title: BMDMs Ezh2 KO, Hepa1-6 CM treated, R2

description: Library name: KO_CM_R2

data_processing:
Atac-seq reads were trimmed using fastp.
Atac-seq reads were aligned to mm10 genome using bowtie2.
Peaks were called using MACS2 with the significance cut-off q-value <= 0.05
Assembly: mm10
Supplementary files format and content: broadPeak

source_name: Bone marrow-derived macrophages

extract_protocol:
Density gradient centrifugation was performed to isolate cell nuclei.
TruePrep DNA Library Prep Kit V2 for Illumina (TD501, Vazyme, Nanjing, China) was used to perform the transposition according to the manufacturer's recommendations. The transposed DNA fragments were purified by MinElute PCR Purification Kit (QIAGEN, Hilden, Germany). Library quality control was performed using the QSep-400 (BiOptic, Taipei, China) and Qubit 3.0 (Thermo Fisher Scientific, Wilmingto, USA). Sequencing was carried out on the Illumina Novaseq X platform (Illumina, San Diego, USA) with paired-end 150 bp (PE150) mode. Library construction and sequencing were performed at Biomarker Technologies (Hongkong) Co., Limited.

value: Bone marrow-derived macrophages

value: Ezh2 KO

value: Hepa1-6 CM


title: HFF_Fractionation_Uninfected_TotalRNA_72hpi_C

status: Public on Feb 22 2026

type: SRA

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description: Library name: Sample 21

library_source: transcriptomic

data_processing:
The reads of the ribo-seq libraries was trimmed to remove the linker CTGTAGGCACCATCAAT by using cutadapt. For the Shishkin protocol libraries the linker was AGATCGGAAGAGCACACGT
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et. al, plus few breakpoints from our STAR runs.
The alignments above was made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et. al. to get all the breakpoints.
genome build: Host: hg19, Merlin: NC_006273.2, TB40: EF999921.1
Supplementary files format and content: csv files of the cytosolic to nuclear ratio, half-life, and footprints of transcripts and the read counts of all transcripts in each experiment. For the tiles screen, a table with the read counts of different tiles in different flow cytometry defined categories.

molecule: total RNA

organism: Homo sapiens

source_name: HFF

extract_protocol:
For RNA-seq, cells were harvested with Tri-Reagent (Sigma-Aldrich), total RNA was extracted, and poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For ribosome profiling, medium was aspirated from dishes, which were immediately placed on ice and rinsed with 10 ml ice-cold PBS supplemented with drugs used in pretreatment of the cells. PBS was aspirated and 800 μl ice-cold lysis buffer (20 mM Tris, pH 7.4, 250 mM NaCl, 15 mM MgCl2, 1 mM dithiothreito, 0.5% Triton X-100 and 24 U / ml Turbo DNase (Ambion, AM2239), along with any drugs used for sample treatment) was dripped onto dishes. Cells were scraped and the lysate was removed and incubated 10 min on ice. The lysate was then clarified by centrifugation for 10 min at 20,000 × g, 4°C and ∼1.1 ml supernatant was recovered.
RNA-seq: mRNA samplewas subjected to DNAseI treatment and 3’ dephpsphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3’ adaptor ligation using T4 ligase (NEB). The ligated products used for reverse transcription with SSIII (Invitrogen) for first strand cDNA synthesis. The cDNA products were 3’ ligated with a second adaptor using T4 ligase and amplified for 8 cycles in a PCR for final library products of 200-300bp. For the tiles screen DNA was extracted from sorted cells and the transfected plasmids were amplified with primers containing the illumina adaptors.
ribosome profiling and targeted PCR of transfected DNA

treatment_protocol: For Ribo-seq libraries, all samples were treated with 100μg/mL CHX for 1 minute. Cells were placed on ice immediately after treatment, washed twice with PBS containing 100μg/mL CHX.

tag: virus strain

tag: cell line

value: HFF

tag: hours post infection


title: WL-COL-MOCK2

city: Shenzhen

first: Yao

last: Peng

address: 1066 Xueyuan Avenue, Nanshan District

country: China

institute: Shenzhen University

data_processing:
Majorbio cloud (https://cloud.majorbio.com/) was used to analyze differentially expressed genes (DEG). Genes with a corrected p-value < 0.05 and absolute log2 fold change > 2 were interpreted as differentially expressed. Venn diagrams, heatmaps and GO enrichment analysis were conducted by R packages.
Assembly: TAIR10.1_NCBI
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: 10-d-old seedlings

growth_protocol: 10-d-old Col-0 and uvr8 seedlings grown in long-day conditions(16 hour light/8 hour dark)

extract_protocol:
Total RNA was isolated using the RNAiso Plus (Takara) kit. RNA quality control was performed by gel electrophoresis. Three biological replicates were independently prepared throughout the processes, from the induction of seed germination to the preparation of RNA-seq libraries.
Generation of RNA libraries using Illumina TruseqTM RNA sample prep Kit followed the manufacturer’s instructions. The average RNA fragment was 300 bp and a 15-cycle PCR amplification was carried out with the primer mixture provided in the kit. Libraries were sequenced using an Illumina Hiseq4000 instrument with 2× 150-bp paired-ends reads by Majorbio.

treatment_protocol: treated with or without 50 uM ABA in white light or white light plus UV-B (5 umol m-2 sec-1)for 3 h.

tag: tissue

value: 10-d-old seedlings

value: seedlings

tag: cell type

tag: genotype

tag: treatment

value: white light


title: BMDMs Ezh2 KO, Hepa1-6 CM treated, R1

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

description: Library name: KO_CM_R1

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

growth_protocol: BMDMs were harvested from the femurs and tibias of Ezh2fl/fl;LysM-Cre+/- (Ezh2 KO) mice and its littermate control mice by flushing. Bine marrow cells were cultured for 7-10 days in Dulbecco's modified Eagle's medium (DMEM, HyClone, Logan, UT, USA) supplemented with 10% fetal bovine serum (Gibco, Grand Island, NY, USA), 1% sodium pyruvate, 1% HEPES, 100 U/ml penicillin/streptomycin, 20% L929 cell conditioned media and 5% horse serum.

treatment_protocol: BMDMs were treated with Hepa1-6 conditioned media for 24 hours. For the control condition, BMDMs were cultured in DMEM complete medium for 24 hours.


title: HFF_Fractionation_Uninfected_TotalRNA_72hpi_B

description: Library name: Sample 20


title: HFF_Fractionation_Uninfected_TotalRNA_72hpi_A

description: Library name: Sample 19


title: mpkCCDc11, Ctnnb1-siRNA, dDAVP, Replicate 2

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

country: USA

institute: Johns Hopkins University School of Medicine

description: Library name: Ctnnb1-dDAVP-2

data_processing:
Raw sequencing reads were subjected to quality control using FastQC, and trimmed with Trimmomatic. The filtered reads were aligned to the GRCm38/mm10 reference genome using HISAT2, and gene expression levels were quantified using StringTie. Differentially expressed genes (DEGs) were identified using DESeq2.
Assembly: mm10
Supplementary files format and content: text file of raw counts and TPM

source_name: Kidney

growth_protocol: The mpkCCDc11 cells were grown in a 1:1 mixture of DMEM and Ham’s F-12 medium (11330032, Thermo Fisher Scientific, Waltham, MA) containing 60 nM sodium selenite (S9133, Sigma, St. Louis, MO), 5 µg/mL transferrin (T8158, Sigma), 50 nM dexamethasone (D8893, Sigma) 1 nM triiodothyronine (T5516, Sigma), 10 ng/mL epidermal growth factor (E4127, Sigma), 5 µg/mL insulin (I5500, Sigma) and 2% heat-inactivated FBS (SV30207.02, Hyclone;Cytiva, Marlborough, MA) at 37℃ and 5% CO2 in a humidified incubator. Cells were grown on semipermeable supports (0.4 µm pore size, Transwell Permeable Supports, 3450, Corning Costar, NY) in a culture medium for 4 days and starved in serum- and hormone-free medium for 24 h. Then, the vasopressin V2 receptor-selective agonist 1-deamino-8-D-arginine vasopressin (dDAVP, V1005, Sigma) was treated to the basolateral side of the cells.

extract_protocol:
Total RNA was extracted using the TRIzolTM reagent (15596018, Invitrogen, Waltham, MA) and assessed for quality using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero H/M/Y Gold (Illumina, San Diego, CA).

treatment_protocol: For siRNA-mediated knockdown of Ctnnb1, mpkCCDc11 cells were transfected with control-siRNA (D-001206-13-20, Dharmacon, Horizon Discovery, Cambridge, UK), TRIM28-siRNA (M-040800-01-0005, Dharmacon) (50 nM), or Ctnnb1-siRNA (L-040628-00-0005, Dharmacon) using DharmaFECT1 (T-2001-03, Dharmacon) on semipermeable filters of the Transwell system (3450, Corning Costar) as previously described. Cells were cultured for 4 days and then incubated in serum- and hormone-free media for 24 h. dDAVP (1 nM) was treated to the basolateral side of the polarized cells for 24 h.

value: Kidney

value: mpkCCDc11 cells

value: kidney collecting duct cells

value: Ctnnb1 Knockdown

value: Vasopressin agonist


title: MMTV-R26Met syngeneic graft tumor S39

city: Marseille

first: Olivier

last: Castellanet

address: 27 boulevard Lei Roure

country: France

institute: Aix Marseille University, CNRS, INSERM

description:
Library name: Tumor_TNBC39
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using Cell Ranger (v6.1.1, 10x Genomics). The cellranger mkfastq command was employed to demultiplex the raw base call files into FASTQ files, followed by alignment to the mouse reference genome (mm10) using the “cellranger count” command, which also produced gene-cell expression matrices for each sample. Quality Control (QC) was performed using multiple approaches to ensure high-quality cell and gene selection. Ambient RNA contamination and cell barcode calling were initially assessed using the knee detection method implemented in Cell Ranger. Barcode rank plots were inspected to confirm appropriate cell versus background separation. Mitochondrial and ribosomal genes were identified based on gene symbols, where mitochondrial genes were defined by the prefix “mt-” and ribosomal genes by the prefix “Rpl” or “Rps,” using pattern matching on the gene annotation metadata. The scater package (v1.26.0) was then used to calculate per-cell quality metrics with “perCellQCMetrics” function, including the percentage of mitochondrial and ribosomal gene expression per cell. Outlier cells were identified and filtered based on library size, number of detected genes, and mitochondrial and ribosomal gene content using the “isOutlier” function from the scater package. This method flags cells that deviate beyond three median absolute deviations (MADs) from the median. Cells identified as outliers were excluded from downstream analyses to ensure data quality. Doublet detection was performed with the DoubletFinder package (v2.0.3), assuming an expected doublet rate of 10%, and clusters with more than 80% predicted doublets were removed. Cell cycle phase assignment was conducted using the “cyclone” function from the scran package (v1.26.0) with the mouse cell cycle marker dataset, categorizing cells into G1, S, and G2/M phases. These QC filters were applied using the Seurat R package (v5), and cells meeting all the criteria were considered high-confidence cells for downstream analysis. Raw sequencing data processing, mappings, and QC were performed at the Cancer Research Center of Marseille Integrative BioInformatics (Cibi) facility.
Assembly: mouse mm10
Supplementary files format and content: RDS file of a Seurat object with all samples integrated, including expression, metadata, clustering, and embeddings

source_name: mammary gland tumor

extract_protocol:
MMTV-R26Met syngeneic tumors were dissected at passage 7 and minced into small fragments, followed by enzymatic digestion for 20-35 min at 37°C. The digestion solution consisted of type IV collagenase (2 mg/ml, Sigma), hyaluronidase (1 mg/ml, Sigma), and DNase I (20 µg/ml, Roche) in DMEM/F12 (Dulbecco's modified Eagle's media/F12, 1/1, ThermoFisher Scientific) supplemented with 10% fetal bovine serum (FBS, Sigma) and penicillin–streptomycin (P/S, 100 U/ml / 0.1 mg/ml, ThermoFisher Scientific). After digestion, samples were centrifuged, and the pellet was incubated on ice for 1 min with red blood cell lysis buffer (ThermoFisher Scientific). They were then washed in PBS and further incubated for 5 min at 37°C with trypsin (0.05%, Gibco). Subsequently, the cells were resuspended in DMEM/F12 + 10% FBS + P/S, and filtered through a 40µm nylon cell strainer to remove aggregates. Cell counting and viability assessment using trypan blue revealed that all samples exhibited viability above 80%, so no sorting was performed. The cell concentration was then adjusted to approximately 1,000 cells/µL for library preparation.
Single-cell RNA sequencing libraries were generated using the 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v3.1, following the manufacturer's protocol. Specifically, 10,000 cells per sample were loaded onto a Chromium Controller to encapsulate individual cells into Gel Beads in Emulsion (GEMs). After cell lysis within the GEMs, mRNA was reverse transcribed to produce cDNA, which was then amplified by PCR. This cDNA was subsequently used for sequencing library preparation. The libraries were sequenced on an Illumina NextSeq 500 and NextSeq 2000 sequencers, targeting a depth of approximately 60,000 reads per cell. The library generation, validation, and sequencing were performed at the "Transcriptomique et Génomique Marseille Luminy (TGML)" platform.

value: mammary gland tumor

tag: Sex

value: female

tag: recipient strain

value: 50% 129S2/SvPasOrlRj, 50% C57BL/6JRj


title: WL-COL-MOCK1


title: Tim3 agonist2

city: Los Angeles

first: Yoshihiro

last: Sakano

state: CA

address: 1450 Biggy street

department: Molecular Microbiology & Immunology

institute: Unversity of Southern California

description:
Library name: Sample_5
21079R-06-20_S0

data_processing:
Partek Flow, version 10.0
Sequence reads were trimmed by quality score (min Phred score 20 from both end, and trimmed reads shorter than 25bp were discarded).
Trimmed reads were mapped to mm10 with GENECODE M25 annotation as a guidance by STAR 2.7.8.
Aligned reads were further quantified to GENCODE M25 with Partek E/M algorithm.
Genes with less than 10 counts in all samples were removed from the analysis. The remaining genes were subjected to differential expression analysis by DESeq2 with median ratio normalization
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw read counts per gene per sample

source_name: lung

extract_protocol:
Cultured ILC2s were recovered, lysed in RLT buffer (Qiagen) and RNA was extracted using the MicroRNeasy kit (Qiagen)
For each sample, a total of 10pg of RNA was used to generate cDNA (SMARTer Ultra Low Input RNA v3 kit, Clontech) for library preparation

value: lung

value: sorted ILC2s

tag: strain

value: Tim-3 agonist


title: mpkCCDc11, Ctnnb1-siRNA, dDAVP, Replicate 1

description: Library name: Ctnnb1-dDAVP-1


title: mpkCCDc11, Ctnnb1-siRNA, dDAVP, Replicate 3

description: Library name: Ctnnb1-dDAVP-3


title: ISO1

description:
Library name: Sample_1
21079R-06-15_S12

value: isotype control


title: BMDMs WT, Hepa1-6 CM treated, R2

description: Library name: WT_CM_R2

value: Bone marrow-derived macrophages

value: WT

value: Hepa1-6 CM


title: MMTV-R26Met syngeneic graft tumor S37

description:
Library name: Tumor_TNBC37
10x Genomics


title: mpkCCDc11, Ctnnb1-siRNA, Vehicle, Replicate 3

description: Library name: Ctnnb1-veh-3

value: Vehicle


title: HFF_Fractionation_Delta27_Nuclear_72hpi_A

description: Library name: Sample 16

value: HFF


title: LPSIFN24h:bone marrow-derived macrophages stimulated with LPS and IFN-γ for 24 hours rep3

city: Kunming

first: Yang

last: Naixue

state: Yunnan

address: 727 South Jingming Road, Chenggong District

department: Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine

institute: LPBR

description: Library name: LPSIFN24h3

data_processing:
Program:featureCounts v2.0.1; Command:"featureCounts" "-T" "10" "-p" "-t" "exon" "-g" "gene_id" "-a" "/nas01/Genome/hisat2_index/grcm38_hisat2/Mus_musculus.GRCm38.84.gtf" "-o"
Assembly: Mus_musculus.GRCm38.84.gtf
Supplementary files format and content: featureCounts

molecule: polyA RNA

source_name: bone marrow-derived macrophages

extract_protocol:
Resuspend the isolated bone marrow cells in bone marrow-derived macrophages (BMDM) growth medium (DMEM+1-%FBS+ 15% filtered (0.2 μm) L-929 cell (ATCC, CCL-1) culture supernatant) at a concentration of 2x106 cells/ml. Seed the cells in 15cm dish. Change fresh BMDM growth medium on day 3. On day 7, assess the formation of mature BMDM using flow cytometry analysis and fluorophore-conjugated antibodies to detect cells expressing CD11b and F4/80.
RNA extraction was performed using FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme RC112-01). Reverse transcription was performed using SMARTScribe Reverse Transcriptase (Clontech) according to the manufacturer’s instructions. The cDNA was amplified and the final library was constructed using TD501 kit (Vazyme).

value: bone marrow-derived macrophages


title: BMDMs WT, Hepa1-6 CM treated, R1

description: Library name: WT_CM_R1


title: mpkCCDc11, Ctnnb1-siRNA, Vehicle, Replicate 2

description: Library name: Ctnnb1-veh-2

value: Kidney

value: mpkCCDc11 cells


title: MMTV-R26Met syngeneic graft tumor S35

description:
Library name: Tumor_TNBC35
10x Genomics


title: RNA-seq of H9C2 cells subjected to hypoxia/reoxygenation with LITAF overexpression, biological replicate 4

city: Chongqing

first: Guo

last: Yang

state: Chongqing

address: No. 1 Jiankang Road, Yuzhong District.

institute: chongqing university

description:
Library name: H_R_OE_4_lib
H9C2 rat cardiomyoblast cells were transduced with a LITAF-overexpressing lentiviral vector and subjected to hypoxia (1% O2 for 8 h) followed by reoxygenation (2 h). Total RNA was extracted for RNA-seq. This sample represents a biological replicate of the hypoxia/reoxygenation plus LITAF overexpression group.

data_processing:
Clean reads were aligned to the Rattus norvegicus reference genome using a splice-aware aligner.
Aligned reads were quantified at the gene level based on the reference gene annotation.
Gene-level raw read counts were generated for each sample and compiled into a single count matrix.
Differential gene expression analysis was performed using DESeq2 and/or edgeR for downstream interpretation.
Assembly: Rattus norvegicus reference genome (Ensembl)
Supplementary files format and content: The processed data file is a tab-delimited text file containing gene-level raw read counts for all samples. Columns include gene name, gene biotype, Ensembl gene ID, and raw read counts for each individual sample.
Supplementary files format and content: Gene identifiers are based on Ensembl Rattus norvegicus gene annotations (ENSRNOG). Raw read counts are suitable for downstream differential expression analysis.

organism: Rattus norvegicus

source_name: heart

growth_protocol: H9C2 rat cardiomyoblast cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum and antibiotics at 37°C in a humidified incubator with 5% CO2 under normoxic conditions.

extract_protocol:
Total RNA was extracted from H9C2 cells using a standard commercial RNA extraction kit according to the manufacturer’s instructions. RNA concentration and purity were assessed by spectrophotometry, and RNA integrity was evaluated using an RNA integrity number (RIN) to ensure suitability for RNA sequencing.
RNA-seq libraries were constructed using a standard Illumina-compatible library preparation protocol. Polyadenylated mRNA was enriched from total RNA using oligo(dT) magnetic beads, fragmented to approximately 300 bp, and reverse transcribed into cDNA. Sequencing adapters were ligated, followed by size selection, PCR amplification, and purification to generate the final sequencing libraries.

treatment_protocol: Cells were divided into three experimental groups: control, hypoxia/reoxygenation (H/R), and hypoxia/reoxygenation plus LITAF overexpression. Control cells were maintained under normoxic conditions without hypoxia/reoxygenation or lentiviral transfection. For H/R treatment, cells were transfected with an empty lentiviral vector and exposed to hypoxia (1% O2) for 8 hours followed by reoxygenation under normoxic conditions for 2 hours. For the H/R plus LITAF overexpression group, cells were transduced with a LITAF-overexpressing lentiviral vector prior to hypoxia (1% O2 for 8 hours) and reoxygenation (2 hours).

value: heart

value: cardiomyoblast

value: LITAF overexpression

value: Hypoxia (1% O2 for 8 h) followed by reoxygenation (2 h); lentivirus-mediated LITAF overexpression

tag: batch


title: HFF_Fractionation_Delta27_Nuclear_72hpi_C

description: Library name: Sample 18


title: LPSIFN24h:bone marrow-derived macrophages stimulated with LPS and IFN-γ for 24 hours rep1

description: Library name: LPSIFN24h1


title: RNA-seq of H9C2 cells subjected to hypoxia/reoxygenation with LITAF overexpression, biological replicate 3

description:
Library name: H_R_OE_3_lib
H9C2 rat cardiomyoblast cells were transduced with a LITAF-overexpressing lentiviral vector and subjected to hypoxia (1% O2 for 8 h) followed by reoxygenation (2 h). Total RNA was extracted for RNA-seq. This sample represents a biological replicate of the hypoxia/reoxygenation plus LITAF overexpression group.


title: HFF_Fractionation_Delta27_Nuclear_72hpi_B

description: Library name: Sample 17


title: HFF_Fractionation_Delta27_Cytosol_72hpi_C

description: Library name: Sample 15


title: mpkCCDc11, Ctnnb1-siRNA, Vehicle, Replicate 1

description: Library name: Ctnnb1-veh-1

value: kidney collecting duct cells

value: Ctnnb1 Knockdown


title: mpkCCDc11, Control-siRNA, dDAVP, Replicate 3

description: Library name: Con-dDAVP-3

value: Vasopressin agonist


title: LPSIFN24h:bone marrow-derived macrophages stimulated with LPS and IFN-γ for 24 hours rep2

description: Library name: LPSIFN24h2


title: HFF_Fractionation_Delta27_Cytosol_72hpi_B

description: Library name: Sample 14


title: mpkCCDc11, Control-siRNA, dDAVP, Replicate 2

description: Library name: Con-dDAVP-2


title: LPS24h: bone marrow-derived macrophages stimulated with LPS for 24 hours rep2

description: Library name: LPS24h2


title: mpkCCDc11, Control-siRNA, dDAVP, Replicate 1

description: Library name: Con-dDAVP-1


title: RNA-seq of H9C2 cells subjected to hypoxia/reoxygenation with LITAF overexpression, biological replicate 2

description:
Library name: H_R_OE_2_lib
H9C2 rat cardiomyoblast cells were transduced with a LITAF-overexpressing lentiviral vector and subjected to hypoxia (1% O2 for 8 h) followed by reoxygenation (2 h). Total RNA was extracted for RNA-seq. This sample represents a biological replicate of the hypoxia/reoxygenation plus LITAF overexpression group.


title: HFF_Fractionation_Delta27_Cytosol_72hpi_A

description: Library name: Sample 13


title: RNA-seq of H9C2 cells subjected to hypoxia/reoxygenation, biological replicate 4

description:
Library name: H_R_4_lib
H9C2 rat cardiomyoblast cells were subjected to hypoxia (1% O2 for 8 h) followed by reoxygenation (2 h) after empty lentiviral vector transfection. Total RNA was extracted for RNA-seq. This sample represents a biological replicate of the hypoxia/reoxygenation group.

value: wild type

value: Hypoxia (1% O2 for 8 h) followed by reoxygenation (2 h); empty lentiviral vector transfection


title: LPS24h: bone marrow-derived macrophages stimulated with LPS for 24 hours rep1

description: Library name: LPS24h1


title: IL413IFN24h:bone marrow-derived macrophages stimulated with IL4, IL13 and IFN-γ for 24 hours rep3

description: Library name: IL413IFN24h3


title: HFF_Fractionation_Delta27_TotalRNA_72hpi_A

description: Library name: Sample 10


title: LPS24h: bone marrow-derived macrophages stimulated with LPS for 24 hours rep3

description: Library name: LPS24h3


title: IL413IFN24h:bone marrow-derived macrophages stimulated with IL4, IL13 and IFN-γ for 24 hours rep2

description: Library name: IL413IFN24h2


title: mpkCCDc11, Control-siRNA, Vehicle, Replicate 2

description: Library name: Con-veh-2


title: RNA-seq of H9C2 cells subjected to hypoxia/reoxygenation, biological replicate 3

description:
Library name: H_R_3_lib
H9C2 rat cardiomyoblast cells were subjected to hypoxia (1% O2 for 8 h) followed by reoxygenation (2 h) after empty lentiviral vector transfection. Total RNA was extracted for RNA-seq. This sample represents a biological replicate of the hypoxia/reoxygenation group.


title: RNA-seq of H9C2 cells subjected to hypoxia/reoxygenation with LITAF overexpression, biological replicate 1

description:
Library name: H_R_OE_1_lib
H9C2 rat cardiomyoblast cells were transduced with a LITAF-overexpressing lentiviral vector and subjected to hypoxia (1% O2 for 8 h) followed by reoxygenation (2 h). Total RNA was extracted for RNA-seq. This sample represents a biological replicate of the hypoxia/reoxygenation plus LITAF overexpression group.


title: HFF_Fractionation_Delta27_TotalRNA_72hpi_C

description: Library name: Sample 12


title: mpkCCDc11, Control-siRNA, Vehicle, Replicate 1

description: Library name: Con-veh-1


title: mpkCCDc11, Control-siRNA, Vehicle, Replicate 3

description: Library name: Con-veh-3


title: RNA-seq of H9C2 cells subjected to hypoxia/reoxygenation, biological replicate 2

description:
Library name: H_R_2_lib
H9C2 rat cardiomyoblast cells were subjected to hypoxia (1% O2 for 8 h) followed by reoxygenation (2 h) after empty lentiviral vector transfection. Total RNA was extracted for RNA-seq. This sample represents a biological replicate of the hypoxia/reoxygenation group.


title: IL413IFN24h:bone marrow-derived macrophages stimulated with IL4, IL13 and IFN-γ for 24 hours rep1

description: Library name: IL413IFN24h1


title: Mouse colon FFPE section for spatial-FFPE-ATAC at a resolution of 50um

city: New Haven

first: Haikuo

last: Li

state: CT

address: 55 Prospect St

institute: Washington University in St. Louis

description: Library name: mouse_colon

data_processing:
Read 2 fastq sequences were first filtered based on linker oligo sequences using bbduk, followed by extraction of spatial Barcode A (8 bp) and spatial Barcode B (8 bp) sequences. Then, The Read 2 fastq file was split into two new fastq files, which indicate genomic DNA sequences and the Barcode A/B sequences, respectively. A reference genome index file was created using chromap (version 0.2.6-r490) against the GRCm38 or GRCh38 primary assembly fasta files. Genome mapping was performed using chromap (chromap --preset atac) against the created index file, in which the 16-bp spatial barcode fastq is set as the barcode file. This pipeline generates a fragment .bed file, which is then compressed with gzip and tabix indexed for downstream analysis.
Patho-DBiT Read 1 sequences were aligned to the reference genome GRCh38 with STAR (version 2.7.7a) and unique molecular identifier (UMI) and spatial barcode sequences were extracted from Read 2 using published scripts (https://github.com/Zhiliang-Bai/Patho-DBiT), followed by generation of a gene-by-pixel count matrix by ST_Pipeline (version 1.7.6).
Assembly: GRCm38 or GRCh38
Supplementary files format and content: .h5ad: Anndata format for data matrix
Supplementary files format and content: .txt: positions of pixels used for analysis; otherwise, the region is blank with no tissues

source_name: adult mouse colon

extract_protocol:
ATAC-seq and CUT&Tag are performed in situ on tissue sections. The tissue is then lysed for library preparation.
Library is constructed with standard Nextera adapters.

value: adult mouse colon

value: Homemade sample


title: RNA-seq of H9C2 cells subjected to hypoxia/reoxygenation, biological replicate 1

description:
Library name: H_R_1_lib
H9C2 rat cardiomyoblast cells were subjected to hypoxia (1% O2 for 8 h) followed by reoxygenation (2 h) after empty lentiviral vector transfection. Total RNA was extracted for RNA-seq. This sample represents a biological replicate of the hypoxia/reoxygenation group.


title: HFF_Fractionation_Delta27_TotalRNA_72hpi_B

description: Library name: Sample 11


title: IL41324h:bone marrow-derived macrophages stimulated with IL4 and IL13 for 24 hours rep2

description: Library name: IL41324h2


title: IL41324h:bone marrow-derived macrophages stimulated with IL4 and IL13 for 24 hours rep3

description: Library name: IL41324h3


title: RNA-seq of H9C2 cells under normoxia, biological replicate 4

description:
Library name: NC_4_lib
H9C2 rat cardiomyoblast cells were cultured under normoxic conditions without hypoxia/reoxygenation or lentiviral transfection. Total RNA was extracted for RNA-seq. This sample represents a biological replicate of the control group.

value: No hypoxia/reoxygenation treatment; no lentiviral transfection


title: Mouse brain sagittal FFPE section for spatial-FFPE-ATAC at a resolution of 50um

description: Library name: mouse_brain_sagittal

source_name: adult mouse brain

value: adult mouse brain

value: Commercialized section


title: RNA-seq of H9C2 cells under normoxia, biological replicate 3

description:
Library name: NC_3_lib
H9C2 rat cardiomyoblast cells were cultured under normoxic conditions without hypoxia/reoxygenation or lentiviral transfection. Total RNA was extracted for RNA-seq. This sample represents a biological replicate of the control group.


title: Mouse brain coronal FFPE section for spatial-FFPE-ATAC at a resolution of 50um

description: Library name: mouse_brain_coronal


title: RNA-seq of H9C2 cells under normoxia, biological replicate 2

description:
Library name: NC_2_lib
H9C2 rat cardiomyoblast cells were cultured under normoxic conditions without hypoxia/reoxygenation or lentiviral transfection. Total RNA was extracted for RNA-seq. This sample represents a biological replicate of the control group.


title: HFF_Fractionation_WT_Cytosol_72hpi_C

description: Library name: Sample 6

value: HFF


title: IL41324h:bone marrow-derived macrophages stimulated with IL4 and IL13 for 24 hours rep1

description: Library name: IL41324h1

value: bone marrow-derived macrophages


title: HFF_Fractionation_WT_Nuclear_72hpi_A

description: Library name: Sample 7


title: P3

city: Guangzhou

first: Li

last: Zhao

state: Guangdong

address: 1838 North Guangzhou Avenue,

department: Department of Cardiovascular Surgery

institute: Nanfang Hospital, Southern Medical University

data_processing:
TruSeq PE Cluster Kit v3 cBot HS
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Illumina Casava 1.8 software used for basecalling.
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: vascular smooth muscle cells

growth_protocol: vascular smooth muscle cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from the samples, and the integrity of the extracted RNA was assessed by agarose gel electrophoresis. The concentration of RNA was accurately determined using NanoDrop.
RNA libraries for RNA-seq were preparded using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

treatment_protocol: Vascular smooth muscle cells were transduced with adenoviral vectors carrying pyruvate dehydrogenase kinase 4 overexpression plasmids or control plasmids.

value: vascular smooth muscle cells

value: Adenoviral vector transfection of pyruvate dehydrogenase kinase 4e overexpression plasmid


title: HFF_Fractionation_WT_Nuclear_72hpi_C

description: Library name: Sample 9


title: HFF_Fractionation_WT_Cytosol_72hpi_B

description: Library name: Sample 5


title: IFN24h:bone marrow-derived macrophages stimulated them with IFN-γ for 24 hours rep3

description: Library name: IFN24h3


title: IFN24h:bone marrow-derived macrophages stimulated them with IFN-γ for 24 hours rep2

description: Library name: IFN24h2


title: RNA-seq of H9C2 cells under normoxia, biological replicate 1

description:
Library name: NC_1_lib
H9C2 rat cardiomyoblast cells were cultured under normoxic conditions without hypoxia/reoxygenation or lentiviral transfection. Total RNA was extracted for RNA-seq. This sample represents a biological replicate of the control group.

value: heart

value: cardiomyoblast


title: P2

value: Adenoviral vector transfection of pyruvate dehydrogenase kinase 4 overexpression plasmid


title: HFF_Fractionation_WT_Nuclear_72hpi_B

description: Library name: Sample 8


title: HFF_Fractionation_WT_Cytosol_72hpi_A

description: Library name: Sample 4


title: IFN24h:bone marrow-derived macrophages stimulated them with IFN-γ for 24 hours rep1

description: Library name: IFN24h1


title: P1

value: pyruvate dehydrogenase kinase 4 overexpression


title: shTTP MeRIPped

city: Wuhan

first: RUI

last: Zhou

address: Donghu Road 185

institute: Wuhan University

description:
Treat_IP
MeRIPped RNA

data_processing:
After obtaining raw data, the raw data is filtered first to obtain high-quality clean data, and the clean data is compared to the reference genome of the project species to obtain comprehensive transcript information and conduct gene expression quantification
And GO, KEGG Pathway analysis. Meanwhile, the results were compared by genome-wide de novo peak calling to study the binding preference of proteins on RNA, and motif analysis of binding sites was conducted.
Assembly: GRCh38
Library strategy: MeRIP-seq

growth_protocol: The human hepatocyte cells HL7702 in DMEM (Gibco), supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
HL7702 cells with stable knockdown of TTP and control cells were collected.
MeRIP-sequencing and following data analyses were mainly supported by Seqhealth Technology.

treatment_protocol: For knockdown, the short hairpin RNAs (shRNAs) of TTP were cloned into pLKO.1 according to instructions.

value: Normal liver


title: C3

value: WT

value: Adenoviral vector transfection of control plasmid


title: HFF_Fractionation_WT_TotalRNA_72hpi_C

description: Library name: Sample 3


title: shTTP Input

description:
Treat_Input
Input RNA


title: HFF_Fractionation_WT_TotalRNA_72hpi_B

description: Library name: Sample 2


title: control rep3

description: Library name: Ctrl3


title: C2


title: shNC MeRIPped

description:
Control_IP
MeRIPped RNA


title: control rep2

description: Library name: Ctrl2


title: HFF_Fractionation_WT_TotalRNA_72hpi_A

description: Library name: Sample 1


title: C1


title: PBMC_OP_17

status: Public on Feb 21 2026

city: Leioa

first: Mariana

last: Astiz

state: Bizkaia

address: Barrio Sarriena s/n, Science Park of the UPV/EHU, Sede Building, 3rd floor

country: Spain

institute: Achucarro Basque Center for Neuroscience

description:
Library name: OP17
PE150 platform
47

data_processing:
Gene expression matrix (features x samples) was filtered for not-expressed genes by excluding all genes that are not detected in 5% of all samples (counts = 0 in > 2 samples) followed by an additional filtering for low-expressed genes excluding all genes that display less than an average of 10 counts to confirm reliable and robust quantification.
A total of 13866 genes are ubiquitously expressed across all samples. Differential expression analysis was performed in DESeq2 (v1.46.0).
For pair-wise comparison between aGCs exposed and control (C) infants, DEG analysis was adjusted for covariates of birth weight and gestational age, since groups displayed significant differences for both confounding factors. Genes were considered differentially expressed with an abs(log2FC) > 1 and p-value < 0.05. Subsequently, raw counts were variance stabilized utilizing variance-stabilizing transformation (VSD) for principal component analysis.
For gene set enrichment analysis (GSEA) to identify gene ontology (GO) terms and transcription factor activity analysis, genes were ranked descending based on log2FoldChange * -log10(p-value) and GSEA for GO terms was performed with clusterProfiler (v4.14.6). GSEA results were adjusted for multiple testing utilizing FDR (0.05). The top active and suppressed GO pathways based on the normalized enrichment score (NES) from each pair-wise comparison were displayed in dot plots. For collapsing related enriched GO-terms within a superior parental term, rrvgo (v1.18.0) was utilized.
For the analysis of inferred transcription factor activity, the vsd counts were included in an univariate linear model (ulm) calculated with the decoupleR (v2.12.0) package as described previously. As transcription factor network, we used the annotated DoRothEA database for human transcription factor-gene interactions from CollecTRI.
Assembly: Fastq files were mapped to the GRCh38 human reference genome with HISAT2.
Supplementary files format and content: Process data files contain data from all samples. Files include DEG analysis, GSEA analysis indentifying GO terms and Transcription factor inferred activity. All these analysis was performed for the comparison between controls and antenatal GCs (aGCs) exposed groups and within the aGCs exposed groups, a comparison depending the time of maternal exposure in-phase (IP) vs out-of-phase (OP)

source_name: Blood

extract_protocol:
RNA was isolated from babies’ PBMCs using the AllPrep DNA/RNA/miRNA Universal Kit (80224, Qiagen, Hilden Germany) following the manufacturer’s protocol.
RNA libraries were then prepared via poly(A) selection and reverse transcription into cDNA, followed by library quality assessment. Sequencing was performed using 150 bp paired-end reads on an Illumina PE150 platform. Quality of sequencing was assessed with fastqc (v0.12.0) and fastq files were mapped to the GRCh38 human reference genome with HISAT2.

value: Blood

value: PBMCs

value: male

tag: birth weight

tag: gestational age

value: aGC out-of-phase (evening)


title: PBMC_OP_16

description:
Library name: OP16
PE150 platform
46

value: female


title: shNC input

description:
Control_Input
Input RNA


title: PBMC_OP_15

description:
Library name: OP15
PE150 platform
45


title: PBMC_OP_14

description:
Library name: OP14
PE150 platform
44


title: PBMC_OP_10

description:
Library name: OP10
PE150 platform
40


title: PBMC_OP_13

description:
Library name: OP13
PE150 platform
43


title: PBMC_OP_12

description:
Library name: OP12
PE150 platform
42


title: control rep1

description: Library name: Ctrl1


title: PBMC_OP_8

description:
Library name: OP8
PE150 platform
38


title: PBMC_OP_7

description:
Library name: OP7
PE150 platform
37


title: PBMC_OP_11

description:
Library name: OP11
PE150 platform
41


title: PBMC_OP_9

description:
Library name: OP9
PE150 platform
39


title: PBMC_OP_4

description:
Library name: OP4
PE150 platform
34


title: PBMC_OP_5

description:
Library name: OP5
PE150 platform
35


title: PBMC_OP_6

description:
Library name: OP6
PE150 platform
36


title: PBMC_OP_3

description:
Library name: OP3
PE150 platform
33


title: PBMC_IP_16

description:
Library name: IP16
PE150 platform
29

value: aGC in phase (morning)


title: PBMC_IP_17

description:
Library name: IP17
PE150 platform
30


title: PBMC_OP_1

description:
Library name: OP1
PE150 platform
31


title: PBMC_OP_2

description:
Library name: OP2
PE150 platform
32


title: PBMC_IP_14

description:
Library name: IP14
PE150 platform
27


title: PBMC_IP_15

description:
Library name: IP15
PE150 platform
28


title: PBMC_IP_13

description:
Library name: IP13
PE150 platform
26


title: PBMC_IP_9

description:
Library name: IP9
PE150 platform
22


title: PBMC_IP_4

description:
Library name: IP4
PE150 platform
17


title: PBMC_IP_8

description:
Library name: IP8
PE150 platform
21


title: PBMC_IP_12

description:
Library name: IP12
PE150 platform
25


title: PBMC_IP_6

description:
Library name: IP6
PE150 platform
19


title: PBMC_Control_13

description:
Library name: C13
PE150 platform
12

value: Control


title: PBMC_IP_10

description:
Library name: IP10
PE150 platform
23


title: PBMC_IP_11

description:
Library name: IP11
PE150 platform
24


title: PBMC_IP_3

description:
Library name: IP3
PE150 platform
16


title: PBMC_IP_5

description:
Library name: IP5
PE150 platform
18


title: PBMC_Control_14

description:
Library name: C14
PE150 platform
13


title: PBMC_Control_12

description:
Library name: C12
PE150 platform
11


title: PBMC_Control_6

description:
Library name: C6
PE150 platform
5


title: PBMC_Control_7

description:
Library name: C7
PE150 platform
6


title: PBMC_IP_7

description:
Library name: IP7
PE150 platform
20


title: PBMC_IP_1

description:
Library name: IP1
PE150 platform
14


title: PBMC_IP_2

description:
Library name: IP2
PE150 platform
15


title: PBMC_Control_8

description:
Library name: C8
PE150 platform
7


title: PBMC_Control_2

description:
Library name: C2
PE150 platform
1


title: PBMC_Control_10

description:
Library name: C10
PE150 platform
9


title: PBMC_Control_11

description:
Library name: C11
PE150 platform
10


title: genomic DNA from whole blood sample collected from medication overuse headache subject 9 at timepoint T2

type: genomic

city: Bologna

first: Paolo

last: Garagnani

state: BO

address: Via San Giacomo 12

department: Department of Medical and Surgical Sciences (DIMEC)

country: Italy

institute: Univeristy of Bologna

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 9 at timepoint T2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged on Illumina iScan scanner using iScan Control Software (ICS) with standard recommended Illumina scanner settings

data_processing:
R v3.6.3
*processed value definition: Average Beta (non normalized, not filtered).

label: Cy3 and Cy5

source_name: genomic DNA from whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from whole blood samples using QIAamp DNA Blood Mini kit (Qiagen) according to manufacturer’s instructions.

value: whole blood

tag: phenotype

value: medication overuse headache

tag: timepoint


title: genomic DNA from whole blood sample collected from medication overuse headache subject 9 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 9 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 9 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 9 at timepoint T3


title: PBMC_Control_4

description:
Library name: C4
PE150 platform
3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 9 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 9 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 8 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 8 at timepoint T3


title: PBMC_Control_9

description:
Library name: C9
PE150 platform
8


title: PBMC_Control_3

description:
Library name: C3
PE150 platform
2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 8 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 8 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 8 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 8 at timepoint T1


title: PBMC_Control_5

description:
Library name: C5
PE150 platform
4


title: genomic DNA from whole blood sample collected from medication overuse headache subject 8 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 8 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 7 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 7 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 7 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 7 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 7 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 7 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 6 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 6 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 6 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 6 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 6 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 6 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 7 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 7 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 5 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 5 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 5 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 5 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 5 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 5 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 4 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 4 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 3 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 3 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 4 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 4 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 3 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 3 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 3 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 3 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 4 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 4 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 6 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 6 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 25 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 25 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 3 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 3 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 23 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 23 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 24 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 24 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 5 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 5 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 23 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 23 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 25 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 25 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 25 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 25 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 23 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 23 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 22 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 22 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 25 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 25 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 22 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 22 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 21 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 21 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 21 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 21 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 22 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 22 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 22 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 22 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 20 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 20 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 20 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 20 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 23 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 23 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 20 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 20 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 18 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 18 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 20 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 20 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 19 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 19 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 18 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 18 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 18 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 18 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 15 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 15 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 16 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 16 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 15 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 15 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 15 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 15 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 18 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 18 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 14 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 14 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 14 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 14 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 15 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 15 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 14 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 14 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 13 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 13 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 17 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 17 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 13 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 13 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 13 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 13 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 13 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 13 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 12 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 12 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 12 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 12 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 11 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 11 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 11 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 11 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 12 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 12 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 12 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 12 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 11 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 11 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 14 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 14 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 11 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 11 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 10 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 10 at timepoint T1


title: genomic DNA from whole blood sample collected from medication overuse headache subject 10 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 10 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 10 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 10 at timepoint T3


title: genomic DNA from whole blood sample collected from medication overuse headache subject 1 at timepoint T2

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 1 at timepoint T2


title: genomic DNA from whole blood sample collected from medication overuse headache subject 10 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 10 at timepoint T0


title: genomic DNA from whole blood sample collected from healthy control subject 9 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from healthy control subject 9 at timepoint T1

value: healthy control


title: genomic DNA from whole blood sample collected from healthy control subject 9 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 9 at timepoint T0


title: genomic DNA from whole blood sample collected from healthy control subject 8 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 8 at timepoint T0


title: genomic DNA from whole blood sample collected from medication overuse headache subject 1 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 1 at timepoint T1


title: MHCII_pool2_BCR

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: Library name: D10_BCR

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and BCR) was performed using the 10x genomics Cell Ranger v7.0.0 multi pipeline and aligning to the mm10-2020-A and vdj_IMGT_mouse mouse reference genomes.
Further processing was performed with Serurat v5.1.0 in R v4.4.1
Assembly: mm10
Supplementary files format and content: 10x Genomics mRNA output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: 10x Genomics BCR output files: all_contigs_annotations.csv
Supplementary files format and content: txt file of Seurat metadata object providing cell annotation and metadata
Library strategy: BCR-Seq

molecule: other

source_name: Spleen

extract_protocol:
Splenocytes were isolated and FACS sorted according to the indicated markers.
10x 5’ scRNA-seq libraries were generated using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics CG000331 Rev E) according to the instructions provided.

treatment_protocol: Mice were infected with influenza PR8 and euthanized 14 days later.

value: Spleen

tag: sorting markers

value: CD11b– F4/80– Thy1.1– Live/Dead– CD19+/mid IgD–

value: CD45.2 MHCII-KO and CD45.1/2 wild-type B cells

value: Influenza PR8

tag: time point

value: Day 14


title: genomic DNA from whole blood sample collected from medication overuse headache subject 1 at timepoint T3

description: bisulfite converted DNA from whole blood isolated from medication overuse headache subject 1 at timepoint T3


title: genomic DNA from whole blood sample collected from healthy control subject 7 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from healthy control subject 7 at timepoint T1


title: Renal pelvis-Wild type mouse

first: Xiaofeng

last: Cheng

address: Chongqing City, Shapingba District, Xinqiao Zheng Street

institute: Army Medical University

description:
Library name: Sample 1
10x Genomics

data_processing:
Reads were aligned to the mouse reference transcriptome (mm10). Gene counts and unique molecular identifier (UMI) counts were generated using the Subread software package (https://sourceforge.net/projects/subread/). These counts were then compiled into expression matrices.
Assembly: Mouse mm10
Supplementary files format and content: barcodes.tsv.gz: list of barcodes
Supplementary files format and content: features: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data

source_name: Renal pelvis

extract_protocol:
Adult C57BL/6 male mice were deeply anesthetized and transcardially perfused with chilled PBS. Thirty renal pelvises were dissected and temporarily stored in tissue preservation solution (Miltenyi Biotec, Cologne, Germany; 130-100-008). After single washes with PBS, samples were digested enzymatically at 37°C for 30 min using a digestion cocktail containing: 2 mg/mL collagenase I, 2 mg/mL collagenase II, 1 mg/mL collagenase IV, 2 mg/mL dispase II, and 50 U/mL DNase I in RPMI 1640 medium (Thermo Fisher Scientific; 11875093). The enzymatic reaction was quenched by adding an equal volume of RPMI-1640 medium. The cell suspension was centrifuged at 500 ×g for 6 min, resuspended in 0.25% Trypsin-EDTA (25200056, Thermo Fisher Scientific), and incubated for 5 min at 37°C. Subsequently, the digested suspension was filtered through a 70-μm cell strainer and centrifuged again at 500 ×g for 6 min. Cells were washed twice with PBS containing 0.03% BSA, and their viability was assessed as 94.2% using an automated cell counter (Countstar BioTech; ALIT Life Sciences, Shanghai, PR China).
Single-cell suspensions were loaded onto a Chromium Controller instrument (10x Genomics, Pleasanton, CA) to generate gel bead-in-emulsions (GEMs) with the Chromium Single Cell 3’ v3.1 Reagent Kit (10x Genomics, 1000268). Reverse transcription within GEMs was performed in a thermal cycler (SimpliAmp, Thermo Fisher Scientific) under the following program: 53°C for 45 min, 85°C for 5 min, and hold at 4°C. Barcoded cDNA was amplified, fragmented, a-tailed, and ligated with Illumina adaptors using a library construction kit (10x Genomics, PN-1000190). Libraries were sequenced on a NovaSeq 6000 system (Illumina, San Diego, CA) with a sequencing depth of ~48,902 reads per cell.

value: Renal pelvis

value: Wild type


title: genomic DNA from whole blood sample collected from healthy control subject 7 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 7 at timepoint T0


title: genomic DNA from whole blood sample collected from healthy control subject 6 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from healthy control subject 6 at timepoint T1


title: genomic DNA from whole blood sample collected from healthy control subject 6 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 6 at timepoint T0


title: genomic DNA from whole blood sample collected from healthy control subject 5 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 5 at timepoint T0


title: MHCII_pool1_GEX

description:
Library name: D9_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and BCR) was performed using the 10x genomics Cell Ranger v7.0.0 multi pipeline and aligning to the mm10-2020-A and vdj_IMGT_mouse mouse reference genomes.
Further processing was performed with Serurat v5.1.0 in R v4.4.1
Assembly: mm10
Supplementary files format and content: 10x Genomics mRNA output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: 10x Genomics BCR output files: all_contigs_annotations.csv
Supplementary files format and content: txt file of Seurat metadata object providing cell annotation and metadata


title: MHCII_pool2_GEX

description:
Library name: D10_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: d14.KO.M.igM.MBC

description: Library name: d14.KO.M.igM.MBC

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: txt file of RPKM normalized read counts for each detected gene

extract_protocol:
Cells were FACS sorted directly into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

treatment_protocol: Animals were infected with influenza PR8 and euthanized 14 days later.  Spleens were isolated and the indicated cell population purified by FACS.

value: Male

value: IgM+ Memory B cell

value: MHC-II KO

value: Influenza PR8 infected


title: d14.KO.M.CS.MBC

description: Library name: d14.KO.M.CS.MBC

value: Class-switched Memory B cell


title: d14.KO.M.ActB

description: Library name: d14.KO.M.ActB

value: Activated B cell


title: genomic DNA from whole blood sample collected from healthy control subject 5 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from healthy control subject 5 at timepoint T1

value: female


title: genomic DNA from whole blood sample collected from healthy control subject 4 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from healthy control subject 4 at timepoint T1

value: whole blood

value: male


title: d14.KO.F.CS.MBC

description: Library name: d14.KO.F.CS.MBC

value: Female


title: genomic DNA from whole blood sample collected from healthy control subject 4 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 4 at timepoint T0

value: healthy control


title: genomic DNA from whole blood sample collected from healthy control subject 8 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from healthy control subject 8 at timepoint T1


title: genomic DNA from whole blood sample collected from healthy control subject 3 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from healthy control subject 3 at timepoint T1


title: d14.KO.F.igM.MBC

description: Library name: d14.KO.F.igM.MBC

value: Spleen


title: d14.KO.F.ActB

description: Library name: d14.KO.F.ActB


title: genomic DNA from whole blood sample collected from healthy control subject 2 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 2 at timepoint T0


title: genomic DNA from whole blood sample collected from healthy control subject 13 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 13 at timepoint T0


title: d14.WT.M.igM.MBC

description: Library name: d14.WT.M.igM.MBC

value: wildtype


title: d14.WT.M.ActB

description: Library name: d14.WT.M.ActB


title: genomic DNA from whole blood sample collected from healthy control subject 11 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from healthy control subject 11 at timepoint T1


title: genomic DNA from whole blood sample collected from healthy control subject 12 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from healthy control subject 12 at timepoint T1


title: d14.WT.F.CS.MBC

description: Library name: d14.WT.F.CS.MBC


title: d14.WT.F.ActB

description: Library name: d14.WT.F.ActB


title: genomic DNA from whole blood sample collected from healthy control subject 12 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 12 at timepoint T0


title: d14.WT.M.CS.MBC

description: Library name: d14.WT.M.CS.MBC


title: genomic DNA from whole blood sample collected from healthy control subject 3 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 3 at timepoint T0


title: genomic DNA from whole blood sample collected from healthy control subject 11 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 11 at timepoint T0


title: d14.WT.F.igM.MBC

description: Library name: d14.WT.F.igM.MBC


title: genomic DNA from whole blood sample collected from healthy control subject 1 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 1 at timepoint T0


title: 024-F4/80

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

institute: institution of microbology

description:
Library name: DSP-1001660018859-B-E01
024-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)

data_processing:
DSP sequencing data were processed with the GeoMx NGS Pipeline (DND). After sequencing, reads were trimmed, merged, and aligned to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicates and duplicate reads, thus converting reads into digital counts. The limit of quantitation (LOQ) was estimated as following: the geometric mean reads of the negative control probes plus 2 geometric standard deviations of the negative control probes. Targets that consistently fell below the LOQ were removed, and the datasets were normalized using upper quartile (Q3) normalization. Differentially expressed genes of each disease group were identified using Wald statistics test, with |fold change| > 1.5 and Benjamini–Hochberg (BH)-adjusted P-value < 0.05 as compared to HC group.
Assembly: GRCm38 (mm10)
Supplementary files format and content: xlsx

source_name: Lung

extract_protocol:
For the NanoString GeoMx Digital Spatial Profiler (DSP) transcriptional assays, slides were prepared following the manufacturer’s instruction from GeoMx DSP Slide Preparation User Manual with some modifications (NanoString, MAN-10115-05 for software v2.3). Briefly, slides were baked at 60°C for 30 minutes. Deparaffinization and rehydration were performed in CitriSolv hybrid solvent, 100% ethanol, and 95% ethanol, sequentially. Target retrieval was performed in 1× Tris EDTA (TE) buffer (pH 9.0). Thereafter, tissue RNA targets were exposed by incubating the slides with 1 µg/mL proteinase K at 37°C. Slides were washed and then immediately placed in 10% neutral buffered formalin, followed by incubation in NBF stop buffer (100 mM Tris-HCl and 100 mM glycine). The Whole Transcriptome Atlas (WTA) probe reagent was diluted and added to each slide, which was covered with a HybriSlip cover (Grace Bio-Labs) and incubated for 15 hours at 37°C in a HybEZ II System (Advanced Cell Diagnostics, USA). Slides were washed and blocked in 200 μL Buffer W (NanoString) for 30 minutes. The optimal dilution solution of morphology markers and nuclear staining SYTO13 (Nanostring) were used for distinguishing various morphology. In detail, slides were covered with 200 μL morphology marker solution, and incubated at RT for 1 hours. Slides were blocked with Buffer W and covered with morphology marker and SYTO13 (1:10), subsequently incubated with HRP polymer and dye. After blocking with HRP blocker, slides were blocked and stained for the next staining cycle. Finally, Slides were then scanned with the NanoString DSP instrument for RNA probes collection. For spatial samples, slides were loaded into the slide holder of the GeoMx DSP machine and secured by closing the slide tray clamp. Each slide was covered with 2 mL of buffer S and the underside of the slides cleaned with 70% ethanol before loading the slide tray into the DSP. The scanning areas were set to only scan the tissues and the tissue boundaries were determined by adjusting the x and y scanning areas and the sensitivity. Each slide was scanned with a 20× objective. ROIs were placed per tissue based on the selection regions and assessment. After approval of the ROIs, the GeoMx DSP photocleaves the ultraviolet-cleavable barcoded linker of the bound RNA probes and collects the individual segmented areas into separate wells in the DSP collection plate. For each experimental group, n = 3–4 individual ROIs of 0.2–0.5 mm2 in area with each containing ~ 300 designated immune cells were collected for subsequent analysis.
DSP collection sample plates were dried down by sealing the plates with aeroseal and placed at RT overnight. The samples were then resuspended with diethyl pyrocarbonate (DEPC)-treated water. 96-well plates were prepared by mixing 2 μL polymerase chain reaction (PCR) mix (NanoString), 4 μL of index primer mix (NanoString), and 4 μL of DSP sample. The following PCR program was used to amplify the Illumina sequencing compatible libraries: 1) 37°C for 30 minutes, 50°C for 10 minutes, and 95°C for 3 minutes; 2) 18 cycles of 95°C for 15 seconds, 65°C for 1 minutes, and 68°C for 30 seconds; 3) 68°C for 5 minutes and a final hold at 4°C. The indexed libraries were pooled into 8-well strip tubes, and incubated with 58 μL AMPure XP beads (Beckman Coulter, Cat# A63880) in a 1:1.2 ratio. The 8-well strip was placed on a magnetic stand before removal of the supernatant. The beads were then washed twice with 80% ethanol and dried before being eluted with 10 μL elution buffer (10mM Tris-HCl pH 8, 0.05% Tween-20). The samples were combined into two pools of 40 μL each and incubated with 48 μL AMPure buffer (2.5 M NaCl, 20% PEG 8000) for 5 minutes. Following magnetic incubation for 5 minutes and removal of supernatants, the beads were washed twice with 80% ethanol and dried for 1 minute before elution with 17 μL elution buffer. The two pools were combined to a final elute of 34 μL. Sequencing library size was assessed with a DNA high sensitivity bioanalyzer assay (Agilent Technologies). Library concentration was assessed with Qubit dsDNA high sensitivity assay (Thermo Fisher Scientific). Total target counts per DSP collection plate for sequencing were calculated from the total sampled areas (μm2) reported in the DSP generated Lab Worksheet. All sequencing libraries were generated with unique indexes allowing pooled sequencing. WTA libraries for sequencing with an Illumina NovaSeq 6000 platform.

value: Lung

value: Macrophages

tag: group


title: 025-F4/80

description:
Library name: DSP-1001660018859-B-E03
025-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 025-CD3

description:
Library name: DSP-1001660018859-B-E02
025-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)

value: T cells


title: genomic DNA from whole blood sample collected from healthy control subject 2 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from healthy control subject 2 at timepoint T1


title: 023-F4_80

description:
Library name: DSP-1001660018859-B-D11
023-F4_80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from healthy control subject 10 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from healthy control subject 10 at timepoint T0


title: 023-CD3

description:
Library name: DSP-1001660018859-B-D10
023-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 9 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 9 at timepoint T1

value: episodic migraine


title: 024-CD3

description:
Library name: DSP-1001660018859-B-D12
024-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 8 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 8 at timepoint T1


title: genomic DNA from whole blood sample collected from episodic migraine subject 9 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 9 at timepoint T0


title: 022-F4/80

description:
Library name: DSP-1001660018859-B-D09
022-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: MHCII_pool1_BCR

description: Library name: D9_BCR

value: CD11b– F4/80– Thy1.1– Live/Dead– CD19+/mid IgD–

value: CD45.2 MHCII-KO and CD45.1/2 wild-type B cells

value: Influenza PR8

value: Day 14


title: genomic DNA from whole blood sample collected from healthy control subject 10 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from healthy control subject 10 at timepoint T1


title: genomic DNA from whole blood sample collected from episodic migraine subject 8 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 8 at timepoint T0


title: genomic DNA from whole blood sample collected from episodic migraine subject 7 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 7 at timepoint T1


title: 021-F4_80

description:
Library name: DSP-1001660018859-B-D07
021-F4_80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 022-CD3

description:
Library name: DSP-1001660018859-B-D08
022-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 7 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 7 at timepoint T0


title: 021-CD3

description:
Library name: DSP-1001660018859-B-D06
021-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 6 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 6 at timepoint T1


title: genomic DNA from whole blood sample collected from episodic migraine subject 6 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 6 at timepoint T0


title: genomic DNA from whole blood sample collected from episodic migraine subject 5 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 5 at timepoint T1


title: genomic DNA from whole blood sample collected from episodic migraine subject 4 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 4 at timepoint T0


title: 019-F4/80

description:
Library name: DSP-1001660018859-B-D03
019-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 4 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 4 at timepoint T1


title: genomic DNA from whole blood sample collected from episodic migraine subject 5 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 5 at timepoint T0


title: 019-CD3

description:
Library name: DSP-1001660018859-B-D02
019-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 018-F4_80

description:
Library name: DSP-1001660018859-B-D01
018-F4_80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 3 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 3 at timepoint T0


title: 017-F4/80

description:
Library name: DSP-1001660018859-B-C11
017-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 018-CD3

description:
Library name: DSP-1001660018859-B-C12
018-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 017-CD3

description:
Library name: DSP-1001660018859-B-C10
017-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 3 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 3 at timepoint T1


title: 020-F4_80

description:
Library name: DSP-1001660018859-B-D05
020-F4_80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 20 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 20 at timepoint T0


title: genomic DNA from whole blood sample collected from episodic migraine subject 2 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 2 at timepoint T1


title: genomic DNA from whole blood sample collected from episodic migraine subject 19 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 19 at timepoint T1


title: 016-F4/80

description:
Library name: DSP-1001660018859-B-C09
016-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 015-F4/80

description:
Library name: DSP-1001660018859-B-C07
015-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 015-CD3

description:
Library name: DSP-1001660018859-B-C06
015-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 016-CD3

description:
Library name: DSP-1001660018859-B-C08
016-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 18 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 18 at timepoint T0


title: 014-CD3

description:
Library name: DSP-1001660018859-B-C04
014-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 20 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 20 at timepoint T1


title: genomic DNA from whole blood sample collected from episodic migraine subject 19 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 19 at timepoint T0


title: 014-F4/80

description:
Library name: DSP-1001660018859-B-C05
014-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 013-F4/80

description:
Library name: DSP-1001660018859-B-C03
013-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 18 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 18 at timepoint T1


title: genomic DNA from whole blood sample collected from episodic migraine subject 17 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 17 at timepoint T1


title: genomic DNA from whole blood sample collected from episodic migraine subject 17 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 17 at timepoint T0


title: 013-CD3

description:
Library name: DSP-1001660018859-B-C02
013-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 15 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 15 at timepoint T1


title: genomic DNA from whole blood sample collected from episodic migraine subject 16 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 16 at timepoint T1


title: 011-CD3

description:
Library name: DSP-1001660018859-B-B10
011-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 012-F4/80

description:
Library name: DSP-1001660018859-B-C01
012-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 15 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 15 at timepoint T0


title: genomic DNA from whole blood sample collected from episodic migraine subject 14 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 14 at timepoint T1


title: genomic DNA from whole blood sample collected from episodic migraine subject 14 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 14 at timepoint T0


title: genomic DNA from whole blood sample collected from episodic migraine subject 13 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 13 at timepoint T1


title: 010-F4/80

description:
Library name: DSP-1001660018859-B-B09
010-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 009-CD3

description:
Library name: DSP-1001660018859-B-B06
009-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 009-F4/80

description:
Library name: DSP-1001660018859-B-B07
009-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 16 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 16 at timepoint T0


title: 008-F4/80

description:
Library name: DSP-1001660018859-B-B05
008-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 12 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 12 at timepoint T0


title: 012-CD3

description:
Library name: DSP-1001660018859-B-B12
012-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 007-F4/80

description:
Library name: DSP-1001660018859-B-B03
007-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 011-F4/80

description:
Library name: DSP-1001660018859-B-B11
011-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 008-CD3

description:
Library name: DSP-1001660018859-B-B04
008-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 010-CD3

description:
Library name: DSP-1001660018859-B-B08
010-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 11 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 11 at timepoint T1


title: 006-CD3

description:
Library name: DSP-1001660018859-B-A12
006-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 13 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 13 at timepoint T0


title: genomic DNA from whole blood sample collected from episodic migraine subject 10 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 10 at timepoint T1


title: genomic DNA from whole blood sample collected from episodic migraine subject 11 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 11 at timepoint T0


title: 007-CD3

description:
Library name: DSP-1001660018859-B-B02
007-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: genomic DNA from whole blood sample collected from episodic migraine subject 10 at timepoint T0

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 10 at timepoint T0


title: 020-CD3

description:
Library name: DSP-1001660018859-B-D04
020-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 006-F4/80

description:
Library name: DSP-1001660018859-B-B01
006-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 004-F4/80

description:
Library name: DSP-1001660018859-B-A09
004-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 005-CD3

description:
Library name: DSP-1001660018859-B-A10
005-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 005-F4_80

description:
Library name: DSP-1001660018859-B-A11
005-F4_80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: JAR_MTX-resistant_rep3

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

country: Japan

institute: Nagoya University

description: Library name: 6

data_processing:
Expression levels for each gene were quantified from the sequencing data by Kallisto software.
The tximport package (ver. 1.18.0) was used to summarize the data.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: a tsv file includes TPM counts of each sample

source_name: JAR

growth_protocol: Cells were maintained in RPMI-1640 medium (Nacalai Tesque, Kyoto, Japan) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany).
The library construction and pair-end sequencing were conducted by Novogene. (Beijing, China.)

treatment_protocol: MTX-resistant JAR cells were established by continuous stepwise exposure to increasing concentrations of MTX. Cells were initially cultured in 10 nM MTX, and the concentration was gradually increased over several months.

tag: cell line

value: JAR

value: choriocarcinoma

value: MTX


title: genomic DNA from whole blood sample collected from episodic migraine subject 1 at timepoint T1

description: bisulfite converted DNA from whole blood isolated from episodic migraine subject 1 at timepoint T1

value: whole blood


title: JAR_MTX-resistant_rep2

description: Library name: 5


title: JAR_MTX-resistant_rep1

description: Library name: 4


title: 003-CD3

description:
Library name: DSP-1001660018859-B-A06
003-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 004-CD3

description:
Library name: DSP-1001660018859-B-A08
004-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 002-F4/80

description:
Library name: DSP-1001660018859-B-A05
002-F4/80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 030-CD68 [DSP-1001660009393-B-H12]

description:
Library name: DSP-1001660009393-B-H12
TB
NanoString GeoMx Digital Spatial Profiling (DSP)

data_processing:
DSP sequencing data were processed with the GeoMx NGS Pipeline (DND). After sequencing, reads were trimmed, merged, and aligned to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicates and duplicate reads, thus converting reads into digital counts. The limit of quantitation (LOQ) was estimated as following: the geometric mean reads of the negative control probes plus 2 geometric standard deviations of the negative control probes. Targets that consistently fell below the LOQ were removed, and the datasets were normalized using upper quartile (Q3) normalization. Differentially expressed genes of each disease group were identified using Wald statistics test, with |fold change| > 1.5 and Benjamini–Hochberg (BH)-adjusted P-value < 0.05 as compared to HC group.
Assembly: GRCh38.p13
Supplementary files format and content: xlsx


title: 001-F4_80

description:
Library name: DSP-1001660018859-B-A03
001-F4_80
NanoString GeoMx Digital Spatial Profiling (DSP)


title: 002-CD3

description:
Library name: DSP-1001660018859-B-A04
002-CD3
NanoString GeoMx Digital Spatial Profiling (DSP)


title: Control

description:
Library name: DSP-1001660018859-B-A01
Control
NanoString GeoMx Digital Spatial Profiling (DSP)

value: Control


title: 029-CD68 [DSP-1001660009393-B-H10]

description:
Library name: DSP-1001660009393-B-H10
TB
NanoString GeoMx Digital Spatial Profiling (DSP)


title: JAR_rep1

description: Library name: 1

value: No treatment


title: JAR_rep3

description: Library name: 3