title: Neuron, mock treated, biological repl 3

data_processing:
Quality check was done by using FastQC v0.11.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.20.1 (--qualified_quality_phred 20 -f 5 -t 5)
Deduplicated reads were removed using fastuniq v1.1
Trimmed and deduplicated reads were mapped to hg38 using STAR v2.7.3a (--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical)
bigWig files were generated by bedtools v2.30.0 (-bga -split -trackline) with uniquely mapped reads
Assembly: hg38
Supplementary files format and content: bigWig

source_name: brain

extract_protocol:
RNA was harvested using Direct-zol RNA Mini prep kit (Zymo research). The ERCC spike-in RNA mixture (Invitrogen) was added.
RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA prep kit (Illumina) following manufacturer's protocols.

value: brain

value: Stem cells-derived neurons

value: Neuronal differentiation


title: HEK293T cells, HuB/C/D triple overexpressing cells, biological replicate 2

status: Public on Oct 20 2023

type: SRA

city: New York

first: Hachung

last: Chung

state: New York

address: 701 W 168th St, HHSC Rm 1506

department: Microbiology & Immunology

country: USA

institute: Columbia University

library_source: transcriptomic

data_processing:
Quality check was done by using FastQC v0.11.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v0.20.1 (--qualified_quality_phred 20 -f 5 -t 5)
Deduplicated reads were removed using fastuniq v1.1
Trimmed and deduplicated reads were mapped to hg38 using STAR v2.7.3a (--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical)
Read counts were performed using featureCounts v1.6.4 (-p  -t exon -g gene_name -s 2) with GENCODE v38 primary assembly annotation file
bigWig files were generated by bedtools v2.30.0 (-bga -split -trackline) with uniquely mapped reads
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw count values for each sample
Supplementary files format and content: bigWig

molecule: total RNA

organism: Homo sapiens

source_name: kidney

extract_protocol:
RNA was harvested using Direct-zol RNA Mini prep kit (Zymo research). The ERCC spike-in RNA mixture (Invitrogen) was added and rRNA was depleted by RiboMinus™ Eukaryote Kit (Invitrogen)
RNA sequencing libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB) following manufacturer's protocols.

tag: tissue

value: kidney

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: genotype

value: HuB/C/D overexpression

tag: treatment

value: Lipofectamine 2000


title: RBE cells

city: Shanghai

first: Yuanyuan

last: Shi

address: changhailu 168

country: China

institute: the First Affiliated Hospital of Naval Medical University

data_processing:
For RNA-seq analysis, 2×150 bp paired-end sequencing (PE150) was performed on an Illumina Novaseq 6000 (LC-Bio).
The Fastp software (https://github.com/OpenGene/fastp) was used to remove reads containing adaptor contamination, low-quality bases, and undetermined bases with default parameters.
HISAT2 (https://ccb.jhu.edu/software/hisat2) was used to map the reads to the reference genome of Homo sapiens GRCh38.
StringTie was used to perform expression levels by calculating FPKM (fragments per kilobase of exon model per million mapped fragments).
Assembly: genes enriched in the proteasome and lysosome pathway
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: RBE

extract_protocol:
RNA was harvested following the standard protocol. 1 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: RBE

value: cancer cell line

value: Untreated cells


title: hypothalamic_maternal inulin treatment_rep3

type: genomic

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

description: maternal inulin treatment

hyb_protocol: Labeled DNA was hybridized to the Arraystar Mouse ReqSeq Promoter Array.

scan_protocol: Array was scanned with Agilent Scanner G2505C.

data_processing: After normalization, raw data was input into SignalMap Software to observe and evaluate the methylation peaks.

label: Cy 5

molecule: genomic DNA

organism: Mus musculus

source_name: MeDIP DNA from maternal inulin treatment

label_protocol: Immunoprecipitated methylated DNA was labeled with Cy5 fluorophere and the input genomic DNA was labeled with Cy3 fluorophere.

extract_protocol: Genomic DNA was extracted from hypothalamic samples using Dneasy Blood & Tissue Kit.

value: hypothalamic tissue

tag: age

value: 16 week

tag: group

value: maternal inulin treatment

tag: molecule type

value: MeDIP DNA

label: Cy 3

source_name: input DNA from maternal inulin treatment

value: input DNA


title: moloch_gibbon_M_input

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

library_source: genomic

data_processing:
Raw reads were aligned to the approporiate reference genome using bowtie2, with default settings
Alignments were converted to bam and filtered to remove low quality mapped reads using samtools
deeptools was used to calculate RPKM normalized signal of each epigenetic mark across the genome and at TAD boundaries
ChromHMM was used to annotate chromatin states using the mouse alignments
Assembly: mm10, mPah1, mCar1, nomLeu4, hMol2
Supplementary files format and content: bigWig; bed

organism: Hylobates moloch

source_name: LCL

extract_protocol: ChIP-seq libraries were contructed using the NEBNext UltraII kit according to manufactor's instructions.

value: LCL

value: ChIP

value: Silvery Gibbon

tag: Sex

value: M

tag: chip antibody

value: input


title: TFK1 cells


title: HEK293T cells, mock treated, biological replicate 2

value: kidney

value: WT


title: HEK293T cells, HuB/C/D triple overexpressing cells, biological replicate 1

value: Human embryonic kidney

value: HuB/C/D overexpression


title: HEK293T cells, mock treated, biological replicate 3

value: Lipofectamine 2000


title: HEK293T cells, mock treated, biological replicate 1


title: HEK293T cells, mock treated, biological repl 3

value: No treatment


title: Neuron, mock treated, biological repl 1

value: brain

value: Stem cells-derived neurons

value: Neuronal differentiation


title: RNA.02_MRTK.103_CTRL_rep2

city: Rotterdam

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam

description:
RNA-seq in MRT organoids P103, after 4 days lentiviral transduction with the Luciferase gene
MRTK_RNAseq_readcounts_normalized_2022-11-10.txt; MRTK_RNAseq_readcounts_unnormalized_2022-11-10.txt

data_processing:
Raw RNA-seq data were mapped against mm10 reference genome using a TopHat2 pipeline (version 2.1.1) (Kim et al., 2013). The mapped reads with mapping quality score <10 were discarded using SAMtools. The read coverage for each gene in “Homo Sapiens GRCm38.92” annotation file was determined using a HTSeq tool (version 0.9.1). The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools. The genes with at least 20 reads in both replicates were kept for further analysis. The filtered expression data were normalized based on the size factors of the individual samples using a DESeq2 package.
Assembly: hg38
Supplementary files format and content: bigWig files, read counts

source_name: MRT organoids P103

growth_protocol: The cell pellets were seeded in growth factor-reduced BME (Trevigen, 3533-010-02) and cultured in kidney organoid medium (AdDF+++ supplemented with 1.5% B27 supplement (Gibco), 10% R-spondin-conditioned medium, EGF (50 ng ml−1, Peprotech), FGF-10 (100 ng ml−1, Peprotech), N-acetylcysteine (1.25 mM, Sigma), Rho-kinase inhibitor Y-27632 (10 µM, Abmole) and A83-01 (5 µM, Tocris Bioscience). Medium was changed every 3–4 days, and organoids were passaged every 1–3 weeks. Depending on organoid morphology, organoids were either passaged using mechanical dissociation (Wilms tumour organoids, MRTK organoids), or TrypLE Express (Invitrogen, 12605036) containing 10 µM Y-27632 (Wilms tumour organoids, RCCs). Following the addition of 5–10 ml AdDF+++ and centrifugation at 250×g, cells were reseeded in BME and topped with kidney organoid medium. All organoid cultures are stored in the biobank of the Princess Máxima Center and made available to the scientific community according to the rules and regulations under which the patients and parents gave informed consent for donating the tissue.

extract_protocol:
RNA was isolated following a standard TRIzol RNA isolation protocol (Ambion). The cells were lysed using 1 ml of TRIzol reagent, and 200 µl chloroform was added to the lysates. The mixture was vortexed and centrifuged at 12,000 g at 4°C for 15 min. Upper phase was homogenized with 0.5 ml of 100% isopropanol, incubated at room temperature for 10 min, and centrifuged at 4°C for 10 min. The resulted RNA pellet was washed with 75% ice-cold ethanol, dried at room temperature for 10 min, and resuspended in RNase-free water. The isolated RNA was treated with DNase using RNeasy Mini Kit (Qiagen)
RNA-seq libraries were prepared using a TruSeq Stranded RNA LT Kit (Illumina).

treatment_protocol: For SMARCB1 re-expression, MRT organoids were lentivirally transduced with pLKO.1-UbC-luciferase-blast40 or pLKO.1-UbC-hSMARCB1-blast lentiviruses. After 2 days, 10 µg/ml blasticidin was added to the culture medium; For BRD9 inhibition experiments, MRT organoids were mechanically dissociated and plated at a density of 10.000 cells/ul in 10ul BME droplets. After 24h, 10µM I-BRD9 inhibitor (MedChemExpress, HY-18975) was added to the organoids.

value: MRT organoids P103

value: Malignant rhabdoid tumor cells

value: Luciferase plasmid


title: 9810 cells

value: cancer cell line

value: Untreated cells


title: HEK293T cells, empty vector transfected, biological replicate 3


title: HEK293T cells, mock treated, biological repl 2


title: moloch_gibbon_F_input

value: LCL

value: ChIP

value: Silvery Gibbon

value: F


title: HEK293T cells, mock treated, biological repl 1

value: kidney

value: WT


title: moloch_gibbon_M_CTCF

description: HMO-gibbon-CTCF.bigwig

data_processing:
Raw reads were aligned to the approporiate reference genome using bowtie2, with default settings
Alignments were converted to bam and filtered to remove low quality mapped reads using samtools
deeptools was used to calculate RPKM normalized signal of each epigenetic mark across the genome and at TAD boundaries
ChromHMM was used to annotate chromatin states using the mouse alignments
Assembly: mm10, mPah1, mCar1, nomLeu4, hMol2
Supplementary files format and content: bigWig; bed
Supplementary files format and content: *-CTCF-peaks-combined-merge200bp-sorted.bed: bed files contain all CTCF peaks unionized between one male and one female replicate, and merged within 200bp.

value: M

value: CTCF


title: Neuron, mock treated, biological repl 2


title: moloch_gibbon_F_H3K27ac


title: PS_3

city: Urumqi

first: Jingzhan

state: Xinjiang

address: NO. 91, Tianchi Road, Tianshan District

department: Dermatology

institute: People’s Hospital of Xinjiang Uygur Autonomous Region

description:
PS_3
KS259-PS.R1.fq.gz

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with P value <0.05 and fold change>1.5 or < 0.67.
The threshold for RASE detection was set to an RASE ratio >0.2 and P-value <0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Kaposi sarcoma lesion

extract_protocol:
Total RNA was extracted from KS lesions and adjacent non-tumor tissues of three patients with KS using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) . Following RNA extraction, the DNA was digested with DNase I. RNA quality was determined by measuring the A260/A280 ratio using a NanodropTM One/OneC spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Electrophoresis (1.5% agarose gel) was performed to confirm the RNA integrity. Qualified RNAs were quantified using the Qubit™ RNA Assay Kit (Life Technologies, Carlsbad, CA, USA).
An RNA-seq library was prepared from 2 µg of total RNA using a KCTM Stranded mRNA Library Prep Kit for Illumina (cat. no. DR08402, Wuhan Seq health Co., Ltd., Wuhan, China). Polymerase chain reaction (PCR) products corresponding to 200–500 bp were enriched.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. A NovaSeq 6000 sequencer (Illumina, San Diego, CA, USA) with a PE150 model was used for quantification and final sequencing.

value: Kaposi sarcoma lesion


title: moloch_gibbon_M_H3K4me1


title: PS_1

description:
PS_1
KS251-PS.R1.fq.gz


title: moloch_gibbon_F_H3K4me1


title: PS_2

description:
PS_2
KS252-PS.R1.fq.gz


title: NC_2

description:
NC_2
KS252-NC.R1.fq.gz

source_name: Kaposi sarcoma adjacent non-tumor tissue


title: moloch_gibbon_F_H3K27me3


title: RPS27_IP-2

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of RPS27 on genome using “ABLIRC” strategy.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include peak information for each group.

growth_protocol: Kaposi's sarcoma tissue were irradiated twice for 800 mJ/cm2, and lysed in ice-cold wash buffer. Cells lysis was performed in cold Wash buffer (1× PBS, 0.5% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate) supplemented with a 200 U/mL RNase inhibitor (Takara) and protease inhibitor cocktail (Bimake) and incubate on ice for 30 min. Clear cell lysate by centrifugation at 10,000 rpm for 10 min at 4°C. Add RQ I (Promega, 1U/μl) to a final concentration of 0.1 U/μl and incubate in a heat block for 30 min at 37°C. Immediately afterward, a stop solution was added to the lysates to quench DNase. The mixture was then vibrated vigorously and centrifuged at 13,000 x g at 4℃ for 20 min to remove cell debris.

extract_protocol:
The immunuprecipitates were further incubated with protein A/G Dynabeads (Thermo Scientific) for 2h at 4 °C. After applying to magnet and removing the supernatants, the beads were sequentially washed with lysis buffer, high-salt buffer (250 mM Tris 7.4, 750 mM NaCl, 10 mM EDTA, 0.1% SDS, 0.5% NP-40 and 0.5 deoxycholate), and PNK buffer (50 mM Tris 7.4, 20 mM EGTA and 0.5% NP-40) for two times, respectively. Resuspend the beads in of Elution buffer (50 nM Tris 8.0, 10 mM EDTA and 1% SDS). Incubate the suspension for 20 min in a heat block at 70°C to release the immunoprecipitated RBP with crosslinked RNA and vortex. Remove the magnetic beads on the separator and transfer the supernatant to a clean 1.5 ml microfuge tube. Add Proteinase K (BBI) into the 1% input（without immunoprecipitated）and immunoprecipitated RBP with crosslinked RNA, with final concentration of 1.2 mg/ml. Incubate for 120 min at 55°C. The RNA was purified with Trizol reagent (Life technologies).
cDNA libraries were prepared with the KAPA RNA Hyper Prep Kit (KAPA, KK8541) according the manufacturer’s procedure. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NovaSeq system for 150 nt paired-end sequencing.

treatment_protocol: For IP, the supernatant was incubated overnight at 4°C with 10 μg RPS27-antibody (cat. no. 15355-1-AP, Proteintech, Rosemont, IL, USA) and control IgG-antibody (cat. no. AC005, ABclonal, Wuhan, China).

tag: rip antibody

value: RPS27-antibody (Proteintech, Rosemont, IL, USA)


title: moloch_gibbon_F_H3K4me3


title: moloch_gibbon_M_H3K27me3


title: moloch_gibbon_M_H3K4me3


title: HiC.02_MRTK.103_SMARCB1

description: Hi-C in MRT organoids P103, after 4 days lentiviral transduction with the SMARCB1 gene

data_processing:
Raw Hi-C data were mapped with HiC-Pro (Servant et al., 2015), which performs mapping, identification of valid Hi-C pairs, generation of contact matrices and ICE normalization (Imakaev et al., 2012).
Assembly: hg38
Supplementary files format and content: hic files

extract_protocol:
Hi-C data were generated using as a previous published protocol (Rao et al., 2014) with minor modifications (Liu et al., 2021). For each template, 10 million cells were harvested and crosslinked using 2% formaldehyde. Crosslinked DNA was digested in nucleus using MboI, and biotinylated nucleotides were incorporated at the restriction overhangs and joined by blunt-end ligation. The ligated DNA was enriched in a streptavidin pull-down.
Hi-C libraries were prepared using a standard end-repair and A-tailing method.

treatment_protocol: For SMARCB1 re-expression, MRT organoids were lentivirally transduced with pLKO.1-UbC-luciferase-blast40 or pLKO.1-UbC-hSMARCB1-blast lentiviruses. After 2 days, 10 µg/ml blasticidin was added to the culture medium.

value: a wild-type full-length SMARCB1 gene plasmid


title: RPS27_input-2

value: IgG-antibody (ABclonal, Wuhan, China).


title: moloch_gibbon_F_HiC

data_processing:
HiC data were subject to quality control and alignment with bowtie2 using the HiCUP pipeline.
Bam files were paired and converted to .cool format using cooltools.
TADs were called using HicExplorer, HicFindTADs with parameters --minDepth 100000, --maxDepth 600000, --delta 0.01, --correctForMultipleTesting fdr
Supplementary_files_format_and_content: BED files with TAD boundary regions

extract_protocol: Arima HiC

value: Silvery gibbon

tag: protocol

value: Arima


title: NC_3

description:
NC_3
KS259-NC.R1.fq.gz

value: Kaposi sarcoma adjacent non-tumor tissue


title: RNA.11_MRTK.78_SMARCB1_rep1

description:
RNA-seq in MRT organoids P78, after 4 days lentiviral transduction with the SMARCB1 gene
MRTK_RNAseq_readcounts_normalized_2022-11-10.txt; MRTK_RNAseq_readcounts_unnormalized_2022-11-10.txt

source_name: MRT organoids P78

value: MRT organoids P78

value: Malignant rhabdoid tumor cells


title: MP_Organoid_24h_2nd

city: Philadelphia

first: Ning

last: Li

state: Pennsylvania

address: 3800 Spruce St.

department: Biomedical Sciences

institute: UPENN

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Data was processed using the 10X Genomics CellRanger pipeline. Sequencing reads were mapped to GRCh38 reference genome.
An initial filtering was performed on the raw gene-barcode matrix output by the Cell Ranger cellranger count function, removing barcodes that have less than 1000 transcripts (quantified by unique molecular identifier (UMI)) and 500 expressed genes (“expressed” means that there is at least 1 transcript from the gene in the cell).
Assembly: GRCh38
Supplementary files format and content: gene_by_cell_count_matrix.txt contains a sparse matrix where rows are genes (with gene information in the gene_annotation.csv), columns are cells (with cell information in the cell_annotation.csv), and values are UMI counts for the given gene in the given cell. cell_annotation.csv contains a data frame with annotations (i.e. 10X barcode, tissue type, cell type, etc.) for each cell. gene_annotation.csv contains a data frame with gene id and gene short name.

source_name: Mixed

growth_protocol: Organoid from adjacent normal colon and tumor were generated by culturing on top of the MatriGel. The medium  contains advanced Dulbecco’s modified Eagle medium/F12 including supplement N2 (Invitrogen; 17502-048), B27 (Invitrogen; 17504-044), N-acetylcysteine (MilliporeSigma; A9165, 1 mM), mEGF (Invitrogen; PMG8041, 50 ng/ml), mNoggin (Peprotech, 250-38, 100 ng/ml), and R-spondin 1 (PeproTech, 315-32).

extract_protocol:
Using the Chromium controller (10x Genomics) and reagents from the Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics), cells were partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs) where each cell's trascriptome was indexed with a specific 10x BarCode. cDNA were amplified and purified for library preparation.
cDNA were used for library preparation using the Chromium Single Cell 3′ Reagent Kit v3 (10x Genomics) according to manufacturer’s protocol.

treatment_protocol: Patient derived monocyte were cultured for 7 days and differentiated into macrophage. Organoid from tumor or normal colon were co-cultured with macrophage for 48 hours in organoid medium before downstream analysis.

value: Mixed

value: mixed

tag: library type

value: mRNA

tag: antibodies/tags


title: Co_Culture_24h_2nd


title: F1_M_15848_hippocampus

city: Cambridge

first: Andreas

middle: F

last: Kautt

state: MA

address: 16 Divinity Ave

institute: Harvard University

data_processing:
Using cutadapt v.2.3, we trimmed very low quality bases (quality score <10) and applied a minimum length cutoff of 25 bp.
We then mapped trimmed reads of P. maniculatus and P. polionotus individuals to their respective reference genome, Pman_2.1 (GCA_003704035.1) or Ppol_1.3.3 (GCA_003704135.2), and in-house annotations generated with Comparative Annotation Toolkit using the GENCODE v15 primary-assembly annotation of Mus musculus (GRCm38 mm10) as reference. We competitively mapped reads from F1 hybrids to a diploid reference genome created by concatenating the two species assemblies and annotations. We performed read mapping with STAR v.2.7.0e (Dobin et al. 2013) in a transcriptome-aware manner.
We estimated gene expression with RSEM v1.3.1 and retained only genes present in both species’ annotations. For F1 samples, allele counts (reads mapped to a diploid reference) were summed up.
Assembly: GCA_003704035.1; GCA_003704135.2
Supplementary files format and content: tab-delimited text file of expected gene counts (rows) for each sample (columns)

organism: Peromyscus maniculatus x Peromyscus polionotus

extract_protocol:
For the whole brain dataset, a cohort of 59–137-day-old virgin male P. maniculatus (n=5) and P. polionotus (n=6) animals were euthanized by CO2 inhalation 7–10 h before the start of the dark period. Whole brain samples were then rapidly dissected, flash-frozen, and stored at -70°C. We homogenized the samples in TRIzol Reagent (Invitrogen, 15596026) using a Bio-Gen PRO200 homogenizer (PRO Scientific, Oxford, USA), and extracted RNA using a Direct-zol™ RNA MiniPrep Plus kit (Zymo Research, R2070), including a DNase I treatment; For the brain subregion dataset, a cohort of 82–85-day-old virgin male and female P. maniculatus, P. polionotus, and their F1 hybrids were euthanized by CO2 inhalation followed by cervical dislocation 3–10 h before the onset of the dark period. One cohort was used for dissection of the cerebellum, hippocampus, and hindbrain samples. In these samples, after the brain was removed, a dorsal-to-ventral incision was made posterior to the cerebrum to release the hindbrain and cerebellum. The cerebellar peduncles were cut, and the hindbrain and cerebellum were placed in tubes and flash frozen in liquid nitrogen. The petri dish with the remaining brain was then placed on ice, and the two cerebral hemispheres were cut apart. For each hemisphere separately, the hippocampus was severed from the dorsal fornix and gently scooped out of the hemisphere with a brush in ventral-to-dorsal direction (Lu, Airey, and Williams 2001), and then flash frozen. For a second cohort of animals, we dissected the brains and then immediately submerged them into embedding compound for cryosectioning (Tissue-Tek O.C.T.) and froze them on dry ice. We sectioned brains on a coronal plane at 150 μm using a cryostat at -20°C (Leica CM3050 S, Leica Biosystems Inc., Buffalo Grove, IL) and stored the sections at -70°C until we dissected the medial prefrontal cortex, septum, striatum, hypothalamus, amygdala, thalamus, and midbrain with sample corers according to anatomical landmarks. The sample cores were immediately transferred into homogenization buffer. After subregion dissection, we homogenized samples for 10 seconds in Maxwell RSC Homogenization Buffer (Promega, Madison, USA) with 2% 1-thioglycerol using a Bio-Gen PRO200 homogenizer (PRO Scientific, Oxford, USA) and then extracted RNA using the Maxwell RSC simplyRNA Tissue Kit (Promega).
We prepared each whole brain sequencing library from 1 μg of total RNA using a PrepX PolyA mRNA Isolation Kit (Wafergen, 40047) on the Apollo 324 NGS Library Prep System (Takara Bio USA Holdings, Mountain View, CA). We added Illumina indices and amplified libraries with 12 cycles of PCR and cleaned them using PCRClean DX beads (Aline Biosciences, Woburn, MA); We prepared brain subregion RNA-Seq libraries using an mRNA HyperPrep kit (Kapa Biosystems, Wilmington, USA) automated on a BioMek FXp (Beckman Coulter, Brea, USA). Post-capture, we fragmented mRNA for 6 min at 94°C for a target insert size of 200-300 base pairs. We amplified dual-indexed adapter-ligated libraries in 11 PCR cycles.

value: brain

tag: brain subregion

value: hippocampus

tag: strain

value: F1 hybrid (P. maniculatus x P. polionotus)


title: Co_Culture_24h_2nd_barcode

description: Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: TotalSeq-B HTO


title: F1_M_15848_hindbrain

value: hindbrain

value: M


title: MP_Organoid_24h_2nd_barcode


title: F1_M_15846_hippocampus


title: CoCulture_36h_2_barcode


title: moloch_gibbon_M_HiC

value: LCL


title: F1_M_15848_cerebellum

value: cerebellum


title: F1_M_15846_hindbrain


title: F1_M_15846_cerebellum


title: CoCulture_36h_1


title: CoCulture_36h_1_barcode


title: hCRC0087_barcode


title: F1_M_15845_hindbrain


title: F1_M_15845_hippocampus


title: hCRC0087


title: F1_M_15836_thalamus

value: thalamus


title: RNA_seq_A2780_Control_rep1

city: Chengdu

first: Lei

last: Tao

address: No.17, Section 3, Renmin Nan Road

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

data_processing:
RNA libraries were sequenced on an Illumina NovaSeq 6000 sequencing machine with 150-base pair (bp) paired-end reads.
Transcript abundance was normalized and measured by FPKM.
DESeq2 (v.1.26.0, RRID:SCR_000154) was used to identify differentially expressed genes
Assembly: hg38
Supplementary files format and content: Excel files include RPKM values for each Sample

source_name: ovarian cancer cells

growth_protocol: A2780 cells were cultured in RPMI 1640 medium (Gibco) with 10% fetal bovine serum (FBS). ES2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) with 10% FBS. All cell lines were maintained in standard conditions at 37 °C and 5% CO2.

extract_protocol:
Total RNA was purified from A2780 and ES2 cells after dimethyl sulfoxide (DMSO) or ZY0511 (1μM) treatment for 24 h and stored in TRIzol (Invitrogen, USA)
RNA-seq libraries were constructed using an Illumina stranded mRNA sample preparation kit (NEB, E7770) according to the manufacturer’s protocol.

treatment_protocol: A2780 and ES2 cells were treated with 1 µM LSD1 inhibitor ZY0511 or DMSO for 24 hours.

value: ovarian cancer cells

value: WT

value: Control


title: F1_M_15845_cerebellum


title: RPS27_input-1

value: Kaposi sarcoma lesion

value: IgG-antibody (ABclonal, Wuhan, China).


title: hCRC0086_barcode

value: Mixed


title: CoCulture_36h_2

value: mixed


title: F1_M_15836_striatum

value: striatum


title: RPS27_IP-1

value: RPS27-antibody (Proteintech, Rosemont, IL, USA)


title: hCRC0086

value: mRNA


title: hCRC0084_barcode


title: F1_M_15836_mPFC

value: brain

value: mPFC

value: F1 hybrid (P. maniculatus x P. polionotus)


title: hCRC0083_barcode

value: TotalSeq-B HTO


title: F1_M_15836_septum

value: septum

value: M


title: F1_M_15836_hypothalamus

value: hypothalamus


title: F1_M_15836_midbrain

value: midbrain


title: hCRC0084


title: F1_M_15836_amygdala

value: amygdala


title: hCRC0083


title: F1_M_15466_thalamus

value: thalamus


title: hCRC0081_barcode


title: F1_M_15466_striatum


title: F1_M_15466_septum


title: hCRC0081


title: hCRC0080_barcode


title: hCRC0080


title: hCRC0049_barcode


title: F1_M_15466_mPFC


title: hCRC0049


title: 4_SCv3_cite_10_31_2019

value: Tumoroid_08_48hr/GTCAACTCTTTAGCG; Tumoroid+Macrophage_08_48hr/TGATGGCCTATTGGG; Tumoroid_28_48hr/TTCCGCCTCTCTTTG; Tumoroid+Macrophage_28_48hr/AGTAAGTTCAGCGTA; Macrophage_48hr/no barcode


title: F1_M_15466_midbrain


title: F1_M_15466_amygdala


title: F1_M_15465_thalamus


title: F1_M_15466_hypothalamus


title: moloch_gibbon_F_CTCF

description: HMO-gibbon-CTCF.bigwig

value: LCL

value: ChIP

value: Silvery Gibbon

value: F

value: CTCF


title: 3_SCv3_cite_10_31_2019

value: Mixed

value: mixed

value: Tumoroid_08_24hr/GTCAACTCTTTAGCG; Tumoroid+Macrophage_08_24hr/TGATGGCCTATTGGG; Tumoroid_28_24hr/TTCCGCCTCTCTTTG; Tumoroid+Macrophage_28_24hr/AGTAAGTTCAGCGTA; Macrophage_24hr/no barcode


title: 2_SCv3_10_31_2019

value: mRNA


title: moloch_gibbon_M_H3K27ac


title: 1_SCv3_10_31_2019


title: F1_M_15465_septum

value: brain

value: F1 hybrid (P. maniculatus x P. polionotus)


title: F1_M_15465_striatum

value: striatum

value: M


title: LiverMet_44

source_name: LiverMet

value: LiverMet


title: F1_M_15465_mPFC

value: mPFC


title: F1_M_15465_midbrain

value: midbrain


title: F1_M_15465_hypothalamus

value: hypothalamus


title: Tumor_44

source_name: Tumor

value: Tumor


title: Liver_44

source_name: Liver

value: Liver


title: NC_1

description:
NC_1
KS250_NC_HT2JWDSX2_L1

value: Kaposi sarcoma adjacent non-tumor tissue


title: Organoid_28

source_name: Organoid

value: Organoid

value: Epithelial


title: Tumoroid_28

source_name: Tumoroid

value: Tumoroid


title: F1_F_15847_thalamus

source_name: brain

value: thalamus

value: F


title: Tumor_28

value: mixed

value: mRNA


title: F1_M_15465_amygdala

value: brain

value: amygdala

value: F1 hybrid (P. maniculatus x P. polionotus)


title: Tumoroid_24


title: Organoid_24


title: F1_F_15847_septum

value: septum


title: F1_F_15847_mPFC

value: mPFC


title: F1_F_15847_midbrain

value: midbrain


title: F1_F_15847_hypothalamus

value: hypothalamus


title: F1_F_15847_amygdala


title: Tumor_26

value: Tumor


title: Tumor_24


title: Tumoroid_08


title: F1_F_15847_striatum

value: striatum


title: Tumor_27


title: F1_F_15844_hippocampus

value: hippocampus


title: F1_F_15844_hindbrain

value: hindbrain


title: Liver_09

value: Liver


title: Organoid_26

value: Organoid

value: Epithelial


title: Tumor_08


title: LiverMet_09

value: LiverMet


title: Tumor_09

value: mixed


title: F1_F_15650_septum

value: F


title: F1_F_15650_thalamus

value: brain

value: thalamus


title: F1_F_15843_hippocampus

value: F1 hybrid (P. maniculatus x P. polionotus)


title: F1_F_15843_cerebellum

value: cerebellum


title: Colon_08

source_name: Colon

value: Colon

value: mRNA


title: Organoid_08


title: LiverMet_27


title: F1_F_15650_striatum


title: Colon_09


title: Tumor_07


title: F1_F_15650_hypothalamus

value: hypothalamus


title: F1_F_15844_cerebellum


title: F1_F_15843_hindbrain


title: Stim_CD4_SevereAsthma_D16toD20_Gex

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

description: Single-cell RNA-seq with 10x Genomics 3' v3 GEX

data_processing:
mkfastq (Cell Ranger 3.0.2) was used to generate FASTQ files with default parameters
count (Cell Ranger 3.0.2) was used to generate the filtered UMI matrix with default parameters
aggr (Cell Ranger 3.0.2) was used to aggregate multiple libraries
Seurat (3.0.2) was used to filter and normalize the UMI matrix
Genome_build: GRCh37 (hg19-3.0.0 from Cell Ranger)
Supplementary_files_format_and_content: sc_cd4resting_annotation.txt.gz meta data for 27771 cells
Supplementary_files_format_and_content: sc_cd4resting_umi.txt.gz UMI count data matrix for 27771 cells
Supplementary_files_format_and_content: sc_cd4stim_annotation.txt.gz meta data for 27583 cells
Supplementary_files_format_and_content: sc_cd4stim_umi.txt.gz UMI count data matrix for 27583 cells

source_name: Bronchoalveolar lavage (BAL)

extract_protocol:
For single-cell RNA-seq (10x Genomics), a maximum of 60,000 total CD4+ T cells from up to 6 donors for resting and stimulation conditions separately and per disease were sorted then pooled into low retention 1.5mL collection tubes, containing 500µL of a 1:1 solution of PBS:FBS supplemented with RNAse inhibitor (1:100). Following sorting, ice-cold PBS was added to make up to a volume of 1400µL. Cells were then centrifuged for 5 minutes (600x g at 4˚C) and the supernatant was carefully removed leaving 5 to 10µL. 25µL of resuspension buffer (0.22µm filtered ice-cold PBS supplemented with ultra-pure bovine serum albumin; 0.04%, Sigma-Aldrich) was added to the tube and the pellet was gently but thoroughly resuspended. Following careful mixing, 33µL of the cell suspension was transferred to a PCR-tube for processing as per the manufacturer’s instructions (10x Genomics).
Single-cell RNA-seq using 10x genomics platform was performed using Chromium™ Single Cell 3' v3 Reagent Kits following the manufacturer’s protocol
Libraries were constructed using Chromium™ Single Cell 3' v3 Reagent Kits following the manufacturer’s protocol; 100 x 100 bp paired-end reads, 3'TAG, Hg19 human reference genome.

treatment_protocol: BAL samples were obtained by instilling a total volume of 120mL of warm 0.9% saline in small aliquots into the right upper lobe segments of the lung using a fiberoptic bronchoscope procedure. Aliquots were pooled together and collected as 1 sample with immediate storage on ice and in liquid nitrogen for long-term storage. To perform this study, BAL samples from each donor were thawed, washed, and diluted to a concentration of 2x10^6 cells/mL with MACS buffer. For the stimulation condition, for each donor, one quarter of the sample was plated in 500µL of T cell culture medium in 24-well culture plate and stimulated for 2h with PMA (20nM)/Ionomycin (1µM). Fo both, resting and stimulation, conditions, cells were sequentially stained with fluorescence-labeled surface antibodies and DNA-barcode-conjugated antibodies (TotalSeq™-A antibody, Biolegend, 0.5µg/condition). We then performed FACS sorting of total CD3+ CD4+ T cells from resting and stimulation condition separately.

tag: donors

tag: stimulation

value: Stimulated

tag: disease state

value: Severe Asthma

tag: molecule subtype

value: polyA RNA 3'end capture


title: Human gut microbiota sample 55

city: izmir

first: leman

last: binokay

address: Mithatpaşa

country: Turkey

institute: İzmir Biyomedicine and Genom Instıtute

data_processing:
library strategy: 16S rRNA-seq
We performed quality control of the raw sequencing reads using the FastQC software v0.11.9 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and filtered out poor-quality reads with Trimmomatic.
For taxonomic profiling, we aligned the reads to target organism genomes using Kraken 2 and the Ribosomal Database Project database.
We used Ampliseq v2.3.1 developed by nf-coreand Nextflow v21.10.6  workflow for bioinformatics analysis. We analyzed optional parameters as "dada_ref_taxonomy 'rdp" and "--picrust," and prepared a metadata document as specified in the nf-core/ampliseq documentation. The pathway analysis was performed with the picrust2 tool v2.5.1, using the default parameters and a custom database.  then established OTU grouping for each sample and obtained a Kraken 2 format output and report file of microbiome compositions with properties varying from kingdom to species. We combined the Kraken 2 reports for each sample using the combine_kreports.py function in KrakenTools.
We created the custom database using the KEGG ortholog IDs with the help of KEGG db.
We used the refineR v1.5.1 package eveloped in the R environment to determine reference intervals for each metabolic pathway.
Assembly: For taxonomic profiling, we aligned the reads to target organism genomes using Kraken 2and the Ribosomal Database Project database.
Supplementary files format and content: Kraken 2 report file which includes counts with tsv file format (lvl_type, name represents Clade level type (R, D, P, C, O, F, G, S....), and name)

organism: human feces metagenome

source_name: Human gut

extract_protocol:
We collected approximately the size of chickpeas feces sample from 57 healthy Turkish volunteers,using a disposable spoon and transferred them into a screw cap tube containing 10 volumes of DNA/RNA Shield (ZymoResearch). We used the ZymoBIOMICS™ DNA Miniprep Kit (Zymo Researches, #D4300) to isolate bacterial DNA from the samples, following the kit's protocol.
We prepared the sequencing library using the 16S Metagenomic Sequencing Library Preparation protocol from Illumina. The library had a size range of about 550 bp and a concentration of at least 10 nM. We sequenced 5ng of DNA from each sample using the iSeq 100 sequencing machine with paired-end (2x150) reading method.

tag: tissue

value: Human gut

value: 16S rRNA


title: F1_F_15467_hippocampus

value: hippocampus


title: Unstim_CD4_MildAsthma_D02toD05_Gex

tag: cell type

value: Unstimulated

value: Mild Asthma


title: Human gut microbiota sample 54


title: Human gut microbiota sample 57


title: Stim_CD4_MildAsthma_D01toD05_Gex


title: Human gut microbiota sample 53


title: F1_F_15650_mPFC

value: mPFC


title: Human gut microbiota sample 52


title: F1_F_15467_cerebellum

value: F


title: Stim_CD3_SevereAsthma_D21toD25_Gex


title: Human gut microbiota sample 56


title: Stim_CD4_SevereAsthma_D26toD31_Gex


title: Human gut microbiota sample 49


title: Human gut microbiota sample 50


title: Human gut microbiota sample 51


title: Human gut microbiota sample 48


title: Colon_07

value: mixed


title: Human gut microbiota sample 47


title: F1_F_15462_striatum

value: brain

value: striatum


title: Unstim_CD4_SevereAsthma_D21toD25_Gex


title: Human gut microbiota sample 46


title: Human gut microbiota sample 45


title: F1_F_15462_septum

value: septum

value: F1 hybrid (P. maniculatus x P. polionotus)


title: Human gut microbiota sample 44


title: Unstim_CD4_SevereAsthma_D26toD31_Gex


title: Human gut microbiota sample 42


title: Human gut microbiota sample 40


title: Human gut microbiota sample 43


title: F1_F_15462_mPFC


title: Human gut microbiota sample 41


title: Stim_CD4_MildAsthma_D06toD10_Gex


title: Human gut microbiota sample 39


title: CD4_Non-TRM_Stim_D07_MildAsthma_S2

description: <400 cells bulk, full-transcriptome (Smart-seq2)

data_processing:
FASTQ was merged and filtered using fastp (v0.20.1)
Reads were aligned with the STAR aligner (v2.7.3a)
samtools (v0.1.19-44428cd) was used to index and sort the BAM files from STAR
QC reports was performed with bamCoverage (v3.3.1) and Qualimap (vv.2.2.2-dev)
Raw and transcripts per million reads (TPM) counts were taken from STAR's BAM aligned output
Genome_build: hg19
Supplementary_files_format_and_content: bulk_counts.txt.gz raw counts for 202 samples in TAB delimited TXT
Supplementary_files_format_and_content: bulk_metadata.txt.gz metadata for 202 samples in TAB delimited TXT
Supplementary_files_format_and_content: bulk_tpm.txt.gz transcripts per million reads (TPM) for 202 samples in TAB delimited TXT

molecule: polyA RNA

extract_protocol:
For bulk RNA-seq, a maximum of 400 cells per population of interest, per donor, and per stimulation condition were sorted individually into low retention 0.2mL PCR tubes, containing 8uL of ice-cold lysis buffer (Triton X-100 [0.1%, Sigma-Aldrich], 1% RNase inhibitor [Takara Bio]). Following sorting, tubes were vortexed for 10s, span for 1min at 3000g, and directly stored at -80°C.
Bulk RNA-seq libraries were prepared for sequencing using the Smart-seq2 protocol adapted for samples with small cell numbers (Rosales et al, 2018) and following standard Illumina protocols. 100 x 100 bp paired-end reads,  Hg19 human reference genome.

treatment_protocol: BAL samples were obtained by instilling a total volume of 120mL of warm 0.9% saline in small aliquots into the right upper lobe segments of the lung using a fiberoptic bronchoscope procedure. Aliquots were pooled together and collected as 1 sample with immediate storage on ice and in liquid nitrogen for long-term storage. To perform this study, BAL samples from each donor were thawed, washed, and diluted to a concentration of 2x10^6 cells/mL with MACS buffer. For the stimulation condition, for each donor, one quarter of the sample was plated, but no more than 500,000 cells, in 500µL of T cell culture medium in 24-well culture plate, and stimulated for 2h with PMA (20nM)/Ionomycin(1µM). Both for resting and stimulation conditions, cells were sequentially stained with fluorescence-labeled surface antibodies and DNA-oligo-conjugated-antibodies (Total-Seq A, Biolegend, 0.5 µg/sample). We then performed FACS sorting of CD103+ CD69+ (CD103+ TRM), CD103– CD69+ (CD103– TRM), and CD103– CD69– (non-TRM) CD4+ T cells from resting and stimulation condition separately.

value: Male

value: Mild asthma

value: PolyAtail captured messenger RNA


title: Human gut microbiota sample 35


title: Human gut microbiota sample 37


title: F1_F_15462_amygdala

value: amygdala


title: Human gut microbiota sample 36


title: Human gut microbiota sample 38


title: Unstim_CD4_MildAsthma_D06toD10_Gex

value: polyA RNA 3'end capture


title: CD4_Non-TRM_Stim_D24_SevereAsthma_S2

value: Stimulated

value: Severe asthma


title: Human gut microbiota sample 34

value: Human gut

value: 16S rRNA


title: F1_F_15462_hypothalamus

value: hypothalamus


title: Bhlhe41dTomato-Cre+/-_CCR2hi rep 3

first: Yaozu

last: Xiang

address: 1239 Siping Road, Yangpu District

institute: Tongji University

data_processing:
Illumina Casava v1.8 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.4.0j with parameters --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 16000000000 --outSAMunmapped Within --twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM --runThreadN 10
Transcripts per million (TPM) were evaluated by a statistical method RSEM (RNA-Seq by Expectation Maximization) using a generative model of RNA-seq reads and the EM algorithm, taking read mapping uncertainty into account and achieving the most accurate abundance estimates
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: heart

extract_protocol:
Total RNA was isolated from the macrophages for analysis using the TRIzol reagent (Invitrogen, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were anesthetized by spontaneous inhalation and maintained under general anesthesia with 1–2% isoflurane. Animals were mechanically ventilated using a rodent ventilator (Harvard Apparatus) connected to an endotracheal tube. The heart was exposed by a left side limited thoracotomy and the LAD was ligated with a 6-0 polyester suture 1 mm from the apex of the normally positioned left auricle.

value: heart

tag: cell line

value: macrophages

tag: genotype

value: male

tag: treatment

value: MI


title: mouse_brain

first: Ryan Mulqueen

last: Mulqueen

state: OR

address: 3181 S.W. Sam Jackson Park Road

department: Molecular and Medical Genetics

institute: Oregon Health and Science

description: single-cell ATAC seq via custom chemistry

library_source: genomic single cell

data_processing:
FastQ files were generated from BCL files using bcl2fastq (v 2.19.0, Illumina Inc.) with the following options with-failed-reads, no-lane-splitting, fastq-compression-level=9, create-fastq-for-index-reads
Data were demultiplexed with scitools (https://github.com/adeylab/scitools) fastq-dump-10x function; briefly FastQ reads were assigned to their expected primer index sequence allowing for sequencing error (Hamming distance ≤2) and indexes were concatenated to form a “cellID”. cellIDs are stored in the FastQ header
Demultiplexed reads were aligned with scitools fastq-align function to a concatenated reference genomes GRCm38 (“mm10”, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2) and GRCh38 (“hg38”,Genome Reference Consortium Human Reference 38 (GCA_000001405.2) via bwa mem (v0.7.15-r1140) .
Aligned reads then underwent a barcode-specific duplicate removal via scitools
Alignment rates of human (hg38) and mouse (mm10) per cellID were then generated with scitools function barnyard-compare and cellIDs were assigned as human, mouse, or mixed.
CellIDs that were assigned to a single genome and realigned to the respective genome (hg38 or mm10), underwent barcode-based removal of duplicates and then filtered to those with >= 10,000 unique reads, and a percentage unique reads of <= 90%.
Persisting barcodes (cellID) were then filtered and fragments files were generated for Signac input.
See "txci-ATAC-seq, a massive-scale single-cell technique to profile chromatin accessibility" methods for further cell type annotation and differential analysis.
Assembly: GRCm38 (“mm10”, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2); GRCh38 (“hg38”,Genome Reference Consortium Human Reference 38 (GCA_000001405.2)
Supplementary files format and content: *_metadata.tsv: Tab-separated file detailing annotations and metadata per cell (each row being a cell).
Supplementary files format and content: *_SeuratObject.PF.Rds: Signac/Seurat R data object files. Can be read in with R function "readRDS" in Signac v 1.0. Contains multiple assays (ATAC, GeneActivity, Chromvar analysis) per cell used in downstream analysis in manuscript.
Supplementary files format and content: *.counts.sparseMatrix.cols.gz;*.counts.sparseMatrix.rows.gz;*.counts.sparseMatrix.values.gz: Sparse Matrix format files of raw fragment counts from called peaks (generated through cellranger)
Supplementary files format and content: *.merged.fragments.tsv.gz,*.merged.fragments.tsv.gz.tbi; Fragment file (modified bed format) with index file generated through samtools and tabix from aligned bam file.

source_name: whole brain

extract_protocol:
Human cortex samples from the middle frontal gyrus were sourced from the Oregon Brain Bank from a 50-year-old female of normal health status. Samples were collected by an OHSU neuropathologist, placed into a labeled cassette, and cryopreserved in an airtight container in a -80 °C freezer. The duration of time between the time of death and brain biopsy sample freezing, or post-mortem interim (PMI), was <24 hours. Mouse brain tissue was collected as discarded tissue from mice used for unrelated studies approved by the OHSU IACUC. Whole mouse brains were dissected from sacrificed C57BL/6J mice and flash-frozen in an isopentane-LN2 double-bath and stored at -80 °C.
At the time of nuclei dissociation, 50 ml of nuclei isolation buffer (NIB-HEPES) was freshly prepared with final concentrations of 10 mM HEPES-KOH (Fisher Scientific, BP310-500 and Sigma Aldrich 1050121000, respectively), pH 7.2, 10 mM NaCl (Fisher Scientific S271-3), 3mM MgCl2 (Fisher Scientific AC223210010), 0.1 % (v/v) IGEPAL CA-630 (Sigma Aldrich I3021), 0.1 % (v/v) Tween-20 (Sigma-Aldrich P-7949) and diluted in PCR-grade Ultrapure distilled water (Thermo Fisher Scientific 10977015). After dilution, two tablets of Pierce™ Protease Inhibitor Mini Tablets, EDTA-free (Thermo Fisher A32955) were dissolved and suspended to prevent protease degradation during nuclei isolation.
An at-bench dissection stage was set up prior to nuclei extraction. A petri dish was placed over dry ice, with fresh sterile razors pre-chilled by dry-ice embedding. 7 ml capacity Dounce homogenizers were filled with 2 ml of NIB-HEPES buffer and held on wet ice. Dounce homogenizer pestles were held in ice-cold 70% (v/v) ethanol (Decon Laboratories Inc 2701) in 15 ml tubes on ice to chill. Immediately prior to use, pestles were rinsed with chilled distilled water. For tissue dissociation, mouse and human brain samples were treated similarly. The still-frozen block of tissue was placed on the clean pre-chilled petri dish and roughly minced with the razors. Razors were then used to transport roughly 1 mg of the minced tissue into the chilled NIB-HEPES buffer within a Dounce homogenizer. Suspended samples were given 5 minutes to equilibrate to the change in salt concentration prior to douncing. Tissues were then homogenized with 5 strokes of a loose (A) pestle, another 5-minute incubation, and 5-10 strokes of a tight (B) pestle. Nuclei were transferred to a 15 ml conical tube and pelleted with a 400 r.c.f centrifugation at 4 °C in a centrifuge for 10 minutes. The supernatant was removed and pellets were resuspended in 5 ml of ATAC-PBS buffer (APB) consisting of 1X PBS (Thermo Fisher 10010) and 0.04mg/ml (f.c.) of bovine serum albumin (BSA, Sigma Aldric A2058). Samples were then filtered through a 35 µm cell strainer (Corning 352235). A 10 μl aliquot of suspended nuclei was diluted in 90 μl APB (1:10 dilution) and manually counted on a hemocytometer with Trypan Blue staining (Thermo Scientific T8154). The stock nuclei suspension was then diluted to a concentration of 2,857 nuclei/μl in APB. Dependent on experimental schema, pools of tagmented nuclei were combined to allow for the assessment of pure samples and to test index collision rates.
Tagmentation plates were prepared by the combination of 1430 μl of TBS with 770 μl nuclei solution. The TBS recipe was described in “Blocking barcode-swapping”, but a different version of Digitonin (Bivision 2082-1) was used here. This solution was mixed briefly on ice. 20 μl of the mixture was placed into the 96-well iTSM plate (see “Sample multiplexing” for details). Tagmentation was performed at 37 °C for 60 minutes on a 300 r.c.f Eppendorf ThermoMixer with a lid heated to 65 °C. Following this incubation, plate temperature was brought down with a 5-minute incubation on ice to stop the reaction. Tagmented nuclei were then pooled into a single 15 ml conical tube. 5 ml of tagmentation wash buffer (TMG) was prepared consisting of a final concentration of 10 mM Tris Acetate pH 7.5 (Sigma 93352 and Sigma A6283, respectively), 5 mM MgAcetate (Sigma M5661), and 10% (v/v) glycerol (Sigma G5516), diluted in PCR grade water. 1 ml of TMG was added on top of the chilled tagmented nuclei. Nuclei were pelleted at 500 r.c.f for 10 minutes at 4 °C. Most of the supernatant was removed with care not to disturb the pellet. Then 500 μl of TMG was added to the pellet and the tube was once again spun at 500 r.c.f. for 5 minutes at 4 °C. 490 μl was removed leading to a low volume of concentrated nuclei. Loading buffer was prepared consisting of 10% (v/v) glycerol, 20 mM NaCl, 10 mM Tris-Cl pH 7.5 (Life technologies AM9855), 0.02 mM EDTA (Fisher Scientific AM9260G), 0.2 mM DTT (VWR 97061-340), and 0.2x (v/v) TB1 (Illumina Inc.). The nuclear pellet was resuspended with an additional 30 μl of loading buffer. An aliquot of 2 μl of sample was diluted 20-50X and quantified with Trypan Blue on a hemocytometer. Depending on the experiment, a 14 μl nuclei solution containing the desired amount of nuclei in the loading buffer was then combined with 1 μl of 75 μM short SBS oligo (Table S8).
The 10X Chromium was then run with the custom nuclei solution as per the manufacturer’s instructions (10x Document CG000209 Rev D) with the following adaptations. In step 2.4e during GEM aspiration and transfer, 100 μl GEM volume was split into two tubes, with one receiving 10 μl and the other 90 μl (henceforth referred to as 10% and 90% samples). In step 2.5.a, GEM incubation cycles were limited to 6. For Pre-PCR wash elution (Step 3.2.j) the 10% sample was eluted in 8.5 μl whereas the 90% sample was eluted in 32.5 μl. For step 3.2.n, the 10% sample had 8 μl transferred to a new strip, while the 90% sample had 32 μl transferred to a new strip. At step 4.1.b, the sample Index PCR mix was split with 11.5 μl and 46 μl being combined with the 10% and 90% samples, respectively. For step 4.1.c, 1 μl and 2 μl of a 10 μM i7 TruSeq primer was used, respectively. For step 4.1.d, 8 and 7 PCR cycles were used, respectively. Libraries were then checked for quality and quantified by Qubit DNA HS assay (Agilent Q32851) and Tapestation D5000 (Agilent 5067-5589) following the manufacturer’s instructions. Libraries were then diluted and sequenced on a NextSeq 500 Mid flow cell or a NovaSeq 6000 S4 flow cell (Illumina Inc.).

value: whole brain


title: F1_F_15462_midbrain

value: brain

value: midbrain

tag: Sex

value: F


title: Human gut microbiota sample 33

tag: molecule type


title: CD4_CD103–TRM_Stim_D12_MildAsthma_S2

value: Male

value: Mild asthma


title: Human gut microbiota sample 32


title: Bhlhe41dTomato-Cre+/-_CCR2hi rep 2


title: Bhlhe41dTomato-Cre+/-_CCR2hi rep 1


title: CD4_CD103–TRM_Stim_D11_MildAsthma_S2

value: PolyAtail captured messenger RNA


title: Human gut microbiota sample 30


title: Human gut microbiota sample 29


title: Human gut microbiota sample 31


title: F1_F_15462_thalamus

value: thalamus

value: F1 hybrid (P. maniculatus x P. polionotus)


title: CD4_CD103–TRM_Stim_D08_MildAsthma_S2

value: Stimulated

value: Female


title: Human gut microbiota sample 28

value: Human gut

value: 16S rRNA


title: Human gut microbiota sample 26


title: CD4_CD103–TRM_Stim_D05_MildAsthma_S2


title: Bhlhe41dTomato-Cre+/-_CCR2low rep 3

value: heart


title: Stim_CD4_MildAsthma_D11toD15_Gex

value: Mild Asthma

value: polyA RNA 3'end capture


title: Human gut microbiota sample 25


title: Bhlhe41dTomato-Cre+/-_CCR2low rep 2

value: macrophages

value: male

value: MI


title: Bhlhe41dTomato-Cre+/-_CCR2low rep 1


title: CD4_CD103–TRM_Stim_D01_MildAsthma_S2


title: Human gut microbiota sample 23


title: CD4_CD103+TRM_Stim_D28_SevereAsthma_S2

value: Severe asthma


title: Human gut microbiota sample 24


title: Human gut microbiota sample 21


title: Aiolos_gd_WT2

city: St. Louis

first: Marco

last: Colonna

state: Missouri

address: 425 S. Euclid

department: Pathology and Immunology

institute: Washington University in St. Louis

data_processing:
Sequencing data were mapped onto mouse genome build mm9 using Bowtie2. Duplicate reads were removed using Picard’s markDuplicates. MACS2 was used for peak calling using a p value threshold of 1 x 10-5.
Assembly: mm9
Supplementary files format and content: bw file
Library strategy: CUT&RUN

source_name: small intestine

extract_protocol:
CUT&RUN-seq was performed using CUTANATM ChIC/CUT&RUN kit (EpiCypher #14-1048) following manufacturer’s instructions. For each procedure, 1mg of antibodies and sorted 0.5x106 cells were used.
Libraries are generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645S) and NEBNext Multiplex Oligos for Illumina (NEB #E7600S) following the manufacture’s protocol

value: Ikzf3 +/+

value: small intestine

value: IEL

tag: chip antibody

value: clone 9D10 (Sigma Aldrich)


title: Human gut microbiota sample 20


title: Aiolos_gd_WT1


title: Human gut microbiota sample 19


title: Aiolos_gd_KO

value: Ikzf3 -/-


title: CD4_CD103+TRM_Stim_D01_MildAsthma_S2

value: Male

value: Mild asthma

value: PolyAtail captured messenger RNA


title: CD4_CD103+TRM_Stim_D05_MildAsthma_S2

value: Stimulated


title: Human gut microbiota sample 16

value: Human gut

value: 16S rRNA


title: Aiolos_DN_WT2


title: Human gut microbiota sample 17


title: Human gut microbiota sample 15


title: Human gut microbiota sample 18


title: Human gut microbiota sample 22


title: Human gut microbiota sample 12


title: Human gut microbiota sample 27


title: Aiolos_DN_WT1


title: CD4_CD103+TRM_Stim_D07_MildAsthma_S2


title: Human gut microbiota sample 14


title: CD4_Non-TRM_Unstim_D20_SevereAsthma_S2

value: Unstimulated


title: Human gut microbiota sample 13


title: CD4_Non-TRM_Unstim_D12_MildAsthma_S2


title: Human gut microbiota sample 11


title: Aiolos_DN_KO


title: gdATAC_WT4

data_processing:
Sequencing data were mapped onto mouse genome build mm9 using Bowtie2. Duplicate reads were removed using Picard’s markDuplicates. MACS2 was used for peak calling using a p value threshold of 1 x 10-5.
Assembly: mm9
Supplementary files format and content: bw file

extract_protocol: 50,000 cells were sorted and processed as per manufacturer’s instructions (Nextera DNA Library Preparation Kit, Illuminia)

value: ATAC


title: Human gut microbiota sample 9


title: CD4_Non-TRM_Unstim_D05_MildAsthma_S2


title: F1_F_15650_amygdala

value: brain

value: amygdala

value: F1 hybrid (P. maniculatus x P. polionotus)

value: F


title: Human gut microbiota sample 8


title: gdATAC_WT3

value: Ikzf3 +/+


title: F1_F_15650_midbrain

value: midbrain


title: CD4_Non-TRM_Unstim_D14_MildAsthma_S2

value: Female


title: CD4_CD103–TRM_Unstim_D10_MildAsthma_S2


title: Human gut microbiota sample 6


title: Human gut microbiota sample 10


title: Human gut microbiota sample 7


title: gdATAC_WT1

value: small intestine

value: IEL


title: Human gut microbiota sample 3


title: Human gut microbiota sample 1


title: gdATAC_KO4

value: Ikzf3 -/-


title: CUTRUN.15_MRTK.103_antiBRD9

description: CUT&RUN in MRT organoids P103

data_processing:
ChIP-seq were mapped to a hg38 reference. The mapped reads with mapping quality score <15 and the optical PCR duplicates were discarded using SAMtools. The coverage files of ChIP-seq data were generated using “normalize to 1X genome coverage” methods in deepTools. Peak calling was performed using MACS2 (version 2.1.1.20160309) (Liu, 2014) at a q-value cutoff of 0.01. CUT&RUN data were mapped to the hg38 reference genome using BWA-MEM (version 0.7.15-r1140). The mapped reads were filtered using SAMtools, discarding reads with mapping quality score <15, as well as optical PCR duplicates. The coverage files were produced using the deepTools (version 3.0) method “normalize to 1X genome coverage”.
Assembly: hg38
Supplementary files format and content: bigWig files
Library strategy: cut&run

source_name: MRT organoids P103

extract_protocol:
ChIP-seq experiments were performed using a published protocol (Liu et al., 2021). For chromatin preparation, the MRT cells were cross-linked by a final concentration of 1% formaldehyde for 10 min. To perform a double-crosslinking reaction, a first cross-linking was performed by adding 2mM disuccinimidyl glutarate (DSG, 20593, Thermo Fisher) for 45 minutes at room temperature and washed once with 1x PBS before second cross-linking reaction. Subsequently, cells were cross-linked with a final concentration of 1% formaldehyde for 10 minutes. The cross-linking reaction was quenched using 2.0 M glycine. The cross-linked cells were then lysed and sonicated to obtain ~300 bp chromatin using Bioruptor Plus sonication device (Diagenode). For ChIP assays, antibodies were first coupled with Protein G beads (ThermoFisher Scientific), and then the sonicated chromatin were incubated overnight at 4oC with the antibody coupled Protein G beads. After over incubation, captured chromatin was washed, eluted and de-crosslinked. The released DNA fragments were purified using MiniElute PCR Purification Kit (Qiagen). The ChIP experiments were performed using the following antibodies: (1) CTCF (07-729, Merck Millipore), (2) RAD21 (ab154769, Abcam), and (3) H3K27ac (ab4729, Abcam).
ChIP-seq libraries were prepared according to the protocol of KAPA HTP Library Preparation Kit (Roche).

value: MRT organoids P103

value: Malignant rhabdoid tumor cells

value: no treatment


title: CUTRUN.14_MRTK.103_antiSS18

description: CUT&RUN in MRT organoids P103


title: Human gut microbiota sample 2

value: Human gut


title: gdATAC_KO2


title: CUTRUN.13_MRTK.103_noAb

description: CUT&RUN in MRT organoids P103


title: CUTRUN.12_MRTK.103_antiBRD9_iBRD9

description: CUT&RUN in MRT organoids P103, after 5 days treatment with iBRD9


title: CD4_CD103–TRM_Unstim_D11_MildAsthma_S2

value: Male

value: Mild asthma

value: PolyAtail captured messenger RNA


title: CD4_CD103+TRM_Unstim_D10_MildAsthma_S2

value: Unstimulated


title: Unstim_CD4_SevereAsthma_D16toD20_Gex

value: Severe Asthma

value: polyA RNA 3'end capture


title: Human gut microbiota sample 5

value: 16S rRNA


title: CD4_CD103–TRM_Unstim_D14_MildAsthma_S2


title: CD4_CD103+TRM_Unstim_D14_MildAsthma_S2


title: CUTRUN.11_MRTK.103_antiBRD9_DMSO

description: CUT&RUN in MRT organoids P103, after 5 days treatment with DMSO

value: DMSO


title: CUTRUN.10_MRTK.103_antiSS18_iBRD9


title: gdATAC_KO1

value: ATAC


title: CD4_CD103–TRM_Unstim_D12_MildAsthma_S2


title: gdATAC_KO3


title: DN_ATAC_WT2

value: Ikzf3 +/+


title: gdATAC_WT2

value: small intestine


title: CD4_CD103–TRM_Unstim_D13_MildAsthma_S2

value: Female


title: CUTRUN.07_MRTK.103_noAb_DMSO


title: CUTRUN.09_MRTK.103_antiSS18_DMSO


title: DN_ATAC_WT3

value: IEL


title: F1_F_15467_hindbrain

value: brain

value: hindbrain

value: F1 hybrid (P. maniculatus x P. polionotus)

value: F


title: CUTRUN.06_MRTK.103_antiBRD9_SMARCB1

description: CUT&RUN in MRT organoids P103, after 4 days lentiviral transduction with the Luciferase gene

value: MRT organoids P103

value: Malignant rhabdoid tumor cells

value: a wild-type full-length SMARCB1 gene plasmid


title: CUTRUN.04_MRTK.103_antiSS18_SMARCB1


title: CD4_CD103+TRM_Unstim_D13_MildAsthma_S2

value: Unstimulated

value: Mild asthma

value: PolyAtail captured messenger RNA


title: CD4_CD103+TRM_Unstim_D12_MildAsthma_S2

value: Male


title: CD4_Non-TRM_Stim_D20_SevereAsthma_S2

value: Stimulated

value: Severe asthma


title: CUTRUN.05_MRTK.103_antiBRD9_CTRL

value: Luciferase plasmid


title: DN_ATAC_WT1

value: small intestine

value: ATAC

value: Ikzf3 +/+


title: CUTRUN.03_MRTK.103_antiSS18_CTRL


title: DN_ATAC_KO4

value: IEL

value: Ikzf3 -/-


title: CD4_Non-TRM_Stim_D19_SevereAsthma_S2

value: Female


title: CUTRUN.01_MRTK.103_noAb_CTRL


title: Human gut microbiota sample 4

value: Human gut

value: 16S rRNA


title: CUTRUN.02_MRTK.103_noAb_SMARCB1

value: MRT organoids P103

value: Malignant rhabdoid tumor cells


title: DN_ATAC_KO3


title: CUTRUN.08_MRTK.103_noAb_iBRD9


title: leucogenys_gibbon_M_CTCF_rep2

description: HMO-gibbon-CTCF.bigwig

organism: Nomascus leucogenys

source_name: LCL

extract_protocol: ChIP-seq libraries were contructed using the NEBNext UltraII kit according to manufactor's instructions.

value: LCL

value: ChIP

value: Northern white-cheecked gibbon

value: M


title: leucogenys_gibbon_M_input_rep1

value: INPUT


title: leucogenys_gibbon_M_input_rep2


title: DN_ATAC_KO2


title: DN_ATAC_KO1


title: leucogenys_gibbon_M_CTCF_rep1

description: HMO-gibbon-CTCF.bigwig


title: leucogenys_gibbon_F_input

data_processing:
Raw reads were aligned to the approporiate reference genome using bowtie2, with default settings
Alignments were converted to bam and filtered to remove low quality mapped reads using samtools
deeptools was used to calculate RPKM normalized signal of each epigenetic mark across the genome and at TAD boundaries
ChromHMM was used to annotate chromatin states using the mouse alignments
Assembly: mm10, mPah1, mCar1, nomLeu4, hMol2
Supplementary files format and content: bigWig; bed

value: F


title: leucogenys_gibbon_M_HiC

value: White cheecked gibbon

tag: protocol

value: Arima


title: leucogenys_gibbon_F_CTCF

description: HMO-gibbon-CTCF.bigwig


title: leucogenys_gibbon_F_HiC


title: FoxP3_Mutant_scATAC

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Sequencing data were converted to fastq files, aligned to the mm10 reference genome, and quantified per cell using Cell Ranger ATAC software (10x Genomics, v1.2).
Hashtag processing followed the original recommendations of the ASAP-seq paper (Mimitou et al, Nature Biotech, 2021), using asap_to_kite (https://github.com/caleblareau/asap_to_kite) to process FASTQs files for downstream quantification by the bustools and kite workflows {Melsted et al, Nature Biotech 2021; Booeshagi et al, bioRxiv, 2022}. We used the HTODemux() (Stoeckius et al, Genome Biology, 2018)  function in the Seurat package (v4.0.2) (Hao et al, Cell, 2021) to remove doublets and call hashtag identities.
To enable comparisons across conditions and datasets, we used a common set of Treg- specific open chromatin regions, defined previously (Chowdhary et al, biorxiv, 2023) by supplementing pan-immunocyte OCRs from the ImmGen consortium (Yoshida et al, Cell, 2019) with additional peaks from Treg scATAC-seq data.
Data analysis was performed using Signac v1.4 (Stuart et al, Nature Methods, 2021). For quality control, only cells with at least 1x10^3 fragments per cell , greater than 50 percent reads in peaks, TSS enrichment score greater than 2, nucleosome signal less than 10, and ratio of blacklist-region reads less than 0.05 were retained for further analysis. Putative doublets identified by ArchR v1.0.1 (Granja et al, Nature Genetics, 2021) and non-Treg contaminant cells were also removed. We used the latent semantic indexing approach as previously described (Cusanovich et al, Cell, 2018; Stuart et al, Cell, 2019). Binarized count matrices were normalized using the term frequency-inverse document frequency (TF-IDF) transformation and reduced in dimensionality by singular value decomposition (SVD). As the first component was highly correlated with sequencing depth, SVD components 2-30 were used to generate a shared nearest neighbor (SNN) graph for clustering and as input into UMAP (McInnes et al, ArXiv, 2018) with cosine distance metric for visualization.
Assembly: mm10
Supplementary files format and content: .mtx ATAC counts matrices, peaks.txt files have OCR locations, barcodes.txt files have cell barcodes
Supplementary files format and content: fragments.tsv.gz files have raw ATAC fragments, fragments.tsv.gz.tbi files are index of fragments files
Supplementary files format and content: Metadata.txt files have relevant metadata, including cell population assignment, UMAP coordinates
Supplementary files format and content: Hashtag_Counts.txt files contain raw counts of ASAPseq hashtags by cell barcode for cells included in ATAC counts matrices

source_name: Spleen

extract_protocol:
Treg were sorted from mice of the appropriate genotype and desired organ, as detailed in experimental design, into DMEM + 5% FCS in DNA Lo-Bind tubes for input in to scATAC-seq/ASAP-seq as detailed in the next step.
For experiments with multiple conditions per scATAC run, we hashtagged cells using a modification of the ASAP-seq strategy (Mimitou et al, Nature Biotech, 2021) for low cell input primary cell samples. Before sorting, cells were hashtagged with TotalSeqA DNA-barcoded hashtag antibodies at the same time as staining with fluorophore-conjugated antibodies (BioLegend). Cells were sorted into DMEM + 5% FCS in DNA Lo-Bind tubes (Eppendorf, cat # 022431021). After spinning down for 5 min at 500g in a refrigerated centrifuge at 4C, cells were resuspended in 100 μl chilled 0.1x Omni Lysis buffer (1x Omni Lysis buffer (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40 substitute/IGEPAL, 0.01% Digitonin, 1% BSA in nuclease free water) diluted 1:10 in Wash/Lysis Dilution Buffer (10mM Tris-HCl, 10mM NaCl, 3 mM MgCl2, 1% BSA in nuclease free water)), gently mixed by pipetting and incubated on ice for 6.5 min. Following lysis, 100 μl chilled wash buffer was added and gently mixed by pipetting. Cells were spun down for 5min at 500g at 4C, all but 5 μl of supernatant was removed, and 45 μl of chilled 1x nuclei buffer (10x Genomics) was added without mixing. After one more centrifugation step at 500g, 4C for 5 min, supernatant was removed, and samples were resuspended in 7ul 1x nuclei buffer for cell counting and input into transposition, barcoding, and library preparation according to the Chromium Next GEM Single Cell ATAC manual (10x Genomics).   Modifications to the original 10X protocol were made as described in the original ASAP-seq publication and as detailed at https://citeseq.files.wordpress.com/2020/09/asap_protocol_20200908.pdf. Briefly, 0.5 μl of 1uM BOA bridge oligo was spiked into the barcoding reaction. During GEM incubation, an additional 5 min incubation at 40C was added to the beginning of the protocol. 43.5 instead of 40.5 μl of Elution Solution I was added during silane bead elution to recover 43 μl. 40 μl was used for SPRI clean up as indicated in the protocol, while 3 μl was set aside. During SPRI cleanup, the supernatant was saved. The bead bound fraction was processed as in the protocol, while for the supernatant fraction, 32 μl SPRI was added for 5 min. Beads were collected on a magnet, washed twice with 80% ethanol, and eluted in 42 μl EB. This 42 μl was combined with the 3 μl set aside from the previous step as input into the HTO indexing reaction. HTO Indexing PCR was run with partial P5 and indexed Rpxx primers as: 95C 3 min, 12-14 cycles of (95C 20 sec, 60C 30 sec, 72C 20 sec), 72C 5 min. The PCR product was cleaned up with 1.6X SPRI purification for quantification and sequencing alongside ATAC libraries.

value: Spleen

value: Treg

value: WT, FOXP3.p.Lys199del, FOXP3.p.R337Q, FOXP3.p.R51Q

value: B6, B6 Foxp3-ires-GFP


title: CD4_Non-TRM_Stim_D04_MildAsthma_S2

value: Stimulated

value: Female

value: Mild asthma

value: PolyAtail captured messenger RNA


title: CD4_Non-TRM_Stim_D09_MildAsthma_S2

value: Male


title: THP-1 cells, G9a_KO, TL, m6A-IP, biol rep 1

city: Chapel Hill

first: Adil

last: Muneer

state: North Carolina

address: 120 Mason Farm Rd, Genetic Medicine Building

department: Biochemistry and Biophysics

institute: University of North Carolina Chapel Hill

data_processing:
The raw sequencing data were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina).
The adapter was trimmed by Trimmomatic-0.32 software.
Input and m6A-IP reads were mapped to human genome version hg38 by STAR v.2.5.2a, and only uniquely mapping reads at the exon level for each gene were quantified and summarized to gene counts, which were further analyzed in R v.3.6.2 using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

growth_protocol: THP-1 cells were maintained in RPMI 1640 media supplemented with 10% fetal bovine serum (FBS) and 100 U/ml penicillin and streptomycin in humidified atmosphere with 5% carbon dioxide at 37 °C.

extract_protocol:
Messenger RNA from 10 ug total RNA extracted from Ctrl, METTL3 KO and G9a KO cell samples was purified with Dynabeads Oligo (dT)25 (Thermo Fisher; 61006). Ten percent of 150 ng mRNA was used as Input mRNA, and the remainder was incubated with 3 ug anti-m6A polyclonal antibody (Synaptic Systems; 202003) which was preconjugated to Dynabeads Protein A (Thermo Fisher; 10001D) in 500uL IP buffer (50 mM Tris, pH 7.4, 150 mM NaCl, 0.1% Igepal CA-630) for 2 hours at 4°C. After washing twice with IP-buffer and twice with High-Saltwash buffer (50 mM Tris pH 7.4, 500 mM NaCl, 0.1% Igepal CA-630) for 5 minutes each, the m6A mRNA was eluted with 100 uL IP-buffer containing 6.7 mM N6-Methyladenosine (Sigma-Aldrich; M2780) and 40 U RNase Inhibitor (NEB, M0314S) and then recovered with RNA Clean and Concentrator-5 spin columns (Zymo; R1015).
The Input mRNA and m6A-IPed mRNA were subjected to library generation using the SMART-seq2 protocol as described (Nature Protocols volume 9, pages171–181). For the synthesis of the first strand cDNA, the mRNA was mixed with 0.25 µL RNase inhibitor and 1 µL CDS primer (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’) and heated to 70 ºC for 2 min. Then the mixture containing 0.5 µL of 100 mM DTT, 0.3 µL of 200 mM MgCl2, 1 µL of 10 mM dNTPs, 0.25 µL RNase inhibitor, 1 µL of 10 µM TSO primer (5’-AAGCAGTGGTATCAACGCAGAGTACATrGrGrG-3’), 2 µL of 5X SMARTScribe RT buffer and 0.5 µL SMARTScribe reverse transcriptase (Takara, 639536) was added for performing reverse transcription. The cDNA was then amplified by Advantage Polymerase Mix (TAKARA, 639201) with IS primer (5’-AAGCAGTGGTATCAACGCAGAGT-3’). After purification with 0.8X AMPure XP beads (Fisher Scientific, A63880), the fragmentation of 100 pg cDNA was performed with EZ Tn5 Transposase (Lucigen, TNP92110). Fragments of cDNA were amplified by KAPA HiFi hotstart readymix (EMSCO/FISHER, KK2601) with the Nextera i7 primer and Nextera i5 primer. The DNA was purified with 0.8X AMPure XP beads and quantified by qPCR with KAPA Library Quantification Kit (Fisher, NC0078468). The DNA from different samples was pooled at equal molar amounts, and the final sequencing library was loaded at concentrations of 2.7 pM, and sequenced on a NextSeq 550 (Illumina) for single-read sequencing.

treatment_protocol:
THP-1 cells were first incubated in the presence of 60 nM PMA overnight to differentiate into macrophages followed by 48 h resting in PMA-free medium.
THP-1 cells were either left unstimulated (‘N’) or subjected to a single LPS stimulation at 1 µg/ml for 15 min (‘NL’)  or first primed with 100 ng/ml LPS to induce endotoxin tolerance for 24 h, followed by the second LPS challenge at 1 µg/ml for 15 min (‘TL’).

value: monocyte

value: G9a knockout

value: TL

tag: m6a ip

value: IP

tag: replicate


title: CD4_Non-TRM_Stim_D03_MildAsthma_S2


title: THP-1 cells, G9a_KO, TL, Input, biol rep 1

value: input


title: Wild-type_heart_CaptureHiC_rep2

data_processing:
Raw capture HiC data was aligned to mm10 genome using HiCUP.
Pairtools was used to further process data and generate interaction matrices across replicates in each genotype.
HiCExplorer python package was used to identify TADs and calculate insulation scores.
Assembly: mm10
Supplementary files format and content: bedgraph files contain insulation scores, which are the result of calling TADs on the replicate-merged, normalized, HiC data using the program hicFindTADs, from the HiCExplorer python package.
Supplementary files format and content: (.cool) Cooler files represent replicate-merged HiC matrices at 10kb resolution with Knight-Ruiz Iterative Correction (IC) normalization.

extract_protocol:
We used the Arima HiC kit to process mouse testis and heart tissues. Briefly, frozen tissue was lysed and conditioned before chromatin digestion. The digested chromatin was then filled in and biotinylated before ligation. Next, chromatin was protein-digested and reverse crosslinking overnight, followed by purification. The purified DNA was then sonicated using the bioruptor pico (Diagenode) and size selected before library preparation using the NEB DNA Ultra II, following Arima’s protocol.
The Hi-C DNA was bound to streptavidin beads before enzymatic end prep, adaptor ligation, DNA release by heat incubation, and lastly, PCR to barcode and amplify the libraries. Capture Hi-C libraries were generated by using the Agilent SureSelect Target Enrichment Kit.
capture Hi-C

value: heart

value: Wild-type


title: B5234_hom_heart_KO_CaptureHiC_rep2


title: CD4_Non-TRM_Stim_D16_SevereAsthma_S2

value: Severe asthma


title: THP-1 cells, G9a_KO, NL, m6A-IP, biol rep 2

value: NL


title: THP-1 cells, G9a_KO, TL, Input, biol rep 2


title: CD4_Non-TRM_Stim_D17_SevereAsthma_S2


title: THP-1 cells, G9a_KO, NL, m6A-IP, biol rep 1


title: B5234_hom_heart_KO_CaptureHiC_rep1


title: CD4_Non-TRM_Stim_D02_MildAsthma_S2


title: THP-1 cells, G9a_KO, NL, Input, biol rep 1


title: CD4_CD103–TRM_Stim_D20_SevereAsthma_S2


title: CD4_CD103–TRM_Stim_D24_SevereAsthma_S2


title: ATXN1-82Q Tg Cerebellum 52 Weeks Old Rep 3

city: New Haven

first: Evrett

middle: Nathanial

last: Thompson

state: CT

address: 333 Cedar Street

department: Cell Biology

institute: Yale School of Medicine

data_processing:
STAR v2.7.7a was used to align reads to the mouse reference genome mm10. Set --outFilterMismatchNmax 2, kept all other parameters default.
The htseq-count v0.13.5 from the HTSeq package was used to count reads from the alignments generated using STAR. Set parameters -s reverse -m union -r pos, all other parameters kept default.
Read counts for each sample were input directly into DESeq2, which was used to carry out normalization and differential gene analysis using default parameters.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw read counts generated by HTSeq per sample.

source_name: Cerebellum

growth_protocol: Not applicable

extract_protocol:
Cerebella were dissected out, flash frozen, and kept at -80°C until further processing. Anatomical location was verified under a dissection microscope. The same individual conducted all tissue extractions to eliminate variability in sample collection. Total RNA was extracted from frozen mouse cerebellum using the Qiagen RNeasy Mini Kit (Qiagen, 74106) per the manufacturer’s protocol. RNA was sent to the Yale Center for Genomic Analysis for library preparation and sequencing.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit following manufacturer's protocol. Briefly, this kit selects for transcripts containing a polyA tail and uses dUTPs to produce a reverse stranded library. Sequencing was conducted using standard Illumina protocols.

value: Cerebellum

value: FVB/NJ

value: ATXN1-82Q Tg

tag: age

value: 52 weeks old


title: THP-1 cells, G9a_KO, NL, Input, biol rep 2


title: THP-1 cells, G9a_KO, N, Input, biol rep 2

value: N


title: ATXN1-82Q Tg Cerebellum 52 Weeks Old Rep 2

tag: strain


title: THP-1 cells, G9a_KO, N, m6A-IP, biol rep 2


title: THP-1 cells, G9a_KO, N, Input, biol rep 1


title: CD4_CD103–TRM_Stim_D19_SevereAsthma_S2

value: Stimulated

value: Female


title: THP-1 cells, G9a_KO, N, m6A-IP, biol rep 1


title: ATXN1-82Q Tg Cerebellum 52 Weeks Old Rep 1


title: CD4_CD103–TRM_Stim_D31_SevereAsthma_S2

value: PolyAtail captured messenger RNA


title: THP-1 cells, METTL3_KO, TL, m6A-IP, biol rep 2

value: monocyte

value: METTL3 knockout


title: THP-1 cells, METTL3_KO, TL, Input, biol rep 2

value: TL


title: THP-1 cells, G9a_KO, TL, m6A-IP, biol rep 2

value: G9a knockout

value: IP


title: WT FVB Cerebellum 52 Weeks Old Rep 3

value: WT


title: WT FVB Cerebellum 52 Weeks Old Rep 2


title: THP-1 cells, METTL3_KO, TL, m6A-IP, biol rep 1


title: CD4_CD103–TRM_Stim_D09_MildAsthma_S2

value: Male

value: Mild asthma


title: THP-1 cells, METTL3_KO, NL, m6A-IP, biol rep 2

value: NL


title: CD4_CD103–TRM_Stim_D16_SevereAsthma_S2

value: Severe asthma


title: THP-1 cells, METTL3_KO, NL, Input, biol rep 2

value: input


title: THP-1 cells, METTL3_KO, NL, Input, biol rep 1


title: WT FVB Cerebellum 52 Weeks Old Rep 1

value: Cerebellum

value: FVB/NJ


title: CD4_CD103–TRM_Stim_D07_MildAsthma_S2


title: THP-1 cells, METTL3_KO, NL, m6A-IP, biol rep 1


title: THP-1 cells, METTL3_KO, N, Input, biol rep 2

value: N


title: THP-1 cells, METTL3_KO, TL, Input, biol rep 1


title: THP-1 cells, METTL3_KO, N, m6A-IP, biol rep 2


title: ATXN1-82Q Tg Cerebellum 20 Weeks Old Rep 2

value: ATXN1-82Q Tg

value: 20 weeks old


title: CD4_CD103–TRM_Stim_D17_SevereAsthma_S2

value: Stimulated

value: PolyAtail captured messenger RNA


title: CD4_CD103–TRM_Stim_D04_MildAsthma_S2

value: Female


title: THP-1 cells, Ctrl_KO, TL, Input, biol rep 2

value: monocyte

value: TL


title: CD4_CD103–TRM_Stim_D03_MildAsthma_S2


title: THP-1 cells, Ctrl_KO, TL, m6A-IP, biol rep 2

value: IP


title: ATXN1-82Q Tg Cerebellum 20 Weeks Old Rep 3


title: THP-1 cells, METTL3_KO, N, Input, biol rep 1

value: METTL3 knockout


title: THP-1 cells, Ctrl_KO, TL, Input, biol rep 1

value: WT


title: THP-1 cells, Ctrl_KO, TL, m6A-IP, biol rep 1


title: CD4_CD103–TRM_Stim_D02_MildAsthma_S2

value: Male

value: Mild asthma


title: THP-1 cells, Ctrl_KO, NL, Input, biol rep 2

value: NL


title: CD4_CD103+TRM_Stim_D24_SevereAsthma_S2

value: Severe asthma


title: THP-1 cells, Ctrl_KO, NL, Input, biol rep 1

value: input


title: WT FVB Cerebellum 20 Weeks Old Rep 1

value: Cerebellum

value: FVB/NJ


title: WT FVB Cerebellum 20 Weeks Old Rep 2


title: THP-1 cells, Ctrl_KO, NL, m6A-IP, biol rep 1


title: CD4_CD103+TRM_Stim_D20_SevereAsthma_S2


title: ATXN1-82Q Tg Cerebellum 12 Weeks Old Rep 3

value: ATXN1-82Q Tg

value: 12 weeks old


title: THP-1 cells, Ctrl_KO, N, Input, biol rep 2

value: N


title: THP-1 cells, METTL3_KO, N, m6A-IP, biol rep 1


title: THP-1 cells, Ctrl_KO, N, m6A-IP, biol rep 2


title: CD4_CD103+TRM_Stim_D19_SevereAsthma_S2

value: Stimulated

value: PolyAtail captured messenger RNA


title: ATXN1-82Q Tg Cerebellum 20 Weeks Old Rep 1

value: 20 weeks old


title: THP-1 cells, Ctrl_KO, N, Input, biol rep 1

value: monocyte


title: ATXN1-82Q Tg Cerebellum 12 Weeks Old Rep 2


title: ATXN1-82Q Tg Cerebellum 12 Weeks Old Rep 1


title: THP-1 cells, Ctrl_KO, N, m6A-IP, biol rep 1

value: IP


title: WT FVB Cerebellum 20 Weeks Old Rep 3


title: 4C.04_MRTK.60_MYC.P_SMARCB1_rep2

description: 4C-seq in MRT organoids P60, after 4 days lentiviral transduction with the SMARCB1 gene

data_processing:
4C-seq: The raw sequence data was mapped using our 4C mapping pipeline (http://github.com/deWitLab/4C_mapping ).
Assembly: hg38
Supplementary files format and content: bedgraph files
Library strategy: 4C-seq

source_name: MRT organoids P60

extract_protocol:
4C-seq was performed as previously described using a two-step PCR method for indexing described in (Geeven et al., 2018; van de Werken et al., 2012). We used DpnII as the first restriction enzyme and Csp6I as the second restriction fragment.
4C-seq libraries were prepared using a two-step PCR method for indexing described in (Geeven et al., 2018; van de Werken et al., 2012).

value: MRT organoids P60

value: Malignant rhabdoid tumor cells

value: a wild-type full-length SMARCB1 gene plasmid


title: THP-1 cells, Ctrl_KO, NL, m6A-IP, biol rep 2

value: WT


title: CD4_CD103+TRM_Stim_D31_SevereAsthma_S2

value: Female


title: 4C.02_MRTK.60_MYC.P_CTRL_rep2

description: 4C-seq in MRT organoids P60, after 4 days lentiviral transduction with the Luciferase gene

value: Luciferase plasmid


title: WT FVB Cerebellum 12 Weeks Old Rep 2


title: CD4_CD103+TRM_Stim_D09_MildAsthma_S2

value: Male

value: Mild asthma


title: CD4_CD103+TRM_Stim_D16_SevereAsthma_S2

value: Severe asthma


title: RNA.13_MRTK.103_DMSO_rep1

description:
RNA-seq in MRT organoids P103, after 5 days with DMSO treatment
MRTK_RNAseq_readcounts_normalized_2022-11-10.txt; MRTK_RNAseq_readcounts_unnormalized_2022-11-10.txt

data_processing:
Raw RNA-seq data were mapped against mm10 reference genome using a TopHat2 pipeline (version 2.1.1) (Kim et al., 2013). The mapped reads with mapping quality score <10 were discarded using SAMtools. The read coverage for each gene in “Homo Sapiens GRCm38.92” annotation file was determined using a HTSeq tool (version 0.9.1). The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools. The genes with at least 20 reads in both replicates were kept for further analysis. The filtered expression data were normalized based on the size factors of the individual samples using a DESeq2 package.
Assembly: hg38
Supplementary files format and content: bigWig files, read counts

extract_protocol:
RNA was isolated following a standard TRIzol RNA isolation protocol (Ambion). The cells were lysed using 1 ml of TRIzol reagent, and 200 µl chloroform was added to the lysates. The mixture was vortexed and centrifuged at 12,000 g at 4°C for 15 min. Upper phase was homogenized with 0.5 ml of 100% isopropanol, incubated at room temperature for 10 min, and centrifuged at 4°C for 10 min. The resulted RNA pellet was washed with 75% ice-cold ethanol, dried at room temperature for 10 min, and resuspended in RNase-free water. The isolated RNA was treated with DNase using RNeasy Mini Kit (Qiagen)
RNA-seq libraries were prepared using a TruSeq Stranded RNA LT Kit (Illumina).

value: MRT organoids P103

value: DMSO


title: CD4_CD103+TRM_Stim_D04_MildAsthma_S2


title: CD4_CD103+TRM_Stim_D17_SevereAsthma_S2


title: RNA.16_MRTK.103_iBRD9_rep2

description:
RNA-seq in MRT organoids P103, after 5 days with iBRD9 treatment
MRTK_RNAseq_readcounts_normalized_2022-11-10.txt; MRTK_RNAseq_readcounts_unnormalized_2022-11-10.txt


title: RNA.14_MRTK.103_DMSO_rep2


title: WT FVB Cerebellum 12 Weeks Old Rep 3

value: Cerebellum

value: FVB/NJ

value: 12 weeks old


title: 4C.08_MRTK.78_MYC.P_SMARCB1_rep2

description: 4C-seq in MRT organoids P78, after 4 days lentiviral transduction with the SMARCB1 gene

source_name: MRT organoids P78

value: MRT organoids P78


title: WT FVB Cerebellum 12 Weeks Old Rep 1


title: 4C.07_MRTK.78_MYC.P_SMARCB1_rep1


title: ATXN1-82Q Tg Cerebellum 5 Weeks Old Rep 4

value: ATXN1-82Q Tg

value: 5 weeks old


title: 4C.06_MRTK.78_MYC.P_CTRL_rep2

description: 4C-seq in MRT organoids P78, after 4 days lentiviral transduction with the Luciferase gene


title: 4C.05_MRTK.78_MYC.P_CTRL_rep1


title: 4C.03_MRTK.60_MYC.P_SMARCB1_rep1

value: MRT organoids P60


title: CD4_CD103+TRM_Stim_D02_MildAsthma_S2

value: Stimulated

value: PolyAtail captured messenger RNA


title: 4C.01_MRTK.60_MYC.P_CTRL_rep1

value: Malignant rhabdoid tumor cells


title: CD4_Non-TRM_Unstim_D08_MildAsthma_S2

value: Unstimulated

value: Female


title: ATXN1-82Q Tg Cerebellum 5 Weeks Old Rep 2


title: brain_UAS-HA-Zld_aZld_rep2

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

data_processing:
Raw CUT&RUN reads were trimmed to remove adapter sequences using NGmerge version 0.3
Trimmed reads were aligned to the Drosophila melanogaster genome (version dm6) using bowtie2 with paramters -k 2 --very-sensitive --no-mixed --no-discordant -X 5000.
Reads with a mapping quality < 30 and reads aligning to the mitochondrial genome or scaffolds were discarded.
Peak calling was performed using MACS2 with parameters –broad -f BAMPE –keep-dup all -g dm.
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters –binSize 10. bigWig files were z-score normalized by subtracting the genome-wide average of all bins from each bin value and dividing by the standard deviation of all bins.
Assembly: dm6
Supplementary files format and content: bigWig files: z-scoore normalized read depth of merged replicates
Supplementary files format and content: narrowPeak files: MACS2 peaks

organism: Drosophila melanogaster

growth_protocol: Flies were raised on standard fly food at 25 °C

extract_protocol:
CUT&RUN was performed using EpiCypher reagents according to the manufacturer protocol. 50 brains were used for each CUT&RUN reaction. Overnight incubation with antibodies was performed in antibody buffer containing 0.05% digitonin. 0.5 µL anti-Zld antibody was used for CUT&RUN.
Libraries were prepared using the NEBNext Ultra II kit (NEB). During library preparation, cleanup steps were performed using a 1.1X ratio of Axygen paramagnetic beads, as recommended by EpiCypher. PCR amplification was performed with the following conditions: 98°C for 45 seconds, then 14 cycles of 98°C for 15 seconds, 60°C for 10 seconds, and a final extension of 72°C for 1 minute.

treatment_protocol: Larvae were grown at 18°C until reaching the L3 stage, then shifted to 33°C for 24 hours to induce Zld overexpression

value: brain

tag: developmental stage

value: L3 larvae

value: Type II neuroblast

tag: antibody

value: anti-Zld


title: CD4_Non-TRM_Unstim_D07_MildAsthma_S2

tag: stimulation

value: Male

tag: disease state

value: Mild asthma


title: ATXN1-82Q Tg Cerebellum 5 Weeks Old Rep 1

tag: tissue

value: Cerebellum

value: FVB/NJ


title: ATXN1-82Q Tg Cerebellum 5 Weeks Old Rep 3


title: brain_brat_aZld_rep1

tag: cell type


title: brain_brat_aZld_rep2


title: titration_S2-Grh-DBD_80_rep2

data_processing:
Raw ATAC-seq reads were trimmed to remove adapter sequences using NGmerge version 0.3.
Trimmed reads were aligned to the Drosophila melanogaster genome (version dm6) using bowtie2 with paramters -k 2 --very-sensitive --no-mixed --no-discordant -X 5000.
Reads with a mapping quality < 30 and reads aligning to the mitochondrial genome or scaffolds were discarded. Only fragments < 100bp were considered for downstream analysis.
Reads were combined across all replicates and peak calling was performed using MACS2 with parameters -f BAMPE --keep-dup all -g dm --call-summits.
featureCounts was used to count the number of reads aligning within 200bp (100bp upstream or downstream) of peak summits.
Differential accessibility analysis was performed using DESeq2. Regions with an adjusted p-value < 0.05 were considered differentially accessible.
bigWig files were generated using deepTools bamCoverage version 3.5.1 with parameters –binSize 10. bigWig files were z-score normalized by subtracting the genome-wide average of all bins from each bin value and dividing by the standard deviation of all bins.
Assembly: dm6
Supplementary files format and content: bigWig files: z-score normalized read depth for merged replicates. Only small fragments (< 100bp) are included.
Supplementary files format and content: narrowPeak files: MACS2 peaks called on combined replicates for all samples within each experiment.

growth_protocol: Drosophila S2 cells were cultured at 27°C in Schneider's medium supplemented with 10% fetal bovine serum  and antibiotic/antimycotic.

extract_protocol:
2×10^5 cells were harvested for ATAC-seq by centrifugation at 600 × g for 3 minutes at RT. Cells were washed once in 100 µL 1X PBS and resuspended in 100 µL ATAC lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2,0.1% NP-40). Cells were centrifuged at 600 × g for 10 minutes at 4°C. Supernatant was removed and pellet was resuspended in 47.5 µL buffer TD (Illumina). 2.5 uL of Tagment DNA Enzyme (Illumina) was added and samples were incubated at 37°C for 30 minutes. Tagmented DNA was purified using MinElute Reaction Cleanup Kit (Qiagen) and eluted in 10 µL of buffer EB.
DNA was PCR amplified for 12 cycles with the following conditions:72°C for 5 minutes, 98°C for 30 seconds, then 12 cycles of 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. Amplified libraries were purified using a 1.2X ratio of Axygen paramagnetic beads.

treatment_protocol: Transcription factor expression was induced by adding CuSO4 to the cell culture media. For all induction experiments, cells were plated at 1×10^6 cells per mL. Experiments were performed with cells harvested 48 hours after induction.

tag: cell line

value: 80uM CuSO4


title: CD4_CD103+TRM_Stim_D03_MildAsthma_S2

tag: molecule subtype


title: titration_S2-Grh-DBD_80_rep1

tag: genotype

tag: treatment


title: WT FVB Cerebellum 5 Weeks Old Rep 3

value: WT


title: brain_UAS-HA-Zld_aZld_rep1


title: CD4_Non-TRM_Unstim_D03_MildAsthma_S2

tag: Sex


title: titration_S2-Zld-DBD_400_rep2

value: 400uM CuSO4


title: titration_S2-Zld-DBD_400_rep1


title: CD4_Non-TRM_Unstim_D02_MildAsthma_S2


title: RNA.15_MRTK.103_iBRD9_rep1

value: MRT organoids P103


title: CD4_CD103–TRM_Unstim_D31_SevereAsthma_S2

value: Severe asthma


title: FHet.B6.GFP.M51WT.reTreg#5

description:
Flow cytometry sorted Mouse Tregs as DAPI–CD19-TCRβ+CD4+Thy1.1-CD25+
Genes_count_table.tsv

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: raw read counts

extract_protocol:
Mouse CD4+ regulatory Tregs in 6-10 weeks old Foxp3 missense mutant mice hemizygous male and heterozygous female were isolated from spleen by flow cytometry, as DAPI–CD19-TCRβ+CD4+CD25+. 1,000 cells were double-sorted directly into lysis buffer for RNA-seq (Smart-seq2)  library preparation following the standard ImmGen low-input protocol (www.immgen.org).
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

tag: genetic background

value: B6 Foxp3-ires-GFP

value: Spleen

tag: cell

value: Treg

tag: age (weeks)


title: FHet.B6.GFP.M51WT.aTreg#5

value: Female


title: WT FVB Cerebellum 5 Weeks Old Rep 1

value: 5 weeks old


title: FHet.R51Q.reTreg#4


title: FHet.R51Q.reTreg#3


title: CD4_CD103–TRM_Unstim_D29_SevereAsthma_S2

value: Unstimulated

value: PolyAtail captured messenger RNA


title: WT_CCR2hi rep 3

value: heart

value: macrophages

value: male

tag: ccr2 status

value: MI


title: FHet.R51Q.aTreg#4


title: CD4_Non-TRM_Unstim_D04_MildAsthma_S2

value: Mild asthma


title: WT FVB Cerebellum 5 Weeks Old Rep 4

value: Cerebellum

value: FVB/NJ

tag: age


title: WT_CCR2hi rep 2

tag: strain

value: WT


title: Wild-type_heart_CaptureHiC_rep1

value: Wild-type


title: FHet.B6.GFP.reTreg#1


title: CD4_CD103–TRM_Unstim_D28_SevereAsthma_S2

value: Male

value: Severe asthma


title: CD4_CD103–TRM_Unstim_D24_SevereAsthma_S2


title: WT_CCR2hi rep 1


title: FHet.B6.GFP.aTreg#1

value: B6 Foxp3-ires-GFP

value: Spleen


title: FHet.R51Q.aTreg#3

value: Treg

value: Female


title: WT FVB Cerebellum 5 Weeks Old Rep 2

value: 5 weeks old


title: FHet.WT.Tconv#1

description:
Flow cytometry sorted Mouse Tconv as DAPI–CD19-TCRβ+CD4+Thy1.1-CD25-
Genes_count_table.tsv

value: Tconv


title: WT_CCR2low rep 3

value: heart


title: FHet.B6.reTreg#2


title: CD4_CD103–TRM_Unstim_D19_SevereAsthma_S2

value: Unstimulated

value: PolyAtail captured messenger RNA


title: FHet.B6.M309WT.reTreg#4


title: CD4_CD103–TRM_Unstim_D20_SevereAsthma_S2


title: WT_CCR2low rep 2

value: macrophages

value: male

value: MI


title: FHet.B6.GFP.M51WT.reTreg#4


title: FHet.B6.aTreg#2


title: CD4_CD103–TRM_Unstim_D17_SevereAsthma_S2


title: FHet.WT.Tconv#2


title: CD4_CD103–TRM_Unstim_D16_SevereAsthma_S2


title: WT_CCR2low rep 1


title: FHet.B6.M309WT.aTreg#4


title: CD4_CD103–TRM_Unstim_D09_MildAsthma_S2

value: Mild asthma


title: FHet.B6.aTreg#1

value: WT


title: FHet.B6.GFP.M51WT.aTreg#4


title: FHet.R309Q.reTreg#5


title: CD4_CD103–TRM_Unstim_D08_MildAsthma_S2


title: M-triple KO4 - 60 min LPS + 120 min ActD

city: Durham

first: Brittany

last: Snyder

state: NC

address: 111 T.W. Alexander Drive

institute: NIEHS

description:
Myeloid-triple_KO_LPS_ActD_raw_counts.txt
Myeloid-triple_KO_LPS_ActD_normalized_counts_per_kb.txt

data_processing:
Base calling performed on-instrument and generation of FASTQ files performed using bcl2fastq2
Read pairs were filtered to remove those where either mate's mean quality score fell below 20
Read pairs were aligned to mm10 reference genome assembly using STAR 2.7.0f
Counts per gene were determined using featureCounts 1.5.1 based on refGene annotations downloaded 2018-06-03
Normalization factors were determined using DESeq2 estimateSizeFactors function, used in conjunction with featureCounts gene length to calculate abundance in normalized reads per kb, applied to coverage tracks generated by STAR
Assembly: mm10
Supplementary files format and content: tab-delimted text, raw counts per gene, normalized counts per kb
Supplementary files format and content: bigWig, normalized read coverage

source_name: Bone marrow-derived macrophage

growth_protocol: Bone marrow-derived macrophages from wild-type (WT) and M-triple knock-out (KO) mice were cultured for 7-10 days until confluency was reached.

extract_protocol:
RNA was extracted using the GE Healthcare Illustra RNAspin mini kit (Cat# 25-0500-72).
RNA libraries were prepared for sequencing using standard Illumina protocols.  Illumina Truseq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 µg of total RNA for the construction of sequencing libraries.

treatment_protocol: Once reaching confluency, macrophages were incubated in serum-starvation medium for 16-18 hours.  After serum-deprivation macrophages were first treated with or without lipopolysaccharide (LPS) for 1 h, followed by treatment with Actinomycin D (ActD) for 10, 20, 30, 45, 60, or 120 min, for a total of 8 timepoints.  Four mice of each genotype were used, and three plates of cells were pooled for each timepoint.

value: Bone marrow-derived macrophage

value: M-triple KO

value: LPS + ActD

tag: time

value: 60 min + 120min


title: M-triple KO4 - 60 min LPS + 60 min ActD

value: 60 min + 60min


title: FHet.R309Q.aTreg#5

value: Spleen

value: Treg