title: RNAseq_NGN2_0h_r2_1846

value: 0 hour mESC (FCS/LIF)

tag: mouse strain

tag: experiment id


title: UGCG-KO_1

status: Public on Aug 07 2025

type: SRA

city: Grand Rapids

first: Robert

last: Fillinger

state: Michigan

address: 333 Bostwick Ave NE

country: USA

institute: Van Andel Institute

description: Library name: sgUgcg_1

library_source: transcriptomic

data_processing:
Concatenate -1 and -2 fastQ files together
Trim reads (Trim Galore 0.6.10)
Alignment (STAR 2.7.10a)
RNA-Seq analysis DESeq2 (1.44.0)
Assembly: mm10
Supplementary files format and content: FastQ

molecule: total RNA

organism: Mus musculus

source_name: Spleen

growth_protocol: NTC and sgUgcg CD8+ OT-I T cells were maintained in IMDM + 10% Nu-Serum IV culture supplement, 50 U/mL penicillin/50 ug/mL streptomycin, 50 uM 2-mercaptoethanol, 6 mM glutamine, and 50 U/mL recombinant murine IL-2 prior to adoptive transfer into C57BL/6J mice.

extract_protocol:
Qiagen RNeasy Plus Universal Mini Kit
Takara SMART-Seq mRNA LP (with UMIs) Kit

treatment_protocol: Following adoptive transfer, mice were immunized intravenously with a sublethal dose of recombinant attenuated Listeria monocytogenes expressing ovalbumin (Lm-OVA; 2e6 colony-forming units/mouse)

tag: tissue

value: Spleen

tag: strain

tag: cell type

value: CD8+ T cells

tag: genotype

value: Ugcg knockout


title: Control_3

description: Library name: NTC_4

value: Control


title: Control_4

description: Library name: NTC_5


title: lib42423

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib42423

data_processing:
Fastq files were aligned to the Ensembl version of the human genome (GRCh38) (GenBank assembly accession id GCA_000001405.15), using TopHat (version 1.4.1). The single-paired flag was set to “single,” while all other TopHat parameters were set to defaults
HTSeq-count was used to generate gene counts with mode as “Intersection (nonempty)” and minimum alignment quality set to 0 and otherwise set to default parameters
For quality control, samples were kept that had human aligned counts >250,000 and median CV coverage < 1.1. Genes were filtered to include those that had a trimmed mean of M values (TMM) normalization count of at least 1 in at least 10% of libraries and were classified as protein coding using BioMart. Normalized counts were transformed to log2 counts per million along with observations level weights using voomWithQualityWeights from the “limma” R package version 3.46
Assembly: GRCh38
Supplementary files format and content: counts_raw.tsv
Supplementary files format and content: hgnc_ensembl_id_mapping.tsv
Supplementary files format and content: modules_normalized_expr.tsv
Supplementary files format and content: voom_normalized_gene_expr.tsv

organism: Homo sapiens

source_name: Nasal lavage

extract_protocol:
Cells were sorted into lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara)
Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina). Single-read sequencing was carried out on a HiSeq2500 sequencer (Illumina), using a HiSeq SBS v4 Kit to generate 58-base reads, with a target of approximately 10 million reads per sample

value: Nasal lavage

tag: Sex

value: female

tag: donorid

tag: treatment

value: Placebo

tag: age months

tag: visit

tag: illness

tag: virus _yn

tag: eos total

tag: lym total

tag: mac total

tag: squ total

tag: epi total

tag: neut total

tag: enitrox


title: lib42424

description: Library name: lib42424

tag: tissue

value: Mepolizumab


title: RNAseq_NGN2mut_24h_r2_1846

city: Basel

first: Sevi

last: Durdu

address: Fabrikstrasse 24

department: Genome Regulation

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing samples generated by Illumina HiSeq sequencing. Illumina RTA 3.4.4 and bcl2fastq2 v2.20 was used for basecalling and demultiplexing samples generated by Illumina NovaSeq sequencing. RNA-seq reads were mapped to mm10 using STAR aligner (Dobin et al, Bioinformatics 2013).
Assembly: mm10
Supplementary files format and content: Rsubread Bioconductor powered by featureCounts function (Liao et al, Nucleic Acids Research, 2019) was used to generate gene count table(s) at the level of "gene_name" based on the gene annotation from the GENCODE release M25 with default parameters.

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma).

extract_protocol:
RNA for RNA-seq was isolated using Norgen Single Cell RNA Purification Kit, following the manufacturer’s instructions.
Sequencing libraries were prepared from purified total RNA for each sample using TruSeq stranded Total RNA Library Prep (Illumina), or TruSeq stranded mRNA Library Prep (Illumina).

treatment_protocol: mESCs were induced for differentiation by expressing NGN2 or MyoD1. 100000 cells per sample was collected for RNA extraction.

value: embryonic stem cells

tag: cell line

tag: cell type

value: mESC

value: 24 hours N2B27(w/oVitA)+dox

tag: mouse strain

tag: experiment id


title: Tal1 (Re4)

city: Helsinki

first: Sami

last: Kilpinen

address: Viikinkaari 9

department: Faculty of Biological and Environmental Sciences

country: Finland

institute: University of Helsinki

description:
Library name: E12R1_Tal1_757_4
E12R1_Tal1_R4

library_source: genomic

data_processing:
Reads were demultiplexed using the dual barcode sequences. Demultiplexed reads were aligned against the Mus musculus genome mm10 and the peak calling was performed, using the nf-core (Ewels et al., 2020) pipeline nf-core/cutandrun.
Following software was used in the nf-core/cutandrun pipeline: adapter trimming with TrimGalore!, aligner bowtie2, duplicate filtering with Picard, peakcaller SEACR.
Assembly: mm10
Supplementary files format and content: bigwig files contain the filtered CUT&Tag reads aligned to the mouse (Mus Musculus) genome version mm10.
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: rhombomere 1

growth_protocol: Embryonic brains were isolated from E12.5 wildtype (ICR) mouse embryos. Embryos were obtained from timed matings, where embryonic day 0.5 (E0.5) was defined as noon of the day of the vaginal plug. All animal experiments were approved by the Laboratory Animal Center, University of Helsinki, and the National Animal Experiment Board in Finland.

extract_protocol:
The samples were processed following the CUT&Tag-It Assay Kit protocol (Active Motif, cat # 53170). Shortly, the cells from freshly dissociated r1 tissues were bound to concanavalin A coated magnetic beads followed by the antibody incubations and washing steps on beads. The following primary antibodies were used: rabbit anti-Gata2 (Abcam, ab109241), rabbit anti-Gata3 (Boster, M00593), rabbit anti-Tal1 (Abcam, ab75739), rabbit anti-Vsx2 (Proteintech, 25825-1-AP-20), rabbit anti-Ebf1 (Boller et al., 2016) rabbit anti-Insm1 (Nordic BioSite, ASJ-IO4DE3-50), rabbit anti-Tead2 (Biorbyt, orb382464), rabbit anti-IgG (Cell Signalling, 66362) and rabbit anti-H3K4me3 (Cell Signalling, 9751).
The library  preparation was done as part of the CUT&Tag-It Assay Kit protocol (Active Motif, cat # 53170) that uses protein A-Tn5 transposomes (pA-Tn5) for tagmentation followed by DNA amplification with Q5 high-fidelity DNA polymerase and dual-barcoding primers. The number of PCR cycles was 14.
The DNA libraries were multiplexed at 10 nM equimolar ratios and sequenced on NextSeq 500 or Aviti. 75 bp paired-end sequences were obtained.

treatment_protocol: r1 tissues were dissected using the constriction at midbrain-hindbrain boundary anteriorly and the extent of cerebellar tissue dorsally as visual landmarks. The ventral part of the r1 was separated and used for the CUT&Tag. r1 tissues from the embryos of one mouse litter were pooled and dissociated together. Cells were then divided between samples, using 200 000 - 250 000 cells per sample. Embryos from different E12.5 mouse litters were used as biological replicates.

value: rhombomere 1

value: E12.5 embryo

value: anterior hindbrain cells

tag: genotype

value: wild-type (ICR)

tag: treatment

value: rabbit anti-Tal1 (Abcam, ab75739)

tag: batch


title: E4.5, 6 histone marks and IgG control, 3 rounds, scMTR-seq, sublibrary4, RNA

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description:
polyA RNA
read1 file contains transcript; read2 files contains cell barcodes, Ab id, UMI and transcript
DNA sublibrary4 and RNA sublibrary4 are from same sample

data_processing:
After sequencing, cell barcodes and UMI information were extracted with modified Reachtools (https://doi.org/10.1038/s41592-021-01060-3). Sequences from fixed positions of Read2 were extracted: 1st-8th for BC3, 39th-46th for BC2, 77th-84th for BC1, 115th-119th for RT-ID in RNA data or for antibody-ID in DNA data, 120th-127th for UMI. Barcode combinations (BC1:BC2:BC3:RT-ID/antibody-ID) were mapped to all possible barcode combinations with Bowtie (version: 1.3.1, doi:10.1186/gb-2009-10-3-r25, version, --norc -m 1 -v 0). Mapped cell IDs and UMI were stored in read names of genome sequences. Trim-galore (version:0.6.10) was used to trim adapter sequences with default settings. Trimmed reads were mapped mapped to GRCh38 for human samples and mm10 for mouse samples using Bowtie2 (version: 2.5.3, DOI: 10.1038/nmeth.1923) for DNA data and STAR (version: 2.7.11b, DOI: 10.1093/bioinformatics/bts635) for RNA data with default settings. Only unique mapped reads were kept by samtools filtering (version: 1.19.2, MAPQ>50 for RNA data and MAPQ>10 for DNA data). For the paired-end mapping data, only proper mapped reads with correct orientation were kept. Duplicated reads were identified by the mapping positions and UMIs for each cellid of RNA data. Duplicated reads were identified by mapping positions only for each cellid of DNA data. RNA deduplicated data were feature counted by custom script with splitpoolquantitation (https://github.com/laurabiggins/nf_yang_wang/tree/main/splitpoolquantitation) and converted to sparse matrix. DNA deduplicated data were converted to fragment files for downstream analyses.
Assembly: mm10 for mouse sample, GRCh38 for human sample
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: single cell RNA data: barcodes.tsv.gz; features.tsv.gz; matrix.mtx.gz
Library strategy: scMTR-seq

molecule: polyA RNA

source_name: Whole embryo

growth_protocol: H9 cells were grown in 5% CO2, 5% O2 at 37°C and maintained in Essential8 medium (ThermoFisher Scientific) on 0.5% Geltrex (ThermoFisher Scientific). Embryos at approximately E3.5 were collected by flushing the uterus with M2 medium (Sigma-Aldrich) 94– to 98-hours after human chorionic gonadotropin injection. Embryos were cultured in KSOM medium (Millipore, MR-121-D) for 24 hours at 37°C in a 5% CO2 incubator under light mineral oil (Millipore, ES-005-C).

extract_protocol:
H9 cells and samples collected from different time points during endoderm differentiation were dissociated into single cells with TrypLE Express (ThermoFisher Scientific). Zona pellucidae was removed from E4.5 embryos using Acidic Tyrode’s solution (Sigma) and washed through three drops of M2 media. Embryos were washed in PBSI (PBS without calcium or magnesium supplemented with 1x Protease Inhibitor Cocktail [PIC], 0.05 U/μL SuperaseIn RNase Inhibitor, 0.1 U/μL Protector RNAse Inhibitor and 0.2% BSA) and dissociated into single cells with TrypLE Express.
Nuclei were prepared with Nuclei Extraction buffer and fixed with 0.2% formaldehyde at room temperature for 5 min. Concanavalin A beads were added to the samples to bind nuclei. Preincubated antibody and proteinA-Tn5-MEBdU were added to the nuclei and incubated at RT for 1 hour or overnight at 4°C. Nuclei were washed three times and tagmented at 37°C for 1 hour in the presence of MgCl2. Reaction was stopped with EDTA. Tagmentation was repeated for sequential tagmentation. Followed, reverse transcription was crried out to capture polyA-mRNA transcripts. Three rounds of split-pool barcoding was performed to add combinatory barcodes for each single cells. Nuclei was counted and aliquoted into sublibraries. Reverse crosslinking was performed at 55°C for 1 hour in reverse crosslinking buffer with proteinase K and RNase inhibtors. PMSF was used to inactivate proteinase K. DNA and cDNA were separated by C1 Streptavidin beads. For DNA library, tagmented genomic DNA fragments were purified with Ampure XP beads. Eluted DNA was performed adapter switching and amplified. For RNA library, templated switch was performed and preammplified. MEA adapters were added to the RNA library by Tn5-MEA mediated tagmentation. The concentration of libraries was measured with a Qubit. Samples were run on a Bioanalyzer to check the size distribution of library fragments before submited for seuqencing.

treatment_protocol: Endoderm differentiation: H9 cells were seeded on Geltrex in Essential8 medium. The next day, cells were washed with 0.1% BSA in DMEM, and then cultured in endoderm induction medium comprised of 50% IMDM (ThermoFisher Scientific), 50% F-12 Nutrient Mix (ThermoFisher Scientific), 1% Chemically Defined Lipids (ThermoFisher Scientific), 0.1% BSA Fraction V (ThermoFisher Scientific), 15μg/mL Transferrin (Merck), 450μM Monothioglycerol (Merck), 0.7μg/mL Insulin (Merck), 100ng/mL Activin-A (Cambridge Stem Cell Institute), 100nM PI-103 (Tocris Bio-Techne), 3μM CHIR99021 (Cambridge Stem Cell Institute),  10ng/mL FGF2 (Cambridge Stem Cell Institute), 3ng/mL BMP4 (R&D Systems) and 10μg/mL Heparin (Merck). After 24 hours, cells were cultured in modified endoderm induction medium whereby CHIR99021 and BMP4 were removed, the concentration of FGF2 was increased to 20ng/mL, and LDN193189 (Axon Medchem) was added to 250nM.

tag: developmental stage

value: E4.5 blastocysts

tag: strain

value: Whole embryo

tag: antibody

tag: library type

value: mRNA


title: Vsx2 (Re3)

description:
Library name: E12R1_Vsx2_3
E12R1_Vsx2_R3

value: rabbit anti-Vsx2 (Proteintech, 25825-1-AP-20)


title: RNAseq_NGN2_0h_r1_1846

value: 0 hour mESC (FCS/LIF)


title: Control_2

description: Library name: NTC_3

value: Spleen

value: CD8+ T cells

value: Control


title: RNAseq_NGN2mut_24h_r1_1846


title: lib42416

description: Library name: lib42416

value: Nasal lavage

tag: Sex

value: female

tag: donorid

value: Mepolizumab

tag: age months

tag: visit

tag: illness

tag: virus _yn

tag: eos total

tag: lym total

tag: mac total


title: E4.5, 6 histone marks and IgG control, 3 rounds, scMTR-seq, sublibrary4, DNA

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains cell barcodes, Ab id, UMI and genomic fragments
DNA sublibrary4 and RNA sublibrary4 are from same sample

tag: cell type

value: gDNA


title: E4.5, 6 histone marks and IgG control, 3 rounds, scMTR-seq, sublibrary3, RNA

description:
polyA RNA
read1 file contains transcript; read2 files contains cell barcodes, Ab id, UMI and transcript
DNA sublibrary3 and RNA sublibrary3 are from same sample


title: lib42413

description: Library name: lib42413

tag: tissue

value: Placebo

tag: squ total

tag: epi total

tag: neut total

tag: enitrox


title: E4.5, 6 histone marks and IgG control, 3 rounds, scMTR-seq, sublibrary3, DNA

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains cell barcodes, Ab id, UMI and genomic fragments
DNA sublibrary3 and RNA sublibrary3 are from same sample

tag: developmental stage

tag: strain

tag: antibody


title: RNAseq_NGN2mut_12h_r1_1846

value: embryonic stem cells

tag: cell line

value: mESC

tag: genotype

tag: treatment

value: 12 hours N2B27(w/oVitA)+dox

tag: mouse strain

tag: experiment id


title: lib42408

description: Library name: lib42408

tag: Sex

tag: donorid

tag: age months

tag: visit

tag: illness

tag: virus _yn

tag: eos total


title: lib42421

description: Library name: lib42421

tag: tissue

tag: lym total

tag: mac total

tag: squ total

tag: epi total

tag: neut total


title: Control_1

description: Library name: NTC_2

tag: strain

tag: cell type

tag: genotype


title: 5xFAD;PU.1-low (FADPU 668)

type: RNA

city: Worcester

first: Violeta

last: Duran Laforet

address: 365 Plantation St

department: Neurobiology

institute: University of Massachusetts Chan Medical School

hyb_protocol: Tissue was washed and hybridized for 15 minutes with DAPI and polyT solution and washed with formamide wash buffer for 10 minutes.

scan_protocol: MERFISH imaging was performed according to Vizgen MERSCOPE instructions

data_processing: Raw data were decoded using Vizgen's MERLIN pipeline incorporated in the MERSCOPE. Vizgen's postprocessing tool was applied to obtain the cell segmentation based on the DAPI staining by using the CellPose algorithim.

source_name: sagittal brain section

label_protocol: Tissue on coverslips was fixed for 15 minutes at room temperature in 4% paraformaldehyde in PBS, followed by three washes with PBS. Tissue was then permeabilized in 70% ethanol for 24 hours. Samples were photobleached for 3h in 70% ethanol followed by an incubation with blocking solution (1 h, RT). Then samples were incubated with the primary antibody solution (Purified Azide Free anti-β-amyloid 6E10, #803004, Biolegend 1:100 plus 10:100 of RNAse inhibitor. Samples were washed three times with 1x PBS and incubated with the secondary amtibody solution  (1 h RT). Samples were washed three times with 1x PBS, fixed (4% PFA in 1× PBS, 15 min, RT) and washed two times with 1x PBS. After a wash with Formamide Wash Buffer  (30% formamide in 2X saline sodium citrate (SSC)), the MERFISH library mix was added and allowed to hybridize to occur for 48 hours. Sample was then washed and incubated at 47°C with Formamide Wash Buffer twice  and then the tissue was embedded in a polyacrylamide gel followed by incubation with tissue clearing solution (2X SSC, 2% SDS, 0.5% v/v Triton X-100, and proteinase K 1:100) overnight at 37°C.

extract_protocol: Mice were anesthetized and euthanized by decapitation. Brains were extracted and immediately transferred to cold OCT. Embedded brains were frozen and stored at -80°C.

value: 5xFAD; Cx3cr1CreErt2/+(Litt);Spi1fl/+

value: M

tag: age

value: 13 months


title: RNAseq_NGN2mut_12h_r2_1846

tag: cell line

tag: treatment

tag: mouse strain

tag: experiment id


title: 5xFAD (FADPU 662)

value: Cx3cr1CreErt2/+(Litt); 5xFAD

tag: Sex

value: 11 months


title: lib42407

description: Library name: lib42407

tag: donorid

tag: age months

tag: visit

tag: illness

tag: virus _yn

tag: enitrox


title: E4.5, 6 histone marks and IgG control, 3 rounds, scMTR-seq, sublibrary2, RNA

description:
polyA RNA
read1 file contains transcript; read2 files contains cell barcodes, Ab id, UMI and transcript
DNA sublibrary2 and RNA sublibrary 2 are from same sample

tag: developmental stage

value: E4.5 blastocysts

value: Whole embryo

tag: antibody

tag: library type

value: mRNA


title: 5xFAD;PU.1-high

data_processing:
Raw data were decoded using Vizgen's MERLIN pipeline incorporated in the MERSCOPE. Vizgen's postprocessing tool was applied to obtain the cell segmentation based on the DAPI staining by using the CellPose algorithim.
counts_and_metadata.csv files contain matrices of cell IDs as rows, genes and metadata as columns. Matrix contains raw counts of detected transcripts. Volume metadata is provided in cubic microns. X and Y metadata are provided in microns.

value: 8 months


title: E4.5, 6 histone marks and IgG control, 3 rounds, scMTR-seq, sublibrary2, DNA

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains cell barcodes, Ab id, UMI and genomic fragments
DNA sublibrary2 and RNA sublibrary 2 are from same sample

tag: strain

tag: cell type


title: RNAseq_NGN2mut_6h_r2_1846

tag: tissue

tag: genotype

value: 6 hours N2B27(w/oVitA)+dox


title: E4.5, 6 histone marks and IgG control, 3 rounds, scMTR-seq, sublibrary1, RNA

description:
polyA RNA
read1 file contains transcript; read2 files contains cell barcodes, Ab id, UMI and transcript
DNA sublibrary1 and RNA sublibrary 1 are from same sample


title: E4.5, 6 histone marks and IgG control, 3 rounds, scMTR-seq, sublibrary1, DNA

description:
Tn5 taggmented DNA
read1 file contains genomic fragment; read2 files contains cell barcodes, Ab id, UMI and genomic fragments
DNA sublibrary1 and RNA sublibrary 1 are from same sample


title: lib42406

description: Library name: lib42406

value: Nasal lavage

value: female

tag: treatment

value: N

tag: eos total

tag: lym total

tag: mac total

tag: squ total

tag: epi total

tag: neut total


title: 5xFAD;PU.1-low

tag: Sex

tag: age

value: 10 months


title: Control (FADPU 663)

value: 12 months


title: RNAseq_NGN2mut_6h_r1_1846

value: embryonic stem cells

tag: cell line

value: mESC

tag: mouse strain

tag: experiment id


title: lib42405

description: Library name: lib42405

tag: donorid

value: Placebo

tag: age months

tag: visit

tag: illness

tag: virus _yn

value: Y

tag: enitrox


title: 5xFAD 2

tag: genotype

value: M


title: RNAseq_NGN2mut_0h_r1_1846

tag: tissue

tag: cell type

tag: treatment

value: 0 hour mESC (FCS/LIF)


title: lib42403

description: Library name: lib42403

value: cold

value: Cold

tag: eos total

tag: lym total

tag: mac total

tag: squ total

tag: epi total


title: 5xFAD 1

value: Cx3cr1CreErt2/+(Litt); 5xFAD

tag: Sex

tag: age


title: Control


title: RNAseq_GFP_24h_r2_1846

tag: cell line

value: 24 hours N2B27(w/oVitA)+dox

tag: mouse strain

tag: experiment id


title: lib42386

description: Library name: lib42386

tag: donorid

tag: age months

tag: visit

tag: illness

tag: neut total


title: RNAseq_GFP_24h_r1_1846

tag: tissue

tag: cell type

tag: genotype


title: LSK (Lin-/Sca+/Kit+) cells - IMQ treated 7

city: New York

first: Dr. Shruti

last: Naik

state: NY

address: 1425 Madison Ave

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

description: Library name: LSK_IMQ7

data_processing:
Demultiplexing of raw sequencing data was performed using Illumina’s bcl2fastq Conversion Software (vX.X), generating sample-specific FASTQ files.
Adaptor sequences were removed using trimmomatic.
Removed duplicate reads (Sambamba).
Bowtie2 was used to align the reads to mm10 genome.
Peak calling to identify open chromatin regions was performed using MACS2
Assembly: mm10
Supplementary files format and content: .bed format, main peak output file containing the full list of called peaks, coordinates and associated statistics (-log10(pvalue))

source_name: Bone Marrow

extract_protocol:
LSK cells were sorted into DMEM media without serum and spun (500g, 5 minutes, 4°C) and flowthrough discarded. Cells were washed once with 200uL cold PBS, spun down (as before) and flowthrough discarded. Pellets were resuspended in 25uL of PBS and quickly added lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% GEPAL CA-630) and centrifuged immidiately at 500 ×g 4°C for 30 seconds. Supernatant was discarded and 39ul of water immediately added, after which were also added 10uL Tagment DNA Buffer and 1uL Tagment DNA Enzyme. Cells were vortexed and incubated for 30 minuted at 37°C
Immediately following transposition, samples were purified using the Qiagen MinElute PCR Purification Kit according to the manufacturer’s instructions. Library construction was performed following Illumina’s standard protocol for sequencing on the NovaSeq 6000 platform, including PCR amplification and addition of sequencing adapters.

value: Bone Marrow

value: LineagenegSca1+Kit+ progenitors

tag: treatment

value: Imiquimod recovery


title: LSK (Lin-/Sca+/Kit+) cells - IMQ treated 6

description: Library name: LSK_IMQ6


title: LSK (Lin-/Sca+/Kit+) cells - IMQ treated 5

description: Library name: LSK_IMQ5


title: lib42384

description: Library name: lib42384

value: Nasal lavage

value: female

value: Mepolizumab

tag: virus _yn

tag: eos total

tag: lym total

tag: mac total

tag: enitrox


title: RNAseq_NGN2mut_0h_r2_1846

tag: cell line


title: LSK (Lin-/Sca+/Kit+) cells - Control 2

description: Library name: LSK_Control_2

value: Petroleum jelly


title: RNAseq_GFP_12h_r2_1846

value: embryonic stem cells

value: 12 hours N2B27(w/oVitA)+dox

tag: mouse strain


title: lib42383

description: Library name: lib42383

tag: Sex

value: N

tag: squ total

tag: epi total


title: LSK (Lin-/Sca+/Kit+) cells - Control 1

description: Library name: LSK_Control_1


title: LSK (Lin-/Sca+/Kit+) cells - Control 3

description: Library name: LSK_Control_3


title: RNAseq_GFP_12h_r1_1846

value: mESC

tag: experiment id


title: lib42378

description: Library name: lib42378

tag: donorid

tag: age months

tag: visit

tag: illness


title: RNAseq_GFP_6h_r2_1846

tag: tissue

tag: cell type

tag: genotype

value: 6 hours N2B27(w/oVitA)+dox


title: lib42373

description: Library name: lib42373

tag: treatment

tag: virus _yn

tag: eos total

tag: neut total


title: B34286 mouse anaplastic thyroid cancer cells

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: Library name: B34286

data_processing:
Illumina (NovaSeq) Exome Variant Detection Pipeline: The data processing pipeline for detecting variants in Illumina NovaSeq data is as follows. First the FASTQ files are processed to remove any adapter sequences at the end of the reads using cutadapt (v1.6). The files are then mapped using the BWA mapper (bwa mem v0.7.12). After mapping the SAM files are sorted and read group tags are added using the PICARD tools. After sorting in coordinate order, the BAM’s are processed with PICARD MarkDuplicates. The marked BAM files are then processed using the GATK toolkit (v 3.2) according to the best practices for tumor normal pairs. They are first realigned using ABRA (v 0.92) and then the base quality values are recalibrated with the BaseQRecalibrator. Somatic variants are then called in the processed BAMs using muTect (v1.1.7) for SNV and the Haplotype caller from GATK with a custom post-processing script to call somatic indels.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel spreadsheet (.xlsx) containing somatic variants in Mutation Annotation Format (MAF).

source_name: cell line derived from recurrent anaplastic thyroid cancer from Tpo-Cre/eYFP/BRaf-CA/Trp53fl/fl genetic engineered mouse

growth_protocol: F12 Coons', 5% FBS, 1% PSG

extract_protocol:
We isolated DNA from tails and cells with the DNeasy Blood & Tissue Kit from Quiagen (Catalogue Number 69504) according to the manufacturers instructions.
100 ng of DNA were used to prepare libraries using the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) with 8 cycles of PCR. After sample barcoding, 340-500 ng of library were captured by hybridization using the SinglePlex Mouse Exome (Twist catalog # 102036) according to the manufacturer’s protocol.

tag: batch


title: B36934 normal tissue control

description: Library name: B36934 NT

source_name: mouse tail

value: tail from Tpo-Cre/eYFP/BRaf-CA/Trp53fl/fl genetic engineered mouse


title: RNAseq_GFP_6h_r1_1846

tag: cell line

tag: mouse strain


title: B36934 mouse anaplastic thyroid cancer cells

description: Library name: B36934

value: cell line derived from recurrent anaplastic thyroid cancer from Tpo-Cre/eYFP/BRaf-CA/Trp53fl/fl genetic engineered mouse


title: B34286 normal tissue control

description: Library name: B34286 NT


title: Cgas KO CD4+CCR7+ thymocytes, TCR-seq

city: Beijing

first: Hang

middle: Hubert

last: Yin

address: Shuangqing Road 30, Haidian District

department: School of Pharmaceutical Sciences

country: China

institute: Tsinghua University

description: Library name: Sample 30

data_processing:
For scRNA-seq analysis, data were analyzed using the Cell Ranger 7.0 Pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome/).
Downstream analysis was conducted using the Seurat v5.1.0, SingleCellExperiment v1.24.0 and SCP v0.5.6 packages.
Assembly: mm10
Supplementary files format and content: Matrix files and tab delimited files
Library strategy: TCR-Seq

source_name: Thymus

extract_protocol:
Thymocytes from Cd4Cre mice and Cd4Cre Cgasfl/fl flow mice were isolated. The resulting cells were filtered through 100-μm cell strainers, washed with PBS, lysed in red blood cell buffer, and resuspended in PBS. CCR7+ Thymocytes were sorted using a FACSAria Fusion flow cytometer (BD Biosciences). The cell suspension (300–600 viable cells per mL) was loaded onto a Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion, following the manufacturer’s protocol.
TCR libraries were prepared using the TCR kit and transcriptome libraries was generated by Single Cell 3’ Library and Gel Bead kit and sequenced on an Illumina NovaSeq 6000 instrument with a paired-end 150-base pair (PE150) reading strategy.

value: Thymus

value: Thymus CD4+CCR7+ cells

value: Cgas knockout


title: B36244 normal tissue control

description: Library name: B36244 NT


title: RNAseq_GFP_0h_r2_1846

value: 0 hour mESC (FCS/LIF)


title: lib42372

description: Library name: lib42372

tag: Sex

value: Y

tag: lym total

tag: mac total

tag: squ total

tag: enitrox


title: RNAseq_GFP_0h_r1_1846

tag: experiment id


title: WT CD4+CCR7+ thymocytes, TCR-seq

description: Library name: Sample 29

value: WT


title: Cgas KO CD4+CCR7+ thymocytes

description: Library name: Sample 28

library_source: genomic single cell

data_processing:
For scRNA-seq analysis, data were analyzed using the Cell Ranger 7.0 Pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome/).
Downstream analysis was conducted using the Seurat v5.1.0, SingleCellExperiment v1.24.0 and SCP v0.5.6 packages.
Assembly: mm10
Supplementary files format and content: Matrix files and tab delimited files


title: lib42370

description: Library name: lib42370

value: Nasal lavage

tag: donorid

tag: age months

tag: visit

tag: illness

tag: epi total


title: LSK (Lin-/Sca+/Kit+) cells - IMQ treated 4

description: Library name: LSK_IMQ4

tag: tissue

value: Bone Marrow

tag: cell type

value: LineagenegSca1+Kit+ progenitors

tag: genotype

tag: treatment

value: Imiquimod recovery


title: Cgas KO tTreg in situ Hi-C, rep4

description: Library name: Sample 26

data_processing:
The reads were aligned to the mm39 genome using the presplit_map.py script in diffHic v1.34.0, with minor modifications.
Technical replicates from multiple sequencing runs of the same library were combined using the mergePairs function in diffHic.
The .hic files were generated using Juicer v1.7.6 and subsequently merged.
Assembly: mm39
Supplementary files format and content: .hic contact matrices

extract_protocol:
In situ Hi-C was performed according to the previously described method by Johanson, T.M.
Library was constructed using DNA library construction kit (Vazyme).

value: Thymus Treg

value: Cgas Knockout


title: RNAseq_NGN2_72h_r4_1558

value: embryonic stem cells

tag: cell line

value: HA36, rtTA/pTRE-humanNgn2 random insertion

value: 72 hours N2B27(w/oVitA)+bFGF/EGF+dox


title: B36244 mouse anaplastic thyroid cancer cells

description: Library name: B36244

tag: batch


title: WT CD4+CCR7+ thymocytes

description: Library name: Sample 27


title: lib42369

description: Library name: lib42369

tag: Sex

value: female

value: Mepolizumab

tag: virus _yn

value: N

tag: eos total

tag: neut total


title: lib42367

description: Library name: lib42367

tag: lym total

tag: mac total

tag: squ total

tag: enitrox


title: WT tTreg in situ Hi-C, rep4

description: Library name: Sample 22

value: Thymus


title: Cgas KO tTreg in situ Hi-C, rep3

description: Library name: Sample 25


title: Cgas KO tTreg in situ Hi-C, rep2

description: Library name: Sample 24


title: Cgas KO tTreg in situ Hi-C, rep1

description: Library name: Sample 23


title: RNAseq_NGN2_72h_r2_1558

value: mESC

tag: mouse strain

tag: experiment id


title: RNAseq_NGN2_72h_r1_1558


title: WT tTreg in situ Hi-C, rep3

description: Library name: Sample 21


title: lib42377

description: Library name: lib42377

tag: donorid

tag: age months

tag: visit

tag: illness

tag: epi total


title: WT tTreg in situ Hi-C, rep2

description: Library name: Sample 20

tag: tissue

tag: cell type

tag: genotype


title: lib42359

description: Library name: lib42359

tag: Sex

tag: treatment

value: Placebo

value: cold

value: Exacerbation

tag: virus _yn


title: WT tTreg in situ Hi-C, rep1

description: Library name: Sample 19

value: WT


title: Cgas KO CTCF CUT&Run, rep2

description: Library name: Sample 17

data_processing:
Filtered reads were mapped to the mouse genome mm10 using Bowtie2 v2.5.357 with the parameters -I 10 -X 1000 -p 16 and --very-sensitive --no-mixed --no-discordant. E. coli spike-in DNA was mapped to the E. coli genome with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --no-overlap --no-dovetail --phred33 -I 10 -X 700.
Peak calling was carried out using SEACR v.1.3 (Sparse Enrichment Analysis for CUT&RUN) with a 0.01 non-stringent option
Assembly: mm39
Supplementary files format and content: Bed file containing called peaks from CUT&Run data
Library strategy: CUT&Run

extract_protocol:
CUT&RUN was performed following the established Bench top CUT&RUN with antibodies-online V6 protocol (https://www.protocols.io/view/bench-top-cut-run-with-antibodies-online-cut-run-s-kqdg3557pv25/v6).
DNA libraries were constructed using the Hyperactive Universal CUT&RUN Assay Kit for Illumina Pro (HD102, Vazyme).


title: lib42353

description: Library name: lib42353

value: Nasal lavage

value: Y

tag: eos total

tag: lym total

tag: neut total


title: RNAseq_NGN2_48h_r3_1558

tag: cell line

value: 48 hours N2B27(w/oVitA)+bFGF/EGF+dox


title: Cgas KO CTCF CUT&Run, rep3

description: Library name: Sample 18

value: Thymus Treg


title: WT CTCF CUT&Run, rep3

description: Library name: Sample 15


title: RNAseq_NGN2_72h_r3_1558

tag: mouse strain


title: Cgas KO CTCF CUT&Run, rep1

description: Library name: Sample 16

value: Cgas Knockout


title: lib42349

description: Library name: lib42349

tag: mac total

tag: squ total

tag: enitrox


title: lib42352

description: Library name: lib42352

tag: donorid

tag: age months

tag: visit


title: RNAseq_NGN2_48h_r1_1558

tag: tissue

value: embryonic stem cells

tag: experiment id


title: WT CTCF CUT&Run, rep2

description: Library name: Sample 14

tag: cell type

tag: genotype


title: Cgas KO tTreg ATAC, rep3

description: Library name: Sample 12

data_processing:
ATAC-seq data was analyzed according to ENCODE guidelines
Adapter and low-quality reads were filtered out using Trimmomatic v0.39 with settings of SLIDINGWINDOW:4:15 MINLEN:65.
Filtered reads were mapped to mouse genome mm39 using Bowtie2 v2.5.360 with parameter -X 1000 and --very-sensitive.
Peak calling was performed on bam file using BAMPE mode with parameter as follows: --nomodel --nolambda --keep-dup all --call-summits.
The peaks were merged using R script createIterativeOverlapPeakSet.R
Assembly: mm39
Supplementary files format and content: Peak file containing called peaks from ATAC data

extract_protocol:
ATAC-seq was performed using modified omni-ATAC protocol.
Library was constructed using DNA library construction kit (Novoprotein).


title: lib42348

description: Library name: lib42348

tag: Sex

tag: treatment

tag: illness

tag: epi total


title: Cgas KO tTreg ATAC, rep2

description: Library name: Sample 11


title: Cgas KO tTreg ATAC, rep1

description: Library name: Sample 10


title: RNAseq_NGN2_36h_r4_1558

value: HA36, rtTA/pTRE-humanNgn2 random insertion

value: 36 hours N2B27(w/oVitA)+bFGF/EGF+dox


title: lib42363

description: Library name: lib42363

value: female

tag: virus _yn

tag: eos total

tag: lym total

tag: neut total


title: lib42346

description: Library name: lib42346

value: Mepolizumab

tag: mac total

tag: squ total


title: WT tTreg ATAC, rep3

description: Library name: Sample 9


title: RNAseq_NGN2_36h_r3_1558

tag: cell line

tag: mouse strain


title: WT tTreg ATAC, rep2

description: Library name: Sample 8


title: WT tTreg ATAC, rep1

description: Library name: Sample 7


title: Cgas KO CD25+Foxp3- preTreg ATAC, rep2

description: Library name: Sample 5

value: Thymus preTreg


title: lib42343

description: Library name: lib42343

tag: donorid

tag: age months

tag: visit

tag: enitrox


title: RNAseq_NGN2_36h_r2_1558

tag: tissue

tag: cell type

tag: genotype

tag: experiment id


title: RNAseq_NGN2_48h_r4_1558

tag: treatment


title: WT CD25+Foxp3- preTreg ATAC, rep3

description: Library name: Sample 3

value: Thymus


title: lib42339

description: Library name: lib42339

tag: Sex

tag: illness

tag: virus _yn

tag: epi total


title: WT CD25+Foxp3- preTreg ATAC, rep2

description: Library name: Sample 2


title: WT CTCF CUT&Run, rep1

description: Library name: Sample 13


title: RNAseq_NGN2_48h_r2_1558

value: mESC


title: Control P5 Cx3cr1-KO barrel cortex [22R_UB]

first: Pinar

last: Ayata

state: New York

department: Neuroscience

institute: Icahn School of Medicine at Mt Sinai

description: Library name: 22R_UB

data_processing:
Sequencing reads were quality checked and trimmed using Trim Galore (v0.6.4; a wrapper program implementing Cutadapt v2.9 and FastQC v0.11.9)
Reads were then mapped to the GRCm38 (mm10) mouse genome using the HISAT2 package (v2.2.0).
Quantification of reads was then performed using featureCounts (v2.0.0) against the Ensembl v99 annotation.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: Barrel cortex

extract_protocol:
The brain tissue was thawed in an ice-cold  glass homogenizer containing 1 mL cell-lysis buffer. After manually homogenizing the samples with 3-5 gentle strokes, samples were  homogenized in a motor-driven overhead stirrer. A post-nuclear supernatant was prepared by centrifugation. Post-mitochondrial supernatant was prepared by centrifugation after NP40 and DHPC treatment. GFP-antibod-coated beads were added to each supernatant. After overnight incubation, the polysome-bound beads were washed with the high-salt buffer. RNA clean-up was performed using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA integrity was assayed using an RNA Pico chip on a Bioanalyzer 2100 (Agilent, Santa Clara, CA), and only samples with RIN>9 were considered for subsequent analysis. Double-stranded cDNA was generated from 1-5 ng of RNA using the Nugen Ovation V2 kit (NuGEN, San Carlos, CA) following the manufacturer’s instructions. Libraries for sequencing were prepared using Nextera XT kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions. The quality of the libraries was assessed by 2200 TapeStation (Agilent).

treatment_protocol: To activate Tamoxifen-inducible Cre (CreErt2), Cx3cr1CreER/+ (Litt); Eef1a1LSL.eGFPL10a/+ mice were orally administered 50 µg tamoxifen (T5648, Sigma, St. Louis, MO) dissolved 10 mg/mL in corn oil (C8267, Sigma) once daily at ages P1, P2, and P3. Aldh1l1EGFP-L10a/+ mice were not injected with tamoxifen. Unilateral whisker lesioning was performed at P4. Mice were euthanized at P5 with CO2, and the barrel cortex region was dissected and flash-frozen for TRAP.

value: Barrel cortex

value: male

value: Tissue

value: Mice were treated with Tamoxifen at P1-3, whiskers on the right side were cauterized at P4.


title: Cgas KO CD25+Foxp3- preTreg ATAC, rep1

description: Library name: Sample 4


title: lib42342

description: Library name: lib42342

value: Nasal lavage

value: Placebo

value: cold

value: Exacerbation

tag: eos total

tag: lym total

tag: mac total

tag: neut total


title: Deprived P5 Cx3cr1-KO barrel cortex [22L_UB]

description: Library name: 22L_UB


title: Cgas KO CD25+Foxp3- preTreg ATAC, rep3

description: Library name: Sample 6

value: Cgas Knockout


title: RNAseq_NGN2_24h_r4_1558

value: embryonic stem cells

tag: cell line

value: 24 hours N2B27(w/oVitA)+bFGF/EGF+dox

tag: mouse strain


title: Control P5 Cx3cr1-KO barrel cortex [19R_UB]

description: Library name: 19R_UB


title: lib42335

description: Library name: lib42335

tag: donorid

tag: age months

tag: visit

value: Cold

value: Y

tag: squ total


title: Deprived P5 Cx3cr1-KO barrel cortex [18L_UB]

description: Library name: 18L_UB

tag: tissue

value: female

tag: cell type

tag: genotype


title: Deprived P5 Cx3cr1-KO barrel cortex [19L_UB]

description: Library name: 19L_UB

tag: Sex

tag: treatment


title: lib42345

description: Library name: lib42345

tag: illness

tag: virus _yn

tag: enitrox


title: RNAseq_NGN2_24h_r3_1558

value: HA36, rtTA/pTRE-humanNgn2 random insertion

tag: experiment id


title: Control P5 Cx3cr1-KO barrel cortex [18R_UB]

description: Library name: 18R_UB


title: RNAseq_NGN2_24h_r2_1558


title: RNAseq_NGN2_36h_r1_1558

value: 36 hours N2B27(w/oVitA)+bFGF/EGF+dox


title: lib42333

description: Library name: lib42333

value: Mepolizumab

value: N

tag: eos total

tag: lym total

tag: mac total

tag: epi total


title: Deprived P5 Cx3cr1-KO barrel cortex [12L_UB]

description: Library name: 12L_UB

value: Barrel cortex

value: male


title: RNAseq_NGN2_24h_r1_1558

tag: cell line

value: mESC

tag: mouse strain


title: RNAseq_NGN2_NOGF24h_r2_1558

value: 24 hours N2B27(w/oVitA)+dox


title: Deprived P5 Cx3cr1-KO barrel cortex microglia [22L]

description: Library name: 22L

value: Microglia

value: Mice were treated with Tamoxifen at P1-3, whiskers on the right side were cauterized at P4.


title: lib42332

description: Library name: lib42332

value: Nasal lavage

tag: donorid

tag: age months

tag: visit

tag: neut total


title: Control P5 Cx3cr1-KO barrel cortex microglia [19R]

description: Library name: 19R

tag: tissue

tag: cell type

tag: genotype


title: RNAseq_NGN2_NOGF24h_r1_1558

tag: treatment


title: Deprived P5 Cx3cr1-KO barrel cortex [7L_UB]

description: Library name: 7L_UB

tag: Sex

value: Tissue


title: Control P5 Cx3cr1-KO barrel cortex microglia [22R]

description: Library name: 22R


title: RNAseq_NGN2_12h_r4_1558

value: embryonic stem cells

value: 12 hours N2B27(w/oVitA)+bFGF/EGF+dox


title: lib42330

description: Library name: lib42330

tag: illness

tag: virus _yn

tag: squ total

tag: enitrox


title: RNAseq_NGN2_nodox12h_r1_1558

value: 12 hours N2B27(w/oVitA)+bFGF/EGF

tag: experiment id


title: Control P5 Cx3cr1-KO barrel cortex [7R_UB]

description: Library name: 7R_UB


title: lib42331

description: Library name: lib42331

tag: eos total

tag: lym total

tag: mac total

tag: epi total


title: Control P5 Cx3cr1-KO barrel cortex microglia [18R]

description: Library name: 18R


title: Deprived P5 Cx3cr1-KO barrel cortex microglia [19L]

description: Library name: 19L


title: lib42328

description: Library name: lib42328

tag: donorid

value: Placebo

tag: age months


title: RNAseq_NGN2_12h_r3_1558

tag: cell line

tag: mouse strain


title: Control P5 Cx3cr1-KO barrel cortex microglia [12R]

description: Library name: 12R

tag: tissue

tag: cell type


title: Deprived P5 Cx3cr1-KO barrel cortex microglia [18L]

description: Library name: 18L

value: female

tag: genotype

tag: treatment


title: RNAseq_NGN2_12h_r2_1558

value: HA36, rtTA/pTRE-humanNgn2 random insertion


title: Deprived P5 Cx3cr1-KO barrel cortex microglia [12L]

description: Library name: 12L

tag: Sex


title: lib42324

description: Library name: lib42324

tag: visit

value: cold

tag: illness

value: Exacerbation

tag: virus _yn

value: Y

tag: neut total


title: RNAseq_NGN2_12h_r1_1558

tag: experiment id


title: Control P5 Cx3cr1-KO barrel cortex microglia [7R]

description: Library name: 7R

value: Barrel cortex


title: lib42323

description: Library name: lib42323

value: N

tag: eos total

tag: lym total

tag: squ total

tag: enitrox


title: Deprived P5 Cx3cr1-KO barrel cortex microglia [7L]

description: Library name: 7L


title: WT CD25+Foxp3- preTreg ATAC, rep1

description: Library name: Sample 1

value: Thymus

value: Thymus preTreg

value: WT


title: LP_mast_cell, replicate 2

city: Seoul

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

country: South Korea

institute: Seoul National University

description:
Library name: LP_MC_2
Chromium GEM-X Single Cell 3’ v4 assay (10X Genomics)

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/8.0/getting-started/cr-what-is-cell-ranger)
Assembly: mm10 (GRCm38)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Small Intestine

extract_protocol:
Single-cell suspensions of small intestinal epithelium and lamina propria were prepared as described . Briefly, the small intestine was isolated and opened longitudinally. Its contents were then rinsed in PBS following removal of Peyer’s patches. The tissue was then cut into 2-3 cm segments and incubated in RPMI media (ThermoFisher) containing 5 mM EDTA, 0.145 mg/mL DTT, and 3% FBS at 37°C with 5% CO2 for 20 min with agitation. Pieces of intestine were washed in RPMI containing 2 mM EDTA to separate the epithelial fraction. Lamina propria digestion was performed using 0.1 mg/mL Liberase TL (Roche #540102001) and 0.5 mg/mL DNAse (DN25, Sigma-Aldrich) in RPMI for 30 min at 37°C with 5% CO2. Digested tissue was sequentially strained through 70 mM and 40 mM strainers and washed in RPMI containing 3% FBS. The epithelial fraction was also subjected to a 30% Percoll density gradient by centrifugation (GE17-0891-01, Sigma Aldrich) in preparation for sorting.  Cells were then stained and sorted via FACS Aria into ice cold 10% FBS in dPBS w/o Ca, Mg, or EDTA. .  Stain:  Fc block, EMA (live/dead), FceRI-PE, CD11b-APC, CD19-APC/efluor780, CD45-efluor450, CD3-Alexa700, CD117-PE/Cy7.  MCs were gated as live, CD45+ CD19- CD11b- CD3- CD117+ FceRI+
GEM-X Single Cell 3’ v4 assay (10X Genomics) according to the manufacturer’s protocol

treatment_protocol: BALB/cJ female mice were sensitized subcutaneously with  5ug endograde OVA + 1mg aluminum hydroxide in 200ul PBS on d0 and d7 under ketamine/xylazine treatment. Mice were then challenged intragastrically with 50mg of OVA (Sigma grade III) in 200ul PBS starting on day 14. These mice were challenged every other day, 5 times in total, by oral gavage.  5 days after the 5th OVA challenge, MCs were sorted via FACS Aria for scRNAseq analysis.

value: Small Intestine

value: Primary cells

value: Sorted Mast Cells

value: BALB/cJ

value: OVAxAlum+5 OVA gavages


title: lib42315

description: Library name: lib42315

value: Nasal lavage

tag: donorid

value: Mepolizumab

tag: age months

value: Cold

tag: mac total

tag: epi total


title: RNAseq_NGN2_nodox6h_1558

tag: tissue

value: embryonic stem cells

tag: cell line

tag: cell type

value: mESC

value: HA36, rtTA/pTRE-humanNgn2 random insertion

value: 6 hours N2B27(w/oVitA)+bFGF/EGF

tag: mouse strain


title: lib42311

description: Library name: lib42311

tag: Sex

value: female

tag: treatment

tag: visit

value: Y


title: RNAseq_ASCL1_r2_24h_3232

description: Library name: Sample99

tag: genotype

value: 24 hours N2B27(w/oVitA)+dox


title: RNAseq_NGN2_ESMnodox6h_r1_1558

value: 6 hours mESC (FCS/LIF) after seeding

tag: experiment id


title: IEL_mast_cell, replicate 2

description:
Library name: IEL_MC_2
Chromium GEM-X Single Cell 3’ v4 assay (10X Genomics)


title: RNAseq_ASCL1_r2_0h_3232

description: Library name: Sample97

value: 0 hour mESC (FCS/LIF)


title: RNAseq_NGN2_ESMnodox6h_r2_1558


title: LP_mast_cell, replicate 1

description:
Library name: LP_MC_1
Chromium GEM-X Single Cell 3’ v4 assay (10X Genomics)

value: Small Intestine


title: RNAseq_ASCL1_r1_24h_3232

description: Library name: Sample98


title: lib42293

description: Library name: lib42293

value: Placebo

tag: illness

tag: virus _yn

value: N

tag: eos total

tag: neut total


title: IEL_mast_cell, replicate 1

description:
Library name: IEL_MC_1
Chromium GEM-X Single Cell 3’ v4 assay (10X Genomics)

value: Primary cells

value: Sorted Mast Cells

value: BALB/cJ


title: RNAseq_NGN2_6h_r4_1558

value: 6 hours N2B27(w/oVitA)+bFGF/EGF+dox


title: lib42314

description: Library name: lib42314

value: Nasal lavage

tag: donorid

value: Mepolizumab

value: Cold

tag: lym total

tag: squ total

tag: enitrox


title: RNAseq_NGN2_6h_r3_1558

tag: tissue

value: embryonic stem cells

value: mESC

value: HA36, rtTA/pTRE-humanNgn2 random insertion


title: lib42294

description: Library name: lib42294

value: female

tag: age months

tag: mac total

tag: epi total


title: RNAseq_ASCL1_r2_48h_3232

description: Library name: Sample95

tag: cell line

tag: cell type

value: 48 hours N2B27(w/oVitA)+dox

tag: mouse strain


title: RNAseq_ASCL1_r1_48h_3232

description: Library name: Sample94

tag: genotype

tag: treatment


title: RNAseq_NGN2_6h_r2_1558

tag: experiment id


title: lib42292

description: Library name: lib42292

tag: Sex

tag: visit

tag: illness

tag: virus _yn

value: Y


title: RNAseq_ASCL1_r1_6h_3232

description: Library name: Sample92

value: 6 hours N2B27(w/oVitA)+dox


title: RNAseq_NGN2_6h_r1_1558


title: ChIPseq_input_ASCL1_6h_r1_3130

description: Library name: Sample 75

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters.
Assembly: mm10
Supplementary files format and content: ExportWig function from the QuasR package was employed to generate the wig files with default parameters except scaling=1e6 and setting shift to 80 as the average of all samples after quantifying the estimated fragment length (half) or 'halfInsert' for paired-end.

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were grown for several passages at 37℃ 7% CO2 seeded on plates coated with 0.2% gelatin (Sigma) and maintained in serum/LIF (Dulbecco’s modified Eagle medium (DMEM, Invitrogen), supplemented with 15% fetal calf serum (Invitrogen), L-glutamine (Gibco), nonessential amino acids (Gibco), 0.001% 2-Mercaptoethanol (Sigma) and leukemia inhibitory factor (produced in-house).

extract_protocol:
DNA was purified with AmpureXP beads.
Immunoprecipitated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina).

treatment_protocol: To induce expression with TETON system, cells were washed with PBS and treated with 1 μg/ml doxycycline (Sigma, no. D989) in induction media, also referred as N2B27w/oVitA, (DMEM/F12/Glutamax (LifeTech, no. 31331-028), 1× B27 without vitamin A (LifeTech, no. 12587-010), 1× N2 supplement (LifeTech, no. 17502-048), ) or in serum/LIF media as indicated.

tag: chip antibody

value: Streptavidin (Thermo Fisher, 11205D)

tag: batch


title: ChIPseq_input_ASCL1_6h_r2_3130

description: Library name: Sample 76


title: RNAseq_ASCL1_r1_0h_3232

description: Library name: Sample96

value: 0 hour mESC (FCS/LIF)


title: ChIPseq_ASCL1_6h_r2_3130

description: Library name: Sample 74


title: lib42288

description: Library name: lib42288

tag: donorid

value: Placebo

value: N

tag: eos total

tag: lym total

tag: squ total

tag: neut total

tag: enitrox


title: ChIPseq_ASCL1_6h_r1_3130

description: Library name: Sample 73

tag: tissue

tag: cell line

tag: cell type


title: ChIPseq_EBF2_NGN2_24h_3897

description: Library name: Sample 66

tag: genotype

tag: treatment

value: 24 hours N2B27(w/oVitA)+dox

value: anti-Ebf2 antibody (R&D Systems, AF7006)


title: RNAseq_NGN2_0h_r4_1558

tag: mouse strain

tag: experiment id


title: lib42286

description: Library name: lib42286

tag: Sex

tag: age months

tag: visit

tag: illness

tag: mac total

tag: epi total


title: lib42285

description: Library name: lib42285

tag: donorid

tag: virus _yn

tag: eos total

tag: lym total


title: RNAseq_NGN2_0h_r1_1558

tag: tissue


title: ChIPseq_MYOD1_6h_ctrl_KD_3897

description: Library name: Sample 63

tag: cell line

value: 24 hours non-targeting siRNA, 6 hours N2B27(w/oVitA)+dox

tag: chip antibody

tag: batch


title: ChIPseq_MYOD1_6h_TCF_KD_3897

description: Library name: Sample 62

tag: cell type

tag: genotype

tag: treatment

value: 24 hours Tcf3/4/12 siRNA, 6 hours N2B27(w/oVitA)+dox


title: ChIPseq_NGN2_24h_ctrl_KD_3897

description: Library name: Sample 65

value: 24 hours non-targeting siRNA, 24 hours N2B27(w/oVitA)+dox


title: lib42283

description: Library name: lib42283

value: Nasal lavage

tag: Sex

value: Mepolizumab

tag: squ total

tag: neut total

tag: enitrox


title: ChIPseq_NGN2_24h_EBF_KD_3897

description: Library name: Sample 64

value: embryonic stem cells

value: mESC

value: 24 hours Ebf2/3 siRNA, 24 hours N2B27(w/oVitA)+dox


title: RNAseq_ASCL1_r2_6h_3232

description: Library name: Sample93

tag: mouse strain

tag: experiment id


title: ChIPseq_POL2_GFP_24h_2053

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters.
Assembly: mm10
Supplementary files format and content: ExportWig function from the QuasR package was employed to generate the wig files with default parameters except scaling=1e6 and setting shift to 80 as the average of all samples after quantifying the estimated fragment length (half).

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were grown for several passages at 37℃ 7% CO2 seeded on plates coated with 0.2% gelatin (Sigma) and maintained in serum/LIF (Dulbecco’s modified Eagle medium (DMEM, Invitrogen), supplemented with 15% fetal calf serum (Invitrogen),L-glutamine (Gibco), nonessential amino acids (Gibco), 0.001% 2-Mercaptoethanol (Sigma) and leukemia inhibitory factor (produced in-house).

extract_protocol:
DNA was purified with AmpureXP beads
Immunoprecipitated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina).

tag: antibody

value: anti-Pol2 antibody (Santa-Cruz, sc899x)


title: DAP_ascl1-tcf4_d2_rep1_3037

description: Library name: Sample 97

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for single-read experiments. Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing for paired-read experiments. ChIP-seq samples were aligned to the mm10 assembly of the mouse genome using QuasR (Gaidatzis et al, Bioinformatics 2015), which internally uses Bowtie 2 (Langmead, Genome Biology 2009). Bowtie was run with QuasR default parameters.
Assembly: mm10
Supplementary files format and content: ExportWig function from the QuasR package was employed to generate the wig files with default parameters except scaling=1e6 and only for single-end experiments setting shift to 120.

growth_protocol: Rosetta(DE3)pLysS Competent Cells (Millipore) were induced to express GST-tagged protein encoded in pGEX-6P-1 plasmids for DAPseq (NGN2, MyoD1, bHLH domains of TCF3-E12,TCF3-E47,TCF4,TCF12). 2ml fresh culture were added into 50ml LB and grow to an OD600 of 0.5 and induced with IPTG for 3 hours at 37DEgC for NGN2 and MyoD1 and 16DegC for TCFs. Cells were lysed and soluble fractions were mixed in combinations. GST tagged proteins were isolated using Promega MagneGST beads.

extract_protocol:
DNA was purified by AMPure beads with a ratio of 2:1 beads to sample volume.
Isolated DNA was subjected to library preparation (NEBNext Ultra II DNA Library Prep Kit, Illumina). In the library preparation protocol, samples were amplified using 12 PCR cycles.

treatment_protocol: Protocol was performed for Small-scale DAP-seq using E. coli-expressed recombinant protein as previously described (Bartlett et al, Nature Protocols, 2017) with modifications. Brielfy, freshly isolated GST-bHLH proteins bound to magnetic beads were incubated with 10ug of gemonic DNA sonicated to an average size range of 150-200bp for 1 hour in PBS. Beads were washed 4x with 200ul of PBS + 0.05%NP40, then washed 2x with 200ul PBS. Finally, beads were resuspended in 30ul 10 mM Tris-Cl, pH 8.5 + 2ul 10mg/ml Proteinase K and incubated at 50DegC for 3 hours.

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-

tag: treatment (proteins)


title: DAP_ascl1-tcf4_d1_rep2_3037

description: Library name: Sample 96


title: RNAseq_NGN2_0h_r3_1558

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing samples generated by Illumina HiSeq sequencing. Illumina RTA 3.4.4 and bcl2fastq2 v2.20 was used for basecalling and demultiplexing samples generated by Illumina NovaSeq sequencing. RNA-seq reads were mapped to mm10 using STAR aligner (Dobin et al, Bioinformatics 2013).
Assembly: mm10
Supplementary files format and content: Rsubread Bioconductor powered by featureCounts function (Liao et al, Nucleic Acids Research, 2019) was used to generate gene count table(s) at the level of "gene_name" based on the gene annotation from the GENCODE release M25 with default parameters.

value: HA36, rtTA/pTRE-humanNgn2 random insertion


title: DAP_ascl1-tcf4_d2_rep2_3037

description: Library name: Sample 98


title: lib42290

description: Library name: lib42290

data_processing:
Fastq files were aligned to the Ensembl version of the human genome (GRCh38) (GenBank assembly accession id GCA_000001405.15), using TopHat (version 1.4.1). The single-paired flag was set to “single,” while all other TopHat parameters were set to defaults
HTSeq-count was used to generate gene counts with mode as “Intersection (nonempty)” and minimum alignment quality set to 0 and otherwise set to default parameters
For quality control, samples were kept that had human aligned counts >250,000 and median CV coverage < 1.1. Genes were filtered to include those that had a trimmed mean of M values (TMM) normalization count of at least 1 in at least 10% of libraries and were classified as protein coding using BioMart. Normalized counts were transformed to log2 counts per million along with observations level weights using voomWithQualityWeights from the “limma” R package version 3.46
Assembly: GRCh38
Supplementary files format and content: counts_raw.tsv
Supplementary files format and content: hgnc_ensembl_id_mapping.tsv
Supplementary files format and content: modules_normalized_expr.tsv
Supplementary files format and content: voom_normalized_gene_expr.tsv

value: female

tag: donorid

tag: age months

tag: visit

tag: illness

tag: virus _yn

tag: eos total

tag: mac total

tag: epi total


title: DAP_ascl1-tcf3e47_d2_rep2_3037

description: Library name: Sample 94

tag: tissue

tag: cell line

tag: cell type

tag: genotype


title: DAP_ascl1-tcf3e47_d2_rep1_3037

description: Library name: Sample 93


title: RNAseq_NGN2_0h_r2_1558

tag: treatment

value: 0 hour mESC (FCS/LIF)


title: DAP_ascl1-tcf4_d1_rep1_3037

description: Library name: Sample 95

tag: mouse strain


title: ChIPseq_POL2_GFP_6h_2326

value: 6 hours N2B27(w/oVitA)+dox

tag: experiment id


title: DAP_ascl1-tcf3e47_d1_rep1_3037

description: Library name: Sample 91


title: lib42273

description: Library name: lib42273

tag: Sex

tag: lym total

tag: squ total

tag: neut total

tag: enitrox


title: lib42272

description: Library name: lib42272

tag: donorid

value: Placebo

tag: age months

tag: visit

tag: illness


title: DAP_ascl1-tcf3e47_d1_rep2_3037

description: Library name: Sample 92

tag: treatment (proteins)


title: ChIPseq_POL2_NGN2_24h_2053

tag: tissue

value: 24 hours N2B27(w/oVitA)+dox

tag: antibody


title: ChIPseq_POL2_MYOD1_6h_2326

tag: cell line

tag: cell type


title: DAP_ascl1-tcf3e12_d2_rep2_3037

description: Library name: Sample 90

tag: genotype


title: DAP_ascl1-tcf3e12_d1_rep1_3037

description: Library name: Sample 87

tag: mouse strain


title: DAP_ascl1-tcf3e12_d2_rep1_3037

description: Library name: Sample 89

tag: experiment id


title: lib42269

description: Library name: lib42269

tag: Sex

tag: treatment

tag: virus _yn

value: Y

tag: eos total

tag: mac total

tag: epi total


title: ChIPseq_POL2_MYOD1_24h_2053


title: lib42268

description: Library name: lib42268

tag: donorid

tag: age months

value: N

tag: lym total

tag: squ total

tag: neut total

tag: enitrox


title: DAP_ascl1-tcf12_d2_rep2_3037

description: Library name: Sample 86

tag: tissue

tag: cell line

tag: treatment (proteins)


title: lib42337

description: Library name: lib42337

tag: visit

tag: illness


title: DAP_ascl1-tcf12_d2_rep1_3037

description: Library name: Sample 85

tag: cell type

tag: genotype

tag: mouse strain

tag: experiment id


title: lib42276

description: Library name: lib42276

tag: Sex

tag: treatment

tag: virus _yn

tag: eos total

tag: mac total


title: ChIPseq_H3K27ac_GFP_24h_1954

tag: antibody

value: anti-H3K27ac antibody (Active Motif, 39133)


title: ChIPseq_H3K27ac_NGN2_24h_1954


title: DAP_ascl1-tcf12_d1_rep1_3037

description: Library name: Sample 83


title: DAP_ascl1-ascl1_d1_rep2_3037

description: Library name: Sample 82


title: ChIPseq_H3K27ac_GFP_24h_2052


title: lib42280

description: Library name: lib42280

tag: donorid

tag: age months

tag: lym total

tag: squ total

tag: epi total

tag: neut total


title: lib42259

description: Library name: lib42259

tag: tissue

tag: visit

tag: illness

value: Cold

tag: enitrox


title: Mouse primary neuron, E15-2, rep2

city: Taipei

first: Pei-Lin

last: Cheng

address: No. 128 Acdemia Rd., Section 2, Nankang

country: Taiwan

institute: Institue of Molecular Biology, Academia Sinica

description:
Library name: sample48
column names in all_expression.TPM.tsv: MsE15_2_S34

data_processing:
The paired-end, 148-bp raw sequencing reads for each sample were aligned to the mouse reference genome (GCF_000001635.26) using STAR (v 2.7.10)
The expected read counts of each gene were estimated by RSEM (v1.3.3)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files includes raw read counts and TPMs of all samples

source_name: Cerebral Cortex

growth_protocol: Primary cortical neurons were prepared from mouse embryos at embryonic day (E) E18 and cultured in neurobasal medium (Gibco; Cat. #21103049) supplemented with Gem21 NeuroPlex (Gemini Bio-Products; Cat. #400-160-010) in humidified chamber with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted utilizing the RNeasy Mini Kit (Qiagen; Cat# 74104) and its concentration was determined using a Nanodrop 2000 spectrophotometer and a Qubit fluorometer (both from ThermoFisher Scientific). The quality of the extracted RNA was evaluated using a 2100 Bioanalyzer (Agilent).
1ug of total RNA per sample was subjected to library preparation using SureSelect XT HS2 mRNA Library Prep Kit (Agilent Technology, USA) on the Agilent Bravo Automated Liquid Handling Platform. Libraries were sequenced using NovaSeq6000 (Illumina) with paired-end 150. 60 million reads per sample was obtained and subjected to RNA-seq analysis.

treatment_protocol: BDNF in 20ng/ml at 2 DIV, Paxillin siRNA or scrambled siRNA were treated at 2 DIV.

value: Cerebral Cortex

tag: cell type

value: cortical neuron

tag: genotype

value: WT


title: lib42266

description: Library name: lib42266

extract_protocol:
Cells were sorted into lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara)
Sequencing libraries were constructed from total RNA using TruSeq RNA Sample Preparation Kits v2 (Illumina) and clustered onto a flowcell using a cBOT amplification system with a HiSeq SR v4 Cluster Kit (Illumina). Single-read sequencing was carried out on a HiSeq2500 sequencer (Illumina), using a HiSeq SBS v4 Kit to generate 58-base reads, with a target of approximately 10 million reads per sample

value: Nasal lavage

tag: Sex

tag: treatment


title: ChIPseq_POL2_NGN2_6h_2326

value: embryonic stem cells

tag: cell line

value: mESC

tag: mouse strain

tag: experiment id


title: ChIPseq_H3K27ac_MYOD1_24h_2052

tag: antibody


title: Mouse primary neuron, E15-1, rep1

description:
Library name: sample47
column names in all_expression.TPM.tsv: MsE15_1_S65


title: DAP_ascl1-tcf3e12_d1_rep2_3037

description: Library name: Sample 88

value: DNMT1-/-; DNMT3a-/-; DNMT3b-/-

tag: treatment (proteins)


title: Mouse primary neuron, Control, BDNF-4, DIV5, rep4

description:
Library name: sample46
column names in all_expression.TPM.tsv: MsD5SCBD4_S13

value: BDNF, scrambled siRNA


title: lib42257

description: Library name: lib42257

value: female

tag: donorid

tag: age months

tag: virus _yn

tag: eos total

tag: lym total

tag: mac total


title: ChIPseq_H3K27ac_GFP_6h_r1_2052

tag: tissue


title: lib42256

description: Library name: lib42256

value: Mepolizumab

tag: visit

tag: illness

tag: squ total

tag: epi total

tag: neut total

tag: enitrox


title: Mouse primary neuron, Control, BDNF-1, DIV5, rep1

description:
Library name: sample43
column names in all_expression.TPM.tsv: MsD5SCBD1_S77

tag: cell type

tag: genotype

tag: treatment


title: DAP_ascl1-tcf12_d1_rep2_3037

description: Library name: Sample 84

tag: cell line

tag: treatment (proteins)

tag: mouse strain

tag: experiment id


title: Mouse primary neuron, Control-3, DIV5, rep3

description:
Library name: sample41
column names in all_expression.TPM.tsv: MsD5SC3_S4

value: scrambled siRNA


title: Mouse primary neuron, Control-4, DIV5, rep4

description:
Library name: sample42
column names in all_expression.TPM.tsv: MsD5SC4_S11


title: lib42250

description: Library name: lib42250

tag: Sex

tag: donorid

tag: age months

tag: virus _yn

tag: eos total


title: DAP_ascl1-ascl1_d1_rep1_3037

description: Library name: Sample 81

tag: tissue


title: ChIPseq_H3K27ac_MYOD1_6h_r2_2052

value: 6 hours N2B27(w/oVitA)+dox

tag: antibody


title: Mouse primary neuron, Control-1, DIV5, rep1

description:
Library name: sample39
column names in all_expression.TPM.tsv: MsD5SC1_S1


title: lib42263

description: Library name: lib42263

value: Placebo

tag: visit

tag: illness

tag: lym total

tag: mac total

tag: squ total

tag: epi total


title: ChIPseq_H3K27ac_MYOD1_6h_r1_2052

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: Mouse primary neuron, PXN KD, BDNF-2, DIV5, rep4

description:
Library name: sample37
column names in all_expression.TPM.tsv: MsD5PXNBD2_S84

value: BDNF, paxillin siRNA


title: lib42258

description: Library name: lib42258

tag: Sex

value: Y

tag: neut total

tag: enitrox


title: Mouse primary neuron, PXN KD, BDNF-4, DIV5, rep5

description:
Library name: sample38
column names in all_expression.TPM.tsv: MsD5PXNBD4_S14


title: Mouse primary neuron, PXN KD, BDNF-11, DIV5, rep3

description:
Library name: sample36
column names in all_expression.TPM.tsv: MsD5PXNBD11_S3


title: Mouse primary neuron, Control-2, DIV5, rep2

description:
Library name: sample40
column names in all_expression.TPM.tsv: MsD5SC2_S2


title: ChIPseq_H3K27ac_GFP_6h_r2_2052

value: anti-H3K27ac antibody (Active Motif, 39133)

tag: mouse strain

tag: experiment id


title: lib42242

description: Library name: lib42242

tag: tissue

tag: donorid

tag: age months

tag: virus _yn

tag: eos total


title: Mouse primary neuron, PXN KD, BDNF-10, DIV5, rep2

description:
Library name: sample35
column names in all_expression.TPM.tsv: MsD5PXNBD10_S31


title: lib42241

description: Library name: lib42241

tag: visit

value: cold

tag: illness

value: Cold

tag: lym total

tag: mac total


title: ChIPseq_H3K27ac_NGN2_6h_r1_2052

tag: cell line

tag: cell type

tag: antibody


title: Mouse primary neuron, Control, BDNF-3, DIV5, rep3

description:
Library name: sample45
column names in all_expression.TPM.tsv: MsD5SCBD3_S9

value: Cerebral Cortex

value: cortical neuron

tag: genotype

tag: treatment


title: Mouse primary neuron, PXN KD, BDNF-1, DIV5, rep1

description:
Library name: sample34
column names in all_expression.TPM.tsv: MsD5PXNBD1_S83

value: WT


title: ChIPseq_GFP_48h_2706

value: embryonic stem cells

value: 48 hours N2B27(w/oVitA)+dox

value: Streptavidin (Thermo Fisher, 11205D)


title: ChIPseq_MYOD1mut_48h_2706

value: mESC


title: Mouse primary neuron, PXN KD-4, DIV5, rep6

description:
Library name: sample33
column names in all_expression.TPM.tsv: MsD5PXN4_S12

value: paxillin siRNA


title: lib42237

description: Library name: lib42237

value: Nasal lavage

tag: Sex

value: female

value: Mepolizumab

tag: squ total

tag: epi total

tag: neut total

tag: enitrox


title: lib42239

description: Library name: lib42239

tag: tissue

tag: donorid

value: Placebo

tag: age months


title: ChIPseq_MYOD1_48h_2706

tag: mouse strain

tag: experiment id


title: Mouse primary neuron, PXN KD-3, DIV5, rep5

description:
Library name: sample32
column names in all_expression.TPM.tsv: MsD5PXN3_S7


title: lib42247

description: Library name: lib42247

tag: visit

tag: illness

tag: virus _yn

tag: eos total

tag: lym total


title: Mouse primary neuron, Control, BDNF-2, DIV5, rep2

description:
Library name: sample44
column names in all_expression.TPM.tsv: MsD5SCBD2_S78

tag: cell type

tag: genotype

value: BDNF, scrambled siRNA


title: ChIPseq_H3K27ac_NGN2_6h_r2_2052

tag: cell line

tag: treatment

value: 6 hours N2B27(w/oVitA)+dox

tag: antibody


title: lib42223

description: Library name: lib42223

tag: Sex

tag: mac total

tag: squ total

tag: epi total

tag: neut total


title: Mouse primary neuron, PXN KD-1, DIV5, rep1

description:
Library name: sample28
column names in all_expression.TPM.tsv: MsD5PXN1_S71

tag: tissue


title: Mouse primary neuron, PXN KD-10, DIV5, rep2

description:
Library name: sample29
column names in all_expression.TPM.tsv: MsD5PXN10_S30


title: lib28722

description: Library name: lib28722

tag: donorid

tag: age months

tag: enitrox


title: Mouse primary neuron, Control, BDNF-2, DIV3, rep2

description:
Library name: sample26
column names in all_expression.TPM.tsv: MsD3SCBD2_S76


title: ChIPseq_MYOD1mut_24h_2706

value: 24 hours N2B27(w/oVitA)+dox

tag: mouse strain

tag: experiment id


title: Mouse primary neuron, Control, BDNF-1, DIV3, rep1

description:
Library name: sample25
column names in all_expression.TPM.tsv: MsD3SCBD1_S75


title: Mouse primary neuron, Control-3, DIV3, rep3

description:
Library name: sample24
column names in all_expression.TPM.tsv: MsD3SC3_S3

value: scrambled siRNA


title: Mouse primary neuron, PXN KD-2, DIV5, rep4

description:
Library name: sample31
column names in all_expression.TPM.tsv: MsD5PXN2_S72


title: ChIPseq_MYOD1_24h_2706


title: Mouse primary neuron, Control-2, DIV3, rep2

description:
Library name: sample23
column names in all_expression.TPM.tsv: MsD3SC2_S67


title: lib28717

description: Library name: lib28717

tag: visit

tag: illness

tag: virus _yn

tag: eos total

tag: lym total


title: Mouse primary neuron, Control, BDNF-3, DIV3, rep3

description:
Library name: sample27
column names in all_expression.TPM.tsv: MsD3SCBD3_S8

tag: cell type

tag: genotype

tag: treatment


title: Mouse primary neuron, Control-1, DIV3, rep1

description:
Library name: sample22
column names in all_expression.TPM.tsv: MsD3SC1_S66


title: Control P5 Cx3cr1-KO barrel cortex [12R_UB]

description: Library name: 12R_UB

value: Barrel cortex

tag: Sex

value: male

value: Tissue

value: Mice were treated with Tamoxifen at P1-3, whiskers on the right side were cauterized at P4.


title: ChIPseq_GFP_6h_2196

value: embryonic stem cells

tag: cell line

tag: antibody


title: Mouse primary neuron, PXN KD, BDNF-2, DIV3, rep4

description:
Library name: sample21
column names in all_expression.TPM.tsv: MsD3PXNBD2_S82

tag: tissue

value: Cerebral Cortex

value: cortical neuron

value: WT

value: BDNF, paxillin siRNA


title: lib28715

description: Library name: lib28715

value: Nasal lavage

tag: donorid

tag: mac total

tag: squ total

tag: epi total

tag: neut total


title: Mouse primary neuron, PXN KD, BDNF-10, DIV3, rep2

description:
Library name: sample19
column names in all_expression.TPM.tsv: MsD3PXNBD10_S29


title: lib28708

description: Library name: lib28708

value: female

tag: age months

tag: visit

tag: enitrox


title: ChIPseq_GFP_24h_2706

value: mESC

value: Streptavidin (Thermo Fisher, 11205D)

tag: mouse strain

tag: experiment id


title: Mouse primary neuron, PXN KD, BDNF-11, DIV3, rep3

description:
Library name: sample20
column names in all_expression.TPM.tsv: MsD3PXNBD11_S1

tag: cell type


title: Mouse primary neuron, PXN KD-11, DIV5, rep3

description:
Library name: sample30
column names in all_expression.TPM.tsv: MsD5PXN11_S2

tag: genotype

value: paxillin siRNA


title: Mouse primary neuron, PXN KD, BDNF-1, DIV3, rep1

description:
Library name: sample18
column names in all_expression.TPM.tsv: MsD3PXNBD1_S81

tag: treatment


title: Mouse primary neuron, PXN KD-3, DIV3, rep5

description:
Library name: sample17
column names in all_expression.TPM.tsv: MsD3PXN3_S6


title: lib28706

description: Library name: lib28706

tag: Sex

value: Mepolizumab

value: cold

tag: illness

value: Exacerbation

tag: virus _yn

value: Y

tag: eos total

tag: lym total


title: Mouse primary neuron, PXN KD-2, DIV3, rep4

description:
Library name: sample16
column names in all_expression.TPM.tsv: MsD3PXN2_S70

tag: tissue


title: ChIPseq_input_MYOD1_6h_2007

tag: cell line

value: 6 hours N2B27(w/oVitA)+dox

tag: antibody

value: input


title: ChIPseq_GFP_6h_2007


title: Mouse primary neuron, PXN KD-10, DIV3, rep2

description:
Library name: sample14
column names in all_expression.TPM.tsv: MsD3PXN10_S28


title: Mouse primary neuron, PXN KD-1, DIV3, rep1

description:
Library name: sample13
column names in all_expression.TPM.tsv: MsD3PXN1_S69


title: lib28716

description: Library name: lib28716

tag: donorid

value: Placebo

tag: mac total

tag: squ total

tag: epi total

tag: neut total


title: lib28705

description: Library name: lib28705

tag: age months

tag: visit

tag: enitrox


title: lib28704

description: Library name: lib28704

tag: treatment


title: ChIPseq_MYOD1_6h_2007

value: embryonic stem cells

tag: cell type

tag: genotype

tag: mouse strain

tag: experiment id


title: lib28703

description: Library name: lib28703

tag: Sex

tag: illness

tag: virus _yn

tag: eos total

tag: lym total


title: Mouse primary neuron, Control, BDNF-2, DIV10, rep2

description:
Library name: sample11
column names in all_expression.TPM.tsv: MsD10SCBD2_S80

tag: tissue

value: Cerebral Cortex

value: BDNF, scrambled siRNA


title: ChIPseq_MYOD1mut_6h_2326

tag: cell line

tag: antibody


title: ChIPseq_GFP_6h_2326


title: ChIPseq_MYOD1_6h_2196


title: lib28700

description: Library name: lib28700

tag: donorid

tag: mac total

tag: squ total

tag: epi total

tag: neut total


title: Mouse primary neuron, Control-6, DIV10, rep3

description:
Library name: sample9
column names in all_expression.TPM.tsv: MsD10SC6_2_S15

tag: cell type

value: cortical neuron

value: WT

tag: treatment

value: scrambled siRNA


title: Mouse primary neuron, Control-3, DIV10, rep2

description:
Library name: sample8
column names in all_expression.TPM.tsv: MsD10SC3_S5

tag: genotype


title: Mouse primary neuron, Control, BDNF-3, DIV10, rep3

description:
Library name: sample12
column names in all_expression.TPM.tsv: MsD10SCBD3_S10


title: ChIPseq_MYOD1_6h_2326

tag: mouse strain

tag: experiment id


title: Mouse primary neuron, PXN KD, BDNF-11, DIV10, rep2

description:
Library name: sample6
column names in all_expression.TPM.tsv: MsD10PXNBD11_S5

value: BDNF, paxillin siRNA


title: ChIPseq_input_NGN2_6h_1849

value: mESC


title: lib28698

description: Library name: lib28698

value: Nasal lavage

tag: Sex

value: female

tag: age months

tag: visit

tag: illness

tag: enitrox


title: Mouse primary neuron, PXN KD, BDNF-10, DIV10, rep1

description:
Library name: sample5
column names in all_expression.TPM.tsv: MsD10PXNBD10_S33

tag: tissue


title: Mouse primary neuron, Control-1, DIV10, rep1

description:
Library name: sample7
column names in all_expression.TPM.tsv: MsD10SC1_S68


title: ChIPseq_GFP_6h_1849

tag: cell line

tag: antibody

value: Streptavidin (Thermo Fisher, 11205D)


title: Mouse primary neuron, PXN KD-11, DIV10, rep3

description:
Library name: sample3
column names in all_expression.TPM.tsv: MsD10PXN11_S4

value: paxillin siRNA


title: lib28699

description: Library name: lib28699

tag: donorid

value: cold

value: Cold

tag: virus _yn

tag: eos total

tag: lym total

tag: mac total


title: Mouse primary neuron, PXN KD-10, DIV10, rep2

description:
Library name: sample2
column names in all_expression.TPM.tsv: MsD10PXN10_S32

tag: cell type

tag: treatment


title: Mouse primary neuron, PXN KD-1, DIV10, rep1

description:
Library name: sample1
column names in all_expression.TPM.tsv: MsD10PXN1_S73

tag: genotype


title: Mouse primary neuron, Control, BDNF-1, DIV10, rep1

description:
Library name: sample10
column names in all_expression.TPM.tsv: MsD10SCBD1_S79


title: ChIPseq_NGN2mut_6h_1849

value: 6 hours N2B27(w/oVitA)+dox

tag: mouse strain

tag: experiment id


title: ChIPseq_NGN2_6h_1849


title: TG_HFD

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

description: Library name: TG_HFD

data_processing:
The FASTQ data files were aligned to the 10x Genomics mouse reference sequence (refdata-gex-mm10-2020-A) using 10X Genomics CellRanger on the NIH HPC Biowulf cluster (http://hpc.nih.gov). Seurat package was used to further analyze the single cell RNA seq data
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: .h5

source_name: Liver

extract_protocol:
The liver samples were homogenized with a gentleMACS Dissociator (Miltenyi), filtered through 70 μm cell strainers, and then centrifuged at 400g through a Percoll density gradient (40% and 70%).
The cells were loaded in the lanes using 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 with a single capture lane per sample targeting recovery of 8,000 cells. All subsequent steps of library preparation and quality control were performed according to the 10X Genomics Chromium Single Cell 3' Reagent Kits User Guide.

value: Liver

tag: Sex

value: male

value: HFD


title: S100a8f/fCx3cr1Cre_HFD5

description:
Library name: S100a8f/fCx3cr1Cre_HFD5
MKO_HFD_vs_WT_HFD.xlsx

data_processing:
FASTQC
TRIMMOMATIC
hisat2
samtools
featureCounts
DEseq2
Assembly: Mus_musculus.GRCm38.102.gtf
Supplementary files format and content: Excel file and raw counts

extract_protocol:
Trizol
PolyA selection for mRNA species (eukaryotic)


title: lib28696

description: Library name: lib28696

value: Placebo

tag: age months

tag: visit

tag: squ total

tag: epi total

tag: neut total


title: ChIPseq_NGN2_ES24h_1848

tag: tissue

value: embryonic stem cells

tag: cell line

value: 24 hours FCS/LIF+dox

tag: antibody


title: WT_HFD

description: Library name: WT_HFD

value: WT


title: lib28694

description: Library name: lib28694

tag: donorid

tag: illness

tag: virus _yn

tag: eos total

tag: enitrox


title: S100a8f/fCx3cr1Cre_HFD3

description:
Library name: S100a8f/fCx3cr1Cre_HFD3
MKO_HFD_vs_WT_HFD.xlsx

tag: genotype

tag: treatment


title: lib28695

description: Library name: lib28695

value: Exacerbation

value: N

tag: lym total

tag: mac total


title: ChIPseq_GFP_24h_1848

tag: cell type

value: mESC

value: 24 hours N2B27(w/oVitA)+dox

tag: mouse strain

tag: experiment id


title: ChIPseq_input_NGN2_24h_1848

value: input


title: Mouse primary neuron, PXN KD-11, DIV3, rep3

description:
Library name: sample15
column names in all_expression.TPM.tsv: MsD3PXN11_S35

value: Cerebral Cortex

value: cortical neuron


title: S100a8f/fCx3cr1Cre_HFD1

description:
Library name: S100a8f/fCx3cr1Cre_HFD1
MKO_HFD_vs_WT_HFD.xlsx

tag: Sex


title: lib28691

description: Library name: lib28691

value: Nasal lavage

value: female

value: Mepolizumab

tag: age months

tag: visit

value: cold

value: Y

tag: squ total

tag: epi total

tag: neut total


title: S100a8f/f_HFD3

description:
Library name: S100a8f/f_HFD3
MKO_HFD_vs_WT_HFD.xlsx

tag: tissue

value: Liver

value: male

value: HFD


title: lib28693

description: Library name: lib28693

tag: donorid

value: Placebo

tag: illness

tag: virus _yn


title: Mouse primary neuron, PXN KD-2, DIV10, rep4

description:
Library name: sample4
column names in all_expression.TPM.tsv: MsD10PXN2_S74

tag: genotype

value: WT

value: paxillin siRNA


title: lib28697

description: Library name: lib28697

tag: treatment

value: N

tag: eos total

tag: enitrox


title: S100a8f/f_HFD5

description:
Library name: S100a8f/f_HFD5
MKO_HFD_vs_WT_HFD.xlsx


title: ChIPseq_NGN2mut_24h_1848

value: embryonic stem cells

tag: cell line

tag: cell type

value: mESC

tag: antibody

value: Streptavidin (Thermo Fisher, 11205D)


title: S100a8f/f_HFD2

description:
Library name: S100a8f/f_HFD2
MKO_HFD_vs_WT_HFD.xlsx

tag: Sex


title: S100a8f/f_HFD4

description:
Library name: S100a8f/f_HFD4
MKO_HFD_vs_WT_HFD.xlsx


title: lib28687

description: Library name: lib28687

tag: age months

tag: lym total

tag: mac total


title: lib28686

description: Library name: lib28686

tag: visit

tag: squ total

tag: epi total


title: S100a8f/f_HFD1

description:
Library name: S100a8f/f_HFD1
MKO_HFD_vs_WT_HFD.xlsx

tag: tissue


title: ChIPseq_NGN2_24h_1848

value: 24 hours N2B27(w/oVitA)+dox

tag: mouse strain

tag: experiment id


title: S100a8f/fCx3cr1Cre_Chow5

description:
Library name: S100a8f/fCx3cr1Cre_Chow5
MKO_HFD_vs_WT_HFD.xlsx

tag: genotype

value: Chow


title: lib28688

description: Library name: lib28688

value: Nasal lavage

tag: donorid

tag: treatment

tag: illness

tag: virus _yn

tag: neut total


title: ChIPseq_NGN2_ES12h_1848

tag: cell line

tag: cell type

value: 12 hours FCS/LIF+dox

tag: antibody


title: S100a8f/fCx3cr1Cre_Chow1

description:
Library name: S100a8f/fCx3cr1Cre_Chow1
MKO_HFD_vs_WT_HFD.xlsx

tag: Sex


title: S100a8f/fCx3cr1Cre_HFD4

description:
Library name: S100a8f/fCx3cr1Cre_HFD4
MKO_HFD_vs_WT_HFD.xlsx


title: lib42336

description: Library name: lib42336

value: female

value: Mepolizumab

tag: age months

value: Cold

tag: eos total

tag: lym total

tag: mac total

tag: enitrox


title: S100a8f/fCx3cr1Cre_Chow3

description:
Library name: S100a8f/fCx3cr1Cre_Chow3
MKO_HFD_vs_WT_HFD.xlsx

tag: tissue

value: Liver


title: S100a8f/fCx3cr1Cre_Chow2

description:
Library name: S100a8f/fCx3cr1Cre_Chow2
MKO_HFD_vs_WT_HFD.xlsx

value: male


title: ChIPseq_GFP_12h_1848

value: 12 hours N2B27(w/oVitA)+dox

tag: mouse strain

tag: experiment id


title: lib28684

description: Library name: lib28684

tag: donorid

tag: visit

tag: squ total

tag: epi total


title: ChIPseq_NGN2mut_12h_1848

tag: genotype

tag: treatment


title: S100a8f/f_Chow5

description:
Library name: S100a8f/f_Chow5
MKO_HFD_vs_WT_HFD.xlsx


title: ChIPseq_NGN2_12h_1848

tag: cell line

tag: cell type


title: ChIPseq_input_NGN2_12h_1848

tag: antibody

value: input


title: S100a8f/f_Chow4

description:
Library name: S100a8f/f_Chow4
MKO_HFD_vs_WT_HFD.xlsx

tag: Sex


title: lib28685

description: Library name: lib28685

tag: age months

tag: illness

tag: virus _yn

tag: eos total

tag: neut total


title: ChIPseq_input_NGN2_ES6h_1848

tag: tissue

value: 6 hours FCS/LIF+dox

tag: mouse strain


title: lib28683

description: Library name: lib28683

tag: donorid

tag: lym total

tag: mac total

tag: enitrox


title: lib28682

description: Library name: lib28682

tag: visit

tag: squ total

tag: epi total


title: S100a8f/f_Chow2

description:
Library name: S100a8f/f_Chow2
MKO_HFD_vs_WT_HFD.xlsx

tag: genotype

tag: treatment


title: HFD_Bcl2TG2

description:
Library name: HFD_Bcl2TG2
HFD_TG_vs_WT.xlsx

tag: Sex

value: HFD


title: lib28679

description: Library name: lib28679

tag: age months

value: N


title: HFD_Bcl2TG6

description:
Library name: HFD_Bcl2TG6
HFD_TG_vs_WT.xlsx


title: HFD_Bcl2TG3

description:
Library name: HFD_Bcl2TG3
HFD_TG_vs_WT.xlsx


title: S100a8f/f_Chow1

description:
Library name: S100a8f/f_Chow1
MKO_HFD_vs_WT_HFD.xlsx


title: HFD_Bcl2TG5

description:
Library name: HFD_Bcl2TG5
HFD_TG_vs_WT.xlsx


title: HFD_Bcl2TG1

description:
Library name: HFD_Bcl2TG1
HFD_TG_vs_WT.xlsx


title: ChIPseq_NGN2_ES6h_1848

value: embryonic stem cells

tag: cell line

tag: cell type

tag: antibody

tag: experiment id


title: lib28672

description: Library name: lib28672

tag: tissue

value: Placebo

tag: illness

tag: virus _yn

tag: eos total

tag: neut total


title: HFD_WT5

description:
Library name: HFD_WT5
HFD_TG_vs_WT.xlsx

value: WT


title: ChIPseq_input_NGN2_6h_1848

value: mESC

value: 6 hours N2B27(w/oVitA)+dox

tag: mouse strain


title: HFD_WT3

description:
Library name: HFD_WT3
HFD_TG_vs_WT.xlsx


title: S100a8f/fCx3cr1Cre_Chow4

description:
Library name: S100a8f/fCx3cr1Cre_Chow4
MKO_HFD_vs_WT_HFD.xlsx

value: Chow


title: HFD_WT4

description:
Library name: HFD_WT4
HFD_TG_vs_WT.xlsx


title: HFD_WT2

description:
Library name: HFD_WT2
HFD_TG_vs_WT.xlsx


title: ChIPseq_GFP_6h_1848

value: Streptavidin (Thermo Fisher, 11205D)


title: Chow_Bcl2TG3

description:
Library name: Chow_Bcl2TG3
HFD_TG_vs_WT.xlsx


title: lib28667

description: Library name: lib28667

value: Nasal lavage

value: female

tag: donorid

tag: visit

value: Y

tag: lym total

tag: mac total

tag: enitrox


title: HFD_WT1

description:
Library name: HFD_WT1
HFD_TG_vs_WT.xlsx

value: Liver

tag: Sex

tag: genotype

tag: treatment


title: lib28664

description: Library name: lib28664

tag: age months

value: cold

value: Cold

tag: squ total

tag: epi total


title: lib28663

description: Library name: lib28663

tag: tissue

value: Mepolizumab


title: AdariΔgut_bio rep3

city: Wuhan

first: pengfei

last: xu

address: Donghu Road 115

institute: Wuhan University

description:
Library name: Sample 6
Ileal crypts isolated from Adarfl/fl;VIlCreERt2 mice were treated with tamoxifen.

data_processing:
Illumina ® TruSeq ® Stranded Total RNA Sample Preparation kits.
Illumina Real Time Analysis software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome.
RNA-seq analysis was performed using Illumina Real Time Analysis software, STAR, and Cufflinks.
Assembly: GRCm38
Supplementary files format and content: Excel files include FPKM values for each Sample.

source_name: ileal crypts

growth_protocol: No in vitro culture.

extract_protocol:
Total RNA was extracted by RNeasy Mini Kit.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Intestinal crypts were isolated from Adarfl/fl or Adarfl/fl;VilCreERt2 mice treated with tamoxifen for three days.

value: ileal crypts

value: Adar1 KO

value: tamoxifen


title: AdariΔgut_bio rep2

description:
Library name: Sample 5
Ileal crypts isolated from Adarfl/fl;VIlCreERt2 mice were treated with tamoxifen.


title: Chow_WT3

description:
Library name: Chow_WT3
HFD_TG_vs_WT.xlsx

value: male


title: Chow_Bcl2TG1

description:
Library name: Chow_Bcl2TG1
HFD_TG_vs_WT.xlsx


title: ChIPseq_NGN2_6h_1848

value: embryonic stem cells

tag: cell line

tag: cell type

tag: antibody

tag: experiment id


title: ChIPseq_input_NGN2_6h_1706

value: input

tag: mouse strain


title: AdariΔgut_bio rep1

description:
Library name: Sample 4
Ileal crypts isolated from Adarfl/fl;VIlCreERt2 mice were treated with tamoxifen.


title: lib28657

description: Library name: lib28657

tag: donorid

value: Placebo

tag: illness

tag: virus _yn

value: N

tag: eos total

tag: neut total


title: Adarfl/fl_bio rep3

description:
Library name: Sample 3
Ileal crypts isolated from Adarfl/fl mice were treated with tamoxifen.

value: WT


title: Chow_WT1

description:
Library name: Chow_WT1
HFD_TG_vs_WT.xlsx

tag: Sex

value: Chow


title: lib28652

description: Library name: lib28652

value: Nasal lavage

tag: visit

tag: lym total

tag: mac total

tag: enitrox


title: ChIPseq_NGN2mut_6h_1706

value: mESC

tag: genotype

tag: treatment

value: 6 hours N2B27(w/oVitA)+dox

value: Streptavidin (Thermo Fisher, 11205D)


title: Adarfl/fl_bio rep2

description:
Library name: Sample 2
Ileal crypts isolated from Adarfl/fl mice were treated with tamoxifen.

tag: tissue


title: Adarfl/fl_bio rep1

description:
Library name: Sample 1
Ileal crypts isolated from Adarfl/fl mice were treated with tamoxifen.


title: control littermate P0 rep4

city: San Diego

first: Zeyu

last: Chen

state: CA

address: 9500 Gilman Drive, BFRII 1217

department: School of Medicine

institute: UCSD

description: littermate control P0 heart

data_processing:
Raw RNA-seq reads were quality-controlled using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and trimmed with Trim Galore (v0.6.7) to remove low-quality bases and adapter sequences, obtaining high-quality clean reads
Trimmed reads were aligned to the mouse genome (GRCm38, Mus musculus) using HISAT2 (v2.2.1, PMID: 31375807).
Gene expression quantification was performed using StringTie (v2.2.1, https://doi.org/10.1038/nbt.3122).
Gene counts were obtained with featureCounts (https://doi.org/10.1093/bioinformatics/btt656) and used for differential expression analysis with DESeq2 (https://doi.org/10.1186/s13059-014-0550-8)
Alternative splicing events from RNA-seq data were identified using rMATS (v4.3.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: control littermate

growth_protocol: Rbpms and Rbpms2 floxed mice were generated with CRISPR-Cas9. Cardiomyocyte (CM)-specific Rbpms or Rbpms2 knockout mice were created by crossing Rbpms or Rbpms2 floxed mice with Xmlc2-Cre mice. CM-specific Rbpms and Rbpms2 double knockout mice were created by crossing Rbpms floxed mice with Rbpms2 floxed mice, and then with Xmlc2-Cre mice.

extract_protocol:
P0 neonatal mouse hearts were homogenized in TRIzol (Invitrogen) for RNA extraction according to the manufacturer’s instructions.
The concentration and quality of purified RNA was assessed by Agilent Bioanalyzer 2100. cDNA libraries were constructed using an Illumina TruSeq stranded mRNA kit according to manufacturer’s instructions. Libraries were sequenced with an Illumina NovaSeq 6000 sequencer to a sequencing depth of 80-100 million reads per sample.

value: heart

tag: strain

value: control littermate

tag: age


title: control littermate P0 rep3

description: littermate control P0 heart


title: ChIPseq_NGN2mut_6h_1848

tag: cell line

tag: cell type

tag: antibody

tag: experiment id


title: ChIPseq_NGN2_6h_1706

tag: mouse strain


title: lib28645

description: Library name: lib28645

value: female

tag: donorid

tag: age months

tag: illness

tag: virus _yn

tag: eos total

tag: squ total

tag: epi total


title: lib28644

description: Library name: lib28644

tag: Sex

tag: visit

tag: lym total

tag: mac total

tag: neut total

tag: enitrox


title: control littermate P0 rep2

description: littermate control P0 heart

tag: tissue

tag: strain

tag: genotype

tag: age


title: lib28660

description: Library name: lib28660

tag: donorid

tag: treatment


title: lib28643

description: Library name: lib28643

tag: age months

tag: illness


title: control littermate P0 rep1

description: littermate control P0 heart


title: Xmlc2-Cre drove CM-specific Rbpms KO  mice P0 rep4

description: CM-specific Rbpms KO P0 heart

source_name: Xmlc2-Cre drove CM-specific Rbpms KO

value: Xmlc2-Cre drove CM-specific Rbpms KO


title: Chow_WT2

description:
Library name: Chow_WT2
HFD_TG_vs_WT.xlsx

value: Liver


title: PBMCs, donor3, 6 month cryopreservation

city: Frederick

first: Tomozumi

last: Imamichi

address: Frederick National Laboratory for Cancer Research

department: Applied and Developmental Research Directorate

institute: National Institutes of Health

description: Library name: PBMC3_6M_GEX

data_processing:
Sequence data were initially processed with Cell Ranger pipeline (v7.0.1, 10x Genomics, Pleasanton, CA, USA) by using human reference GRCh38-2020-A (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: CellRanger output files: mRNA_barcodes.tsv.gz, mRNA_features.tsv.gz, mRNA_matrix.mtx.gz. features_reference.csv

source_name: blood

extract_protocol:
Briefly, 30 mL of leucocytes suspension was laid on to 10 mL of Lymphocyte Separation Medium (MP Biomedicals, Fountain Pkwy, Solon, OH, USA) and span at 700 xg for 30 min at room temperature with the brake off. The lymphocyte layers were corrected and then washed with PBS (Quality Biological Inc, Gaithersburg, MD, USA) three times at 500 xg for 5 min at room temperature.
The scRNA-Seq libraries were constructed using the Chromium Next GEM Single Cell 5′ Reagent Kit V2 (Dual Index) (10x Genomics, Pleasanton, CA, USA) following the manufacturer’s instructions.

value: blood

tag: cell type

value: PBMC


title: ChIPseq_GFP_6h_1706

value: embryonic stem cells

tag: cell line

tag: antibody

tag: mouse strain

tag: experiment id


title: PBMCs, donor3, 12 month cryopreservation

description: Library name: PBMC3_12M_GEX


title: PBMCs, donor3, fresh

description: Library name: PBMC3_fresh_GEX


title: lib28640

description: Library name: lib28640

source_name: Nasal lavage

tag: Sex

value: Mepolizumab

tag: visit

value: Exacerbation

tag: virus _yn

value: Y

tag: eos total

tag: lym total

tag: squ total

tag: epi total


title: PBMCs, donor2, fresh

description: Library name: PBMC2_fresh_GEX

tag: tissue


title: Chow_Bcl2TG2

description:
Library name: Chow_Bcl2TG2
HFD_TG_vs_WT.xlsx

value: male

tag: genotype


title: lib28651

description: Library name: lib28651

tag: donorid

tag: treatment

value: Placebo

tag: mac total

tag: neut total

tag: enitrox


title: lib28641

description: Library name: lib28641

value: Nasal lavage

tag: age months

value: cold

tag: illness


title: Xmlc2-Cre drove CM-specific Rbpms KO  mice P0 rep2

description: CM-specific Rbpms KO P0 heart

tag: strain

tag: age


title: Xmlc2-Cre drove CM-specific Rbpms KO  mice P0 rep3

description: CM-specific Rbpms KO P0 heart


title: PBMCs, donor2, 12 month cryopreservation

description: Library name: PBMC2_12M_GEX

tag: cell type


title: PBMCs, donor2, 6 month cryopreservation

description: Library name: PBMC2_6M_GEX


title: lib28639

description: Library name: lib28639

tag: Sex

tag: visit

tag: virus _yn


title: lib28638

description: Library name: lib28638

tag: eos total

tag: lym total

tag: squ total


title: lib28637

description: Library name: lib28637

tag: tissue

value: N

tag: epi total


title: PBMCs, donor1, fresh

description: Library name: PBMC1_fresh_GEX


title: Xmlc2-Cre drove CM-specific Rbpms KO  mice P0 rep1

description: CM-specific Rbpms KO P0 heart

tag: genotype


title: control littermate rep4

source_name: heart

extract_protocol:
Embryonic or neonatal mouse hearts were homogenized in TRIzol (Invitrogen) for RNA extraction according to the manufacturer’s instructions.
The concentration and quality of purified RNA was assessed by Agilent Bioanalyzer 2100. cDNA libraries were constructed using an Illumina TruSeq stranded mRNA kit according to manufacturer’s instructions. Libraries were sequenced with an Illumina NovaSeq 6000 sequencer to a sequencing depth of 80-100 million reads per sample.

value: Wild type

tag: time


title: PBMCs, donor1, 6 month cryopreservation

description: Library name: PBMC1_6M_GEX


title: PBMCs, donor1, 12 month cryopreservation

description: Library name: PBMC1_12M_GEX


title: lib28628

description: Library name: lib28628

tag: donorid

tag: treatment

value: Cold

tag: mac total

tag: neut total


title: lib28626

description: Library name: lib28626

tag: age months

tag: illness

tag: enitrox


title: control littermate rep2

value: heart

tag: strain


title: lib28642

description: Library name: lib28642

tag: Sex

value: female

tag: visit