H3K27me3.bigWig
HNES1_d0_R1_peaks_H3K27me3.xls
HNES1_d0_R2_peaks_H3K27me3.xls

value: embryo-derived HNES1

value: embryo-derived naive hPSC


title: ANT1 KO Control 3

value: ANT1 knockout (KO)


title: Y5

description: TableCPM

value: Vehicle


title: HNES1_d10_rep2, H3K27me3


title: HNES1_d0_rep1, H3K27me3


title: Pt6_omentum3

description:
ICA001-07329A-001-E15-C01-NGS001_S15_L001_R1_001
Pt6_data file(RPM).xlsx

source_name: omentum

value: EV


title: H9_EOS_rep2, H3K27me3

description:
H9_EOS_R1.mLb.clN_H3K27me3.bigWig
H9_EOS_R2.mLb.clN_H3K27me3.bigWig
H9_EOS_R1_peaks_H3K27me3.xls
H9_EOS_R2_peaks_H3K27me3.xls


title: Y3

description: TableCPM


title: Pt6_omentum2

description:
ICA001-07329A-001-E14-C01-NGS001_S14_L001_R1_001
Pt6_data file(RPM).xlsx


title: Y4

description: TableCPM


title: ANT1 KO Control 2

value: Bronchial epithelial cell

value: Control


title: Wildtype Control 3

value: Wildtype


title: H9_EOS_rep1, H3K27me3


title: ANT1 KO Bleomycin 3

value: Bleomycin


title: ANT1 KO Control 1


title: Pt6_omentum1

description:
ICA001-07329A-001-E13-C01-NGS001_S13_L001_R1_001
Pt6_data file(RPM).xlsx

value: surface


title: LN-Negative-2

description:
Gene-expression data from peri-tumoral tonsillar tissue not including tumor tissue
LN2

tag: disease state

value: lymph node of oropharyngeal cancer


title: Y2

description: TableCPM

value: WT

value: mPFC

tag: cell type


title: ANT1 KO Bleomycin 2


title: Pt6_pelvis3

description:
ICA001-07329A-001-E21-C01-NGS001_S21_L001_R1_001
Pt6_data file(RPM).xlsx

source_name: pelvis


title: cR_H9_EOS_d20X_rep2, H3K27me3

description:
cR_H9_EOS_d20X_R1.mLb.clN_H3K27me3.bigWig
cR_H9_EOS_d20X_R2.mLb.clN_H3K27me3.bigWig
cR_H9_EOS_d20X_R1_peaks_H3K27me3.xls
cR_H9_EOS_d20X_R2_peaks_H3K27me3.xls

value: chemically reset cR-H9-EOS

value: N2B27 + 2uM XAV939 + 3ng/ml Activin A + 10ng/ml FGF2 (XAF)


title: cR_H9_EOS_d20X_rep1, H3K27me3

value: chemically reset hPSC


title: ANT1 KO Bleomycin 1


title: Y1

description: TableCPM

value: microglia (CD45/CD11b/P2ry12)


title: Pt6_pelvis2

description:
ICA001-07329A-001-E20-C01-NGS001_S20_L001_R1_001
Pt6_data file(RPM).xlsx


title: Arsenic_multi-omic (ATAC)

city: Jinan

first: Yang

last: Xiuhui

state: Shandong

address: NO.1500,ShunHua Road

department: School of Software

country: China

institute: Shandong University

description:
Single Cell Multiome (ATAC)
10x Genomics
dmerged.h5ad

library_source: genomic single cell

data_processing:
The single-cell RNA-seq data was preprocessed with the Cellranger toolset. Cell Ranger (v6.1.2) module ‘mkfastq’ with default parameters was used to demultiplex raw base call (BCL) files generated by Illumina sequencers into FASTQ files. Multiple FASTQ files from the same library and strand were concatenated into a single file. Cell Ranger (v6.1.2) module ‘count’ with default parameters was employed for the subsequent read processing. The Cellranger toolset performed a series of operations to quantify the raw gene expression, which includes reads alignment, read, reads filtering, barcode and UMI counting. Specifically, reads were first aligned to the mouse reference genome mm10. Control and Arsenic libraries were integrated using the 10x genomics ‘aggr’ function with default parameters. Integrated chromium cellular barcodes were used to generate a combined raw cell-by-gene expression matrix required for subsequent analyses.
A python library Scanpy (v1.8.2) was utilized for quality control of the single-cell data. Cells expressing less than 200 or more than 2500 genes, as well as those with more than 10% mitochondrial reads, were considered lousy and thus removed from the downstream analyses. The remaining cell-by-gene expression matrix was composed of 2605 cells for RNAseq only data (1392 cells from the Arsenic library and 1211 cells from the control library, respectively) and 16636 genes. As for RNAseq in sc-multiomics data, the remaining cell-by-gene expression matrix was composed of 5284 cells (2192 cells from the Arsenic library and 3092 cells from the control library, respectively) and 18050 genes.
The filtered Cell-by-gene expression matrix was normalized to account for the difference in library size, which was further log-transformed using the Scanpy (v1.8.2) python library with default parameters. The normalized expression matrix was then subject to principal components analysis (PCA) for linear dimension reduction. The top principal components were subject to exploratory analysis to identify contributions to variance at the level of cell type. Feature selection of principal components was conducted, and a shared nearest neighbor network of cells was then constructed based on Euclidean distances between cells in multidimensional PC space, opting for 15 neighbors per cell, which was further reduced with the UMAP method of Scanpy (v1.8.2) to generate a two-dimensional (2D) embeddings for cell visualizations with default parameters.
The cell-by-gene expression matrix was clustered (by cells) to obtain the cell clusters (cell populations) using the Leiden method implemented in Scanpy (v1.8.2) with default parameters. For each obtained cell cluster, we identified the top expressed genes (potential signature genes) associated with the cluster and annotate the cell type information using the Cellar tool (v1.12) that previously developed with default parameters, which compared the signature genes associated with each cluster with known cell type markers curated in public databases such as CellMarker, PanglaoDB, and GSEA to infer the cell identities. The enriched GO terms and pathways associated with the signature genes of each cell cluster were also employed as additional evidence for confident cell type annotation.
SDREM (v1.2.0) was used to generate the receptor-TF signaling network. Signaling and Dynamic Regulatory Events Miner (SDREM) is a powerful computational approach for identifying which signaling pathways and transcription factors control the temporal cellular response to a stimulus. The input file contains receptors that were generated earlier (see cell-cell interaction section in Methods), transcription factors (TFs) from scRNAseq were generated with scdiff (v2) and that from sc-ATACseq in the multiomics data were generated with cisTopic (v2.1.0) R (4.1.2) packages. After two steps of path-generation and SDREM training, a regulatory network between receptors, internal genes, and TFs was generated and saved. The software Cytoscape (v3.9.1) was used to generate the organic plot with the output sif files.
Assembly: mm10
Supplementary files format and content: The h5ad file provides an extensible way to record data and its annotations. The h5ad of single-cell sequencing is divided into multiple parts such as X, obs, var, uns, etc., each storing different information. Where X is the expression matrix; obs contains cell metadata, which describes the results of cells from different directions, such as the cell type to which they belong; var contains gene metadata, which describes the results of genes from different directions. X, obs, and var are all stored in dataframe format; uns is an unstructured annotation with can store other unstructured information.

source_name: aorta and aortic sinus plaque

extract_protocol:
After 13 weeks of exposure, mice were injected with a BB515-conjugated anti-CD45 antibody via tail vein to stain circulating leukocytes and euthanized within the following 10 minutes. Aorta were perfused (intracardiac) with ice-cold PBS. The aortic arch was carefully separated from the perivascular adipose tissue along with the brachiocephalic artery and the carotids, opened and plaque was isolated. Next, the heart was dissected to isolate the plaque from the root of aortic sinus. Both control and treated samples were obtained by pooling the plaques from four mice each for scRNA sequencing. The isolated plaques were digested using a cocktail of enzymes (450U/ml liberase, 125U/ml collagenase and 60U/ml hyaluronidase) at 37˚C for an hour, then passed through a 70 μm cell strainer to obtain single cell suspensions. The cells were then blocked for 30 minutes at 4°C with anti-mouse CD16/CD32 to block non-specific binding of antibodies to Fc Receptors, then stained for CD45+ cells, but with an antibody conjugated with BV785 to distinguish plaque-resident leukocytes from those found in the blood. Lastly, 4′,6-diamidino-2-phenylindole (DAPI) was added to exclude dead cells. These plaque resident CD45+ live cells were sorted on a FACS sorter using a 100um nozzle and sent to the Genome Quebec- Centre for single-cell RNA sequencing.
Cells were manually counted, and viability was assessed using Trypan Blue on a hemocytometer. Libraries were generated using the Chromium Next GEM Single Cell 3 Kit v3.1 kit (10X Genomics) as per the manufacturer’s recommendations. The targeted cell recovery was aimed at 2000 cells. Adapters and PCR primers were purchased from 10X Genomics and libraries were quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems). The average size fragment was determined using a LabChip GXII (PerkinElmer) instrument. Next, the libraries were normalized, pooled, denatured in 0.05N NaOH and neutralized using HT1 buffer. The pool was loaded at 225pM on an Illumina NovaSeq SP Lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 2x100 cycles (paired-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed with RTA v3.4.4. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate FASTQ reads.

tag: tissue

value: aorta and aortic sinus plaque

value: CD45+ immune cells

value: apoE-/-

value: male

tag: age

value: 18 weeks

value: 200 ppb arsenic for 13 weeks


title: Control_multi-omic (ATAC)

tag: genotype


title: cR_H9_EOS_d20E_rep2, H3K27me3

description:
cR_H9_EOS_d20E_R1.mLb.clN_H3K27me3.bigWig
cR_H9_EOS_d20E_R2.mLb.clN_H3K27me3.bigWig
cR_H9_EOS_d20E_R1_peaks_H3K27me3.xls
cR_H9_EOS_d20E_R2_peaks_H3K27me3.xls


title: SV Rep 2

city: Chicago

first: Donald

last: Vander Griend

state: IL

address: 909 S. Wolcott Ave, COMRB Room 5051

department: Pathology

institute: The University of Illinois at Chicago

description: cell barcodes end in -8

data_processing:
Fastq.gz files were generated and demultiplexed with CellRanger 5.0.0
A custom reference index was made using Gencode’s GRCh38 genome and v35 gene models (equivalent to Ensembl release 101) using 10X Genomics’ Cell Ranger software v 5.0.0 and reads aligned to the index and cell called using the standard cellranger count pipeline. Next cellranger aggr was used with --normalize=none to aggregate all samples together
Assembly: Gencode GRCh38 primary assembly, v35 primary gene annotation
Supplementary files format and content: barcodes.tsv.gz - gzipped tab-separated list of cell barcodes
Supplementary files format and content: features.tsv.gz - gzipped tab-separated list of gene symbols and ENSEMBL IDs
Supplementary files format and content: matrix.mtx.gz - gzipped sparce matrix format of UMI counts per feature & cell barcode
Supplementary files format and content: aggregation.csv - comma-separated file of sample aggregation order

source_name: Seminal Vesicle

extract_protocol:
Fresh biopsy tissues were minced into 1-2mm pieces, digested overnight in collagenase solution, and further dissociated using 0.25% trypsin. After dissociation to single cells, cells were cultured in epithelial selection media (KSFM) until they reached 70-80% confluency (4-8 days).). Cells from each biopsy were passaged one time for expansion before freezing. Prior to the scRNA-seq experiment, the PrECs were thawed, passaged, and maintained in KSFM for 3-4 days until they reached 70% confluency.
Cell partitioning, library preparation, and sequencing was performed in a single batch using the 10X Genomics platform. 10X gem generation and barcoding was performed according to the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D for a targeted cell recovery of 5000 cells per sample (4 groups with two replicates each for 8 samples total). Post GEM-RT cleanup was performed on all samples according to the 10X protocol, followed by cDNA amplification (12 cycles), and quantification using Agilent TapeStation. 3’ gene expression dual index library construction was performed using dual index plate TT set A, according to the 10X protocol.

value: Seminal Vesicle

value: Basal epithelial

tag: prostate zone


title: SV Rep 1

description: cell barcodes end in -7


title: Pt6_pelvis1

description:
ICA001-07329A-001-E19-C01-NGS001_S19_L001_R1_001
Pt6_data file(RPM).xlsx

tag: type

value: EV


title: cR_H9_EOS_d20E_rep1, H3K27me3

tag: day of_formative_transition


title: cR_H9_EOS_d10_rep2, H3K27me3

description:
cR_H9_EOS_d10_R1.mLb.clN_H3K27me3.bigWig
cR_H9_EOS_d10_R2.mLb.clN_H3K27me3.bigWig
cR_H9_EOS_d10_R1_peaks_H3K27me3.xls
cR_H9_EOS_d10_R2_peaks_H3K27me3.xls

tag: biological replicate

value: N2B27 and 2uM XAV939


title: SV18359-0738

status: Public on Oct 09 2023

city: Boston

first: Joanne

last: Sordillo

state: MA

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

institute: Mass General Brigham

data_processing:
The ExceRpt pipeline was used for quality control (QC) of the RNA-seq data
miRNAs with less than five mapped reads in at least 50% of subjects were removed prior to analysis
subjects with less than 100k mapped reads were dropped.
Assembly: hg38, miRBase v22
Supplementary files format and content: tab-delimited text file with raw counts of miRNA x Sample.

source_name: serum

extract_protocol:
Total RNA was isolated from archival serum samples using the miRNeasy kit (Qiagen, Germantown, MD) according to the manufacturer's instructions
small RNA-seq libraries were prepared by using the Norgen Biotek Small RNA Library Prep Kit (Norgen Biotek, Therold, Canada), and sequenced on the Illumina NextSeq 500 platform.
NextSeq 500/550 High Output Kit v2 (51 Cycles using a 75-Cylce Kit)

value: serum

tag: batch

tag: Sex

value: F

tag: pctpred fev1_pre_bd

tag: inhaled steroids

tag: bdrbase


title: TZ Rep 2

description: cell barcodes end in -6

source_name: Prostate

value: Prostate

value: Transition


title: Pt5_ascites3

description:
ICA001-07329A-001-E12-C01-NGS001_S12_L001_R1_001
Pt5_data file(RPM).xlsx

source_name: ascites

tag: treatment

value: pre-operation


title: Pt5_ascites2

description:
ICA001-07329A-001-E11-C01-NGS001_S11_L001_R1_001
Pt5_data file(RPM).xlsx


title: Arsenic_RNA-only

description:
Gene Expression
10x Genomics
dmerged_RNA.h5ad


title: Control_multi-omic (GEX)

description:
Single Cell Multiome (GEX)
10x Genomics
dmerged.h5ad


title: Arsenic_multi-omic (GEX)


title: cR_H9_EOS_d10_rep1, H3K27me3

tag: cell line

value: chemically reset cR-H9-EOS

value: chemically reset hPSC

tag: culture condition


title: cR_H9_EOS_d0_rep2, H3K27me3

description:
cR_H9_EOS_d0_R1.mLb.clN_H3K27me3.bigWig
cR_H9_EOS_d0_R2.mLb.clN_H3K27me3.bigWig
cR_H9_EOS_d0_R1_peaks_H3K27me3.xls
cR_H9_EOS_d0_R2_peaks_H3K27me3.xls

tag: histone modification


title: TZ Rep 1

description: cell barcodes end in -5

tag: cell type


title: PZ Rep 2

description: cell barcodes end in -4

tag: tissue

value: Peripheral


title: Pt5_liver-surface3

description:
ICA001-07329A-001-E09-C01-NGS001_S9_L001_R1_001
Pt5_data file(RPM).xlsx

tag: location

value: surface


title: Pt5_ascites1

description:
ICA001-07329A-001-E10-C01-NGS001_S10_L001_R1_001
Pt5_data file(RPM).xlsx


title: Control_RNA-only

value: aorta and aortic sinus plaque

value: CD45+ immune cells

tag: genotype

value: apoE-/-

tag: age


title: Pt5_liver-surface2

description:
ICA001-07329A-001-E08-C01-NGS001_S8_L001_R1_001
Pt5_data file(RPM).xlsx

tag: type


title: PZ Rep 1

description: cell barcodes end in -3

tag: prostate zone


title: CZ Rep 2

description: cell barcodes end in -2

value: Central


title: Pt5_liver-surface1

description:
ICA001-07329A-001-E07-C01-NGS001_S7_L001_R1_001
Pt5_data file(RPM).xlsx


title: HNES1_d10_rep2, H3K27ac

description:
HNES1_d10_R1.mLb.clN_H3K27ac.bigWig
HNES1_d10_R2.mLb.clN_H3K27ac.bigWig
HNES1_d10_R1_peaks_H3K27ac.xls
HNES1_d10_R2_peaks_H3K27ac.xls

value: embryo-derived HNES1

value: embryo-derived naive hPSC

tag: biological replicate

tag: day of_formative_transition


title: HNES1_d10_rep1, H3K27ac


title: Pt5_omentum3

description:
ICA001-07329A-001-E06-C01-NGS001_S6_L001_R1_001
Pt5_data file(RPM).xlsx

value: EV


title: CZ Rep 1

description: cell barcodes end in -1

value: Basal epithelial


title: Pt5_omentum2

description:
ICA001-07329A-001-E05-C01-NGS001_S5_L001_R1_001
Pt5_data file(RPM).xlsx


title: DetB_4

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
Rna-seq reads were aligned with STAR-aligner using the genome build Ensembl Mus musculus GRCm38.p5
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: Ensembl Mus musculus GRCm38.p5
Supplementary files format and content: tab-delimited .txt files include 2 columns: ensemble feature identifier and count number.

source_name: Skin

extract_protocol:
Mouse skin sections were collected and stored in RNAlater (Agilent). Skin sections were transferred into the appropriate amount of Qiazol lysis buffer (Qiagen), homogenized using gentleMACS Dissociator (Miltenyi Biotec) and gentleMACS M tubes (Miltenyi Biotec), The total RNA was isolated using the RNeasy Plus Universal Minikit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

tag: strain

value: 8-12 weeks old

value: Detergent B


title: DetB_5


title: Pt5_pelvis3

description:
ICA001-07329A-001-E03-C01-NGS001_S3_L001_R1_001
Pt5_data file(RPM).xlsx


title: Pt5_pelvis2

description:
ICA001-07329A-001-E02-C01-NGS001_S2_L001_R1_001
Pt5_data file(RPM).xlsx


title: DetB_3


title: H9_EOS_rep2, H3K27ac

description:
H9_EOS_R1.mLb.clN_H3K27ac.bigWig
H9_EOS_R2.mLb.clN_H3K27ac.bigWig
H9_EOS_R1_peaks_H3K27ac.xls
H9_EOS_R2_peaks_H3K27ac.xls

source_name: H9-EOS (parental line for cR-H9-EOS)

value: H9-EOS (parental line for cR-H9-EOS)

value: conventional hPSC


title: Pt5_omentum1

description:
ICA001-07329A-001-E04-C01-NGS001_S4_L001_R1_001
Pt5_data file(RPM).xlsx


title: H9_EOS_rep1, H3K27ac


title: DetA_6

value: Detergent A


title: HNES1_d0_rep1, H3K27ac

description:
HNES1_d0_R1.mLb.clN_H3K27ac.bigWig
HNES1_d0_R2.mLb.clN_H3K27ac.bigWig
HNES1_d0_R1_peaks_H3K27ac.xls
HNES1_d0_R2_peaks_H3K27ac.xls

value: N2B27 and 2uM XAV939


title: cR_H9_EOS_d0_rep1, H3K27me3

source_name: chemically reset cR-H9-EOS

value: chemically reset cR-H9-EOS

value: chemically reset hPSC


title: cR_H9_EOS_d20X_rep2, H3K27ac

description:
cR_H9_EOS_d20X_R1.mLb.clN_H3K27ac.bigWig
cR_H9_EOS_d20X_R2.mLb.clN_H3K27ac.bigWig
cR_H9_EOS_d20X_R1_peaks_H3K27ac.xls
cR_H9_EOS_d20X_R2_peaks_H3K27ac.xls

value: N2B27 + 2uM XAV939 + 3ng/ml Activin A + 10ng/ml FGF2 (XAF)


title: Pt5_pelvis1

description:
ICA001-07329A-001-E01-C01-NGS001_S1_L001_R1_001
Pt5_data file(RPM).xlsx

value: surface


title: DetA_5


title: DetB_6


title: Pt4_ascites3

description:
ICA001-07328A-001-E24-C01-NGS001_S24_L001_R1_001
Pt4_data file(RPM).xlsx

value: pre-operation


title: Pt4_ascites2

description:
ICA001-07328A-001-E23-C01-NGS001_S23_L001_R1_001
Pt4_data file(RPM).xlsx


title: DetA_4


title: cR_H9_EOS_d20E_rep1, H3K27ac

description:
cR_H9_EOS_d20E_R1.mLb.clN_H3K27ac.bigWig
cR_H9_EOS_d20E_R2.mLb.clN_H3K27ac.bigWig
cR_H9_EOS_d20E_R1_peaks_H3K27ac.xls
cR_H9_EOS_d20E_R2_peaks_H3K27ac.xls


title: HNES1_d0_rep2, H3K27ac


title: DetB_2


title: DetA_2


title: cR_H9_EOS_d10_rep2, H3K27ac

description:
cR_H9_EOS_d10_R1.mLb.clN_H3K27ac.bigWig
cR_H9_EOS_d10_R2.mLb.clN_H3K27ac.bigWig
cR_H9_EOS_d10_R1_peaks_H3K27ac.xls
cR_H9_EOS_d10_R2_peaks_H3K27ac.xls


title: Pt4_liver-surface3

description:
ICA001-07328A-001-E21-C01-NGS001_S21_L001_R1_001
Pt4_data file(RPM).xlsx


title: Pt4_ascites1

description:
ICA001-07328A-001-E22-C01-NGS001_S22_L001_R1_001
Pt4_data file(RPM).xlsx


title: cR_H9_EOS_d20X_rep1, H3K27ac


title: DetA_1


title: cR_H9_EOS_d10_rep1, H3K27ac


title: Pt4_liver-surface2

description:
ICA001-07328A-001-E20-C01-NGS001_S20_L001_R1_001
Pt4_data file(RPM).xlsx


title: Pt4_omentum3

description:
ICA001-07328A-001-E18-C01-NGS001_S18_L001_R1_001
Pt4_data file(RPM).xlsx


title: Pt4_liver-surface1

description:
ICA001-07328A-001-E19-C01-NGS001_S19_L001_R1_001
Pt4_data file(RPM).xlsx


title: CTRL_6

value: PBS


title: HNES1_d10_rep2, H3K9me3

description:
HNES1_d10_R1.mLb.clN_H3K9me3.bigWig
HNES1_d10_R2.mLb.clN_H3K9me3.bigWig
HNES1_d10_R1_peaks_H3K9me3.xls
HNES1_d10_R2_peaks_H3K9me3.xls

value: embryo-derived HNES1


title: Pt4_omentum2

description:
ICA001-07328A-001-E17-C01-NGS001_S17_L001_R1_001
Pt4_data file(RPM).xlsx


title: cR_H9_EOS_d0_rep2, H3K27ac

description:
cR_H9_EOS_d0_R1.mLb.clN_H3K27ac.bigWig
cR_H9_EOS_d0_R2.mLb.clN_H3K27ac.bigWig
cR_H9_EOS_d0_R1_peaks_H3K27ac.xls
cR_H9_EOS_d0_R2_peaks_H3K27ac.xls


title: CTRL_5


title: CTRL_4


title: cR_H9_EOS_d20E_rep2, H3K27ac


title: CTRL_3


title: DetA_3


title: CTRL_2


title: Pt4_omentum1

description:
ICA001-07328A-001-E16-C01-NGS001_S16_L001_R1_001
Pt4_data file(RPM).xlsx


title: HNES1_d0_rep2, H3K9me3

description:
HNES1_d0_R1.mLb.clN_H3K9me3.bigWig
HNES1_d0_R2.mLb.clN_H3K9me3.bigWig
HNES1_d0_R1_peaks_H3K9me3.xls
HNES1_d0_R2_peaks_H3K9me3.xls

value: embryo-derived naive hPSC


title: Pt4_pelvis3

description:
ICA001-07328A-001-E15-C01-NGS001_S15_L001_R1_001
Pt4_data file(RPM).xlsx

value: EV


title: Pt4_pelvis2

description:
ICA001-07328A-001-E14-C01-NGS001_S14_L001_R1_001
Pt4_data file(RPM).xlsx


title: HNES1_d0_rep1, H3K9me3


title: cR_H9_EOS_d0_rep1, H3K27ac


title: IAV/Sp/AMX_biol rep3

city: Lille

first: Yasmine

last: Zeroual

state: Nord

address: 1 Rue du professeur Calmette, 59000 Lille (Institut pasteur de Lille)

country: France

institute: INSERM

data_processing:
STAR-2.7.10a
Genome index was generated using fasta file GRCm39.fa and annotation file gencode.vM30.chr_patch_hapl_scaff.annotation.gtf through STAR-2.7.10a (sjdbOverhang 149)
Sequence reads were mapped to generated genome using STAR-2.7.10a (--quantMode GeneCounts)
ReadsPerGene.out.tab file with four columns (gene ID, counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA, counts for the 2nd read strand aligned with RNA)  was generated by STAR for each sample
Assembly: GRCm39
Supplementary files format and content: TAB files include read counts for each sample (only first two columns were used :Gene ID and read counts for unstranded RNA-seq)

source_name: Bone marrow

growth_protocol: CX3CR1gfp/+mice were infected intranasally (i.n.). with influenza A virus (IAV) and seven days later withS. pneumoniae(Sp).

extract_protocol:
RNA was harvested using NucleoSpin RNA kit by MN
RNA libraries for RNA-seq were prepared using QIAseq stranded mRNA library kit (Qiagen). 200 ng of total RNA.

treatment_protocol:
Mice were treated intragastrically (i.g.) with amoxicillin (AMX) 12 h after Sp infection (IAV/Sp/AMX) or left untreated (IAV/Sp)
Bone marrow mature neutrophils were sorted by FACS 12h post-treatment. Each biological replicate (biol rep) represents a pool of 3 mice. Subsequently RNA was purified for RNA-seq analysis

value: Bone marrow

value: Mature Neutrophiles

tag: agent

value: influenza A virus (IAV) and Streptococcus pneumoniae

tag: condition

value: amoxicillin (AMX)-treated infected mice (IAV/Sp/AMX)


title: Pt4_pelvis1

description:
ICA001-07328A-001-E13-C01-NGS001_S13_L001_R1_001
Pt4_data file(RPM).xlsx


title: HNES1_d10_rep1, H3K9me3


title: Pt4_tumor-surface3

description:
ICA001-07328A-001-E12-C01-NGS001_S12_L001_R1_001
Pt4_data file(RPM).xlsx

source_name: primary cancer


title: cR_H9_EOS_d20X_rep2, H3K9me3

description:
cR_H9_EOS_d20X_R1.mLb.clN_H3K9me3.bigWig
cR_H9_EOS_d20X_R2.mLb.clN_H3K9me3.bigWig
cR_H9_EOS_d20X_R1_peaks_H3K9me3.xls
cR_H9_EOS_d20X_R2_peaks_H3K9me3.xls


title: cR_H9_EOS_d20X_rep1, H3K9me3


title: Pt4_tumor-surface2

description:
ICA001-07328A-001-E11-C01-NGS001_S11_L001_R1_001
Pt4_data file(RPM).xlsx


title: Pt3_ascites2

description:
ICA001-07328A-001-E08-C01-NGS001_S8_L001_R1_001
Pt3_data file(RPM).xlsx


title: cR_H9_EOS_d20E_rep2, H3K9me3

description:
cR_H9_EOS_d20E_R1.mLb.clN_H3K9me3.bigWig
cR_H9_EOS_d20E_R2.mLb.clN_H3K9me3.bigWig
cR_H9_EOS_d20E_R1_peaks_H3K9me3.xls
cR_H9_EOS_d20E_R2_peaks_H3K9me3.xls


title: Pt4_tumor-surface1

description:
ICA001-07328A-001-E10-C01-NGS001_S10_L001_R1_001
Pt4_data file(RPM).xlsx


title: cR_H9_EOS_d20E_rep1, H3K9me3


title: sorted STINGgt/gt BMDCs, +Tem+anti-CD3 stimulated 1hr 3

city: Cincinnati

first: Chandrashekhar

last: Pasare

state: Ohio

address: 250 Albert Sabin Way

department: Immunology

institute: Cincinnati Children's Hospital Medical Center

description: BMDC-sting-gt-1hr_overlap.conservative_peak.narrowPeak.gz

data_processing:
Raw fastq files were processed and aligned to the mm10 genome, and analyzed using ENCODE ATAC-seq pipeline v2.2.0  (DOI: 10.5281/zenodo.5598324; DOI: 10.1093/nar/gkz1062; DOI: 10.1038/nature11247)
Assembly: mm10
Supplementary files format and content: Encode v2.0.0 generated overlap peak files for each sample

source_name: bone marrow derived

growth_protocol: BMDCs grown in 5% FCS containing RPMI for 7 days. Naïve CD4+ T cells expanded with anti-CD3, anti-CD28 coated plate + IL-2 for 5 days. Effector T cells then rested 2 days with IL-2 to create effector memory T (Tem) cell population.

extract_protocol:
Transposase Tn5 with adapter sequences was used to cut the accessible DNA (Buenrostro et al 2015)
The accessible DNA sequences with adaptor sequences were isolated, and libraries were prepared using the OMNI ATAC protocol (Corces et al 2017)

treatment_protocol: BMDCs were treated with Tem cells +/- anti-CD3 for 1 hr, then sorted away from Tem cells for sequencing.

value: bone marrow derived

value: dendritic cells

value: Tem cells + anti-CD3


title: CTRL_1

value: Skin

value: 8-12 weeks old


title: cR_H9_EOS_d10_rep2, H3K9me3

description:
cR_H9_EOS_d10_R1.mLb.clN_H3K9me3.bigWig
cR_H9_EOS_d10_R2.mLb.clN_H3K9me3.bigWig
cR_H9_EOS_d10_R1_peaks_H3K9me3.xls
cR_H9_EOS_d10_R2_peaks_H3K9me3.xls

value: chemically reset cR-H9-EOS

value: chemically reset hPSC

value: N2B27 and 2uM XAV939


title: Pt3_ascites1

description:
ICA001-07328A-001-E07-C01-NGS001_S7_L001_R1_001
Pt3_data file(RPM).xlsx

value: pre-operation


title: cR_H9_EOS_d10_rep1, H3K9me3


title: sorted STINGgt/gt BMDCs, +Tem+anti-CD3 stimulated 1hr 2


title: H9_EOS_rep2, H3K9me3

description:
H9_EOS_R1.mLb.clN_H3K9me3.bigWig
H9_EOS_R2.mLb.clN_H3K9me3.bigWig
H9_EOS_R1_peaks_H3K9me3.xls
H9_EOS_R2_peaks_H3K9me3.xls

value: H9-EOS (parental line for cR-H9-EOS)

value: conventional hPSC


title: IAV/Sp (control)_biol rep1

value: infected mice left untreated (IAV/Sp)


title: IAV/Sp (control)_biol rep2


title: IAV/Sp/AMX_biol rep2


title: IAV/Sp (control)_biol rep3


title: Pt3_pelvis3

description:
ICA001-07328A-001-E06-C01-NGS001_S6_L001_R1_001
Pt3_data file(RPM).xlsx

value: EV

value: surface


title: sorted STINGgt/gt BMDCs, +Tem+anti-CD3 stimulated 1hr 1


title: IAV/Sp/AMX_biol rep1

value: Bone marrow

value: Mature Neutrophiles


title: Pt3_pelvis2

description:
ICA001-07328A-001-E05-C01-NGS001_S5_L001_R1_001
Pt3_data file(RPM).xlsx


title: H9_EOS_rep1, H3K9me3


title: Pt3_ascites3

description:
ICA001-07328A-001-E09-C01-NGS001_S9_L001_R1_001
Pt3_data file(RPM).xlsx


title: sorted STINGgt/gt BMDCs, +Tem unstimulated control 3

description: BMDC-sting-gt-us_overlap.conservative_peak.narrowPeak.gz

value: Tem cells unstimulated


title: cR_H9_EOS_d0_rep2, H3K9me3

description:
cR_H9_EOS_d0_R1.mLb.clN_H3K9me3.bigWig
cR_H9_EOS_d0_R2.mLb.clN_H3K9me3.bigWig
cR_H9_EOS_d0_R1_peaks_H3K9me3.xls
cR_H9_EOS_d0_R2_peaks_H3K9me3.xls


title: cR_H9_EOS_d0_rep1, H3K9me3


title: sorted STINGgt/gt BMDCs, +Tem unstimulated control 2

value: bone marrow derived


title: Pt3_omentum3

description:
ICA001-07328A-001-E03-C01-NGS001_S3_L001_R1_001
Pt3_data file(RPM).xlsx


title: Pt3_pelvis1

description:
ICA001-07328A-001-E04-C01-NGS001_S4_L001_R1_001
Pt3_data file(RPM).xlsx


title: HNES1_d10_rep2, H3K4me3

description:
HNES1_d10_R1.mLb.clN_H3K4me3.bigWig
HNES1_d10_R2.mLb.clN_H3K4me3.bigWig
HNES1_d10_R1_peaks_H3K4me3.xls
HNES1_d10_R2_peaks_H3K4me3.xls

source_name: embryo-derived HNES1

value: embryo-derived HNES1

value: embryo-derived naive hPSC


title: sorted STINGgt/gt BMDCs, +Tem unstimulated control 1

value: dendritic cells


title: Pt3_omentum2

description:
ICA001-07328A-001-E02-C01-NGS001_S2_L001_R1_001
Pt3_data file(RPM).xlsx


title: HNES1_d10_rep1, H3K4me3


title: HNES1_d0_rep2, H3K4me3

description:
HNES1_d0_R1.mLb.clN_H3K4me3.bigWig
HNES1_d0_R2.mLb.clN_H3K4me3.bigWig
HNES1_d0_R1_peaks_H3K4me3.xls
HNES1_d0_R2_peaks_H3K4me3.xls


title: sorted WT BMDCs, +Tem+anti-CD3 stimulated 1hr 3

description: BMDC-wt-1hr_overlap.conservative_peak.narrowPeak.gz

value: Tem cells + anti-CD3


title: Pt3_omentum1

description:
ICA001-07328A-001-E01-C01-NGS001_S1_L001_R1_001
Pt3_data file(RPM).xlsx


title: sorted WT BMDCs, +Tem+anti-CD3 stimulated 1hr 2


title: Pt2_saliva-postope3

description:
ICA001-00171A-001-E01-C01-NGS001_S19_L001_R1_001
Pt2_data file(RPM).xlsx

source_name: saliva

value: post-operation


title: sorted WT BMDCs, +Tem+anti-CD3 stimulated 1hr 1


title: HNES1_d0_rep1, H3K4me3


title: Pt2_saliva-postope2

description:
ICA001-00170A-001-E01-C01-NGS001_S18_L001_R1_001
Pt2_data file(RPM).xlsx


title: H9_EOS_rep2, H3K4me3

description:
H9_EOS_R1.mLb.clN_H3K4me3.bigWig
H9_EOS_R2.mLb.clN_H3K4me3.bigWig
H9_EOS_R1_peaks_H3K4me3.xls
H9_EOS_R2_peaks_H3K4me3.xls


title: H9_EOS_rep1, H3K4me3


title: sorted WT BMDCs, +Tem unstimulated control 3

description: BMDC-wt-us_overlap.conservative_peak.narrowPeak.gz


title: Pt2_saliva-postope1

description:
ICA001-00169A-001-E01-C01-NGS001_S17_L001_R1_001
Pt2_data file(RPM).xlsx


title: sorted WT BMDCs, +Tem unstimulated control 2


title: Pt2_urine-postope3

description:
ICA001-00168A-001-E01-C01-NGS001_S16_L001_R1_001
Pt2_data file(RPM).xlsx

source_name: urine


title: sorted WT BMDCs, +Tem unstimulated control 1


title: Pt2_urine-postope2

description:
ICA001-00167A-001-E01-C01-NGS001_S15_L001_R1_001
Pt2_data file(RPM).xlsx


title: cR_H9_EOS_d20X_rep2, H3K4me3

description:
cR_H9_EOS_d20X_R1.mLb.clN_H3K4me3.bigWig
cR_H9_EOS_d20X_R2.mLb.clN_H3K4me3.bigWig
cR_H9_EOS_d20X_R1_peaks_H3K4me3.xls
cR_H9_EOS_d20X_R2_peaks_H3K4me3.xls

value: chemically reset cR-H9-EOS

value: chemically reset hPSC

value: N2B27 + 2uM XAV939 + 3ng/ml Activin A + 10ng/ml FGF2 (XAF)


title: biol FAD/Tet1(+/-)_4

city: Atlanta

middle: J

last: Armstrong

state: Georgia

address: 615 Michael St

institute: Emory University

data_processing:
RNA sequencing reads were trimmed using Trimmomatic/0.36. Illumina adapters were removed from the reads. The leading and trailing ends of reads were trimmed if the base quality dropped below a Phred score of 20, and a sliding window 4:15
Sequenced reads were aligned to the mouse genome mm10 using STAR/2.7.0f with the default parameters.
Genes with less than 20 reads were dropped and differential gene expression analysis was performed with DESeq2.
DESeq2 was also used to generate VST normalized read counts for each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Cortex

extract_protocol:
To isolate RNA, mouse cortex was homogenized in 1mL of TRIzol and RNA was purified using chloroform and Isopropyl alcohol
Poly(A)+ transcripts were isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module kit according to the manufacturer’s protocol (New England BioLabs Inc., Massachusetts, USA). RNA samples were randomly primed (5’ d(N6) 3’ [N=A,C,G,T]) and fragmented. The first strand was synthesized with Protoscript II Reverse Transcription with a modified extension period as to what is stated in the manufacturer’s protocol (30 minutes at 42⁰C). The remaining steps of library generation were carried out according to the manufacturer’s protocol NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA).

value: Cortex

tag: Sex

value: male


title: cR_H9_EOS_d20X_rep1, H3K4me3


title: Wildtype Bleomycin 2

value: Bronchial epithelial cell

value: Wildtype

tag: treatment

value: Bleomycin


title: Pt2_serum-postope3

description:
ICA001-00174A-001-E01-C01-NGS001_S22_L001_R1_001
Pt2_data file(RPM).xlsx

value: EV


title: cR_H9_EOS_d20E_rep2, H3K4me3

description:
cR_H9_EOS_d20E_R1.mLb.clN_H3K4me3.bigWig
cR_H9_EOS_d20E_R2.mLb.clN_H3K4me3.bigWig
cR_H9_EOS_d20E_R1_peaks_H3K4me3.xls
cR_H9_EOS_d20E_R2_peaks_H3K4me3.xls

tag: cell line


title: cR_H9_EOS_d20E_rep1, H3K4me3

tag: culture condition


title: biol FAD/Tet1(+/-)_2


title: Pt2_serum-postope2

description:
ICA001-00173A-001-E01-C01-NGS001_S21_L001_R1_001
Pt2_data file(RPM).xlsx


title: Pt2_urine-postope1

description:
ICA001-00166A-001-E01-C01-NGS001_S14_L001_R1_001
Pt2_data file(RPM).xlsx


title: cR_H9_EOS_d10_rep2, H3K4me3

description:
cR_H9_EOS_d10_R1.mLb.clN_H3K4me3.bigWig
cR_H9_EOS_d10_R2.mLb.clN_H3K4me3.bigWig
cR_H9_EOS_d10_R1_peaks_H3K4me3.xls
cR_H9_EOS_d10_R2_peaks_H3K4me3.xls

value: N2B27 and 2uM XAV939

tag: histone modification


title: biol FAD/Tet1(+/-)_3


title: biol FAD/Tet1(+/-)_1


title: Pt2_serum-postope1

description:
ICA001-00172A-001-E01-C01-NGS001_S20_L001_R1_001
Pt2_data file(RPM).xlsx


title: cR_H9_EOS_d10_rep1, H3K4me3

tag: cell type


title: biol Tet1(+/-)_2

tag: tissue


title: cR_H9_EOS_d0_rep2, H3K4me3

description:
cR_H9_EOS_d0_R1.mLb.clN_H3K4me3.bigWig
cR_H9_EOS_d0_R2.mLb.clN_H3K4me3.bigWig
cR_H9_EOS_d0_R1_peaks_H3K4me3.xls
cR_H9_EOS_d0_R2_peaks_H3K4me3.xls


title: cR_H9_EOS_d0_rep1, H3K4me3


title: biol Tet1(+/-)_1


title: biol 5xFAD2

value: FAD


title: Pt2_saliva2

description:
ICA001-00103A-001-E01-C01-NGS001_S23_L001_R1_001
Pt2_data file(RPM).xlsx

value: pre-operation


title: H9_EOS_rep2, H3K4me1

description:
H9_EOS_R1.mLb.clN_H3K4me1.bigWig
H9_EOS_R2.mLb.clN_H3K4me1.bigWig
H9_EOS_R1_peaks_H3K4me1.xls
H9_EOS_R2_peaks_H3K4me1.xls

value: H9-EOS (parental line for cR-H9-EOS)

value: conventional hPSC


title: Pt2_saliva1

description:
ICA001-00102A-001-E01-C01-NGS001_S22_L001_R1_001
Pt2_data file(RPM).xlsx


title: biol 5xFAD1


title: H9_EOS_rep1, H3K4me1


title: Pt2_urine3

description:
ICA001-00101A-001-E01-C01-NGS001_S21_L001_R1_001
Pt2_data file(RPM).xlsx


title: biol WT4

value: WT


title: Pt2_urine2

description:
ICA001-00100A-001-E01-C01-NGS001_S20_L001_R1_001
Pt2_data file(RPM).xlsx


title: biol WT3


title: cR_H9_EOS_d20X_rep1, H3K4me1

description:
cR_H9_EOS_d20X_R1.mLb.clN_H3K4me1.bigWig
cR_H9_EOS_d20X_R2.mLb.clN_H3K4me1.bigWig
cR_H9_EOS_d20X_R1_peaks_H3K4me1.xls
cR_H9_EOS_d20X_R2_peaks_H3K4me1.xls


title: cR_H9_EOS_d20X_rep2, H3K4me1


title: Pt2_serum3

description:
ICA001-00095A-001-E01-C01-NGS001_S15_L001_R1_001
Pt2_data file(RPM).xlsx


title: Pt2_urine1

description:
ICA001-00099A-001-E01-C01-NGS001_S19_L001_R1_001
Pt2_data file(RPM).xlsx


title: Pt2_saliva3

description:
ICA001-00104A-001-E01-C01-NGS001_S24_L001_R1_001
Pt2_data file(RPM).xlsx


title: biol WT2


title: biol WT1


title: cR_H9_EOS_d20E_rep2, H3K4me1

description:
cR_H9_EOS_d20E_R1.mLb.clN_H3K4me1.bigWig
cR_H9_EOS_d20E_R2.mLb.clN_H3K4me1.bigWig
cR_H9_EOS_d20E_R1_peaks_H3K4me1.xls
cR_H9_EOS_d20E_R2_peaks_H3K4me1.xls


title: cR_H9_EOS_d20E_rep1, H3K4me1


title: Pt2_ascites3

description:
ICA001-00098A-001-E01-C01-NGS001_S18_L001_R1_001
Pt2_data file(RPM).xlsx


title: Pt2_serum1

description:
ICA001-00092A-001-E01-C01-NGS001_S13_L001_R1_001
Pt2_data file(RPM).xlsx


title: ABL2KO Ctrl - bio rep 2

city: Maywood

first: wei

last: Qiu

department: Surgery

institute: Loyola University Chicago

description: 4276 - ABL2 KO Ctrl

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: excel file contains read counts

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver

value: ABL2 KO

value: Control


title: Pt2_meta-inner3

description:
ICA001-00085A-001-E01-C01-NGS001_S6_L001_R1_001
Pt2_data file(RPM).xlsx

data_processing:
CLC Genomics Workbench version 9.5.3 program
Sequence reads were trimmed and mapped to the miRbase 21 database allowing up to two mismatches
Reads per million mapped reads (RPM) method was used for normalization.
Assembly: miRbase 21

source_name: metastatic cancer

extract_protocol:
The EV sheet was fabricated from cellulose nanofibers. The EV capture process from moistened organs using the EV sheet consists of the following steps: EV capture by absorption of ascites on organs, EV storage by drying, washing, and EV release. Then, total RNA was extracted using RNA purification kit (Norgen Biotek Corp, Thorold,  Canada). To obtain tissue RNA, tissues were shredded using the gentleMACS Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany) and total RNAs was extracted by using the miRNeasy Plus Mini Kit (QIAGEN, Hilden, Germany).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA). Then, PCR products were separated by electrophoresis (120 V, 60 min), and DNA fragments corresponding to 140–160 bp (the length of small non-coding RNA plus the adaptors) were recovered.

tag: location

value: inner


title: Pt2_serum2

description:
ICA001-00093A-001-E01-C01-NGS001_S14_L001_R1_001
Pt2_data file(RPM).xlsx


title: ABL2KO EtOH - bio rep 2

description: 5955 - ABL2 KO EtOH

tag: genotype

value: EtOH


title: HNES1_d10_rep2, H3K4me1

description:
HNES1_d10_R1.mLb.clN_H3K4me1.bigWig
HNES1_d10_R2.mLb.clN_H3K4me1.bigWig
HNES1_d10_R1_peaks_H3K4me1.xls
HNES1_d10_R2_peaks_H3K4me1.xls

value: embryo-derived HNES1

value: embryo-derived naive hPSC


title: cR_H9_EOS_d10_rep1, H3K4me1

description:
cR_H9_EOS_d10_R1.mLb.clN_H3K4me1.bigWig
cR_H9_EOS_d10_R2.mLb.clN_H3K4me1.bigWig
cR_H9_EOS_d10_R1_peaks_H3K4me1.xls
cR_H9_EOS_d10_R2_peaks_H3K4me1.xls

value: chemically reset cR-H9-EOS

value: chemically reset hPSC


title: ABL2KO Ctrl - bio rep 3

description: 4278 - ABL2 KO Ctrl


title: Pt2_ascites1

description:
ICA001-00096A-001-E01-C01-NGS001_S16_L001_R1_001
Pt2_data file(RPM).xlsx


title: cR_H9_EOS_d10_rep2, H3K4me1


title: DetB_1

value: Skin

tag: age

value: 8-12 weeks old

value: Detergent B


title: Pt2_meta-inner1

description:
ICA001-00083A-001-E01-C01-NGS001_S4_L001_R1_001
Pt2_data file(RPM).xlsx

tag: type

value: EV


title: ABL2KO Ctrl - bio rep 1

description: 4277 - ABL2 KO Ctrl


title: cR_H9_EOS_d0_rep2, H3K4me1

description:
cR_H9_EOS_d0_R1.mLb.clN_H3K4me1.bigWig
cR_H9_EOS_d0_R2.mLb.clN_H3K4me1.bigWig
cR_H9_EOS_d0_R1_peaks_H3K4me1.xls
cR_H9_EOS_d0_R2_peaks_H3K4me1.xls

value: N2B27 and 2uM XAV939


title: HNES1_d10_rep1, H3K4me1


title: Pt2_meta-surface3

description:
ICA001-00082A-001-E01-C01-NGS001_S3_L001_R1_001
Pt2_data file(RPM).xlsx

value: surface


title: HNES1_d0_rep1, H3K4me1

description:
HNES1_d0_R1.mLb.clN_H3K4me1.bigWig
HNES1_d0_R2.mLb.clN_H3K4me1.bigWig
HNES1_d0_R1_peaks_H3K4me1.xls
HNES1_d0_R2_peaks_H3K4me1.xls


title: Pt2_ascites2

description:
ICA001-00097A-001-E01-C01-NGS001_S17_L001_R1_001
Pt2_data file(RPM).xlsx

value: pre-operation


title: Pt2_meta-inner2

description:
ICA001-00084A-001-E01-C01-NGS001_S5_L001_R1_001
Pt2_data file(RPM).xlsx


title: ABL2KO EtOH - bio rep 3

description: 5957 - ABL2 KO EtOH


title: WT EtOH - bio rep 2

description: 4247 - ABL2 WT EtOH

value: WT


title: ABL2KO EtOH - bio rep 1

description: 4142 - ABL2 KO EtOH

value: liver


title: WT Ctrl - bio rep 3

description: 4206 - ABL2 WT Ctrl


title: WT EtOH - bio rep 1

description: 4246 - ABL2 WT EtOH


title: Pt2_meta-surface2

description:
ICA001-00081A-001-E01-C01-NGS001_S2_L001_R1_001
Pt2_data file(RPM).xlsx


title: ZNF611.

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

institute: EPFL

description: Naive WIBR3

data_processing:
Peak were called on mapped data using MACS2
Assembly: hg19
Supplementary files format and content: .fq : Raw fastq file, .bed : bed file containing unfiltered raw peaks

source_name: Naïve WIBR3 overexpressing ZNF611

growth_protocol:
4i media
Conventional (primed) human ESC lines were maintained in mTSER for H1 (Male)on Matrigel, for WIBR3 (Female) on irradiated inactivated mouse embryonic fibroblast (MEF) feeders in human ESC medium (hESM) and passaged with collagenase and dispase, followed by sequential sedimentation steps in hESM to remove single cells while naïve ES cells and primed H1 were passaged by Accutase in single cells. hES media composition: DMEM/F12 supplemented with 15% fetalbovine serum, 5% KnockOut Serum Replacement, 2 mM L-glutamine, 1% nonessential amino acids, 1% penicillin-streptomycin (Lonza), 0.1 mM β-mercaptoethanol and 4 ng/ml FGF2. Naïve media composition: 500 mL of medium was generated by including: 240 mL DMEM/F12, 240 mL Neurobasal, 5 mL N2 supplement, 10 mL B27 supplement, 2 mM L-glutamine, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1% penicillin-streptomycin, 50 μg/ml BSA. In addition for KN/2i media: PD0325901 (1 μM), CHIR99021 (1 μM), 20 ng/ml hLIF and Doxycycline (2 µg/ml).

extract_protocol:
Cells were cross-linked for 10 minutes at room temperature by the addition of one-tenth of the volume of 11% formaldehyde solution to the PBS followed by quenching with glycine. Cells were washed twice with PBS, then the supernatant was aspirated and the cell pellet was conserved in -80°C. Pellets were lysed, resuspended in 1mL of LB1 on ice for 10 min (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100, protease inhibitors), then after centrifugation resuspend in LB2 on ice for 10 min (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitors). After centrifugation, resuspend in LB3 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.1% SDS and protease inhibitors) for histone marks and SDS shearing buffer (10 mM Tris pH8, EDTA 1mM, SDS 0.15% and protease inhibitors) for transcription factor and sonicated (Covaris settings: 5% duty, 200 cycle, 140 PIP, 20 min), yielding genomic DNA fragments with a bulk size of 100-300bp. Coating of the beads with the specific antibody and carried out during the day at 4°C, then chromatin was added overnight at 4°C for histone marks while antibody for transcription factor is incubated with chromatin first with 1% Triton and 150mM NaCl. Subsequently, washes were performed with 2x Low Salt Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 150mM NaCl, 0.15% SDS), 1x High Salt Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 500 mM NaCl, 0.15% SDS), 1x LiCl buffer (10 mM Tris pH 8, 1 mM EDTA, 0.5 mM EGTA, 250 mM LiCl, 1% NP40, 1% NaDOC) and 1 with TE buffer. Final DNA was purified with Qiagen Elute Column. Up to 10 nanograms of ChIPed DNA or input DNA (Input) were prepared for sequencing. Library was quality checked by DNA high sensitivity chip (Agilent). Quality controlled samples were then quantified by picogreen (Qubit® 2.0 Fluorometer, Invitrogen). Cluster amplification and following sequencing steps strictly followed the Illumina standard protocol.  Libraries were ligated with Illumina adaptors
Illumina HiSeq 2500 (Illumina), with each library sequenced in 100-bp reads run.

treatment_protocol: Primed H1 were transduced with GFP or KLF4-containing lentiviral vectors and split after 48h then selected using blasticydin for the 3 following days. Naïve WIBR3dPE hESC cells in KN/2iL media were transduced with GFP or ZNF611-containing lentiviral vectors, split after 96h, then selected for a couple of passages with blasticydin on irradiated Mouse Embryonic Blasticidin-resistant (MMMbz).

tag: genotype/variation

value: WIBR3  hESC

tag: antibody

value: HA


title: HNES1_d0_rep2, H3K4me1

tag: biological replicate

tag: day of_formative_transition


title: WT Ctrl - bio rep 2

description: 4275 - ABL2 WT Ctrl

value: Control


title: GFP

description: Primed H1

source_name: Primed H1 overexpressing KLF4

growth_protocol:
hESM media
Conventional (primed) human ESC lines were maintained in mTSER for H1 (Male)on Matrigel, for WIBR3 (Female) on irradiated inactivated mouse embryonic fibroblast (MEF) feeders in human ESC medium (hESM) and passaged with collagenase and dispase, followed by sequential sedimentation steps in hESM to remove single cells while naïve ES cells and primed H1 were passaged by Accutase in single cells. hES media composition: DMEM/F12 supplemented with 15% fetalbovine serum, 5% KnockOut Serum Replacement, 2 mM L-glutamine, 1% nonessential amino acids, 1% penicillin-streptomycin (Lonza), 0.1 mM β-mercaptoethanol and 4 ng/ml FGF2. Naïve media composition: 500 mL of medium was generated by including: 240 mL DMEM/F12, 240 mL Neurobasal, 5 mL N2 supplement, 10 mL B27 supplement, 2 mM L-glutamine, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1% penicillin-streptomycin, 50 μg/ml BSA. In addition for KN/2i media: PD0325901 (1 μM), CHIR99021 (1 μM), 20 ng/ml hLIF and Doxycycline (2 µg/ml).

value: H1  hESC


title: Pt2_tumor-fluid3

last: Yoshida

institute: Nagoya University

description:
ICA001-00088A-001-E01-C01-NGS001_S9_L001_R1_001
Pt2_data file(RPM).xlsx

source_name: tumor fluid


title: WT EtOH - bio rep 3

description: 4250 - ABL2 WT EtOH

value: EtOH


title: WT Ctrl - bio rep 1

description: 4321 - ABL2 WT Ctrl


title: cR_H9_EOS_d0_rep1, H3K4me1


title: Pt2_tumor-fluid2

description:
ICA001-00087A-001-E01-C01-NGS001_S8_L001_R1_001
Pt2_data file(RPM).xlsx


title: Pt2_tumor-fluid1

description:
ICA001-00086A-001-E01-C01-NGS001_S7_L001_R1_001
Pt2_data file(RPM).xlsx


title: Pt2_tumor-surface2

description:
ICA001-00090A-001-E01-C01-NGS001_S11_L001_R1_001
Pt2_data file(RPM).xlsx


title: INPUT

description: Naive WIBR3

value: DNA INPUT


title: Pt2_tumor-surface3

description:
ICA001-00091A-001-E01-C01-NGS001_S12_L001_R1_001
Pt2_data file(RPM).xlsx


title: C57BL/6-tumor_TCR

city: shanghai

first: Qing

last: Li

state: Shanghai

address: 320 Yueyang Road

institute: Chinese Academy of sciences

description: 10x Genomics TCR library

data_processing:
Basecalls performed using CASAVA version 1.8
For5' GEX library, cellranger (v6.1.10) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table. Seurat package (version: 4.0.3 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data. PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. CCA analysis in Seurat package was applied for combining 3’ scRNA-Seq data and 5’ scRNA-Seq data. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
For TCR library, cellranger (v6.1.1) was used to obtain the nucleotide sequences of α and β chain in each T cell. Then CDR3 sequence was annotated to calculate the frequency of each clonotype.
Assembly: GRCm38
Supplementary files format and content: scRNA-seq: text file transcript counts; scTCR-seq: text file with amino acid CDR3 sequence, nucleotide CDR3 sequence, and clone ID

source_name: Tumor

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 5' R2-only Instrumen and Immune Profiling reagents (10x Genomics) according to manufacturer's protocol.
Libraries were generated and prepared for sequencing using standard Illumina protocols

treatment_protocol: Kb-/-Db-/- mice and C57BL/6 mice were i.v. injected with B16F10 cells (3×105). The tumor bearing Kb-/-Db-/- mice were i.p. injected with Ia-MSCs (1×106) or Ia+MSCs (1×106) every 3 days starting on day 0. After 9 days, splenic CD8+ T cells from Ia-MSCs treated Kb-/-Db-/- mice (Ia-MSCs-spleen), splenic CD8+ T cells from Ia+MSCs treated Kb-/-Db-/- mice (Ia+MSCs-spleen), tumor infiltrated CD8+ T cells from Ia+MSCs treated Kb-/-Db-/- mice (Ia+MSCs-tumor), splenic CD8+ T cells from C57BL/6 mice (C57BL/6-spleen), and tumor infiltrated CD8+ T cells from C57BL/6 mice (C57BL/6-tumor) were isolated using magnet beads and subjected to single cell RNA sequencing.

value: Tumor

value: CD8+ T cells

value: Wild type


title: C57BL/6-spleen_TCR

description: 10x Genomics TCR library

source_name: Spleen

value: Spleen


title: Ia+MSCs-tumor_TCR

description: 10x Genomics TCR library

value: Ia+MSCs


title: KLF4.1

description: Primed H1

value: H1 hESC


title: M17 cells, Miat4

first: Bing

last: Yao

address: 615 Michael Street

department: Department of Human Genetics

data_processing:
All total reads were mapped to hg38 by TopHat2 with default parameter followed by gene expression quantification and differential expression analysis using Cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: fpkm table

growth_protocol: The BE(2)-M17 human neuroblastoma line and SH-SY5Y line (both are from ATCC) were propagated in DMEM/F12 medium containing 10% fetal bovine serum (FBS) (HyClone).

extract_protocol:
Cultured cells were harvested then centrifuged at 1,500 g and cell pellets were used for RNA isolation. Cell pellet was homogenized in TRIzol using a hand-held pestle homogenizer and incubated in TRIzol for at least 5 minutes. Chloroform (1:5 ratio) was added, mixed well and incubated at room temperature for 15 minutes. Samples were then centrifuged at 12,000 g for 15 minutes at 4°C. The top aqueous layer was transferred to a clean tube, and the RNA was precipitated in 3 M NaAc pH 5.2 (10:1 ratio), 4 ml of glycogen (5 mg/ml), 100% isopropanol (1:1 ratio) overnight at -80°C. The next day, the samples were centrifuged at 20,000 g for 20 minutes at 4°C. The resulting RNA pellet was washed once in 75% ethanol, centrifuged at 7,500 g for 10 minutes at 4°C. The washed RNA pellet was dissolved in nuclease-free water. RNA was quantified by NanoDrop and the quality was confirmed by agarose gel.
An amount of 1ug total RNA per sample was processed for library preparation using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. Libraries were sequenced on a HiSeq with a read length configuration of 150 PE, targeting 100M total reads per sample.

treatment_protocol: Cells were transfected with 100 pmol siRNA, miRNA mimics, or miRNA inhibitors, including Hsa-miR-137 (Ambion, mc10513), has-miR-100 (Ambion, mc10188) and has-anti-miR-137 (Dharmacon, IH-310413-07-0005), using Lipofectamine 2000 (Invitrogen) following manufacturer’s instructions.

value: neuroblastoma cells

value: GOMAFU knockdown


title: Pt2_meta-surface1

first: Kosuke

address: 65 Tsuruma-cho

description:
ICA001-00080A-001-E01-C01-NGS001_S1_L001_R1_001
Pt2_data file(RPM).xlsx

value: EV

value: surface


title: Ia+MSCs-spleen_TCR

description: 10x Genomics TCR library


title: M17 cells, Miat3


title: Ia-MSCs-spleen_TCR

description: 10x Genomics TCR library

value: Ia-MSCs


title: KLF4.3

description: Primed H1


title: Pt2_tumor-surface1

description:
ICA001-00089A-001-E01-C01-NGS001_S10_L001_R1_001
Pt2_data file(RPM).xlsx


title: C57BL/6-tumor

description: 10x Genomics 5' GEX library


title: M17 cells, Con_4

value: control


title: M17 cells, Miat2


title: M17 cells, Con_2


title: Pt1_urine-postope3

description:
ICA001-00064A-001-E01-C01-NGS002_S9_L001_R1_001
Pt1_data file(RPM).xlsx

value: post-operation


title: Pt1_urine-postope2

description:
ICA001-00063A-001-E01-C01-NGS002_S8_L001_R1_001
Pt1_data file(RPM).xlsx


title: Ia+MSCs-tumor

description: 10x Genomics 5' GEX library


title: KLF4.2

description: Primed H1

value: HA


title: M17 cells, Con_3


title: C57BL/6-spleen

description: 10x Genomics 5' GEX library


title: G41_control_2

city: New York

first: Rajal

last: Sharma

address: 1425 Madison Ave., Room 16-52

institute: ISMMS

data_processing:
Basecalls performed using CASAVA version 1.4
Read sequences were filtered by Trimmomatic 0.36
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie v1.0.1
Peaks were called using MACS with Input as control with the following setting: pvalue cutoff (1.00e-05), model fold (10, 30).
For RNA-Seq: Tophat (v2.1.0) alignment was performed using the mm9 reference genome. HT-seq was used to find read counts across genes. DESeq2 was used to find differentially expressed genes with FDR < 0.1 and Fold-change > 1.5.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files generated by computing feature density over a 5 bp window across the genome. http://genome.ucsc.edu/goldenPath/help/wiggle.html For RNA-Seq: Tab-delimited text file of normalized counts for all samples.

source_name: HCT116 cells

extract_protocol:
For ChIP-Seq: Whole cell lysates were sonicated and protein-DNA complexes were isolated with antibodies. For RNA-Seq: Compound treated cells were collected and RNA was extracted using TRIzol.
ChIP-sequencing for GAS41, c-Myc, H3K27cr and H3K27ac and RNA-sequencing in HCT116 cells with and without Dox treatment were performed on the Illumina HiSeq 2500v4 platform with 100bp read length under rapid run mode. Two to three biological replicates were prepared for each treatment condition. Specifically, for these genomic sequencing samples, ChIP-DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 200-300bp size fractions were excised from 2% agarose gel stained with GelStar. Adaptor-modified fragments were enriched by 16 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size. Additionally, RNA-sequencing for HCT116 GAS41 wt and GAS41 KO cells, or GAS41 KO cells stably expressing GFP-Flag-GAS41 wt (wt rescue), or GFP-Flag-GAS41 Y74A/W93A (mutant rescue), was performed using an BGISEQ-500 platform at BGI. Three biological replicates were prepared for each treatment. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and single-end read of 50 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA. nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method

tag: replicate

tag: chip antibody


title: Pt1_urine3

city: Nagoya

description:
ICA001-00061A-001-E01-C01-NGS002_S6_L001_R1_001
Pt1_data file(RPM).xlsx

value: pre-operation


title: Pt1_urine2

description:
ICA001-00060A-001-E01-C01-NGS002_S5_L001_R1_001
Pt1_data file(RPM).xlsx


title: Ia-MSCs-spleen

description: 10x Genomics 5' GEX library


title: G41_control_1


title: Pt1_urine1

description:
ICA001-00059A-001-E01-C01-NGS002_S4_L001_R1_001
Pt1_data file(RPM).xlsx


title: CR_doxo_2

value: Dox 500 nM

value: H3K27cr (PTM-Bio 526)


title: Preadipocytes from iWAT (HFD-KO3) [KO3-RNA-seq]

city: California

first: Sona

last: Kang

state: Berkeley

address: Morgan Hall 321

department: Nutritional Sciences & Toxicology

institute: University of California, Berkeley

description: RNAseq.xlsx

data_processing:
WGBS:
trim_galore, Version 0.6.6, trim_base1=10 trim_base2=15
mapping to the in silico bisulfite converted GRCm39, Bismark, Version 0.23.0
DMRs detection, DSS, version 2.44.0, p-value 0.01, minlen=200, minCG=5, dis.merge=50, pct.sig=0.5
Assembly: MM39 (WGBS); MM10 (RNA-seq)
Supplementary files format and content: WGBS.xlsx, DMRs for Pooled WT-WGBS, Pooled KO-WGBS
Supplementary files format and content: Readcount.xlsx, excel, readcount for WT1-RNA-seq, WT2-RNA-seq, WT3-RNA-seq, KO1-RNA-seq, KO2-RNA-seq, KO3-RNA-seq
RNA-seq:
RNA alignment, Hisat2, Version 2.2.1, Default
Feature count, Htseq, Version 0.9.1, Default
Differential gene expression analysis, Deseq2, Version 1.36.0, Default

source_name: iWAT

extract_protocol:
WGBS: Preadipocytes were isolated from SVF of iWAT using flow cytometry and genomic DNA was purified using DNeasy blood & tissue kit (Cat#. 69506)
WGBS: Genomic DNA is sonicated and proceed to bisulfite conversion with ZYMO EZ DNA Methylation Lightning Kit (cat#11-338). The library is prepped with Swift Biosciences ACCEL-NGS MethylSeq DNA library kit Cat#30096)
RNA-seq:Preadipocytes were isolated from SVF of iWAT using flow cytometry and RNA was purified using RNAqueous®-Micro Kit (Cat#. AM1931)
RNA-seq:Poly(A) RNA Selection Kit V1.5

treatment_protocol:
WGBS: High fat diet (14 weeks)
RNA-seq: High fat diet (6 weeks)

value: iWAT

tag: Sex

value: male

value: preadipocytes (CD45-, CD31-, TER119-, PDGFRa+)

value: Pdgfra-Tet3 KO

value: High fat diet (6 weeks)


title: Ia+MSCs-spleen

description: 10x Genomics 5' GEX library

value: Spleen

value: CD8+ T cells

tag: treatment

value: Ia+MSCs


title: Preadipocytes from iWAT (HFD-KO2) [KO2-RNA-seq]

description: RNAseq.xlsx


title: Pt1_serum3

description:
ICA001-00058A-001-E01-C01-NGS002_S3_L001_R1_001
Pt1_data file(RPM).xlsx

source_name: serum

value: EV


title: CR_doxo_1

state: NY

tag: cell line


title: Pt1_serum2

description:
ICA001-00106A-001-E01-C01-NGS002_S2_L001_R1_001
Pt1_data file(RPM).xlsx


title: Pt1_serum1

description:
ICA001-00105A-001-E01-C01-NGS002_S1_L001_R1_001
Pt1_data file(RPM).xlsx


title: Preadipocytes from iWAT (HFD-KO1) [KO1-RNA-seq]

description: RNAseq.xlsx


title: Preadipocytes from iWAT (HFD-WT3) [WT3-RNA-seq]

description: RNAseq.xlsx

value: Tet3 f/f


title: Preadipocytes from iWAT (HFD-WT2) [WT2-RNA-seq]

description: RNAseq.xlsx


title: Pt1_urine-postope1

description:
ICA001-00062A-001-E01-C01-NGS002_S7_L001_R1_001
Pt1_data file(RPM).xlsx