title: Subject P155 (P155-T1F)


title: Subject P154 (P154-T1F)

status: Public on Aug 06 2026

type: protein

city: Stanford

first: Paul

middle: Joseph

last: Utz

state: California

address: 269 Campus Dr

country: USA

institute: Stanford University School of Medicine

description:
reason for sample removal: NA
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.
Luminex™ FLEXMAP 3D™

hyb_protocol: A fluorescent secondary antibody was added to a PBS solution containing conjugated beads bound to antibodies.

scan_protocol: A Luminex FlexMAP 3D instrument was used to quantify autoantibody levels in each sample by measuring fluorescence (in MFI) from each barcoded bead.

data_processing: See methods section for detailed description. MFI values for unconjugated beads were subtracted from MFI values for antigen conjugated bead IDs, with MFI averages calculated after background subtraction.

label: R-PE conjugated goat anti-human IgG secondary antibody

molecule: protein

organism: Homo sapiens

source_name: Serum/Plasma

label_protocol: Secondary antibody with a conjugated fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.

extract_protocol: Blood was collected from patients and healthy controls. Blood was then processed into serum or plasma.

tag: tissue

value: Serum/Plasma

tag: condition

value: Patient


title: LCA1.DMSO.PC.2f

type: SRA

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description:
Library name: LCA1.DMSO.PC.2f
transcriptome of DMSO treated LCA retinal organoid

library_source: transcriptomic

data_processing:
Illumina bulk RNAseq reads were quality checked and aligned to Ensembl reference transcriptomes of Homo sapiens (version 115) for control and treated samples of patient derived retinal organoids (CEP290-LCA). Analysis pipeline has been described previously (Song, et al. 2025). Briefly, transcriptome alignments were performed with Kallisto and processed with the R package tximport, before differential expression analysis with edgeR and limma.
Differentially expressed genes (DEG) were identified by setting a p-value filter of 0.05 and selecting the top 500 over and under expressing genes with at least 1.2-fold change. DEGs were mapped to KEGG pathways using gProfiler and filtered to identify pathways that had minimum 3 DEG mappings and at least 5% of the pathway impacted by differential genes.
Assembly: GRCh38.p14/ENSv115
Supplementary files format and content: Comma-delimited text files containing transcript level counts, gene level counts, normalized gene level counts-per-million results, or diffierential expressed gene results.

molecule: polyA RNA

source_name: Retinal organoid

growth_protocol: Human induced pluripotent stem cell (iPSC) lines were generated from fibroblasts obtained from a familial control individual and an LCA10 patient (designated LCA-1), derived from skin biopsy samples. Reprogramming was performed using a non-integrating Sendai virus system at the iPSC Core Facility of the National Heart, Lung, and Blood Institute, following established protocol. Retinal organoids were generated from human iPSC using a modified differentiation protocol as previously described (Kelley, et al. 2020). Briefly, small cell aggregates obtained from one well of a six-well plate were resuspended in mTeSRTM1 basal medium supplemented with 10 μM Y-27632 (Tocris) and transferred onto a 10cm hESC-qualified Matrigel-coated dish to initiate differentiation. From day 0 to day 3 (D0-D3), cultures were maintained in neural induction medium (NIM) (DMEM/F-12 (1:1)) (ThermoFisher Scientific), supplemented with 1x N2, 1x NEAA, and 5mM Nicotinamide. At D4, the medium was fully replaced with NIM (Regent, et al. 2022). Beginning at D10, cultures were transitioned to retinal induction medium (RIM) consisting of DMEM/F-12 supplemented with 1x B27 without Vitamin A (ThermoFisher Scientific), 1% antibiotic-antimycotic solution (ThermoFisher Scientific), 1% GlutaMAX and 1x NEAA with daily media changes until D17. At D17, adherent cells were mechanically lifted and transferred as small clusters (<5 mm2) into 90mm suspension culture dishes (SUMITOMO BAKELITE CO, Ltd). Floating aggregates were subsequently cultured in RIM supplemented with IGF1 (ThermoFisher Scientific) until D41. From D42 to D62, the medium was further supplemented with 10% fetal bovine serum, 20ng/ml IGF-1, and 1 mM taurine (Sigma). Between D63 and D91, 1 μM 9-cis retinal was added at each media change. After D91, the concentration of 9-cis retinal was adjusted to 0.5 μM and maintained until the completion of differentiation. Following the transition to suspension culture, a partial media change was carried out every 2–3 days. At each step, media were freshly supplemented with IGF-1, taurine, and 9-cis retinal under dim light.

extract_protocol:
Total RNA was isolated from homogenized retinal organoids using RNeasy Mini Kit (QIAGEN), following the manufacturer’s instructions. RNA quality was evaluated using the TapeStation system (Agilent), and only samples with high quality (RNA RIN ≥9) were used for the downstream applications.
For library preparation, 100 ng of total RNA was used to generate  strand-specific mRNA sequencing libraries using the TruSeq stranded RNA Kit (Illumina).

treatment_protocol: Details of treatment can be found in the accompanying manuscript.

value: Retinal organoid

tag: group

tag: donor

value: PEN1B (Patient)

tag: treatment

value: DMSO


title: SJRHB013759_C10_DYE2108

city: Memphis

first: Michael

last: Dyer

state: TN

address: 262 Danny Thomas

institute: St. Jude Children's Research Hospital

description: Library name: SJRHB013759_C10

library_source: transcriptomic single cell

data_processing:
Single-cell (scRNA-seq) and single-nucleus (snRNA-seq) RNA sequencing data were generated from patient tumors, patient-derived xenografts (PDXs), and in vitro culture models (2D, 3D, and Cancer Cell Line Factory [CCLF]) representing multiple pediatric solid tumor types. Analyses were conducted using consistent methodological principles within an evolving computational framework. Although individual datasets were processed with slightly different versions of analytical tools, all followed a unified workflow for alignment, quality control, normalization, integration, and downstream analysis as described below.
Raw sequencing reads in FASTQ format were first assessed for quality using FASTQC (v0.11.5). Alignment and gene quantification were performed using Cell Ranger (v7.0.0 or v8.0.1, 10x Genomics) against the appropriate genome references. Patient samples were aligned to the human GRCh38 reference genome, whereas xenograft and mixed-origin datasets (PDX, 3D) were aligned to a dual human–mouse reference (GRCh38 + mm10 or GRCh38 + GRCm39). In all cases, intronic reads were included during counting to enhance transcript detection sensitivity. For rhabdomyosarcoma samples, the cell count parameter in Cell Ranger was fixed at 10,000 to mitigate barcode overestimation.
Comprehensive quality control (QC) filtering was applied to remove debris, damaged cells, multiplets, and nonhuman contaminants. Cells were excluded based on a combination of criteria, including the number of detected genes, total UMI counts, and the proportion of mitochondrial reads. Typical thresholds included the retention of cells with at least 100–1,000 detected genes and ≥500 UMIs, and exclusion of cells with >5–25% mitochondrial transcripts, depending on dataset type (≤10% for most scRNA-seq, ≤1% for snRNA-seq). For select samples, Outlier cells exceeding three median absolute deviations (MADs) from the median number of detected genes or UMIs were also removed.For select samples, doublets were detected and filtered using demuxafy (PMID 38622708) and Seurat-based outlier identification. In xenograft and culture samples, potential mouse contamination was addressed by removing barcodes showing predominant alignment to the mouse genome. For select tumor datasets, background ambient RNA contamination was further reduced using CellBender (v0.2.0) (PMID 37550580).
Quality-controlled gene expression matrices were processed using Seurat (v4.4.0 or v5.0; Hao et al., 2021). Data were normalized using the NormalizeData() function (log-normalization with a scale factor of 10,000) and scaled via linear regression to account for differences in sequencing depth and mitochondrial content. Highly variable genes (typically 2,000–3,000 per dataset) were identified for downstream analysis. Dimensionality reduction was performed using principal component analysis (PCA), with the top 30 principal components retained for nonlinear projection via Uniform Manifold Approximation and Projection (UMAP). Graph-based clustering was implemented using the Leiden algorithm (Traag et al., 2019) through Seurat’s FindClusters() function at resolutions between 0.1 and 0.4.
To integrate datasets across experimental models, replicates, and biological conditions, multiple batch-correction frameworks were employed, including Harmony (Korsunsky et al., 2019), Reciprocal PCA (RPCA) (Stuart et al., 2019), fastMNN (Haghverdi et al., 2018), and scVI (Lopez et al., 2018). The choice of integration method was dataset-dependent and guided by visual inspection of inter-sample mixing and Local Inverse Simpson’s Index (LISI) metrics (Korsunsky et al., 2019). All integrated datasets were subsequently clustered and analyzed uniformly.
Automated annotation was performed using SingleR (Aran et al., 2019) by comparison with the Human Cell Atlas and the Database of Immune Cell Expression (DICE). Clusters identified as immune populations or doublets were excluded prior to reintegration. For select datasets, copy-number variation (CNV) inference was carried out using inferCNV (https://github.com/broadinstitute/inferCNV/wiki), supplemented by Numbat for single-nucleus variant calling (PMID 36163550). In some analyses, cell cycle scores were computed using Seurat’s CellCycleScoring() function to quantify the proportion of S- and G2/M-phase genes. Differential gene expression analysis was performed using Seurat’s FindMarkers() function (Wilcoxon rank-sum test) with thresholds of log₂ fold change ≥ 0.25, a minimum expression frequency of 0.1, and adjusted p < 0.01.Additionally, cells were annotated using known gene expression profiles from a reference dataset (Patel et al., 2022) using scRNA-seq reference label transfer method, FindTransferAnchors(), from Seurat, enabling the classification of cells in query datasets at specified clustering resolution.
For multi-tumor cohorts (Ewing sarcoma, neuroblastoma, osteosarcoma, and rhabdomyosarcoma), analyses were executed using the Snap workflow (https://github.com/stjude-dnb-binfcore/sc-rna-seq-snap), a containerized and reproducible pipeline maintained by the St. Jude Bioinformatics Core. All dependencies were configured for R v4.4.0 and Seurat v4.4.0, ensuring full computational reproducibility (see GitHub repository for versioning reports). Each cohort was subdivided into three analytical groups: 1. Dual-genome cohort (PDX and 3D samples): aligned to GRCh38 + GRCm39 and filtered for low-quality and mouse-derived cells. 2. Human-genome cohort (patient, 2D, CCLF samples): aligned to GRCh38 and processed using identical QC parameters. 3. Integrated cohort: merged from the two above and analyzed jointly after Harmony-based integration. Cells with fewer than 500 UMIs, fewer than 300–1,000 genes (depending on tumor type), or >10% mitochondrial reads were removed prior to normalization and scaling. Highly variable features (n = 3,000) were used for PCA, followed by clustering with Leiden at resolution 0.1. Marker genes were identified per cluster, and top-ranked genes were examined for biological interpretability.
Interactive visualization and exploratory analysis were facilitated using ShinyCell (v2.1.0) (Ouyang et al., 2021). Processed datasets and interactive R Shiny applications are available through institutional repositories and project-specific GitHub resources (URLs to be provided upon publication).
Assembly: hg38
Supplementary files format and content: barcodes, matrix, features

molecule: total RNA

source_name: cells

growth_protocol: Cells dissociated from O-PDX tumors were seeded onto PrimeSurface 96-well low-adhesion U-bottom plates at 25,000-50,000 cells/well (S-Bio, MS-9096UZ). Plates were centrifuged at 300xg for 3 minutes to aggregate the cells in each well. After 5-7 days, organoids had formed and were transferred to 0.5% geltrex- (Thermo, A14133-02) coated 10cm standard tissue culture plates. Cells that migrate from the organoid were considered a 2D culture and referred to as passage 0. Additional organoids were collected for downstream applications and cryopreserved in 90% FBS and 10% DMSO. After 7-10 days, 2D cells were passaged to fresh geltrex-coated 10cm dishes for 5-7 days and harvested for downstream molecular assays and cryopreserved stocks.

extract_protocol:
Extract protocol: To dissociate organoids into single-cell suspension 40U papain was added to 400uL of papain buffer(1mM L-cystein, 0.5mM EDTA in PBS -/-) and incubated at 37°C for ~5 min. The organoids were added and incubating at 37°C for ~5 min with occasional flicking until the organoid dissociated to the point of floating. 40uL of DNase was added and the dissociated cells were incubated at 37 °C for an additional 5 min. The cell suspension was filtered with a 40-μm mesh cell strainer and washed with 2mL PBS−/−. The filtered cells were slowly added to a 5 ml BSA cushion medium (4% BSA in Retinal Explant media) and spun at 500g for 10 min at 4 °C to separate the cells from the debris. The supernatant was removed and resuspend the cell pellet in 400 μl of explant culture medium. To generate single-nucleus suspensions from flash-frozen tissue frozen fragments were manually dissociated using Noyes spring scissors in 1 mL TST buffer (73 mM sodium chloride, 5 mM Tris [pH 8.0], 0.5 mM calcium chloride, 10.5 mM magnesium chloride, 0.01% bovine serum albumin, 0.03% Tween-20). Nuclear suspensions were filtered through a 40 μm strainer and diluted with an additional 1 mL TST buffer and 3 mL ST buffer (73 mM sodium chloride, 5 mM Tris [pH 8.0], 0.5 mM calcium chloride, 10.5 mM magnesium chloride) and centrifuged at 500xg at 4°C for 5 min. The nuclear pellet was resuspended in ST buffer and filtered through a 40 μm strainer to generate single-nuclear suspensions for snRNA-seq. To generate single-cell suspensions from fresh tissue, samples were rinsed with PBS -/-, minced with a scalpel, and processed using the Papain Dissociation System (Worthington). The tumors were incubated in 5 mL papain-DNase I solution at 37°C for 15-30 min, filtered through a 40 μm strainer, and centrifuged at 500 x g for 5 min. The cell pellets were then resuspended in 3.1 mL resuspension buffer (2.7 mL Earle’s buffered saline solution, 300 μL albumin-ovomucoid inhibitor, 150 μL DNase I) and layered over 5 mL albumin-ovomucoid inhibitor cushion and centrifuged at 100xg for 6 min. The pellet was resuspended in PBS and filtered through a 40 μm strainer.
Single cell RNA sequencing and library preparation was preformed using the 10X genomics 3’ gene expression kits.

value: cells

tag: disease

value: RMS

tag: cell type

tag: batch


title: SJNBL012407_C1_DYE4089

description: Library name: SJNBL012407_C1

value: NBL


title: Subject P136 (P136-T2F)


title: Subject P150 (P150-T1F)


title: WT2head, exercised, 5 dpf, rep3

city: wuhan

first: guihua

last: wang

address: hubei

country: China

institute: Huazhong University of Science and Technology

description: Library name: WT2

data_processing:
Pathway analyses, specifically Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and Gene Ontology (GO) enrichment analyses were performed using DAVID
Assembly: GRCz11
Supplementary files format and content: To measure gene expression, HT-seq-count (intersection-strict mode) was used for mapping reads. Differentially expressed mRNAs were identified using DESeq2, applying a cut-off value of FC≥2 and adjusted P-value of ≤0.05

organism: Danio rerio

source_name: head

extract_protocol:
We conducted RNA-seq analysis using three biological replicates for both WT and pnkp-/- zebrafish. For each replicate, 30 fishes each replicate (5 dpf larvae) was dissected. The tail tissue was used for genotyping, and the heads of homozygote mutant were selected for RNA extraction. Total RNA of WT and pnkp-/- zebrafish heads was isolated and subsequently used for cDNA synthesis. Illumina sequencing, with library construction from Novogene (China), was used for the RNA-seq process.
The RNA-seq data were mapped to the zebrafish GRCz11 genome using the Hisat2 v2.0.4 software. To measure gene expression, HT-seq-count (intersection-strict mode) was used for mapping reads. Differentially expressed mRNAs were identified using DESeq2, applying a cut-off value of FC≥2 and adjusted P-value of ≤0.05.

value: head


title: LCA1.HAL.PA.8e

description:
Library name: LCA1.HAL.PA.8e
transcriptome of HAL treated LCA retinal organoid

value: HAL


title: Subject P140 (P140-T2F)


title: LCA1.DMSO.PC.1f

description:
Library name: LCA1.DMSO.PC.1f
transcriptome of DMSO treated control retinal organoids


title: Subject P136 (P136-T1F)


title: WT1head, exercised, 5 dpf, rep3

description: Library name: WT1


title: WT3head, exercised, 5 dpf, rep3

description: Library name: WT3


title: Subject P129 (P129-T2F)


title: Control.DMSO.PB.1b

description:
Library name: Control.DMSO.PB.1b
transcriptome of DMSO treated control retinal organoids

value: PEN8E (Control)


title: Subject P137 (P137-T1F)


title: Subject P119 (P119-T2F)


title: day5itapre1

city: XIAMEN

first: Peida

last: Yang

state: 福建

address: XIAMEN UNIVERSITY

institute: XIAMEN UNIVERSITY

description: Library name: Z116

data_processing:
Program:featureCounts v2.0.3; Command:"featureCounts" "-a" "GCF_017639785.1_BCM_Maur_2.0_genomic.gtf" "-o" "output.txt" "-t" "exon" "-g" "gene_id" "-p" "-B" "-C" "--largestOverlap" "--fracOverlap" "0.5"
Assembly: GCF_017639785.1(BCM_Maur_2.0)
Supplementary files format and content: txt files includes counts for each sample

organism: Mesocricetus auratus

source_name: Pre-exposure intranasal ITA prophylaxis group at 5 dpi lung tissue

extract_protocol:
lung tissue was homogenized and RNA extraction was performed using the QIAamp Viral RNA Mini Kit (Qia-gen) following the manufqcturer’s instructions. The RNA samples were then sent to Shanghai OE Biotechnology Co., Ltd. for sequencing.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufqcturer's protocols.

value: Lung


title: Subject P142 (P142-T1F)


title: Recovered skin CD4⁺ T cells (HFD) — snATAC-seq, replicate 1

city: San Francisco

first: Sagar

last: Bapat

state: CA

address: 513 Parnassus Ave

institute: UCSF

description:
Library name: HFD_CD4_snATAC_recovered_RUN3
Single-nucleus ATAC sequencing of FACS-isolated CD4⁺ T cells from ear skin following recovery from IMQ-induced inflammation in mice fed a high-fat diet.

library_source: genomic

data_processing:
Raw FASTQ files were processed using the Cell Ranger ATAC (10x Genomics) “atac count” pipeline.
Reads were aligned to the mouse reference genome (GRCm39) to generate fragment files and filtered peak-barcode matrices.
Quality control metrics including fragment size distribution, transcription start site (TSS) enrichment, and number of fragments per cell were evaluated.
Downstream analysis was performed using ArchR (v1.0.3). Arrow files were generated from fragment files using high-quality barcodes passing Cell Ranger filtering.
Peak calling was performed using addGroupCoverages and addReproduciblePeakSet functions (MACS2-based). Dimensionality reduction was performed using iterative LSI, followed by clustering and UMAP visualization. Differentially accessible regions (DARs) were identified using ArchR marker testing with FDR < 0.05.
Assembly: GRCm39 (mouse)
Supplementary files format and content: Processed data include fragment files (.tsv.gz) containing genomic coordinates and cell barcode assignments; peak coordinate files (.bed) representing reproducible accessible chromatin regions; and peak-by-cell accessibility matrices (HDF5 format, filtered_peak_bc_matrix.h5) containing quantitative accessibility counts for each peak across individual nuclei.
Supplementary files format and content: ArchR Arrow files (HDF5 format) contain integrated chromatin accessibility data, quality control metrics, dimensionality reduction embeddings, cluster annotations, and accessibility matrices used for downstream analysis and visualization.

molecule: genomic DNA

organism: Mus musculus

source_name: ear skin

growth_protocol: Mice (wild-type C57BL/6J) were maintained under specific pathogen-free conditions with ad libitum access to food and water. Animals were housed under standard 12-hour light/dark cycles.

extract_protocol:
Ear skin was harvested and mechanically and enzymatically dissociated into single-cell suspensions. CD4-positive T cells were isolated by fluorescence-activated cell sorting (FACS). Nuclei were subsequently isolated from sorted CD4-positive T cells according to the 10x Genomics Chromium Single Cell ATAC v2 protocol.
Single-nucleus ATAC libraries were generated using the Chromium Single Cell ATAC v2 kit (10x Genomics) following the manufacturer’s instructions. Briefly, isolated nuclei were transposed using Tn5 transposase, barcoded through droplet-based partitioning on the Chromium Controller, and amplified to generate sequencing libraries. Libraries were sequenced on an Illumina NovaSeq X platform to produce paired-end reads.

treatment_protocol: Mice were fed either low-fat diet (10% kcal fat) or high-fat diet (60% kcal fat) during topical imiquimod (IMQ)-induced psoriasiform inflammation. After resolution of inflammation, ear skin tissue was collected during the recovery phase for downstream analysis.

value: ear skin

value: CD4-positive T cells

tag: genotype

value: wild type C57BL/6J

value: high-fat diet (60% kcal fat) during IMQ treatment; recovered after inflammation


title: Recovered skin CD4⁺ T cells (LFD) — snATAC-seq

description:
Library name: LFD_CD4_snATAC_recovered_RUN3
Single-nucleus ATAC sequencing of FACS-isolated CD4⁺ T cells from ear skin following recovery from IMQ-induced inflammation in mice fed a low-fat diet.

value: Low-fat diet (10% kcal fat) during IMQ treatment; recovered after inflammation


title: Subject P133 (P133-T2F)

value: Serum/Plasma


title: Control.DMSO.PA.3b

description:
Library name: Control.DMSO.PA.3b
transcriptome of DMSO treated control retinal organoids


title: Subject P111 (P111-T3F)

value: Patient


title: Subject P133 (P133-T1F)


title: Multiplexed CD45+ immune cells from LFD- and HFD-fed mice (IMQ day 6)

description:
Library name: CD45_Flex_multiplexed_LFD_HFD
CD45+ immune cells from LFD- and HFD-fed mice were multiplexed into a single Chromium Single Cell 3′ Fixed RNA Profiling (Flex) library (10x Genomics). The pooled library was sequenced across two lanes. Demultiplexing of LFD and HFD samples was performed using Cell Ranger multi with probe barcode reference (SagarProbes.csv). Separate filtered gene-barcode matrices were generated for LFD and HFD samples using the GRCm39 reference genome.

data_processing:
Raw FASTQ files were processed using the Cell Ranger multi pipeline (10x Genomics).
Reads were aligned to the Mus musculus reference genome (GRCm39), and gene expression matrices were generated for each demultiplexed condition (LFD and HFD).
Filtered feature-barcode matrices were generated using Cell Ranger default quality control parameters.
Downstream quality control and clustering analyses were performed using Scanpy. Low-quality cells (fewer than 200 detected genes) and genes expressed in fewer than three cells were removed. Doublets were identified and removed computationally.
Data were normalized and log-transformed prior to clustering using the Leiden algorithm and visualization by UMAP. Differential gene expression analysis was performed using rank-based statistical testing.
Assembly: GRCm39
Supplementary files format and content: Processed data consist of filtered gene-by-cell count matrices in HDF5 (.h5) format generated by Cell Ranger. Separate matrices are provided for LFD and HFD samples demultiplexed from the same multiplexed Flex library.

growth_protocol: C57BL/6J mice were maintained under specific pathogen-free conditions with ad libitum access to food and water. Mice were fed either low-fat diet (10% kcal fat) or high-fat diet (60% kcal fat) for 1 week prior to and during induction of psoriasis inflammation.

extract_protocol:
Lesional ear skin was enzymatically digested into single-cell suspensions using collagenase and DNase. Live CD45⁺ immune cells were isolated by fluorescence-activated cell sorting (FACS) prior to single-cell library preparation.
Single-cell gene expression libraries were generated using the Chromium Single Cell 3′ Fixed RNA Profiling (Flex) platform (10x Genomics) according to the manufacturer’s instructions. Fixed single-cell suspensions were processed using the Chromium Controller to generate barcoded gel bead-in-emulsions, followed by reverse transcription and library construction per the 10x Genomics Flex protocol. LFD and HFD samples were multiplexed into a single Flex library using probe-based sample indexing. Libraries were sequenced on an Illumina NovaSeq X platform to generate paired-end reads.

treatment_protocol: Psoriasiform skin inflammation was induced by topical application of 5% imiquimod (IMQ) cream to the ear daily for 6 consecutive days. On day 6 of treatment, lesional ear skin was harvested for analysis.

value: CD45+ immune cells

value: Low-fat diet (10% kcal fat) or high-fat diet (60% kcal fat) for 1 week; topical 5% imiquimod for 6 days

value: Single multiplexed 10x Chromium Flex library


title: Subject P119 (P119-T1F)


title: Subject P131 (P131-T1F)


title: epiBmpr1aKO uninfected 2

city: Berlin

last: Sigal

address: Augustenburger Platz 1

department: Dept. Hepatology and Gastroenterology

country: Germany

institute: Charité Universitätsmedizin

description: Library name: A5313_SP258_036_44

data_processing:
Raw sequencing data was processed using 10x Genomics CellRanger v9.0.1 software, using genome reference GRCm39-2024-A and Chromium Mouse Transcriptome Probe Set v1.1.1.
Assembly: GRCm39
Supplementary files format and content: Raw sequences in FASTQ (R1,R2) and filtered count matrices as generated by CellRanger.

source_name: Stomach antrum

extract_protocol:
Cells were obtained from antral gastric glands for the Bmpr1a-KO mouse and from both antrum and corpus for the H.py infection experiment. Once gastric glands were isolated, samples were treated with TrypLE at 37 °C for 8 minutes, in order to obtain a single-cell suspension. Stromal and epithelial cells were sorted independently and combined later on. Cells were further processed with Chromium Fixed RNA Profiling kits (10x Genomics) according to the manufacturer’s instructions. For each condition, two biological replicates were analyzed.
Libraries were constructed using Single Cell 3' Library & Gel Bead Kit v3 and the A Chip Kit (10x genomics) according to the manufacturer's instructions. Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).

value: Stomach antrum

value: Axin2CreErt2-Bmpr1afl/fl KO


title: Control.DMSO.PA.2b

description:
Library name: Control.DMSO.PA.2b
transcriptome of DMSO treated control retinal organoids

value: Retinal organoid

value: DMSO


title: Control.DMSO.PA.3c

description:
Library name: Control.DMSO.PA.3c
transcriptome of DMSO treated control retinal organoids


title: Subject P100 (P100-T3F)


title: Control.DMSO.PB.1a

description:
Library name: Control.DMSO.PB.1a
transcriptome of DMSO treated control retinal organoids


title: Subject P124 (P124-T2F)


title: Mock, 30 min rep 1

city: University Park

first: Grace

last: Schmidt

state: PA

address: 323 AVBS Bldg

institute: Penn State University

description: Library name: Sample B1

data_processing:
). Read quality was assessed with FastQC (v0.12.1), and adaptor trimming was performed using Trim Galore (v0.6.10). Reads were aligned to the bGalGal1.mat.broiler.GRCg7b reference genome using STAR (v2.7.11b). Gene-level counts were extracted with HTSeq (v2.0.5) and analyzed in R using edgeR (v3.40.2). Counts were normalized using the TMM method, and low-expression genes were filtered by CPM thresholds.
Assembly: bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: tab delimited .txt files contains raw counts for each sample

organism: Gallus gallus

growth_protocol: Cells were cultured at 25* C in DMEM supplemented with 10% FBS and 1% antibiotic-antimycotic at 5% atmospheric CO2

extract_protocol:
Total RNA was extracted using the Direct-Zol RNA miniprep kit by Zymo
Directional mRNA library preparation (poly A enrichment) was done by Novogene

tag: cell line

value: Embryonic fibroblast

value: Wildtype

tag: time

value: 30 min


title: epiBmpr1aWT uninfected 2

description: Library name: A5313_SP258_036_40

value: Axin2CreErt2-Bmpr1afl/fl WT


title: Subject P116 (P116-T2F)


title: epiBmpr1aKO uninfected 1

description: Library name: A5313_SP258_036_39


title: epiBmpr1aWT uninfected 1

description: Library name: A5313_SP258_036_38


title: 11_1094-3 P2_1

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib100967

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
The FASTQs were aligned to the University of California Santa Cruz (UCSC) Human genome assembly version 19, using STAR v.2.4.2a and gene counts were generated using HTSeq-count (v0.4.1) (57, 58). Quality metrics were compiled from PICARD (v1.134FASTQC (v0.11.3) Samtools (v1.2)8, and HTSeq-count.
Assembly: Homo sapiens GRCh38.77 (version 77)
Supplementary files format and content: Gene count matrix with genes in columns and samples in rows

source_name: airway epithelial cells

extract_protocol:
Airway epithelial cells  were cultured in room air or hyperoxia conditions
We generated full-length cDNA from total RNA (0.5 ng). We amplified cDNA using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) and constructed sequencing libraries using the NexteraXT DNA Library prep kit (Illumina).

value: airway epithelial cells

tag: Sex

value: female

tag: donorid

tag: collection timepoint

tag: studygroup

value: BPD


title: 10_1094-2 P2 O2 48h_2

description: Library name: lib100966

value: O2 48 hours


title: Subject P102 (P102-T2F)

value: Serum/Plasma


title: Subject P114 (P114-T3F)

value: Patient


title: Subject P093 (P093-T2F)


title: Stromal IL1r1 WT Hpy 2m inf 2

description: Library name: A5313_SP258_036_Il1r1WT-2

source_name: Stomach corpus and antrum

value: Stomach corpus and antrum

value: Col1a2CreErt2-Il1r1fl/fl WT

value: 2m infection with H.pylori


title: 12_1094-3 P2_2

description: Library name: lib100968


title: Subject P091 (P091-T2F)


title: 9_1094-2 P2 O2 48h_1

description: Library name: lib100965


title: Subject P086 (P086-T1F)


title: Subject P113 (P113-T2F)


title: Subject P100 (P100-T2F)


title: 7_1094-2 P2 O2 24h_1

description: Library name: lib100963

value: O2 24 hours


title: Subject P079 (P079-T1F)


title: 6_1094-2 P2 RA_2

description: Library name: lib100962

value: room air


title: 8_1094-2 P2 O2 24h_2

description: Library name: lib100964


title: Stromal IL1r1 WT uninfected 2

description: Library name: A5313_SP258_036_73WT

value: uninfected


title: Stromal IL1r1 WT Hpy 2m inf 1

description: Library name: A5313_SP258_036_Il1r1WT-1


title: Subject P084 (P084-T1F)


title: Subject P070 (P070-T1F)


title: Subject P086 (P086-T2F)


title: Stromal IL1r1 WT uninfected  1

description: Library name: A5313_SP258_036_14_WT


title: Subject P082 (P082-T1F)


title: Lesional skin CD4+ T cells from HFD-fed mice (reaction 2)

description: Library name: HFD2

data_processing:
Raw fastq files were mapped to the mouse transcriptome (UCSC mm10) using PIPseeker68 (Fluent BioSciences, version 3.2) pipeline that performs barcode whitelisting, alignment with STAR, molecular index correction, and generates barcode-feature counts matrices. After alignment and sensitivity calling (sensitivity_5 was chosen for all three samples), 2103 cells were recovered from the LFD condition and 5232 (HFD1 and HFD2 two reactions combined) were recovered from the HFD condition. After QC filtering (doublets and non-CD4+ T cell contamination), 1769 CD4+ T cells remained in the LFD condition, and 4450 CD4+ T cells remained in the HFD condition (HFD1 and HFD2 two reactions combined), with over 1,500 median genes per cell. Seurat69 (version 5.1.0) was used for downstream analysis. The filtered expression matrices for LFD, HFD1, and HFD2 samples were loaded and processed to create Seurat objects for each condition. The HFD1 and HFD2 datasets were merged into a single HFD Seurat object, which was subsequently merged with the LFD dataset. The combined dataset was then normalized using the NormalizeData function with default settings. Variable features were identified using the “vst” method with 2,000 features. Data scaling was performed using ScaleData, followed by principal component analysis (PCA) using the top 2,000 variable features. To correct for batch effects between the different conditions, Harmony70 (version 1.2.0) was applied on the PCA embeddings, using the condition labels (LFD, HFD1, HFD2) as a covariate. Batch-corrected embeddings were used for downstream analyses, including clustering and visualization. Clustering was performed by constructing a shared nearest neighbor (SNN) graph using the FindNeighbors function on the Harmony-corrected embeddings, followed by clustering using the FindClusters function with a resolution of 0.5. Uniform Manifold Approximation and Projection (UMAP) was used for visualization of the clusters, based on the Harmony embeddings. For downstream analysis, clusters identified as potential contaminations (clusters 9 and 10, likely monocytes and skin regulatory cell types) were removed, and clustering was redone. Differential expression analysis was conducted using the FindAllMarkers function with the following parameters: only positive markers (only.pos = TRUE), minimum fraction of cells expressing a gene (min.pct = 0.25), and a log fold change threshold of 0.25. The top five markers for each cluster were identified and visualized using a dot plot (DotPlot). To assess TH17 pathogenicity, we calculated a TH17 pathogenicity score based on published gene signatures associated with pathogenic TH17 cells38,39. Gene sets from both studies, comprising key regulators and effector genes that define pathogenic TH17 cells, were curated and used to evaluate the pathogenic potential of TH17 cells in our dataset. We first identified the genes present in our single-cell RNA-seq dataset that overlapped with the published pathogenic TH17 gene sets. Using the AddModuleScore function in Seurat, we calculated the TH17 pathogenicity score for each cell in the TH17 cluster.
Assembly: UCSC Mouse  mm10
Supplementary files format and content: Tab-separated value files. Features, barcodes. and matrix files

source_name: Ear skin

extract_protocol:
4 μL cell suspension (5000 cells max) with 20 units of RNase inhibitor was added to each PIP tube reaction, followed by vortexing to generate single bead to cell emulsion
We performed 16 cycles of PCR for cDNA amplification after cDNA synthesis, and 25% of each cDNA sample was carried into transcriptome library preparation. PIPseq T2 3ʹ Single Cell gene expression libraries were subject to standard Illumina paired-end sequencing targeting 20,000 reads per input cell using NovaSeq X.

value: Ear skin

value: CD4+ T cells

value: WT

value: IMQ


title: 5_1094-2 P2 RA_1

description: Library name: lib100961


title: Subject P070 (P070-T2F)


title: Subject P069 (P069-T3F)


title: Subject P085 (P085-T1F)


title: Subject P074 (P074-T2F)


title: Subject P074 (P074-T1F)


title: 3_1093-2 P1 O2 24h_1

description: Library name: lib100959

value: male


title: Subject P078 (P078-T1F)


title: Subject P069 (P069-T1F)


title: 4_1093-2 P1 O2 24h_2

description: Library name: lib100960

value: airway epithelial cells


title: Lesional skin CD4+ T cells from HFD-fed mice (reaction 1)

description: Library name: HFD1


title: Lesional skin CD4+ T cells from LFD-fed mice

description: Library name: LFD


title: 2_1093-2 P1 RA_2

description: Library name: lib100958


title: Subject P062 (P062-T1F)


title: 1108-3 #1 P2 O2-96h

description: Library name: lib109743

extract_protocol:
Airway epithelial cells from airway brushings pediatric patients  were cultured in room air or hyperoxia conditions
We generated full-length cDNA from total RNA (0.5 ng). We amplified cDNA using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) and constructed sequencing libraries using the NexteraXT DNA Library prep kit (Illumina).


title: Subject P046 (P046-T1F)


title: E.coli RNA-seq extracted from a microfluidic device, replicate 4

city: Wurzburg

first: Elise

last: Bornet

address: Josef-Schneider Strasse 2

institute: Helmholtz Insitute

description: Library name: EC_4_MF

data_processing:
Sequence reads were trimmed for Nextera adapter and MATQ-Seq primers using bbmap. bbduk.sh -Xmx10g t=20
Trimmed reads were then mapped to the reference genome using bowtie2 version 2.3.4.1. bowtie2 -p 30
features were assigned using featureCounts.
Read counts extraction was performed using feature counts version 2.0.1
Assembly: GCF_000011065.1 for Bacteroides thetaiotaomicron and GCF_904425475.1 for E.coli
Supplementary files format and content: tab delimited text file contains raw counts for each sample

organism: Escherichia coli

source_name: E. coli MG1655

growth_protocol: Cells were grown in M9 mininal media comlemented with amylopectin

extract_protocol:
RNA was extracted following the MATQ-seq protocol
MATQ-Seq and ribosomal RNA depletion with DASH. Cells were lysed using mechanical sonication and 5U lysozyme per well. cDNA librairies were obtained using the MATQ-Seq reverse transcription protocol. Ribosomal cDNA was depleted from the cDNA librairies using DASH.

treatment_protocol: 100% RNAlater

value: E. coli MG1655

value: Mars-Red

value: fixed in 100% RNAlater


title: E.coli RNA-seq extracted from a microfluidic device, replicate 3

description: Library name: EC_3_MF


title: Subject P052 (P052-T1F)

value: Serum/Plasma


title: Subject P052 (P052-T2F)

value: Patient


title: E.coli RNA-seq extracted from a microfluidic device, replicate 2

description: Library name: EC_2_MF


title: 1_1093-2 P1 RA_1

description: Library name: lib100957

value: BPD


title: Subject P071 (P071-T1F)


title: Subject P061 (P061-T1F)


title: Subject P057 (P057-T1F)


title: Subject P044 (P044-T1F)


title: E.coli RNA-seq extracted from a microfluidic device, replicate 1

description: Library name: EC_1_MF


title: E.coli RNA-seq extracted from liquid culture, replicate 4

description: Library name: EC_4_LC


title: 1108-3 #1 P2 RA

description: Library name: lib109739

value: RA


title: Subject P056 (P056-T2F)


title: 1108-3 #1 P2 O2-72h

description: Library name: lib109741


title: Subject P050 (P050-T1F)


title: E.coli RNA-seq extracted from liquid culture, replicate 3

description: Library name: EC_3_LC


title: 1107-2 #2 P2 O2-72h

description: Library name: lib109740

value: female


title: Subject P054 (P054-T1F)


title: 1107-2 #2 P2 O2-96h

description: Library name: lib109742


title: 1107-2 #2 P2 RA

description: Library name: lib109738


title: E.coli RNA-seq extracted from liquid culture, replicate 1

description: Library name: EC_1_LC


title: Subject P026 (P026-T1F)


title: Subject P053 (P053-T1F)


title: P23H.F.DMSO.31503R

description:
Library name: P23H.F.DMSO.31503R
transcriptome of DMSO treated P23H female retina

data_processing:
Illumina bulk RNAseq reads were quality checked and aligned to Ensembl reference transcriptomes of Rattus norvegicus (version 115) for control and treated samples of Rho P23H/- retinas. Analysis pipeline has been described previously (Song, et al. 2025). Briefly, transcriptome alignments were performed with Kallisto and processed with the R package tximport, before differential expression analysis with edgeR and limma.
Differentially expressed genes (DEG) were identified by setting a p-value filter of 0.05 and selecting the top 500 over and under expressing genes with at least 1.2-fold change. DEGs were mapped to KEGG pathways using gProfiler and filtered to identify pathways that had minimum 3 DEG mappings and at least 5% of the pathway impacted by differential genes.
Assembly: GRCr8/ENSv115
Supplementary files format and content: Comma-delimited text files containing transcript level counts, gene level counts, normalized gene level counts-per-million results, or diffierential expressed gene results.

organism: Rattus norvegicus

source_name: Retina

growth_protocol: Hemizygous P23H-1 rats were generated and previously characterized through in-house breeding at EyeCRO by crossing transgenic P23H line 1 rats with wild-type Long Evans rats obtained from Charles River, in order to model the clinical progression of adRP (Song, et al. 2025). Animals were housed in ventilated cages in groups of 2-3 under controlled 12-hour light/dark cycle, with free access to food and water.

extract_protocol:
Total RNA was isolated from homogenized rat retinas using RNeasy Mini Kit (QIAGEN), following the manufacturer’s instructions. RNA quality was evaluated using the TapeStation system (Agilent), and only samples with high quality (RNA RIN ≥9) were used for the downstream applications.
For library preparation, 100 ng of total RNA was used to generate  strand-specific mRNA sequencing libraries using the TruSeq stranded RNA Kit (Illumina).

treatment_protocol: P23H-1 rats underwent anesthesia via intraperitoneal injection of ketamine (85 mg/kg) and xylazine (4 mg/kg) cocktail, followed by pupillary dilation using standard ophthalmic procedures. Intravitreal injections were carried out under a stereomicroscope to allow precise positioning of the needle. A volume of 5 µL (20-100 μM) was introduced into the vitreous cavity via the pars plana using a 33-gauge needle attached to a Hamilton syringe. Bilateral injections were performed in all animals.

value: Retina

value: F

tag: strain

value: DMSO


title: Subject P030 (P030-T1F)


title: Subject P024 (P024-T1F)


title: Subject P056 (P056-T1F)


title: E.coli RNA-seq extracted from liquid culture, replicate 2

description: Library name: EC_2_LC


title: Subject P032 (P032-T1F)


title: TART3 O2-96h

description: Library name: lib109737

value: control


title: Subject P025 (P025-T1F)


title: TART2 O2-96h

description: Library name: lib109736


title: Subject P048 (P048-T1F)


title: P23H.F.HAL.30725R

description:
Library name: P23H.F.HAL.30725R
transcriptome of HAL treated P23H female retina

value: HAL


title: TART1 O2-96h

description: Library name: lib109735


title: P23H.F.DMSO.31502R

description:
Library name: P23H.F.DMSO.31502R
transcriptome of DMSO treated P23H female retina


title: Subject P042 (P042-T2F)


title: TART3 O2-72h

description: Library name: lib109734


title: P23H.F.HAL.30724R

description:
Library name: P23H.F.HAL.30724R
transcriptome of HAL treated P23H female retina


title: P23H.F.DMSO.31103R

description:
Library name: P23H.F.DMSO.31103R
transcriptome of DMSO treated P23H female retina


title: TART2 O2-72h

description: Library name: lib109733


title: Subject P017 (P017-T1F)

description:
reason for sample removal: NA
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.
Luminex™ FLEXMAP 3D™


title: Subject P016 (P016-T1F)


title: WT.F.NOTREAT.32010L

description:
Library name: WT.F.NOTREAT.32010L
transcriptome of untreated WT female retina

value: SDxLE

value: WT

value: NOTREAT


title: Subject P015 (P015-T3F)


title: Subject P042 (P042-T1F)


title: Subject P039 (P039-T1F)


title: Subject P037 (P037-T1F)


title: Subject P015 (P015-T1F)


title: TART1 O2-72h

description: Library name: lib109732

value: airway epithelial cells


title: Subject P034 (P034-T2F)


title: TART3 RA

description: Library name: lib109731

value: male


title: Subject P011 (P011-T1F)


title: WT.F.NOTREAT.32009L

description:
Library name: WT.F.NOTREAT.32009L
transcriptome of untreated WT female retina


title: Subject P033 (P033-T1F)


title: Subject P029 (P029-T1F)


title: P23H.F.DMSO.30948R

description:
Library name: P23H.F.DMSO.30948R
transcriptome of DMSO treated P23H female retina


title: P23H.F.DMSO.31102R

description:
Library name: P23H.F.DMSO.31102R
transcriptome of DMSO treated P23H female retina


title: TART1 RA

description: Library name: lib109729


title: Subject P010 (P010-T2F)


title: TART2 RA

description: Library name: lib109730


title: Subject P010 (P010-T1F)


title: Subject P021 (P021-T3F)


title: Subject P021 (P021-T1F)


title: Subject P007 (P007-T1F)


title: TART15_5

description: Library name: lib105975

tag: cell morphology

value: AEC


title: TART15_4

description: Library name: lib105974


title: Dicer1f/f, Mock 500uM, 0h chase

city: Irvine

first: Annie

last: Trinh

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: Library name: Dicer1f/f, Mock 500uM 0h chase

data_processing:
For BrdU-labeled samples loaded on R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN114 or FLO-PRO114M) and unlabeled samples loaded on R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-PRO114M), basecalling and alignment to the hg19 human reference genome were performed using Dorado v0.6.2. Chimeric reads were removed using samtools v1.15.1. To identify BrdU-containing reads, DNAscent v4.1.1 was used to detect the nucleoside analog within individual reads. CpG methylation and hydroxymethylation were called using Dorado v0.6.2. Nanoplot v1.41.6 was used to assess and visualize read-level statistics such as the number of reads, read length N50, mean and median read length, and mean and median read quality.
Please note that the raw BAM files are basecalled but unaligned. We chose to submit unaligned BAM files to allow users to align the reads to the reference genome or assembly of their choice. Therefore, they are not aligned to a reference genome, and no genome assembly is associated with these BAM files. The "GRCh37 (hg19)" refers to the reference genome used for our downstream alignment and analysis of the processed data, but it doesn't apply to the uploaded raw BAM files.
Assembly: GRCh37 (hg19)
Supplementary files format and content: Processed data are available in bedMethyl files (.bed) and read-level calls (.tsv).
Supplementary files format and content: The uploaded BED files in the folder are the output of modkit pileup (Oxford Nanopore Technologies), and they are in the UCSC bedMethyl format, which is an extended BED format for base modification data. They retain the standard BED coordinate fields and can be visualized in genome browsers that support bedMethyl tracks, including the UCSC Genome Browser.

source_name: Dicer1f/f mBMMSC

growth_protocol: HUES64 and HUES8 TKO hESCs were cultured on Geltrex (Thermo Fisher Scientific, A1413302) coated tissue culture plates with mTeSR (STEMCELL Technologies) media. Cells were incubated at 37°C with 5% CO2. Media was changed daily and cells were passaged upon reaching 80% confluency using ReleSR (STEMCELL Technologies). H9 hESCs (WiCell) were cultured on tissue culture plates coated with Cultrex Reduced Growth Factor Basement Membrane Extract (R&D Systems, 343301001) in StemFlex medium (Thermo Fisher Scientific, A3349401). Cells were maintained at 37°C with 5% CO2. Medium was changed daily or every other day, and cells were passaged at ~80% confluency using Accutase (Innovative Cell Technologies, AT104). Following passaging, 2µM Thiazovivin (Selleck Chemicals LLC, S1049) was added for 24 h only. MDA-MB-231 breast cancer cells were maintained in DMEM (Gibco) media supplemented with 10% Fetal Bovine Serum (FBS, Seradigm). Cells were incubated at 37°C with 5% CO2. Media was changed every other day and cells were passaged upon reaching 80% confluency using  TrypLE (Gibco). BJ human fibroblasts were expanded in Fibroblast Growth Medium (FGM-2, Lonza Bioscience). Cells were maintained at 37°C with 5% CO₂. Medium was changed every other day, and cells were passaged upon reaching approximately 80% confluency using TrypLE (Gibco). THP-1 cells were maintained in suspension in RPMI 1640 medium (Gibco, A10491-01) supplemented with 10% FBS and 0.1% β-mercaptoethanol. Cells were incubated at 37°C with 5% CO₂ and subcultured by dilution as needed to maintain an appropriate cell density. Human bone marrow-derived mesenchymal stem cells (hBMMSCs, PCS-500-012) were obtained from ATCC and cultured in ATCC Mesenchymal Stem Cell Basal Medium (ATCC, PCS-500-030) plus Mesenchymal Stem Cell Growth Kit (ATCC, PCS-500-041). Cells were maintained at 37°C with 5% CO₂. Medium was changed every other day, and cells were passaged upon reaching approximately 80% confluency using 0.05% Trypsin-EDTA (Gibco). Dicer1-positive mouse bone marrow-derived mesenchymal stem cells (mBMMSC mBMMSCs, CRL-3220) were obtained from ATCC and cultured in α-Minimum Essential Medium supplemented with 10% FBS. Cells were maintained at 37°C with 5% CO₂. Medium was changed every other day, and cells were passaged upon reaching approximately 80% confluency using 0.05% Trypsin-EDTA (Gibco).

extract_protocol:
Genomic DNA was isolated using the Puregene Cell Kit (Qiagen, 158043) according to the manufacturer’s instructions.
For samples labeled with 500 µM BrdU and samples not labeled with BrdU, libraries were prepared using a Ligation Sequencing Kit (Oxford Nanopore Technologies, SQK-LSK114) according to the manufacturer’s instructions. Libraries generated from labeled samples were loaded onto R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN114 or FLO-PRO114M) and sequenced using a MinION Mk1b device or a PromethION P2 solo device (Oxford Nanopore Technologies). Libraries for samples labeled with BrdU and samples not labeled with BrdU were loaded onto R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-PRO114M) and sequenced on a PromethION P2 solo device for 72 hours. Minimum read length was set to 1000 bp. All sequencing data was collected using MinKNOW v23.07.5.

treatment_protocol: For the nocodazole experiment, hESCs were arrested with 1 µg/ml nocodazole for 16h, stained with the Live/Dead Fixable Violet Dead Cell Stain Kit (Invitrogen, L34964), fixed in  75% ethanol, counterstained with Propidium Iodide (Invitrogen, P3566), and live G2/M cells were isolated by FACS before genomic DNA extraction. For the BrdU pulse-chase experiments, BrdU pulses are conducted by adding BrdU to the culture medium at the desired final concentration and incubating for the specified durations (10 minutes, 30 minutes, or 1 hour). Cells are then either collected immediately (0h chase) or washed three times with DPBS and incubated in fresh mTeSR medium for 16 hours (16h chase). For mock treatments, BrdU is replaced with an equivalent volume of Ultrapure H2O. Cells subjected to mock treatments undergo the same incubation times as their BrdU-treated counterparts, with samples collected at 0h or following an 8h or 16h incubation.

value: Dicer1f/f mBMMSC

value: mesenchymal stem cell

value: Mock 500 µM, 10m pulse, 0h chase


title: Subject P004 (P004-T2F)

tag: tissue

value: Serum/Plasma

value: Patient


title: P23H.F.HAL.30722R

description:
Library name: P23H.F.HAL.30722R
transcriptome of HAL treated P23H female retina


title: Dicer1f/f, BrdU 500uM, 16h chase

description: Library name: Dicer1f/f, BrdU 500 uM 16h chase

value: 500 µM BrdU, 10m pulse, 16h chase


title: P23H.F.HAL.30718R

description:
Library name: P23H.F.HAL.30718R
transcriptome of HAL treated P23H female retina

value: Retina


title: Subject P004 (P004-T1F)

tag: condition


title: TART15_2

description: Library name: lib105972


title: Dicer1f/f, BrdU 500uM, 8h chase

description: Library name: Dicer1f/f, BrdU 500 uM 8h chase

value: 500 µM BrdU, 10m pulse, 8h chase


title: TART15.

description: Library name: lib105971

value: RA


title: Subject P013 (P013-T1F)


title: Subject P125 (P125-T1F)


title: Subject P006 (P006-T1F)


title: Subject P005 (P005-T1F)


title: Subject P006 (P006-T2F)


title: Subject P156 (P156-T1F)


title: SNCA-GR mouse M8279, anterior brain (both hemispheres), bulk ONT PCR-cDNA (barcode 24)

city: Seattle

first: Benjamin

last: Logsdon

address: 1150 Eastlake Ave E Ste 600/700

institute: Cajal Therapeutics

description:
Library name: LL3-250218-01_barcode24
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 7.7, RNA prep RN3-250203-32), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP24.

data_processing:
Raw ONT signal was written as POD5 and basecalled in real time by MinKNOW on a PromethION P2 Solo (R10.4.1 flow cell; ONT run LL3-250218-01, 2025-02-18) with per-sample demultiplexing by barcode (BP01-BP24).
Basecalled FASTQ reads per barcode were aligned to a mouse reference with minimap2 in splice-aware mode (-ax splice -uf -k14) and coordinate-sorted with samtools (LL3-250218-01_barcode<NN>_minimap2_sorted.bam).
SNCA 5'UTR transcript-isoform read counts (dIRE1..7, IRE, total SNCA locus, housekeeping genes Hprt1/Snap25/Gapdh, and total minimap2-aligned reads) were tabulated per library from the sorted BAMs. Results are deposited as bulk_ONT_SNCA_isoform_counts.tsv (see companion README).
Assembly: GRCh38 (GenBank assembly accession GCA_000001405.15, primary assembly/no-alt analysis set)
Supplementary files format and content: LL3-250218-01_barcode<NN>_minimap2_sorted.bam: coordinate-sorted BAM of splice-aware minimap2 alignments of ONT basecalls to GRCm39. Read sequences and per-base Q-scores are retained (BAM can be converted to FASTQ with `samtools fastq` if raw reads are requested separately).
Supplementary files format and content: bulk_ONT_SNCA_isoform_counts.tsv: per-library SNCA transcript-isoform read counts covering the 23 deposited libraries. Sample 1 (BP01 / M8274 R-OB) is present in the table with '.' placeholders because that library is not in the deposit. Companion bulk_ONT_SNCA_isoform_counts_README.txt documents the analysis pipeline and full column dictionary.

source_name: anterior brain (both hemispheres)

extract_protocol:
Brain regions (right olfactory bulb, right midbrain, right hippocampus, and 'Brain-Both-Anterior' = anterior brain, both hemispheres) were microdissected from six SNCA-GR homozygous mice (M8274-M8279) at three collection timepoints (olfactory bulb 2024-01-24; midbrain 2024-01-27; hippocampus + anterior brain 2025-02-03). Total RNA was extracted per lab SOP (TRIzol + column purification), quantified by NanoDrop and BioAnalyzer; RIN 7.7-9.2.
500 ng total RNA per sample was reverse-transcribed with Maxima H Minus Reverse Transcriptase (ThermoFisher EP0751) with strand-switching, then barcoded and amplified with the ONT cDNA-PCR Barcoding Kit 24 V14 (SQK-PCB114.24) and LongAmp Hot Start Taq 2X Master Mix (NEB M0533S): 13 PCR cycles per sample using 5 uL of RT product and 0.75 uL of the kit-supplied barcode primer BP01-BP24. Barcoded amplicons were pooled equimolar after Qubit quantification and BioAnalyzer sizing, SPRIselect-cleaned, and sequenced per the SQK-PCB114.24 workflow.

value: anterior brain (both hemispheres)

tag: age

value: 48 days

value: female

value: SNCA-GR homozygous (humanized SNCA gene-replacement knock-in; JAX #39166)

value: SNCA-GR (JAX #39166)

tag: mouse id

tag: barcode


title: Subject P126 (P126-T1F)


title: TART14_4

description: Library name: lib105970

value: airway epithelial cells

value: control

tag: treatment


title: Subject P063 (P063-T1F)


title: TART14_3

description: Library name: lib105969

tag: cell type

value: male

value: AEC


title: SNCA-GR mouse M8278, anterior brain (both hemispheres), bulk ONT PCR-cDNA (barcode 23)

description:
Library name: LL3-250218-01_barcode23
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.1, RNA prep RN3-250203-31), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP23.


title: TART14_2

description: Library name: lib105968


title: Subject P085 (P085-T2F)


title: SNCA-GR mouse M8277, anterior brain (both hemispheres), bulk ONT PCR-cDNA (barcode 22)

description:
Library name: LL3-250218-01_barcode22
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.1, RNA prep RN3-250203-30), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP22.


title: Subject P124 (P124-T1F)


title: Subject P111 (P111-T1F)


title: MEC1 epicardial cells, Independent replicate sample 4, IgG antibody

city: Oxford

first: Andia

middle: Nicole

last: Redpath

address: IDRM IMS-Tetsuya Nakamura Building, Roosevelt Dr, Headington

country: United Kingdom

institute: University of Oxford

description: Library name: EPI_IgG_Sample4

data_processing:
NGS data were demultiplexed using Illumina bcl2fastq, and processed with the nf-core/cut&run v2 pipeline using TrimGalore, Bowtie2, Samtools, Picard, deepTools, Bedtools, and SEACR. TrimGalore removed adaptor sequences, polyG+ sequences and low-quality reads, and Bowtie2 aligned reads to the mouse genome (mm10) with default parameters. Filtering was conducted with Samtools and Picard to exclude low-quality alignments (MAPQ ≥ 20 for WT1/IgG, MAPQ ≥ 10 for histone modifications), genomic blacklist regions, and duplicate reads. Peaks were called using SEACR, normalizing against IgG controls and scaling background control by a factor of 0.8. Read normalization was performed using Counts Per Million (CPM) with binsize 1, and consensus peaks were computed from at least two biological replicates.
Assembly: Mouse mm10
Supplementary files format and content: bigWig (.bigWig); BigWig files were created by bedGraphtoBigWig (UCSC) as part of the nf-core/cut&run v2 pipeline.
Library strategy: CUT&Run

source_name: MEC1 Mouse Embryonic Epicardial Cell Line

growth_protocol: MEC1, an epicardium-derived cell line, was cultured on 0.1% bovine gelatine in MEC1 expansion medium (10% EmbryoMax ES Cell Qualified FBS, 1% Penicillin/Streptomycin, EmbryoMAX DMEM high glucose) at 37°C in 5% CO2.

extract_protocol:
MEC1 epicardial cells cultured for 2 days in expansion medium were harvested from T75 flasks using 0.05% Trypsin-EDTA (2-3 minutes at 37°C). Cell viability was estimated at >95%, and cells were divided based on immunogen (1x106 cells/reaction). CUT&RUN was performed using the CUT&RUN Assay Kit (Cell Signaling Technologies), following the manufacturer’s instructions with minor modifications. Input DNA samples (1x105 cells/reaction) were prepared using DNA extraction buffer (containing Proteinase K and RNase A) according to the Cell Signaling protocol. Samples were incubated at 55°C for 1 hour with shaking (500 RPM, Eppendorf ThermoMixer), cooled on ice, then sonicated using a Diagenode Bioruptor Pico set to “Easy Mode” (25 cycles of 30 sec on/off at 4°C).
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs), with modifications guided by the protocol "Library Prep for CUT&RUN with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645) V.2" (dx.doi.org/10.17504/protocols.io.bagaibse). Less than 6 ng CUT&RUN DNA was used as input. NEBNext End Prep was performed at 20°C for 30 minutes and 50°C for 60 min. Adaptor concentrations were adjusted to input amounts (e.g., 3 µM NEBNext adaptor for 6 ng CUT&RUN DNA). Ligations were performed at 20°C for 15 min, and USER enzyme was used to cleave the uracil loop (37°C for 15 min). DNA cleanup steps used 1.75X SPRIselect beads for WT1/IgG CUT&RUN and 1.1X for histone modifications (H3K27ac, H3K4me3). To amplify the library, the ligation product was mixed with 2x Ultra II Q5 mix, universal primer and index primers; detailed in the key resources table. PCR amplification was typically 12 - 15 cycles (WT1/IgG: 98°C for 30 sec, 12 - 15 cycles of 98°C for 10 sec, 65°C for 10 sec, final extension at 65°C for 5 min; histone modifications: 13sec annealing/extension). Double size selection (0.8X, 1.2X SPRIselect beads) was used for WT1 and IgG, while single size selection (1.1X beads) was applied for histone modifications. Input DNA samples (50 ng input) followed the standard NEBNext Ultra II DNA Library Prep Kit protocol. Libraries were assessed using a High Sensitivity DNA Kit on a on Bioanalyser instrument (Agilent) and quantified using the KAPA Library Quantification Kit. Next-generation sequencing (NGS) was conducted on equimolar pooled libraries using the NextSeq 500/550 High Output v2.5 kit (75 cycles) (Illumina), with paired-end reads (42 bp x 2) and 6 bp single index reads.

tag: cut&run antibody

value: Rabbit (DA1E) mAb IgG XP® Isotype Control


title: TART14.

description: Library name: lib105967


title: SNCA-GR mouse M8276, anterior brain (both hemispheres), bulk ONT PCR-cDNA (barcode 21)

description:
Library name: LL3-250218-01_barcode21
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.0, RNA prep RN3-250203-29), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP21.

value: 55 days

tag: genotype


title: TART15 for BPD

description: Library name: lib105966


title: SNCA-GR mouse M8275, anterior brain (both hemispheres), bulk ONT PCR-cDNA (barcode 20)

description:
Library name: LL3-250218-01_barcode20
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.1, RNA prep RN3-250203-28), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP20.


title: Subject P114 (P114-T1F)

extract_protocol: Blood was collected from patients and healthy controls. Blood was then processed into serum or plasma.

value: Serum/Plasma


title: Subject P078 (P078-T3F)

value: Patient


title: TART14 for BPD

description: Library name: lib105965


title: SNCA-GR mouse M8274, anterior brain (both hemispheres), bulk ONT PCR-cDNA (barcode 19)

description:
Library name: LL3-250218-01_barcode19
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.2, RNA prep RN3-250203-27), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP19.


title: Subject P115 (P115-T1F)


title: Subject P107 (P107-T1F)


title: Subject P113 (P113-T1F)


title: SNCA-GR mouse M8279, right hippocampus, bulk ONT PCR-cDNA (barcode 18)

description:
Library name: LL3-250218-01_barcode18
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.8, RNA prep RN3-250203-26), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP18.

source_name: right hippocampus

value: right hippocampus


title: Subject P093 (P093-T1F)

description:
reason for sample removal: NA
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.
Luminex™ FLEXMAP 3D™


title: T383 p2

description: Library name: lib105963


title: Subject P101 (P101-T1F)


title: SNCA-GR mouse M8277, right hippocampus, bulk ONT PCR-cDNA (barcode 17)

description:
Library name: LL3-250218-01_barcode17
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 7.9, RNA prep RN3-250203-25), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP17.


title: Subject P104 (P104-T1F)


title: Subject P039 (P039-T2F)


title: T3032 P3_3

description: Library name: lib105961


title: Subject P092 (P092-T1F)


title: SNCA-GR mouse M8275, right hippocampus, bulk ONT PCR-cDNA (barcode 15)

description:
Library name: LL3-250218-01_barcode15
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.4, RNA prep RN3-250203-23), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP15.


title: SNCA-GR mouse M8276, right hippocampus, bulk ONT PCR-cDNA (barcode 16)

description:
Library name: LL3-250218-01_barcode16
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.1, RNA prep RN3-250203-24), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP16.


title: T3031 P2_3

description: Library name: lib105962


title: Subject P102 (P102-T1F)


title: Subject P103 (P103-T1F)


title: MEC1 epicardial cells, Independent replicate sample 1, H3K27ac antibody

description: Library name: EPI_H3K27ac_Sample1

value: Acetyl-Histone H3 (Lys27) (D5E4)

tag: cell line

value: MEC1 Mouse Embryonic Epicardial Cell Line


title: MEF2C-KO, non-treated, differentiation 1, clone D9 (scRNA-seq)

city: New York

first: Anna

last: Podlesny-Drabiniok

state: NY

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

description: Library name: D9_KO_NT

data_processing:
Raw base call files were demultiplexed into FASTQ files using PIPseeker (Fluent Biosciences). Reads were aligned to the human reference genome (GRCh38), followed by barcode assignment and UMI counting to generate feature-barcode matrices. Sensitivity setting 3 was used
Quality control, normalization, clustering, and visualization were performed using Seurat v4.0. Cells were filtered based on the following criteria: <100 detected genes, <500 UMIs, >95% of UMIs from a single gene, or >10% mitochondrial reads. Count data were normalized using SCTransform (v0.4.1) with regression for mitochondrial gene percentage. Principal component analysis (PCA) was used for dimensionality reduction.
Assembly: hg38
Supplementary files format and content: barcode.tsv, features.tsv, matrix.mtx files provided for each sample

growth_protocol: iPSC lines were differentiated to hematopoietic precursor cells (HPCs) using StemDiff kit (StemCell Technologies). 20,833 cells/cm2 HPCs were plated and differentiated for 24 days to microglia (iMGL) in iMGL media (DMEM/F12, 2xB27, 0.5xN2, 2xITSG, 400uM monothioglycerol, 5ug/ml insulin, 1xNEAA, 1xGlutaMax) supplemented with three factors (IL34 (100ng/ml), TGFb (50ng/ml), and MCSF (25ng/ml). iMGLs were fed Monday, Wednesday and Friday with 1ml of iMGL media with three factors. Cells were splitted in 1:2 ratio if too confluent. Day 24 iMGLs were lifted with gentle pipetting and Accutase and plated 62,500 cells/cm2 in 1ml of conditioned media and 1ml of fresh media iMGL media with three factors supplemented additionally with two factors (CX3CL1 and CD200 100ng/ml each) for 3 additional days (day 25, day 26,  day 27). At day 26 of iMGL differentiation, iMGL received 1ml of five factor iMGL media and treatment with myelin or LPS. Cells were collected at day 27.

extract_protocol:
Cells were washed with PBS and dissociated using Accutase (Stemcell Technologies, cat. 07920) for 10 minutes at 37°C. Cells were centrifuged at 400 × g for 5 minutes and resuspended in 1.0% PBS/bovine serum albumin (BSA). The cell suspension was filtered through a 40 μm cell strainer to remove aggregates. Cell number and viability were assessed using trypan blue exclusion and an automated cell counter (Countess, Thermo Fisher Scientific). Only samples with high viability (typically >90%) were used for downstream processing.
Single cells were partitioned into PIP droplets using the PIPseq T20 3’ Single Cell RNA Kit v4.0 (Fluent Biosciences, Watertown, MA, USA) according to the manufacturer’s instructions. Briefly, approximately 40,000 live cells were combined with template beads, gently mixed, vortexed for 3 minutes to generate stable PIP emulsions, and processed following the recommended workflow. Captured mRNA was released upon cell lysis within the droplets, followed by reverse transcription, cDNA amplification, cDNA purification, and library preparation. Libraries were sequenced by Azenta (New Jersey, USA) on an Illumina NovaSeq X platform, generating ~50,000 reads per cell (~2 billion reads per sample).

treatment_protocol: Day 26 iMGL were treated with myelin fragments (20ug/ml, 24) and harvested the following day.

value: iPSC-derived microglia

value: non-treated

tag: batch


title: T3027 P2_3

description: Library name: lib105960

value: RA

tag: Sex


title: SNCA-GR mouse M8274, right hippocampus, bulk ONT PCR-cDNA (barcode 14)

description:
Library name: LL3-250218-01_barcode14
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.5, RNA prep RN3-250203-22), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP14.


title: Subject P007 (P007-T2F)

data_processing: See methods section for detailed description. MFI values for unconjugated beads were subtracted from MFI values for antigen conjugated bead IDs, with MFI averages calculated after background subtraction.


title: SNCA-GR mouse M8278, right midbrain, bulk ONT PCR-cDNA (barcode 13)

description:
Library name: LL3-250218-01_barcode13
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.6, RNA prep RN3-250203-21), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP13.

source_name: right midbrain

value: right midbrain

value: 48 days

value: female


title: T3031 P2_2

description: Library name: lib105959

value: airway epithelial cells

tag: donorid


title: Subject P091 (P091-T1F)

source_name: Serum/Plasma


title: T3032 P3_2

description: Library name: lib105958

value: control

tag: collection timepoint


title: TART15_3

description: Library name: lib105973

value: male

tag: studygroup


title: Subject P083 (P083-T1F)


title: Subject P_NA (P_NA (null))

description:
reason for sample removal: Polyreactive sample
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.
Luminex™ FLEXMAP 3D™


title: SNCA-GR mouse M8279, right midbrain, bulk ONT PCR-cDNA (barcode 12)

description:
Library name: LL3-250218-01_barcode12
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.8, RNA prep RN3-240127-06), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP12.

value: SNCA-GR homozygous (humanized SNCA gene-replacement knock-in; JAX #39166)

tag: strain

value: SNCA-GR (JAX #39166)


title: Dicer1f/f, BrdU 500uM, 0h chase

description: Library name: Dicer1f/f, BrdU 500 uM 0h chase

value: Dicer1f/f mBMMSC

value: mesenchymal stem cell

value: 500 µM BrdU, 10m pulse, 0h chase


title: Subject P071 (P071-T3F)

value: Serum/Plasma

value: Patient


title: Subject HC022 (HC022)

value: Healthy control


title: Subject P088 (P088-T1F)


title: Subject P073 (P073-T1F)


title: Subject P053 (P053-T3F)


title: T3027 P2_2

description: Library name: lib105957

tag: cell morphology

value: AEC


title: Subject HC083 (HC083)

tag: tissue


title: SNCA-GR mouse M8278, right hippocampus, bulk ONT PCR-cDNA (barcode 11)

description:
Library name: LL3-250218-01_barcode11
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.7, RNA prep RN3-240127-05), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP11.

value: right hippocampus


title: SNCA-GR mouse M8277, right midbrain, bulk ONT PCR-cDNA (barcode 10)

description:
Library name: LL3-250218-01_barcode10
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.8, RNA prep RN3-240127-04), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP10.


title: Subject HC079 (HC079)

tag: condition


title: T3032 P3

description: Library name: lib105955

value: RA


title: T3031 P2

description: Library name: lib105956


title: Subject HC020 (HC020)


title: SNCA-GR mouse M8276, right midbrain, bulk ONT PCR-cDNA (barcode 09)

description:
Library name: LL3-250218-01_barcode09
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.0, RNA prep RN3-240127-03), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP09.

value: right midbrain

tag: age

value: 55 days


title: Subject HC069 (HC069)


title: SNCA-GR mouse M8275, right midbrain, bulk ONT PCR-cDNA (barcode 08)

description:
Library name: LL3-250218-01_barcode08
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.8, RNA prep RN3-240127-02), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP08.

tag: mouse id


title: Subject HC082 (HC082)


title: Subject P166 (P166-T1F)


title: Subject P121 (P121-T1F)


title: Subject HC019 (HC019)


title: Subject HC066 (HC066)


title: SNCA-GR mouse M8274, right midbrain, bulk ONT PCR-cDNA (barcode 07)

description:
Library name: LL3-250218-01_barcode07
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.5, RNA prep RN3-240127-01), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP07.

tag: barcode


title: 1107-2 #1 P2_3

description: Library name: lib105951

value: female

value: BPD

tag: treatment


title: Subject HC076 (HC076)


title: SNCA-GR mouse M8278, right olfactory bulb, bulk ONT PCR-cDNA (barcode 05)

description:
Library name: LL3-250218-01_barcode05
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.5, RNA prep RN3-240124-05), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP05.

source_name: right olfactory bulb

value: right olfactory bulb

value: 48 days


title: 1108-2 #2 P2 spindle

description: Library name: lib105952

tag: cell type

value: airway epithelial cells

value: male

value: fibroblast


title: Subject HC059 (HC059)


title: 1108-3 #1 P3

description: Library name: lib105953


title: Subject HC063 (HC063)


title: Subject HC058 (HC058)


title: SNCA-GR mouse M8279, right olfactory bulb, bulk ONT PCR-cDNA (barcode 06)

description:
Library name: LL3-250218-01_barcode06
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.8, RNA prep RN3-240124-06), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP06.

value: SNCA-GR homozygous (humanized SNCA gene-replacement knock-in; JAX #39166)

value: SNCA-GR (JAX #39166)


title: Subject HC054 (HC054)

value: Serum/Plasma


title: 1108-3 #1 P2_2

description: Library name: lib105950


title: Subject HC047 (HC047)


title: Subject HC078 (HC078)


title: GSC17- 203440060042_R07C01

status: Public on Aug 07 2026

type: genomic

city: Amsterdam

first: Bart A.

last: Westerman

address: van der Boechorststraat 6b

department: Human Genetics

country: Netherlands

institute: Amsterdam UMC

description: Methylation array of surgically removed GBM modelsample that was cultured without experimental treatment

hyb_protocol: According to Infinium Methylation HD EPIC manufacturers protocol

data_processing:
CNV analysis and graphing was done using the Bioconductor minfi and conumee R packages 28 or by using Python pylluminator==2.2. Gene locations for annotation were derived with the UCSC genome browser database, using the Table browser tool 29. Assembly hg19 was used as reference genome.
Processed values consist of NOOB background-corrected and nonlinear dye-bias-corrected DNA-methylation beta values for Infinium MethylationEPIC CpG probes, together with corresponding pOOBAH detection P values. Beta values range from 0 to 1 and represent the proportion of methylated signal at each CpG site. Detection P values indicate whether the measured probe signal is distinguishable from background.

label: Cy3, Cy5

source_name: Human GBM brain tumor

growth_protocol: According to Krishna P L Bhat. Mesenchymal differentiation mediated by NF-κB promotes radiation resistance in glioblastoma. Cancer Cell 2013 Sep 9;24(3):331-46.

extract_protocol: Genomic DNA was isolated from untreated cell pellets using the DNeasy Blood & Tissue Kit (Qiagen, 69504), according to manufacturer’s protocol. Additionally, samples were treated with RNase A (DNase and protease-free, 10 mg/mL, Thermo Scientific™, EN0531) to remove RNA from samples.

treatment_protocol: Cells were grown in steady state

value: Human GBM brain tumor

value: GBM tumor cell culture model

value: -1.48 to 2.45EGFR min to max

value: None (steady state culture)


title: SNCA-GR mouse M8277, right olfactory bulb, bulk ONT PCR-cDNA (barcode 04)

description:
Library name: LL3-250218-01_barcode04
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 9.0, RNA prep RN3-240124-04), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP04.


title: T3011 p2 (spindly)

description: Library name: lib105964

value: RA

value: control


title: 1107-2 #1 P2_2

description: Library name: lib105949

value: AEC


title: Subject HC038 (HC038)

description:
reason for sample removal: NA
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.
Luminex™ FLEXMAP 3D™

value: Healthy control


title: T3027 P2

description: Library name: lib105954

value: female


title: SNCA-GR mouse M8276, right olfactory bulb, bulk ONT PCR-cDNA (barcode 03)

description:
Library name: LL3-250218-01_barcode03
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 9.2, RNA prep RN3-240124-03), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP03.

value: right olfactory bulb

value: 55 days


title: 1108-3 #1 P2

description: Library name: lib105948

value: airway epithelial cells

value: BPD


title: Subject HC050 (HC050)


title: SNCA-GR mouse M8275, right olfactory bulb, bulk ONT PCR-cDNA (barcode 02)

description:
Library name: LL3-250218-01_barcode02
Bulk brain-region RNA sequenced as one of 24 pooled barcoded libraries on ONT run LL3-250218-01 (PromethION P2 Solo, R10.4.1 flow cell FLO-PRO114M, kit SQK-PCB114.24). cDNA input: 500 ng total RNA (RIN 8.8, RNA prep RN3-240124-02), RT with Maxima H Minus, 13-cycle barcoding PCR with LongAmp Hot Start Taq and PCB114.24 barcode primer BP02.

value: male


title: Subject HC040 (HC040)


title: Subject HC045 (HC045)


title: Subject HC034 (HC034)


title: Subject HC041 (HC041)


title: SNCA-GR mouse M9378, SNc-VTA (midbrain), snRNA-seq ONT long-read

description:
Library name: LL3-250509-05
ONT long-read cDNA sequencing of 10 ng of amplified 10x 5' cDNA (from the same Chromium GEM-RT amplicon used for LX3-250506-05) with custom 5' partial-Read1 forward primer and partial-TSO reverse primer, LongAmp Hot Start Taq amplification, Ligation Sequencing Kit V14 (SQK-LSK114) on PromethION P2 Solo (R10.4.1 chemistry, FLO-PRO114M). Reads carry the 10x cell barcode + UMI at the 5' end. No gene- or isoform-level quantification is deposited. Only the minimap2-sorted BAM is deposited (as both raw and processed data); the BAM retains basecalled read sequences and per-base Q-scores, from which FASTQ can be regenerated with `samtools fastq`. Full basecalled FASTQs are archived in the source bucket and available on reasonable request.

data_processing:
[10X] Bcl -> FASTQ demultiplexing with Illumina DRAGEN BCL Convert v3.10.4 on BaseSpace, one FASTQ set per NextSeq 2000 P3 flow cell (RX1-0227 / RX1-0228 / RX1-0229). Per-sample FASTQs from all three runs were merged before Cell Ranger input.
[10X] cellranger count --include-introns --chemistry fiveprime (Cell Ranger v6.1.1; martian v4.0.6) against a mouse reference (confirm exact build). Outputs: filtered_feature_bc_matrix {barcodes,features,matrix} + .h5, metrics_summary.csv, web_summary.html, analysis/ (clustering, PCA, tSNE, UMAP, diffexp).
[ONT] Real-time basecalling with MinKNOW on PromethION P2 Solo, R10.4.1 chemistry, LSK114 kit; POD5 signals recorded; basecalls written to <libID>_live_basecall.fastq.gz.
[ONT] minimap2 alignment of ONT basecalls with splice-aware parameters (-ax splice -uf -k14) against the same mouse reference used for Cell Ranger. Alignments sorted and indexed with samtools. No gene- or isoform-level quantification is included in this Series.
Assembly: GRCh38 (GenBank assembly accession GCA_000001405.15, primary assembly/no-alt analysis set)
Supplementary files format and content: [10X] For each 10x library: three 10x Market Exchange files (<libID>_barcodes.tsv.gz cell barcodes, <libID>_features.tsv.gz gene features, <libID>_matrix.mtx.gz sparse UMI matrix), the same matrix in HDF5 (<libID>_filtered_feature_bc_matrix.h5), and <libID>_metrics_summary.csv Cell Ranger QC metrics.
Supplementary files format and content: [ONT] <libID>_live_basecall_minimap2_sorted.bam: coordinate-sorted BAM of minimap2 splice-aware alignments of ONT basecalls to the same mouse reference; retains 10x cell-barcode + UMI, basecalled read sequences, and per-base Q-scores. Same BAM is listed as the *raw file for each ONT library -- basecalled FASTQ can be regenerated with `samtools fastq`. Full FASTQs are archived in the source bucket and available on reasonable request.

molecule: nuclear RNA

source_name: Substantia nigra pars compacta / ventral tegmental area (SNc-VTA), midbrain

extract_protocol:
Brains from three SNCA-GR homozygous male mice (JAX #39166; DOB 2025-03-04; sacrificed 2025-04-28 at age 55 days) were flash-frozen and stored at -80 C. On 2025-04-30 (M9376) and 2025-05-01 (M9377, M9378), 50 um coronal sections were cut on a dry-ice-cooled sectioning stage and the substantia nigra / VTA and olfactory bulb were microdissected under a stereo microscope from both hemispheres, then homogenized in 1 mL Homogenization Buffer (NIM pH 8.0 with 0.2 U/uL RNase Inhibitor, 1x protease inhibitor cocktail, 0.1 mM DTT) using a Dounce homogenizer (10 loose + 10 tight strokes). Nuclei were purified by Debris Removal Solution gradient (Miltenyi), washed in 2X BSA/PBS, filtered through a 30 um strainer, and resuspended in 1% BSA blocking buffer. Nuclei counts (Trypan blue, Neubauer hemocytometer) were adjusted to 200-700 nuclei/uL for 10x loading.
[10X] 10x Genomics Chromium Next GEM Single Cell 5' v2: nuclei loaded onto a Chromium Next GEM Chip K at target recovery of 7,500 cells (12,000 loaded). GEM-RT, Dynabead cleanup, and 13-cycle cDNA amplification per manufacturer protocol. Gene expression libraries constructed from 50 ng of amplified cDNA with the 10x Library Construction Kit; 14-cycle indexing PCR with Dual Index Kit TT Set A wells A1-A6 (one index per sample).
[ONT] 10 ng of the same amplified 10x cDNA per sample was re-amplified (7 cycles, LongAmp Hot Start Taq 2X, 66->58 C ramp, 6 min extension) with custom oligos Fwd_3580_partial_read1_defined_for_5'_cDNA (5'-/5phos/ACTTGCCTGTCGCTCTATCTTCCTACACGACGCTCTTCCGATCT-3') and Rev_PR2_partial_TSO_defined_for_5'_cDNA (5'-/5phos/TTTCTGTTGGTGCTGATATTGCAAGCAGTGGTATCAACGCAGAG-3') to add ONT-compatible ends preserving the 10x cell barcode + UMI at the 5' of the read. Products bead-cleaned (1x SPRIselect), end-prepped (NEBNext Ultra II End Repair / dA-tailing), ligated to ONT LSK114 sequencing adapters with Salt-T4 DNA Ligase; cleaned with SPRIselect (0.4x) and eluted in 34 uL Elution Buffer.

value: nuclei

value: SNCA-GR homozygous (humanized SNCA gene-replacement knock-in; JAX #39166)


title: SNCA-GR mouse M9378, olfactory bulb, snRNA-seq ONT long-read

description:
Library name: LL3-250509-06
ONT long-read cDNA sequencing of 10 ng of amplified 10x 5' cDNA (from the same Chromium GEM-RT amplicon used for LX3-250506-06) with custom 5' partial-Read1 forward primer and partial-TSO reverse primer, LongAmp Hot Start Taq amplification, Ligation Sequencing Kit V14 (SQK-LSK114) on PromethION P2 Solo (R10.4.1 chemistry, FLO-PRO114M). Reads carry the 10x cell barcode + UMI at the 5' end. No gene- or isoform-level quantification is deposited. Only the minimap2-sorted BAM is deposited (as both raw and processed data); the BAM retains basecalled read sequences and per-base Q-scores, from which FASTQ can be regenerated with `samtools fastq`. Full basecalled FASTQs are archived in the source bucket and available on reasonable request.

source_name: Olfactory bulb

value: Olfactory bulb

value: SNCA-GR (JAX #39166)


title: Subject HC033 (HC033)

value: Serum/Plasma


title: Subject HC028 (HC028)


title: Subject HC039 (HC039)


title: 1104-4 #1 P2_3

description: Library name: lib105945


title: SNCA-GR mouse M9377, olfactory bulb, snRNA-seq ONT long-read

description:
Library name: LL3-250509-04
ONT long-read cDNA sequencing of 10 ng of amplified 10x 5' cDNA (from the same Chromium GEM-RT amplicon used for LX3-250506-04) with custom 5' partial-Read1 forward primer and partial-TSO reverse primer, LongAmp Hot Start Taq amplification, Ligation Sequencing Kit V14 (SQK-LSK114) on PromethION P2 Solo (R10.4.1 chemistry, FLO-PRO114M). Reads carry the 10x cell barcode + UMI at the 5' end. No gene- or isoform-level quantification is deposited. Only the minimap2-sorted BAM is deposited (as both raw and processed data); the BAM retains basecalled read sequences and per-base Q-scores, from which FASTQ can be regenerated with `samtools fastq`. Full basecalled FASTQs are archived in the source bucket and available on reasonable request.


title: Subject HC035 (HC035)


title: C57BL6-Spleen-NK-2

city: Winnipeg

first: Peter

last: Thompson

state: MB

address: 715 McDermot ave

department: Physiology & Pathophysiology

country: Canada

institute: University of Manitoba

description: Library name: C57BL6-2

data_processing:
Read alignment
Normalize read counts
Assembly: mm10
Supplementary files format and content: Differential_expression_analysis_table.csv

source_name: Spleen

extract_protocol:
Trizol total RNA (ZymoResearch RNA microprep kit)
paired end 150 bp

treatment_protocol: Freshly isolated splenocytes

value: Spleen

value: NK cell

value: wild-type


title: 1104-4 #1 P2_2

description: Library name: lib105944


title: Subject HC032 (HC032)


title: 1104-4 #1 P2

description: Library name: lib105943

value: RA


title: Subject HC026 (HC026)


title: 1103-2 #2 P3_2

description: Library name: lib105942

value: AEC


title: SNCA-GR mouse M9377, SNc-VTA (midbrain), snRNA-seq ONT long-read

description:
Library name: LL3-250509-03
ONT long-read cDNA sequencing of 10 ng of amplified 10x 5' cDNA (from the same Chromium GEM-RT amplicon used for LX3-250506-03) with custom 5' partial-Read1 forward primer and partial-TSO reverse primer, LongAmp Hot Start Taq amplification, Ligation Sequencing Kit V14 (SQK-LSK114) on PromethION P2 Solo (R10.4.1 chemistry, FLO-PRO114M). Reads carry the 10x cell barcode + UMI at the 5' end. No gene- or isoform-level quantification is deposited. Only the minimap2-sorted BAM is deposited (as both raw and processed data); the BAM retains basecalled read sequences and per-base Q-scores, from which FASTQ can be regenerated with `samtools fastq`. Full basecalled FASTQs are archived in the source bucket and available on reasonable request.

value: Substantia nigra pars compacta / ventral tegmental area (SNc-VTA), midbrain


title: Subject HC023 (HC023)

value: Healthy control


title: Subject HC024 (HC024)


title: Subject HC021 (HC021)


title: SNCA-GR mouse M9376, SNc-VTA (midbrain), snRNA-seq ONT long-read

description:
Library name: LL3-250509-01
ONT long-read cDNA sequencing of 10 ng of amplified 10x 5' cDNA (from the same Chromium GEM-RT amplicon used for LX3-250506-01) with custom 5' partial-Read1 forward primer and partial-TSO reverse primer, LongAmp Hot Start Taq amplification, Ligation Sequencing Kit V14 (SQK-LSK114) on PromethION P2 Solo (R10.4.1 chemistry, FLO-PRO114M). Reads carry the 10x cell barcode + UMI at the 5' end. No gene- or isoform-level quantification is deposited. Only the minimap2-sorted BAM is deposited (as both raw and processed data); the BAM retains basecalled read sequences and per-base Q-scores, from which FASTQ can be regenerated with `samtools fastq`. Full basecalled FASTQs are archived in the source bucket and available on reasonable request.


title: 1103-2 #2 P3

description: Library name: lib105941

value: female


title: WT8_proli_NS

city: montpellier

first: Jean-Philippe

last: Hugnot

address: 141 rue de la Cardonille

country: France

institute: Institut de génomique fonctionnelle

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. Version v1.5.2. Parameters -l 15 -q 0.2 -n 0.05
Remove the reads containing the adaptor(adaptor pollution)
Remove reads whose N content is greater than 5%
Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads)
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: excel file containing FPKM, TPM and read count

source_name: Spinal Cord

growth_protocol: Spinal cord neural stem cells were maintained in DMEM-F12 medium supplemented  with N2, L-glutamine, Ciprofloxaine, Gentamycin, B27, Funzine. For proliferation condition Heparine, EGF and FGF2 were added to the culture media

extract_protocol:
cells were collected and lysate according to the RNeasy kit from QIAGEN
Stranded mRNA Library construction procedure are listed below: 1) mRNA enrichment and purification: Oligo dT Selection (mRNA enrichment): Use oligo dT beads to enrich mRNA with poly A tail. 2) RNA fragment and reverse transcription/ Fragment the RNA and first-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP. 3) End repair, add A and adaptor ligation: The synthesized cDNA was subjected to end-repair and then was 3' denylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 4) PCR amplification: Prior to PCR amplification, the dUTP-marked strand is selectively degraded by Uracil-DNA-Glycosylase(UDG). The remaining strand is amplified to generate a cDNA library suitable for sequencing. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer; 5) Single strand separation and cyclization: Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase; 6) DNA nanoball synthesis; 7) Sequencing on DNBSEQ (DNBSEQ Technology) platform

treatment_protocol: Cells were infected with an adenovirus CMV-Cre to induce YAP1 recombination. RNA sequencing were performed on neurospheres (7 days of proliferation) or after 5 days of differentiation.

value: Spinal Cord

value: neural stem cells


title: Subject HC015 (HC015)

city: Stanford

last: Utz

address: 269 Campus Dr

institute: Stanford University School of Medicine


title: Subject HC_NA (HC_NA (null))

description:
reason for sample removal: Healthy state misclassification
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.
Luminex™ FLEXMAP 3D™


title: 1103-2 #2 P2_7

description: Library name: lib105940

source_name: airway epithelial cells

value: airway epithelial cells

value: BPD


title: Subject HC014 (HC014)


title: Subject HC017 (HC017)


title: 1103-2 #2 P2_5

description: Library name: lib105938


title: Subject HC013 (HC013)


title: WT7_proli_NS


title: Subject HC010 (HC010)


title: 1103-2 #2 P2_4

description: Library name: lib105937


title: WT7_diff


title: Subject HC004 (HC004)


title: Subject HC042 (HC042)


title: Subject HC003 (HC003)


title: SOD1G93A Uninfected MM155 M10

city: Hamilton

first: Imran

middle: Syed

last: Ahmed

state: Ontario

address: 1280 Main Street West

institute: McMaster University

description:
Library name: Sample 3
Colum name in MM_RNAseq_mouse_STAR_Grcm39_reverseStranded_edit_ANNonly_GeneSorted_SUM_GroupSorted_FilterByExpr_VOOM-TMM.xlsx: X3.MM155.M10 (SOD1G93A Uninfected)

data_processing:
The reads were trimmed using TrimGalore and then aligned with GRCm39 reference using STAR83. Next, the reads were counted by using HTSeq count. Genes, showing low levels of expression were removed using EdgeR package in R, resulting in 12,503 genes. Counts for these remaining genes were normalized with TMM normalization method and then transformed using voom transformation. The limma package in R was used to identify genes differentially expressed between the infected and the uninfected groups SOD1G93A mice.
For differential expression analysis, corrected p-values < 0.05 were considered to be significant.
Assembly: GRCm39
Supplementary files format and content: MM_RNAseq_mouse_STAR_Grcm39_reverseStranded_edit_ANNonly_GeneSorted_SUM_GroupSorted_FilterByExpr_VOOM-TMM.xlsx contains log2 transformed expression values

source_name: Lumbar Spinal Cord

growth_protocol: Mice were maintained on a 12 hour light/dark cycle and low-fat dietary chow and water was provided ad libitum. Breeding pairs consisted of male SOD1G93A mice and female WT mice, and mice were bred up to the second generation. Litters were weaned at 21 days of age and housed at a maximum of five mice per cage.

extract_protocol:
The spinal cord was removed at 30 days post-infection (90 days of age) and cut immediately distal to the 13th rib to isolate the lumbar spine. The lumbar spinal cord was hydraulically removed from the vertebrae using 5 mL of PBS and flash frozen in liquid nitrogen. Once frozen, samples within a cryotube were disrupted using a pestle and homogenized by pipetting with 600 µL of RLT buffer (Qiagen). Homogenized samples were then transferred to a Qiashredder spin column (Qiagen), and the flowthrough was subsequently spun in a gDNA eliminator column (Qiagen). Equal volume of 70% ethanol was added and RNA isolation was carried out as per the RNeasy instruction manual (Qiagen)
Sample libraries were prepared using the NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina and cDNA libraries were sequenced using an Illumina HiSeq machine (2x50 bp sequence reads).

treatment_protocol: WT and SOD1G93A mice were anesthetized using isoflurane and infected with IAV i.n. in a 40 µL inoculum of PBS. Mice were infected with 300 plaque forming units (PFU) of IAV, equating to a 0.1 median lethal dose (LD50) infection. Mice were monitored for weight loss upto 14 days post-infection.

value: Lumbar Spinal Cord

tag: disease state

value: SOD1G93A mouse model

value: Uninfected


title: Subject P009 (P009-T1F)

first: Paul

value: Patient


title: 1103-2 #2 P2_2

description: Library name: lib105935


title: WT6_diff


title: WT5_proli_NS


title: 1103-2 #2 P2

description: Library name: lib105934


title: Subject P167 (P167-T1F)

value: Serum/Plasma


title: Subject P164 (P164-T1F)


title: Subject P162 (P162-T1F)


title: 1102-2 #2 P2_4

description: Library name: lib105933

value: male


title: Subject P163 (P163-T1F)


title: WT5_diff


title: WT4_proli_NS


title: Subject P157 (P157-T1F)


title: Subject P159 (P159-T1F)


title: 1102-2 #1 P2_3

description: Library name: lib105932


title: WT4_diff


title: Subject P152 (P152-T1F)


title: Subject P020 (P020-T2F)


title: 1102-2 #1 P2_2

description: Library name: lib105931


title: KO8_proli_NS


title: Subject P149 (P149-T2F)


title: Subject P153 (P153-T1F)


title: 1102-2 #1 P2

description: Library name: lib105930


title: KO8_diff


title: Subject P148 (P148-T1F)


title: Subject P149 (P149-T1F)


title: 1100-2 #1 P2

description: Library name: lib105929