title: KO7_proli_NS


title: Subject P_NA (P_NA6 (null))

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: Disease 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™

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: 1097-4 #1#2 P2

type: SRA

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib105928

library_source: transcriptomic

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

molecule: total RNA

source_name: airway epithelial cells

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).

tag: cell type

value: airway epithelial cells

value: RA

tag: Sex

value: female

tag: donorid

tag: studygroup

value: BPD

tag: collection timepoint

tag: cell morphology

value: AEC

tag: treatment


title: Subject P068 (P068-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: KO7_diff

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

organism: Mus musculus

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 P144 (P144-T2F)


title: 1097-4 #1#2 P3

description: Library name: lib105927


title: Subject P144 (P144-T1F)


title: KO6_proli_NS


title: Subject P145 (P145-T1F)


title: 1113-3 #2 P2

description: Library name: lib114836

tag: study group


title: KO6_diff


title: Subject P139 (P139-T1F)


title: Subject P135 (P135-T1F)


title: Subject P130 (P130-T1F)


title: Subject P134 (P134-T3F)


title: KO5_proli_NS


title: Subject P108 (P108-T1F)


title: TART14

description: Library name: lib114833

value: male

value: control


title: KO5_diff


title: Subject P134 (P134-T1F)


title: Subject P105 (P105-T3F)


title: KO4_proli_NS


title: Subject P132 (P132-T1F)


title: Subject P097 (P097-T2F)


title: TART3

description: Library name: lib114832


title: KO4_diff


title: Subject P128 (P128-T1F)


title: Subject P096 (P096-T1F)


title: TART2

description: Library name: lib114831


title: TART1

description: Library name: lib114830


title: sublibrary16

city: STANFORD

first: Xiaochen

last: Xiong

state: CA

address: 327 Campus Drive

institute: Stanford University

description: Library name: scRNA_seq_sub16

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the Parse Biosciences data analysis pipeline, split-pipe/ParseBiosciences-Pipeline v1.2.1, to demultiplex reads and generate single-cell transcript count matrices. Transcriptome reads were aligned to the mouse reference genome mm39 to generate single-cell gene count matrices.
Single-cell gene expression matrices were processed using Seurat v5.3.0 in R. Genes were required to be expressed in at least 3 cells, and cells were required to contain a minimum of 100 detected features. Cells were retained if they had between 300 and 10,000 detected features and mitochondrial content below 10%. Potential doublets were identified and removed using DoubletFinder v2.0.4, followed by manual removal of doublet clusters.
Filtered data were normalized using the LogNormalize method with a scale factor of 10,000. The top 2,000 highly variable genes were identified using the variance-stabilizing transformation selection method. Data were scaled across all genes, and principal component analysis was performed. UMAP visualization was generated using the top 30 principal components. Clustering was performed using the Leiden algorithm on a shared nearest-neighbor graph constructed with k = 20 neighbors. Cells were manually annotated into major lineages and specific subtypes based on canonical marker expression.
Assembly: mm39
Supplementary files format and content: expression_raw_counts.mtx.gz contains the raw gene-by-cell UMI count matrix in sparse Matrix Market format. genename.tsv.gz contains the gene names corresponding to the rows of the matrix. cellname.tsv.gz contains the cell barcodes/cell IDs corresponding to the columns of the matrix. metadata.tsv.gz contains per-cell metadata, including sample identity, treatment condition, cell-type annotation, and other quality-control information.

molecule: polyA RNA

source_name: lung

extract_protocol:
Lung tissues were minced and enzymatically dissociated in digestion buffer containing Collagenase IV, Dispase, 0.25% Trypsin-EDTA, and DNase I in HBSS for 30 minutes at 37 °C. The suspension was neutralized with an ice-cold quench solution containing heat-inactivated FBS, DNase I, and L15 medium, then passed through a 40 μm filter. Following centrifugation at 500 rcf for 10 minutes, the cell pellet was subjected to red blood cell lysis with ACK lysing buffer (Gibco A1049201) for 5 minutes at room temperature. Single cells were washed with PBS and re-pelleted. Cells were then resuspended in FACS buffer containing DAPI, and live single cells were isolated by FACS sorting for scRNA-seq.
scRNA-seq libraries were prepared using the Evercode Whole Transcriptome (WT) v3 kit (Parse Biosciences) according to the manufacturer’s instructions. Briefly, sorted live single-cell suspensions were fixed and permeabilized using the Evercode Fixation v3 kit. Fixed samples were frozen until split-pool combinatorial barcoding. In the first round, transcripts underwent in situ reverse transcription using well-specific barcoded oligo(dT) and random hexamer primers. Cells were then pooled, split into new plates, and subjected to two additional rounds of in situ barcode ligation. Following the third round, cells were partitioned into sub-libraries and lysed. Barcoded cDNA was amplified and fragmented. Final sequencing libraries were generated through end repair, A-tailing, adapter ligation, and final PCR amplification, during which a fourth sample-specific barcode was introduced. Libraries were converted to Ultima adapters, evaluated for quality, pooled, and sequenced on an Ultima platform.

value: lung

value: treated with vehicle, 6-OHDA, or BIBO3304, both in the presence and absence of seeded PDAC cells.


title: Subject P120 (P120-T3F)


title: sublibrary15

description: Library name: scRNA_seq_sub15


title: 1113-3 #2 P3 LB O2-96h

description: Library name: lib114829


title: Subject P089 (P089-T2F)


title: sublibrary14

description: Library name: scRNA_seq_sub14


title: Subject P109 (P109-T2F)


title: Subject P089 (P089-T1F)


title: sublibrary13

description: Library name: scRNA_seq_sub13


title: Subject P099 (P099-T2F)


title: Subject P080 (P080-T1F)


title: 1113-3 #2 P3 LB

description: Library name: lib114827


title: Subject P098 (P098-T1F)


title: sublibrary12

description: Library name: scRNA_seq_sub12


title: Subject P082 (P082-T2F)


title: 1113-2 #1 P3 LB

description: Library name: lib114826


title: Subject P077 (P077-T1F)


title: sublibrary11

description: Library name: scRNA_seq_sub11


title: Subject P066 (P066-T3F)


title: sublibrary10

description: Library name: scRNA_seq_sub10


title: Subject P094 (P094-T1F)


title: 1113-2 #2 P3 LB

description: Library name: lib114825


title: 1113-1 #1 AEC P2

description: Library name: lib114824


title: Subject P066 (P066-T1F)


title: Subject P087 (P087-T1F)


title: Subject P095 (P095-T3F)


title: Subject P064 (P064-T1F)


title: 1112-3 #1#2 P2 spindle

description: Library name: lib114823

value: fibroblast


title: 1112-2 #2 P2 spindle

description: Library name: lib114822


title: sublibrary8

description: Library name: scRNA_seq_sub8


title: Subject P081 (P081-T1F)


title: sublibrary7

description: Library name: scRNA_seq_sub7


title: Subject P076 (P076-T1F)


title: Subject P051 (P051-T1F)


title: Subject P075 (P075-T2F)


title: Subject P090 (P090-T2F)


title: sublibrary6

description: Library name: scRNA_seq_sub6


title: Subject P127 (P127-T2F)


title: 1112-2 #1 P2 AEC spindle mixed

description: Library name: lib114821

value: mixed


title: TART15 P3

description: Library name: lib114820


title: Subject P049 (P049-T1F)


title: Subject P072 (P072-T1F)


title: sublibrary5

description: Library name: scRNA_seq_sub5


title: Subject P043 (P043-T1F)


title: TART14 P3

description: Library name: lib114819


title: sublibrary4

description: Library name: scRNA_seq_sub4


title: Subject P068 (P068-T2F)


title: corrected #1

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

description: Library name: Sh15_SLF2_a7

data_processing:
Illumina bcl2fastq (v2.20) were performed for converting fastq files and separation by samples with default setting
Adapter sequences were trimmed using Cutadapt (v1.14).
Reads mapped to ribosomal RNA were removed using Bowtie2 (v2.2.5) and SAMtools (v1.2).
The reads were mapped by STAR  (v2.5.3a)
gene-level read counts were generated using HTSeq (v0.6.1)
Assembly: GRCh38
Supplementary files format and content: Raw gene-level read counts
Supplementary files format and content: DESeq2 nomalized count values for each sample

source_name: Human iPS derived hematopoietic stem and progenitor cells

extract_protocol:
miRNeasy micro kit (Qiagen)
Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus

tag: genotype

value: corrected


title: sublibrary3

description: Library name: scRNA_seq_sub3


title: Subject P041 (P041-T1F)


title: Subject P040 (P040-T1F)


title: Subject P138 (P138-T1F)


title: 1113-3 #2 P3 LB RA

description: Library name: lib114828


title: corrected #3

description: Library name: Sh14_SLF2_a3

value: Human iPS derived hematopoietic stem and progenitor cells


title: sublibrary2

description: Library name: scRNA_seq_sub2


title: corrected #2

description: Library name: Sh13_SLF2_a1


title: Subject P067 (P067-T1F)

value: Serum/Plasma


title: Subject P059 (P059-T1F)

value: Patient


title: Subject P038 (P038-T1F)


title: sublibrary1

description: Library name: scRNA_seq_sub1


title: 1107-2 #1 P2

description: Library name: lib105947

value: airway epithelial cells


title: mutant #1-3

description: Library name: Sh12_SLF2_C1_3

value: mutant


title: WT Control, rep 3

city: Houston

first: Xiao

last: Zhao

state: Texas

address: 6550 Bertner Avenue

department: Head and Neck Surgery

institute: MD Anderson Cancer Center

description:
Library name: Control C
FPKM.Control_g1C_g1

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We used HISAT2 to map reads to the genome of ftp://ftp.ensembl.org/pub/release-112/fasta/mus_musculus/dna/.
Assembly: The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts.
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

growth_protocol: ROC6 oral squamous cell cancer cells were maintained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using RNEasy mini kit (Qiagen)
Poly(A) RNA sequencing library was prepared following Illumina's TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

tag: cell line

value: Oral squamous

value: WT Control


title: shPgk1_3

city: Wuhan

first: Tinglin

last: Yang

state: Hubei

address: 1277 Jie Fang Avenue, Jianghan District

department: Department of Breast and Thyroid Surgery

country: China

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description:
Library name: Sample 6
4T1 cells with PGK1 knockdown (shPGK1), replicate 3

data_processing:
Primary processing and gene expression quantification were performed using DNBC4tools (BGI). The count matrix was analyzed using Seurat (v4) in R. Low-quality cells (<200 or >4000 detected genes, >30000 UMIs or >20% mitochondrial reads) were removed. Data were normalized using LogNormalize with a scale factor of 10000, and the top 2000 variable genes were identified by variance-stabilizing transformation. Harmony was used for batch correction across samples.
Assembly: GRCh38 (hg38) - Genome Reference Consortium Human Build 38
Supplementary files format and content: Processed data are provided in Market Exchange (MEX) format: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene identifiers), and matrix.mtx.gz (sparse count matrix). Filtered matrices contain only high-quality cells passing QC thresholds.

source_name: breast cancer

extract_protocol:
Single-cell suspensions with viability >80% (assessed by 0.4% trypan blue staining) were used for library preparation. Cells were encapsulated into droplets for lysis, mRNA capture, and reverse transcription on the TaiM4 scRNA platform.
cDNA was amplified, fragmented, and processed for library construction. The libraries were converted into circular forms to produce single-stranded DNA, which was then amplified into DNA nanoballs. These were placed onto patterned nanoarrays and sequenced using cPAS technology on the BGI DNBSEQ platform with paired-end sequencing. Separate cDNA and oligo capture libraries were prepared for each sample.

treatment_protocol: Cells were transduced with lentiviral particles expressing either non-targeting shRNA (shNC) or PGK1-targeting shRNA (shPgk1). After 48 hours, cells were selected with puromycin (2 ug/mL) for 7 days to establish stable knockdown lines.

value: breast cancer

value: breast cancer cell line

value: epithelial

value: PGK1 knockdown (shPGK1)


title: Subject P058 (P058-T3F)


title: 1103-2 #1 P2_4

description: Library name: lib105946

value: RA

value: female

value: BPD

value: AEC


title: mutant #1-2

description: Library name: Sh11_SLF2_C1_2


title: sublibrary9

description: Library name: scRNA_seq_sub9

value: lung

value: treated with vehicle, 6-OHDA, or BIBO3304, both in the presence and absence of seeded PDAC cells.


title: shPgk1_2

description:
Library name: Sample 5
4T1 cells with PGK1 knockdown (shPGK1), replicate 2


title: mutant #1-1

description: Library name: Sh10_SLF2_C1_1

value: Human iPS derived hematopoietic stem and progenitor cells


title: WT Control, rep 2

description:
Library name: Control B
FPKM.Control_g1B_g1


title: Subject P023 (P023-T1F)

value: Serum/Plasma


title: SNCA-GR mouse M9376, olfactory bulb, snRNA-seq ONT long-read

city: Seattle

first: Benjamin

last: Logsdon

address: 1150 Eastlake Ave E Ste 600/700

institute: Cajal Therapeutics

description:
Library name: LL3-250509-02
ONT long-read cDNA sequencing of 10 ng of amplified 10x 5' cDNA (from the same Chromium GEM-RT amplicon used for LX3-250506-02) 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: Olfactory bulb

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: Olfactory bulb

value: nuclei

tag: age

value: 55 days

value: male

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

tag: strain

value: SNCA-GR (JAX #39166)


title: WT Control, rep 1

description:
Library name: Control A
FPKM.Control_g1A_g1

value: Oral squamous

value: WT Control


title: Subject HC027 (HC027)

value: Healthy control


title: shPgk1_1

description:
Library name: Sample 4
4T1 cells with PGK1 knockdown (shPGK1), replicate 1

value: breast cancer

value: breast cancer cell line

value: epithelial

value: PGK1 knockdown (shPGK1)


title: Subject P058 (P058-T1F)

value: Patient


title: shNC_3

description:
Library name: Sample 3
4T1 cells transduced with non-targeting shRNA control, replicate 3

value: wild type


title: corrected #2-2

description: Library name: AT_Sh13_a1

library_source: genomic

data_processing:
Illumina bcl2fastq (v2.20) were performed for converting fastq files and separation by samples with default setting
Reads were trimmed for adapters and low-quality bases using Trim Galore (v0.6.10).
Trimmed reads were aligned to the human hg38 reference genome using Bowtie2 (v2.5.1).
PCR duplicates were removed using Picard (v3.0.0), mitochondrial reads were removed using Samtools (version 1.19), and ENCODE blacklisted regions were filtered out using bedtools2 (version 2.31.1).
Filtered reads were used for peak calling with MACS2 (v2.2.9.1) using a q-value cutoff of 0.05.
Assembly: GRCh38
Supplementary files format and content: bed.files

molecule: genomic DNA

extract_protocol:
QIAGEN MinElute PCR Purification Kit
Fast-ATAC protocol

value: Human iPS derived hematopoietic stem and progenitor cells

value: corrected

tag: batch


title: Subject P060 (P060-T1F)

value: Serum/Plasma


title: Subject P031 (P031-T1F)


title: CSMD3, KO guide 2, rep 3

description:
Library name: KO g2 C
FPKM.Knockout_g2C

value: CSMD3 knockout


title: corrected #1-2

description: Library name: AT_Sh14_a7


title: CSMD3, KO guide 2, rep 2

description:
Library name: KO g2 B
FPKM.Knockout_g2B


title: WT8_diff

value: Spinal Cord

value: neural stem cells


title: 1103-2 #2 P2_6

description: Library name: lib105939

value: airway epithelial cells

value: female

value: BPD

value: AEC


title: Subject HC009 (HC009)

value: Healthy control


title: Subject P022 (P022-T1F)


title: shNC_2

description:
Library name: Sample 2
4T1 cells transduced with non-targeting shRNA control, replicate 2

value: breast cancer


title: CSMD3, KO guide 2, rep 1

description:
Library name: KO g2 A
FPKM.Knockout_g2A

value: Oral squamous


title: Subject P047 (P047-T2F)


title: mutant #1-2

description: Library name: AT_Sh12_C1

value: mutant


title: corrected #2-1

description: Library name: AT_Sh16_a1


title: Subject P018 (P018-T1F)


title: WT6_proli_NS


title: CSMD3, KO guide 1, rep 3

description:
Library name: KO g1 C
FPKM.Knockout_g1C


title: patient with sepsis-associated ARDS 4

city: Nanning City

first: Qicheng

last: Long

state: Guangxi Zhuang Autonomous Region

address: No.6 Shuangyong Road

department: Department of Intensive Care Unit

institute: The First Affiliated Hospital of Guangxi Medical University

description: Library name: SA4

data_processing:
Raw sequencing reads were filtered using SOAPnuke to remove adapter contamination, low-quality reads, and reads containing excessive ambiguous bases. Clean reads were aligned to the human reference genome (GRCh38) using Bowtie. Known miRNAs were identified based on miRBase, and novel miRNAs were predicted using miRDeep. Read counts for each miRNA were calculated, and expression levels were normalized as transcripts per million (TPM). Differential expression analysis was performed using DESeq2 based on the raw read counts.
The processed expression matrices include both known miRNAs annotated in miRBase and putative novel miRNAs predicted by miRDeep. Novel miRNAs are represented by their miRDeep-assigned identifiers.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts and RPM table for all Samples

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted from peripheral whole blood samples using a commercially available RNA extraction kit according to the manufacturer’s instructions. The concentration and purity of the extracted RNA were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent Bioanalyzer or equivalent platform. Only RNA samples that met the quality control requirements were used for subsequent library construction.
small RNA libraries were constructed separately. Briefly, small RNAs were ligated with 3′ and 5′ adapters, reverse-transcribed into cDNA, amplified by PCR, and purified to obtain the final small RNA libraries.

value: Peripheral blood

tag: disease state

value: patient with sepsis-associated ARDS


title: shNC_1

description:
Library name: Sample 1
4T1 cells transduced with non-targeting shRNA control, replicate 1

value: breast cancer cell line

value: epithelial

value: wild type


title: CSMD3, KO guide 1, rep 2

description:
Library name: KO g1 B
FPKM.Knockout_g1B


title: Subject HC002 (HC002)

value: Serum/Plasma


title: Subject P045 (P045-T2F)

value: Patient


title: SK-MEL-28, 10 uM ASO550 (dIRE), biol rep 2

description:
Library name: MB107-10uM-ASO550-rep2-31
column MB107-10uM-ASO550-rep2-31 in MB107_deseq2_tmm_norm_counts.tsv

data_processing:
Bcl -> FASTQ demultiplexing performed by Azenta (bcl2fastq).
Transcript-level quantification with Salmon v1.10.0 against the GENCODE human transcriptome (confirm release).
Transcript counts aggregated to gene level with tximport.
Gene-level counts normalized in DESeq2 v1.38.3 (TMM); differential expression testing by DESeq2 Wald test.
Assembly: GRCh38 (GENCODE release to be confirmed)
Supplementary files format and content: MB107_deseq2_tmm_norm_counts.tsv: tab-delimited gene x sample matrix of DESeq2 TMM-normalized counts. 14,892 Ensembl gene IDs x 36 samples; column names match *library name values (with ASO2-REP2-29 and ASO2-REP2-30 corresponding to library indices 29 and 30 -- see naming note in accompanying documentation).

growth_protocol: SK-MEL-28 cells (ATCC HTB-72; working stock SKMEL28_P4) cultured in EMEM (ATCC 30-2003) + 10% FBS (Atlas Biologicals F-0500-A) + 1% Penicillin/Streptomycin (Thermo Scientific 15140122). Cells were thawed at passage 4 in a 10 cm plate at 1.478e6 cells (~2.6e4 cells/cm^2), grown 3 days, then plated on 2025-09-29 into 24-well plates at 80,000 cells/well in 550 uL medium and grown ~24 h before transfection.

extract_protocol:
Cell pellets were lysed in 1 mL cold Trizol (Invitrogen 15596026) on ice, vortexed 2 x 30 s, incubated 5 min at RT; 200 uL chloroform added, shaken 15 s, incubated 3 min at RT, centrifuged 15 min at 12,000 x g / 4 C. The aqueous phase was mixed 1:1 with 70% ethanol and purified on Qiagen RNeasy MinElute Micro columns per the UPenn Trizol/Qiagen hybrid protocol (Buffer RW1 wash, two RPE washes, 80% EtOH wash, 5 min dry spin, elution in 15 uL nuclease-free water). RNA was quantified by NanoDrop (A260/A280 1.98-2.05, A260/A230 1.83-2.22 across 36 samples).
Total RNA (12 uL per sample, 160-427 ng/uL) was submitted to Azenta Life Sciences (project 30-1251841615) for standard bulk poly(A) RNA-Seq library preparation. Illumina 2x150 bp paired-end, ~25-35 M reads/sample. (Exact kit and stranded chemistry to be confirmed with Azenta; likely NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.)

treatment_protocol: On 2025-09-30, cells were transfected with one of four ASOs (ASO2 non-targeting control, ASO43 SNCA-dIRE-selective, ASO550 SNCA-dIRE-selective from Biospring; ASO387 SNCA-IRE-selective from IDT) at 0.2 uM, 2 uM, or 10 uM final concentration in the well. ASO stocks were pre-diluted to 2 mM in PBS, then serially diluted in water. For each transfection, 5.5 uL of 100x ASO in Opti-MEM (Gibco 31985062) and 1.5 uL Lipofectamine RNAiMAX (Thermo Fisher 13778150) in Opti-MEM were mixed 1:1, incubated 5 min at RT, and 50 uL of the ASO/lipid complex added dropwise to 500 uL of medium per well. n=3 biological replicates per (ASO x dose) condition. Cell pellets were collected 3 days post-transfection (2025-10-03) using Accutase, centrifuged at 500 x g / 5 min / 4 C, and stored at -80 C.

value: melanoma (metastatic melanoma-derived)

value: SNCA-dIRE-selective ASO (ASO0550, Biospring; 2'-O-methoxyethyl/DNA gapmer); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation

tag: dose

value: 10 uM

tag: replicate


title: corrected #1-1

description: Library name: AT_Sh17_a7

value: Human iPS derived hematopoietic stem and progenitor cells

value: corrected


title: mutant #1-1

description: Library name: AT_Sh15_C1


title: Subject P014 (P014-T2F)

tag: tissue

tag: condition


title: CSMD3, KO guide 1, rep 1

description:
Library name: KO g1 A
FPKM.Knockout_g1A

tag: cell type

value: CSMD3 knockout


title: patient with sepsis-associated ARDS 3

description: Library name: SA3


title: Subject P045 (P045-T1F)


title: FOXL2-deltaCter, dox, rep3

city: PARIS

first: Anne Laure

last: Todeschini

address: 15 rue hélène brion

institute: CNRS/Université Paris Cité

description: Library name: Sample 15

data_processing:
primary analysis based on AOZAN software (ENS, Paris) was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5)
Fastq files were then aligned using STAR algorithm (version 2.7.11b)
Reads were then counted using RSEM (v1.3.3)
the statistical analyses on the read counts were performed with R (version 4.4.2) and the DESeq2 package (DESeq2_1.42.1)
Assembly: Ensembl release 113, GRCh38
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: KGN FOXL2WT/WT

growth_protocol: KGN cells were maintained in DMEM-F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA extractions were performed with the TRI-reagent supplier’s instructions (Life technologies, 15596-018).
350 ng of high-quality total RNA sample (RIN =10) was processed using Stranded mRNA Prep kit (Illumina) according to manufacturer instructions, Illumina Nextseq 2000 instrument using 59 base-length reads in a paired-end mode

treatment_protocol: treated with 500 ng/ml doxycycline for 24 h before RNA extraction

value: KGN FOXL2WT/WT

value: Granulosa cell line

value: 500 ng/ml doxycycline, 24h


title: patient with sepsis-associated ARDS 1

description: Library name: SA1


title: Tumor, CD45+ CD3-, Combo treated

city: Dallas

first: Qiao

last: Jian

state: TX

address: 6000 Harry Hines Blvd

department: department of pathology

institute: University of Texas southwestern medical center

description:
Library name: Combo-tumor CD45+ CD3-
10X Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger (version 7.1.0, 10x Genomics) to generate feature-barcode matrices.
Assembly: mm10
Supplementary files format and content: HDF5 feature-barcode matrix

source_name: tumor

extract_protocol:
C57BL/6J mice (n = 6 per group) were inoculated with B16-cEGFR cells and treated with PBS, 5μg of CmAb-IL2 and 80μg of CmAb-(IL10)2 by intraperitoneal injection on days 9 and 12. The tumor tissues were collected and digested on day 14. The CD45+ cells from CmAb-(IL10)2 and CmAb-IL2 combination therapy treated B16-cEGFR tumor were isolated by with CD45 (TIL) selection kit (STEMCELL). CD3+ and CD3- live cells were sorted from enriched CD45+ cells by BD FACSMelody™.
Single-cell suspensions were loaded onto a Chromium Single Cell Chip (10x Genomics) according to the manufacturer’s instructions for coencapsulation with barcoded gel beads at a target capture rate of approximately 10,000 individual cells per sample. Captured mRNA was barcoded during cDNA synthesis, and the barcoded cDNA was converted into pooled single-cell RNA-seq libraries for Illumina sequencing by using the Chromium Single Cell 5′ Library & Gel Bead Kit (10x Genomics) according to the manufacturer’s instructions. All libraries were sequenced with a NovaSeq 6000 sequencing platform.

treatment_protocol: CmAb-(IL10)2 and CmAb-IL2 combination treatment

value: tumor

value: immune cells


title: FOXL2-deltaCter, dox, rep2

description: Library name: Sample 14


title: Tumor, CD45+ CD3+, Combo treated

description:
Library name: Combo-tumor CD45+ CD3+
10X Genomics

value: CmAb-(IL10)2 and CmAb-IL2 combination treatment


title: Subject P036 (P036-T2F)


title: patient with sepsis without ARDS 4

description: Library name: SWA4

value: Peripheral blood

value: patient with sepsis without ARDS


title: FOXL2-deltaCter, dox, rep1

description: Library name: Sample 13


title: Tumor, CD45+ CD3-, untreated

description:
Library name: Control-tumor CD45+ CD3-
10X Genomics

value: untreated


title: Subject P012 (P012-T1F)

value: Serum/Plasma


title: FOXL2-S101D, dox, rep3

description: Library name: Sample 12

value: FOXL2WT/WT, pLVX-TetOne-Puro-FOXL2S101D


title: patient with sepsis without ARDS 2

description: Library name: SWA2


title: FOXL2-S101D, dox, rep2

description: Library name: Sample 11


title: patient with sepsis without ARDS 1

description: Library name: SWA1


title: CAMCB4

city: Boston

first: Maeva

middle: general

last: Chauvin

state: MA

address: 55 fruit st

institute: general hosp corp d/b/a mass general hosp

description: Library name: CAMCB4

data_processing:
high-quality total RNA was used for mRNA enrichment using poly(A) selection (or rRNA depletion if applicable, if you know it). The enriched RNA was then fragmented and reverse-transcribed to generate first-strand and second-strand cDNA.
Libraries were sequenced on an Illumina platform to generate paired-end reads.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Omentum

extract_protocol:
Primary mesothelial cells were isolated from fresh omentum of C57BL/6J mice. Tissue samples were mechanically minced and enzymatically digested in DMEM supplemented with 5% serum, 2 mg/mL collagenase type I, and 40 U/mL DNase I at 37°C for 30 minutes. The resulting suspension was transferred into a dissociation tube and further processed using the gentleMACS dissociator system to facilitate tissue dissociation. The cell suspension was then filtered through a 70 µm cell strainer, washed, and plated in culture conditions.  Cells were cultured for one week prior to experimental treatment. Cancer-associated mesothelial cells (CAMCC and CAMCB) were generated by exposing primary mesothelial cells (MCs) to standardized cancer cell-conditioned media from two cell lines KPCA.C and KPCA.B respectively  for 72 hours.  Total RNA was extracted using the Qiagen RNA extraction kit following the manufacturer’s instructions.
RNA-seq libraries were prepared by Novogene using a standard Illumina-compatible library preparation protocol.

value: Omentum

value: Primary MC

value: Primary Mesothelial cells

value: KPCA condition media


title: Subject P036 (P036-T1F)

value: Patient


title: ACCs - P5

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

description: Library name: Auto-fluorescent Cluster Complexes - ACCs

data_processing:
Single cell RNA-Seq libraries were sequenced to 50,000 reads per cell on an Illumina NovaSeq 6000
The BCL files were de-multiplexed using CellRanger mkfastq version 3.01 and then aligned and quan-tify them against GRCh38 using Cellranger count
We performed quality control checks for each sample in R for each sample and removed any cells with fewer than 1000 reads or 500 genes or greater than 10% mitochondrial reads. Any cells which expressed haemoglobin genes were also removed from the analysis. Doublets were predicted using DoubletFinder and filtered from the data.
The Seurat R package (version 4.3.0) was then used to process the data prior to integration. Firstly the raw data was normalised using the standard parameters.
Assembly: GRCh38
Supplementary files format and content: csvFile containing filtered count matrix for each cell
Supplementary files format and content: csv with metadata for each cell, contains cell identifcation
Supplementary files format and content: Cellranger filtered matix files

source_name: Retina

extract_protocol:
All samples were isolated and dissociated to single cells using a neurosphere dissociation kit (Miltenyi Biotech).
Libraries generated using the Chromium Single Cell 3’ Library & Gel Bead Kit (version 3, 10x Genomics)

value: Retina

value: FACS sorted based on auto-fluorescence


title: FOXL2-S101D, dox, rep1

description: Library name: Sample 10

value: KGN FOXL2WT/WT

value: Granulosa cell line


title: Subject P148 (P148-T2F)


title: CAMCB3

description: Library name: CAMCB3


title: healthy control 4

description: Library name: HC4

value: healthy control


title: FOXL2-S101A, dox, rep3

description: Library name: Sample 9

value: FOXL2WT/WT, pLVX-TetOne-Puro-FOXL2S101A

value: 500 ng/ml doxycycline, 24h


title: Subject P035 (P035-T1F)


title: CAMCB2

description: Library name: CAMCB2


title: healthy control 3

description: Library name: HC3

value: Peripheral blood


title: Subject P122 (P122-T1F)


title: CAMCB1

description: Library name: CAMCB1


title: Subject P028 (P028-T1F)


title: FOXL2-S101A, dox, rep1

description: Library name: Sample 7


title: CAMCC4

description: Library name: CAMCC4


title: FOXL2-WT, dox, rep3

description: Library name: Sample 6

value: FOXL2WT/WT, pLVX-TetOne-Puro-FOXL2WT


title: Subject P123 (P123-T3F)


title: patient with sepsis-associated ARDS 4

description: Library name: SA4

data_processing:
For mRNA and lncRNA analysis, raw sequencing reads were filtered using SOAPnuke to remove adapter contamination, low-quality reads, and reads containing excessive ambiguous bases. Clean reads were aligned to the human reference genome using HISAT2. Novel transcripts were assembled using StringTie and compared with the reference annotation using Cuffcompare to identify putative novel lncRNA transcripts. Gene-level read counts were generated using featureCounts based on the final gene annotation. Gene expression levels were normalized and reported as fragments per kilobase of transcript per million mapped reads (FPKM). Differential expression analysis was performed using DESeq2 based on the raw read counts.Novel transcripts were assembled using StringTie and compared with the reference annotation using Cuffcompare. The processed expression matrices include both annotated genes and putative novel transcripts. Novel transcripts are represented by StringTie-generated XLOC identifiers.
For circRNA analysis, raw sequencing reads were filtered using SOAPnuke. Clean reads were aligned to the reference genome using both Bowtie2 and BWA. Candidate circular RNAs were identified independently using find_circ and CIRI, and the integrated results were used for downstream analysis. CircRNA expression levels were normalized as reads per million mapped reads (RPM). Differentially expressed circRNAs were identified using NOISeq.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM or RPM table for all Samples

extract_protocol:
Total RNA was extracted from peripheral whole blood samples using a commercially available RNA extraction kit according to the manufacturer’s instructions. The concentration and purity of the extracted RNA were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent Bioanalyzer or equivalent platform. Only RNA samples that met the quality control requirements were used for subsequent library construction.
ribosomal RNA was removed from total RNA, and strand-specific transcriptome libraries were constructed following the standard protocol. The purified RNA was fragmented and reverse-transcribed into cDNA, followed by end repair, adaptor ligation, PCR amplification, and library purification

value: patient with sepsis-associated ARDS


title: CAMCC3

description: Library name: CAMCC3


title: FOXL2-WT, dox, rep2

description: Library name: Sample 5


title: patient with sepsis-associated ARDS 3

description: Library name: SA3


title: Subject P027 (P027-T1F)

value: Serum/Plasma


title: Subject P123 (P123-T1F)


title: CAMCC1

description: Library name: CAMCC1


title: Subject P019 (P019-T1F)


title: FOXL2-WT, without dox treatment, rep3

description: Library name: Sample 3

value: without Doxycycline


title: MPMC3

description: Library name: MPMC3

value: Omentum


title: patient with sepsis without ARDS 4

description: Library name: SWA4

value: patient with sepsis without ARDS


title: FOXL2-WT, without dox treatment, rep2

description: Library name: Sample 2


title: FOXL2-WT, without dox treatment, rep1

description: Library name: Sample 1


title: Subject P117 (P117-T1F)


title: Subject P_NA (P_NA4 (null))

description:
reason for sample removal: Disease 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: MPMC2

description: Library name: MPMC2

value: Primary MC

value: Primary Mesothelial cells


title: patient with sepsis without ARDS 3

description: Library name: SWA3


title: Subject P041 (P041-T3F)

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: Patient


title: H1155 cells, chimera bio rep 2

first: Lance

last: Terada

address: 5323 Harry Hines Blvd, MC 8448

institute: University of Texas Southwestern

description: Library name: TA_2

data_processing:
Adaptors were trimmed (TrimGalore v0.6.4) and reads aligned to the human genome (GRCh38) using STAR (v2.7.3a).
Gene expression quantification was performed using the featurecount function from the Subread package (v1.6.3).
DESeq2 R Bioconductor package was used to normalize read counts and identify differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file including counts for each sample

extract_protocol:
Total RNA was extracted using RNeasy from Qiagen
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina).  Poly-A RNA was purified and fragmented before strand specific cDNA synthesis.

value: Lung carcinoma

value: chimera


title: patient with sepsis without ARDS 2

description: Library name: SWA2


title: Primary microglia, caspase-3/7 inhibitor, 120min, rep3

city: Seville

first: Miguel

last: Burguillos

address: Antonio Maura Montaner

country: Spain

institute: IBiS-CSIC

description:
Library name: INH_3
primary microglia isolated from whole brain excluding cerebellum

data_processing:
NovaSeq Control Software v1.8 was used for basecalling
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQ Generation based on bcl2fastq with default parameters. Reads were mapped to murine genome assembly (GRCm39) using HISAT2  using default parameters but specifying --rna-strandness RF
Differential expressed genes between samples were analysed using edgeR, genes positions were obtained from the GTF file from GENCODE (M36, GRCm39)
Assembly: GRCm39
Supplementary files format and content: Feature count files for each sample from edgeR

source_name: brain

growth_protocol: Postnatal P1–P4 mice were sacrificed, and brains were carefully dissected with meninges and cerebellum removed. Cortices were washed in ice-cold calcium- and magnesium-free Hank's Buffered Salt Solution (HBSS; Biowest). Brains were then minced and resuspended in ice-cold HBSS. After washing, tissues were incubated for 15 minutes at 37ºC in HBSS containing 0.1% trypsin and 0.05% DNase, then resuspended in DMEM (high glucose, GlutaMAX, Gibco) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S). Cells from one brain were seeded into T25 flasks; cells pooled from 4–5 brains were seeded into T75 flasks. Medium was fully replaced 24 hours after seeding. GM-CSF (5 ng/mL) was added 7 days after seeding. Microglial cells were harvested from confluent astrocyte monolayers, 10–12 days after the initial seeding, by tapping the side of the culture flask. These microglial cells found in the medium were plated into 24-well dishes. Experiments were performed 24 h after the final plating.

extract_protocol:
Total RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen, Cat# 80204), according to the manufacturer's instructions. Cells were lysed directly in the culture flasks using the provided lysis buffer containing guanidine thiocyanate. Homogenized lysates were passed through the AllPrep spin columns to separate DNA and RNA. RNA was eluted in RNase-free water and stored at -80C until use. RNA concentration and purity were assessed using a NanoDrop spectrophotometer and RNA integrity was confirmed using an Agilent Bioanalyzer.
Total RNA-Seq libraries were prepared using Illumina Stranded Total Prep with Ribo Zero Plus

treatment_protocol: Cells were treated with vehicle or 40uM caspase-3/7 inhibitor (Cayman Chemical; Cat# 14464) for 120 minutes

value: brain

value: microglia

value: wild type

value: caspase-3/7 inhibitor (40 uM, 120 min)


title: Subject P_NA (P_NA3 (null))

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.

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


title: H1155 cells, chimera bio rep 1

description: Library name: TA_1


title: patient with sepsis without ARDS 1

description: Library name: SWA1


title: Primary microglia, vehicle, 120min, rep3

description:
Library name: C_3
primary microglia isolated from whole brain excluding cerebellum

value: vehicle (120 min)


title: healthy control 4

description: Library name: HC4

value: Peripheral blood

value: healthy control


title: Subject P055 (P055-T1F)


title: H1155 cells, control bio rep 2

description: Library name: control_2

value: vector


title: Primary microglia, caspase-3/7 inhibitor, 120min, rep2

description:
Library name: INH_2
primary microglia isolated from whole brain excluding cerebellum


title: H1155 cells, control bio rep 1

description: Library name: control_1


title: Subject P008 (P008-T2F)

value: Serum/Plasma


title: SK-MEL-28, 10 uM ASO2 (NTC), biol rep 1

description:
Library name: MB107-10uM-ASO2-rep1-25
column MB107-10uM-ASO2-rep1-25 in MB107_deseq2_tmm_norm_counts.tsv

value: melanoma (metastatic melanoma-derived)

value: Non-targeting control ASO (ASO0002, Biospring); transfected with Lipofectamine RNAiMAX in Opti-MEM; 3-day incubation

value: 10 uM


title: 50 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 3, H3K27ac CUT&Tag

first: Yi-Lan

last: Weng

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

description: Library name: SS0630YC070

data_processing:
Raw paired-end reads were assessed for sequencing quality and adapter contamination, and low-quality bases and adapter sequences were trimmed using Trimmomatic.
RNA-seq reads were aligned to the human GRCh38/hg38 reference genome using the STAR aligner. Gene-level read counts were generated using STAR, followed by normalization and differential-expression analysis using DESeq2.
CUT&Tag reads were aligned to the human GRCh38/hg38 reference genome using STAR. Duplicate reads were handled and low-quality alignments were filtered before normalization. H3K27ac-enriched regions were identified by peak calling with MACS2.
Assembly: GRCh38/hg38
Supplementary files format and content: RNA-seq processed data include a gene-expression matrix and differential-expression analysis results in tab-delimited text format.
Supplementary files format and content: CUT&Tag processed data include genome-browser signal tracks in bigWig format.
Library strategy: CUT&Tag

growth_protocol: HMC3 human microglial cells were obtained from ATCC. Cells were maintained in high-glucose DMEM supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
For RNA-seq, total RNA was extracted using TRIzol reagent. For CUT&Tag, nuclei or permeabilized cells were prepared according to the CUT&Tag workflow, and tagmented DNA was purified using ampure beads.
RNA-seq libraries were prepared using the Smart-seq2 protocol with poly(A) RNA selection from 100 ng RNA, followed by amplification, indexing, and library purification. H3K27ac CUT&Tag libraries were generated using an anti-H3K27ac antibody and a protein A/G–Tn5 transposase-based CUT&Tag workflow, followed by PCR amplification, indexing, and library purification. All libraries were sequenced using paired-end sequencing.

treatment_protocol: HMC3 cells were treated with vehicle control or PFOS at 25 or 50 µM for 24 hours. For recovery samples, PFOS-containing medium was removed after 24 hours, cells were washed as appropriate, and fresh PFOS-free medium was added for an additional 24-hour recovery period.

value: microglial cell

value: 50 µM PFOS; 24 h treatment followed by 24 h recovery


title: Subject P110 (P110-T3F)

value: Patient


title: 50 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 2, H3K27ac CUT&Tag

description: Library name: SS0630YC066


title: Primary microglia, vehicle, 120min, rep2

description:
Library name: C_2
primary microglia isolated from whole brain excluding cerebellum


title: Primary microglia, caspase-3/7 inhibitor, 120min, rep1

description:
Library name: INH_1
primary microglia isolated from whole brain excluding cerebellum


title: healthy control 1

description: Library name: HC1


title: 22_T397_P3ALI

description: Library name: lib45769

data_processing:
Base-calling was performed using CASAVA v.1.8.2.
FASTQ reads were trimmed using fastq-mcf (ea-utils, v.1.1.2) to remove SMARTer adapter sequences.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0); duplicate alignments were marked and removed using Picard MarkDuplicates.
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, 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

extract_protocol:
Airway epithelial cells from school age children or neonates were cultured in ALI or submerged 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: culture

value: air liquid interface

tag: age group

value: child

tag: donor id


title: 25 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 3, H3K27ac CUT&Tag

description: Library name: SS0630YC058

value: 25 µM PFOS; 24 h treatment followed by 24 h recovery


title: Subject P138 (P138-T2F)


title: 21_T392_P3ALI

description: Library name: lib45768


title: WT2

city: zhengzhou

first: Fang yuan

last: Zhen

state: henan

address: 河南省郑州市

institute: Sichuan Provincial People's Hospital

description: Library name: Sample7

data_processing:
Downstream analysis was performed using a combination of programs including Bowtie2, Tophat2, HTseq, Cufflink and our wrapped scripts. Alignments were parsed using Tophat program and differential expressions were determined through DESeq/DEGseq. GO and KEGG enrichment were implemented by the GOseq R package and KOBAS. Gene fusion and difference of alternative splicing event were detected by MISO and SOAPfuse software
Assembly: Reference genome and gene model annotation files were downloaded from genome website browser (mm10 (GRCm38)) directly. Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9. Bowtie uses a BWT(Burrows-Wheeler Transformer) algorithm for mapping reads to the genome and Tophat can generate a database of splice junctions based on the gene model annotation file and thus achieve a better mapping result than other non-splice mapping tools.
Supplementary files format and content: The processed data will be provided as a tab-delimited text file. The file contains a matrix of gene expression counts, with rows representing genes identified by their official gene symbols and columns representing individual samples. The numerical values within the matrix represent normalized gene expression levels (e.g., FPKM ) for each gene in each sample.

source_name: eyeball

extract_protocol:
First, take the retinal tissue sample (fresh or flash-frozen) and immediately place it into a microcentrifuge tube containing lysis buffer from an RNA extraction kit. Homogenize the tissue thoroughly using a homogenizer to ensure all cells are completely lysed and all RNA is released. This is a critical step for high yield. After homogenization, centrifuge the sample briefly to pellet any debris.  Next, add ethanol to the lysate and transfer the mixture to a spin column from the kit. Centrifuge the column to allow the RNA to bind to the membrane while proteins and other impurities flow through. Wash the column multiple times with different wash buffers provided in the kit to remove any residual DNA and contaminants.  Finally, place the column into a new collection tube. Add pre-warmed, RNase-free water or elution buffer directly onto the center of the column membrane. Wait for a minute to ensure the RNA is fully dissolved, then centrifuge to collect the highly purified total RNA.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: eyeball

value: wildtype


title: Subject P002 (P002-T2F)

first: Paul

last: Utz

address: 269 Campus Dr

institute: Stanford University School of Medicine


title: 50 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 1, H3K27ac CUT&Tag

description: Library name: SS0630YC062


title: WT1

description: Library name: Sample6


title: 20_T389_P3ALI

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib45767


title: Subject P127 (P127-T1F)


title: HET2

description: Library name: Sample5

value: heterozygous


title: 19_T385_P3ALI

description: Library name: lib45766


title: vehicle control, 24 h treatment followed by 24 h recovery, biological replicate 3, H3K27ac CUT&Tag

description: Library name: SS0630YC046

value: vehicle control; 24 h treatment followed by 24 h recovery


title: Subject P_NA (P_NA2 (null))

description:
reason for sample removal: Disease 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: HET1

description: Library name: Sample4


title: KO3

description: Library name: Sample3

value: knockout


title: vehicle control, 24 h treatment followed by 24 h recovery, biological replicate 2, H3K27ac CUT&Tag

description: Library name: SS0630YC042


title: vehicle control, 24 h treatment followed by 24 h recovery, biological replicate 1, H3K27ac CUT&Tag

description: Library name: SS0630YC038


title: Subject P105 (P105-T1F)


title: KO2

description: Library name: Sample2


title: 16_T392_P3sub

description: Library name: lib45763

value: submerged


title: 50 µM PFOS, 24 h treatment, biological replicate 3, H3K27ac CUT&Tag

description: Library name: SS0630YC034

value: 50 µM PFOS; 24 h treatment


title: KO1

description: Library name: Sample1


title: 15_T389_P3sub

description: Library name: lib45762


title: patient with sepsis without ARDS 3

description: Library name: SWA3

value: Peripheral blood

value: patient with sepsis without ARDS


title: Subject P003 (P003-T2F)

value: Serum/Plasma


title: healthy control 2

description: Library name: HC2

value: healthy control


title: FOXL2-S101A, dox, rep2

description: Library name: Sample 8

value: KGN FOXL2WT/WT

value: Granulosa cell line

value: FOXL2WT/WT, pLVX-TetOne-Puro-FOXL2S101A

value: 500 ng/ml doxycycline, 24h


title: Subject P014 (P014-T1F)

value: Patient


title: 50 µM PFOS, 24 h treatment, biological replicate 2, H3K27ac CUT&Tag

description: Library name: SS0630YC030

value: microglial cell


title: SI, 20w Naïve KO

city: Beijing

first: Jie

state: Beijing

address: No. 1, Qinghuayuan, Haidian District

department: Institute for Immunology

institute: Tsinghua University

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope(https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline.
STAR v2.6.1a was used to map reads to the reference genome GRCm38 (mm10)
UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1,and used to generate expression matrix files for subsequent analysis
Assembly: GRCm38 (mm10)
Supplementary files format and content: matrix.mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary files format and content: barcodes.tsv, cell names (colname names of the count matrix)
Supplementary files format and content: genes.tsv, gene names (row names of the count matrix)

source_name: small intestine

extract_protocol:
The cell suspension is injected into the SCOPE-chip™ microfluidic chip, where single cells are separated based on the principle of the "Poisson distribution." Cells fall into specially designed chip micro-wells under the influence of gravity, ensuring that only one cell falls into each micro-well. Subsequently, millions of magnetic beads carrying unique cell tags (Cell Barcodes) are added to the chip micro-wells, ensuring that only one magnetic bead falls into each micro-well. After cell lysis, the magnetic beads with unique cell tags (Barcodes) and molecular tags (UMI) capture mRNA by binding to the poly(A) tail of mRNA, labeling both the cells and the mRNA
Collect the magnetic beads from the chip, and reverse transcribe the captured mRNA into cDNA and amplify it.The cDNA is then fragmented, connected with adapters, and sequenced on Illumina novaseq 6000  with 150 bp paired end reads.

treatment_protocol: About 0.5 cm length of small intestine was cut at ~10 cm to the cecum, washed with PBS, Use sCelLiVE™ tissue dissociation solution to dissociate tissue samples into a single cell suspension, and dilute the cells to an appropriate concentration, generally 2-2.5 × 10^5 Cells/mL

value: small intestine

value: 20 week old naive


title: 14_T385_P3sub

description: Library name: lib45761

value: airway epithelial cells

value: child


title: Subject P109 (P109-T1F)


title: 50 µM PFOS, 24 h treatment, biological replicate 1, H3K27ac CUT&Tag

description: Library name: SS0630YC026


title: SI, 20w Naïve WT


title: 13_T384_P3sub

description: Library name: lib45760


title: 25 µM PFOS, 24 h treatment, biological replicate 3, H3K27ac CUT&Tag

description: Library name: SS0630YC022

value: 25 µM PFOS; 24 h treatment


title: TRF2 Rep 2

city: Madison

first: Jeffrey

last: Dilworth

email: jdilworth@ohri.ca, fdilworth@wisc.edu

state: WI

address: 1111 Highland Ave - WIMR II 4518

department: Cell and Regenerative Biology

institute: University of Wisconsin - Madison

data_processing:
Nextera adapters were trimmed from sequenced reads with Cutadapt 4.4 (Python 3.9.6).
Trimmed sequences were aligned to mm10 using Bowtie2 version 2.4.4 with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Duplicates, non-uniquely aligned reads were marked with Picard (3.1.1) and filtered from BAMs using Samtools v1.10 (htslib 1.10). Retained mapped and properly paired reads with greater than 10 Q-score.
Genome coverage was calculated using bamCoverage v3.5.3 (deepTools v3.5.3) with the following parameters: --effectiveGenomeSize 2467481108 --binSize 1 --normalizeUsing 'RPGC' --ignoreForNormalization 'chrM' --extendReads.
Peaks were called using MACS (3.0.0) with parameters: -f BAMPE -g 2467481108 -q 0.05.
Assembly: GRCm38_mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

source_name: Skeletal muscle - Tibialis Anterior Muscle

growth_protocol: Animals were housed and bred in a local animal facility at a 12-hour dark/12-hour light cycle.

extract_protocol:
Tn5-PA tagemented DNA was treated with proteinase K, extracted with phenol chloroform, and precipitated with ethanol.
Extracted DNA was amplified with barcoded i5 and i7 compatible primers

treatment_protocol: 10 µl of Notexin was injected into TA muscles in samples from 3 days post-injury.

value: Primary cells

value: Muscle stem cells

value: Wildtype

value: 3 days-post notexin injury

tag: antibody

value: Rabbit anti-TRF-2 Novus Biologicals Cat# NB100-57130


title: Subject P065 (P065-T1F)

city: Stanford

value: Serum/Plasma


title: 12_1050-3_P3ALI

city: Seattle,

description: Library name: lib45759

value: air liquid interface

value: neonate


title: Subject P_NA (P_NA5 (null))


title: 25 µM PFOS, 24 h treatment, biological replicate 2, H3K27ac CUT&Tag

description: Library name: SS0630YC018

tag: treatment


title: TRF2 Rep 1

value: Skeletal muscle - Tibialis Anterior Muscle


title: 11_1045-4_P3ALI

description: Library name: lib45758


title: 25 µM PFOS, 24 h treatment, biological replicate 1, H3K27ac CUT&Tag

description: Library name: SS0630YC014


title: Subject P112 (P112-T1F)


title: IgG

value: Rabbit IgG Santa Cruz SC-2027


title: vehicle control, 24 h treatment, biological replicate 3, H3K27ac CUT&Tag

description: Library name: SS0630YC010

value: vehicle control; 24 h treatment


title: SAA_CsA_RvE1

city: Albany

first: Katherine

middle: C

last: MacNamara

state: NY

address: 47 New Scotland Avenue

department: Immunology and Microbial Disease

institute: Albany Medical College

description:
Library name: Sample 4
10X Genomics

data_processing:
Samples were demultiplexed using bases2fastq version 2.1.0.1522407762. Genome alignment, barcode processing, and gene counting were performed in Partek Flow (version 12.8.2) using Cell Ranger - Gene Expression 9.0.0.
Assembly: Mouse mm10
Supplementary files format and content: Processed single-cell gene expression data are provided as 10x Genomics Cell Ranger–generated HDF5 (.h5) files. Each file contains the filtered feature-barcode count matrix in sparse format, along with the associated feature metadata (gene IDs, gene names, and feature types) and barcode metadata (cell barcodes that passed Cell Ranger filtering). The files follow the standard 10x Genomics HDF5 structure, with the count matrix and its indexing components stored under the /matrix group (see https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/analysis/outputs/outputs-h5-matrices).

source_name: Bone Marrow

extract_protocol:
Bone marrow cells were isolated from femurs and tibias via centrifugation and RBCs lysed. Total bone marrow was then resuspended in HBSS at 1200 cells/µL for downstream 10X Genomics scRNAseq preparation.
Library construction was performed following the manufacturer’s protocol for the 10X Genomics Chromium GEM-X Single Cell 5’ Kit v3. Briefly, single-cell suspension of bone marrow were combined with the master mix and loaded into a Chromium Next GEM Chip together with gel beads and partitioning oil to generate Gel Beads-in-Emulsion (GEMs). Within each GEM, cells were lysed and poly-adenylated RNA were reversed-transcribed using barcoded oligonucleotides on the gel beads, incorporating the cell barcode, UMI, and Illumina Read 1 sequence. After GEM dissolution, the barcoded cDNA was recovered, cleaned up with Silane DynaBeads, and amplified by PCR. Size-selected cDNA fragments (SPRIselect) were then used for 5’ gene expression library construction following the 10x protocol, during which the Illumina P5, P7, samples index, and Read 2 sequences were added.

treatment_protocol: Hybrid F1 (C57BL/6;Balb/c) mice, at 7- to 8 weeks of age, were exposed to sub-lethal radiation (350 RADs,137Cs source) and received 6.5x106 C57BL/6 splenocytes from age- and gender-matched donors via intraperitoneal injection 3-4 hours post radiation. SAA-induced mice were then treated with 10mg/kg Cyclosporine A (CsA) and/or 0.00125 mg/kg Resolvin E1 (RvE1) every other day by intraperitoneal injection starting on day 7 post-irradiation, for a total of five treatments. Healthy mice received no treatment.

value: Bone Marrow

value: Total Bone Marrow

tag: timepoint

value: 45 days post-irradiation


title: Subject P096 (P096-T2F)

source_name: Serum/Plasma

value: Patient


title: vehicle control, 24 h treatment, biological replicate 2, H3K27ac CUT&Tag

description: Library name: SS0630YC006

value: microglial cell


title: SAA_CsA

description:
Library name: Sample 3
10X Genomics

tag: genotype

value: 350 Rads + 6.5e7 C57BL/6 Splenocytes + 10mg/kg CsA day 7,9,11,13,15


title: Subject P027 (P027-T2F)


title: 10_1043-2_P3ALI

description: Library name: lib45757

source_name: airway epithelial cells

value: airway epithelial cells


title: vehicle control, 24 h treatment, biological replicate 1, H3K27ac CUT&Tag

description: Library name: SS0630YC002

tag: cell line


title: 9_1055-2_P3ALI

description: Library name: lib45756


title: SAA_RvE1

description:
Library name: Sample 2
10X Genomics


title: 7_1050-4_P2ALI

description: Library name: lib45754


title: Subject P120 (P120-T1F)


title: Subject P003 (P003-T3F)


title: 50 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 3

description: Library name: SS0630YC090

data_processing:
Raw paired-end reads were assessed for sequencing quality and adapter contamination, and low-quality bases and adapter sequences were trimmed using Trimmomatic.
RNA-seq reads were aligned to the human GRCh38/hg38 reference genome using the STAR aligner. Gene-level read counts were generated using STAR, followed by normalization and differential-expression analysis using DESeq2.
CUT&Tag reads were aligned to the human GRCh38/hg38 reference genome using STAR. Duplicate reads were handled and low-quality alignments were filtered before normalization. H3K27ac-enriched regions were identified by peak calling with MACS2.
Assembly: GRCh38/hg38
Supplementary files format and content: RNA-seq processed data include a gene-expression matrix and differential-expression analysis results in tab-delimited text format.
Supplementary files format and content: CUT&Tag processed data include genome-browser signal tracks in bigWig format.

value: 50 µM PFOS; 24 h treatment followed by 24 h recovery


title: 6_1050-3_P2sub

description: Library name: lib45753

value: submerged


title: Healthy

description:
Library name: Sample 1
10X Genomics


title: 8_1041-3_P3ALI

description: Library name: lib45755


title: Subject P076 (P076-T2F)


title: 50 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 2

description: Library name: SS0630YC089


title: Irinotecan-treated Gsdme-deficient mice 4

city: Shimotsuke

first: Tadayoshi

last: Karasawa

address: 3311-1, Yakushiji

institute: Jichi Medical University

description: Library name: KO4

data_processing:
Paired-end reads were aligned to the mouse reference genome (GRCm38) using HISAT2 v[2.2.2] with default parameters.
Aligned reads were sorted by coordinate and indexed using SAMtools v[1.23].
Gene-level read counts were quantified using featureCounts (Subread package v[2.1.1])based on the Ensembl GRCm38.102 GTF annotation.
Differential expression analysis was performed using DESeq2 v[1.46.0] in R v[4.4.1].
Assembly: GRCm38
Supplementary files format and content: DESeq2-normalized gene expression counts. Tab-delimited text file with gene IDs (Ensembl gene ID) in rows and sample names in columns.

source_name: ileum

extract_protocol:
Total RNA was prepared using FastGene RNA premium Kit (NIPPON Genetics, Tokyo, Japan) according to the manufacturer’s instruction.
Strand-specific RNA sequencing libraries were prepared from total RNA using poly(A) selection for mRNA enrichment, by Genewiz (Suzhou, China), following the manufacturer's standard protocol.

value: ileum

value: Gsdme-/-

value: irinotecan


title: 5_1045-4_P2sub

description: Library name: lib45752


title: Subject P012 (P012-T2F)

value: Serum/Plasma


title: 50 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 1

description: Library name: SS0630YC088


title: Irinotecan-treated Gsdme-deficient mice 3

description: Library name: KO3


title: 4_1043-2_P2sub

description: Library name: lib45751

value: neonate


title: Subject P095 (P095-T1F)


title: Irinotecan-treated Gsdme-deficient mice 2

description: Library name: KO2


title: 25 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 3

description: Library name: SS0630YC087

value: 25 µM PFOS; 24 h treatment followed by 24 h recovery


title: 3_1055-2_P2sub

description: Library name: lib45750


title: Subject P090 (P090-T1F)


title: 25 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 2

description: Library name: SS0630YC086


title: Irinotecan-treated Gsdme-deficient mice 1

description: Library name: KO1


title: 2_1041-3_P2sub

description: Library name: lib45749


title: Rat 72 (GRC)

city: Research Triangle Park

first: Colette

last: Miller

state: NC

address: 109 TW Alexander

institute: U.S. Environmental Protection Agency

description:
Library name: index30-72-Chemical-Ozone008ppm_S1.fastq
index30-72-Chemical-Ozone008ppm_S1
Partek_GRC_351_Filter_observations_Sex_is_Females.txt

data_processing:
Partek Flow NGS analysis software (Build 11.0.24.0102) was used to demultiplex data, trim adapters, and remove low quality bases.
Processed reads were aligned using STAR 2.6.1d to rn6 (Ensembl release 104 v2).
Differentially expressed genes (DEGs) were determined using DESeq2 following median ratio normalization and statistical significance was set at Storey q-value < 0.05.
Assembly: rn6
Supplementary files format and content: tab-delimited text file contains normalized counts for each sample

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Total RNA was isolated from liver using the Direct-Zol RNA Miniprep kit (Zymo Research) and concentrations were determined by Qubit (ThermoFisher Scientific).
RNA quality was determined using Bioanalyzer (Beckman Coulter, Inc.), with RIN values > 7. Hepatic RNA samples were processed on Apollo324 for polyA selection prior to library preparation, which was performed using the PrepX mRNA library prep kit for Illumina (Takara Bio USA, Inc.). Sample products were measured for quality and quantity using the Bioanalyzer High Sensitivity DNA chips, with final pooled libraries quantified using the Qubit High Sensitivity kit.

treatment_protocol: On the mornings of GD 5 and 6 (0700 – 1100), pregnant rats were exposed to either filtered air or 0.8 ppm ozone for 4 hours (n = 12 per group). A silent air discharge generator (OREC) was used to generate ozone, which was then delivered to Rochester-style “Hinners” chambers using a mass flow controller. Ozone concentrations were continuously monitored during the exposures using an API Model 400 ozone analyzer (Teledyne Instruments; City of Industry, CA). Chambers were controlled for temperature (~22°C) and humidity (~50%). In offspring, exposures to filtered air or ozone occurred weekly following weaning on postnatal weeks 5 – 7. Due to the size of the offspring, the concentration of ozone used on the first week (postnatal week 5) was 0.4 ppm. The following exposures on postnatal weeks 6 and 7 occurred using 0.8 ppm.

value: Liver

value: Female

value: Ozone + Ozone


title: 25 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 1

city: Houston

description: Library name: SS0630YC085


title: Irinotecan-treated WT mice 4

description: Library name: WT4

value: Gsdme+/+


title: 1_1056-4_P1sub

description: Library name: lib45748


title: Rat 69 (GRC)

description:
Library name: index29-69-Chemical0-0Ozone0080ppm_S9.fastq
index29-69-Chemical0-0Ozone0080ppm_S9
Partek_GRC_351_Filter_observations_Sex_is_Females.txt


title: vehicle control, 24 h treatment followed by 24 h recovery, biological replicate 3

description: Library name: SS0630YC084

value: vehicle control; 24 h treatment followed by 24 h recovery


title: Irinotecan-treated WT mice 3

description: Library name: WT3


title: TA bio rep 3, input

description: Library name: TA3_input

data_processing:
Reads were aligned to GRCh38 using BWA v0.7.12, filtered for quality, and analyzed using Samtools version 1.3 and Sambamba version 0.6. Relaxed peaks were called using MACS version 2.1.0 with a p-value of 1x10-2 for H3K27ac and H3K27me3 and SPP version 1.4 with an IDR = 0.01 for each other sample.
Assembly: GRCh38
Supplementary files format and content: narrowPeak files for each sample except input

extract_protocol:
5 x 105 cells were crosslinked and chromatin was sheared using a Bioruptor UCD-200 (Diagenode).
Chromatin was immunoprecipitated using the MAGnify ChIP System (Invitrogen), and libraries prepared and barcoded. ChIP’ed and input samples were run on an Illumina HiSeq 2500 using 50SR SBS v3 reagents.

value: Lung carcinoma

value: chimera


title: patient with sepsis-associated ARDS 2

description: Library name: SA2

data_processing:
Raw sequencing reads were filtered using SOAPnuke to remove adapter contamination, low-quality reads, and reads containing excessive ambiguous bases. Clean reads were aligned to the human reference genome (GRCh38) using Bowtie. Known miRNAs were identified based on miRBase, and novel miRNAs were predicted using miRDeep. Read counts for each miRNA were calculated, and expression levels were normalized as transcripts per million (TPM). Differential expression analysis was performed using DESeq2 based on the raw read counts.
The processed expression matrices include both known miRNAs annotated in miRBase and putative novel miRNAs predicted by miRDeep. Novel miRNAs are represented by their miRDeep-assigned identifiers.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes raw counts and RPM table for all Samples

extract_protocol:
Total RNA was extracted from peripheral whole blood samples using a commercially available RNA extraction kit according to the manufacturer’s instructions. The concentration and purity of the extracted RNA were assessed using a NanoDrop spectrophotometer, and RNA integrity was evaluated using an Agilent Bioanalyzer or equivalent platform. Only RNA samples that met the quality control requirements were used for subsequent library construction.
small RNA libraries were constructed separately. Briefly, small RNAs were ligated with 3′ and 5′ adapters, reverse-transcribed into cDNA, amplified by PCR, and purified to obtain the final small RNA libraries.

value: Peripheral blood

value: patient with sepsis-associated ARDS


title: Rat 68 (GRC)

description:
Library name: index28-68-Chemical0-0Ozone0080ppm_S21.fastq
index28-68-Chemical0-0Ozone0080ppm_S21
Partek_GRC_351_Filter_observations_Sex_is_Females.txt


title: vehicle control, 24 h treatment followed by 24 h recovery, biological replicate 2

description: Library name: SS0630YC083

value: microglial cell


title: Irinotecan-treated WT mice 2

description: Library name: WT2


title: Subject P077 (P077-T2F)

value: Patient


title: TA bio rep 3, H3K27me3 ChIP

description: Library name: TA3_me3


title: Rat 66 (GRC)

description:
Library name: index27-66-Chemical0-0Ozone0080ppm_S15.fastq
index27-66-Chemical0-0Ozone0080ppm_S15
Partek_GRC_351_Filter_observations_Sex_is_Females.txt


title: vehicle control, 24 h treatment followed by 24 h recovery, biological replicate 1

description: Library name: SS0630YC082


title: Irinotecan-treated WT mice 1

description: Library name: WT1

value: ileum


title: TA bio rep 3, HA ChIP

description: Library name: TA3_HA


title: 50 µM PFOS, 24 h treatment, biological replicate 3

description: Library name: SS0630YC081

value: 50 µM PFOS; 24 h treatment


title: Rat 65 (GRC)

description:
Library name: index26-65-Chemical0-0Ozone0080ppm_S2.fastq
index26-65-Chemical0-0Ozone0080ppm_S2
Partek_GRC_351_Filter_observations_Sex_is_Females.txt


title: 6OHDA_5

city: STANFORD

first: Xiaochen

last: Xiong

address: 327 Campus Drive

institute: Stanford University

description: Library name: 6OHDA_barcode_11

data_processing:
Reads were processed to identify a 4-nucleotide cell line identifier (CLID) and a 16-nucleotide random clonal barcode (rBC). Reads were strictly filtered to retain those matching the expected structural motif. To mitigate library preparation errors, the filtered sequences were clustered using bartender.
Assembly: Custom construct
Supplementary files format and content: Clustering results from bartender, with barcode and assocaited counts.

source_name: lung

extract_protocol:
Genomic DNA was extracted from weighed, frozen metastasis-bearing tissues, following the addition of a benchmark spike-in cell line, using Proteinase K (Life Technologies AM2544) digestion and the Qiagen Puregene Kit (158063).
Sequencing libraries were prepared from 32 μg of genomic DNA per sample by amplifying the U6-CLID-rBC-sgRNA in a single-step, 27-cycle PCR with NEBNext Ultra II Q5 Master Mix (New England Biolabs M0544X) and custom Illumina-compatible primers containing unique dual i5/i7 indexes, followed by double-sided SPRIselect bead (Beckman Coulter B23317) purification and Agilent TapeStation quality assessment.

value: lung


title: TA bio rep 3, H3K27ac ChIP

description: Library name: TA3_ac


title: Rat 63 (GRC)

description:
Library name: index25-63-Chemical-Ozone008ppm_S5.fastq
index25-63-Chemical-Ozone008ppm_S5
Partek_GRC_351_Filter_observations_Sex_is_Females.txt


title: CAMCC2

description: Library name: CAMCC2

data_processing:
high-quality total RNA was used for mRNA enrichment using poly(A) selection (or rRNA depletion if applicable, if you know it). The enriched RNA was then fragmented and reverse-transcribed to generate first-strand and second-strand cDNA.
Libraries were sequenced on an Illumina platform to generate paired-end reads.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Primary mesothelial cells were isolated from fresh omentum of C57BL/6J mice. Tissue samples were mechanically minced and enzymatically digested in DMEM supplemented with 5% serum, 2 mg/mL collagenase type I, and 40 U/mL DNase I at 37°C for 30 minutes. The resulting suspension was transferred into a dissociation tube and further processed using the gentleMACS dissociator system to facilitate tissue dissociation. The cell suspension was then filtered through a 70 µm cell strainer, washed, and plated in culture conditions.  Cells were cultured for one week prior to experimental treatment. Cancer-associated mesothelial cells (CAMCC and CAMCB) were generated by exposing primary mesothelial cells (MCs) to standardized cancer cell-conditioned media from two cell lines KPCA.C and KPCA.B respectively  for 72 hours.  Total RNA was extracted using the Qiagen RNA extraction kit following the manufacturer’s instructions.
RNA-seq libraries were prepared by Novogene using a standard Illumina-compatible library preparation protocol.

value: Omentum

value: Primary MC

value: Primary Mesothelial cells

value: KPCA condition media


title: 50 µM PFOS, 24 h treatment, biological replicate 2

description: Library name: SS0630YC080


title: 6OHDA_4

description: Library name: 6OHDA_barcode_10


title: Rat 23 (GRC)

description:
Library name: index4-23-Chemical0-0Ozone0080ppm_S14.fastq
index4-23-Chemical0-0Ozone0080ppm_S14
Partek_GRC_351_Filter_observations_Sex_is_Females.txt

value: Liver

value: Female

value: Air + Ozone


title: MPMC4

description: Library name: MPMC4


title: control bio rep 3, input

description: Library name: control3_input

value: vector


title: 50 µM PFOS, 24 h treatment, biological replicate 1

description: Library name: SS0630YC079


title: 6OHDA_3

description: Library name: 6OHDA_barcode_9


title: control bio rep 3, H3K27me3 ChIP

description: Library name: control3_me3

value: Lung carcinoma


title: Rat 22 (GRC)

description:
Library name: index3-22-Chemical0-0Ozone0080ppm_S6.fastq
index3-22-Chemical0-0Ozone0080ppm_S6
Partek_GRC_351_Filter_observations_Sex_is_Females.txt


title: 6OHDA_2

description: Library name: 6OHDA_barcode_8


title: 25 µM PFOS, 24 h treatment, biological replicate 3

description: Library name: SS0630YC078

value: 25 µM PFOS; 24 h treatment


title: Rat 18 (GRC)

description:
Library name: index2-18-Chemical-Ozone008ppm_S21.fastq
index2-18-Chemical-Ozone008ppm_S21
Partek_GRC_351_Filter_observations_Sex_is_Females.txt


title: 25 µM PFOS, 24 h treatment, biological replicate 2

description: Library name: SS0630YC077


title: control bio rep 3, Aiolos ChIP

description: Library name: control3_Aio


title: 6OHDA_1

description: Library name: 6OHDA_barcode_7


title: control bio rep 3, H3K27ac ChIP

description: Library name: contro3_ac


title: 25 µM PFOS, 24 h treatment, biological replicate 1

description: Library name: SS0630YC076


title: Rat 17 (GRC)

description:
Library name: index48-17-Chemical0-0Ozone0080ppm_S4.fastq
index48-17-Chemical0-0Ozone0080ppm_S4
Partek_GRC_351_Filter_observations_Sex_is_Females.txt


title: TA bio rep 2, input

description: Library name: TA2_input

value: chimera


title: vehicle_6

description: Library name: 6OHDA_barcode_6


title: vehicle control, 24 h treatment, biological replicate 3

description: Library name: SS0630YC075

value: vehicle control; 24 h treatment


title: Rat 16 (GRC)

description:
Library name: index47-16-Chemical-Ozone008ppm_S7.fastq
index47-16-Chemical-Ozone008ppm_S7
Partek_GRC_351_Filter_observations_Sex_is_Females.txt


title: TA bio rep 2, H3K27me3 ChIP

description: Library name: TA2_me3


title: vehicle_5

description: Library name: 6OHDA_barcode_5


title: Subject P001 (P001-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™

value: Serum/Plasma


title: vehicle control, 24 h treatment, biological replicate 2

description: Library name: SS0630YC074

value: microglial cell


title: vehicle_4

description: Library name: 6OHDA_barcode_4


title: Rat 97 (GRC)

description:
Library name: index43-97-Chemical0-0Ozone0080ppm_S22.fastq
index43-97-Chemical0-0Ozone0080ppm_S22
Partek_GRC_351_Filter_observations_Sex_is_Males.txt

value: Male

value: Ozone + Ozone


title: Primary microglia, vehicle, 120min, rep1

description:
Library name: C_1
primary microglia isolated from whole brain excluding cerebellum

value: brain

value: microglia

value: wild type

value: vehicle (120 min)


title: TA bio rep 2, HA ChIP

description: Library name: TA2_HA


title: Rat 15 (GRC)

description:
Library name: index46-15-Chemical-Ozone008ppm_S16.fastq
index46-15-Chemical-Ozone008ppm_S16
Partek_GRC_351_Filter_observations_Sex_is_Females.txt


title: vehicle_3

description: Library name: 6OHDA_barcode_3

value: lung


title: vehicle control, 24 h treatment, biological replicate 1

description: Library name: SS0630YC073


title: TA bio rep 2, H3K27ac ChIP

description: Library name: TA2_ac


title: Rat 96 (GRC)

description:
Library name: index42-96-Chemical-Ozone008ppm_S3.fastq
index42-96-Chemical-Ozone008ppm_S3
Partek_GRC_351_Filter_observations_Sex_is_Males.txt

value: Liver


title: 011SFh-miRNAcount

city: Toronto

first: Sowmya

last: Viswanathan

address: 60 Leonard Avenue

country: Canada

institute: University Health Network

data_processing:
Sequencing data alignment and microRNA counts generation was performed as described by Potla et al. (PMID: 36475076).
Assembly: miRBase v22.1
Supplementary files format and content: raw counts for each sample

source_name: bone marrow-derived mesenchymal stromal cells

growth_protocol: Biobanked MSC(M) were thawed and plated on 24-well plates at 50,000 cells/well and cultured for 72 h in proliferation medium.

extract_protocol:
After 24 h, RNA extraction was performed on cell samples using a miRNeasy Mini Kit (Qiagen, Hilden, Germany) and stored at -30°C until analysis.
Libraries of cDNA were prepared using the QIAseq miRNA Library Kit (Qiagen) according to the manufacturer's instructions. The libraries were quantified using a DS-11 Spectrophotometer (DeNovix, Wilmington, USA) and assessed for quality using a high-sensitivity DNA chip on the Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: Cells were then washed with phosphate-buffered saline (PBS) and treated with low-glucose DMEM (Sigma) supplemented with or without synovial fluid. To treat cells with synovial fluid, samples were collected from unrelated late-stage OA patients (KL 3-4) outside of the clinical trial cohort (REB #14–7483), pooled from eight patients, and stored at ‑80°C until use, as previously described (82). For treated wells, DMEM was supplemented with 30% (v/v) synovial fluid.

value: Synovial fluid-treated

tag: subject id

value: Cell Donor 11


title: vehicle_2

description: Library name: 6OHDA_barcode_2


title: control bio rep 2, input

description: Library name: control2_input

value: vector


title: 011h-miRNAcount

value: bone marrow-derived mesenchymal stromal cells

value: Untreated


title: control bio rep 2, H3K27me3 ChIP

description: Library name: control2_me3

value: Lung carcinoma


title: vehicle_1

description: Library name: 6OHDA_barcode_1


title: Rat 95 (GRC)

description:
Library name: index41-95-Chemical-Ozone008ppm_S24.fastq
index41-95-Chemical-Ozone008ppm_S24
Partek_GRC_351_Filter_observations_Sex_is_Males.txt


title: 010SFh-miRNAcount

value: Cell Donor 10


title: Rat 91 (GRC)

description:
Library name: index40-91-Chemical0-0Ozone0080ppm_S8.fastq
index40-91-Chemical0-0Ozone0080ppm_S8
Partek_GRC_351_Filter_observations_Sex_is_Males.txt


title: TRF2KO-ATAC-seq-MuSCs_0hr_2

description: Library name: Trf2-KO-0hr-2

data_processing:
Pre-trimmed sequences were aligned to mm10 using Bowtie2 version 2.5.4 with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
Duplicates and non-uniquely aligned reads were marked with Picard (3.1.1) from BAMs using Samtools v1.10 (htslib 1.10). Mapped and properly paired reads with greater than 10 Q-score were retained, excluding duplicates.
Genome coverage was calculated using bamCoverage v3.5.3 (deepTools v3.5.3) with the following parameters: --effectiveGenomeSize 2494787038 --binSize 10 --normalizeUsing 'RPGC' --ignoreForNormalization 'chrM'.
Peaks were called using MACS3 version 3.0.2 with callpeak parameters “–nomodel --nolambda –keep-dup-all –format BEDPE -gsize 2494787038 –qvalue 0.05”, SEACR version 1.3 with parameters “non stringent 0.01”, and GoPeaks version 1.0.0.
Consensus peaks were merged using DiffBind version 3.10.1.
Assembly: GRCm38_mm10
Supplementary files format and content: bigWig, bed, narrowPeak

source_name: Skeletal Muscle - hind limb

value: Skeletal Muscle - hind limb

value: Primary cells

value: Muscle stem cells

value: Wildtype


title: control bio rep 2, Aiolos ChIP

description: Library name: control2_Aio


title: 010h-miRNAcount


title: TRF2KO-ATAC-seq-MuSCs_0hr_1

description: Library name: Trf2-KO-0hr-1


title: Rat 88 (GRC)

description:
Library name: index39-88-Chemical0-0Ozone0080ppm_S13.fastq
index39-88-Chemical0-0Ozone0080ppm_S13
Partek_GRC_351_Filter_observations_Sex_is_Males.txt

value: Male

value: Ozone + Ozone


title: control bio rep 2, H3K27ac ChIP

description: Library name: control2_ac


title: 007SFh-miRNAcount

value: Cell Donor 7


title: Rat 87 (GRC)

description:
Library name: index38-87-Chemical0-0Ozone0080ppm_S16.fastq
index38-87-Chemical0-0Ozone0080ppm_S16
Partek_GRC_351_Filter_observations_Sex_is_Males.txt


title: Control-ATAC-seq-MuSCs_0hr_2

description: Library name: Control-0hr-2


title: 25 µM PFOS, 24 h treatment followed by 24 h recovery, biological replicate 1, H3K27ac CUT&Tag

description: Library name: SS0630YC050

value: microglial cell

value: 25 µM PFOS; 24 h treatment followed by 24 h recovery


title: TA bio rep 1, input

description: Library name: TA1_input

value: chimera


title: Rat 48 (GRC)

description:
Library name: index17-48-Chemical-Ozone008ppm_S13.fastq
index17-48-Chemical-Ozone008ppm_S13
Partek_GRC_351_Filter_observations_Sex_is_Males.txt

value: Liver

value: Air + Ozone


title: 007h-miRNAcount


title: Control-ATAC-seq-MuSCs_0hr_1

description: Library name: Control-0hr-1


title: Rat 46 (GRC)

description:
Library name: index16-46-Chemical0-0Ozone0080ppm_S23.fastq
index16-46-Chemical0-0Ozone0080ppm_S23
Partek_GRC_351_Filter_observations_Sex_is_Males.txt


title: 006SFh-miRNAcount

value: Synovial fluid-treated

value: Cell Donor 6


title: TA bio rep 1, HA ChIP

description: Library name: TA1_HA


title: CLP_SPREVs2

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

institute: Saga University

description: Library name: Sample 6

data_processing:
Obtained FASTQ-formatted data was trimmed using trimmomatic 0.39 and reads were mapped into GRCm38.p4 mus musculus reference genome using hisat 2.1.0, followed by counted using featureCounts 2.0.6  and cuffdiff 2.2.1.
Assembly: GRCm38.p4
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Spleen

extract_protocol:
Cells were lysed with Trizol (thermofisher scientific), and total RNAs were extracted using QuickGene AutoS and AutoS RNA Cultured Cell Kit (KURABO) following manufacturer's protocols.
The cDNA library was constructed using TruSeq stranded mRNA Library Prep kit (illumina), and sequencing was performed using 101-base single-read mode of NovaSeq X plus (illumina).

treatment_protocol: CLP was operated in each mice, and injected EVs or SPLEVs or PBS at tail vein after operation. Ten days after the operation, the mice was dissected and the spleen removed.

value: Spleen

value: Splenocytes

value: WT

value: CLP operation and injected SPREVs


title: 006h-miRNAcount

value: bone marrow-derived mesenchymal stromal cells

value: Untreated


title: 18_T384_P3ALI

description: Library name: lib45765

value: airway epithelial cells

value: air liquid interface

value: child


title: CLP_SPREVs1

description: Library name: Sample 5


title: Rat 43 (GRC)

description:
Library name: index15-43-Chemical0-0Ozone0080ppm_S20.fastq
index15-43-Chemical0-0Ozone0080ppm_S20
Partek_GRC_351_Filter_observations_Sex_is_Males.txt

value: Male


title: 005SFh-miRNAcount

value: Cell Donor 5


title: CLP_EV2

description: Library name: Sample 4

value: CLP operation and injected EVs


title: control bio rep 1, input

description: Library name: control1_input

value: Lung carcinoma

value: vector


title: Rat 41 (GRC)

description:
Library name: index14-41-Chemical0-0Ozone0080ppm_S10.fastq
index14-41-Chemical0-0Ozone0080ppm_S10
Partek_GRC_351_Filter_observations_Sex_is_Males.txt

value: Liver

value: Air + Ozone


title: TA bio rep 1, H3K27ac ChIP

description: Library name: TA1_ac

value: chimera


title: Subject P001 (P001-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.

value: Serum/Plasma

value: Patient


title: 17_T397_P3sub

description: Library name: lib45764

value: submerged


title: 005h-miRNAcount


title: Rat 39 (GRC)

description:
Library name: index13-39-Chemical-Ozone008ppm_S10.fastq
index13-39-Chemical-Ozone008ppm_S10
Partek_GRC_351_Filter_observations_Sex_is_Males.txt


title: control bio rep 1, H3K27me3 ChIP

description: Library name: control1_me3


title: Rat 37 (GRC)

description:
Library name: index11-37-Chemical-Ozone008ppm_S15.fastq
index11-37-Chemical-Ozone008ppm_S15
Partek_GRC_351_Filter_observations_Sex_is_Males.txt


title: CLP_EV1

description: Library name: Sample 3

value: Spleen

value: Splenocytes

value: WT


title: 004SFh-miRNAcount

value: bone marrow-derived mesenchymal stromal cells

value: Synovial fluid-treated

value: Cell Donor 4


title: CLP_PBS2

description: Library name: Sample 2

value: CLP operation and injected PBS