title: CD4_CD103–TRM_Unstim_D07_MildAsthma_S2

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

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.

value: Male


title: FHet.R309Q.reTreg#4

status: Public on Oct 20 2023

type: SRA

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

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

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

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: genotype

tag: genetic background

tag: tissue

value: Spleen

tag: cell

value: Treg

tag: Sex

value: Female

tag: age (weeks)


title: M-triple KO4 - 60 min LPS + 45 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.

tag: cell type

value: Bone marrow-derived macrophage

value: M-triple KO

tag: treatment

value: LPS + ActD

tag: time

value: 60 min + 45min


title: FHet.R309Q.aTreg#4


title: FHet.R51Q.reTreg#2

value: B6 Foxp3-ires-GFP


title: FHet.B6.reTreg#1

value: WT


title: CD4_CD103–TRM_Unstim_D06_MildAsthma_S2

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

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

molecule: polyA RNA

organism: Homo sapiens

source_name: Bronchoalveolar lavage (BAL)

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.

tag: stimulation

value: Unstimulated

tag: disease state

value: Mild asthma

tag: molecule subtype

value: PolyAtail captured messenger RNA


title: FHet.R51Q.aTreg#2


title: M-triple KO4 - 60 min LPS + 30 min ActD

value: 60 min + 30min


title: FHet.R51Q.reTreg#1


title: M-triple KO4 - 60 min LPS + 10 min ActD

value: 60 min + 10min


title: M-triple KO4 - 60 min LPS + 20 min ActD

value: 60 min + 20min


title: FHet.R51Q.aTreg#1


title: Male.M200WT.reTreg.4


title: WT.Tconv.1

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

value: Tconv


title: M-triple KO4 - 60 min LPS

value: LPS


title: CD4_CD103–TRM_Unstim_D04_MildAsthma_S2


title: WT.Tconv.2

value: Spleen

value: Male


title: Male.M200WT.aTreg.4

value: Treg


title: M-triple KO4 - untreated

value: Bone marrow-derived macrophage


title: Male.M51WT.reTreg.4


title: CD4_CD103–TRM_Unstim_D02_MildAsthma_S2


title: Male.M51WT.aTreg.4


title: Male.M200.aTreg.4


title: WT4 - 60 min LPS + 120 min ActD

value: 60 min + 120min


title: CD4_CD103+TRM_Unstim_D31_SevereAsthma_S2

value: Female

value: Severe asthma


title: Male.M51.reTreg.5

value: B6 Foxp3-ires-GFP


title: Male.M51.reTreg.4


title: WT4 - 60 min LPS + 60 min ActD

value: WT

value: LPS + ActD

value: 60 min + 60min


title: CD4_CD103–TRM_Unstim_D05_MildAsthma_S2

value: Unstimulated

value: Mild asthma

value: PolyAtail captured messenger RNA


title: WT4 - 60 min LPS + 45 min ActD

value: 60 min + 45min


title: CD4_CD103+TRM_Unstim_D28_SevereAsthma_S2


title: Male.M200.reTreg.5


title: Male.M200.reTreg.4


title: Male.M51.aTreg.5


title: CD4_CD103+TRM_Unstim_D24_SevereAsthma_S2


title: WT4 - 60 min LPS + 30 min ActD

value: 60 min + 30min


title: Male.M200.aTreg.5


title: CD4_CD103–TRM_Unstim_D03_MildAsthma_S2


title: Cortex #donor 5

type: RNA

city: Kobe

first: Hijiri

last: Fujioka

address: 6-7-5, Minatojimaminamimachi, Chuouku,

country: Japan

institute: NBI

description: BLK

hyb_protocol: Hybridazation to GeneChip was done by GeneCHip Hybridization, Wash and Stain Kit and GeneChip HybridazationOven 645 at 45 degree celcius 60 rpm for 16 hr

scan_protocol: GeneChips were scanned using GenCHip Scanner 3000 7G

data_processing:
The data were analyzed with GeneSpring GX 14.9.1 using MAS 5.0 as normalization method. Probes with Present and/or Marginal flags in at least 1 samples were used for gene-level analysis and their signal values were averaged by arithmetic mean in GeneSpring GX 14.9.1.
Average of MAS 5.0 signal intensity on each gene. ID_REF columun in Matrix Template contains probe IDs with Entrez Gene ID of each gene.

label: biotin

source_name: Cortex #donor 5

label_protocol: Biotin-labeled cRNA were prepared from 100 ng total RNA by GenCHip 3'IVT PLUS Reagent Kit according to the Thermo Fisher Scientific 's protocol

growth_protocol: BLK

extract_protocol: Total RNA was extracted and purified by using an RNeasy Mini kit (QIAGEN) according to manufacturer’s standard protocol.

treatment_protocol: BLK

value: kidney cortex

tag: protocol

value: autopsy


title: CD4_CD103+TRM_Unstim_D20_SevereAsthma_S2

value: Male


title: WT4 - 60 min LPS + 20 min ActD

value: 60 min + 20min


title: FHet.M309.aTreg.3

value: Spleen

value: Treg


title: Male.M51.aTreg.4


title: FHet.M309.reTreg.2

value: Female


title: Cortex #donor 3

description: BLK

source_name: Cortex #donor 3


title: WT4 - 60 min LPS

value: Bone marrow-derived macrophage

value: LPS


title: Cortex #donor 4

description: BLK

source_name: Cortex #donor 4


title: FHet.M309.aTreg.2


title: CD4_CD103+TRM_Unstim_D17_SevereAsthma_S2

value: Severe asthma


title: CD4_CD103+TRM_Unstim_D29_SevereAsthma_S2


title: Cortex #donor 2

description: BLK

source_name: Cortex #donor 2


title: CD4_CD103+TRM_Unstim_D16_SevereAsthma_S2


title: Cortex #donor 1

description: BLK

source_name: Cortex #donor 1

value: biopsy


title: WT4 - untreated

value: WT


title: FHet.M309.reTreg.1


title: CD4_CD103+TRM_Unstim_D09_MildAsthma_S2

value: Unstimulated


title: M-triple KO3 - 60 min LPS + 120 min ActD

value: M-triple KO

value: LPS + ActD

value: 60 min + 120min


title: M-triple KO3 - 60 min LPS + 60 min ActD

value: 60 min + 60min


title: 3D RPTEC spheroid_day5  #Lot1

description: BLK

source_name: 3D RPTEC spheroid_day5  #Lot1

value: Renal Proximal Tubule Epithelial Cells

value: 3D culture_day5


title: FHet.M309.aTreg.1


title: 3D RPTEC spheroid_day32 #Lot1

description: BLK

source_name: 3D RPTEC spheroid_day32 #Lot1

value: 3D culture_day32


title: WT4 - 60 min LPS + 10 min ActD

value: 60 min + 10min


title: FHet.M337WT.aTreg.2

value: Spleen


title: CD4_CD103+TRM_Unstim_D19_SevereAsthma_S2

value: PolyAtail captured messenger RNA


title: CD4_CD103+TRM_Unstim_D08_MildAsthma_S2

value: Female

value: Mild asthma


title: 3D RPTEC spheroid_day20 #Lot1

description: BLK

source_name: 3D RPTEC spheroid_day20 #Lot1

value: 3D culture_day20


title: FHet.M337WT.reTreg.2

value: Treg


title: M-triple KO3 - 60 min LPS + 30 min ActD

value: Bone marrow-derived macrophage

value: 60 min + 30min


title: FHet.M337WT.reTreg.1

value: WT


title: 3D RPTEC spheroid_day14 #Lot2

description: BLK

source_name: 3D RPTEC spheroid_day14 #Lot2

value: 3D culture_day14


title: CD4_CD103+TRM_Unstim_D06_MildAsthma_S2

value: Unstimulated

value: Male


title: M-triple KO3 - 60 min LPS + 20 min ActD

value: M-triple KO

value: LPS + ActD

value: 60 min + 20min


title: CD4_CD103+TRM_Unstim_D07_MildAsthma_S2


title: M-triple KO3 - 60 min LPS + 10 min ActD


title: CD4_CD103+TRM_Unstim_D05_MildAsthma_S2


title: FHet.M309WT.aTreg.1


title: 3D RPTEC spheroid_day12 #Lot1

description: BLK

source_name: 3D RPTEC spheroid_day12 #Lot1

value: Renal Proximal Tubule Epithelial Cells

value: 3D culture_day12


title: 2D RPTEC_day2_#Lot1

description: BLK

source_name: 2D RPTEC_day2_#Lot1

value: 2D culture_day2


title: CD4_CD103+TRM_Unstim_D03_MildAsthma_S2

value: PolyAtail captured messenger RNA


title: CD4_CD103+TRM_Unstim_D04_MildAsthma_S2

value: Female


title: FHet.M337WT.aTreg.1

value: Spleen


title: M-triple KO3 - untreated


title: FHet.M337.aTreg.2


title: M-triple KO3 - 60 min LPS

value: LPS


title: 2D RPTEC_day12 #Lot1

description: BLK

source_name: 2D RPTEC_day12 #Lot1

value: 2D culture_day12


title: M-triple KO3 - 60 min LPS + 45 min ActD

value: Bone marrow-derived macrophage

value: 60 min + 45min


title: CD4_CD103+TRM_Unstim_D02_MildAsthma_S2

value: Mild asthma


title: WT3 - 60 min LPS + 120 min ActD

value: WT

value: 60 min + 120min


title: FHet.M337.reTreg.1

value: Treg


title: FHet.M309WT.reTreg.1


title: 3D RPTEC CI_24hr #Lot1

description: BLK

source_name: 3D RPTEC CI_24hr #Lot1

value: Reseed after 3D culture


title: CD4_Non-TRM_Stim_D19_SevereAsthma_S1

value: Stimulated

value: Severe asthma


title: WT3 - 60 min LPS + 60 min ActD

value: LPS + ActD

value: 60 min + 60min


title: CD4_Non-TRM_Stim_D17_SevereAsthma_S1

value: Male


title: WT3 - 60 min LPS + 45 min ActD


title: 3D RPTEC CI_24hr #Lot3

description: BLK

source_name: 3D RPTEC CI_24hr #Lot3

value: Renal Proximal Tubule Epithelial Cells


title: WT3 - 60 min LPS + 30 min ActD

value: 60 min + 30min


title: FHet.M337.aTreg.1

value: Spleen

value: Female


title: CD4_Non-TRM_Stim_D16_SevereAsthma_S1

value: PolyAtail captured messenger RNA


title: FHet.M51WT.reTreg.1


title: 3D RPTEC CI 24hr #Lot2

description: BLK

source_name: 3D RPTEC CI 24hr #Lot2


title: FHet.M51WT.aTreg.1


title: 3D RPTEC spheroid_day14 #Lot3

description: BLK

source_name: 3D RPTEC spheroid_day14 #Lot3

value: 3D culture_day14


title: CD4_Non-TRM_Stim_D09_MildAsthma_S1

source_name: Bronchoalveolar lavage (BAL)


title: Sample_12_CART_KD1

city: Malmo

first: Dmytro

last: Kryvokhyzha

address: Jan Waldenströms gata 35

department: Clinical Sciences

country: Sweden

institute: Lund University

data_processing:
QC with fastQC 0.10
mapping with STAR 2.3.0
counting with featureCounts v1.4.4
Assembly: Rnor_5.0.75
Supplementary files format and content: raw counts in multiple sample tab-delimited table

organism: Rattus norvegicus

extract_protocol:
NucleoSpin RNA (Macherey Nagel, Prod# 740955.250)
Illumina truSeq stranded total RNA prep, LT Ribo zero

treatment_protocol: INS-1 cells were treated with negative control siRNA (NC2) and an siRNA for Cartpt (CART_KD).

tag: cell line

value: pancreatic beta-cell line


title: WT3 - 60 min LPS + 10 min ActD

source_name: Bone marrow-derived macrophage

value: Bone marrow-derived macrophage

value: 60 min + 10min


title: FHet.M51.reTreg.3


title: Sample_11_NC2


title: FHet.M51.aTreg.3


title: Sample_10_CART_KD1


title: CD4_Non-TRM_Stim_D04_MildAsthma_S1

value: Mild asthma


title: FHet.M51.reTreg.2

value: Treg


title: CD4_Non-TRM_Stim_D20_SevereAsthma_S1


title: WT3 - untreated

value: WT


title: WT3 - 60 min LPS

value: LPS


title: FHet.M337.reTreg.3


title: Sample_9_NC2


title: CD4_Non-TRM_Stim_D02_MildAsthma_S1

value: Stimulated


title: CD4_Non-TRM_Stim_D03_MildAsthma_S1


title: Sample_8_CART_KD1


title: Sample_7_NC2


title: CD4_CD103–TRM_Stim_D31_SevereAsthma_S1

value: Severe asthma


title: Male.M51.reTreg.3

value: B6 Foxp3-ires-GFP


title: CD4_CD103–TRM_Stim_D20_SevereAsthma_S1

value: Male


title: Sample_6_CART_KD1


title: M-triple KO2 - 60 min LPS + 30 min ActD

value: M-triple KO

value: LPS + ActD


title: CD4_CD103–TRM_Stim_D24_SevereAsthma_S1


title: M-triple KO2 - 60 min LPS + 60 min ActD

value: 60 min + 60min


title: WT3 - 60 min LPS + 20 min ActD

value: 60 min + 20min


title: Sample_4_CART_KD1


title: CD4_CD103–TRM_Stim_D19_SevereAsthma_S1

value: Female

value: PolyAtail captured messenger RNA


title: M-triple KO2 - 60 min LPS + 20 min ActD


title: CD4_CD103–TRM_Stim_D17_SevereAsthma_S1


title: M-triple KO2 - 60 min LPS + 120 min ActD

value: 60 min + 120min


title: Male.M51.aTreg.2

value: Spleen


title: FHet.M51.aTreg.2


title: CD4_CD103–TRM_Stim_D16_SevereAsthma_S1


title: M-triple KO2 - 60 min LPS + 10 min ActD

value: Bone marrow-derived macrophage

value: 60 min + 10min


title: M-triple KO2 - 60 min LPS + 45 min ActD

value: 60 min + 45min


title: M-triple KO2 - 60 min LPS


title: M-triple KO2 - untreated


title: Male.M51.aTreg.1

value: Treg


title: CD4_Non-TRM_Stim_D13_MildAsthma_S1

value: Mild asthma


title: Sample_2_CART_KD1

value: pancreatic beta-cell line


title: Sample_3_NC2


title: Sample_1_NC2


title: Male.M51.reTreg.1


title: WT2 - 60 min LPS + 60 min ActD

value: WT


title: Male.WT.lit327fs.GFPp.CD25neg.2

value: B6 Foxp3-ires-GFP


title: Male.WT.lit327fs.GFPp.CD25neg.3

value: Male


title: Sample_5_NC2


title: CD4_Non-TRM_Stim_D14_MildAsthma_S1

value: Stimulated


title: CD4_CD103–TRM_Stim_D07_MildAsthma_S1


title: Male.M51.aTreg.3


title: Male.WT.lit327fs.GFPp.CD25neg.1


title: Male.M51WT.aTreg.1


title: Sample 32_CC_FIN_8

city: Irvine

first: Anne

last: Calof

state: CA

address: Biological Sciences III, 519 Ring Rd

department: Developmental & Cell Biology

institute: University of California, Irvine

library_source: transcriptomic single cell

data_processing:
For samples 17-32, cellranger count was run using the mm10 reference genome and default parameters to call cells and map transcripts.
For samples 33-36, cellranger aggr was run, using default paramters, to aggregate samples.
For samples 37-42, cellranger aggr was run, using default parameters, to aggregate samples. Cells exceeding three median absolute deviations in number of transcripts, number of genes, and percent mitochondrial genes expressed were considered low-quality cells and filtered out.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz contain list of all cell barcodes in that library; features.tsv.gz contain list of all genes from reads mapped onto  reference genome; matrix.tsv.gz; contain UMI count per gene per cell.

source_name: intraembryonic mouse embryo

extract_protocol:
Whole embryos were dissected from pregnant dams in 1X phoshate buffered saline (PBS). Parietal and visceral yolk sacs were removed for DNA extraction and PCR genotyping. Extraembryonic tissue was removed for genotyping by X-gal stain. Intraembryonic tissues from embryos were transferred into 1.5 ml DNA LoBind tubes, washed with 1X PBS, incubated in 1X TrypLE Express at 37°C for 20 min (cardiac crescent) min, dissociated into single cells by passage through pipette, quenched with 1X PBS, underlayed with hanks balanced salt solution + 1% deaceytlated bovine serum albumin, and spun at 1200 rpm for 5 min in a swing bucket centrifuge. The resulting upper supernatant layer was discarded by pipette and the cells were spun again at 1200 rpm for 5 min. The resulting supernatant was again discarded. The cells were washed in 1X PBS by raising them in 1X PBS, spinning them at 1200 rpm for 5 min, and discarding the resulting supernatant.  The cells were then re-suspended in 1X PBS.
Single cell RNA libraries were constructed using 10X Genomics Chromium Single Cell 3' Reagents Kit v2 protocol and paired-end sequenced with single-indexing on the Illumina HiSeq 4000 to a minimum of 50,000 reads per cell using its standard protocol.

tag: strain

tag: developmental stage

value: cardiac crescent (E7.75)

value: intraembryonic mouse embryo

value: Nipbl FIN/+


title: WT2 - 60 min LPS + 45 min ActD

value: LPS + ActD


title: Sample 30_CC_FIN_6


title: CD4_Non-TRM_Stim_D12_MildAsthma_S1

value: PolyAtail captured messenger RNA


title: Male.WT.lit327fs.GFPhi.CD25p.3


title: WT2 - 60 min LPS + 120 min ActD

value: 60 min + 120min


title: WT2 - 60 min LPS + 30 min ActD

value: 60 min + 30min


title: WT2 - 60 min LPS + 20 min ActD

value: Bone marrow-derived macrophage

value: 60 min + 20min


title: Sample 28_CC_FIN_4


title: Male.WT.lit327fs.GFPhi.CD25p.2

value: Spleen


title: CD4_CD103–TRM_Stim_D09_MildAsthma_S1


title: CD4_CD103–TRM_Stim_D04_MildAsthma_S1

value: Female


title: Sample 29_CC_FIN_5


title: Male.KO.M327fs.GFPlo.CD25p.3

value: Treg


title: CD4_Non-TRM_Stim_D11_MildAsthma_S1

value: Mild asthma


title: Male.WT.lit327fs.GFPhi.CD25p.1

value: WT


title: CD4_Non-TRM_Stim_D08_MildAsthma_S1


title: Sample 31_CC_FIN_7


title: WT2 - untreated


title: CD4_CD103–TRM_Stim_D03_MildAsthma_S1


title: CD4_Non-TRM_Stim_D06_MildAsthma_S1


title: Sample 25_CC_FIN_1


title: Sample 27_CC_FIN_3


title: M-triple KO1 - 60 min LPS + 120 min ActD

value: M-triple KO


title: CD4_CD103+TRM_Stim_D31_SevereAsthma_S1

value: Severe asthma


title: Male.B6.Lit.M327fs.GFPneg.3

value: B6 Foxp3-ires-GFP

value: Male


title: Male.KO.M327fs.GFPp.CD25neg.1


title: Male.KO.M327fs.GFPlo.CD25p.2


title: Sample 24_CC_FLOX_8

value: cardiac crescent (E7.75)

value: intraembryonic mouse embryo

value: Nipbl Flox/+


title: M-triple KO1 - 60 min LPS + 60 min ActD

value: LPS + ActD

value: 60min + 60 min


title: Sample 23_CC_FLOX_7


title: CD4_Non-TRM_Stim_D05_MildAsthma_S1

value: Stimulated

value: PolyAtail captured messenger RNA


title: WT2 - 60 min LPS

value: Bone marrow-derived macrophage

value: LPS


title: Male.KO.M327fs.GFPhi.CD25p.1

value: Spleen


title: CD4_CD103+TRM_Stim_D24_SevereAsthma_S1


title: Sample 26_CC_FIN_2

value: Nipbl FIN/+


title: CD4_Non-TRM_Stim_D01_MildAsthma_S1

value: Mild asthma


title: M-triple KO1 - 60 min LPS + 45 min ActD

value: 60 min + 45min


title: Sample 21_CC_FLOX_5


title: Sample 20_CC_FLOX_4


title: FHet.WT.lit327fs.GFPp.CD25neg.1

value: WT

value: Treg

value: Female


title: FHet.WT.lit327fs.GFPp.CD25lo.2

value: B6 Foxp3-ires-GFP


title: Sample 22_CC_FLOX_6

value: cardiac crescent (E7.75)


title: M-triple KO1 - 60 min LPS + 10 min ActD

value: M-triple KO

value: 60 min + 10min


title: CD4_Non-TRM_Stim_D07_MildAsthma_S1

value: Male


title: M-triple KO1 - 60 min LPS


title: M-triple KO1 - 60 min LPS + 30 min ActD

value: LPS + ActD

value: 60 min + 30min


title: Sample 19_CC_FLOX_3

value: intraembryonic mouse embryo

value: Nipbl Flox/+


title: M-triple KO1 - 60 min LPS + 20 min ActD

value: Bone marrow-derived macrophage

value: 60 min + 20min


title: CD4_Non-TRM_Stim_D24_SevereAsthma_S1

value: Stimulated

value: Severe asthma

value: PolyAtail captured messenger RNA


title: CD4_CD103+TRM_Stim_D19_SevereAsthma_S1


title: FHet.KO.M327fs.GFPneg.2

value: Spleen


title: CD4_CD103–TRM_Stim_D28_SevereAsthma_S1


title: Sample 17_CC_FLOX_1


title: M-triple KO1 - untreated


title: FHet.KO.M327fs.GFPneg.1

value: Treg


title: WT1 - 60 min LPS + 120 min ActD

value: WT

value: 60 min + 120min


title: FHet.WT.lit327fs.GFPneg.1

value: B6 Foxp3-ires-GFP

value: Female


title: FHet.KO.M327fs.GFPp.CD25neg.3


title: CD4_CD103+TRM_Stim_D16_SevereAsthma_S1


title: G3 scRNA-seq

city: Stanford

first: Yang

last: Zhao

address: Beckman B169B, 279 Campus Drive

department: MCP

institute: Stanford University

description: IL-10 HER2 CAR-T in spleen

data_processing:
The fastq files were generated and demultiplexed by CeleScope rna from Singleron (version 3.0.1) and primary data analysis was performed with CeleScope (version 1.10.0) using a custom reference package based on reference genome (Mus_musculus_ensembl_92).
Assembly: mm10 for G1 and G2, Mus_musculus_ensembl_92 for G3
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: Spleen

extract_protocol:
MC38-HER2 bearing mice were sublethally lymphodepleted by total body irradiation (4 Gy) on day 5, followed by i.v. adoptive transfer of HER2 CAR-T or IL-10 HER2 CAR-T cells on day 6. On day 18, mice were sacrificed, and CAR-T cells were isolated from tumors or spleens as described above. NSG mice were inoculated (s.c.) with PANC1-CD19 cells (2 × 106) and received i.v. adoptive cell transfer of CD19 CAR-T or IL-10 CD19 hCAR-T cells (1 × 106) on day 8. On day 39, mice were sacrificed, and CAR-T cells were isolated from spleens as described above. Sorted HER2 CAR-T cells from tumors were then pelleted for 5 min at 400 relative centrifugal force and washed once in PBS with BSA (0.04% wt/v). Afterward, HER2 CAR-T or IL-10 HER2 CAR-T cells were suspended in 100 μl of Cell Multiplexing Oligo (LMO, 10x Genomics), respectively. LMO-barcode labeling was performed for 10 min at room temperature, and then cells were washed twice with PBS, resuspended in PBS with BSA (0.04% wt/v), filtered, and pooled. Labeled cells were subjected to single cell encapsulation using a Chromium Single Cell Instrument and reagents. Sorted CD19 hCAR-T cells or IL-10 CD19 hCAR-T cells from spleens were subjected to single cell encapsulation using a Chromium Single Cell Instrument and reagents separately.
For G1and G2, A Chromium Next GEM Chip G was loaded with the appropriate number of cells and the sequencing libraries prepared using 10x Genomics reagents according to the manufacturer’s instructions and passed quality control. For G3, cells were subjected to single cell partitioning using microchip, mRNA Capture and sequencing libraries were prepared using GEXSCOPE Single Cell RNA Library Kit Cell V2 reagents (Singleron Biotechnologies GmbH) according to the manufacturer’s instructions and passed quality control.

value: T cells

value: Immune cells


title: WT1 - 60 min LPS + 60 min ActD

value: LPS + ActD

value: 60 min + 60min


title: CD4_CD103–TRM_Stim_D12_MildAsthma_S1

value: Male

value: Mild asthma


title: FHet.KO.M327fs.GFPp.CD25neg.2


title: G2 scRNA-seq

description: IL-10 HER2 CAR-T in tumor

source_name: Tumor

value: Tumor


title: FHet.KO.M327fs.GFPneg.3


title: WT1 - 60 min LPS + 45 min ActD

value: Bone marrow-derived macrophage

value: 60 min + 45min


title: WT1 - 60 min LPS + 30 min ActD

value: 60 min + 30min


title: FHet.KO.M327fs.GFPp.CD25neg.1


title: CD4_CD103–TRM_Stim_D11_MildAsthma_S1

value: Stimulated

value: PolyAtail captured messenger RNA


title: WT1 - 60 min LPS + 20 min ActD

value: 60 min + 20min


title: G1 scRNA-seq

description: HER2 CAR-T in tumor

value: WT


title: CD4_CD103+TRM_Stim_D09_MildAsthma_S1


title: mouse_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

molecule: genomic DNA

source_name: Liver

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

value: Liver

value: ChIP

value: House Mouse

value: M

tag: chip antibody

value: input


title: WT2 - 60 min LPS + 10 min ActD

tag: genotype

value: LPS + ActD

value: 60 min + 10min


title: FHet.KO.M327fs.GFPp.CD25lo.3

tag: genetic background

value: B6 Foxp3-ires-GFP

value: Spleen

value: Treg

value: Female


title: mouse_F_input

tag: tissue

value: F


title: FHet.KO.M327fs.GFPp.CD25lo.2

tag: cell


title: Sample 18_CC_FLOX_2

value: cardiac crescent (E7.75)

value: intraembryonic mouse embryo

value: Nipbl Flox/+


title: mouse_M_CTCF

description:
mouse-CTCF.bigwig
mouse-liver-8-chromatin-states.bed

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.

tag: Sex

value: CTCF


title: WT1 - 60 min LPS + 10 min ActD

value: Bone marrow-derived macrophage

value: WT


title: mouse_F_CTCF

value: Liver

value: ChIP


title: WT1 - 60 min LPS

value: LPS


title: CD4_CD103–TRM_Stim_D08_MildAsthma_S1

value: Stimulated

value: Mild asthma

value: PolyAtail captured messenger RNA


title: CD4_CD103–TRM_Stim_D14_MildAsthma_S1


title: FHet.WT.lit327fs.GFPp.CD25lo.1

value: B6 Foxp3-ires-GFP

tag: age (weeks)


title: FHet.WT.lit327fs.GFPp.CD25hi.2

value: Spleen


title: WT1 - untreated

tag: cell type


title: CD4_CD103+TRM_Stim_D03_MildAsthma_S1


title: mouse_M_H3K27ac

description:
mouse-H3K27ac.bigwig
mouse-liver-8-chromatin-states.bed

value: House Mouse

value: M


title: FHet.WT.lit327fs.GFPp.CD25hi.1

value: Treg

value: Female


title: TTP KO4 - 60 min LPS + 120 min ActD

description:
Myeloid-TTP_KO_LPS_ActD_raw_counts.txt
Myeloid-TTP_KO_LPS_ActD_normalized_counts_per_kb.txt

growth_protocol: Bone marrow-derived macrophages from wild-type (WT) and M-TTP 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.

value: M-TTP KO

tag: treatment

value: LPS + ActD

value: 60 min + 120min


title: mouse_F_H3K27ac

value: F


title: CD4_CD103–TRM_Stim_D13_MildAsthma_S1


title: TTP KO4 - 60 min LPS + 60 min ActD

value: Bone marrow-derived macrophage

tag: time

value: 60 min + 60min


title: FHet.KO.M327fs.GFPp.CD25lo.1


title: CD4_CD103+TRM_Stim_D04_MildAsthma_S1

tag: stimulation


title: CD4_CD103–TRM_Stim_D05_MildAsthma_S1

value: Male

tag: disease state


title: mouse_M_H3K4me1

description:
mouse-H3K4me1.bigwig
mouse-liver-8-chromatin-states.bed

value: Liver

value: ChIP


title: Male.KO.M327fs.GFPneg.1


title: mouse_M_H3K27me3

description:
mouse-H3K27me3.bigwig
mouse-liver-8-chromatin-states.bed


title: mouse_F_H3K27me3


title: CD4_CD103–TRM_Stim_D06_MildAsthma_S1

value: Stimulated

value: Mild asthma

tag: molecule subtype


title: TTP KO4 - 60 min LPS + 45 min ActD

value: 60 min + 45min


title: FHet.reTreg.B6.lit327.2

value: WT

value: B6 Foxp3-ires-GFP

value: Spleen


title: CD4_CD103+TRM_Stim_D02_MildAsthma_S1

value: PolyAtail captured messenger RNA


title: TTP KO4 - 60 min LPS + 30 min ActD

value: 60 min + 30min


title: FHet.reTreg.B6.lit327.1

value: Treg

value: Female


title: mouse_F_H3K4me3

description:
mouse-H3K4me3.bigwig
mouse-liver-8-chromatin-states.bed

value: House Mouse


title: mouse_M_H3K4me3

value: M


title: CD4_CD103–TRM_Stim_D01_MildAsthma_S1


title: FHet.aTreg.B6.lit327.2


title: TTP KO4 - 60 min LPS + 10 min ActD

value: Bone marrow-derived macrophage

value: M-TTP KO

value: LPS + ActD

value: 60 min + 10min


title: FHet.aTreg.B6.lit327.1


title: TTP KO4 - 60 min LPS + 20 min ActD

value: 60 min + 20min


title: CD4_CD103+TRM_Stim_D13_MildAsthma_S1

value: Stimulated


title: TTP KO4 - 60 min LPS

value: LPS


title: mouse_M_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: Liver

value: House mouse

tag: protocol

value: Arima


title: FHet.reTreg.KO.M327fs.3

value: B6 Foxp3-ires-GFP

value: Spleen


title: FHet.reTreg.KO.M327fs.2


title: mouse_F_HiC


title: TTP KO4 - untreated


title: FHet.reTreg.KO.M327fs.1


title: Ctrl_3st

city: LanZhou

first: yingshi

last: du

address: NO.1 Donggang West Road

department: First Department of Geriatrics

country: China

institute: The First Hospital of Lanzhou University

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 FC>2  Qvalue < =0.05
Genome_build: rat ensembl v6
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: PC12 cells

growth_protocol: PC-12 cells line (Procell Life Science & Technology Co., Ltd.,China) was cultured at 37℃ with 5% CO 2 in RPMI-1640 with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, 100 U/mL penicillin. SiRNA transfection of PC-12 cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48h for RT-qPCR analysis.

extract_protocol:
Total RNAs were treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1 μg of total RNA was used for RNA-seq library preparation with KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (#KK8544). Polyadenylated mRNAs were purified with VAHTS mRNA capture Beads (N401-01), and fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted Roche Adaptor (KK8726). Ligation products corresponding to 300-500bps were amplified, purified, quantified, and stored at -80 ℃ before sequencing.

treatment_protocol: shRNA against NQO1 transfection of PC2 cells was performed using lipofectAMINE 2000

tag: cell line

value: PC12 cells

value: control plasmid


title: CD4_CD103+TRM_Stim_D07_MildAsthma_S1

value: Male

value: Mild asthma

value: PolyAtail captured messenger RNA


title: TTP WT4 - 60 min LPS + 120 min ActD

value: Bone marrow-derived macrophage

value: WT

value: 60 min + 120min


title: TTP WT4 - 60 min LPS + 60 min ActD

value: LPS + ActD

value: 60 min + 60min


title: CD4_CD103+TRM_Stim_D05_MildAsthma_S1

value: Stimulated


title: Ctrl_1st


title: Ctrl_2st


title: CD4_CD103+TRM_Stim_D11_MildAsthma_S1


title: TTP WT4 - 60 min LPS + 30 min ActD

value: 60 min + 30min


title: TTP WT4 - 60 min LPS + 45 min ActD

value: 60 min + 45min


title: Male.B6.Lit.M327fs.GFPneg.2

value: Treg


title: CD4_CD103+TRM_Stim_D06_MildAsthma_S1


title: CD4_CD103+TRM_Stim_D14_MildAsthma_S1

value: Female


title: CD4_CD103+TRM_Stim_D01_MildAsthma_S1


title: TTP WT4 - 60 min LPS + 20 min ActD

value: 60 min + 20min


title: shNQO1_3st

value: NQO1 knockdown


title: shNQO1_2st

value: PC12 cells


title: FHet.aTreg.KO.M327fs.3

value: B6 Foxp3-ires-GFP

value: Spleen


title: shNQO1_1st


title: TTP WT4 - 60 min LPS + 10 min ActD

value: 60 min + 10min


title: Male.reTreg.M62.1

value: Male


title: CD4_Non-TRM_Unstim_D08_MildAsthma_S1

value: Unstimulated

value: Mild asthma

value: PolyAtail captured messenger RNA


title: CD4_CD103+TRM_Stim_D28_SevereAsthma_S1

value: Severe asthma


title: CD4_Non-TRM_Unstim_D04_MildAsthma_S1


title: Male.KO.M327fs.GFPneg.2


title: TTP WT4 - 60 min LPS

value: Bone marrow-derived macrophage

value: WT

value: LPS


title: CD4_Non-TRM_Unstim_D02_MildAsthma_S1


title: Male.B6.Lit.M327fs.GFPneg.1


title: TTP KO3 - 60 min LPS + 120 min ActD

value: M-TTP KO

value: LPS + ActD

value: 60 min + 120min


title: TTP WT4 - untreated


title: Male.aTreg.M62.1

value: Treg


title: Male.reTreg.M27.2


title: CD4_CD103–TRM_Unstim_D29_SevereAsthma_S1


title: Male.reTreg.M27.1


title: CD4_CD103–TRM_Unstim_D31_SevereAsthma_S1

value: Female


title: TTP KO3 - 60 min LPS + 60 min ActD

value: 60 min + 60min


title: NRK-49F cells, YWCH-4A-2

city: Guangzhou

first: Xinrong

last: Hu

state: Guangdong

address: Zhong shan Road II

institute: Nephrology, The First Affiliated Hospital, Sun Yat-sen University

description:
all.genes.group.expression.annot.txt
all.genes.expression.annot.txt

data_processing:
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software. RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
Supplementary files format and content: Tab-delimited txt files include fpkm and raw counts for all samples or for all biological replicates per sample.

extract_protocol:
Total RNA was isolated from NRK-49F cells with or without the incubation of TGF-β1 for 48 h using Trizol (15596026, Invitrogen) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversely transcribed into cDNA using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, USA, NEB #7530). The purified double-stranded cDNA fragments were end repaired, a base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X). Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.

value: renal fibroblast

value: wt


title: TTP KO3 - 60 min LPS + 45 min ActD

value: 60 min + 45min


title: TTP KO3 - 60 min LPS + 30 min ActD

value: 60 min + 30min


title: Male.aTreg.M27.2

value: Spleen

value: Male


title: CD4_CD103–TRM_Unstim_D24_SevereAsthma_S1

value: Unstimulated

value: PolyAtail captured messenger RNA


title: Male.aTreg.M62.2


title: CD4_CD103–TRM_Unstim_D28_SevereAsthma_S1

value: Severe asthma


title: Male.aTreg.M27.1


title: TTP KO3 - 60 min LPS + 20 min ActD

value: Bone marrow-derived macrophage

value: 60 min + 20min


title: HK-2 cell, 24hr, high sodium, replicate 1

city: Shang hai

first: Jie

last: Gu

address: No. 12, middle Urumqi Road, Shanghai

institute: Division of Nephrology, Huashan Hospital, Fudan University, Shanghai, China.

description: Gene expression after 24hr in high sodium group

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyzearray images to get raw data. Genespring (version 14.8, Agilent Technologies) were employedto finish the basic analysis with the raw data. To begin with, the raw data was normalizedwith the quantile algorithm. The probes that at least 1 conditions out of 2 conditions haveflags in “Detected” were chosen for further data analysis. Differentially expressed geneswere then identified through fold change as well as P value calculated with t-test. Thethreshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.Afterwards, GO analysis and KEGG analysis were applied to determine the roles of thesedifferentially expressed mRNAs. Finally, Hierarchical Clustering was performed to displaythe distinguishable genes' expression pattern among samples.

source_name: HK-2 cell,24hr,high sodium,replicate 1

label_protocol: Total RNA were transcribed to double strand cDNA, then synthesizedinto cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray.After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

growth_protocol: Human proximal tubule epithelial (HK-2) cells were maintained in DMEM/ F12 medium (Gibco; Thermo Fisher Scientific) plus 10% fetal calf serum (FBS) and 1% penicillin/streptomycin.

extract_protocol: RNA was prepared using theTrizol Reagent (Invitrogen, CA)  following the manufacturer's recommendations. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integritywas assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: After culture of the confluent or subconfluent cells, the cells were made quiescent in DMEM/F12 medium with 0.5% FBS for 24 hours at 37 ºC in a humidified incubator with 5% CO2.Quiescent cells were treated with different concentrations of phosphorus/sodium for 24 hours.

tag: group

value: high sodium


title: NRK-49F cells, YEXX-2A-3


title: Male.Tconv.B6.lit337.1

value: WT

value: Tconv


title: HK-2 cell, 24hr, normal, replicate 1

description: Gene expression after 24hr in normal group

source_name: HK-2 cell,24hr,normal,replicate 1

value: normal


title: HK-2 cell, 24hr, high phosphate, replicate 1

description: Gene expression after 24hr in high phosphate group

source_name: HK-2 cell,24hr,high phosphate,replicate 1

value: high phosphate


title: TTP KO3 - 60 min LPS + 10 min ActD

value: M-TTP KO

value: LPS + ActD

value: 60 min + 10min


title: NRK-49F cells, YEXX-2A-2

value: renal fibroblast

value: wt


title: CD4_CD103–TRM_Unstim_D19_SevereAsthma_S1

value: Female


title: CD4_CD103–TRM_Unstim_D20_SevereAsthma_S1

value: Male


title: CD4_CD103–TRM_Unstim_D17_SevereAsthma_S1

value: Unstimulated


title: FHet.aTreg.KO.M327fs.1

value: B6 Foxp3-ires-GFP

value: Spleen

value: Treg


title: FHet.aTreg.KO.M327fs.2


title: NRK-49F cells, YWCH-4A-3


title: NRK-49F cells, YEXX-2A-1


title: TTP KO3 - untreated

value: Bone marrow-derived macrophage


title: NRK-49F cells, YWCH-4A-1


title: TTP KO3 - 60 min LPS

value: LPS


title: CD4_CD103–TRM_Unstim_D16_SevereAsthma_S1

value: Severe asthma

value: PolyAtail captured messenger RNA


title: NRK-49F cells, TGF-b1-3


title: CD4_CD103–TRM_Unstim_D09_MildAsthma_S1

value: Mild asthma


title: Male.reTreg.M62.2


title: NRK-49F cells, TGF-b1-1


title: TTP WT3 - 60 min LPS + 60 min ActD

value: WT

value: 60 min + 60min


title: NRK-49F cells, TGF-b1-2


title: TTP WT3 - 60 min LPS + 120 min ActD

value: LPS + ActD

value: 60 min + 120min


title: Male.reTreg.B6.lit337.1


title: TTP WT3 - 60 min LPS + 45 min ActD

value: 60 min + 45min


title: CD4_Non-TRM_Unstim_D29_SevereAsthma_S1


title: CD4_Non-TRM_Unstim_D24_SevereAsthma_S1


title: Male.reTreg.M337.1


title: TTP WT3 - 60 min LPS + 30 min ActD

value: 60 min + 30min


title: CD4_CD103–TRM_Unstim_D08_MildAsthma_S1

value: Female


title: 6M TAM QC, mRNA-derived cDNA 4

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
TAMQC_4_R_barcodes.tsv.gz
TAMQC_4_R_features.tsv.gz
TAMQC_4_R_matrix.mtx.gz

data_processing:
Cell Ranger v3.0.2 (10x Genomics) was used to align reads to the mm10 mouse pre-mRNA reference genome and to generate feature-barcode matrices.
Further processing was done with Seurat v4.1.1 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis, gene set enrichment analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Brain

growth_protocol: Mice were housed in groups of 2-4, under a 12 h light/dark cycle at 21°C, with food and water ad libitum.

extract_protocol:
Briefly, tissues were subjected to dissociation using the Neural Tissue Dissociation Kit (P) (#130-092-628, Miltenyi) following the manufacturer’s specifications. The cell suspension with 5 μM Actinomycin D (A1410, Sigma)  was filtered over a 70-μm cell strainer (#542070, Greiner) with ice-cold FACS buffer (PBS, 2% FCS, 2 mM EDTA, 5 μM Actinomycin D). The filtered suspension was further centrifuged at 300g at 4 °C for 15 min. We suspended the cell pellet with 30% Percoll (#17-5445-02, GE Healthcare) and spun the suspension at 300g at 4 °C for 15 min. Myelin layers were formed on top of the supernatant and were removed with a Pasteur pipette. The cell pellet was suspended in FACS buffer with anti-mouse CD11b-PE (1:50, REA592, Miltenyi), anti-mouse CD45-BV421 (1:500, #563890, BD Biosciences) and the cell viability marker e780 (1:2000, #65-2860-40, eBioscience) and incubated at 4 °C for 30 min. For the  single-cell experiments, we added a specific hashtag antibody (A0301-A0304, Biolegend) for each individual sample during the antibody incubation. Microglia were washed and sorted on a Miltenyi MACSQuant Tyto cell sorter. Alive microglia expressing CD11b and medium level CD45 but e780 negative were sorted (not shown). At the end, ~15,000 microglia from each GSKO, GSWT, TAM_QC or Ctrl_QC mouse were sorted for the single-cell mRNA library preparation.
We suspended the cells in a final concentration of 1000 cells/μl. We pooled ~2,000 cells from each of the samples (each labeled with a specific hashtag antibody, Biolegend) for library construction using the 10X Genomics single-cell gene expression profiling kit (CG000204_Chromium Single Cell 3' v3.1) combined with HyDrop microfluidic platform. All cDNA libraries were then sequenced on a DNBSEQ PE100 sequencing platform.
Prepare equimolar pools of all 3M RNA libraries, 7M RNA libraries and TAMQC RNA libraries separately. For each RNA library a hash library is included. Hash libraries are spiked in for 10% with the corresponding RNA library (90%). So as an example: the hash library 7M-1_H_S1  was spiked in (10%) into the 7M-1_R_S1 RNA library (90%).

treatment_protocol: Mice were treated with tamoxifen (single dose of 2 mg /kg per day) or vehicle (corn oil) by i.p. injection for 5 consective days at 1 month of age and sacrificed at the indicated time points.

value: Brain

value: Microglia

tag: library type

value: mRNA

tag: antibodies/tags

tag: rounds of_sequencing


title: Male.aTreg.M337.3

tag: genotype

tag: genetic background

value: Spleen

value: Male


title: 6M TAM QC, mRNA-derived cDNA 5

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
TAMQC_5_R_barcodes.tsv.gz
TAMQC_5_R_features.tsv.gz
TAMQC_5_R_matrix.mtx.gz

tag: tissue


title: 6M TAM QC APP-NLGF, mRNA-derived cDNA 3

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
TAMQC_3_R_barcodes.tsv.gz
TAMQC_3_R_features.tsv.gz
TAMQC_3_R_matrix.mtx.gz


title: CD4_Non-TRM_Unstim_D20_SevereAsthma_S1

value: Unstimulated

tag: Sex


title: Male.aTreg.M337.2

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

tag: cell

value: Treg

tag: age (weeks)


title: TTP WT3 - 60 min LPS + 10 min ActD

tag: cell type

value: Bone marrow-derived macrophage

tag: treatment

value: 60 min + 10min


title: Male.aTreg.M337.1


title: CD4_CD103–TRM_Unstim_D07_MildAsthma_S1

tag: stimulation

value: Mild asthma

value: PolyAtail captured messenger RNA


title: 6M TAM QC APP-NLGF, mRNA-derived cDNA 2

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
TAMQC_2_R_barcodes.tsv.gz
TAMQC_2_R_features.tsv.gz
TAMQC_2_R_matrix.mtx.gz


title: TTP WT3 - 60 min LPS

value: WT

value: LPS

tag: time


title: 6M TAM QC, HTO-derived cDNA 5

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
TAMQC_5_R_barcodes.tsv.gz
TAMQC_5_R_features.tsv.gz
TAMQC_5_R_matrix.mtx.gz

value: HTO

value: Anti CD45 + Anti MHC classI :Male C57Bl6 Aph1-cKO/TotalSeq-A0301 ; Male C57Bl6 Ctrl/TotalSeq-A0302 ; Male C57Bl6 Ctrl/TotalSeq-A0303 ; Male Ctrl/TotalSeq-A0304


title: CD4_Non-TRM_Unstim_D14_MildAsthma_S1

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

tag: disease state

tag: molecule subtype


title: Male.reTreg.B6.lit324.1

value: B6 Foxp3-ires-GFP


title: CD4_CD103–TRM_Unstim_D06_MildAsthma_S1


title: 6M TAM QC C57Bl6, mRNA-derived cDNA 1

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
TAMQC_1_R_barcodes.tsv.gz
TAMQC_1_R_features.tsv.gz
TAMQC_1_R_matrix.mtx.gz


title: Male.reTreg.M337.2


title: Male.Tconv.B6.lit324.1

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

value: Tconv


title: TTP WT3 - untreated

description:
Myeloid-TTP_KO_LPS_ActD_raw_counts.txt
Myeloid-TTP_KO_LPS_ActD_normalized_counts_per_kb.txt


title: TTP KO2 - 60 min LPS + 120 min ActD

value: M-TTP KO

value: LPS + ActD

value: 60 min + 120min


title: 6M TAM QC, HTO-derived cDNA 4

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
TAMQC_4_R_barcodes.tsv.gz
TAMQC_4_R_features.tsv.gz
TAMQC_4_R_matrix.mtx.gz

value: Brain

value: Microglia

value: Anti CD45 + Anti MHC classI :Male C57Bl6 Aph1-cKO/TotalSeq-A0301 ; Female C57Bl6 Ctrl/TotalSeq-A0302 ; Male APP-NLGF Ctrl/TotalSeq-A0303


title: 6M TAM QC APP-NLGF, HTO-derived cDNA 3

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
TAMQC_3_R_barcodes.tsv.gz
TAMQC_3_R_features.tsv.gz
TAMQC_3_R_matrix.mtx.gz

value: Anti CD45 + Anti MHC classI :Female Aph1-cKO/TotalSeq-A0301 ; Male Aph1-cKO/TotalSeq-A0302 ; Female Ctrl/TotalSeq-A0304


title: TTP WT3 - 60 min LPS + 20 min ActD

value: Bone marrow-derived macrophage

value: 60 min + 20min


title: TTP KO2 - 60 min LPS + 60 min ActD

value: 60 min + 60min


title: Male.aTreg.B6.lit337.1

value: Spleen

value: Treg

value: Male


title: CD4_CD103–TRM_Unstim_D04_MildAsthma_S1

value: Unstimulated

value: Female

value: Mild asthma

value: PolyAtail captured messenger RNA


title: TTP KO2 - 60 min LPS + 45 min ActD

value: M-TTP KO

value: 60 min + 45min


title: 6M TAM QC APP-NLGF, HTO-derived cDNA 2

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
TAMQC_2_R_barcodes.tsv.gz
TAMQC_2_R_features.tsv.gz
TAMQC_2_R_matrix.mtx.gz

value: HTO


title: Male.Tconv.M337.1

value: Tconv


title: TTP KO2 - 60 min LPS + 30 min ActD

value: LPS + ActD

value: 60 min + 30min


title: CD4_Non-TRM_Unstim_D12_MildAsthma_S1


title: CD4_CD103–TRM_Unstim_D03_MildAsthma_S1


title: 6M TAM QC C57Bl6, HTO-derived cDNA 1

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
TAMQC_1_R_barcodes.tsv.gz
TAMQC_1_R_features.tsv.gz
TAMQC_1_R_matrix.mtx.gz

value: Brain

value: Microglia

value: Anti CD45 + Anti MHC classI :Female Aph1-cKO/TotalSeq-A0301 ; Male Aph1-cKO/TotalSeq-A0302 ; Female Ctrl/TotalSeq-A0303 ; Male Ctrl/TotalSeq-A0304


title: 7M APP-NLGF, mRNA-derived cDNA 2

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
7M-2_R_barcodes.tsv.gz
7M-2_R_features.tsv.gz
7M-2_R_matrix.mtx.gz

value: mRNA


title: Male.reTreg.M337.3

value: Spleen


title: TTP KO2 - 60 min LPS + 20 min ActD

value: Bone marrow-derived macrophage

value: 60 min + 20min


title: CD4_Non-TRM_Unstim_D17_SevereAsthma_S1

value: Unstimulated

value: Male

value: Severe asthma


title: Male.reTreg.M324.2

value: B6 Foxp3-ires-GFP

value: Treg


title: CD4_CD103–TRM_Unstim_D05_MildAsthma_S1

value: Mild asthma

value: PolyAtail captured messenger RNA


title: 7M APP-NLGF, HTO-derived cDNA 2

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
7M-2_R_barcodes.tsv.gz
7M-2_R_features.tsv.gz
7M-2_R_matrix.mtx.gz

value: HTO


title: Male.aTreg.B6.lit324.1

value: WT


title: Male.reTreg.M324.1


title: CD4_CD103–TRM_Unstim_D02_MildAsthma_S1


title: 7M APP-NLGF, mRNA-derived cDNA 1

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
7M-1_R_barcodes.tsv.gz
7M-1_R_features.tsv.gz
7M-1_R_matrix.mtx.gz


title: TTP KO2 - 60 min LPS

value: M-TTP KO

value: LPS


title: CD4_Non-TRM_Unstim_D05_MildAsthma_S1


title: TTP KO2 - 60 min LPS + 10 min ActD

value: LPS + ActD

value: 60 min + 10min


title: TTP WT2 - 60 min LPS + 120 min ActD

value: 60 min + 120min


title: Male.aTreg.M324.2

value: Spleen


title: CD4_CD103+TRM_Unstim_D31_SevereAsthma_S1

value: Female


title: 3M APP-NLGF Ctrl, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
3M_TAM1_barcodes.tsv.gz
3M_Ctrl2_features.tsv.gz
3M_Ctrl2_matrix.mtx.gz

value: Brain

value: Microglia

value: Anti CD45 + Anti MHC classI :Female/TotalSeq-A0301 ; Female/TotalSeq-A0302 ; Male/TotalSeq-A0303 ; Male/TotalSeq-A0304


title: CD4_Non-TRM_Unstim_D16_SevereAsthma_S1

value: Unstimulated

value: Severe asthma


title: Male.aTreg.B6.lit324.3

value: B6 Foxp3-ires-GFP

value: Treg

value: Male


title: 3M APP-NLGF Ctrl, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
3M_TAM1_barcodes.tsv.gz
3M_Ctrl2_features.tsv.gz
3M_Ctrl2_matrix.mtx.gz

value: mRNA


title: TTP WT2 - 60 min LPS + 60 min ActD

value: Bone marrow-derived macrophage

value: WT

value: 60 min + 60min


title: CD4_CD103+TRM_Unstim_D29_SevereAsthma_S1

value: PolyAtail captured messenger RNA


title: 3M C57Bl6 Ctrl, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
3M_TAM1_barcodes.tsv.gz
3M_Ctrl1_features.tsv.gz
3M_Ctrl1_matrix.mtx.gz

value: HTO

value: Anti CD45 + Anti MHC classI :Male/TotalSeq-A0301 ; Male/TotalSeq-A0302 ; Female/TotalSeq-A0303 ; Female/TotalSeq-A0304


title: TTP WT2 - 60 min LPS + 45 min ActD

value: LPS + ActD

value: 60 min + 45min


title: FHet.reTreg.M324.2

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

value: Spleen

value: Female


title: TTP WT2 - 60 min LPS + 30 min ActD

value: 60 min + 30min


title: FHet.reTreg.M324.1


title: CD4_CD103+TRM_Unstim_D28_SevereAsthma_S1

value: Unstimulated


title: FHet.reTreg.M324.3


title: CD4_Non-TRM_Unstim_D13_MildAsthma_S1

value: Mild asthma


title: TTP WT2 - 60 min LPS + 20 min ActD

value: 60 min + 20min


title: TTP KO2 - untreated

value: M-TTP KO


title: 7M APP-NLGF, HTO-derived cDNA 1

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
7M-1_R_barcodes.tsv.gz
7M-1_R_features.tsv.gz
7M-1_R_matrix.mtx.gz

value: Brain

value: Microglia

value: Anti CD45 + Anti MHC classI :Female Aph1-cKO/TotalSeq-A0301 ; Male Aph1-cKO/TotalSeq-A0302 ; Female Ctrl/TotalSeq-A0303 ; Male Ctrl/TotalSeq-A0304


title: Male.aTreg.M324.3

value: B6 Foxp3-ires-GFP

value: Treg

value: Male


title: 3M APP-NLGF Aph1-cKO Tamoxifen Treated, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
3M_TAM2_barcodes.tsv.gz
3M_TAM2_features.tsv.gz
3M_TAM2_matrix.mtx.gz

value: HTO

value: Anti CD45 + Anti MHC classI :Female/TotalSeq-A0301 ; Female/TotalSeq-A0302 ; Male/TotalSeq-A0303 ; Male/TotalSeq-A0304


title: CD4_Non-TRM_Unstim_D11_MildAsthma_S1

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

value: PolyAtail captured messenger RNA


title: Male.Tconv.M324.1

value: Tconv


title: 3M APP-NLGF Aph1-cKO Tamoxifen Treated, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
3M_TAM2_barcodes.tsv.gz
3M_TAM2_features.tsv.gz
3M_TAM2_matrix.mtx.gz

value: mRNA


title: Male.reTreg.M324.3

value: Spleen


title: CD4_CD103+TRM_Unstim_D24_SevereAsthma_S1

value: Severe asthma


title: TTP WT2 - 60 min LPS + 10 min ActD

value: Bone marrow-derived macrophage

value: WT

value: LPS + ActD

value: 60 min + 10min


title: 3M C57Bl6 Aph1-cKO Tamoxifen Treated, HTO-derived cDNA

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
3M_TAM1_barcodes.tsv.gz
3M_TAM1_features.tsv.gz
3M_TAM1_matrix.mtx.gz

value: Brain

value: Anti CD45 + Anti MHC classI :Male/TotalSeq-A0301 ; Male/TotalSeq-A0302 ; Female/TotalSeq-A0303 ; Female/TotalSeq-A0304


title: FHet.aTreg.M324.3

value: Female


title: CD4_CD103+TRM_Unstim_D20_SevereAsthma_S1

value: Unstimulated


title: 3M C57Bl6 Aph1-cKO Tamoxifen Treated, mRNA-derived cDNA.

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
3M_TAM1_barcodes.tsv.gz
3M_TAM1_features.tsv.gz
3M_TAM1_matrix.mtx.gz

value: Microglia


title: CD4_CD103+TRM_Unstim_D19_SevereAsthma_S1


title: Male.reTreg.B6.lit309.1

value: Treg

value: Male


title: TTP KO1 - 60 min LPS + 120 min ActD

description:
Myeloid-TTP_KO_LPS_ActD_raw_counts.txt
Myeloid-TTP_KO_LPS_ActD_normalized_counts_per_kb.txt

value: M-TTP KO

value: 60 min + 120min


title: 3M C57Bl6 Ctrl, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
3M_TAM1_barcodes.tsv.gz
3M_Ctrl1_features.tsv.gz
3M_Ctrl1_matrix.mtx.gz


title: CD4_CD103+TRM_Unstim_D17_SevereAsthma_S1

value: PolyAtail captured messenger RNA


title: Male.aTreg.B6.lit309.1


title: CD4_CD103–TRM_Unstim_D27_SevereAsthma_S1


title: Male.Tconv.M309.1

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

value: Tconv


title: TTP WT2 - 60 min LPS

value: LPS


title: delta-Sisdbp, biol rep 2

city: Qingdao

first: Qihong

last: Huang

state: Shandong

address: 72 Binhaidadao, Aoshanwei, Jimo

institute: Shandong University

description: The Sisdbp deletion strain, biol rep 2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome S. islandicus REY15A (Guo, et al., 2011) and its gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value
Assembly: REY15A
Supplementary files format and content: tab-delimited text files
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Saccharolobus islandicus

source_name: microbial cells

growth_protocol: S. islandicus strains were grown in MTSUV medium (Basic mineral medium+Typtone+Sucrose+Uracil+Vatamin) at 75 oC.

extract_protocol:
Cells were pelleted at 6,000 g for 10 min and washed in PBS, then frozen with liquid nitrogen and transported with dry ice. Total RNA was extracted using the Trizol reagent (Ambion, Austin, TX, USA) and assessed by Aagilent 2100 bioanalyzer.
mRNA was purified from total RNA using probes to remove rRNA. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. And in the DNA polymerase I system, use dUTP to replace the dNTP of dTTP as the raw material to synthesize the second strand of cDNA. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. Then USER Enzyme was used to degrade the second strand of cDNA containing U, In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: microbial cells

tag: cell line

value: Sisdbp knockout

value: no treatment


title: CD4_CD103+TRM_Unstim_D16_SevereAsthma_S1

value: Severe asthma


title: Male.reTreg.M309.1

value: Spleen


title: TTP KO1 - 60 min LPS + 30 min ActD

value: Bone marrow-derived macrophage

value: LPS + ActD

value: 60 min + 30min


title: Male.reTreg.M309.2


title: TTP KO1 - 60 min LPS + 40 min ActD

value: 60 min + 45min


title: delta-Sisssb, biol rep 2

description: The Sisssb deletion strain, biol rep 2

value: Sisssb knockout


title: TTP WT2 - untreated

value: WT


title: delta-Sisdbp, biol rep 1

description: The Sisdbp deletion strain, biol rep 1


title: CD4_CD103–TRM_Unstim_D26_SevereAsthma_S1

value: Unstimulated

value: Male


title: TTP KO1 - 60 min LPS + 10 min ActD

value: M-TTP KO

value: 60 min + 10min


title: delta-Sisssb, biol rep 3

description: The Sisssb deletion strain, biol rep 3


title: delta-Sisssb, biol rep 1

description: The Sisssb deletion strain, biol rep 1


title: Male.aTreg.M309.2

value: Treg


title: Male.aTreg.M309.1


title: delta-Sisdbp, biol rep 3

description: The Sisdbp deletion strain, biol rep 3


title: E233S, biol rep 3 (delta-Sisssb control)

description: The wild type strain E233S, biol rep 3


title: CD4_CD103–TRM_Unstim_D14_MildAsthma_S1

value: Female

value: Mild asthma

value: PolyAtail captured messenger RNA


title: Male.Tconv.B6.lit200.1

value: B6 Foxp3-ires-GFP

value: Tconv


title: CD4_CD103+TRM_Unstim_D09_MildAsthma_S1


title: TTP KO1 - 60 min LPS + 60 min ActD

value: 60 min + 60min


title: E233S, biol rep 2 (delta-Sisssb control)

description: The wild type strain E233S, biol rep 2

value: microbial cells

value: no treatment


title: TTP KO1 - untreated

value: Bone marrow-derived macrophage


title: TTP KO1 - 60 min LPS + 20 min ActD

value: LPS + ActD

value: 60 min + 20min


title: CD4_CD103–TRM_Unstim_D10_MildAsthma_S1


title: E233S, biol rep 1 (delta-Sisssb control)

description: The wild type strain E233S, biol rep 1

value: WT


title: TTP WT1 - 60 min LPS + 120 min ActD

value: 60 min + 120min


title: FHet.aTreg.M324.1

value: Spleen


title: TTP WT1 - 60 min LPS + 60 min ActD


title: TTP WT1 - 60 min LPS + 45 min ActD

value: 60 min + 45min


title: CD4_CD103+TRM_Unstim_D30_SevereAsthma_S1

value: Unstimulated

value: Severe asthma


title: TTP KO1 - 60 min LPS

value: M-TTP KO

value: LPS


title: BW_M_15763_thalamus

city: Cambridge

first: Andreas

middle: F

last: Kautt

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

source_name: brain

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: thalamus

tag: strain

value: BW

value: M


title: FHet.aTreg.M324.2

value: B6 Foxp3-ires-GFP

value: Treg

value: Female


title: Male.Tconv.B6.lit309.1

value: Tconv

value: Male


title: Male.Tconv.M200.1


title: TTP WT1 - 60 min LPS + 20 min ActD

value: Bone marrow-derived macrophage

value: WT

value: LPS + ActD

value: 60 min + 20min


title: Male.reTreg.B6.lit200.1

value: Spleen


title: TTP WT1 - 60 min LPS + 10 min ActD

value: 60 min + 10min


title: BW_M_15763_striatum

value: striatum


title: BW_M_15763_septum

value: septum


title: Male.reTreg.M200.1


title: CD4_CD103+TRM_Unstim_D07_MildAsthma_S1

value: Unstimulated

value: Mild asthma

value: PolyAtail captured messenger RNA


title: CD4_CD103–TRM_Unstim_D12_MildAsthma_S1


title: BW_M_15763_mPFC

value: brain

value: mPFC

value: BW

value: M


title: CD4_CD103+TRM_Unstim_D06_MildAsthma_S1


title: Male.aTreg.M200.3

value: B6 Foxp3-ires-GFP

value: Treg


title: CD4_CD103–TRM_Unstim_D23_SevereAsthma_S1

value: Male

value: Severe asthma


title: BW_M_15763_midbrain

value: midbrain


title: BW_M_15763_hypothalamus

value: hypothalamus


title: CD4_CD103–TRM_Unstim_D11_MildAsthma_S1


title: CD4_CD103+TRM_Unstim_D08_MildAsthma_S1

value: Female


title: Male.aTreg.M200.2

value: Spleen


title: TTP WT1 - untreated

value: Bone marrow-derived macrophage

value: WT


title: CD4_CD103+TRM_Unstim_D05_MildAsthma_S1

value: Unstimulated


title: TTP WT1 - 60 min LPS + 30 min ActD

value: LPS + ActD

value: 60 min + 30min


title: BW_M_15763_amygdala

value: brain

value: amygdala


title: CD4_CD103+TRM_Unstim_D10_MildAsthma_S1

value: Mild asthma

value: PolyAtail captured messenger RNA


title: FHet.reTreg.M200.3

value: B6 Foxp3-ires-GFP


title: Male.aTreg.B6.lit200.1

value: Treg


title: BW_M_15740_striatum

value: striatum

value: BW

value: M


title: CD4_CD103+TRM_Unstim_D23_SevereAsthma_S1

value: Male

value: Severe asthma


title: BW_M_15740_thalamus

value: thalamus


title: Male.aTreg.M200.1

value: Spleen


title: CD4_CD103+TRM_Unstim_D04_MildAsthma_S1

value: Female


title: KO1_scRNAseq

city: St. Louis

first: Marco

last: Colonna

state: Missouri

address: 425 S. Euclid

department: Pathology and Immunology

institute: Washington University in St. Louis

description: 10x Genomics

data_processing:
Cell ranger was used to align samples to the reference mm10 genome and generate gene-cell expression matrices.
Assembly: mm10
Supplementary files format and content: Cell ranger output files

source_name: small intestine

extract_protocol:
CD45+ cells were sorted then cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 10-14 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  GEX libraries were prepared as recommended by the 10x Genomics Chromium Single Cell V(D)J Reagent Kits (v1 Chemistry) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.
the Chromium Single Cell 5’ Library and Gel Bead Kit v1 (PN-1000006), Chromium Single Cell A Chip Kit (PN-1000152) and Chromium Single Index Kit T (PN-1000213) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.

value: IEL

value: small intestine

value: Ikzf3 -/-

tag: age

value: 10 weeks


title: FHet.reTreg.B6.lit200.1

value: WT


title: FHet.aTreg.B6.lit200.1


title: CD4_CD103+TRM_Unstim_D14_MildAsthma_S1

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

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.

value: Unstimulated

value: Mild asthma


title: WT2_scRNAseq

description: 10x Genomics

value: Ikzf3 +/+


title: WT1_scRNAseq

description: 10x Genomics


title: BW_M_15740_midbrain

value: brain

value: midbrain


title: CD4_CD103+TRM_Unstim_D03_MildAsthma_S1

value: PolyAtail captured messenger RNA


title: FHet.reTreg.M200.2

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.

value: B6 Foxp3-ires-GFP

value: Treg


title: CD4_CD103+TRM_Unstim_D13_MildAsthma_S1


title: H3K27ac_DNKO4

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

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: DN IEL

tag: chip antibody

value: EpiCypher SKU 13-0045


title: KO2_scRNAseq

description: 10x Genomics

tag: genotype


title: BW_M_15740_hypothalamus

value: hypothalamus

value: BW

value: M


title: FHet.aTreg.M200.1

tag: genetic background

value: Spleen

value: Female


title: CD4_CD103+TRM_Unstim_D02_MildAsthma_S1

value: Male


title: H3K27ac_DNKO3

value: Ikzf3 -/-

tag: tissue

value: small intestine


title: BW_M_15740_amygdala

value: amygdala

tag: Sex


title: Male.aTreg.B6.lit168.1

value: WT

tag: cell


title: BW_M_15740_mPFC

value: brain

value: mPFC


title: H3K27ac_DNKO2


title: negative_control

value: Ikzf3 +/+

value: IEL

value: rabbit IgG negative control antibody (SKU 13-0042k)


title: BW_M_15514_hippocampus

value: hippocampus


title: FHet.aTreg.B6.lit168.2

value: Treg

tag: age (weeks)


title: pahari_M_input

organism: Mus pahari

value: Liver

value: ChIP

value: Shrewlike Mouse

value: input


title: BW_M_15514_hindbrain

value: hindbrain

value: BW

value: M


title: CD4_CD103+TRM_Unstim_D12_MildAsthma_S1

tag: cell type

value: Unstimulated

value: Male

value: Mild asthma

value: PolyAtail captured messenger RNA


title: H3K27ac_DNKO1

value: Ikzf3 -/-

value: small intestine

value: DN IEL

value: EpiCypher SKU 13-0045


title: pahari_F_input

value: F


title: H3K27ac_DNWT4

value: Ikzf3 +/+


title: H3K27ac_DNWT3


title: FHet.reTreg.M200.1

value: B6 Foxp3-ires-GFP

value: Spleen

value: Treg

value: Female


title: FHet.aTreg.B6.lit168.1

value: WT


title: BW_M_15514_cerebellum

value: brain

value: cerebellum

value: BW


title: BW_M_15513_hippocampus

value: hippocampus

value: M


title: FHet.aTreg.M200.3


title: BW_M_15513_hindbrain

value: hindbrain


title: pahari_F_CTCF

description: pahari-CTCF.bigwig

value: Liver

value: ChIP

value: Shrewlike Mouse

value: CTCF


title: H3K27ac_DNWT2

value: small intestine

value: DN IEL

value: EpiCypher SKU 13-0045


title: BW_M_15513_cerebellum


title: H3K27ac_gdKO4

value: Ikzf3 -/-

value: gd IEL


title: FHet.aTreg.M200.2

value: B6 Foxp3-ires-GFP

value: Spleen

value: Treg

value: Female


title: Male.Tconv.M168.1

value: Tconv

value: Male


title: pahari_M_H3K27ac

value: M


title: H3K27ac_gdKO3


title: CD4_CD103–TRM_Unstim_D13_MildAsthma_S1

value: Unstimulated

value: Mild asthma

value: PolyAtail captured messenger RNA


title: Male.aTreg.M168.3


title: H3K27ac_gdKO2


title: Male.aTreg.M168.2


title: pahari_M_H3K4me1

value: Liver

value: ChIP

value: Shrewlike Mouse


title: pahari_F_H3K4me1

value: F


title: pahari_M_CTCF

description: pahari-CTCF.bigwig

value: CTCF


title: H3K27ac_gdKO1

value: Ikzf3 -/-

value: small intestine

value: EpiCypher SKU 13-0045


title: FHet.reTreg.M168.3

value: Spleen


title: H3K27ac_gdWT4

value: Ikzf3 +/+

value: gd IEL


title: H3K27ac_gdWT3


title: H3K27ac_gdWT2


title: BW_M_15512_hippocampus

value: brain

value: hippocampus

value: BW


title: BW_M_15512_cerebellum

value: cerebellum

value: M


title: pahari_M_H3K4me3


title: BW_M_15512_hindbrain

value: hindbrain


title: BW_M_15507_septum

value: septum


title: H3K27ac_gdWT1


title: BW_M_15507_striatum

value: striatum


title: pahari_F_H3K27me3

value: Liver

value: ChIP

value: Shrewlike Mouse


title: Male.aTreg.M168.1

value: Treg

value: Male


title: BW_M_15507_thalamus

value: thalamus


title: pahari_F_H3K27ac

value: F


title: pahari_F_H3K4me3


title: BW_M_15507_mPFC

value: mPFC


title: FHet.reTreg.M168.1

value: Spleen

value: Female


title: BW_M_15740_septum

value: brain


title: FHet.reTreg.M168.2


title: RNAseq_gd_WT3

data_processing:
Sequences were aligned and gene count tables were produced using STAR aligner.
Assembly: mm10
Supplementary files format and content: log normalized counts using DESeq2

extract_protocol:
50,000 cells of wild-type or Aiolos-deficient γδ IEL and DN IEL were sorted, and RNA was extracted with an RNeasy Micro Kit (QIAGEN) following manufacture’s instructions
ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacture’s protocol.

value: small intestine

value: gd IEL

value: Ikzf3 +/+


title: FHet.aTreg.M168.3


title: RNAseq_gd_WT2


title: BW_M_15507_midbrain

value: midbrain

value: BW

value: M


title: pahari_mouse_M_HiC

value: Liver

tag: protocol

value: Arima


title: FHet.aTreg.M168.2


title: Male.reTreg.M168.3


title: pahari_M_H3K27me3

value: ChIP

value: Shrewlike Mouse


title: pahari_mouse_F_HiC


title: BW_M_15507_hypothalamus

value: hypothalamus


title: BW_M_15507_amygdala

value: amygdala


title: RNAseq_gd_WT1


title: RNAseq_gd_KO3

value: Ikzf3 -/-


title: BW_F_15690_hippocampus

value: hippocampus

value: F


title: Male.reTreg.M168.1

value: Spleen

value: Treg

value: Male


title: PO_M_16809_wholebrain

organism: Peromyscus polionotus

value: brain

value: wholebrain

value: PO


title: RNAseq_DN_WT2

value: small intestine

value: DN IEL

value: Ikzf3 +/+


title: TTP WT1 - 60 min LPS

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

value: Bone marrow-derived macrophage

value: WT

tag: treatment

value: LPS


title: RNAseq_gd_KO2

value: gd IEL


title: BW_F_15690_cerebellum

value: cerebellum

value: BW


title: BW_F_15690_hindbrain

value: hindbrain


title: PO_M_16872_wholebrain

value: M


title: PO_M_16598_wholebrain


title: BW_F_15526_hippocampus

value: hippocampus

value: F


title: PO_M_16620_wholebrain


title: RNAseq_DN_WT1


title: BW_F_15526_cerebellum


title: BW_F_15526_hindbrain


title: PO_M_16537_wholebrain


title: Male.reTreg.M168.2

value: Spleen

value: Treg

value: Male


title: RNAseq_DN_WT3


title: RNAseq_DN_KO3

value: Ikzf3 -/-


title: PO_M_17003_wholebrain

value: brain

value: wholebrain

value: PO


title: PO_M_15921_thalamus

value: thalamus


title: PO_M_15921_striatum

value: striatum


title: FHet.aTreg.M168.1

value: Female


title: G45WT_7Gy_1d_rep4

city: New York

first: Constantinos

last: Broustas

state: NY

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.2 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 026655_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia 24 h post-irradiation. Each sample  was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

value: male

value: 7 Gy of x-rays


title: BW_F_15520_thalamus

value: BW


title: RNAseq_gd_KO1

value: small intestine

value: gd IEL


title: G45WT_7Gy_1d_rep5


title: BW_F_15520_striatum


title: PO_M_15921_septum

value: septum

value: M


title: BW_F_15520_septum

value: F


title: BW_F_15520_mPFC

value: mPFC


title: PO_M_15921_mPFC


title: G45WT_7Gy_1d_rep3


title: RNAseq_DN_KO1

value: DN IEL


title: PO_M_15921_midbrain

value: midbrain


title: MI_E_horizontal_cross_section, spatial transcriptomics

city: Shanghai

first: Yaozu

last: Xiang

address: 1239 Siping Road, Yangpu District

institute: Tongji University

description: 10x Genomics

data_processing:
Raw data were demultiplexed using SpaceRanger (v1.2.1, 10x Genomics).
Read alignment, tissue detection, fiducial detection and feature-barcode matrix generation were performed using SpaceRanger. UCSC mm10 reference genome, provided by 10x Genomics, was used for alignment.
Raw counts data was imported into Python/R for downstream processing.
Assembly: mm10
Supplementary files format and content: Hdf5 format files containing raw read count values for every gene and every spot, and H&E images.

source_name: Heart

extract_protocol:
OCT-embedded freshly frozen hearts of MI and MI-E were used for Visium Spatial Gene Expression platform (10X Genomics). The 10-µm vertical and horizontal sections from MI and MI-E hearts were placed on the pre-chilled Visium Spatial Tissue Optimization slides, followed by optimization of tissue permeabilization according to the manufacturer’s protocol, which established an optimal tissue permeabilization time of 18 minutes for four heart sections. After hematoxylin and eosin (H&E) staining, permeabilization, reverse transcription and second-strand cDNA synthesis, the Visium Spatial Single Cell 3′ Gene Expression libraries were constructed, sequencing of which were performed on Illumina NovaSeq 6000.
The barcoded libraries were prepared under Visium Spatial Gene Expression Slide & Reagent Kit (10X Genomics) according to the manufacturer’s protocol.

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: cross section type

value: Horizontal

tag: model

value: MI-E

value: 8-9 weeks


title: PO_M_15921_hypothalamus

value: brain

value: hypothalamus

value: PO


title: MI_vertical_cross_section, spatial transcriptomics

description: 10x Genomics

value: Vertical

value: MI


title: BW_F_15520_midbrain

value: BW


title: PO_M_15921_amygdala

value: amygdala


title: BW_F_15520_amygdala


title: MI_horizontal_cross_section, spatial transcriptomics

description: 10x Genomics


title: BW_F_15520_hypothalamus


title: PO_M_15920_hippocampus

value: hippocampus


title: BW_F_15515_thalamus

value: thalamus


title: G45WT_0Gy_1d_rep5

value: male


title: G45WT_7Gy_1d_rep1

value: 7 Gy of x-rays


title: G45WT_7Gy_1d_rep2


title: MI-E, scRNAseq

description: 10x Genomics

data_processing:
Raw data were demultiplexed using Cellranger (v5.0.1, 10x Genomics).
UCSC mm10 reference genome, provided by 10x Genomics, was used for alignment and unique molecular identifier (UMI) quantification.
Gene level quantification was completed using Cellranger count.
Raw counts data was imported into Python/R for downstream processing.
Assembly: mm10
Supplementary files format and content: Matrix table with raw read count values for every gene and every cell.

extract_protocol:
For 10X Genomics scRNA-seq, immune cells were isolated by FACS based on CD45 staining from heart of Sham, MI and MI-E. The barcoded libraries were prepared under Single Cell 3’ Reagents Kit v3.1 (10X Genomics) according to the manufacturer’s protocol. Single cell suspensions were loaded on Chromium Controller (10X Genomics) to form single cell gel beads in emulsion (GEMs). The libraries were further controlled via Agilent 2100 Bioanalyzer (Agilent Technologies). After passing quality control, the libraries were sequenced on NovaSeq 6000 (Illumina) to generate 150 bp paired-end reads.
The barcoded libraries were prepared under Single Cell 3’ Reagents Kit v3.1 (10X Genomics) according to the manufacturer’s protocol.

value: Immune cells

value: 8-9 weeks old


title: RNAseq_DN_KO2

value: small intestine

value: DN IEL

value: Ikzf3 -/-


title: PO_M_15920_hindbrain

value: hindbrain

value: M


title: G45WT_0Gy_1d_rep3


title: MI_E_vertical_cross_section, spatial transcriptomics

description: 10x Genomics

value: Heart

value: MI-E

value: 8-9 weeks


title: G45WT_0Gy_1d_rep4


title: G45WT_0Gy_1d_rep2


title: MI, scRNAseq

description: 10x Genomics

value: MI


title: G45WT_0Gy_1d_rep1


title: PO_M_15920_cerebellum

value: brain

value: cerebellum

value: PO


title: G45KO_7Gy_1d_rep9


title: BW_F_15515_striatum

value: striatum

value: BW

value: F


title: BW_F_15515_septum

value: septum


title: PO_M_15820_hippocampus

value: hippocampus


title: PO_M_15820_hindbrain


title: ChIP.06_MRTK.103_antiH3K27ac_SMARCB1

city: Rotterdam

first: Ning Qing

last: Liu

address: Wytemaweg 80

department: Hematology

country: Netherlands

institute: Erasmus University Medical Center Rotterdam

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

data_processing:
ChIP-seq data 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.
Assembly: hg38
Supplementary files format and content: bigWig files

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:
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. 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).

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: MRT organoids P103

value: Malignant rhabdoid tumor cells

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


title: PO_M_15820_cerebellum


title: G45KO_7Gy_1d_rep8

value: male

value: 7 Gy of x-rays


title: BW_F_15515_mPFC

value: mPFC


title: BW_F_15515_midbrain

value: midbrain


title: ChIP.04_MRTK.103_antiRAD21_SMARCB1


title: PO_M_15819_hippocampus

value: M


title: G45KO_7Gy_1d_rep7


title: ChIP.03_MRTK.103_antiRAD21_CTRL

description: ChIP-seq in MRT organoids P103, after 4 days lentiviral transduction with the Luciferase gene

value: Luciferase plasmid


title: BW_F_15515_amygdala

value: brain

value: amygdala


title: BW_F_15515_hypothalamus

value: hypothalamus


title: PO_M_15819_hindbrain

value: hindbrain

value: PO


title: ChIP.02_MRTK.103_antiCTCF_SMARCB1

value: anti-CTCF


title: G45KO_7Gy_1d_rep5


title: BW_F_15508_hippocampus

value: BW

value: F


title: Sham, scRNAseq

description: 10x Genomics

value: Immune cells

value: Heart

value: 8-9 weeks old

value: Sham


title: G45KO_7Gy_1d_rep3

value: male

value: 7 Gy of x-rays


title: ChIP.05_MRTK.103_antiH3K27ac_CTRL

value: MRT organoids P103

value: Malignant rhabdoid tumor cells


title: ChIP.01_MRTK.103_antiCTCF_CTRL

value: Luciferase plasmid


title: BW_F_15508_hindbrain

value: brain


title: PO_M_15765_hippocampus

value: hippocampus

value: M


title: G45KO_7Gy_1d_rep6


title: ATAC.18_MRTK.78_SMARCB1_rep3

description:
ATAC-seq in MRT organoids P78, after 4 days lentiviral transduction with the SMARCB1 gene
MRTK_ATACseq_peak_coordinates_2022-11-10.txt; MRTK_ATACseq_readcounts_unnormalized_2022-11-10.txt; MRTK_ATACseq_readcounts_normalized_2022-11-10.txt

data_processing:
ATAC-seq data were were mapped against the hg38 reference genome using BWA-MEM. The mapped reads with mapping quality score <15, as well as optical PCR duplicates, were discarded using SAMtools. The coverage files were generated using “normalize to 1X genome coverage” methods in deepTools.
Assembly: hg38
Supplementary files format and content: bigWig files, read counts

source_name: MRT organoids P78

extract_protocol:
ATAC-seq libraries were prepared following a published protocol (Liu et al. 2017). 100 k organoid cells are harvested. Nuclei were isolated, permeabilized, and tagmented using in-house produced Tn5 transposase.
The resulted DNA fragments underwent two sequential 9-cycle PCR amplification and the fragments < 700 bp were purified using SPRI beads (Liu et al., 2017).

value: MRT organoids P78

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


title: ATAC.17_MRTK.78_SMARCB1_rep2


title: PO_M_15765_cerebellum

value: cerebellum

value: PO


title: G45KO_7Gy_1d_rep1


title: G45KO_7Gy_1d_rep2


title: BW_F_15508_cerebellum

value: BW

value: F


title: PO_M_15765_hindbrain

value: hindbrain


title: G45KO_0Gy_1d_rep5


title: ATAC.16_MRTK.78_SMARCB1_rep1


title: BW_F_15504_striatum

value: striatum


title: ATAC.15_MRTK.78_CTRL_rep3

description:
ATAC-seq in MRT organoids P78, after 4 days lentiviral transduction with the Luciferase gene
MRTK_ATACseq_peak_coordinates_2022-11-10.txt; MRTK_ATACseq_readcounts_unnormalized_2022-11-10.txt; MRTK_ATACseq_readcounts_normalized_2022-11-10.txt