title: Enteric neuro-glial culture; IL-13 + IL-4 (24h); replicate 7

description: Library name: IL13_IL4_7

data_processing:
After sequencing, the Terra platform was used to run Cumulus (Li B, et al. Nat Methods. 2020.) and broadinstitute_gtex workflows: cumulus/bcl2fastq (V.5) was used for demultiplexing BCL files into individual libraries, broadinstitute_gtex/fastqc_v1-0_BETA (V.2) was used for quality control of fastq files, and broadinstitute_gtex/rnaseq_fastq_star_rsem_rnaseqc_v1-2_BETA was used for STAR alignment (Dobin, et al. Bioinformatics. 2013.) against the mouse reference genome (GRCm38 / mm10) and transcript quantification with RSEM (Li B, et al. BMC Bioinformatics. 2011.). RSEM expected count data was used to generate count matrices and expected counts were rounded to the nearest whole number. Samples with fewer than 1 million reads were excluded from analysis.
For data visualized in associated manuscript, DESeq2 (Love MI, et al. Genome Biol. 2014.) was used to perform differential gene expression analysis based on the negative binomial distribution. DESeq2 Log10(adjusted p-values) and Log2(fold-change) were used to generate volcano plots, and normalized counts of biological replicates from the DESeq2 object were used to plot individual gene expression. Prism v9 was used to generate volcano plots and DESeq2-normalized gene expression scatter and box plots.
Assembly: GRCm38 / mm10
Supplementary files format and content: .tsv file of count matrix and ensembl gene IDs

source_name: Primary culture from neonatal small intestines

extract_protocol:
Newborn P0 mouse pups were euthanized and the small intestine with mesentery was isolated, cleaned, and placed in holding buffer—i.e., HBSS without Ca2+ and Mg2+ (Gibco), 5% FCS, 10mM HEPES (Gibco), 100 units mL-1 Pen-strep (Gibco), 100 μg mL-1 Gentamycin (Lonza)—until all tissues were collected. Small intestines were then minced with scissors and digested for 30 min at 37C with magnetic stirring at 550 rpm in digestion buffer—i.e., HBSS with Ca2+ and Mg2+ (Gibco), 5% FCS, 10mM HEPES (Gibco), 100 μg mL-1 DNase I (Roche), 200 μg mL-1 Liberase TH (Roche). After digestion, samples were gently triturated with 2-3 passes through an 18G needle, filtered with a 40μm strainer, and quenched by washing 3-times with ice-cold sterile DMEM/F-12 media (Gibco). Cells from each mouse were then plated in distinct wells of a 12-well low-adhesion plate and incubated at 37C with 5-10% CO2 for 6-7 days in Neurosphere Culture Media—i.e., DMEM/F-12 (Gibco), 10mM HEPES (Gibco), 100 units mL-1 Pen-strep (Gibco), 100 μg mL-1 Gentamycin (Lonza), 2mM Glutamine (Gibco), 55μM β-mercaptoethanol (Gibco), 1x B-27 Plus supplement (Thermo Scientific), 1x N2 supplement (Thermo Scientific), 20 ng mL-1 recombinant FGF-basic (PeproTech), 20 ng mL-1 recombinant EGF (PeproTech), 50 ng mL-1 recombinant GDNF (R&D Systems). Debris and dead cells were then gently removed with 2-3 media washes, centrifuging at 80 x g for 1-2 min to enrich the precipitate for neurospheres. Neurospheres were dissociated in Accutase (Stem Cell Technologies) for 15-20 min with gentle trituration. After counting cells, dissociated neurospheres were plated in 96-well flat-bottom plates (10,000-20,000 cells per well) or 8-well imaging slide chambers (Ibidi; 20,000-40,000 cells per well) coated with Matrigel (BD; 1:100 dilution in DMEM/F-12 for 2 hrs at 37C) and incubated at 37C with 5-10% CO2 in Neuron Differentiation Media—i.e., Neurobasal A medium (Gibco), 10mM HEPES (Gibco), 100 units mL-1 Pen-strep (Gibco), 100 μg mL-1 Gentamycin (Lonza), 2mM Glutamine (Gibco), 55μM β-mercaptoethanol (Gibco), 1x B-27 Plus supplement (Thermo Scientific), 1x N2 supplement (Thermo Scientific), 50 ng mL-1 recombinant GDNF (R&D Systems). Experiments with cytokine and drug incubations began after day 10 and visible inspection of neuronal networks in culture. After the conclusion of experiment, wells were washed once gently with PBS and RNA from cultures was isolated for bulk RNA sequencing or RT-qPCR by the addition of 5-7 μL of Buffer TCL (Qiagen) supplemented with 1% β-mercaptoethanol (Sigma-Aldrich), snap-frozen on dry ice, and stored at -80C until further processing.
A modified version of the SMART-Seq2 protocol (Picelli, et al. Nat Protoc. 2014.) was applied to generate full-length transcriptomic data from low-input samples—processed by the Klarman Cell Observatory and the Broad Institute Genomics Platform (GP). Briefly, RNA from lysates were cleaned-up using Agencourt RNAClean XP SPRI magnetic beads (Beckman Coulter, A63987) and first strand cDNA synthesis was performed using Maxima H-minus Reverse Transcriptase (Thermo Fisher Scientific, EP0753) and amplified using KAPA HiFi HotStart PCR ReadyMix (KAPA Biosystems, KK2602). cDNA concentration was assessed using Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) and subsequently normalized to 0.25 ng μL-1. Library preparation was performed using the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096), confirmed to have a size of 500 bp using a BioAnalyzer (Agilent), and pooled libraries were normalized to 2nM and denatured using 0.1 N NaOH prior to sequencing. Flow cell cluster amplification and sequencing were performed according to the manufacturer’s protocols using the paired-end Illumina sequencing (2 x 38 bp) with 75 cycle Nextseq 500 high output V2 kit (Illumina).

treatment_protocol: Enteric neuro-glial cultures were treated with or without indicated cytokines or cytokine combinations (50 ng/mL per cytokine) for 24 hours.

tag: div (post-neurosphere_dissociation)

value: not provided

tag: culture replicate

value: Differentiated enteric neurons and glia

value: Wild-type (C57Bl/6J)

value: IL-13 + IL-4 (50 ng/mL, each)


title: blood, Day 3, UGA4, 011

status: Public on Jun 25 2025

type: SRA

city: Bethesda

first: Megan

last: Hockman

state: MD

address: 50 South Drive

department: NIAID

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
Sequencing reads were aligned using the nf-core RNASeq pipeline, version 3.0, and standard parameters. Alignment and quanficiation were performed using STAR and Salmon.
Assembly: GRCh38
Supplementary files format and content: Length scaled gene counts. Rows = Genes, Columns = Subjects

molecule: total RNA

organism: Homo sapiens

source_name: Whole Blood

extract_protocol:
For each study day, total RNA was isolated from blood samples in randomized batches using the PAXgene Blood RNA kit (QIAGEN, Hilden, Germany) according to the manufacturer’s recommendations. Isolated RNA was stored at -80° C in a LoBind twin-tec 96-well PCR plate (Eppendorf). Sample concentrations were determined using the Qubit BR RNA Assay on a Qubit 2.0 Fluorometer (Thermo Fisher Scientific). Sample fragment size distributions were measured using an RNA Screentape on a 4200 TapeStation System.
Sequencing libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB), according to the manufacturer’s protocols. In cases of sufficient RNA concentration, 1 μg of input RNA was used, but in cases of low-yield samples, the maximum possible input mass was used. AMPure XP Beads (Beckman Coulter) were used in place of the supplied NEBNext Sample Purification Beads. Libraries for each study day were prepared in separate batches across multiple 96-well plates due to high sample number. Each plate included two negative controls to monitor for reagent or sample-to-sample contamination. Libraries were barcoded with NEBNext Multiplex Oligos for Illumina (NEB), with each pool containing a unique set of barcodes. Libraries were quantified using the Qubit dsDNA HS Assay on a Qubit 2.0 Fluorometer and fragment size was measured with an HSD1000 Screentape (Agilent) on a 4200 TapeStation System to ensure sufficient molarity and quality for pooling and sequencing. Libraries were pooled with equimolar input to a final concentration of 3nM.

tag: tissue

value: Whole Blood

tag: time

value: Day 3

tag: Sex

value: female

tag: vaccine response

value: Non Responder

tag: bmi

tag: age


title: WT_2

city: New York

first: Genomics-core-facility

last: WCM

state: NY

address: 1300 York Ave.

institute: Weill Cornell Medicine

description:
Library name: Sample 2
wild type mouse 2

data_processing:
Raw sequencing reads in BCL format were processed through bcl2fastq 2.20 (Illumina) for FASTQ conversion and demultiplexing. FASTQ files were trimmed for adaptor sequences and low-quality bases using cutadapt. Trimmed reads were aligned to the mouse reference genome (GRCm38) using STAR aligner. Raw gene counts were quantified using HTSeq-count.
Assembly: GRCm38
Supplementary files format and content: tab-delimited txt file includes gene counts for each sample

organism: Mus musculus

source_name: Kidney

extract_protocol:
Cortices of kidneys from 3 - 4 mice from each of the cohorts were dissected for mRNA-seq. Five -10 mg of each cortex section was transferred into a tube containing beads (Benchmark Scientific Prefilled Tubes for Homogenizer, Catalogue #, D1032-15) and a 500 μl mixture of RLT (from Qiagen RNeasy Plus Mini Kit (Cat. No. 74134)) and β-mercaptoethanol. Tissues were homogenized twice for 30 seconds each with a Bead Bug homogenizer (Benchmark Scientific, Fort Lauderdale, FL). After homogenization, total RNA was extracted by following the protocol from the kit. Total RNA from RCC4 cells was extracted by following the protocol from the kit.
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina), following manufacturer's protocols.

value: Kidney

tag: genotype

value: Wild Type


title: Enteric neuro-glial culture; IL-13 + IL-4 (24h); replicate 6

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

description: Library name: IL13_IL4_6

molecule: polyA RNA

value: Primary culture from neonatal small intestines

tag: cell type

tag: treatment

tag: batch


title: (Rosa26) Wild type chondrocytes, biological rep 3

city: Farmington

first: Ernesto

last: Canalis

state: CT

address: 263 Farmington Avenue

department: Orthopaedic Surgery

institute: UConn Health

description: Library name: Canalis-3

data_processing:
Libraries were validated for length and adapter dimer removal using the Agilent TapeStation 4200 D1000 High Sensitivity assay (Agilent Technologies), and then they were quantified and normalized using the dsDNA High Sensitivity Assay for Qubit 3.0 (Thermo Fisher Scientific).
Sample libraries were prepared for Illumina sequencing by denaturing and diluting the libraries per manufacturer’s protocol (Illumina).
All samples were pooled into one sequencing pool, equally normalized, and run as one sample pool across the Illumina NextSeq 500 using version 2.5 chemistry.
Target read depth was achieved for each sample with paired end 75bp reads.
Raw reads were trimmed with Sickle, with a quality threshold of 30 and length threshold of 45, following that the trimmed reads were mapped to Mus Musculus genome (GRCm38) with HISAT2 .
The resulting SAM files then converted into BAM format using samtools, and the PCR duplicates were removed using PICARD (http://broadinstitute.github.io/picard/).
The counts were generated against the features with htseq-count.
The differential expression of genes between conditions was evaluated using DESeq2.
Covariates were introduced in the DESeq2 analysis to increase the accuracy of results, and genes showing less than 10 counts across the compared samples were excluded from the analysis.
Genes with a false discovery rate (FDR) < 0.05 were considered significant and used in the downstream analysis.
Assembly: Mus Musculus genome (GRCm39 ensembl release 105)
Supplementary files format and content: COUNTS File (*.counts) and counts

source_name: Chondrocyte

growth_protocol: Plated wt cells on tissue culture treated plates.

extract_protocol:
Cells were lifted and the RNA extracted using Qiagen Rneasy Mini Kit.
Total RNA samples were prepared for mRNA-Sequencing using the Illumina TruSeq Stranded mRNA Sample Preparation kit following the manufacturer’s protocol (Illumina, San Diego, CA).

treatment_protocol: 24 hr adenoviral GFP and Cre infection for RosaNICD2 with 24 hr recovery

value: Chondrocyte

value: Wild type

value: AdenoGFP


title: Notch2tm1.1Ecan Experimental chondrocytes, biological rep 1

description: Library name: Hajdu-5

value: no treatment


title: blood, Day 3, UGA4, 324

value: High Responder


title: WT_1

description:
Library name: Sample 1
wild type mouse 1


title: Enteric neuro-glial culture; IL-13 + IL-4 (24h); replicate 5

description: Library name: IL13_IL4_5


title: WT_5

description:
Library name: Sample 5
wild type mouse 5


title: Enteric neuro-glial culture; IL-13 + IL-4 (24h); replicate 3

description: Library name: IL13_IL4_3


title: Enteric neuro-glial culture; IL-13 + IL-4 (24h); replicate 1

description: Library name: IL13_IL4_1


title: blood, Day 3, UGA4, 219

value: male


title: ATACseq: Setdb2KO mouse Bone-marrow derived macrophages treated with B-glucan and Lipopolysaccharide Rep 3

first: Laszlo

last: Halasz

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description: Library name: mm_ATACseq_BMDM_Setdb2KO_GLULPS_Rep3

library_source: genomic

data_processing:
RNA-seq data was performed by nf-core/rnaseq pipeline (version 3.9). In brief, adapters and low quality reads were filtered by trimgalore (0.6.6). Cleaned reads were aligned to the mouse reference genome with STAR and genes were quantified using Salmon.
ATAC-seq data was performed by nf-core/atacseq pipeline (version 1.2.2) using default parameters. In brief, adapter trimming using  by trimgalore (0.6.6). Cleaned reads were aligned using BWA aligner, duplicates were marked by picard and bigWig tracks were generated by BEDTools.
Assembly: mm10
Supplementary files format and content: RNAseq: processed raw and normalized count matrix
Supplementary files format and content: ATACseq: processed coverage files (bigwigs)

molecule: genomic DNA

source_name: BMDM

extract_protocol:
RNA-seq: Total RNA was isolated from SETDB2mKO and WT BMDMs using the RNAeasy kit (Quiagen) according to the manufacturer’s instructions. The quality of the RNA was measured by Agilent BioAnalyzer. High quality RNA samples were submitted to genetic resource core facility (GRCF) Johns Hopkins University for following library preparation and sequencing. Briefly, mRNAs were enriched by removing ribosomal RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490S, New England BioLabs) as per manufacturer’s instructions. ATAC-seq: After β-glucan training, BMDMs were detached from the plate and counted. 60,000 cells per treatment condition were used for the experiment. Cells were washed with ice-cold PBS and nuclei were isolated using lysis buffer (1% Triton-X-100,150 mM NaCl, 0.1% SDS, 1 mM EDTA, and 20 mM Tris-HCl pH 8.0). Tagmentation was performed in nuclei, using Tn5 transposase in a reaction mixture containing 10.5 μl H2O, 12.5 μl TD buffer, and 2 μl Tn5 transposase (Illumina) at 37°C for 30 minutes. Tagmentation reactions were stopped by adding 75 μl TE buffer. DNA was further isolated using Qiagen Minelute columns and amplified by PCR using Nextera primers. PCR reaction clean-up was performed with the addition of 90 μl AMPure XP beads to a 50 μl PCR reaction.
RNA-seq: RNA-Seq libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S, New England BioLabs). Sequencing was performed on the Novaseq-6000 instrument (Illumina). At least three biological replicates were used from all treatment types for sequencing. ATAC-seq: Samples were submitted to genetic resource core facility (GRCF) Johns Hopkins University for following fragment analysis by bioanalyzer and sequencing. Libraries were sequenced 1.6B paired end reads on a Novaseq-6000 instrument (Illumina).

value: BMDM

value: GLULPS


title: Enteric neuro-glial culture; IL-13 + IFNg (24h); replicate 9

description: Library name: IL13_IFNg_9

value: not provided

value: Differentiated enteric neurons and glia

value: Wild-type (C57Bl/6J)

value: IL-13 + IFNg (50 ng/mL, each)


title: blood, Day 3, UGA4, 170

value: Whole Blood

value: Day 3

value: female


title: ATACseq: Setdb2KO mouse Bone-marrow derived macrophages treated with B-glucan and Lipopolysaccharide Rep 2

description: Library name: mm_ATACseq_BMDM_Setdb2KO_GLULPS_Rep2


title: PruKoAP2X-1_Rep2

city: Lanzhou

first: JinLei

last: Wang

address: yanchangbao

country: China

institute: LVRI

description:
Library name: PruKoAP2X-1_Rep2
Parasite of PruΔap2X-1 strain grown in HFF

data_processing:
Raw reads in fastq format were processed using fastp (v0.20.0) and clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from the raw data.
Clean reads were aligned to the ME49 genome using BWA (v0.7.12)
Only uniquely mapped (MAPQ ≥ 13) and de-duplicated reads were used for further analysis.
The peak calling was performed with MACS2 (v2.1.0) and ChIPseeker was used to retrieve the nearest genes around the peak and annotate the genomic region of the peak.
Visualization of peak distribution along genomic regions of genes of interest was performed with IGV.
Assembly: Toxoplasma gondii ME49
Supplementary files format and content: bw

organism: Toxoplasma gondii

source_name: Pru

growth_protocol: Parasites were maintained at 37 ℃ in confluent monolayers of human foreskin fibroblast (HFF) cells

extract_protocol:
Briefly, ~ 107 intracellular tachyzoites were collected and the parasite nuclei were isolated by resuspension of the washed parasite pellet in NE Buffer. The nuclei were then processed according to the manufacturer’s protocol and libraries were constructed using ‘TD903 Hyperactive Universal CUT&Tag Assay Kit for Illumina’ and ‘TD202 TruePrep Index Kit V2 for Illumina’ from Vazyme Biotech (#TD202, China)
Libraries were sequenced on Illumina Novaseq platform at Novogene Science and Technology Co., Ltd (Beijing, China) and 150 bp paired-end reads were generated.

tag: cell line

value: Pru

value: Parasites in HFF

value: Type 2

value: Parasite grown in HFF without  IAA

value: single


title: (Notch2) Wild type chondrocytes, biological rep 3

description: Library name: WT-3

value: Chondrocyte

value: Wild type

value: no treatment


title: Pru_Rep2

description:
Library name: Pru_Rep2
Parasite of Pru strain grown in HFF


title: ATACseq: Setdb2KO mouse Bone-marrow derived macrophages treated with B-glucan and Lipopolysaccharide Rep 1

description: Library name: mm_ATACseq_BMDM_Setdb2KO_GLULPS_Rep1

value: BMDM


title: Enteric neuro-glial culture; IL-13 + IFNg (24h); replicate 7

description: Library name: IL13_IFNg_7

value: Primary culture from neonatal small intestines


title: blood, Day 3, UGA4, 207

value: male

value: High Responder


title: Enteric neuro-glial culture; IL-13 + IFNg (24h); replicate 6

description: Library name: IL13_IFNg_6

value: not provided

value: Differentiated enteric neurons and glia

value: Wild-type (C57Bl/6J)


title: AP2X-1-mAID-HA_-IAA_MORC-2Ty-Rep2

description:
Library name: AP2X-1-mAID-HA_-IAA_MORC-2Ty-Rep2
Parasite of PruAP2X-1-mAID-HA-MORC-2Ty strain grown in HFF without  IAA


title: ATACseq: Setdb2KO mouse Bone-marrow derived macrophages treated with Lipopolysaccharide Rep 3

description: Library name: mm_ATACseq_BMDM_Setdb2KO_LPS_Rep3

value: LPS


title: blood, Day 3, UGA4, 424

value: Whole Blood

value: Day 3


title: AP2X-1-mAID-HA_+IAA_MORC-2Ty-Rep2

description:
Library name: AP2X-1-mAID-HA_+IAA_MORC-2Ty-Rep2
Parasite of PruAP2X-1-mAID-HA-MORC-2Ty strain grown in HFF with IAA

value: Pru

value: Parasites in HFF

value: Parasite grown in HFF with IAA


title: Enteric neuro-glial culture; IL-13 + IFNg (24h); replicate 5

description: Library name: IL13_IFNg_5

value: IL-13 + IFNg (50 ng/mL, each)


title: PruKoAP2X-1-Rep1 [ATAC-Seq]

description: Parasite of PruΔap2X-1 strain grown in HFF

data_processing:
Raw reads in fastq format were processed using fastp (v0.20.0) and clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from the raw data.
Clean reads were aligned to the ME49 genome using BWA (v0.7.12)
Only uniquely mapped (MAPQ ≥ 13) and de-duplicated reads were used for further analysis.
The peak calling was performed with MACS2 (v2.1.0) and ChIPseeker was used to retrieve the nearest genes around the peak and annotate the genomic region of the peak.
Visualization of peak distribution along genomic regions of genes of interest was performed with IGV.
Assembly: Toxoplasma gondii ME49
Supplementary files format and content: bw, bam

extract_protocol:
The ATAC-seq assay was conducted using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme Biotech, #TD701, China). Briefly, approximately 1×108 intracellular tachyzoites (Pru and PruΔap2X-1) were prepared using HFF cell monolayers in a T75 format, which was freshly scraped, gently passage through a 27-gauge needle and centrifuged at 500 × g. The tachyzoites washed twice with pre-cooled TW Buffer and lysed with pre-cooled lysis buffer on ice for 1 h to prepare the nuclei. After that the nucleir resuspended in pre-cooled tagmentation Mix (TW Buffer, 10% Tween 20, 1% Digitonin, Nuclease-free ddH2O, 5 × TTBL, TTE Mix V50) and incubated at 37 °C for 30 min in water bath. Tagmentation was stopped by adding Stop Buffer at room temperature for 5min. Then nuclei were then incubated ATAC DNA Extract Beads at room temperature for 5min, samples were plated on a magnet and unbound liquid was removed. Beads were gently rinsed twice with 80% ethanol and DNA was eluted with double-distilled water. Then the parasite nuclei were processed to construct libraries using TruePrep Index Kit V2 for Illumin from Vazyme Biotech (#TD202, China).
Libraries were sequenced on Illumina Novaseq platform at Novogene Science and Technology Co., Ltd (Beijing, China) and 150 bp paired-end reads were generated.

value: Type 2

value: Parasites in HFF without IAA


title: Enteric neuro-glial culture; IL-13 + IFNg (24h); replicate 3

description: Library name: IL13_IFNg_3


title: ATACseq: Setdb2KO mouse Bone-marrow derived macrophages treated with Lipopolysaccharide Rep 1

description: Library name: mm_ATACseq_BMDM_Setdb2KO_LPS_Rep1


title: blood, Day 3, UGA4, 335

value: female

value: Low Responder


title: ATACseq: Setdb2KO mouse Bone-marrow derived macrophages treated with Lipopolysaccharide Rep 2

description: Library name: mm_ATACseq_BMDM_Setdb2KO_LPS_Rep2

value: BMDM


title: Pru -Rep1 [ATAC-Seq]

description: Parasite of Pru strain grown in HFF


title: blood, Day 3, UGA4, 384


title: ATACseq: Setdb2KO mouse Bone-marrow derived macrophages treated with B-glucan Rep 3

description: Library name: mm_ATACseq_BMDM_Setdb2KO_GLU_Rep3

value: GLU


title: blood, Day 3, UGA4, 298

value: Non Responder


title: Enteric neuro-glial culture; IL-13 + IFNg (24h); replicate 1

description: Library name: IL13_IFNg_1

value: Primary culture from neonatal small intestines

value: not provided


title: ATACseq: Setdb2KO mouse Bone-marrow derived macrophages treated with B-glucan Rep 2

description: Library name: mm_ATACseq_BMDM_Setdb2KO_GLU_Rep2


title: blood, Day 3, UGA4, 306


title: Enteric neuro-glial culture; IL-13 (24h); replicate 9

description: Library name: IL13_9

value: Differentiated enteric neurons and glia

value: Wild-type (C57Bl/6J)


title: AP2X-1-2Ty

description: Parasite of PruAP2X-1-2Ty strain grown in HFF

data_processing:
Raw reads in fastq format were processed using fastp (v0.20.0) and clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from the raw data.
Clean reads were aligned to the ME49 genome using BWA (v0.7.12)
Only uniquely mapped (MAPQ ≥ 13) and de-duplicated reads were used for further analysis.
The peak calling was performed with MACS2 (v2.1.0) and ChIPseeker was used to retrieve the nearest genes around the peak and annotate the genomic region of the peak.
Visualization of peak distribution along genomic regions of genes of interest was performed with IGV.
Assembly: Toxoplasma gondii ME49
Supplementary files format and content: bw, bam
Library strategy: CUT&Tag

value: Parasites in HFF with IAA


title: ATACseq: Setdb2KO mouse Bone-marrow derived macrophages treated with B-glucan Rep 1

description: Library name: mm_ATACseq_BMDM_Setdb2KO_GLU_Rep1


title: AP2X-1-mAID-HA_-IAA_MORC-2Ty-Rep1

description: Parasite of PruAP2X-1-mAID-HA-MORC-2Ty strain grown in HFF without  IAA


title: blood, Day 3, UGA4, 129

value: Whole Blood

value: Day 3

value: High Responder


title: Enteric neuro-glial culture; IL-13 (24h); replicate 8

description: Library name: IL13_8


title: blood, Day 3, UGA4, 283


title: Enteric neuro-glial culture; IL-13 (24h); replicate 7

description: Library name: IL13_7


title: AP2X-1-mAID-HA_+IAA_MORC-2Ty-Rep1

description: Parasite of PruAP2X-1-mAID-HA-MORC-2Ty strain grown in HFF with IAA

value: Pru

value: Parasites in HFF


title: Pru

source_name: Parasite of Pru strain grown in HFF

extract_protocol:
Briefly, 1×10^7  intracellular tachyzoites were collected and the parasite nuclei were isolated by resuspension of the washed parasite pellet in NE Buffer. The nuclei were then processed according to the manufacturer’s protocol and libraries were constructed using ‘TD903 Hyperactive Universal CUT&Tag Assay Kit for Illumina’ and ‘TD202 TruePrep Index Kit V2 for Illumina’ from Vazyme Biotech (#TD202, China)
Libraries were sequenced on Illumina Novaseq platform at Novogene Science and Technology Co., Ltd (Beijing, China) and 150 bp paired-end reads were generated.

value: Type 2


title: ATACseq: Setdb2KO mouse Bone-marrow derived macrophages Control Rep 3

description: Library name: mm_ATACseq_BMDM_Setdb2KO_CTRL_Rep3

value: CTRL


title: blood, Day 3, UGA4, 403

value: female


title: Enteric neuro-glial culture; IL-13 (24h); replicate 6

description: Library name: IL13_6


title: ATACseq: Setdb2KO mouse Bone-marrow derived macrophages Control Rep 2

description: Library name: mm_ATACseq_BMDM_Setdb2KO_CTRL_Rep2


title: AP2X-1-6HA_Rep2

source_name: Parasite of PruAP2X-1-6HA strain grown in HFF


title: Enteric neuro-glial culture; IL-13 (24h); replicate 5

description: Library name: IL13_5


title: ATACseq: Setdb2KO mouse Bone-marrow derived macrophages Control Rep 1

description: Library name: mm_ATACseq_BMDM_Setdb2KO_CTRL_Rep1


title: AP2X-1-6HA_Rep1


title: ATACseq: Wildtype mouse Bone-marrow derived macrophages treated with B-glucan and Lipopolysaccharide Rep 3

description: Library name: mm_ATACseq_BMDM_WT_GLULPS_Rep3

value: Wildtype

value: GLULPS


title: ATACseq: Wildtype mouse Bone-marrow derived macrophages treated with B-glucan and Lipopolysaccharide Rep 2

description: Library name: mm_ATACseq_BMDM_WT_GLULPS_Rep2

value: BMDM


title: Enteric neuro-glial culture; IL-13 (24h); replicate 4

description: Library name: IL13_4


title: blood, Day 3, UGA4, 405


title: Aggresome RNA, replicate 3

city: Wuhan

first: linsen

last: pei

state: Hubei

address: Shui guohu

institute: Wuhan University

description: Library name: Aggr-3

data_processing:
Clean data was mapped to the MG1655 k12 genome using the BWA aligner software (version 0.7.17-r1188, https://github.com/lh3/bwa.git) ,Then we converted the sam files to bam files using samtool.
Assembly: E.coli MG1655 K12
Supplementary files format and content: DEG-Cytosol-Aggresome

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli MG1655

extract_protocol:
After treated with arsenite for 30 minutes, aggresome and cytosol were isolated and purified, and aggresome RNA and cytosol RNA were distributed and extracted
Library was performed accarding to the Materials and Methods section.

value: Escherichia coli MG1655

value: WT


title: Enteric neuro-glial culture; IL-13 (24h); replicate 3

description: Library name: IL13_3

value: Primary culture from neonatal small intestines

value: not provided


title: blood, Day 3, UGA4, 118

value: Low Responder


title: Aggresome RNA, replicate 2

description: Library name: Aggr-2


title: ATACseq: Wildtype mouse Bone-marrow derived macrophages treated with B-glucan and Lipopolysaccharide Rep 1

description: Library name: mm_ATACseq_BMDM_WT_GLULPS_Rep1


title: blood, Day 3, UGA4, 387

value: male

value: Non Responder


title: Aggresome RNA, replicate 1

description: Library name: Aggr-1


title: Enteric neuro-glial culture; IL-13 (24h); replicate 2

description: Library name: IL13_2

value: Differentiated enteric neurons and glia

value: Wild-type (C57Bl/6J)


title: ATACseq: Wildtype mouse Bone-marrow derived macrophages treated with Lipopolysaccharide Rep 3

description: Library name: mm_ATACseq_BMDM_WT_LPS_Rep3

value: LPS


title: Cytosol RNA, replicate 3

description: Library name: Cyto-3


title: Enteric neuro-glial culture; IL-13 (24h); replicate 1

description: Library name: IL13_1


title: blood, Day 3, UGA4, 161

value: Whole Blood

value: Day 3


title: ATACseq: Wildtype mouse Bone-marrow derived macrophages treated with Lipopolysaccharide Rep 2

description: Library name: mm_ATACseq_BMDM_WT_LPS_Rep2


title: Enteric neuro-glial culture; IL-4 (24h); replicate 9

description: Library name: IL4_9


title: blood, Day 3, UGA4, 407

value: High Responder


title: blood, Day 3, UGA4, 375


title: ATACseq: Wildtype mouse Bone-marrow derived macrophages treated with Lipopolysaccharide Rep 1

description: Library name: mm_ATACseq_BMDM_WT_LPS_Rep1


title: Enteric neuro-glial culture; IL-4 (24h); replicate 8

description: Library name: IL4_8


title: Cytosol RNA, replicate 1

description: Library name: Cyto-1


title: blood, Day 3, UGA4, 278


title: blood, Day 3, UGA4, 271


title: Cytosol RNA, replicate 2

description: Library name: Cyto-2


title: ATACseq: Wildtype mouse Bone-marrow derived macrophages treated with B-glucan Rep 3

description: Library name: mm_ATACseq_BMDM_WT_GLU_Rep3

value: GLU


title: Enteric neuro-glial culture; IL-4 (24h); replicate 6

description: Library name: IL4_6


title: blood, Day 3, UGA4, 034

value: female


title: Kcnip3 KO-5xFAD, Replicate 3

city: Mexico City

first: David

last: Valle-Garcia

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan

country: Mexico

institute: National Institute of Neurology and Neurosurgery

data_processing:
Paired-end RNA-seq reads were QC’d using fastQC v. 0.11.9
Reads were aligned against the mouse transcriptome (Ensembl annotation v99, based on mm10) with HISAT 2.1.0 using the following non-standard parameters: --no-unal –no-mixed –no-discordant
Alignments with QS <10 or falling within Encode blacklisted regions were eliminated.
Read count tables were obtained with featureCounts from the Rsubred package (2.10.5, R version 4.2.1) using the following parameters: isGTFAnnotationFile=T, useMetaFeatures=T, minMQS=10, largestOverlap=T, isPairedEnd=T, requireBothEndsMapped=T, with the Ensembl annotation v99 as reference
The read count table was analyzed with edgeR v3.38.4. Lowly expressed genes (cpm<3) were eliminated. After calculating normalization factors and estimating dispersion, differentially expressed genes between the four groups were calculated using glm modeling. Only genes with an absolute log2 fold change > 0.5 and a FDR <1e-2 were considered as DEG
Assembly: mm10
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample
Supplementary files format and content: tab-delimited txt file includes log2(TPM)  for each sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted from freshly dissected hippocampus using Trizol, following manufacturer’s instructions (these samples are the opposite hemisphere of the ones used for the proteomics analyses). Triplicates of the following genotypes were used: WT; Kcnip3 -/-; 5XFAD; 5XFAD/Kcnip3 -/-
Libraries were made using the TruSeq mRNA Library prep kit

value: hippocampus

value: Kcnip3 KO/5xFAD


title: Kcnip3 KO-5xFAD, Replicate 2


title: blood, Day 3, UGA4, 148


title: Enteric neuro-glial culture; IL-4 (24h); replicate 5

description: Library name: IL4_5


title: ATACseq: Wildtype mouse Bone-marrow derived macrophages treated with B-glucan Rep 1

description: Library name: mm_ATACseq_BMDM_WT_GLU_Rep1

value: BMDM

value: Wildtype


title: Enteric neuro-glial culture; IL-4 (24h); replicate 4

description: Library name: IL4_4

value: Primary culture from neonatal small intestines


title: blood, Day 3, UGA4, 151


title: Kcnip3 KO-5xFAD, Replicate 1


title: ATACseq: Wildtype mouse Bone-marrow derived macrophages Control Rep 3

description: Library name: mm_ATACseq_BMDM_WT_CTRL_Rep3

value: CTRL


title: Enteric neuro-glial culture; IL-4 (24h); replicate 3

description: Library name: IL4_3

value: not provided


title: 5xFAD, Replicate 3


title: blood, Day 3, UGA4, 439


title: blood, Day 3, UGA4, 411

value: male


title: Enteric neuro-glial culture; IFNg (24h); replicate 9

description: Library name: IFNg_9

value: IFNg (50 ng/mL)


title: ATACseq: Wildtype mouse Bone-marrow derived macrophages Control Rep 1

description: Library name: mm_ATACseq_BMDM_WT_CTRL_Rep1


title: ATACseq: Wildtype mouse Bone-marrow derived macrophages Control Rep 2

description: Library name: mm_ATACseq_BMDM_WT_CTRL_Rep2


title: 5xFAD, Replicate 1


title: blood, Day 3, UGA4, 177

value: Low Responder


title: RNAseq: Setdb2KO mouse Bone-marrow derived macrophages treated with B-glucan and Lipopolysaccharide Rep 3

description: Library name: mm_RNAseq_BMDM_Setdb2KO_GLULPS_Rep3

value: GLULPS


title: blood, Day 3, UGA4, 400

value: Non Responder


title: Kcnip3 KO, Replicate 3

value: Kcnip3 KO


title: Enteric neuro-glial culture; IL-4 (24h); replicate 2

description: Library name: IL4_2

value: Differentiated enteric neurons and glia

value: Wild-type (C57Bl/6J)


title: RNAseq: Setdb2KO mouse Bone-marrow derived macrophages treated with B-glucan and Lipopolysaccharide Rep 2

description: Library name: mm_RNAseq_BMDM_Setdb2KO_GLULPS_Rep2


title: 5xFAD, Replicate 2


title: Enteric neuro-glial culture; IFNg (24h); replicate 7

description: Library name: IFNg_7


title: blood, Day 3, UGA4, 077

value: Whole Blood

value: Day 3

value: High Responder


title: Kcnip3 KO, Replicate 2

value: hippocampus


title: RNAseq: Setdb2KO mouse Bone-marrow derived macrophages treated with B-glucan and Lipopolysaccharide Rep 1

description: Library name: mm_RNAseq_BMDM_Setdb2KO_GLULPS_Rep1

value: BMDM


title: ATACseq: Wildtype mouse Bone-marrow derived macrophages treated with B-glucan Rep 2

description: Library name: mm_ATACseq_BMDM_WT_GLU_Rep2

value: Wildtype

value: GLU


title: TRACK_2

description:
Library name: Sample 12
TRAnsgenic model of Cancer of the Kidney (TRACK) mouse 2

value: Kidney

value: TRACK


title: Enteric neuro-glial culture; IFNg (24h); replicate 6

description: Library name: IFNg_6

value: Primary culture from neonatal small intestines

value: not provided


title: Kcnip3 KO, Replicate 1


title: blood, Day 3, UGA4, 365

value: female


title: RNAseq: Setdb2KO mouse Bone-marrow derived macrophages treated with Lipopolysaccharide Rep 3

description: Library name: mm_RNAseq_BMDM_Setdb2KO_LPS_Rep3

value: LPS


title: Enteric neuro-glial culture; IFNg (24h); replicate 5

description: Library name: IFNg_5

value: IFNg (50 ng/mL)


title: RNAseq: Setdb2KO mouse Bone-marrow derived macrophages treated with Lipopolysaccharide Rep 2

description: Library name: mm_RNAseq_BMDM_Setdb2KO_LPS_Rep2


title: blood, Day 3, UGA4, 008


title: WT, Replicate 3

description: RNA-hipocampo-WT-C

value: WT


title: Enteric neuro-glial culture; IFNg (24h); replicate 3

description: Library name: IFNg_3

value: Differentiated enteric neurons and glia


title: WT, Replicate 2

description: RNA-hipocampo-WT-B


title: SW1990 cells, Erianin 100nM, 48h, rep2

city: Tianjin

first: Minghan

last: Qiu

state: Tianjin

address: Department of Oncology, Tianjin Union Medical Center of Nankai Univercity, 190 Jieyuan Street, Hongqiao District, Tianjin, China.

department: Department of Oncology

data_processing:
Raw reads were filtered and cleaned by fastp software.
Gene expression levels were quantified with featureCounts v2.0.1,referencing the GENCODE28 annotations.
Sequences were then aligned to the GRCh38 reference genome using STAR.
Transcript assembly and abundance estimation were performed using StringTie v2.2.1.
R was used for visualization.
Assembly: GRCh38
Supplementary files format and content: table-delimited text file includes raw counts for each sample
Supplementary files format and content: table-delimited text file includes FPKM values for each sample

source_name: cell line

growth_protocol: SW1990 cells were maintained  in DMEM, all ith 10% FBS, penicillin (100U/ml), and streptomycin (100 μg/ml) in a 5% CO2 atmosphere at 37°C.

extract_protocol:
Total RNA was extracted using TRIzol reagent
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: SW1990 cells were treated with 100nM Erianin for 48 hours, with an equal concentration of DMSO as the control.

value: cell line

value: pancreas cancer cell

value: Erianin 100nM, 48h


title: Enteric neuro-glial culture; IFNg (24h); replicate 8

description: Library name: IFNg_8

value: Wild-type (C57Bl/6J)


title: RNAseq: Setdb2KO mouse Bone-marrow derived macrophages treated with Lipopolysaccharide Rep 1

description: Library name: mm_RNAseq_BMDM_Setdb2KO_LPS_Rep1


title: WT, Replicate 1

description: RNA-hipocampo-WT-A

value: hippocampus


title: Enteric neuro-glial culture; IFNg (24h); replicate 1

description: Library name: IFNg_1


title: SW1990 cells, Erianin 100nM, 48h, rep1

institute: Tianjin Union Medical Center of Nankai Univercity


title: SW1990 cells, DMSO, 48h, rep2


title: Enteric neuro-glial culture; Control (media only); replicate 9

description: Library name: Control_9

value: Media (Control)


title: RNAseq: Setdb2KO mouse Bone-marrow derived macrophages treated with B-glucan Rep 2

description: Library name: mm_RNAseq_BMDM_Setdb2KO_GLU_Rep2

value: BMDM


title: Enteric neuro-glial culture; Control (media only); replicate 8

description: Library name: Control_8


title: Enteric neuro-glial culture; Control (media only); replicate 7

description: Library name: Control_7


title: RNAseq: Setdb2KO mouse Bone-marrow derived macrophages Control Rep 3

description: Library name: mm_RNAseq_BMDM_Setdb2KO_CTRL_Rep3

value: CTRL


title: Enteric neuro-glial culture; Control (media only); replicate 6

description: Library name: Control_6


title: Enteric neuro-glial culture; Control (media only); replicate 3

description: Library name: Control_3


title: Enteric neuro-glial culture; Control (media only); replicate 4

description: Library name: Control_4


title: RNAseq: Setdb2KO mouse Bone-marrow derived macrophages Control Rep 1

description: Library name: mm_RNAseq_BMDM_Setdb2KO_CTRL_Rep1


title: Control group, rep 1, scRNAseq

city: Philadelphia

first: Dan Dongeun

last: Huh

state: Pennsylvania

address: 210 S 33rd Street 315S Skirkanich Hall

department: Bioengineering

institute: University of Pennsylvania

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw FASTQ files containing sequence reads were pre-processed in the CellRanger pipeline (10X Genomics, v3.1.0). Reads produced from the gene expression profiling were aligned to the human GRCh38 reference genome. The feature-barcode matrices were generated using default parameters for each sample. The quality of cells was assessed based on the proportion of mitochondrial gene counts and the number of genes detected per cell. Low-quality cells were filtered out if the proportion of mitochondrial gene counts was higher than 20%. In addition, only cells with number of features larger than 200 but less than 5000 were kept for subsequent analysis to avoid capture of possible doublet or multiplet. The R package Seurat (v3.2.0) was used to filter out low-quality cells, normalize the raw counts data to account for sequencing depth, scale and identify highly variable features, cluster upon dimensionality reduction. Briefly, the gene-count matrix was first normalized by cell-specific size factor, log-transformed, and then scaled to unit variance and zero mean. Samples from the same experiment were integrated for cell type identification and direct comparisons. Principal components were calculated using the data decomposition technique of Latent Semantic Indexing (LSI) and used to reduce the dataset into two dimensions. Unsupervised hierarchical clustering of cells was generated and visualized using Uniform Manifold Approximation and Projection (UMAP) in Seurat.
Assembly: Human genome GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Microengineered lung tumor infused with CAR T cells

extract_protocol:
The tumor constructs were carefully separated from the stroma and then removed and pooled together for subsequent processing. The sample suspension was digested using a tumor digestion buffer (TTDR, BD Horizon) according to the manufacturer’s instructions and incubated on a rocker in a cell culture incubator for one hour with vigorous pipetting every 10 minutes. The same digestion buffer was added to the microdevices without the tumor constructs to digest the stroma gels, which were separately collected and pooled together to obtain single cell suspensions. All cell suspensions were passed through 70 µm nylon mesh cell strainers to remove undigested clusters and multiplets.
The isolated cells were collected and washed with PBS, and then loaded onto a Chromium Single Cell Chip (10x Genomics) according to the manufacturer’s instructions for co-encapsulation with barcoded beads. The capture of RNA transcripts in the barcoded cells and reverse transcription of cDNA were performed using the manufacturer’s standard protocols. The Agilent TapeStation High Sensitivity D5000 ScreenTape was used for QC of generated cDNA. The barcoded cDNA was converted into single-cell RNA-seq libraries for sequencing using the Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics) according to the manufacturer’s instructions. The Agilent TapeStation High Sensitivity D1000 ScreenTape was used for QC of prepared libraries for sizing (bp) and concentration. The final libraries were pooled together and sequenced by Illumina NovaSeq sequencer with a SP v1.5 FlowCell (100 cycles).

value: epithelial cells, fibroblasts, endothelial cells, T cells


title: Meso group, rep 1, scRNAseq

description: 10x Genomics

value: Microengineered lung tumor infused with CAR T cells

value: A549 overexpressing mesothelin


title: Mesothelioma explant group, rep 1, scRNAseq

description: 10x Genomics

source_name: Microengineered mesothelioma tumor infused with CAR T cells


title: 4T1 cells, fully edited, gene expression library

city: Cambridge

first: Kathryn

last: Yost

state: Massachusetts

address: 455 Main St

department: Biology

institute: Whitehead Institute

description: Library name: PEtracer_4T1_fully_edited_GEX

data_processing:
All scRNA-seq data was processed using the Cellranger software package (version 7.1.0). To capture lineage information a custom reference genome was constructed by appending the 2171 lineage tracing cassette sequences to the human hg38 genome build. Both gene expression and lineage tracing cassette libraries were then aligned to this reference using default parameters. Since the reference contains all 2171 30bp barcode sequences the integration barcode (intBC) of each lineage tracing cassette read can be determined based on which element in the reference it aligns to. A custom Python script was used to extract lineage information from the bam alignment file generated by Cellranger. This script iterated through all reads aligned to a tracing cassette sequence. For each read the lineage mark (LM) sequence at each edit site was determined based on the alignment. For each UMI the number of supporting reads was calculated and the LM for each site set to the LM with the most read support (ties broken randomly). UMIs were then aggregated by intBC, cellBC, and the set of LMs detected across the three edit sites to generate a final LM table. scRNA-seq data for puromycin and blasticidin barcode libraries was aligned using Cellranger to a custom reference. This reference included puromycin and blasticidin resistance cassette sequences with ‘N’s indicating the positions of the 10nt random barcodes. A custom Python script was used to extract the barcode sequence from each read aligned to these elements, generate a consensus barcode for each UMI, and aggregate UMIs by barcode for each cell. To separate barcode calls corresponding to real integrations from sequencing errors and ambient RNA, for each 10x capture a Gaussian mixture model was fitted to the distribution of UMIs per barcode per cell. Barcode calls corresponding to the lower peak were excluded as likely errors. pegRNA libraries were processed using the “CRISPR Guide Capture” feature of Cellranger. pegRNA protospacer mismatch calls supported by <3 UMIs were filtered out and careful quality control performed to exclude cells with multiple pegRNA integrations as these cells could confound our estimation of protospacer mismatch kinetics. Cells with multiple pegRNA calls were removed as well as cells with lineage cassette reads where more than one edit site had an LM installed.
Assembly: mm10
Supplementary files format and content: Processed data barcodes/features/matrix and filtered_counts.h5 files contain the filtered_feature_bc_matrix transcript count matrix outputs from Cellranger. BlastBC_counts.csv, PuroBC_counts.csv, allele_counts.csv, and mapping_counts.csv files contain unfiltered static barcode, lineage tracing cassette allele, and intBC mapping count data.

extract_protocol:
Single cell suspensions were washed with PBS + 0.04% BSA and captured using the 10X Genomics Next GEM Single Cell 3ʹ Kit v3.1
Gene expression libraries were prepared using the 10X Genomics Next GEM Single Cell 3ʹ Kit v3.1 according to the manufacturer's instructions. Targeted lineage tracing cassette, puromycin/blasticidin barcode, and pegRNA libraries were prepared from amplified cDNA using two or three rounds of PCR with target-specific amplification primers and sample indexing primers.


title: RNAseq: Wildtype mouse Bone-marrow derived macrophages treated with B-glucan and Lipopolysaccharide Rep 3

description: Library name: mm_RNAseq_BMDM_WT_GLULPS_Rep3

value: Wildtype

value: GLULPS


title: Enteric neuro-glial culture; Control (media only); replicate 1

description: Library name: Control_1

value: Primary culture from neonatal small intestines

value: not provided


title: Ileal muscularis ILC2s; cKO; replicate 4; H. polygyrus (7 d.p.i.)

description: Library name: Musc_ILC2_cKO_4

data_processing:
After sequencing, the Terra platform was used to run Cumulus (Li B, et al. Nat Methods. 2020.) and broadinstitute_gtex workflows: cumulus/bcl2fastq (V.5) was used for demultiplexing BCL files into individual libraries, broadinstitute_gtex/fastqc_v1-0_BETA (V.2) was used for quality control of fastq files, and broadinstitute_gtex/rnaseq_fastq_star_rsem_rnaseqc_v1-2_BETA was used for STAR alignment (Dobin, et al. Bioinformatics. 2013.) against the mouse reference genome (GRCm38 / mm10) and transcript quantification with RSEM (Li B, et al. BMC Bioinformatics. 2011.). RSEM expected count data was used to generate count matrices and expected counts were rounded to the nearest whole number. Samples with fewer than 1 million reads were excluded from analysis.
For data visualized in associated manuscript, DESeq2 (Love MI, et al. Genome Biol. 2014.) was used to perform differential gene expression analysis based on the negative binomial distribution. DESeq2 Log10(adjusted p-values) and Log2(fold-change) were used to generate volcano plots, and normalized counts of biological replicates from the DESeq2 object were used to plot individual gene expression. Prism v9 was used to generate volcano plots and DESeq2-normalized gene expression scatter and box plots.
Assembly: GRCm38 / mm10
Supplementary files format and content: .csv file of count matrix and gene annotations

source_name: Small intestinal muscularis propria (ileum)

extract_protocol:
Mice were euthanized by CO2 narcosis and perfused with PBS through the left ventricle. The distal 12-centimeters of small intestines were dissected on ice, cut longitudinally along the mesenteric border, and laid flat (luminal side down) on C-fold towels dampened with ice-cold holding buffer (HBSS without Ca2+ and Mg2+, 5% FCS, 10mM HEPES) on a metal tray in an ice bucket. Muscularis propria were isolated from lamina propria by stereomicroscope-aided microdissection performed on an ice-cold metal block lined with buffer-dampened C-fold towels, rinsed 2-3x in holding buffer to limit epithelial cell contaminants, and processed separately from lamina propria samples. The lamina propria samples were stripped of epithelial cells by sequential washing and occasional vortexing in ice-cold IEC isolation buffer with DTE (HBSS without Ca2+ and Mg2+, 5% FCS, 10mM HEPES, 5mM EDTA, 1mM DTE) followed by 2-3 additional washes of the same buffer without DTE, and finally rinsed with PBS without EDTA. Both the muscularis and lamina propria samples were separately minced with scissors and digested in digestion buffer (HBSS with Ca2+ and Mg2+, 5% FCS, 10mM HEPES, 100 μg mL-1 DNase I, Liberase TL enzyme) for 15-30 minutes at 37°C in flasks with stir-bars spinning at 550 rpm. Liberase TL concentrations of 100 μg mL-1 and 200 μg mL-1 were used for muscularis and lamina propria samples, respectively. After digestion, samples were gently triturated with 3-5 passes through an 18G needle attached to a syringe and single-cell suspensions were strained through 40μm nylon meshes, washed, and further processed for FACS purification. ILC2s were defined as viability dye-negative, singlet, CD45+, CD90.2+, Lineage(Ter119, NK1.1, B220, CD19, CD3e)-negative, KLRG1+ cells and sorted on a FACSAria II sorter (BD Biosciences). Between 215 to 2,000 FACS-purified ILC2s (depending on the cellular recovery from each tissue) were sorted directly into 5 μL of Buffer TCL (Qiagen) supplemented with 1% β-mercaptoethanol (Sigma-Aldrich), vortexed, spun down, snap-frozen on dry ice, and stored in -80C until further processing.
A modified version of the SMART-Seq2 protocol (Picelli, et al. Nat Protoc. 2014.) was applied to generate full-length transcriptomic data from low-input samples—processed by the Klarman Cell Observatory and the Broad Institute Genomics Platform (GP). Briefly, FACS-purified cells were lysed in 5 μL of Buffer TCL (Qiagen) supplemented with 1% β-mercaptoethanol (Sigma-Aldrich) and snap-frozen until ready for processing. RNA from lysate was cleaned-up using Agencourt RNAClean XP SPRI magnetic beads (Beckman Coulter, A63987) and first strand cDNA synthesis was performed using Maxima H-minus Reverse Transcriptase (Thermo Fisher Scientific, EP0753) and amplified using KAPA HiFi HotStart PCR ReadyMix (KAPA Biosystems, KK2602). cDNA concentration was assessed using Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) and subsequently normalized to 0.25 ng μL-1. Library preparation was performed using the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096), confirmed to have a size of 500 bp using a BioAnalyzer (Agilent), and pooled libraries were normalized to 2nM and denatured using 0.1 N NaOH prior to sequencing. Flow cell cluster amplification and sequencing were performed according to the manufacturer’s protocols using the paired-end Illumina sequencing (2 x 38 bp) with 75 cycle Nextseq 500 high output V2 kit (Illumina). Two rounds of sequencing were performed to generate sufficient read depth.

treatment_protocol: Calb2-cre; Il13ra1 flox/flox (Calb2ΔIl13ra1) cKO mice (n = 4) and littermate control Il13ra1 flox/flox mice (n = 5) were administered 200 L3 H. polygyrus larvae by oral gavage and euthanized at 7 d.p.i.

value: 19 weeks 2 days

value: Male

tag: well

value: Muscularis ILC2s

value: Calb2 cre/+; Il13ra1 flox/flox (cKO)

value: 200 L3 H. polygyrus larvae


title: RNAseq: Setdb2KO mouse Bone-marrow derived macrophages treated with B-glucan Rep 1

description: Library name: mm_RNAseq_BMDM_Setdb2KO_GLU_Rep1

value: GLU


title: RNAseq: Wildtype mouse Bone-marrow derived macrophages treated with B-glucan and Lipopolysaccharide Rep 2

description: Library name: mm_RNAseq_BMDM_WT_GLULPS_Rep2


title: RNAseq: Setdb2KO mouse Bone-marrow derived macrophages treated with B-glucan Rep 3

description: Library name: mm_RNAseq_BMDM_Setdb2KO_GLU_Rep3


title: VPL/VPM, Coll-3, Days 14

city: ZHENGZHOU

first: Sen

last: Zhao

state: HENAN

address: 100 Science Avenue

institute: ZHENGZHOU UNIVERSITY

data_processing:
Quality Control: Quality assessment of raw reads was performed using FastQC. Reads containing adapter sequences and low-quality reads (those with >10% N bases or >50% bases with quality score Q≤10) were removed to obtain high-quality Clean Data.
Alignment: Clean Reads were aligned to the reference genome (Mus_musculus.GRCm38_release95.genome.fa) using HISAT2 (version 2.2.1), with alignment efficiency ranging between 96.26% and 97.17%. Only Mapped Reads aligned to the reference genome were retained.
Expression Quantification: Gene expression levels were quantified using StringTie, which assembled the transcripts and calculated FPKM values for each gene.
Differential Expression Analysis: Differential expression analysis was conducted using DESeq2 (for samples with biological replicates) with Fold Change ≥2 and FDR as the criteria, generating a list of differentially expressed genes.
Functional Annotation and Enrichment Analysis: Differentially expressed genes were annotated to GO and KEGG databases for functional enrichment analysis, providing insights into biological processes, molecular functions, and cellular components.
Assembly: Mus_musculus.GRCm38_release95.genome.fa
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each sample

source_name: VPL/VPM

extract_protocol:
Use the SteadyPure Universal RNA Extraction Kit (AG, China) to extract RNA from VPL/VPM tissues. RNA with a concentration greater than 2 nM is used for subsequent sequencing libraries.
(1) Enrich eukaryotic mRNA using magnetic beads with Oligo (dT); (2) Add Fragmentation Buffer to randomly fragment the mRNA; (3) Use mRNA as a template to synthesize the first cDNA strand with random hexamer primers, then add buffer, dNTPs, RNase H, and DNA polymerase I to synthesize the second cDNA strand, and purify the cDNA using AMPure XP beads; (4) The purified double-stranded cDNA is then end-repaired, A-tailed, and ligated to sequencing adapters, followed by size selection using AMPure XP beads; (5) Finally, enrich the cDNA library through PCR.

treatment_protocol: Using a stereotaxic device, we injected 10 nL of type IV collagenase (sigma) or saline into the right VPL/VPM of mice. After fourteen days, the mice were anesthetized with 3% isoflurane. We then promptly dissected the VPL/VPM brain tissues and preserved them in liquid nitrogen to prevent RNA degradation.

value: VPL/VPM

value: WT

value: collagenase IV


title: VPL/VPM, Coll-2, Days 14


title: RNAseq: Wildtype mouse Bone-marrow derived macrophages treated with B-glucan and Lipopolysaccharide Rep 1

description: Library name: mm_RNAseq_BMDM_WT_GLULPS_Rep1

value: BMDM


title: Ileal muscularis ILC2s; cKO; replicate 3; H. polygyrus (7 d.p.i.)

description: Library name: Musc_ILC2_cKO_3

value: Small intestinal muscularis propria (ileum)


title: RNAseq: Wildtype mouse Bone-marrow derived macrophages treated with Lipopolysaccharide Rep 3

description: Library name: mm_RNAseq_BMDM_WT_LPS_Rep3

value: LPS


title: SW1990 cells, DMSO, 48h, rep1

value: cell line

value: pancreas cancer cell


title: Ileal muscularis ILC2s; cKO; replicate 2; H. polygyrus (7 d.p.i.)

description: Library name: Musc_ILC2_cKO_2

value: Female


title: VPL/VPM, Coll-1, Days 14


title: Biol Rep 2 – Ws

city: Cuernavaca

first: Gustavo

last: Rodriguez-Alonso

state: Morelos

address: Av.Universidad 2001, Col. Chamilpa

department: Biología Molecular de Plantas

institute: Instituto de Biotecnología

description: Raw reads of whole root from 10dpg seedlings of the WS genotype

data_processing:
The raw reads were analyzed with FastQC, trimmed and processed to discard bases with low-confindence value. Reads shorter than 35 nt were discarded. The processed reads were mapped against the Arabidopsis reference genome (TAIR10). RPKM value for each gene was obtained from mapping counts by using CLC Genomics workbench v 7.5.
Assembly: TAIR10
Supplementary files format and content: Count data was prepared as a csv file containing RPKM values.

organism: Arabidopsis thaliana

source_name: Whole root

growth_protocol: All plants were grown at 21°C, under a 16/8 h light/dark photoperiod with a light intensity of 105 μmol photons m–2 s–1 on vertical petri dishes with LS growth medium supplemented with vitamins.

extract_protocol:
Total RNA was extracted from 8-10 dpg roots of Wt and atx1setm seedlings using TRIzol reagent (Invitrogen-Thermo Fisher Scientific, Waltham, MA, USA), according to the manufacturer's instructions.
Library was constructed at BGI-Hong Kong, following the Illumina Library Preparation protocol.
RNA-Seq was carried out on roots of the atx1setm and the Wt of 10 dpg plants (two biological replicates). Library preparation was done at BGI-Tech, Hong Kong. Moreover, 50 cycles of single-end sequencing were achieved on HiSeq 2000 (Illumina) platform.

value: Whole root


title: Biol Rep 1 – Ws


title: Ileal muscularis ILC2s; cKO; replicate 1; H. polygyrus (7 d.p.i.)

description: Library name: Musc_ILC2_cKO_1


title: VPL/VPM, Saline-2, Days 14

value: Saline


title: RNAseq: Wildtype mouse Bone-marrow derived macrophages treated with Lipopolysaccharide Rep 1

description: Library name: mm_RNAseq_BMDM_WT_LPS_Rep1

value: Wildtype


title: Biol Rep 2 – Setm

description: Raw reads of whole root from 10dpg seedlings of the atx1setm genotype


title: Ileal muscularis ILC2s; Control; replicate 5; H. polygyrus (7 d.p.i.)

description: Library name: Musc_ILC2_Control_5

value: 19 weeks 2 days

value: Male

value: Il13ra1 flox/flox (control)


title: VPL/VPM, Saline-1, Days 14


title: Biol Rep 1 – Setm


title: Ileal muscularis ILC2s; Control; replicate 4; H. polygyrus (7 d.p.i.)

description: Library name: Musc_ILC2_Control_4

value: Muscularis ILC2s

value: 200 L3 H. polygyrus larvae


title: DBLab_ChIP_seq_delta_anti_SegB_2

city: York

first: Daniela

last: Barilla`

address: Wentworth Way

country: United Kingdom

institute: University of York

data_processing:
Sequence reads were mapped to the S. solfataricus P2 genome (NCBI Reference Sequence: NC_002754) with Bowtie 1.0.0-5 (Langmead et al 2009 PMID: 19261174) using the following command:   bowtie -m 1 -n 1 --best --strata -p 4 --chunkmbs 512 NC_002754_bowtie --sam *.fastq > output.sam  Samtools 0.1.19-1 and Bedtools 2.17.0-1 (Li et al 2009 PMID:  19505943, Quinland et al 2010 PMID: 20110278) were used to compute and extract the sequencing coverage using the following command:  samtools faidx NC_002754.fna  samtools import NC_002754.fna.fai *.sam output.bam  samtools sort output.bam output.sorted  samtools index output.sorted.bam  bedtools genomecov -d -ibam output.sorted.bam -g NC_002754.fna > coverage_output.txt
Peak calling - Homer v4.9.1
Genome_build: NC_002754
Supplementary_files_format_and_content: Files ending with _coverage.txt: tab-delimited text file of nucleotide-resolution coverage from ChIP-seq data (column 1: genome ID, column 2: nucleotide position, column 3: coverage)

organism: Saccharolobus solfataricus P2

source_name: Sulfolobus solfataricus P2

growth_protocol: S. solfataricus P2, PBL2025 and ∆Sso_segB strains were grown at 75 °C in 200 ml Brock media, pH 3.0 and supplemented with 0.1% of tryptone. When the cells reached mid-exponential growth phase (OD600nm 0.4 – 0.6), the cultures were taken from 75 °C and cooled down at room temperature before cross-linking with 1% formaldehyde, shaking at 37 °C for 30 minutes. The cross-linked reactions were stopped by adding 125 mM glycine and incubated at 37 °C, shaking for further 15 minutes.

extract_protocol:
DNA was purified from samples using PCR purification kit (Qiagen) and eluted in 40 µl 0.1 x EB buffer (Qiagen).
To construct ChIP-Seq libraries, NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs). Standard library construction for Illumina Miseq (paired end 75bp reads) or Hiseq3000 (paired end 150 bp reads) sequencing platform

treatment_protocol:
Exponentially-growing cells were crosslinked with 1% formadehyde, washed 3 times with 1x PBS then resuspended in 1 ml of Buffer 1 (20 mM HEPES pH 7.9, 50 mM KCl, 10 % glycerol plus EDTA-free protease inhibitors). Cells were then sonicated to shear the DNA. Sample was incubated  with polyclonal anti-SegB rabbit antibodies. Crosslinked products were reversed and DNA was purified.
Exponentially-growing cells were crosslinked with 1% formadehyde, washed 3 times with 1x PBS then resuspended in 1 ml of Buffer 1 (20 mM HEPES pH 7.9, 50 mM KCl, 10 % glycerol plus EDTA-free protease inhibitors). Cells were then sonicated to shear the DNA. Sample was incubated with polyclonal anti-SegB rabbit antibodies. Crosslinked products were reversed and DNA was purified (Detailed protocols are listed in the Supplementary Materials)

tag: developmental stage

value: No synchronization, mixed population of cells, exponential phase

tag: antibody

value: SegB


title: RNAseq: Wildtype mouse Bone-marrow derived macrophages treated with B-glucan Rep 2

description: Library name: mm_RNAseq_BMDM_WT_GLU_Rep2

value: GLU


title: DBLab_ChIP_seq_delta_anti_SegB_1


title: Ileal muscularis ILC2s; Control; replicate 3; H. polygyrus (7 d.p.i.)

description: Library name: Musc_ILC2_Control_3


title: Col-0, Time 60 min, replicate 3

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

country: Brazil

institute: University of São Paulo (ESALQ/USP)

description: Library name: UR033

data_processing:
Read quality was assessed using FastQC version 0.11.8, and low-quality reads and adapter sequences were removed with Trimmomatic version 0.36. The resulting high-quality reads were then aligned to the TAIR10 reference genome using HISAT2 version 2.2.0, and raw read counts were quantified using the featureCounts function from the Sub-read package version 2.0.0.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: leaf

growth_protocol: Seeds were sown on Sungro Propagation Mix Question soil and placed in 4°C cold room for 3 days prior to being transferred to a short-day growth room with 23°C/19°C day/night temperatures and 45% humidity. Plants were watered weekly and placed in random block design to reduce the impact of environmental factors.

extract_protocol:
RNA extraction was performed using TRIzol reagent
Libraries were prepared using using the TruSeq RNA library prep kit (Illumina) according to the manufacturer’s protocol.

value: leaf

tag: ecotype

value: wild-type


title: RNAseq: Wildtype mouse Bone-marrow derived macrophages Control Rep 2

description: Library name: mm_RNAseq_BMDM_WT_CTRL_Rep2

value: BMDM

value: CTRL


title: VPL/VPM, Saline-3, Days 14

value: VPL/VPM

value: WT


title: RNAseq: Wildtype mouse Bone-marrow derived macrophages treated with Lipopolysaccharide Rep 2

description: Library name: mm_RNAseq_BMDM_WT_LPS_Rep2

value: LPS


title: Ileal lamina propria ILC2s; cKO; replicate 4; H. polygyrus (7 d.p.i.)

description: Library name: LP_ILC2_cKO_4

source_name: Small intestinal lamina propria (ileum)

value: Small intestinal lamina propria (ileum)

value: LP ILC2s

value: Calb2 cre/+; Il13ra1 flox/flox (cKO)


title: Col-0, Time 60 min, replicate 1

description: Library name: UR031


title: Ileal lamina propria ILC2s; cKO; replicate 3; H. polygyrus (7 d.p.i.)

description: Library name: LP_ILC2_cKO_3

value: 19 weeks 2 days

value: Male


title: RNAseq: Wildtype mouse Bone-marrow derived macrophages Control Rep 1

description: Library name: mm_RNAseq_BMDM_WT_CTRL_Rep1

value: Wildtype


title: Col-0, Time 30 min, replicate 3

description: Library name: UR024


title: female_Cdel_4_S20_R1_001

city: Suita

first: Yasunori

last: Shintani

state: Osaka

address: 6-1, Kishibe Shimmachi

department: Molecular Pharmacology

country: Japan

institute: National Cerebral and Cardiovascular Center

description: Library name: female_Cdel_4_S20_R1_001

data_processing:
Sequenced reads were mapped to the mouse reference genome sequence (GRCm38_p6). BAM files were then each converted into one integrated count file using FeatureCounts (ver 2.0.0).
Assembly: GRCm38_P6
Supplementary files format and content: Tab-delimited text file including raw_counts

source_name: skeletal muscle

extract_protocol:
RNA was isolated from mice hearts using RNeasy fibrous kit (QIAGEN)
Libraries were prepared for sequencing using a TruSeq Stranded mRNA sample prep kit (Illumina) according to the manufacturer's instructions.

value: skeletal muscle

tag: strain

value: female

value: c-del


title: Ileal lamina propria ILC2s; cKO; replicate 2; H. polygyrus (7 d.p.i.)

description: Library name: LP_ILC2_cKO_2

value: Female

value: 200 L3 H. polygyrus larvae


title: Col-0, Time 30 min, replicate 2

description: Library name: UR023

value: leaf

value: wild-type


title: Ileal lamina propria ILC2s; cKO; replicate 1; H. polygyrus (7 d.p.i.)

description: Library name: LP_ILC2_cKO_1


title: Col-0, Time 30 min, replicate 1

description: Library name: UR022


title: Ileal lamina propria ILC2s; Control; replicate 5; H. polygyrus (7 d.p.i.)

description: Library name: LP_ILC2_Control_5

value: Il13ra1 flox/flox (control)


title: Col-0, Time 0, replicate 3

description: Library name: UR014


title: RNAseq: Wildtype mouse Bone-marrow derived macrophages treated with B-glucan Rep 3

description: Library name: mm_RNAseq_BMDM_WT_GLU_Rep3

value: BMDM

value: GLU


title: female_Cdel_3_S19_R1_001

description: Library name: female_Cdel_3_S19_R1_001


title: RNAseq: Wildtype mouse Bone-marrow derived macrophages Control Rep 3

description: Library name: mm_RNAseq_BMDM_WT_CTRL_Rep3

value: CTRL


title: RNAseq: Wildtype mouse Bone-marrow derived macrophages treated with B-glucan Rep 1

description: Library name: mm_RNAseq_BMDM_WT_GLU_Rep1


title: Col-0, Time 60 min, replicate 2

description: Library name: UR032


title: Col-0, Time 0, replicate 2

description: Library name: UR013


title: Ileal muscularis ILC2s; Control; replicate 2; H. polygyrus (7 d.p.i.)

description: Library name: Musc_ILC2_Control_2

value: Small intestinal muscularis propria (ileum)

value: Muscularis ILC2s


title: female_control_3_S16_R1_001

description: Library name: female_control_3_S16_R1_001

value: mock


title: Ileal muscularis ILC2s; Control; replicate 1; H. polygyrus (7 d.p.i.)

description: Library name: Musc_ILC2_Control_1

value: 19 weeks 2 days


title: SNL-rep 3

city: Guangzhou

first: Xiao-Long

last: Zhang

address: 106 Zhongshan 2nd Road

institute: Guangdong Provincial People’s Hospital

description: Library name: sample-15

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Dorsal root ganglion

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dorsal root ganglion

value: WT

value: Spinal nerve ligation (SNL)


title: Ileal lamina propria ILC2s; Control; replicate 3; H. polygyrus (7 d.p.i.)

description: Library name: LP_ILC2_Control_3

value: Small intestinal lamina propria (ileum)

value: LP ILC2s


title: SNL-rep 2

description: Library name: sample-14


title: female_control_2_S15_R1_001

description: Library name: female_control_2_S15_R1_001

value: skeletal muscle

value: female


title: Ileal lamina propria ILC2s; Control; replicate 2; H. polygyrus (7 d.p.i.)

description: Library name: LP_ILC2_Control_2

value: Female

value: 200 L3 H. polygyrus larvae


title: SNL-rep 1

description: Library name: sample-13


title: female_control_1_S14_R1_001

description: Library name: female_control_1_S14_R1_001


title: PTX-rep 3

description: Library name: sample-12

value: Paclitaxel (PTX)


title: Cdel_S8_R1_001

description: Library name: Cdel_S8_R1_001

value: male

value: c-del


title: female_Cdel_1_S17_R1_001

description: Library name: female_Cdel_1_S17_R1_001


title: female_Cdel_2_S18_R1_001

description: Library name: female_Cdel_2_S18_R1_001


title: NOD-lymphnode-vehicle-mouse6rep10

city: Indianapolis

first: Carmella

last: Evans-Molina

state: Indiana

address: 16 Tech Innovation Bldg 1; 1210 Waterway Blvd Ste 4100

department: Pediatrics

institute: Indiana University School of Medicine

data_processing:
Fastq files were processed to dcc files using GeoMx NGS pipeline software. Using the dcc files, spatial transcriptomics analysis was conducted in R studio v4.2.1 using the GeomxTools 3.4.0 package
The GeoMx whole mouse transcriptome atlas was used as the probe assay metadata
Sequencing quality was assessed using the default quality control (QC) parameter cut-offs, namely: minimum number of reads (1000); minimum percentage of reads trimmed (80%), stitched (80%), and aligned (80%); sequencing saturation (50%); negative control counts (10); maximum counts observed in no treatment control (NTC) well (1000); minimum number of nuclei estimated (100); and minimum segment area (5000). Any ROI that did not satisfy the above criteria was removed as part of QC filtering.
Following segment QC, probe QC was also performed to remove any outlier either globally or locally before generating gene-level count data.
The limit of quantification was determined per segment using the value recommended in the workflow, and segments with less than 1-5% of genes detected were removed. Furthermore, only genes that were detected in at least 1% of segments were retained.
The data was normalized using the quartile 3 method and log transformed.
For each organ, a linear mixed model without random slope was used to identify differentially expressed genes between vehicle and treatment groups for both the 3- and 7-day timepoints. Genes with linear scale fold change ³ 1.5 and p-value < 0.05 were considered as differentially expressed.
Assembly: GeoMx mouse whole transcriptome assay v1
Supplementary files format and content: .dcc files = Digital count conversion file (dcc file)
Supplementary files format and content: Rawcounts_LCMV.txt = raw counts for LCMV mouse dataset
Supplementary files format and content: q3 normalized counts_LCMV.txt = q3 normalized and log transformed values for LCMV mouse dataset
Supplementary files format and content: Rawcounts_NOD.txt = raw counts for NOD mouse dataset
Supplementary files format and content: q3 normalized counts_NOD.txt = q3 normalized and log transformed values for NOD mouse dataset
Library strategy: Spatial transcriptomics

source_name: lymph node

growth_protocol: RIP-LCMV-GP mice were purchased from Jackson Laboratory and bred in-house. Five-week-old female NOD/ShiLT mice were purchased from Jackson Laboratory and acclimated at the IU Laboratory Animal Research Center (LARC) for at least one week prior to treatment.

extract_protocol:
Mouse pancreas sections (5 µm) were fixed, sectioned, and mounted on positively charged slides. The slideswere deparaffinized, heated in antigen retrieval solution (Thermo Fisher Scientific) at 100 °C for 20 min, and treated with 1 µg/mL proteinase K at 37 °C for 15 min. Mouse transcriptomics was visualized using the GeoMx mouse whole transcriptome atlas (NanoString Technologies, GMX-RNA-NGS-MsWTA). An overnightin situhybridization was performed with a mouse WTA probe, and the next day, the slides were washed twice at 37 °C for 25 min with 50% formamide/2X SSC buffer to remove unbound probes. The slides were then washed twice with 2X SSC buffer for 2 minutes at RT and blocked with blocking buffer containing Buffer W (Nanostring) with 1% Fc-Receptor blocker (Milteny) and 5% Normal Donkey Serum (Jackson Laboratories) as described previously (98). The slides were incubated with guinea pig anti-insulin (Dako), 1:200 rabbit anti-CD3 (Abcam), mouse anti-CD68 (Santa Cruz).The slides were washed twice with 2xSSC and incubated with secondary antibodies (1:400 goat-anti-guinea pig Alexa-488; 1:200 goat-anti rabbit Alexa-594 and 1:200 goat-anti mouse Alexa-647) for 30 minutes. Then, the slides were washed four times with 2xSSC for 3 minutes and counter-stainedwith 1:20,000 Syto83 (Invitrogen) for 1 h at room temperature. Stained slides were loaded onto the GeoMx instrument and scanned. After visual inspection using the GeoMx Digital Spatial Profiler (DSP; NanoString Technologies), geometrical ROIs (100 μm diameter) with different histologies were selected for oligonucleotide collection. Photocleaved oligonucleotides from each spatially resolved ROI were sequenced with the Illumina NextSeq500 sequencer (Illumina).
The GeoMx libraries were prepared according to the GeoMx DSP NGS Readout User Manual. Briefly, for each plate, 4 μl of a GeoMx DSP sample was used for amplification. Each GeoMx DSP sample in a well was uniquely indexed with dual indexes. 4 μL of each resulting PCR product, including the NTC negative control, were pooled and purified with AMPure XP beads (Beckman Coulter). The final libraries were qualified and quantified using TapeStation and Qubit, respectively. The libraries were sequenced on an Illumina NextSeq 500 to generate 27 bp paired-end sequence reads.

treatment_protocol: Eight-week-old maleRIP-LCMV-GPmice werepre-treated with TYK2i (BMS-986202, 30 mg/kg) or vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse) by oral gavage two days prior to inoculation with LCMV. Mice continued to receive TYK2i treatment daily until the study endpoint. Six-week-old female NOD mice were treated with BMS-986202 (30 mg/kg) or vehicle for 6 weeks by oral gavage.Themice from each group were euthanized after 6 weeks of TYK2i treatment (12-weeks of age), and the pancreas was harvested and fixed for downstream analysis as described previously(80).

tag: mouse number

value: lymph node

tag: roi

value: NOD/ShiLT

value: 6-week old


title: PTX-rep 2

description: Library name: sample-11

tag: tissue


title: Ileal lamina propria ILC2s; Control; replicate 4; H. polygyrus (7 d.p.i.)

description: Library name: LP_ILC2_Control_4

tag: Sex

value: Il13ra1 flox/flox (control)


title: PTX-rep 1

description: Library name: sample-10


title: Cdel_S6_R1_001

description: Library name: Cdel_S6_R1_001


title: NOD-pancreas-vehicle-mouse6rep13

source_name: pancreas

value: pancreas

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: LLC-rep 3

description: Library name: sample-9

value: Dorsal root ganglion

value: WT

value: Lewis lung carcinoma (LLC)


title: NOD-pancreas-vehicle-mouse6rep14


title: Cdel_S5_R1_001

description: Library name: Cdel_S5_R1_001


title: LLC-rep 2

description: Library name: sample-8


title: Col-0, Time 0, replicate 1

description: Library name: UR012

value: leaf

tag: time

value: wild-type


title: Ileal lamina propria ILC2s; Control; replicate 1; H. polygyrus (7 d.p.i.)

description: Library name: LP_ILC2_Control_1

value: Small intestinal lamina propria (ileum)

value: 19 weeks 2 days

value: LP ILC2s


title: mock_S4_R1_001

description: Library name: mock_S4_R1_001

value: skeletal muscle

value: mock


title: NOD-pancreas-vehicle-mouse6rep11

value: Female


title: mock_S3_R1_001

description: Library name: mock_S3_R1_001

value: male


title: NOD-pancreas-vehicle-mouse6rep12

value: NOD/ShiLT


title: LLC-rep 1

description: Library name: sample-7


title: Cdel_S7_R1_001

description: Library name: Cdel_S7_R1_001

value: c-del


title: mock_S2_R1_001

description: Library name: mock_S2_R1_001


title: NOD-pancreas-vehicle-mouse6rep9

value: 6-week old


title: CFA-rep 3

description: Library name: sample-6

value: Complete Freund's adjuvant (CFA)


title: CFA-rep 2

description: Library name: sample-5


title: NOD-pancreas-vehicle-mouse6rep10

value: pancreas

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: NOD-pancreas-vehicle-mouse7rep7


title: Naïve-rep 3

description: Library name: sample-3

value: Dorsal root ganglion

value: WT

value: No treatment


title: TLQP21_4

first: Huang

last: Shuying

address: 中国广州市中山二路74号中山大学广州校区北校园

institute: Sun Yat-Sen University

data_processing:
RNA quantification and qualification: Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Library preparation for Transcriptome sequencing: Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.
Quality Control: In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.
Clustering and sequencing: After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.
Reads mapping to the reference genome: 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) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genes with counts < 5 in more than 70% of samples were classified as low-expression genes and excluded from further analysis. Normalization of the reads and the analysis of differentially expressed genes (DEGs) were performed using DESeq2 (version 1.32.0) in R. DEGs were selected with a cutoff value of p < 0.01.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: tab-delimited text files include counts for each Sample ...

source_name: KPC

growth_protocol: KPC cells were grown at 37°C in 5% CO2 and were revived and passaged for 2-3 generations until they reached approximately 70%-80% confluence. Subsequently, these cells were utilized for orthotopic tumor implantation.

extract_protocol:
Tumor samples were harvested from orthotopic pancreatic ductal adenocarcinoma model mice after two weeks of TLQP21 or saline treatment. RNA extraction was carried out using the RNAeasy Plus Universal Kit (Qiagen).
The samples underwent library construction by the NEBNext Ultra RNA Library Prep Kit for Illumina, and were loaded onto an Illumina NovaSeq 6000 for 150 bp paired-end sequencing.

treatment_protocol: Two weeks of TLQP21 or saline treatment

value: KPC

value: Pancreatic cancer cells


title: CFA-rep 1

description: Library name: sample-4


title: NOD-pancreas-vehicle-mouse7rep5


title: Naïve-rep 2

description: Library name: sample-2


title: TLQP21_3

address: 中国广州市中山二路74号中山大学广州校区北校园


title: mock_S1_R1_001

description: Library name: mock_S1_R1_001


title: TLQP21_2

address: 中国广州市中山二路74号中山大学广州校区北校园


title: TLQP21_1

address: 中国广州市中山二路74号中山大学广州校区北校园


title: Naïve-rep 1

description: Library name: sample-1


title: Healthy individual 32

type: genomic

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

description: DNA extracted from peripheral blood of healthy individuals

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised 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: Data were processed in R, normalized using BMIQ normalization.

label: Cy5 and Cy3

source_name: Peripheral Blood

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA from the whole blood samples was extracted using salting out method.

value: F


title: NOD-pancreas-vehicle-mouse7rep6


title: NOD-pancreas-vehicle-mouse7rep4


title: NOD-pancreas-vehicle-mouse7rep3


title: db/db5

city: Shanghai

first: Jingyi

state: --None--

address: Shanghai General Hospitol

department: School of Medicine

institute: Shanghai Jiao Tong University

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: retina

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 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: retina


title: Saline4

address: 中国广州市中山二路74号中山大学广州校区北校园

value: Saline


title: db/db4


title: RNAseq: Setdb2KO mouse Bone-marrow derived macrophages Control Rep 2

city: New York

first: Laszlo

institute: Mount Sinai Icahn School of Medicine

description: Library name: mm_RNAseq_BMDM_Setdb2KO_CTRL_Rep2

data_processing:
RNA-seq data was performed by nf-core/rnaseq pipeline (version 3.9). In brief, adapters and low quality reads were filtered by trimgalore (0.6.6). Cleaned reads were aligned to the mouse reference genome with STAR and genes were quantified using Salmon.
ATAC-seq data was performed by nf-core/atacseq pipeline (version 1.2.2) using default parameters. In brief, adapter trimming using  by trimgalore (0.6.6). Cleaned reads were aligned using BWA aligner, duplicates were marked by picard and bigWig tracks were generated by BEDTools.
Assembly: mm10
Supplementary files format and content: RNAseq: processed raw and normalized count matrix
Supplementary files format and content: ATACseq: processed coverage files (bigwigs)

source_name: BMDM

extract_protocol:
RNA-seq: Total RNA was isolated from SETDB2mKO and WT BMDMs using the RNAeasy kit (Quiagen) according to the manufacturer’s instructions. The quality of the RNA was measured by Agilent BioAnalyzer. High quality RNA samples were submitted to genetic resource core facility (GRCF) Johns Hopkins University for following library preparation and sequencing. Briefly, mRNAs were enriched by removing ribosomal RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490S, New England BioLabs) as per manufacturer’s instructions. ATAC-seq: After β-glucan training, BMDMs were detached from the plate and counted. 60,000 cells per treatment condition were used for the experiment. Cells were washed with ice-cold PBS and nuclei were isolated using lysis buffer (1% Triton-X-100,150 mM NaCl, 0.1% SDS, 1 mM EDTA, and 20 mM Tris-HCl pH 8.0). Tagmentation was performed in nuclei, using Tn5 transposase in a reaction mixture containing 10.5 μl H2O, 12.5 μl TD buffer, and 2 μl Tn5 transposase (Illumina) at 37°C for 30 minutes. Tagmentation reactions were stopped by adding 75 μl TE buffer. DNA was further isolated using Qiagen Minelute columns and amplified by PCR using Nextera primers. PCR reaction clean-up was performed with the addition of 90 μl AMPure XP beads to a 50 μl PCR reaction.
RNA-seq: RNA-Seq libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S, New England BioLabs). Sequencing was performed on the Novaseq-6000 instrument (Illumina). At least three biological replicates were used from all treatment types for sequencing. ATAC-seq: Samples were submitted to genetic resource core facility (GRCF) Johns Hopkins University for following fragment analysis by bioanalyzer and sequencing. Libraries were sequenced 1.6B paired end reads on a Novaseq-6000 instrument (Illumina).

value: BMDM

value: CTRL


title: Saline3

address: 中国广州市中山二路74号中山大学广州校区北校园


title: db/db3


title: NOD-pancreas-vehicle-mouse7rep1

value: Female


title: Healthy individual 31


title: Saline2

address: 中国广州市中山二路74号中山大学广州校区北校园


title: Saline1

address: 中国广州市中山二路74号中山大学广州校区北校园


title: NOD-pancreas-vehicle-mouse7rep2

value: NOD/ShiLT


title: NOD-lymphnode-vehicle-mouse6rep8

value: lymph node


title: WT5


title: db/db1


title: 3121_WT_5

first: Richard

middle: Theodore

last: Lee

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

data_processing:
sequences were trimmed using trimmomatic v0.39 (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36)
trimmed reads were pseudoaligned with Kallisto v0.50.1 using the standard kallisto index for mouse ( 200 bootstraps)
abundance files were summerized and imported as a matric using tximport v1.0.3
raw counts were created using DESeq2
common gene annotations were retreived using ensembl biomart
Assembly: mm10
Supplementary files format and content: tab delimited counts fromT, annotated with ensembl gene, transcript, and gene synonym

source_name: liver

extract_protocol:
QIAGEN RNeasy Kits
Prepared by Azenta Biosciences

value: liver


title: NOD-lymphnode-vehicle-mouse6rep7

value: 6-week old


title: WT4


title: 3120_WT_4


title: NOD-pancreas-vehicle-mouse6rep8

value: pancreas


title: Healthy individual 30

value: M


title: Healthy individual 25


title: Healthy individual 24


title: NOD-lymphnode-vehicle-mouse6rep9

value: vehicle (100 µL of 0.5% Methyl Cellulose-4M per mouse)


title: WT3


title: WT2


title: NOD-lymphnode-vehicle-mouse6rep6


title: NOD-pancreas-vehicle-mouse6rep7


title: 3118_WT_3

value: WT


title: WT1


title: 3117_WT_2


title: Healthy individual 28


title: 3116_WT_1


title: NOD-lymphnode-vehicle-mouse6rep5


title: NOD-lymphnode-vehicle-mouse6rep4


title: Healthy individual 27


title: 3154_C247S_KI_5

value: KI - C247S


title: Healthy individual 18


title: Healthy placebo treated quadricep biological replicate 4

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

institute: University of Kentucky

data_processing:
Raw FASTQ files underwent pre-alignment quality control, then were aligned using STAR aligner (reference genome: GRCm38/mm10) in Partek Flow with requrement of junction reads to match introns and strict paired-end compatibility. Quantified reads went through a noise reduction filter with maximum feature exclusion set less than or equal to 10 and were analyzed to obtain differential gene expression using DESeq2 (minimum read cutoff of 50).  Differential gene expression was calculated comparing ACLT and Control limbs for both CSF1-Ri and placebo treatment
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Skeletal muscle

extract_protocol:
Mouse quadricep RNA was isolated using TRIzol and the Zymo MicroPrep Kit and prepared for RNA-sequencing
Conducted at NovoGene

treatment_protocol: Mice received 40mg/kg of CSF1-R inhibitor or .5% sucrose in drinking water for 7 days following ACL transection

value: Skeletal muscle


title: Healthy individual 19


title: 3112_C247S_KI_4


title: E10.5 posterior

city: London

first: Sergio

last: Menchero

address: 1 Midland Road

institute: The Francis Crick Institute

description: 10X Genomics

data_processing:
Quantification by kallisto (0.46.2) bustools (0.40.0) workflow
Cell selection using DropletUtils (1.12.1)
Analysis using Seurat (4.0.3)
Assembly: ASM229v1 with Y chromosome
Supplementary files format and content: kallisto bustools expression matrix in cell ranger-format in tarball
Supplementary files format and content: 10x loupe for embryonic cells
Supplementary files format and content: Seurat rds object for embryonic cells
Supplementary files format and content: Metadata table for embryonic cells in CSV format

organism: Monodelphis domestica

source_name: embryo (posterior region)

extract_protocol:
Samples were incubated on FACSmax Cell Dissociation Solution (Amsbio, T200100) with 10% Papain (30 U/mg, Sigma-Aldrich, 10108014001) for 11-12 min at 37°C to dissociate the cells. Samples were then resuspended in HBSS with 5% FBS, 10 µM rock inhibitor (Stemcell Technologies, Y-27632), and 1x non-essential aminoacids (Life Technologies, 11140050). Cells were filtered through 35 µm cell strainers (Falcon, 352235) and 20 µm filters (Miltenyi Biotec, 130-101-812).
Libraries were prepared using the Single Index Kit T Set A (PN-1000213) from the 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 (PN-1000121)

value: embryo (posterior region)

value: wildtype


title: NOD-lymphnode-vehicle-mouse6rep3


title: 3097_C247S_KI_3


title: NOD-lymphnode-vehicle-mouse6rep2


title: E10.5 anterior

description: 10X Genomics

source_name: embryo (anterior region)

value: embryo (anterior region)


title: Healthy placebo treated quadricep biological replicate 3


title: Healthy individual 22


title: ACLT placebo treated quadricep biological replicate 3


title: 3096_C247S_KI_2


title: Healthy individual 26

value: F


title: Healthy individual 7


title: Healthy individual 8


title: NOD-lymphnode-vehicle-mouse6rep1


title: ACLT placebo treated quadricep biological replicate 2


title: E9.5

description: 10X Genomics

source_name: embryo

value: embryo


title: Healthy individual 12


title: Healthy individual 21


title: Healthy individual 20


title: Healthy individual 9


title: 1288_KO_5

value: KO - Txnip


title: Healthy individual 10


title: Healthy individual 23


title: 3082_C247S_KI_1


title: NOD-pancreas-vehicle-mouse6rep5

value: Female


title: ACLT placebo treated quadricep biological replicate 1


title: Healthy placebo treated quadricep biological replicate 2


title: 1254_KO_4


title: NOD-pancreas-vehicle-mouse6rep4

value: NOD/ShiLT


title: Healthy placebo treated quadricep biological replicate 1


title: Healthy individual 4


title: 1253_KO_3


title: 1252_KO_2


title: ACLT CSF1R treated quadricep biological replicate 4


title: Healthy individual 2


title: INTS11 ChIP-seq, 72h, rep2, input

city: Gainesville

first: Conner

middle: Mark

last: Traugot

state: FL

address: 2033 Mowry Rd, CGRC 265

institute: University of Florida

description:
Library name: INTS11 ChIP-seq_72h_rep2_input
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)

data_processing:
Adapter sequences were first trimmed using Trimmomatic v0.39 to remove sequencing adapters. This step also removed reads smaller than 20 bp and reads with quality lower than 20.
Forward and reverse reads were paired and combined into a single read using PEAR (v0.9.2). PCR Duplicates were collapsed using fastx-collapser from fastx_toolkit (v0.0.14) and UMIs were removed using cutadapt (v5.0).
Reads were mapped to the human and KSHV reference genomes using HISAT2 (v2.2.1) with default parameters.
ChIP-seq peaks were called using MACS2 (v2.2.7.1) and files for visualization of the data were generated using bamCoverage and computeMatrix from Deeptools2 (v3.5.2).
Assembly: Human: hg38, KSHV: GQ994935.1
Supplementary files format and content: ChIP-seq samples include bigwig visualizations of mapped reads.

growth_protocol: iSLK.219 cells were maintained in DMEM supplemented with 10% fetal bovine serum, 1% penicillin and streptomycin, 250 μg/mL G418, 400 μg/mL hygromycin and 10 μg/mL puromycin. They were cultured at in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Cells were crosslinked by incubating with standard growth media supplemented with 1% formaldeyde for 10 min. Crosslinking was quenched by adding glycine to a concentration of 125 mM. Cells were centrifuged and sonicated to generate cell lysate and shear DNA.
Sheared DNA samples were incubated overnight with 5 μg of INTS11 or control IgG antibody for the immunoprecipitation. The resulting DNA was extracted using phenol/chloroform/isoamyl alcohol. The libraries were generated using the Takara ThruPLEX Tag-seq Kit according the manufacturer protocols.

value: Human epithelial


title: INTS11 ChIP-seq, 72h, rep2

description:
Library name: INTS11 ChIP-seq_72h_rep2
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: INTS11 ChIP-seq, 72h, rep1

description:
Library name: INTS11 ChIP-seq_72h_rep1
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: NOD-pancreas-vehicle-mouse6rep6


title: INTS11 ChIP-seq, 72h, rep1, input

description:
Library name: INTS11 ChIP-seq_72h_rep1_input
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: Healthy CSF1R treated quadricep biological replicate 4


title: 1176_KO_1

value: liver


title: NOD-pancreas-vehicle-mouse6rep1

value: 6-week old


title: INTS11 ChIP-seq, 48h, rep2

description:
Library name: INTS11 ChIP-seq_48h_rep2
iSLK.219 cells are latently infected with recombinant human herpesvirus (KSHV)


title: ACLT CSF1R treated quadricep biological replicate 3


title: NOD-pancreas-vehicle-mouse6rep3

value: pancreas