title: Patient 2_ROI 022_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-G07
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal thyroid 2, DGCR8-mutated, VIM+

value: Patient 2_Normal thyroid 2_ VIM+

value: Patient 2


title: mu4K_AD, s5

status: Public on Dec 10 2025

type: SRA

city: Toulouse

first: Aurélie

last: Mougel

address: Avenue des arènes romaines CHU Purpan 31300 Toulouse

country: France

institute: INSERM

description: Library name: 090S-305

library_source: transcriptomic

data_processing:
nf-core/rna-seq pipeline v3.12.0
Raw reads were trimmed for adapters and low-quality sequences using trimgalore.
Contaminant rRNAs were removed with SortMeRNA.
Filtered reads were aligned to the genome using the STAR aligner.
Reads were counted with Salmon.
Assembly: mm39, annotation v107
Supplementary files format and content: counts_genes.txt includes raw counts for each sample, TPM counts and gene length
Supplementary files format and content: counts_transcripts.txt includes raw counts for each sample, TPM counts and transcripts length
Supplementary files format and content: salmon_tx2gene.tsv gives correspondence between genes and transcripts

molecule: total RNA

organism: Mus musculus

source_name: skin

extract_protocol:
RNA was harvested using RNeasy Lipid Tissue Kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA librairies for RNA-seq were prepared using the llumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit following manufacturer's protocol.

tag: tissue

value: skin


title: IR+4-OI_3

city: wuhan

first: hao

last: tian

state: hubei

address: No.9, Zhangzhidong Road, Wuchang District

country: China

institute: Renmin Hospital of Wuhan University

description:
Library name: Sample6
IROI_3

data_processing:
SOAPnuke (V2.1.0) was used to filter the sequencing data as follows:   (1) Reads containing sequencing joints were removed;   (2) Reads with N ratio greater than 0.5% were removed;   (3) Removal of low-quality reads (those with Qphred≤20 bases accounting for more than 50% of the length of the entire reads).   Clean reads are obtained after filtering.
HISAT2 (V2.1.0) was used to compare clean reads with the reference genome, and Bowtie2 (V2.3.5) was used to align the quality controlled sequence to the reference transcription sequence.
Using RSEM, the bowtie2 comparison results were used for statistics, and the number of Reads compared to each transcript of each sample was obtained, and FPKM (Fragments Per Kilobase Per Million bases) conversion was performed.
DESeq2（V1.22.2）/edgeR（V3.6.8）was used for differential expression significance analysis, and the screening threshold was FDR（false discovery rate）＜ 0.05，log2FC（fold change）＞1 or ＜-1.
Assembly: mm10
Supplementary files format and content: xls files include raw counts for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted using the Trizol(Invitrogen, CA, USA), RNA purity and integrity was monitored by NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and a Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA contamination was assessed by 1.5% agarose gel.
The mRNA was purified from the total RNA using poly‐T oligo‐attached magnetic beads. Sequencing libraries were generated from the purified mRNA using the V AHTS Universal V6 RNA-seq Library Kit for MGI (V azyme, Nanjing, China) following the manufacturer's recommendations with unique index codes. The Library quantification and size was assessed using  Qubit  3.0  Fluorometer (Life Technologies, Carlsbad, CA, USA) and Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Subsequently, sequencing was performed on a MGI-SEQ 2000 platform by Frasergen Bioinformatics Co., Ltd. (Wuhan, China).

value: heart

tag: genotype

value: WT

tag: treatment

value: heart transplantation+4-OI


title: Patient 2_ROI 022_ PanCK+

city: Hospitalet de Llobregat

first: Barbara

last: Rivera

address: Granvia de l'Hospitalet de Llobregat, 199

country: Spain

institute: IDIBELL

description:
Library name: Sample_DSP-1001660005657-A-G06
FFPE spatial transcriptomics (NanoString DSP WTA)

data_processing:
Fastq files containing sequencing of UV-cleaved probes were processed into Digital count conversion (DCC) files using the Nanostring GeoMx NGS Pipeline v2.3.3.10. The DCC files were imported into R v4.3.0 for further analysis. Using GeomxTools v3.3.0, areas of Illumination (AOI) were assessed for sequencing quality. AOIs retained for analysis if they met the following criteria: Minimum reads per AOI greater than 1000, the percentage of trimmed reads, stitched reads and aligned reads all greater than 80%, the sequencing saturation greater than 50%, the minimum count of negative control probes greater 0.5, No Template Control (NTC) counts greater than 1300, number of nuclei per AOI is greater than 100, the area per AOI is greater than 1000 µm, and greater than 5% of genes detected above limit of quantification (LOQ, mean of negative control counts + 2 standard deviation). 6 AOIs were discarded for not meeting the criteria, for a total of 78 AOIs. Genes were retained in the analysis if detected above LOQ in at least 5% of AOIs for a total of 12236 genes. Counts were normalized using the quartile 3 (Q3) method.
Assembly: GRCh38
Supplementary files format and content: Matrix of Q3-normalized counts for the 78 AOIs
Library strategy: Spatial Transcriptomics

organism: Homo sapiens

source_name: Normal thyroid 2, DGCR8-mutated, PanCK+

extract_protocol:
GeoMx™ digital spatial profiling was performed as per the supplier’s protocol using the human Whole Transcriptome Atlas probe set with read-out by next-generation sequencing (Nanostring Technologies). Briefly, 5 µm FFPE sections of a sporadic DICER1-thyroid case and a germline DGCR8- thyroid case, were processed through deparaffinization, antigen retrieval (Tris-EDTA ph9 for 20 min at 98°C), and Proteinase K digestion (1 ug/mL Proteinase K for 15 min at 37°C) prior to overnight incubation at 37°C with the human Whole Transcriptome Atlas diluted in hybridization Buffer R. The next day, slides were washed twice in 2XSSC/formamide (25 min at 37°C), blocked with Buffer W (30 min at RT) and incubated with an antibody cocktail consisting of PanCK-AF532, CD45-AF594, VIM-AF647, and SYTO13 for 1 hr in a humidity chamber. Slides were washed 3 times in 2XSSC and then scanned on the GeoMx™ DSP instrument (at 20X), after which regions-of-interest (ROIs) in each case were laid down to capture different histological components in triplicates at least. For the DICER1-case, this included a tumour core from a DICER1-mutated PDTC, the tumor’s capsule, a non-neoplastic nodular area (DICER1-wildtype benign thyroid lesion) and normal area (DICER1-wildtype). For the DGCR8-case, this included a tumour core from a DGCR8-mutated microPTC, a normal adjacent area, non-neoplastic nodular areas (DGCR8-mutated benign thyroid lesions) and normal area (DGCR8-mutated). A total of 51 ROIs were selected and were segmented further into PanCK+ and/or VIM+ areas, and Whole Transcriptome barcodes were released from these distinct populations by UV light illumination and microfluidic collection.
The UV-released barcodes from each of the 84 area-of-illuminations (AOIs) were PCR-amplified to add unique dual-index Illumina i5 and i7 indices and bead-purified twice using AMPure XP beads (Beckman Coutler, A63881). Pooled libraries were sequenced on two 75-cycle High Output flowcells on an Illumina NextSeq sequencer, generating 916M unique raw reads. FASTQ files were converted to DCC files and uploaded onto the GeoMx™ DSP for trimming, stitching, aligning, and deduplication.

value: Patient 2_Normal thyroid 2_ PanCK+

tag: patient

tag: histological type

value: Normal thyroid

tag: Sex

value: Male

tag: label (panck/vim)

value: PanCK+ (Cy3)


title: 574T

city: Tokyo

first: Yu-Yu

last: Liu

address: 5-1-1 Tsukiji, Chūō district

country: Japan

institute: National Cancer Center Research Institute

description:
Library name: 574TA
Column name in GEOrsem_expected_count.csv: 574TA

data_processing:
The sequencing data were subjected to quality control filtering, trimming, and adapter removal using fastp (v0.24.0) with default parameters.
The filtered paired-end reads were aligned to the human reference genome (hg38) using STAR (v2.7.11b), and gene-level read counts were quantified using RNA-Seq by Expectation-Maximization (v1.3.1).
Genes with FDR < 0.05 and log Fold-change > 1 or < -1 were considered as differentially expressed genes.
Assembly: hg38
Supplementary files format and content: csv file includes rsem expected count for each sample
Supplementary files format and content: Tab delimited files including rsem results for each sample

source_name: Collecting duct carcinoma

extract_protocol:
For samples processed at Macrogen, total RNA was extracted using QIAzol Lysis reagent (QIAGEN). For samples processed at BGI, total RNA was extracted using TRIzol Reagent (Invitrogen).
For samples processed at Macrogen, libraries were constructed from the total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina). For samples processed at BGI, libraries were prepared using the DNBSEQ Eukaryotic Strand-specific mRNA library protocol.

value: Collecting duct carcinoma


title: mu4K_AD, s4

description: Library name: 090S-304


title: Patient 2_ROI 021_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-G05
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal thyroid 1, DGCR8-mutated, VIM+

value: Patient 2_Normal thyroid 1_ VIM+

value: VIM+ (Cy5)


title: IR+4-OI_1

description:
Library name: Sample4
IROI_1


title: 573T

description:
Library name: 573TA
Column name in GEOrsem_expected_count.csv: 573TA

source_name: Clear cell renal cell carcinoma

value: Clear cell renal cell carcinoma


title: Patient 2_ROI 021_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-G04
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal thyroid 1, DGCR8-mutated, PanCK+

value: Patient 2_Normal thyroid 1_ PanCK+


title: mu4K_AD, s3

description: Library name: 090S-303


title: Patient 2_ROI 020_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-G03
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 1_3, DGCR8-mutated, VIM+

value: Patient 2_Non-neoplastic nodular area 1_3_ VIM+

value: Non-neoplastic nodular area


title: IR_2

description:
Library name: Sample2
IR_2

value: heart transplantation


title: IR_3

description:
Library name: Sample3
IR_3


title: mu4K_AD, s2

description: Library name: 090S-302


title: Patient 2_ROI 020_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-G02
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 1_2, DGCR8-mutated, PanCK+

value: Patient 2_Non-neoplastic nodular area 1_2_ PanCK+

value: Patient 2


title: mu4K_AD, s1

description: Library name: 090S-301

value: skin


title: 566T

description:
Library name: 566TA
Column name in GEOrsem_expected_count.csv: 566TA


title: 564T

description:
Library name: 564TA
Column name in GEOrsem_expected_count.csv: 564TA


title: IR_1

description:
Library name: Sample1
IR_1

value: heart

value: WT


title: 563T

description:
Library name: 563TA
Column name in GEOrsem_expected_count.csv: 563TA


title: control_AD, s6

description: Library name: 090S-106


title: 576T

description:
Library name: 576TA
Column name in GEOrsem_expected_count.csv: 576TA

source_name: Papillary renal cell carcinoma

value: Papillary renal cell carcinoma


title: Patient 2_ROI 023_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-G08
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal thyroid 3, DGCR8-mutated, PanCK+

value: Patient 2_Normal thyroid 3_ PanCK+

value: Normal thyroid


title: 555T

description:
Library name: 555TA
Column name in GEOrsem_expected_count.csv: 555TA


title: 554T

description:
Library name: 554TA
Column name in GEOrsem_expected_count.csv: 554TA


title: control_AD, s5

description: Library name: 090S-105


title: Patient 2_ROI 018_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-F12
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 3_2, DGCR8-mutated, VIM+

value: Patient 2_Non-neoplastic nodular area 3_2_ VIM+

value: Male


title: P21 Human Small Airway Epithelial Cells biol rep 3

city: Guangzhou

first: Mingyue

last: Jiang

address: No. 74, Zhongshan Second Road, Yuexiu District, Zhongshan University North Campus

institute: Sun Yat-sen University

description: Library name: HSAECs_P21C

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5)  by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 1%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 40%, afterwards clean reads were obtained and stored in FASTQ format.
Assembly: The clean data were mapped to the reference genome by HISAT (v2.2.1)
Supplementary files format and content: txt files include FPkM, TPM values and read counts for each Sample

source_name: airway epithelium

extract_protocol:
Total RNA was extracted from HBECs (P3, P6, P9, and P13) and HSAECs (P2, P7, P14, and P21) using TRIzol reagent (Invitrogen, 15596026CN) according to the manufacturer's instructions.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

value: airway epithelium

tag: cell line

value: human small airway epithelial cell

tag: cell type

value: basal stem cell

value: cultured in a novel medium (sfBSC)


title: IR+4-OI_2

description:
Library name: Sample5
IROI_2

value: heart transplantation+4-OI


title: P21 Human Small Airway Epithelial Cells biol rep 2

description: Library name: HSAECs_P21B


title: control_AD, s4

description: Library name: 090S-104


title: Patient 2_ROI 017_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-F11
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 3_1, DGCR8-mutated, VIM+

value: Patient 2_Non-neoplastic nodular area 3_1_ VIM+

value: Non-neoplastic nodular area

value: VIM+ (Cy5)


title: Patient 2_ROI 016_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-F09
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 2_7, DGCR8-mutated, PanCK+

value: Patient 2_Non-neoplastic nodular area 2_7_ PanCK+

value: Patient 2

value: PanCK+ (Cy3)


title: 552T

description:
Library name: 552TA
Column name in GEOrsem_expected_count.csv: 552TA

value: Clear cell renal cell carcinoma


title: Patient 2_ROI 015_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-F08
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 2_6, DGCR8-mutated, PanCK+

value: Patient 2_Non-neoplastic nodular area 2_6_ PanCK+


title: 547T

description:
Library name: 547TA
Column name in GEOrsem_expected_count.csv: 547TA


title: P21 Human Small Airway Epithelial Cells biol rep 1

description: Library name: HSAECs_P21A


title: control_AD, s3

description: Library name: 090S-103

value: skin


title: P14 Human Small Airway Epithelial Cells biol rep 3

description: Library name: HSAECs_P14C


title: P14 Human Small Airway Epithelial Cells biol rep 2

description: Library name: HSAECs_P14B


title: Patient 2_ROI 014_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-F06
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 2_4, DGCR8-mutated, PanCK+

value: Patient 2_Non-neoplastic nodular area 2_4_ PanCK+


title: 545T

description:
Library name: 545TA
Column name in GEOrsem_expected_count.csv: 545TA


title: control_AD, s2

description: Library name: 090S-102

source_name: skin


title: 544T

description:
Library name: 544TA
Column name in GEOrsem_expected_count.csv: 544TA


title: P14 Human Small Airway Epithelial Cells biol rep 1

description: Library name: HSAECs_P14A


title: control_vehicle, s6

description: Library name: 090S-206


title: Patient 2_ROI 013_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-F05
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 2_3, DGCR8-mutated, VIM+

value: Patient 2_Non-neoplastic nodular area 2_3_ VIM+


title: 543T

description:
Library name: 543TA
Column name in GEOrsem_expected_count.csv: 543TA


title: control_AD, s1

description: Library name: 090S-101


title: P7 Human Small Airway Epithelial Cells biol rep 3

description: Library name: HSAECs_P7C


title: 541T

description:
Library name: 541TA
Column name in GEOrsem_expected_count.csv: 541TA


title: Patient 2_ROI 013_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-F04
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 2_2, DGCR8-mutated, PanCK+

value: Patient 2_Non-neoplastic nodular area 2_2_ PanCK+

value: Male


title: control_vehicle, s5

description: Library name: 090S-205


title: P7 Human Small Airway Epithelial Cells biol rep 2

description: Library name: HSAECs_P7B

value: airway epithelium

value: human small airway epithelial cell


title: Patient 2_ROI 012_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-F03
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 2_1, DGCR8-mutated, PanCK+

value: Patient 2_Non-neoplastic nodular area 2_1_ PanCK+


title: control_vehicle, s3

description: Library name: 090S-203


title: P7 Human Small Airway Epithelial Cells biol rep 1

description: Library name: HSAECs_P7A

value: basal stem cell

value: cultured in a novel medium (sfBSC)


title: 540T

description:
Library name: 540TA
Column name in GEOrsem_expected_count.csv: 540TA


title: P2 Human Small Airway Epithelial Cells biol rep 3

description: Library name: HSAECs_P2C


title: control_vehicle, s2

description: Library name: 090S-202


title: Patient 2_ROI 011_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-F02
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 1_1, DGCR8-mutated, VIM+

value: Patient 2_Non-neoplastic nodular area 1_1_ VIM+

value: Non-neoplastic nodular area


title: P2 Human Small Airway Epithelial Cells biol rep 2

description: Library name: HSAECs_P2B


title: Patient 2_ROI 010_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-F01
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal adjacent 3, DGCR8-mutated, VIM+

value: Patient 2_Normal adjacent 3_ VIM+

value: Normal adjacent

value: VIM+ (Cy5)


title: 530T

description:
Library name: 530TA
Column name in GEOrsem_expected_count.csv: 530TA

source_name: Clear cell renal cell carcinoma

value: Clear cell renal cell carcinoma


title: Patient 2_ROI 014_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-F07
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 2_5, DGCR8-mutated, VIM+

value: Patient 2_Non-neoplastic nodular area 2_5_ VIM+

value: Patient 2


title: control_vehicle, s1

description: Library name: 090S-201

value: skin


title: Patient 2_ROI 09_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-E11
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal adjacent 2, DGCR8-mutated, VIM+

value: Patient 2_Normal adjacent 2_ VIM+


title: Patient 2_ROI 010_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-E12
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal adjacent 3, DGCR8-mutated, PanCK+

value: Patient 2_Normal adjacent 3_ PanCK+

value: PanCK+ (Cy3)


title: heart, control

city: Columbus

first: Katherine

middle: E

last: Miller

state: OH

address: 700 Children's Dr.

department: Institute for Genomic Medicine

country: USA

institute: Nationwide Children's Hospital

description:
Library name: Het
10X Fixed RNA Profiling

library_source: transcriptomic single cell

data_processing:
Demultiplexed FASTQ files were generated on-board the Singular G4 sequencer. Alignment to the Chromium Mouse Transcriptome Probe Set v1.0.1, filtering, barcode counting, and UMI counting was performed using Cell Ranger multi v7.1.0 following the default parameters.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: heart

extract_protocol:
Using aseptic, RNA-preserving conditions, control Db/db and T2D db/db mouse hearts were gravity-fed perfusion fixed under deep isoflurane anesthesia (3%) by ~15 seconds of a PBS flush, followed by ~15 seconds of 4% paraformaldehyde (PFA), and finished with 4% PFA with 60 mM KCl until cardiac arrest in diastole. Tissues were fixed for 24 hours in 4% PFA at 4°C and stored in 70% ethanol until paraffin embedding.
Six 50 µm scrolls were cut from one control Db/db and one diabetic db/db formalin-fixed and paraffin-embedded (FFPE) heart blocks. Cells were isolated from scrolls by following the Isolation of Cells from FFPE Tissue Sections for Chromium Fixed RNA Profiling protocol from 10X Genomics (CG000632 RevB) using the gentleMACS Octo Dissociator method. Approximately 200,000 isolated cells for each sample were used as input for the Chromium Fixed RNA Profiling kit from 10X Genomics (CG000477 RevD) according to the manufacturer’s protocol. Briefly, cells were hybridized overnight with mouse BC001 probe set (Singleplex, ThermoFisher Scientific), followed by GEM generation and barcoding, and Illumina compatible library preparation. Libraries were sequenced on the Singular Genomics G4 benchtop sequencer; therefore, the Illumina libraries were converted using Singular Genomics conversion PCR primers. We targeted 25,000 read pairs per 10,000 cells for each sample and used a run recipe of: 28x10x10x50 (read1:i7index:i5index:read2).

value: heart

value: Db/db

value: male


title: heart, diabetic

description:
Library name: Db
10X Fixed RNA Profiling

value: db/db


title: P2 Human Small Airway Epithelial Cells biol rep 1

description: Library name: HSAECs_P2A

value: airway epithelium

value: human small airway epithelial cell

value: basal stem cell

value: cultured in a novel medium (sfBSC)


title: 509T

description:
Library name: 509TA
Column name in GEOrsem_expected_count.csv: 509TA


title: Patient 2_ROI 09_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-E10
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal adjacent 2, DGCR8-mutated, PanCK+

value: Patient 2_Normal adjacent 2_ PanCK+

value: Normal adjacent

value: Male


title: control_vehicle, s4

description: Library name: 090S-204


title: 8-week old C57BL/6J mouse lung papain+ sorted cells - GEX

city: BETHESDA

first: Beatriz

last: León

state: MD

address: 10 CENTER DR

department: Division of Intramural Research (DIR)

institute: National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH)

description:
Library name: C57BL-6J_mouse_lung_papain_positive_sorted_cells_GEX
10x Genomics

data_processing:
The single-cell 3’ v3 gene expression library was sequenced on a NovaSeq 6000 101 cycle + 101 cycle symmetric run.  The OpenOmics/cell-seek pipeline v2.0.1 leveraging 10x Genomics Cell Ranger v8.0.0 generated matrices from FASTQ files using the 10x Genomics GRCm39-2024-A transcriptome reference and performed Seurat QC filtering using Seurat v5.1.0 in R v4.3.3.  The Seurat filtering was performed to remove low count cells and potential doublets by applying 3 median absolute deviations from the median log-library size filter to the gene and read counts.  The same filtering was applied to the mitochondrial percentage with only an upper threshold.  Cells were log10 normalized, dimension reduction performed using 30 principal components, and data visualized using Uniform Manifold Approximation and Projections (UMAP).  Unsupervised clustering was performed using a resolution of 0.6.
Assembly: GRCm39-2024-A
Supplementary files format and content: 10x Genomics Cell Ranger Output Files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Seurat Processed File: seuratv5.rds

source_name: Lung

extract_protocol:
Eight-week-old C57BL/6J mice (species Mus musculus) were treated intranasally with 10 µg of Alexa Fluor 647-labeled cysteine protease papain in a 100 µL volume. Twenty-four hours later, lungs were processed into a single-cell suspension, and papain⁺ cells were isolated using fluorescence-activated cell sorting (FACS).
Cell suspension and 10x barcoded gel beads were loaded into the 10x Chromium™ Single Cell Chip G (PN 1000120) to capture single cells in nanoliter-scale oil droplets using the 10x Genomics Chromium X Controller with Chromium Next GEM Single Cell 3’ v3.1 reagents (PN-1000268). The single-cell gene expression libraries were constructed following the 10x Genomics 3’ Next GEM 3.1 kit instructions. The libraries were then sequenced on an Illumina NovaSeq 6000, targeting 20,000 reads per cell.
10x Single Cell Genomics

value: Lung

tag: strain

value: mouse lung papain+ cells

tag: age

value: 8-weeks old

tag: library type

value: GEX


title: P13 Human Bronchial Epithelial Cells biol rep 3

description: Library name: HBEC_P13C

source_name: airway epithelium

value: human bronchial epithelial cell


title: 528T

description:
Library name: 528TA
Column name in GEOrsem_expected_count.csv: 528TA

value: Clear cell renal cell carcinoma


title: P13 Human Bronchial Epithelial Cells biol rep 2

description: Library name: HBEC_P13B


title: Patient 2_ROI 08_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-E08
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal adjacent 1, DGCR8-mutated, PanCK+

value: Patient 2_Normal adjacent 1_ PanCK+

value: Patient 2

value: PanCK+ (Cy3)


title: 536T

description:
Library name: 536TA
Column name in GEOrsem_expected_count.csv: 536TA


title: Citeseq, Pam mature AML, GEX, ADT

city: Philadelphia

first: Ramkrishna

last: Mitra

state: Pennsylvania

address: 233 S 10th street

institute: Thomas Jefferson University

description:
Library name: Pam_mature
GEX, ADT

library_source: other

data_processing:
CITE-seq files were demultiplexed using cellranger mkfastq
Demultiplexed data were processed using the cellranger count pipeline
Assembly: mm10
Supplementary files format and content: cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: bone marrow

extract_protocol:
Bone marrow cells were isolated from treated mice and FACs sorted for either CD45.2+Lin-CD117+ (HSPC) or CD45.2+CD11b+ (mature) cells.
Cells with ADTs and encapsulated in gel-beads in emulsion (GEMs) using the 10x Controller and Next Gem Chip G. The CITE-seq protocol using manufacter settings from the Chromium Next Gem Single Cell 3' Kit v3.1 (10x Genomics - CG00206D)

treatment_protocol: Mice were treated with either 100µL PBS or 100µg Pam3CSK4. Mice were sacrificed 24 hours after treatment

value: bone marrow

value: leukemic myeloid cells

value: mRNA, ADT

tag: adt

value: TotalSeq-A 0114 anti-mouse F4/80, TotalSeq-A 0116 anti-mouse Ly-6G/Ly-6C (Gr1), TotalSeq-A 0117 anti-mouse MHCII (I-A/I-E), TotalSeq-A 0849 anti-mouse CD80, TotalSeq-A 0200 anti-mouse CD86, TotalSeq-A 0951 anti-mouse PE Streptavidin (for biotinylated Tlr2)


title: Patient 2_ROI 08_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-E09
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal adjacent 1, DGCR8-mutated, VIM+

value: Patient 2_Normal adjacent 1_ VIM+

value: VIM+ (Cy5)


title: 508T

description:
Library name: 508TA
Column name in GEOrsem_expected_count.csv: 508TA

source_name: Chromophobe renal cell carcinoma

value: Chromophobe renal cell carcinoma


title: P13 Human Bronchial Epithelial Cells biol rep 1

description: Library name: HBEC_P13A

value: airway epithelium

value: basal stem cell

value: cultured in a novel medium (sfBSC)


title: P9 Human Bronchial Epithelial Cells biol rep 3

description: Library name: HBEC_P9C


title: Citeseq, PBS mature AML, GEX, ADT

description:
Library name: PBS_mature
GEX, ADT

value: PBS


title: 503T

description:
Library name: 503TA
Column name in GEOrsem_expected_count.csv: 503TA


title: Patient 2_ROI 07_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-E07
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: microPTC 6, DGCR8-mutated, VIM+

value: Patient 2_microPTC 6_ VIM+

value: microPTC

value: Male


title: Patient 2_ROI 07_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-E06
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: microPTC 6, DGCR8-mutated, PanCK+

value: Patient 2_microPTC 6_ PanCK+


title: P9 Human Bronchial Epithelial Cells biol rep 2

description: Library name: HBEC_P9B

value: human bronchial epithelial cell


title: 513T

description:
Library name: 513TA
Column name in GEOrsem_expected_count.csv: 513TA

source_name: TFE3-rearranged/TFEB-altered renal cell carcinoma


title: Citeseq, PBS HSPC AML, GEX, ADT

description:
Library name: PBS_HSPC
GEX, ADT

value: TotalSeq-A 0109 anti-mouse CD16/32, TotalSeq-A 0130 anti-mouse Ly-6A/E (Sca-1), TotalSeq-A 0857 anti-mouse CD34, TotalSeq-A 0012 anti-mouse CD117, TotalSeq-A 0951 anti-mouse PE Streptavidin (for biotinylated Tlr2)


title: P9 Human Bronchial Epithelial Cells biol rep 1

description: Library name: HBEC_P9A


title: 502T

description:
Library name: 502TA
Column name in GEOrsem_expected_count.csv: 502TA

source_name: Unclassified type of renal cell carcinoma


title: Patient 2_ROI 06_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-E05
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: microPTC 5, DGCR8-mutated, VIM+

value: Patient 2_microPTC 5_ VIM+

value: Patient 2


title: 497T

description:
Library name: 497TA
Column name in GEOrsem_expected_count.csv: 497TA

source_name: Papillary renal cell carcinoma

value: Papillary renal cell carcinoma


title: Patient 2_ROI 06_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-E04
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: microPTC 5, DGCR8-mutated, PanCK+

value: Patient 2_microPTC 5_ PanCK+

value: PanCK+ (Cy3)


title: P6 Human Bronchial Epithelial Cells biol rep 3

description: Library name: HBEC_P6C


title: C57BL/67_liver_KO_HFPODA_replication3

city: 北京

first: 丽娟

last: 游

state: 北京Beijing

address: 潘家园南里7号楼

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400276-KO_HFPODA_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TMP values for each sample

source_name: liver

growth_protocol: The animal research protocol adhered to the guidelines for the care and use of laboratory animals (IACUC), and was approved by the Animal Care and Use Committee of the China Food Safety Risk Assessment Center (No. 2023058). Wild-type and macrophage PPARγ gene knockout male mice aged 10 to 13 weeks, with a C57BL/6J background, were purchased from Shanghai Southern Model Biological Technology Co., Ltd. The macrophage PPARγ gene knockout mice were generated by crossing PPARg-Flox male mice with Lyz2-Cre female mice. The animals were housed in an environment of 20°C with a 12-hour light/dark cycle and relative humidity of 50-60%, and were fed a standard diet.

extract_protocol:
Total RNA was extracted from  cultured cells withTRIzol reagent.mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(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, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: In the oral toxicity study, wild-type (WT) and macrophage PPARγ knockout (Mac-ko) mice were randomly divided into 4 groups(n=6-8), each receiving an oral gavage of PFOA, PFUnDA, and HFPODA at a dose of 1 mg/kg bw/day, along with 0.1% DMSO, for 35 days. This dose was based on the no observed adverse effect level (NOAEL) for oral administration of PFOA and PFUnDA in mice, which is 1 mg/kg bw/day (ATSDR, 2021). HFPODA was used as a substitute for PFOA, maintaining the same gavage dosage. A 0.1% DMSO group served as the control (CT). Mouse body weight was recorded weekly, and at the end of the experiment, blood samples were collected via retro-orbital venipuncture. Subsequently, cervical dislocation was performed for euthanasia, and the organs of the mouse are isolated and weighed. Then, the liver was divided into three parts: the first part was fixed in 10% neutral buffered formalin for histopathological examination and immunohistochemical analysis; the second part was quickly frozen in liquid nitrogen and stored at -80°C for liver tissue RNA sequencing; the third part was washed with PBS and used for flow cytometry analysis.

value: liver

value: PPARg KO

value: oral gavage HFPODA(1mg/kg bw/day


title: 496T

description:
Library name: 496TA
Column name in GEOrsem_expected_count.csv: 496TA

source_name: Clear cell renal cell carcinoma

value: Clear cell renal cell carcinoma


title: Patient 2_ROI 05_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-E03
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: microPTC 4, DGCR8-mutated, VIM+

value: Patient 2_microPTC 4_ VIM+

value: VIM+ (Cy5)


title: C57BL/67_liver_KO_HFPODA_replication2

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400275-KO_HFPODA_2


title: P6 Human Bronchial Epithelial Cells biol rep 2

description: Library name: HBEC_P6B

value: airway epithelium

value: basal stem cell

value: cultured in a novel medium (sfBSC)


title: P6 Human Bronchial Epithelial Cells biol rep 1

description: Library name: HBEC_P6A


title: 504T

description:
Library name: 504TA
Column name in GEOrsem_expected_count.csv: 504TA


title: 487T

description:
Library name: 487TA
Column name in GEOrsem_expected_count.csv: 487TA


title: C57BL/67_liver_KO_PFUnDA_replication3

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400273-KO_PFUnDA_3

value: oral gavage PUnDA(1mg/kg bw/day


title: Patient 2_ROI 04_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-D12
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: microPTC 3, DGCR8-mutated, PanCK+

value: Patient 2_microPTC 3_ PanCK+

value: microPTC

value: Male


title: 469T

description:
Library name: 469TA
Column name in GEOrsem_expected_count.csv: 469TA


title: C57BL/67_liver_KO_PFUnDA_replication2

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400272-KO_PFUnDA_2


title: P3 Human Bronchial Epithelial Cells biol rep 2

description: Library name: HBEC_P3B

value: human bronchial epithelial cell


title: Patient 2_ROI 04_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-E01
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: microPTC 3, DGCR8-mutated, VIM+

value: Patient 2_microPTC 3_ VIM+

value: Patient 2


title: 464T

description:
Library name: 464TA
Column name in GEOrsem_expected_count.csv: 464TA


title: Citeseq, Pam HSPC AML, GEX, ADT

description:
Library name: Pam_HSPC
GEX, ADT

value: bone marrow

value: leukemic myeloid cells

value: mRNA, ADT

value: TotalSeq-A 0109 anti-mouse CD16/32, TotalSeq-A 0130 anti-mouse Ly-6A/E (Sca-1), TotalSeq-A 0857 anti-mouse CD34, TotalSeq-A 0012 anti-mouse CD117, TotalSeq-A 0951 anti-mouse PE Streptavidin (for biotinylated Tlr2)


title: C57BL/67_liver_KO_PFUnDA_replication1

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400271-KO_PFUnDA_1

value: liver

value: PPARg KO


title: Patient 2_ROI 02_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-D08
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: microPTC 2, DGCR8-mutated, VIM+

value: Patient 2_microPTC 2_ VIM+

value: VIM+ (Cy5)


title: C57BL/67_liver_KO_PFOA_replication3

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400270-KO_PFOA_3

value: oral gavage PFOA(1mg/kg bw/day


title: P3 Human Bronchial Epithelial Cells biol rep 1

description: Library name: HBEC_P3A

source_name: airway epithelium

value: airway epithelium

value: basal stem cell

value: cultured in a novel medium (sfBSC)


title: P3 Human Bronchial Epithelial Cells biol rep 3

description: Library name: HBEC_P3C


title: male 3n group3 replicate 6

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

description:
Library name: G97-11
G97-11

data_processing:
Quality check of raw paired-end fastq reads was carried out by FastQC.
The Illumina adapters clipping and quality trimming of raw fastq reads were performed using cutadapt v4.3 with settings --quality-base=33 -q 0,20 -m 35 -M 250. Trimmed RNA-Seq reads were mapped to the reference genome using STAR v2.7.3a as a splice-aware short read aligner and default parameters except for --outFilterMismatchNoverLmax 0.1 and --twopassMode Basic.
Quality control after alignment concerning the number and percentage of uniquely- and multi-mapped reads, rRNA contamination, mapped regions, read coverage distribution, strand specificity, gene biotypes, and PCR duplication was performed using several tools – namely, RSeQC v4.0.0, Picard toolkit v2.25.6, and Qualimap v.2.2.2. All statistics were processed by MultiQC v1.10.1.
Mapped read counts were obtain using featureCounts from the Subread package v2.0.
Assembly: Carassius auratus genome (ASM336829v1) with Ensembl annotation (release 104)
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples

organism: Carassius gibelio

source_name: testes

extract_protocol:
Total RNA was isolated using PureLink® RNA Mini Kit (Ambion) with Trizol reagent (Thermo Fisher Scientific, Waltham, MA, USA) and on-column PureLink DNase treatment was used according to the manufacturer´s protocol. Reagent and buffer volumes were adjusted according to the weight of tissue entering the isolation process (30 mg on average). The final elution was performed using 100 µl of RNAse-free water in the first step and the primal eluate in the second step. The yield and concentration of RNA isolates were checked using a QubitTM 4 fluorometer (Invitrogen by Thermo Fisher Scientific, Waltham, MA, USA) and Qubit RNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA, USA). The quality and integrity of RNA were analysed using RNA 6000 Nano Kit on a 2100 Bioanalyser instrument (Agilent Technologies, Santa Clara, CA, USA). All RNA isolates were normalized by dilution at a uniform concentration of 20 ng/µl with RNase-free water. They served as templates for DNA library preparation in twice the reaction volume recommended by the manufacturer.
RNA integrity (RIN > 7) was checked for each sample on the Fragment Analyzer using RNA Kit 15 nt (Agilent Technologies). First, 250-500 ng of total RNA was used for mRNA enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Subsequently, full-length RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) with xGen™ CS adapters (IDT) containing UMIs. Quality control for library quantity and size distribution was done using QuantiFluor dsDNA System (Promega) and High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies). Final library pool was sequenced on NovaSeq 6000 (Illumina) in paired-end 150bp mode, resulting in an average of 30 million reads per sample.

value: testes

value: triploid males

value: sampled at 22 °C, offspring of a female with wide range of temperature-induced female-male sex reversal


title: Patient 2_ROI 03_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-D11
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: high stromal area, DGCR8-mutated, VIM+

value: Patient 2_high stromal area_ VIM+

value: high stromal area

value: Male


title: 411T

description:
Library name: 411TdaiA
Column name in GEOrsem_expected_count.csv: 411TdaiA

value: Clear cell renal cell carcinoma


title: 463T

description:
Library name: 463TA
Column name in GEOrsem_expected_count.csv: 463TA


title: Patient 2_ROI 02_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-D07
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: microPTC 2, DGCR8-mutated, PanCK+

value: Patient 2_microPTC 2_ PanCK+

value: Patient 2

value: microPTC

value: PanCK+ (Cy3)


title: 409T

description:
Library name: 409T_23000714A
Column name in GEOrsem_expected_count.csv: 409T_23000714A


title: Patient 2_ROI 01_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-D06
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: microPTC 1, DGCR8-mutated, VIM+

value: Patient 2_microPTC 1_ VIM+


title: male 3n group3 replicate 4

description:
Library name: G95-11
G95-11


title: C57BL/67_liver_KO_PFOA_replication1

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400268-KO_PFOA_1

value: liver

value: PPARg KO


title: C57BL/67_liver_KO_HFPODA_replication1

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400274-KO_HFPODA_1

value: oral gavage HFPODA(1mg/kg bw/day


title: Patient 1_ROI 024_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-D04
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 9, DICER1-mutated, VIM+

value: Patient 1_PDTC 9_ VIM+

value: Patient 1

value: PDTC

value: Female

value: VIM+ (Cy5)


title: C57BL/67_liver_KO_CT_replication3

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400279-KO_CT_3

value: oral gavage 0.1%DMSO


title: 382T

description:
Library name: 382TA
Column name in GEOrsem_expected_count.csv: 382TA


title: C57BL/67_liver_KO_CT_replication2

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400278-KO_CT_2


title: 461T

description:
Library name: 461TA
Column name in GEOrsem_expected_count.csv: 461TA


title: male 3n group3 replicate 3

description:
Library name: G94-11
G94-11

value: testes

value: triploid males

value: sampled at 22 °C, offspring of a female with wide range of temperature-induced female-male sex reversal


title: male 3n group3 replicate 2

description:
Library name: G109-12
G109-12


title: male 3n group3 replicate 1

description:
Library name: G108-12
G108-12


title: 253T

description:
Library name: 253T_23000713A
Column name in GEOrsem_expected_count.csv: 253T_23000713A

value: Clear cell renal cell carcinoma


title: Patient 1_ROI 024_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-D03
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 9, DICER1-mutated, PanCK+

value: Patient 1_PDTC 9_ PanCK+


title: C57BL/67_liver_KO_CT_replication1

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400277-KO_CT_1


title: male 3n group2 replicate 5

description:
Library name: G84-11-31
G84-11-31

value: sampled at 28-31 °C, offspring of a female with wide range of temperature-induced female-male sex reversal


title: C57BL/67_liver_WT_HFPODA_replication3

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400288-WT_HFPODA_3

value: wild type


title: 235T

description:
Library name: 235TA
Column name in GEOrsem_expected_count.csv: 235TA


title: male 3n group3 replicate 5

description:
Library name: G96-11
G96-11


title: C57BL/67_liver_KO_PFOA_replication2

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400269-KO_PFOA_2

value: oral gavage PFOA(1mg/kg bw/day


title: male 3n group2 replicate 4

description:
Library name: G83-11-31
G83-11-31


title: 230T

description:
Library name: 230TA
Column name in GEOrsem_expected_count.csv: 230TA


title: 402T

description:
Library name: 402TA
Column name in GEOrsem_expected_count.csv: 402TA


title: Patient 2_ROI 01_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-D05
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: microPTC 1, DGCR8-mutated, PanCK+

value: Patient 2_microPTC 1_ PanCK+

value: Patient 2

value: microPTC

value: Male

value: PanCK+ (Cy3)


title: Patient 1_ROI 021_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-C11
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: macrophage, NA, VIM+

value: Patient 1_macrophage_ VIM+

value: Patient 1

value: macrophage


title: male 3n group2 replicate 3

description:
Library name: G82-11-31
G82-11-31


title: C57BL/67_liver_WT_HFPODA_replication1

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400286-WT_HFPODA_1

value: liver

value: oral gavage HFPODA(1mg/kg bw/day


title: male 3n group2 replicate 2

description:
Library name: G37-11-31
G37-11-31

value: testes

value: triploid males


title: 207T

description:
Library name: 207TA
Column name in GEOrsem_expected_count.csv: 207TA

value: Clear cell renal cell carcinoma


title: Patient 1_ROI 020_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-C10
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 7, DICER1-mutated, VIM+

value: Patient 1_PDTC 7_ VIM+

value: PDTC

value: Female

value: VIM+ (Cy5)


title: C57BL/67_liver_WT_PFUnDA_replication3

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400285-WT_PFUnDA_3

value: wild type

value: oral gavage PUnDA(1mg/kg bw/day


title: 187T

description:
Library name: 187TA
Column name in GEOrsem_expected_count.csv: 187TA


title: Patient 1_ROI 023_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-D02
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 8, DICER1-mutated, VIM+

value: Patient 1_PDTC 8_ VIM+


title: C57BL/67_liver_WT_PFUnDA_replication2

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400284-WT_PFUnDA_2

source_name: liver


title: male 3n group2 replicate 1

description:
Library name: G36-11-31
G36-11-31

value: sampled at 28-31 °C, offspring of a female with wide range of temperature-induced female-male sex reversal


title: 154T

description:
Library name: 154TA
Column name in GEOrsem_expected_count.csv: 154TA

source_name: Clear cell renal cell carcinoma


title: Patient 1_ROI 019_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-C08
FFPE spatial transcriptomics (NanoString DSP WTA)


title: Patient 1_ROI 023_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-D01
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 8, DICER1-mutated, PanCK+

value: Patient 1_PDTC 8_ PanCK+

value: PanCK+ (Cy3)


title: male 3n group1 replicate 5

description:
Library name: G76-4-28
G76-4-28

value: sampled at 28-31 °C, offspring of a female with female-male sex reversal only at high temperature


title: C57BL/67_liver_WT_PFUnDA_replication1

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400283-WT_PFUnDA_1


title: Patient 1_ROI 018_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-C07
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Capsule 6, NA, VIM+

value: Patient 1_Capsule 6_ VIM+

value: Patient 1

value: Tumor Capsule


title: male 3n group1 replicate 4

description:
Library name: G52-5-28
G52-5-28

value: testes


title: 147T

description:
Library name: 147TnaiA
Column name in GEOrsem_expected_count.csv: 147TnaiA


title: C57BL/67_liver_WT_HFPODA_replication2

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400287-WT_HFPODA_2

value: liver

value: oral gavage HFPODA(1mg/kg bw/day


title: C57BL/67_liver_WT_PFOA_replication3

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400282-WT_PFOA_3

value: oral gavage PFOA(1mg/kg bw/day


title: 143T

description:
Library name: 143TA
Column name in GEOrsem_expected_count.csv: 143TA

value: Clear cell renal cell carcinoma


title: 218T

description:
Library name: 218TA
Column name in GEOrsem_expected_count.csv: 218TA


title: male 3n group1 replicate 3

description:
Library name: G90-5-31
G90-5-31

value: triploid males


title: C57BL/67_liver_WT_PFOA_replication2

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400281-WT_PFOA_2


title: Patient 1_ROI 016_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-C05
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Capsule 4, NA, VIM+

value: Patient 1_Capsule 4_ VIM+

value: Female

value: VIM+ (Cy5)


title: Patient 1_ROI 020_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-C09
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 7, DICER1-mutated, PanCK+

value: Patient 1_PDTC 7_ PanCK+

value: PDTC


title: male 3n group1 replicate 2

description:
Library name: G89-6-31
G89-6-31


title: 141T

description:
Library name: 141TA
Column name in GEOrsem_expected_count.csv: 141TA


title: C57BL/67_liver_WT_PFOA_replication1

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400280-WT_PFOA_1

value: wild type


title: Patient 1_ROI 017_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-C06
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Capsule 5, NA, VIM+

value: Patient 1_Capsule 5_ VIM+


title: Patient 1_ROI 015_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-C04
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Capsule 3, NA, VIM+

value: Patient 1_Capsule 3_ VIM+


title: male 3n group1 replicate 1

description:
Library name: G81-4-31
G81-4-31

source_name: testes

value: sampled at 28-31 °C, offspring of a female with female-male sex reversal only at high temperature


title: C57BL/67_liver_WT_CT_replication3

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400291-WT_CT_3

value: oral gavage 0.1%DMSO


title: C57BL/67_liver_WT_CT_replication2

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400290-WT_CT_2


title: 114T

description:
Library name: 114TA
Column name in GEOrsem_expected_count.csv: 114TA


title: male 2n replicate 10

description:
Library name: G66-108
G66-108

value: diploid males

value: sampled at 22 °C


title: C57BL/67_liver_WT_CT_replication1

institute: 国家食品安全风险评估中心

description: Library name: L1EIG2400289-WT_CT_1

value: liver


title: Patient 1_ROI 013_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-C02
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Capsule 1, NA, VIM+

value: Patient 1_Capsule 1_ VIM+

value: Patient 1

value: Tumor Capsule


title: male 2n replicate 9

description:
Library name: G88-108
G88-108

value: testes


title: Sample 543

type: genomic

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC (850K) Beadchip (Illumina) arrays using standard Illumina protocol

scan_protocol: Standard Illumina scanner and settings

data_processing: All methylation analyses were conducted in R (version 4.4.1). EPICv1 and EPICv2 array data were merged and preprocessed using the minfi package (version 1.52.0). Single-sample Noob normalization was performed. Probes with poor performance were excluded based on detection p-values prior to downstream analyses. Additionally, probes targeting the X and Y chromosomes, those containing single nucleotide polymorphisms (SNPs), and cross-reactive probes were filtered out. The data were further corrected for material type (FFPE/FFT) using the limma package (version 3.62.0).

label: Cy3 and Cy5

molecule: genomic DNA

source_name: FFPE

label_protocol: Standard Illumina protocol

extract_protocol: Tumoral DNA from fresh frozen tissue (FFT) samples was isolated with the DNeasy Blood and Tissue Qiagen kit and tumoral DNA from archived formalin-fixed, paraffin-embedded (FFPE) material was isolated using the QIAamp DNA FFPE Tissue Kit

tag: project

value: This study

value: Male

tag: tumor type

value: Minimally invasive follicular thyroid carcinoma (MIFTC)

tag: tissue type

value: FFPE


title: Patient 1_ROI 012_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-C01
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 6, DICER1-mutated, VIM+

value: Patient 1_PDTC 6_ VIM+

value: PDTC

value: Female

value: VIM+ (Cy5)


title: Sample 584

value: Poorly differentiated thyroid carcinoma (PDTC)


title: Patient 1_ROI 012_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-B12
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 6, DICER1-mutated, PanCK+

value: Patient 1_PDTC 6_ PanCK+

value: PanCK+ (Cy3)


title: Patient 1_ROI 011_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-B11
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 5, DICER1-mutated, VIM+

value: Patient 1_PDTC 5_ VIM+


title: APOE_HFD, scRNA_seq

city: Hangzhou

first: Cong

last: Qiu

state: Zhejiang

address: No.866 Yuhangtang Road

institute: Zhejiang University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrex files

source_name: Aorta

extract_protocol:
All animals were anaesthetized by isoflurane inhalation (3%) and euthanized by exsanguination. Aortas from 4 mice of each group were harvested and dissected into small pieces. Tissues were digested in a 1.5 mL digestive solution containing 1.5 mg/mL Collagenase A (Roche, 10103578001) and 0.5 mg/mL Elastase (Sigma-Aldrich, E1250) dissolved in DMEM (Gibco) with 10% FBS (Noverse, NFBS2500A) at 37°C for 3 h. Suspension was slowly pipetted up and down using sterile pipette tips every half-hour. After digestion, the solution was transferred into flow tubes, and 3 mL of flow buffer (i.e., PBS with 10% FBS) was added to terminate the digestion. After centrifugating at 500 g for 5 min at 4°C, the supernatant was discarded, and the pellet was washed with 1 mL flow buffer followed by centrifugation as described above. Cell pellets were then resuspended in 150 μL flow buffer and incubated with fluorochrome-coupled antibodies against CD31 (Invitrogen, 11-0311-82) and CD45 (Invitrogen, 12-0451-82) at 1:100 for 30 mins on ice in the dark. After incubation, cells were washed with 1 mL flow buffer and resuspended in 300 μL PBS. 4,6-Diamidino-2-phenylindole (DAPI) (1:1000) was added to mark dead cells before sorting. The resulting cell suspension was filtered using 40 μm cell strainers. The CD45− and CD31+ living cells were then acquired using a flow sorter (BD FACS ORP ARIA II).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Aorta

value: Endothelial cells

value: Apoe knock out

value: 8 weeks-old mice fed with high fat diet for 16 week


title: male 2n replicate 7

description:
Library name: G63-14
G63-14

value: testes

value: diploid males

value: sampled at 22 °C


title: Sample 592

value: This study

value: Male

value: Thyroid follicular nodular disease (TFND)


title: PMID-31937902_Case1

value: FFPE


title: Sample 585


title: Patient 1_ROI 014_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-C03
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Capsule 2, NA, VIM+

value: Patient 1_Capsule 2_ VIM+

value: Patient 1

value: Tumor Capsule

value: Female


title: Patient 1_ROI 011_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-B10
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 5, DICER1-mutated, PanCK+

value: Patient 1_PDTC 5_ PanCK+

value: PDTC

value: PanCK+ (Cy3)


title: WT_SFD, scRNA_seq

value: Aorta

value: Endothelial cells

value: WT

value: 8 weeks-old mice fed with standard fat diet for 16 week


title: male 2n replicate 5

description:
Library name: G61-14
G61-14

value: testes

value: diploid males


title: Sample 591

value: This study


title: HC_AG_rep2, scATAC

city: Blacksburg

first: Timothy

last: Jarome

address: Mail Stop: 0306,ANIMAL SCIENCES  MC0306,LITTON REEVES   STE 3490

institute: Virginia Tech

description: single nuclei multiome sequencing (snATAC-seq)

library_source: genomic

data_processing:
The raw sequencing reads were trimmed and aligned to mouse reference genome (mm10) using cellranger-arc (10x genomics, v.2.0.1) and quantified using ‘cellranger -arc count’.
The count matrix was further processed using the R package Seurat (v.5.0.1) and Signac (v.1.13.0). Quality control steps were performed to remove low quality nuclei.
The raw count matrix data from snRNA-seq was further processed using the R package Seurat (v.5.0.3)
Assembly: mm10
Supplementary files format and content: tab-separated value files and matrix files
Library strategy: single nuclei multiome (snRNA-seq and snATAC-seq)

source_name: amygdala

growth_protocol: Adult male C57BL/6J mice (12 weeks) were purchased from Jaxson laboratory and maintained in a 12-hour light/dark cycle under standard pathogen-free conditions.

extract_protocol:
Mice were harvested and fresh hippocampus and amygdala tissues were dissected and used to prepare debris-free single nuclei suspension.
Single nuclei RNA-seq (snRNA-seq) and single nuclei ATAC-seq (snATAC-seq) libraries were simultaneously constructed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (10x Genomics, cat# 1000285) according to the manufacturer’s User Guide (CG000338).

treatment_protocol: Adult C57BL/6 male mice (12~15 weeks) were subjected to contextual fear conditioning (CFC), mice without foot shock were used as context control (CC), and mice stayed in the home cage until sample harvest were used as home cage control (HC). Mice were harvested 1h or 4h after foot shock on the training day (day 0) and 4h after memory retrieval on day 1 to assess fear memory consolidation and reconsolidation.

value: amygdala

value: wild-type


title: male 2n replicate 6

description:
Library name: G62-14
G62-14

value: sampled at 22 °C


title: Sample 590

value: Male

value: Thyroid follicular nodular disease (TFND)

value: FFPE


title: male 2n replicate 4

description:
Library name: G65-108
G65-108


title: Sample 593


title: Patient 1_ROI 010_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-B09
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 4, DICER1-mutated, VIM+

value: Patient 1_PDTC 4_ VIM+

value: Patient 1

value: Female

value: VIM+ (Cy5)


title: male 2n replicate 8

description:
Library name: G86-108
G86-108


title: Patient 1_ROI 009_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-B07
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 3, DICER1-mutated, VIM+

value: Patient 1_PDTC 3_ VIM+

value: PDTC


title: CFC_d1_4h_AG_rep2, scATAC


title: APOE_SFD, scRNA_seq

value: Aorta

value: Endothelial cells

value: Apoe knock out


title: male 2n replicate 2

description:
Library name: G75-14
G75-14

value: testes

value: diploid males


title: HC_AG_rep1, scATAC

value: amygdala


title: CFC_d1_4h_AG_rep1, scATAC

value: wild-type


title: Patient 1_ROI 009_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-B06
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 3, DICER1-mutated, PanCK+

value: Patient 1_PDTC 3_ PanCK+

value: PanCK+ (Cy3)


title: AAV8-Cre, slide7

type: RNA

city: Pittsburgh

first: Shuchang

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: AAV8-Cre, slide7

hyb_protocol: Protocal provided and performed by resolve biosciences (https://your.resolve-biosciences.com/), with reference paper PMID: 35021063. The probe set is illustrated in the supplementary file.

data_processing:
Gene count per cell were identified by QuPath
mm10
CSV file for gene by cell count matrix

source_name: liver

extract_protocol: Frozen tissue preserved in 2-methyl-butane from 1 individual tumor bearing control and 1 individual tumor bearing Glul-KO mouse 7-weeks post-virus infection were sectioned at -17oC using a cryostat that cut 10 μm sections placed onto a Resolve Biosciences slide.

value: liver

value: Cre


title: CC_d1_4h_AG_rep2, scATAC


title: AAV8-Cre, slide6

description: AAV8-Cre, slide6


title: AAV8-Cre, slide8

description: AAV8-Cre, slide8


title: daf-2(e1370);bcl-11(bon144), the first day of young adult, rep 4

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1/99

country: Germany

institute: DZNE, German Center for Neurodegenerative Diseases

description:
Library name: Sample 24
daf2bcl11_NormalizedCounts_rLog.csv

data_processing:
Sequencing was executed in PE75 on a NextSeq 2000 System (Illumina) with a NextSeq 2000 P4 XLEAP-SBS™ Reagent Kit (300 Cycles) chemistry.
Raw sequencing data were demultiplexed using bcl2fastq2 v2.20 and aligned against C. elegans reference genome (Ensembl release 109) using Kallisto v048.0.
Assembly: WBcel235
Supplementary files format and content: csv files include normalized counts for each sample.

organism: Caenorhabditis elegans

source_name: nematodes

growth_protocol: Worms were grown on OP50-1 at 20℃.

extract_protocol:
Adult nematodes were dissolved in 1ml Trizol (Invitrogen). Total RNA was extracted using miRNeasy Micro Kit (Qiagen).
SMART-Seq2 protocol (Picelli et al., 2014) was used to prepare cDNA libraries.

value: nematodes

tag: time point

value: the first day of young adult

tag: batch


title: CC_d1_4h_AG_rep1, scATAC

tag: tissue

tag: genotype


title: Patient 1_ROI 008_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-B05
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 2, DICER1-mutated, VIM+

value: Patient 1_PDTC 2_ VIM+

tag: patient

value: Patient 1

value: Female


title: AAV8-Cre, slide4

description: AAV8-Cre, slide4


title: daf-2(e1370);bcl-11(bon144), the first day of young adult, rep 3

description:
Library name: Sample 23
daf2bcl11_NormalizedCounts_rLog.csv


title: AAV8-Cre, slide5

description: AAV8-Cre, slide5


title: male 2n replicate 3

description:
Library name: G107-106
G107-106

tag: treatment

value: sampled at 22 °C


title: Patient 1_ROI 007_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-B03
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 1, DICER1-mutated, VIM+

value: Patient 1_PDTC 1_ VIM+

tag: histological type

value: PDTC

tag: Sex

value: VIM+ (Cy5)


title: Patient 1_ROI 010_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-B08
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 4, DICER1-mutated, PanCK+

value: Patient 1_PDTC 4_ PanCK+

tag: label (panck/vim)


title: CFC_d0_4h_AG_rep2, scATAC


title: Patient 1_ROI 007_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-B02
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 1, DICER1-mutated, PanCK+

value: Patient 1_PDTC 1_ PanCK+


title: CFC_d0_4h_AG_rep1, scATAC

value: amygdala


title: Patient 1_ROI 008_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-B04
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: PDTC 2, DICER1-mutated, PanCK+

value: Patient 1_PDTC 2_ PanCK+


title: daf-2(e1370);bcl-11(bon144), the first day of young adult, rep 2

description:
Library name: Sample 22
daf2bcl11_NormalizedCounts_rLog.csv


title: AAV8-Cre, slide2

description: AAV8-Cre, slide2


title: AAV8-Cre, slide1

description: AAV8-Cre, slide1


title: Patient 1_ROI 006_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-B01
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 3, non-DICER1-mutated, VIM+

value: Patient 1_Non-neoplastic nodular area 3_ VIM+

value: Non-neoplastic nodular area


title: CC_d0_4h_AG_rep1, scATAC

value: wild-type


title: Patient 1_ROI 006_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-A12
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 3, non-DICER1-mutated, PanCK+

value: Patient 1_Non-neoplastic nodular area 3_ PanCK+

value: PanCK+ (Cy3)


title: male 2n replicate 1

description:
Library name: G73-14
G73-14

source_name: testes

value: testes

value: diploid males


title: daf-2(e1370);bcl-11(bon125), the first day of young adult, rep 4

description:
Library name: Sample 20
daf2bcl11_NormalizedCounts_rLog.csv

value: nematodes

value: the first day of young adult


title: daf-2(e1370);bcl-11(bon125), the first day of young adult, rep 2

description:
Library name: Sample 18
daf2bcl11_NormalizedCounts_rLog.csv


title: daf-2(e1370);bcl-11(bon144), the first day of young adult, rep 1

description:
Library name: Sample 21
daf2bcl11_NormalizedCounts_rLog.csv


title: HC_HP_rep1, scATAC

description: single nuclei multiome sequencing (snATAC-seq)

source_name: hippocampus

value: hippocampus


title: daf-2(e1370);bcl-11(bon125), the first day of young adult, rep 3

description:
Library name: Sample 19
daf2bcl11_NormalizedCounts_rLog.csv


title: HC_HP_rep2, scATAC


title: AAV8-GFP control, slide 8

description: AAV8-GFP control, slide 8

value: liver

value: GFP


title: Patient 1_ROI 005_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-A10
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 2, non-DICER1-mutated, PanCK+

value: Patient 1_Non-neoplastic nodular area 2_ PanCK+

value: Patient 1

value: Female


title: Patient 1_ROI 005_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-A11
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 2, non-DICER1-mutated, VIM+

value: Patient 1_Non-neoplastic nodular area 2_ VIM+

value: VIM+ (Cy5)


title: AAV8-Cre, slide3

description: AAV8-Cre, slide3

value: Cre


title: daf-2(e1370);bcl-11(bon125), the first day of young adult, rep 1

description:
Library name: Sample 17
daf2bcl11_NormalizedCounts_rLog.csv


title: AAV8-GFP control, slide 7

description: AAV8-GFP control, slide 7


title: CFC_d1_4h_HP_rep2, scATAC


title: Patient 1_ROI 004_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-A09
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 1, non-DICER1-mutated, VIM+

value: Patient 1_Non-neoplastic nodular area 1_ VIM+

value: Non-neoplastic nodular area


title: CFC_d1_4h_HP_rep1, scATAC

value: wild-type


title: AAV8-GFP control, slide 6

description: AAV8-GFP control, slide 6


title: Patient 1_ROI 004_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-A08
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Non-neoplastic nodular area 1, non-DICER1-mutated, PanCK+

value: Patient 1_Non-neoplastic nodular area 1_ PanCK+

value: PanCK+ (Cy3)


title: daf-2(e1370), the first day of young adult, rep 3

description:
Library name: Sample 15
daf2bcl11_NormalizedCounts_rLog.csv


title: daf-2(e1370), the first day of young adult, rep 4

description:
Library name: Sample 16
daf2bcl11_NormalizedCounts_rLog.csv


title: Patient 1_ROI 003_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-A07
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal thyroid 3, non-DICER1-mutated, VIM+

value: Patient 1_Normal thyroid 3_ VIM+

value: Normal thyroid


title: CC_d0_4h_AG_rep2, scATAC

source_name: amygdala

value: amygdala


title: AAV8-GFP control, slide 4

description: AAV8-GFP control, slide 4

source_name: liver


title: CC_d1_4h_HP_rep2, scATAC

value: hippocampus


title: daf-2(e1370), the first day of young adult, rep 2

description:
Library name: Sample 14
daf2bcl11_NormalizedCounts_rLog.csv

source_name: nematodes

value: nematodes

value: the first day of young adult


title: CC_d1_4h_HP_rep1, scATAC


title: daf-2(e1370), the first day of young adult, rep 1

description:
Library name: Sample 13
daf2bcl11_NormalizedCounts_rLog.csv


title: AAV8-GFP control, slide 3

description: AAV8-GFP control, slide 3

value: liver

value: GFP


title: Patient 1_ROI 002_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-A04
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal thyroid 2, non-DICER1-mutated, VIM+

value: Patient 1_Normal thyroid 2_ VIM+

value: Patient 1

value: Female


title: CFC_d0_4h_HP_rep2, scATAC


title: AAV8-GFP control, slide 2

description: AAV8-GFP control, slide 2


title: Patient 1_ROI 002_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-A03
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal thyroid 2, non-DICER1-mutated, PanCK+

value: Patient 1_Normal thyroid 2_ PanCK+


title: bcl-11(bon144), the first day of young adult, rep 3

description:
Library name: Sample 11
bcl11_NormalizedCounts_rLog.csv


title: bcl-11(bon144), the first day of young adult, rep 4

description:
Library name: Sample 12
bcl11_NormalizedCounts_rLog.csv


title: Patient 1_ROI 001_ VIM+

description:
Library name: Sample_DSP-1001660005657-A-A02
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal thyroid 1, non-DICER1-mutated, VIM+

value: Patient 1_Normal thyroid 1_ VIM+

value: VIM+ (Cy5)


title: CC_d0_4h_HP_rep2, scATAC

description: single nuclei multiome sequencing (snATAC-seq)

value: wild-type


title: CFC_d0_4h_HP_rep1, scATAC


title: AAV8-GFP control, slide 1

description: AAV8-GFP control, slide 1


title: daf-16(mu86);daf-2(e1370);bcl-11(bon125), eggs, rep 4

description: Library name: Sample 12

data_processing:
Sequencing was executed in PE75 on a NovaSeq X Plus system (Illumina) using a NovaSeq X Series 10B Reagent Kit (300 cycles)
Raw sequencing data were demultiplexed using bcl2fastq2 v2.20 and aligned against C. elegans reference genome (Ensembl release 109) using Kallisto v048.0.
Assembly: WBcel235
Supplementary files format and content: csv file includes normalized counts for each sample.

source_name: eggs

growth_protocol: Eggs were extracted from nematodes grown on OP50-1 at 20℃.

extract_protocol:
Total RNA was extracted using miRNeasy Micro Kit (Qiagen). 5ng of total RNA was prepared for the construction of cDNA libraries.
SMART-Seq2 protocol (Picelli et al., 2014) was used to prepare cDNA libraries.

treatment_protocol: Eggs were incubated at 27℃ for 2h after bleaching.

value: eggs

value: incubated at 27℃ for 2h after extraction


title: bcl-11(bon144), the first day of young adult, rep 2

description:
Library name: Sample 10
bcl11_NormalizedCounts_rLog.csv


title: AAV8-GFP control, slide 5

description: AAV8-GFP control, slide 5


title: daf-16(mu86);daf-2(e1370);bcl-11(bon125), eggs, rep 3

description: Library name: Sample 11


title: bcl-11(bon144), the first day of young adult, rep 1

description:
Library name: Sample 9
bcl11_NormalizedCounts_rLog.csv


title: Patient 1_ROI 001_ PanCK+

description:
Library name: Sample_DSP-1001660005657-A-A01
FFPE spatial transcriptomics (NanoString DSP WTA)

source_name: Normal thyroid 1, non-DICER1-mutated, PanCK+

value: Patient 1_Normal thyroid 1_ PanCK+

value: PanCK+ (Cy3)


title: bcl-11(bon125), the first day of young adult, rep 4

description:
Library name: Sample 8
bcl11_NormalizedCounts_rLog.csv


title: CC_d0_4h_HP_rep1, scATAC


title: HepG2, Tunicamycin, rep5

city: Tartu

first: Tiit

last: Örd

address: Riia 23b/2

department: Institute of Genomics

country: Estonia

institute: University of Tartu

description: Library name: HepG2-Tunicamycin_rep5

data_processing:
Sequencing reads were processed using the nf-core RNA-Seq pipeline (version 1.4.2; https://nf-co.re/rnaseq) with the hg19 reference genome and Ensembl release 87 transcript definitions.
Assembly: hg19
Supplementary files format and content: tab-delimited text file containing raw counts

growth_protocol: HepG2 cells were cultured in Dulbecco’s Modified Eagle Medium (4.5 g/l D-glucose; Gibco) supplemented with 10% fetal bovine serum and 1× penicillin-streptomycin.

extract_protocol:
The RNeasy Midi Kit with on-column DNase digestion (Qiagen) was used to extract total RNA.
RNA-seq libraries were prepared from 250 ng of total RNA using the Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina (FWD).

treatment_protocol: Cells were treated with growth medium supplemented with 2 µg/ml tunicamycin (Sigma) or regular growth medium (as control) for 17h.

tag: cell line

value: Tunicamycin

tag: replicate


title: HC_AG_rep2, snRNA

description: single nuclei multiome sequencing (snRNA-seq)

molecule: nuclear RNA

value: amygdala


title: daf-16(mu86);daf-2(e1370);bcl-11(bon125), eggs, rep 2

description: Library name: Sample 10


title: HC_AG_rep1, snRNA


title: daf-16(mu86);daf-2(e1370);bcl-11(bon125), eggs, rep 1

description: Library name: Sample 9


title: HepG2, Tunicamycin, rep4

description: Library name: HepG2-Tunicamycin_rep4


title: daf-2(e1370);bcl-11(bon125), eggs, rep 4

description: Library name: Sample 8


title: bcl-11(bon125), the first day of young adult, rep 3

description:
Library name: Sample 7
bcl11_NormalizedCounts_rLog.csv

value: nematodes


title: HepG2, Tunicamycin, rep3

description: Library name: HepG2-Tunicamycin_rep3


title: bcl-11(bon125), the first day of young adult, rep 2

description:
Library name: Sample 6
bcl11_NormalizedCounts_rLog.csv

value: the first day of young adult


title: HepG2, Tunicamycin, rep2

description: Library name: HepG2-Tunicamycin_rep2


title: CFC_d1_4h_AG_rep1, snRNA


title: daf-2(e1370);bcl-11(bon125), eggs, rep 3

description: Library name: Sample 7


title: CFC_d1_4h_AG_rep2, snRNA


title: wt(N2), the first day of young adult, rep 4

description:
Library name: Sample 4
bcl11_NormalizedCounts_rLog.csv


title: HepG2, Tunicamycin, rep1

description: Library name: HepG2-Tunicamycin_rep1


title: HepG2, Control, rep5

description: Library name: HepG2-Ctrl_rep5

value: Control


title: daf-2(e1370);bcl-11(bon125), eggs, rep 2

description: Library name: Sample 6


title: CC_d1_4h_AG_rep2, snRNA


title: daf-2(e1370);bcl-11(bon125), eggs, rep 1

description: Library name: Sample 5


title: CC_d1_4h_AG_rep1, snRNA


title: daf-2(e1370), eggs, rep 4

description: Library name: Sample 4


title: CFC_d0_4h_AG_rep2, snRNA


title: wt(N2), the first day of young adult, rep 3

description:
Library name: Sample 3
bcl11_NormalizedCounts_rLog.csv


title: HepG2, Control, rep4

description: Library name: HepG2-Ctrl_rep4


title: wt(N2), the first day of young adult, rep 2

description:
Library name: Sample 2
bcl11_NormalizedCounts_rLog.csv


title: CFC_d0_4h_AG_rep1, snRNA


title: wt(N2), the first day of young adult, rep 1

description:
Library name: Sample 1
bcl11_NormalizedCounts_rLog.csv


title: daf-2(e1370), eggs, rep 3

description: Library name: Sample 3


title: HepG2, Control, rep3

description: Library name: HepG2-Ctrl_rep3


title: CC_d0_4h_AG_rep2, snRNA


title: HepG2, Control, rep2

description: Library name: HepG2-Ctrl_rep2


title: daf-2(e1370), eggs, rep 2

description: Library name: Sample 2


title: CC_d0_4h_AG_rep1, snRNA


title: daf-2(e1370), eggs, rep 1

description: Library name: Sample 1


title: HepG2, Control, rep1

description: Library name: HepG2-Ctrl_rep1


title: HC_HP_rep2, snRNA

value: hippocampus


title: set-24 Mutant,YA, 20 degrees, ChIP input 2

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

description: Library name: SX3735_2_input

data_processing:
RNASeq- Quality and Adaptor Trimming - Trimmomatc
RNASeq- Read alignment and counting - Salmon
RNASeq- Differential expression analysis - DESEq2
ChIP-Seq- Quality and Adaptor Trimming - Cutadapt
ChIP-Seq- Read aligment- BWA
ChIP-Seq- Peak calling and bdg generations- MACS3
ChIP-Seq- Differential enrichment analysis- DiffBind
Assembly: Ensembl - WBCel235
Supplementary files format and content: raw_counts.txt - This file contains the raw counts obtained from Salmon alignment  for each sample in matrix fromat
Supplementary files format and content: regularized_log_normalised_counts.txt - This file contain rlog normalsed counts for each sample n matrix format
Supplementary files format and content: All bdgs - These files contain the log2 normalized enrichments in bedgraph format.

source_name: Whole Organism

extract_protocol:
RNAs were extracted using Trizol, chloroform, and isopropanol and treated with DNase I. DNA Chromatin was crosslinbked with formalaldehyde and fragmented by sonnication. Specific fragments were inmunoprecipitated with it's coresponding antibody.
mRNAs were purified from total RNA using PolyT oligo-attached beads and converted to cDNAs for library preparation. cDNA libraries were sequenced using a paired-end 150 bp sequencing strategy. ChIP-Seq libraries were prepared from the inmunoprecipitated fragments using a standard paired end 150bp DNA sequencing strategy.

value: Whole Organism

tag: chip antibody


title: bcl-11(bon125), the first day of young adult, rep 1

description:
Library name: Sample 5
bcl11_NormalizedCounts_rLog.csv


title: 755209_ev_9

city: Tarrytown

first: Kaitlyn

last: Gayvert

state: NY

address: 777 Old Saw Mill River Rd

department: Molecular Profiling & Data Science

institute: Regeneron Pharmaceuticals

description:
Library name: 755209
experiment3_empty-vector_spleen_mouse9

data_processing:
FASTQ files were aligned and quantified using Omicsoft ArrayStudio
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM for  each Sample/gene

source_name: spleen

extract_protocol:
Tissues/Cells were homogenized in TRIzol and chloroform was used for phase separation. The aqueous phase, containing total RNA, was purified using MagMAX™-96 for Microarrays Total RNA Isolation Kit (Ambion by Life Technologies) according to manufacturer’s specifications. Genomic DNA was removed using RNase-Free DNase Set (Qiagen) on the Kingfisher Flex machine (Thermofisher).
Experiment 1-2: The strand-specific RNA-seq libraries were prepared from 500 ng RNA using KAPA stranded mRNA-Seq Kit (KAPA Biosystems). The libraries were amplified by twelve-cycle PCR. Sequencing was performed on Illumina HiSeq®2500 (Illumina) by multiplexed single-read run with 33 cycles.  Experiment 3: mRNA was enriched from 4 ug total RNA using two rounds of Dynabeads® Oligo (dT)25 mRNA purification (Invitrogen). Half of the resulting mRNA was converted to mRNA-seq libraries using the ScriptSeq™ mRNA-Seq Library Preparation Kit (EPICENTRE Biotechnologies). The libraries were amplified by twelve-cycle PCR. Sequencing was performed on Illumina HiSeq®2500 (Illumina) by multiplexed single-read run with 33 cycles.

value: spleen

value: empty-vector


title: HC_HP_rep1, snRNA


title: Healthy_Control #14

city: Southport

first: Natalie

last: Eaton-Fitch

state: Queensland

address: Parklands Dr

country: Australia

institute: Griffith University

hyb_protocol: Processed according to nCounter manufacturers instructions

data_processing:
Raw gene expression data was normalised against positive and negative controls to account for background noise and platform-associated variation. Normalisation and analysis were performed using Rosalind Bio (San Diego, CA, USA) using geometric means of housekeeping genes (ABCF1, ALAS1, EEF1G, G6PD, GAPDH, GUSB, HPRT1, OAZ1, POLR1B, POLR2A, PPIA, RPL19, SDHA, TBP, TUBB) (Supplementary Material 1). Differential expression is reported between ME/CFS and long COVID with HC.
Ingenuity Pathway Analysis (IPA) (Qiagen Digital Insights, California, USA) was used for the interpretation of RNA in biological pathways and networks. The following filters were applied to all analyses, a fold change (FC) >1.5 or <-1.5 and a P-value <0.05.   Normality of participant data was determined using the Shapiro-Wilk test. Normally distributed continuous data was compared using one-way analysis of variance (ANOVA) corrected using Bonferroni, and non-normally distributed continuous data was compared using the Kruskal-Wallis test with Dunn’s corrections. Continuous data are presented as mean ± standard deviation (SD) unless otherwise stated. Categorical variables were compared using the Chi-Square test and the Fisher’s exact test. Participant demographic data was analysed using SPSS (version 27). Cell profile abundance scores were compared using one-way ANOVA corrected using Bonferroni or the Kruskal-Wallis test with Dunn’s corrections using GraphPad Prism (version 10). Significance is set at p<0.05. Adjusted (Adj.) p-values are provided unless otherwise stated.

source_name: Primary Whole Blood, PBMCs

growth_protocol:
[culture protocol]  Human primary cells
10^7 PBMCs were resuspended in fetal bovine serum (FBS) (Invitrogen Life Technologies, Carlsbad, CA, USA) containing 10% dimethyl sulfoxide (DMSO) for storage at -80oC until ribonucleic acid (RNA) extraction. Frozen PBMCs were thawed and immediately pelleted by centrifugation.

extract_protocol: Total RNA was isolated from PBMC pellets (5-10x106 cells) using either Trizol or an RNeasy Mini kit (Qiagen, Hilden, Germany) according to manufacturer instructions. The concentration and quality of the RNA were checked using Nanodrop.

value: blood

tag: cell type

value: PBMCs

tag: age (years)

value: Male

tag: disease

value: Healthy control


title: Healthy_Control #15

scan_protocol: Processed according to nCounter manufacturers instructions


title: 755208_ev_8

description:
Library name: 755208
experiment3_empty-vector_spleen_mouse8


title: N2, YA, 20 degrees, ChIP input 2

description: Library name: n2_2_input

value: Wild-type N2


title: Healthy_Control #13


title: set-24 Mutant, YA, 20 degrees, ChIP input 1

description: Library name: SX3735_1_input


title: CFC_d1_4h_HP_rep2, snRNA

source_name: hippocampus

value: wild-type


title: N2, YA, 20 degrees, ChIP input 1

description: Library name: n2_1_input


title: CFC_d1_4h_HP_rep1, snRNA


title: CC_d1_4h_HP_rep2, snRNA


title: 755206_IL9_5

description:
Library name: 755206
experiment3_IL9_spleen_mouse5


title: set-24 Mutant, YA, 20 degrees, H3K4me3 pulldown 2

description: Library name: SX3735_2_H3K4me3_chip

value: H3K4me3 (Active Motif, #39159)


title: 755205_IL9_4

description:
Library name: 755205
experiment3_IL9_spleen_mouse4


title: CC_d1_4h_HP_rep1, snRNA


title: Healthy_Control #11


title: set-24 Mutant, YA, 20 degrees, H3K4me3 pulldown 1

description: Library name: SX3735_1_H3K4me3_chip


title: Healthy_Control #10


title: 755210_ev_10

description:
Library name: 755210
experiment3_empty-vector_spleen_mouse10


title: Healthy_Control #9


title: 755204_IL9_3

description:
Library name: 755204
experiment3_IL9_spleen_mouse3


title: N2, YA, 20 degrees, H3K4me3 pulldown 2

description: Library name: n2_2_H3K4me3_chip


title: CFC_d0_4h_HP_rep2, snRNA


title: Healthy_Control #8


title: CFC_d0_4h_HP_rep1, snRNA


title: 755203_IL9_2

description:
Library name: 755203
experiment3_IL9_spleen_mouse2


title: N2, YA, 20 degrees, H3K4me3 pulldown 1

description: Library name: n2_1_H3K4me3_chip


title: 755202_IL9_1

description:
Library name: 755202
experiment3_IL9_spleen_mouse1


title: Healthy_Control #12


title: ZNF354A H2O2

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

description:
Library name: ChIP_K562_pTRE_ZNF354A_D_4h
K562 ZNF354A H2O2 1

data_processing:
Adapter trimming with Cutadapt (TruSeq adapters: R1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; R2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT).
Peak files from conditions were merged using BEDTools v2.30.0 (bedtools multiinter) to obtain consensus regions.
Signal values over peak regions were extracted from bigWig files with deepTools v3.5.1 (computeMatrix); peaks with excessively high signal were filtered (maxThreshold = 15).
Heatmaps were generated with deepTools (plotHeatmap) to visualize signal distributions and guide filtering/merging.
Final high-confidence peaks were retained after additional intensity filtering (maxThreshold = 150); resulting list saved as sorted_regions_3.bed.
Assembly: hg19 (GRCh37).
Supplementary files format and content: BED peak files per sample and the final merged peak set (sorted_regions_3.bed) with genomic coordinates of enriched regions.

source_name: bone marrow

growth_protocol: K562 cells were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37 °C with 5% CO₂.

extract_protocol:
Chromatin was crosslinked with 1% formaldehyde for 10 min, quenched with glycine, and sequentially lysed and sonicated to 100–300 bp fragments. Immunoprecipitation was performed with anti-HA magnetic beads (Pierce, 88837) (Mesquita et al, Nature Communications 2025)
ChIP and input DNA were processed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, cat. no. E7645) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with 50 µM H₂O₂ for 4 h or left untreated.

value: bone marrow

value: Myeloid

tag: ip reagent

value: Anti-HA Magnetic Beads Thermo Fisher Scientific Cat# 88837, RRID:AB_2861411


title: 990758_IL13_4

description:
Library name: 990758
experiment2_IL13_spleen_mouse4


title: CC_d0_4h_HP_rep1, snRNA

description: single nuclei multiome sequencing (snRNA-seq)


title: 755207_ev_7

description:
Library name: 755207
experiment3_empty-vector_spleen_mouse7


title: CC_d0_4h_HP_rep2, snRNA


title: Healthy_Control #7


title: GFP H2O2

description:
Library name: ChIP_K562_pTRE_GFP_D_4h
K562 GFP H2O2 1

value: Anti-HA Magnetic Beads Thermo Fisher Scientific Cat# 88837, RRID:AB_2861403


title: KO-mus liver,HFD,16weeks,rep2

city: Zhuhai

first: Yang

last: Zhe

address: Kangning Street No.79

institute: Jinan University

data_processing:
HISAT2 RNA-sequencing alignment software was used for for mapping next-generation sequencing reads to mouse genome
fastp was used for filtering and RseQC sorting mapped reads
Differentially expressed genes and normalized reads were determined using DeSeq2
FeatureCounts was used for counting reads in features
Data was normalized with R and Limma-Voom and log2-transformed
Assembly: mm10
Supplementary files format and content: Matrix table with normalized gene counts for each gene in each sample.
Supplementary files format and content: Matrix table with raw gene counts for each gene in each sample

extract_protocol:
the total RNA was extracted using trizol reagent
RNA libraries for RNA-seq were prepared using NEB Library Prep Kit following manufacturer's protocols.

treatment_protocol: WT and hepatocyte-specific HIF-2α KO were treated by HFD for 16 weeks

value: liver

value: hepatocyte-specific HIF-2alpha knockout

value: high fat diet


title: 990757_IL13_3

description:
Library name: 990757
experiment2_IL13_spleen_mouse3


title: KO-mus liver,HFD,16weeks,rep3


title: Healthy_Control #6


title: 990752_IL13_2

description:
Library name: 990752
experiment2_IL13_spleen_mouse2


title: 990751_IL13_1

description:
Library name: 990751
experiment2_IL13_spleen_mouse1


title: Healthy_Control #4


title: GFP untreated

description:
Library name: ChIP_K562_pTRE_GFP_D_0h
K562 GFP untreated 1

value: Anti-HA Magnetic Beads Thermo Fisher Scientific Cat# 88837, RRID:AB_2861399

value: Control


title: Healthy_Control #5


title: KO-mus liver,HFD,16weeks,rep1


title: PT6_10uM_OTA+5uM_tBHQ_3

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

description: Library name: PT6_TO3

data_processing:
Read quality was assessed using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and then reads were aligned to the Ensembl GRCh38 patch release 27 genome using the HISAT2 aligner .
Reads were imported into R, summarized as reads/gene using the Bioconductor Rsubread package , and then analyzed using the limma-voom  pipeline. An additional fold change criterion was included in the analysis to restrict to those genes with likely biologically meaningful changes in expression .
Assembly: GRCh38 patch release 27 genome
Supplementary files format and content: All counts are provided in a single file called Counts.txt, with samples in columns and genes in rows. The first column provides the Ensembl Gene ID for that row.

source_name: kidney

growth_protocol: Human primary tubule epithelial cells were cultured in DMEM (Gibco, 1130-032) with 1x ITS-A (Gibco, 51300044), 50 nM hydrocortisone (Sigma, H6909) and 1x Antimicrobic-Antimycotic (Gibco, 2520056) until confluence. Cells were passaged using 0.05% trypsin-EDTA (Gibco, 25200056) and neutralized with defined trypsin inhibitor (Gibco, R007100), centrifuged at 400g for 5 minutes, and re-plated with supplemented DMEM solution. Cells are incubated at 37°C and 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004) and converted to cDNA with 20 the SMART-Seq v4 Ultra Low Input RNA Kit (Takara, 634891).
Sequencing libraries were constructed using the SMARTer ThruPlex DNA-Seq Kit (Takara, R400676) and sequenced on a NovaSeq 6000 or NovaSeq X instrument (Illumina, San Diego, CA).

treatment_protocol: PTECs, in triplicate, were plated in two 24-well plates (Costar, 3548) in supplemented DMEM medium and grown to confluence. Treatment group samples were pre-treated for 48 hours with DMEM medium and either sulforaphane (Sigma, S4441), or tBHQ (Sigma, 112941) and controls were treated with supplemented DMEM medium. Then, plates were treated for 72 hours with ochratoxin-A (Sigma, O1877) in either supplemented DMEM, supplemented DMEM + sulforaphane, or supplemented DMEM + tBHQ. Following 72-hour incubation, cells were lysed with Buffer RLT (Qiagen, 74004).

value: kidney

value: primary proximal tubule epithelial cells


title: Healthy_Control #3

value: blood

value: PBMCs


title: Healthy_Control #2

value: Male

value: Healthy control


title: WT-mus liver,HFD,16weeks,rep3

value: WT


title: Healthy_Control #1


title: PT6_10uM_OTA+5uM_tBHQ_2

description: Library name: PT6_TO2


title: 990744_IL4_4

description:
Library name: 990744
experiment2_IL4_spleen_mouse4

value: spleen


title: WT-mus liver,HFD,16weeks,rep2


title: 990743_IL4_3

description:
Library name: 990743
experiment2_IL4_spleen_mouse3


title: PT6_10uM_OTA+5uM_tBHQ_1

description: Library name: PT6_TO1


title: PT6_5uM_tBHQ_3

description: Library name: PT6_T3


title: WT-mus liver,HFD,16weeks,rep1


title: DRG, EndoS,  timepoint 0.5d, scRNAseq 6

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

description: 10x Genomics

data_processing:
Pooled libraries were sequenced on Illumina sequencing platform NovaSeq 6000 system on SP-100 flowcells with 91 bp sequenced into the 3’ end (5’ to 3’) of the mRNAs in National Genomics Infrastructure (SciLifeLab). Raw sequencing data were de-multiplexed, converted into fastq format, and aligned to mouse reference mm10 using the STAR aligner to generate the gene-cell matrices.
Samples were aligned with Cellranger 5.1.0 to the mm10 10X reference.
Data was analized using Seurat 4, for cell filtering, dimension reduction and clustering. RDS object also includes final cell type annotations.
Assembly: mm10
Supplementary files format and content: h5 files from Cellranger 5.0.1 output genome assembly mm10 of the filtered feature and barcode matrixes.
Supplementary files format and content: RDS file containing a Seurat object of the final dataset used for analysis, su_seurat.rds

source_name: Dorsal root ganglion

extract_protocol:
C57BL/6N mice (8-10 wk, Charles River, Sweden) were sacrificed with overdosage of isoflurane. Spines were removed and fresh cervical and lumbar dorsal root ganglia (DRGs) were dissected in a 6 cm Petri-dish with DPBS (Sigma) on ice. And 2 male mice were included for each suspension experiment. The following DRG single cell suspension was performed according to our previous protocol with modifications (5). Briefly, dissected DRGs were chopped with microscissors 1-2 times in 2mL Papain (25 unit/mL, Worthington Biochemical) and then incubated at 37 °C, with a mixture of digestion enzymes of Papain/Collagenase/Dispase (Papain, 25 unit/mL, 4 mL; DNase I, 55 unit/mL, 0.5 mL, Worthington Biochemical; and Collagenase and Dispase 20 mg/mL, 800 uL, Worthington Biochemical). The DRGs were triturated up and down 10 times of every 10 min using glass Pasteur pipettes with decreasing diameter (pre-coated with 0.5% BSA). Cell suspension was filtered through a 30 µm cell strainer (CellTrics, Sysmex) and washed with additional 1.5 mL artificial cerebrospinal fluid (ACSF,  87 mM NaCl, 2.5 mM KCl, NaH2PO4 1.25 mM, NaHCO3 26 mM, Sucrose 75 mM, Glucose 20 mM, CaCl2 0.5 mM, MgSO4 4 mM) and 0.5 mL DPBS. Cells were pelleted by centrifugation (300 g 6 min, 4 °C) and resuspended with 1.5 mL cold ACSF with 0.5 mL DPBS. The cell suspension was carefully loaded on top of the same volume of OptiPrep density gradient medium (Sigma) and centrifuged with 700 g ×10 min at 4 °C. The cell pellet was resuspended with 3 mL cold ACSF. SYTOX Blue (Invitrogen, ThermoFisher Scientific) was added to stain dead cells. Thereafter, alive SYTOX Blue-negative cells were sorted with fluorescence activated cell sorting (FACS, BD FACSAria Fusion / BD FACSAria III) at 4 °C. Cells were concentrated by centrifugation (300 g × 5 min, 4 °C) and resuspended with proper volume (~1 000 cells/ µL) of ACSF solution.
Sorted cells were loaded onto the 10× Chromium chip G to yield single cell droplet with v3.1 kit (10× genomics). Targeted cell recovery for each well was settled to 5 000 cells (10% neurons). Reverse transcription, cDNA amplification and library construction were performed according to the user guide provided by 10× genomics.

value: DRG cells

value: Dorsal root ganglion

tag: strain

tag: age

value: 8-10 weeks old

tag: timepoint


title: Gulf War Illness #20

tag: tissue

value: Gulf War Illness


title: Gulf War Illness #19


title: Gulf War Illness #18


title: 990742_IL4_2

description:
Library name: 990742
experiment2_IL4_spleen_mouse2

tag: batch


title: DRG, EndoS,  timepoint 0.5d, scRNAseq 5

description: 10x Genomics


title: 990741_IL4_1

description:
Library name: 990741
experiment2_IL4_spleen_mouse1


title: ZNF354A untreated

description:
Library name: ChIP_K562_pTRE_ZNF354A_D_0h
K562 ZNF354A untreated 1

value: bone marrow

value: Myeloid

value: Anti-HA Magnetic Beads Thermo Fisher Scientific Cat# 88837, RRID:AB_2861407


title: PT6_5uM_tBHQ_1

description: Library name: PT6_T1


title: DRG, Neg.control,  timepoint 0.5d, scRNAseq 4

description: 10x Genomics


title: 990740_Tslp_5

description:
Library name: 990740
experiment2_Tslp_spleen_mouse5

value: Tslp


title: PT6_10uM_OTA+20uM_SFN2_3

description: Library name: PT6_SO3


title: Gulf War Illness #17


title: 990745_IL4_5

description:
Library name: 990745
experiment2_IL4_spleen_mouse5


title: Gulf War Illness #15


title: Gulf War Illness #16


title: 990739_Tslp_4

description:
Library name: 990739
experiment2_Tslp_spleen_mouse4


title: DRG, RA+IFN blocking,  timepoint 0.5d, scRNAseq 1

description: 10x Genomics


title: 990738_Tslp_3

description:
Library name: 990738
experiment2_Tslp_spleen_mouse3


title: DRG, RA, timepoint 63d, scRNAseq 2

description: 10x Genomics


title: DRG, RA+IFN blocking,  timepoint 0.5d, scRNAseq 2

description: 10x Genomics


title: DRG, Neg.control,  timepoint 0.5d, scRNAseq 3

description: 10x Genomics


title: 990737_Tslp_2

description:
Library name: 990737
experiment2_Tslp_spleen_mouse2


title: PT6_10uM_OTA+20uM_SFN2_2

description: Library name: PT6_SO2


title: PT6_20uM_SFN2_2

description: Library name: PT6_S2


title: PT6_10uM_OTA+20uM_SFN2_1

description: Library name: PT6_SO1


title: DRG, RA, timepoint 63d, scRNAseq 1

description: 10x Genomics


title: 990708_IL33_3

description:
Library name: 990708
experiment2_IL33_spleen_mouse3


title: PT6_20uM_SFN2_1

description: Library name: PT6_S1


title: Gulf War Illness #13


title: PT6_5uM_tBHQ_2

description: Library name: PT6_T2


title: Gulf War Illness #14


title: PT6_20uM_SFN2_3

description: Library name: PT6_S3


title: DRG, RA, timepoint 33d, scRNAseq 10

description: 10x Genomics


title: PT6_10uM_OTA_3

description: Library name: PT6_O3


title: 990736_Tslp_1

description:
Library name: 990736
experiment2_Tslp_spleen_mouse1


title: Gulf War Illness #12


title: DRG, RA, timepoint 33d, scRNAseq 9

description: 10x Genomics


title: Gulf War Illness #11


title: 990706_IL33_1

description:
Library name: 990706
experiment2_IL33_spleen_mouse1


title: PT6_10uM_OTA_2

description: Library name: PT6_O2