title: KO.Veh_8998

description: Library name: Sample_8998


title: plt2 5 nM RGF1 rep3

status: Public on Jul 09 2025

type: SRA

city: Tainan

first: Masashi

last: Yamada

address: No. 100, Sec. 1, Guiren 13th Rd., Guiren Dist.,

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

library_source: transcriptomic

data_processing:
The sequencing reads were mapped to Arabidopsis genome TAIR10 using HISAT2 v2.1.0.
The read counts of genes were compared with the Araport11 genome annotation using featureCounts (subread v2.0.3).
The normalized expression values of genes were performed using DESeq (v1.34.0)
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Root meristematic zone

growth_protocol: Arabidopsis seeds were grown on MS plate for 6 days.

extract_protocol:
The seedings were aligned onto a 2% agarose plate for root tips collection. Using an ophthalmic scalpel (Feather), the meristematic zone of the seedlings were precisely dissected under a dissecting microscope (Axio Zoom, Zeiss). Total RNA was extracted from 50 root sections using the RNeasy Micro Kit (Qiagen). All total RNA samples were treated with DNaseI during RNA extraction.
RNA libraries were prepared using Universal RNA-Seq with NuQuant library preparation kit following manufacture's protocols

treatment_protocol: The seedings were transferred into 1/2 MS media and treated with mock, 0.3nM RGF1 or 5nM RGF1 for 24h.

tag: tissue

value: Root meristematic zone

tag: time

value: 24 hr

tag: genotype

tag: treatment

value: 5 nM RGF1


title: IP_1_1_White_Kontrol

city: Budapest

first: István

last: Likó

address: Üllői út 26.

country: Hungary

institute: Semmelweis University

description: Library name: IP-1-1

library_source: genomic

data_processing:
The raw data from the sequencer, the reads collected in the fastq file (short sequencing reads), were subjected to qualitative analysis using the Fastqc (Babraham Bioinformatics) program.
The reads were trimmed using Trim Galore and Cutadapt to remove bases where the PHRED quality value was less than 20. Trimmed sequences were removed if they become shorter than 50 bases.
reads were aligned to wheat reference genome using Burrows‐Wheeler Aligner (BWA)
The analysis of the enriched methylated DNA locus was performed with bedtools and R statistical tools.
Assembly: GCF_018294505.1_IWGSC_CS_RefSeq_v2.1_genomic.fna     Triticum aestivum (bread wheat)
Supplementary files format and content: cvs, coverage count data by locus

molecule: genomic DNA

organism: Triticum aestivum

source_name: leaf

extract_protocol:
The genomic DNA samples were isolated with NucleoSpin® Plant II Kit (MACHEREY-NAGEL GmbH, Düren, Germany) according to the manufacturer’s instructions.
The DNA sequencing library was prepared using immunoprecipitated (12 samples) and pooled, fragmented IP input DNAs (4 pooled samples) with xGen™ ssDNA & Low-Input DNA Library Preparation Kit (Integrated DNA Technologies (IDT), Inc., Coralville, IA, USA) according to the manufacturer's instructions.
The normalized, pooled, and denatured library samples were sequenced on the Illumina NextSeq platform (Illumina, Inc., San Diego, CA, United States) using 75 + 75 bp paired-end chemistry with NextSeq 500/550 HiOutput Kit v2.5 (150 Cycles)

value: leaf

tag: cell line

tag: cell type

value: variety Mv Beres


title: KO.Tx_8999

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

country: USA

institute: University of Michigan

description: Library name: Sample_8999

data_processing:
University of Michigan Bioinformatics Core RNA-seq pipeline "Watermelon" version 2.4.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v4.8.
FastQC v0.11.8 was used to ensure the quality of data
Trimmed sequence reads were mapped to GRCm38 (ENSEMBL) using STAR v2.7.8a
Quantitative count estimates to genes performed with RSEM v1.3.3
Assembly: GRCm38
Supplementary files format and content: tab-delimited table with raw counts, filtered to remove genes with 0 counts in all samples.

molecule: polyA RNA

organism: Mus musculus

source_name: liver

extract_protocol:
RNA was isolated using phenol/chloroform. 200 nanograms total RNA was used for the construction of sequencing libraries.
Library prep and sequencing were done at Innomics, Inc. Oligo dT beads were used  to enrich mRNA with poly A tail, then mRNA molecules were fragmented into small pieces. The fragmented mRNA was synthesized into first strand cDNA using random primers. The second strand cDNA was synthesized with dUTP instead of dTTP. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments, then the fragments were PCR amplified. After quality control,  Libraries were circularized, then amplified to make DNA nanoball (DNB).

value: liver

tag: Sex

value: female

value: Rescue


title: KO.Tx_8974

description: Library name: Sample_8974


title: plt2 5 nM RGF1 rep2


title: CLV_Control_6

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

description: Library name: 01T0036

data_processing:
The raw sequences were quality controlled using FastQC.
Fastp software was used to remove Illumina adapters and poly-A sequences. Reads shorter than 36 bp and reads with a quality lower thanthe default of 20 were removed from the dataset.
Cleaned sequences were aligned to the Chicken genome (assembly bGalGal1.mat.broiler.GRCg7b) with reference annotation containing more than 17K genes listed in the Ensembl database.
Alignment and estimation of gene expression level were made using the RSEM package supported by STAR aligner.
Differentially expressed genes, gene isoforms and their corresponding p-values were determined using the statistical methods DESeq2
Assembly: GCA_016699485.1
Supplementary files format and content: genes_chicken_filtered.csv.gz
Supplementary files format and content: res-liver.tsv.gz
Supplementary files format and content: res-heart.tsv.gz

organism: Gallus gallus

source_name: Liver

growth_protocol: Birds were kept on litter at a density of 10 individuals per pen; During the pre-experimental period (weeks 1-3), birds were fed Sal-free diets.  After the pre-experimental period (week 4-5), birds were selected and classified into two groups: the Sal-exposed and the control group and fed respective diets ad libitum.

extract_protocol:
Total RNA isolation was done by Maxwell RSC instrument (Promega, USA) using Maxwell® RSC simplyRNA Tissue Kit (Promega, USA).
The Hieff NGS Ultima Dual-mode mRNA Library Prep Kit (Yeasen Biotechnology, China) was used to construct libraries according to manufacturer's protocol.

treatment_protocol: The Sal-exposed group received an experimental diet with Sal ad libitum. Sal was administered in-feed at the concentration of 10.5 mg/kg feed during weeks 4-5. The estimated daily dose was 0.9 mg/kg b.w.

value: Liver

value: Control


title: KO.Tx_8967

description: Library name: Sample_8967


title: plt2 5 nM RGF1 rep1


title: CLV_Control_5

description: Library name: 01T0035


title: plt2 0.3 nM RGF1 rep5

value: 0.3 nM RGF1


title: KO.Tx_8959

description: Library name: Sample_8959


title: CLV_Control_4

description: Library name: 01T0034


title: KO.Veh_794

description: Library name: Sample_794

value: Vehicle


title: plt2 0.3 nM RGF1 rep4


title: B16_CX5461_rep2

city: Melbourne

first: Pacman

last: Szeto

state: VIC

address: 89 Commercial Road

department: Medicine

country: Australia

institute: Monash University

data_processing:
Sequncing reads were processed using RNAsik pipeline https://github.com/MonashBioinformaticsPlatform/RNAsik-pipe
Fastq files were aligned to GRCM38
Gene read counts were extracted
Assembly: GRCM38/mm10
Supplementary files format and content: tab-delimited text files include gene count values for each sample

growth_protocol: DMEM+10% FBS+1% penicillin/streptomycin

extract_protocol: Isolate II RNA mini kit

treatment_protocol: DMSO or 1 uM CX5461 for 3 days

value: melanoma cell line


title: B16_CX5461_rep1


title: KO.Tx_793

description: Library name: Sample_793


title: KO.Tx_796

description: Library name: Sample_796


title: plt2 0.3 nM RGF1 rep3


title: CLV_Control_3

description: Library name: 01T0033


title: plt2 0.3 nM RGF1 rep1


title: KO.Tx_484

description: Library name: Sample_484


title: B16_DMSO_rep3

value: DMSO


title: CLV_Control_1

description: Library name: 01T0031


title: KO.Tx_690

description: Library name: Sample_690


title: B16_DMSO_rep2


title: plt2 0.3 nM RGF1 rep2


title: 182_Male_Control_20wks

city: Jefferson

first: Volodymyr

last: Tryndyak

address: 3900 NCTR Rd

department: Division of Biochemical Toxicology

institute: US-FDA National Center for Toxicological Research

data_processing:
Sequencing was performed in an Illumina NextSeq 500 sequencing machine (Illumina) at a 2 × 74 bp paired-end resolution.
Sequence reads were mapped to the mouse reference genome (NCBI38/mm10) using Illumina RNA-Seq Alignment v2.0.2 software with default parameters in the Illumina BaseSpace environment.
Transcript abundance estimates (read counts) Illumina RNA-Seq Alignment v2.0.2 software with default parameters in the Illumina BaseSpace environment.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include read counts values for each Sample

extract_protocol:
Livers were removed and flash frozen on dry ice. Total RNA was extracted from liver tissue samples using miRNeasy Mini kits (Qiagen, Valencia, CA, USA).
RNA libraries for RNA-sequencing were prepared from 500 ng RNA using Illumina Stranded Total RNA Prep Ligation with Ribo-zero Plus library preparation kits as recommended in the manufacturer’s protocol.

treatment_protocol: Mice in the experimental group were maintained on the obesogenic high-fat and high-sucrose (HF/HS) diets (Teklad Custom Diet - TD.88137, Envigo, Madison, WI, USA) for 20, 40 and 60 weeks.  This diet contains 42% Kcal from milkfat high in palmitic acid, 0.2% of total cholesterol, and is high in sucrose (>30%).  Mice in the control group received an ingredient-matched low-fat and reduced sucrose diet (Teklad Custom Diet – TD.08485, Envigo).

value: tissue

value: Male

tag: time point

value: 20 weeks


title: 181_Male_Control_20wks


title: CLV_SAL_exposed_6

description: Library name: 01T0018

value: SAL exposed


title: B16_DMSO_rep1


title: CLV_SAL_exposed_5

description: Library name: 01T0017


title: mus-B16-LPC-1-9-14

data_processing:
FASTQ files were processed using Laxy (https://zenodo.org/record/3767372) which encompasses the RNAsik pipeline (https://joss.theoj.org/papers/10.21105/joss.00583). Briefly, GRCm38 reference genome was used for STAR alignment (PubmedID: 23104886)
Assembly: GRCm38
Supplementary files format and content: Raw gene count matrix

source_name: melanoma

growth_protocol: The B16 mouse melanoma cell line was obtained from ATCC and maintained in culture in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Total cell RNA was extracted from FACS-purified LPC or HPC populations using the PureLink RNA Mini kit (ThermoFisher), according to the manufacturer’s instructions, including an on-column DNase treatment.
RNA was quantitated using Qubit RNA HS (Thermo Fisher Scientific) and 100 ng total RNA input was used for library preparation according to standard protocols (QuantSeq 3’ mRNA-Seq FWD, Lexogen). Indexed libraries were pooled and sequenced on a NextSeq 500 sequencer (Illumina).

value: mouse melanoma cell line

value: Low-pigmented


title: E-KO-4, replicate 4, scRNA seq

city: Dalian

first: Chunxiu

last: Du

address: Lushunkou District

country: China

institute: Dalian medical university

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
Basecalls performed using CASAVA version 1.8
To quantify the gene expression of the single-cell data, we used STARsolo (version 2.7.10a) along with mouse genome.
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria: MT% < 30%; Cell Gene Number < Median Gene Number * 2;Cell Gene Number > 200.PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: Single cell matrix files

source_name: aorta

extract_protocol:
The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 0.65 U/mL dispase, 0.56 U/mL elastase, 100 U/mL collagenase I, 100 U/mL collagenase II, 100 U/mL collagenase IV, 50 U/mL DNase I, 100U/mL hyaluronidase, 0.2% BSA and 5% FBS for 35 min at 37°C, with agitation. After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences).
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: aorta

value: Goblet cells

value: The mice were given a high-salt diet for 3 weeks


title: B16_CX5461_rep3


title: plt2 mock rep5

value: Root meristematic zone

value: 24 hr

value: Mock


title: plt2 mock rep4


title: E-KO-3, replicate 3, scRNAseq

description: BD Rhapsody


title: CLV_SAL_exposed_4

description: Library name: 01T0016

value: Liver


title: CLV_Control_2

description: Library name: 01T0032

value: Control


title: plt2 mock rep3


title: mus-B16-LPC-18-8-14


title: CLV_SAL_exposed_3

description: Library name: 01T0015


title: plt2 mock rep2


title: mus-B16-LPC-16-9-15


title: E-KO-2, replicate 2, scRNAseq

description: BD Rhapsody


title: E-KO-1, replicate 1, scRNAseq

description: BD Rhapsody


title: mus-B16-HPC-1-9-14

value: High-pigmented


title: CLV_SAL_exposed_2

description: Library name: 01T0014


title: CLV_SAL_exposed_1

description: Library name: 01T0013


title: mus-B16-HPC-18-8-14


title: WT3, replicate 3, scRNAseq

description: BD Rhapsody


title: WT2, replicate 1, scRNAseq

description: BD Rhapsody


title: CHR_Control_6

description: Library name: 01T0024

source_name: Heart

value: Heart


title: WT1, replicate 1, scRNAseq

description: BD Rhapsody


title: plt2 mock rep1


title: CHR_Control_5

description: Library name: 01T0023


title: mus-B16-HPC-16-9-15


title: T cells, wild-type, replicate 3

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

country: Germany

institute: University Medical Center - Mainz

description: Sample R8406

data_processing:
Sequences from the microfluidic droplet platform were demultiplexed and aligned using CellRanger version 3.0.2, available from 10x Genomics with default parameters (using mm10 as reference genome).
Single-cell sequences were identified by detecting deviations from the expression profile of the ambient solution, using the function `emptyDrops` from the `DropletUtils` package.
The dataset was annotated to gene-level information based on ENSEMBL v92. Quality control was per- formed on each dataset independently to remove poor-quality cells, using the `scater` package (McCarthy et al., 2017).
The proportion of mitochondrial gene content was used as a proxy for damaged cells, using three median absolute deviations as a threshold. Low number of reads per cell, low number of detected genes, and high percentage of mitochondrial gene content were used as criteria for filtering, as suggested in the OSCA online resource (https://osca.bioconductor.org).
Normalization of cell-specific biases was performed on the remaining sets of cells using the deconvolution method of Lun et al., 2016 implemented in the `scran` package.
Counts were divided by size factors to obtain normalized expression values that were log-transformed after adding a pseudocount of one.
Data integration across different samples, split by cell type of origin, was performed with the `fastMNN` function, implementing the mutual nearest neighbors method proposed by Haghverdi et al., 2018.
Highly variable genes were identified on the pooled set of cells after modeling the technical noise as Poisson-distributed, and were provided as input for the MNN-based integration.
The results of the MNN integration were then provided as initialization to the t-SNE algorithm (Van der Maaten et al., 2008) to obtain a reduced dimensionality representation of the data.
To identify clusters of cells, we built a shared nearest neighbor graph (Xu et al., 2015) and used the louvain community finding algorithm with default resolution.
Automated cell type annotation was performed with the `SingleR` package, matching the generated expression profiles against the data provided by the `ImmGen` database, as provided via the `celldex` package.
Additionally, we identified marker genes for each cluster using the function `findMarkers` from the `scran` package, which performs Welch t-tests on the log expression values for every gene and between every pair of clusters.
All visualizations were generated with the `iSEE` package (Rue-Albrecht et al., 2018), which was also utilized to construct the deployed instances of an interactive expression browser, providing as input the merged TAMs dataset (including wild-type and PAR2 G37I mutants) and the merged TILs dataset, respectively.
Assembly: mm10
Supplementary files format and content: sce_TAMs.rds, R binary format
Supplementary files format and content: sce_TILs.rds, R binary format
Supplementary files format and content: sparsematrix_TAMs.mtx.gz, rownames_TAMs.txt, colnames_TAMs.txt - plain text sparse counts matrix
Supplementary files format and content: sparsematrix_TILs.mtx.gz, rownames_TILs.txt, colnames_TILs.txt - plain text sparse counts matrix

source_name: tumor

growth_protocol: spontaneous breast canncer model MMTV-PyMT

extract_protocol:
bead-selection of CD11c+ or CD4/CD8 T cells from single cell suspension of digested tumors
10x Genomics platform

treatment_protocol: no additional treatment

value: tumor

value: CD8/CD4 T cells

value: wild-type


title: T cells, wild-type, replicate 2

description: Sample R8405


title: CHR_Control_4

description: Library name: 01T0022


title: PHN_9

city: Beijing

first: Zhenhua

last: Chen

state: China

address: West Beichen Road, Olympic Village, Beijing

department: State Key Laboratory of Molecular Development Biology

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Raw sequencing reads from DIPSEQ T-series sequencer were filtered and demultiplexed using PISA (v0.10) (https://github.com/shiquan/PISA). To identify the positive cells in Fos-TRAP2::Ai9 mice, we inserted the tdTomato sequences (download from : tdTomato Sequence and Map (snapgene.com)) into GRCm38 reference genome. Reads were aligned to the modified GRCm38 mouse genome using STAR (v2.7.4a) (https://github.com/alexdobin/STAR) and sorted using Sambamba (v0.7.0) (1). A nucleus versus gene UMI count matrix was generated by PISA for downstream analysis. Cells expressing tdTomato mRNA were judged to be positive cells.
Seurat R package (v4) was used for analysis.
Assembly: mm10
Supplementary files format and content: phn_neu.rds are serialized R objects of the Bioconductor class ExpressionSet that contains the final data used to generate the results. It can be imported into R with `readRDS(“phn_neu.rds”)`. It contains the gene counts, sample metadata, and feature metadata for single cells that passed quality control.

source_name: Brian

extract_protocol:
To isolate single nuclei from PHN of Fos-TRAP2::Ai9 mice treated with panic attacks, we immersed the tissues in ice-cold homogenization buffer containing 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris-HCl, 0.1 mM DTT, 1% BSA, 0.1% NP-40, and ribonuclease inhibitor (0.4 U/μl). The tissues were then mechanically homogenized using a glass homogenizer for 10 cycles to obtain a single-nucleus suspension for snRNA-seq.
Single-nucleus RNA-seq libraries were prepared using DNBSEQ technology platforms (BGI Genomics, China) and the DNBelab C4 Single-Cell Library Prep Set (MGI Tech, #1000021082).

value: Brian


title: T cells, wild-type, replicate 1

description: Sample R8402


title: CHR_Control_3

description: Library name: 01T0021


title: PP-γδ 3

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Used in this paper.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Peyer's patches

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

value: T cells


title: CHR_Control_2

description: Library name: 01T0020


title: PP-CD4 3

description: Used in this paper.


title: PHN_10


title: PHN_7


title: T cells, PAR2 G37I mutant, replicate 2

description: Sample R8178

value: PAR2 G37I mutant


title: CHR_Control_1

description: Library name: 01T0019


title: T cells, PAR2 G37I mutant, replicate 3

description: Sample R8194


title: PHN_8


title: CHR_SAL_exposed_6

description: Library name: 01T0006

value: SAL exposed


title: T cells, PAR2 G37I mutant, replicate 1

description: Sample R8177


title: CHR_SAL_exposed_5

description: Library name: 01T0005


title: PHN_5


title: CD11c+ cells, PAR2 G37I mutant, replicate 3

description: Sample R8162

value: macrophages, DCs


title: PHN_4


title: CHR_SAL_exposed_4

description: Library name: 01T0004


title: PHN_3


title: CHR_SAL_exposed_3

description: Library name: 01T0003


title: CD11c+ cells, PAR2 G37I mutant, replicate 1

description: Sample R8110


title: PP-CD8 3

description: Used in this paper.


title: CHR_SAL_exposed_2

description: Library name: 01T0002


title: CD11c+ cells, wild-type, replicate 3

description: Sample R7971


title: PP-CD8 2

description: Used in this paper.


title: PHN_6


title: CD11c+ cells, wild-type, replicate 2

description: Sample R7960


title: PHN_1


title: PP-CD4 2

description: Used in this paper.


title: PP-DNT 2

description: Used in this paper.


title: PP-DNT 3

description: Used in this paper.


title: PP-γδ 2

description: Used in this paper.


title: PP-CD8 1

description: Used in this paper.


title: Brain cells recovered after papain treatment with P8

city: Isehara

first: Takatoshi

last: Iijima

address: 143 Shimokasuya

department: School of Medicine

institute: Tokai University

description: 10x Genomics

data_processing:
Libraries were converted and sequenced on a DNBSEQ-G400 (MGI, Guangdong, China).
The barcoded processing and gene counting were made using the Cell Range software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: neocortex and hippocampus

extract_protocol:
We prepared the libraries using the 10x Single Cell Chromium Next GEM Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 (10x Genomics, Pleasanton, CA, USA) according to the manufacturer’s protocol.
Amplified cDNA was fragmented, end-repaired, PCR-amplified with sample indexing primers, and purified with SPRIselect beads (BECKMAN COULTER, Brea, CA, USA).

value: neocortex and hippocampus

tag: strain

tag: developmental stage

value: male


title: CD11c+ cells, PAR2 G37I mutant, replicate 2

description: Sample R8125


title: CD11c+ cells, wild-type, replicate 1

description: Sample R7958


title: N_183

city: Seoul

first: Jeong-Woon

last: Lee

address: Gwanak-ro 1

country: South Korea

institute: Seoul National University

data_processing:
All of pre-processing steps including trimming, alignment, generation of signal track, peak calling and diverse type of QC were performed using ENCODE ATAC-seq processing pipeline (https://github.com/ENCODE-DCC/atac-seq)
Assembly: canFam3.1
Supplementary files format and content: bigwig file

organism: Canis lupus familiaris

source_name: Mammary gland

growth_protocol: Blood samples were collected from healthy dogs and dogs clinically diagnosed with mammary tumors using EDTA-coated tubes. To isolate PBMCs, 1-2 mL of blood was carefully layered onto Ficoll-Paque PLUS (GE Healthcare, 17144002) at a 1:2 ratio and centrifuged at 400 g.

extract_protocol:
Approximately 2500 cells per sample were collected and washed twice with 1× cold phosphate-buffered saline (PBS) to remove any residual media. The cells were then lysed in 200 µL of cold lysis buffer, consisting of 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl₂, and 0.1% NP-40. The lysate was incubated on ice for 10 minutes. After lysis, the cell suspension was centrifuged at 500 ×g for 5 minutes at 4°C. The supernatant was carefully removed, and the cell pellet was resuspended in 50 µL of Tn5 transposase buffer for ATAC-seq. To this suspension, 2.5 µL of Tn5 transposase (Illumina, Cat. No. FC-121-1030) was added. The mixture was incubated at 37°C for 30 minutes with gentle shaking to facilitate transposition into accessible chromatin regions.
For ATAC-seq library preparation, the PCR reaction was set up by combining 10 µL of the purified transposed chromatin with 25 µL of 2× NEBNext High-Fidelity PCR Master Mix (Cat. No. M0541L). ATAC-seq libraries were sequenced as 101-bp paired-end reads on an Illumina HiSeq 2500 system.

value: Mammary gland

value: Female

tag: breed

value: Maltese


title: N_182

value: Shih-Tzu


title: PP-DNT 1

description: Used in this paper.


title: PDX tissue from L7p3

city: Taipei

first: Bing-Ying

last: Ho

address: Rm. 102, No.81, Changxing St.

department: Molecular Imaging Center

institute: National Taiwan University

description: Library name: L7_P3

data_processing:
The sequence was determined using Illumina's sequencing-by-synthesis (SBS) technology (Illumina, USA). Sequencing data (FASTQ reads) were generated using Welgene Biotech's pipeline based on Illumina's basecalling program bcl2fastq v2.20.
Assembly: GRCh38 and GRCm38 reference sequence used for read alignment.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

organism:
Homo sapiens
Mus musculus

source_name: PDX

growth_protocol: PDX tumors were harvested when they reached approximately 2000 mm3. Excised tumors were re-implanted into new mice to establish serial passages.

extract_protocol:
The purified RNA was quantitated at OD260 nm using a ND-1000 spectrophotometer (Nanodrop Technology,USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with the RNA 6000 Nano kit(Agilent Technology, USA).
Illumina's TruSeq Stranded Total RNA Library Prep Gold Kit (Cat. 20020598)  was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection.

treatment_protocol: No treatment

value: PDX

tag: batch


title: PP-γδ 1

description: Used in this paper.


title: PP-CD4 1

description: Used in this paper.


title: 100596, 2 Kidney

city: Jackson

state: MISSISSIPPI

address: 2500 N state street

institute: Molecular and Genomics Core Facility

description:
Library name: P1117B_8_2K_100596
10X genomics

data_processing:
The raw sequencing reads were processed using Cell Ranger v7.0 (10x Genomics). The cellranger mkfastq pipeline was used to demultiplex the FASTQ base call files. The outputs were then used to run cellranger count which aligns the sequencing reads to the reference transcriptome built from the Ensembl Rnor6.0 genome.
Assembly: Rnor6.0
Supplementary files format and content: Tab separated values file and matrix files

molecule: nuclear RNA

organism: Rattus norvegicus

source_name: Kidney

extract_protocol:
Nuclei were isolated from archived kidney (same animals for Methylseq) using a central section/biopsy (cortex and medulla were included) collected at 4 weeks of age from HSRA-S (n=3) and HSRA-C (n=4) per 10X Chromium Nuclei Isolation Kit (PN-1000493). Single nuclei samples were processed through the 10X Genomics Chromium Single Cell 3’ protocol v3.1 per manufacturers’ instruction to capture 5000 cells per sample. Single-cell droplets (GEMs) were produced using the 10X Genomics Chromium Controller and barcoded for sample identification.
Final libraries were validated on the QIAxcel DNA High Sensitivity bioanalyzer to visualize the expected insert size, and concentration. The pooled 10X library (n=7 samples) was subsequently sequenced twice on the Illumina NextSeq 2000 per 10X Genomics specifications (28x91 cycles) using a P3 100-cycle Kit. Our snRNAseq approach captured an average of 5,293 cells per sample, with an average of 55,945 reads per cell, detecting a median of 1,180 genes per cell.

value: Kidney


title: CHR_SAL_exposed_1

description: Library name: 01T0001

value: Heart


title: PHN_2


title: 100595, 2 Kidney

description:
Library name: P1117B_7_2K_100595
10X genomics


title: CNS GCT 02

city: Barretos

first: LENILSON

last: SILVA

state: SP

address: Rua Antenor Duarte Viléla, 1331

department: Molecular oncology research center

country: Brazil

institute: Barretos Cancer Hospital

hyb_protocol: 300 µL of total RNA were used. Hybridization was performed for 24 hours at 65°C, after which the samples were loaded onto the nCounter Prep Station for binding and washing.

scan_protocol: The samples were then scanned, capturing 550 fields of view using the nCounter Digital Analyzer (NanoString Technologies).

data_processing: Data was analyzed using ROSALIND®. Normalization with housekeeping genes was performed based on the geNorm algorithm

label: Capture and reporter probes

organism: Homo sapiens

source_name: Germ cell tumor

label_protocol: Capture and reporter probes were used for 24 hours to label the mRNA (300

extract_protocol: RNA was isolated using the RecoverAll Total Nucleic Acid Isolation Kit (Thermo Fisher Scientific), following the manufacturer's instructions. The purity and concentration of total RNA were assessed using NanoDroPVR 2000 (Thermo Fisher Scientific) and Qubit 2.0 instrument (Thermo Fisher Scientific).

tag: histology

value: CNS mixed tumor

tag: gender

value: M

tag: location

value: Central Nervous System

tag: age

value: 17 years


title: PDX tissue from L7p0

description: Library name: L7_P0


title: CNS GCT 03

value: 11 years


title: 100242, 1 Kidney

description:
Library name: P1117_6_1K_100242
10X genomics


title: AP97854

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description: Moderate-plane of nutrition

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (ARS-UCD1.2) using STAR (v2.6.1), incorporating the quantmode function to determine the number of mapped reads.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
A false discovery rate (FDR) of <0.1 was applied as a threshold to call genes with differential expression levels.
Assembly: ARS-UCD1.2
Supplementary files format and content: Tab delimited txt file of merged gene read counts

organism: Bos taurus

source_name: anterior pituitary

growth_protocol: Holstein-Friesian bull calves were fed differentially either a High plane of nutrition (n=15) or a Moderate plane of nutrition (n=15)  from 2-12 weeks of age. Calves on the High plane of nutrition were expected to grow at 1.0 kg/day, with the Moderate plane of nutrition expected to gain 0.5 kg/day.

extract_protocol:
RNA was  precipitated and purified from anterior pituitary samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the Illumina TruSeq stranded RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

treatment_protocol: Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates. The Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 0.5 kg of concentrates.

value: anterior pituitary

value: Holstein-Friesian

value: Moderate


title: 100253, 1 Kidney

description:
Library name: P1117_4_1K_100253
10X genomics


title: N_172


title: AP97821

description: Moderate-plane of nutrition


title: CONTROL 04

value: Control

value: Testis

value: 16 years


title: CNS GCT 01

value: F

value: 14 years


title: N_103

value: Mammary gland

value: Female

value: Schnauzer


title: CONTROL 03

value: Ovary

value: 18 years


title: AP87886

description: Moderate-plane of nutrition


title: plt2/gPLT2C212S-GFP 5 nM RGF1 rep5

data_processing:
The sequencing reads were mapped to Arabidopsis genome TAIR10 using HISAT2 v2.1.0.
The read counts of genes were compared with the Araport11 genome annotation using featureCounts (subread v2.0.3).
The normalized expression values of genes were performed using DESeq (v1.34.0)
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes FPKM values for each sample

extract_protocol:
The seedings were aligned onto a 2% agarose plate for root tips collection. Using an ophthalmic scalpel (Feather), the meristematic zone of the seedlings were precisely dissected under a dissecting microscope (Axio Zoom, Zeiss). Total RNA was extracted from 50 root sections using the RNeasy Micro Kit (Qiagen). All total RNA samples were treated with DNaseI during RNA extraction.
RNA libraries were prepared using Universal RNA-Seq with NuQuant library preparation kit following manufacture's protocols

value: Root meristematic zone

value: 24 hr

value: 5 nM RGF1


title: 100241, 2 Kidney

description:
Library name: P1117_3_2K_100241
10X genomics

value: Kidney


title: 100236, 1 Kidney

description:
Library name: P1117_2_1K_100236
10X genomics


title: C_9

value: Dachshund


title: N_173

value: Maltese


title: CONTROL 01

value: 13 years


title: AP61973

description: Moderate-plane of nutrition

value: anterior pituitary

value: Holstein-Friesian

value: Moderate


title: 100235, 2 Kidney

description:
Library name: P1117_1_2K_100235
10X genomics


title: CONTROL 02

value: Control

value: M

value: Testis

value: 01 year


title: AP73759

description: Moderate-plane of nutrition


title: N_174

value: Mammary gland

value: Female


title: 101459, 2 Kidney,OxBS (DNA Oxidation)

description:
Library name: P1278_12oxBS_1K
Ovation RRBS Methyl-Seq

data_processing:
After sequencing, TrimGalore was used for adaptor and quality trimming. A custom Python script was used to remove the sequence diversity added by the Ovation RRBS adaptor. Bismark was used for alignment to a reference genome (mRatBn7) and the methylation extractor function was used to process the BAM files and extract the methylation call for each cytosine analyzed
Assembly: mRatBN7
Supplementary files format and content: Cov files

extract_protocol:
DNA was isolated from 4-week-old male HSRA-C (n=6) and HSRA-S (n=6) kidney samples using the PureLink Genomic DNA Mini Kit (Invitrogen) and quantified with the Qubit High-Sensitivity DNA Assay Kit. A total of 100 ng of genomic DNA was used as input for each sample in duplicate and libraries were processed using the Ovation RRBS Methylseq System 1-16 per manufacturer’s instruction with a single adapter/index. Paired samples were subjected to either bisulfite conversion (RRBS) as well as the optional DNA oxidation procedure (oxRRBS). This allowed for the determination of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) modifications of genomic DNA. RRBS measures 5mC and 5hmC but does not differentiate between the two, while oxRRBS only measures 5mC modifications.
Final libraries were validated by bioanalyzer (QIAxcel-DNA High Sensitivity) and concentrations were measured by fluorescence (Qubit HS DNA Assay Kit). Final libraries averaged ~300 base pairs in length and were normalized to 10nM for sequencing. Libraries were sequenced on Illumina NextSeq 2000 per Ovation RRBS Methyl-Seq specifications (100 PE reads) using a P2 200 cycle reagent kit.


title: C_47

value: Schnauzer


title: 101459, 2 Kidney,Mock (Bisulfite conversion RRBS)

description:
Library name: P1278_12mock_1K
Ovation RRBS Methyl-Seq


title: Dysgerminoma 05

value: Dysgerminoma

value: F

value: Ovary

value: 14 years


title: Dysgerminoma 06


title: Dysgerminoma 04

value: 12 years


title: C_44

value: Cocker Spaniel


title: AP61965

description: Moderate-plane of nutrition


title: AP57826

description: Moderate-plane of nutrition


title: C_153

value: Maltese


title: AP57867

description: Moderate-plane of nutrition

value: anterior pituitary


title: 101446, 2 Kidney,OxBS (DNA Oxidation)

description:
Library name: P1278_11oxBS_1K
Ovation RRBS Methyl-Seq

value: Kidney


title: C_148


title: Dysgerminoma 02

value: 10 years


title: C_138

value: Chihuahua


title: Dysgerminoma 03


title: AP47874

description: Moderate-plane of nutrition

value: Holstein-Friesian

value: Moderate


title: C_70


title: 101431, 2 Kidney,Mock (Bisulfite conversion RRBS)

description:
Library name: P1278_10mock_1K
Ovation RRBS Methyl-Seq


title: 101431, 2 Kidney,OxBS (DNA Oxidation)

description:
Library name: P1278_10oxBS_1K
Ovation RRBS Methyl-Seq


title: Dysgerminoma 01

value: 17 years


title: C_132

value: Mammary gland


title: Embryonal carcinoma 03

value: Embryonal carcinoma

value: 15 years


title: AP47825

description: Moderate-plane of nutrition


title: C_10

value: Female


title: AP41971

description: Moderate-plane of nutrition


title: 100253, 2 Kidney,OxBS (DNA Oxidation)

description:
Library name: P1278_9oxBS_1K
Ovation RRBS Methyl-Seq


title: 100253, 2 Kidney,Mock (Bisulfite conversion RRBS)

description:
Library name: P1278_9mock_1K
Ovation RRBS Methyl-Seq


title: AP37865

description: Moderate-plane of nutrition


title: Embryonal carcinoma 01

value: F

value: 18 years


title: AP51980

description: Moderate-plane of nutrition


title: B_87


title: 101446, 2 Kidney,Mock (Bisulfite conversion RRBS)

description:
Library name: P1278_11mock_1K
Ovation RRBS Methyl-Seq


title: 100236, 2 Kidney,OxBS (DNA Oxidation)

description:
Library name: P1278_8oxBS_1K
Ovation RRBS Methyl-Seq


title: AP21978

description: Moderate-plane of nutrition


title: 100236, 2 Kidney,Mock (Bisulfite conversion RRBS)

description:
Library name: P1278_8mock_1K
Ovation RRBS Methyl-Seq


title: Yolk sac tumor 05

value: Yolk sac tumor

value: M

value: Testis

value: 0.7 years


title: Yolk sac tumor 04

value: Ovary


title: AP12937

description: Moderate-plane of nutrition

value: anterior pituitary


title: B_84

value: Shih-Tzu


title: B_73

value: Maltese


title: 100242, 2 Kidney,Mock (Bisulfite conversion RRBS)

description:
Library name: P1278_7mock_1K
Ovation RRBS Methyl-Seq

value: Kidney


title: 100242, 2 Kidney,OxBS (DNA Oxidation)

description:
Library name: P1278_7oxBS_1K
Ovation RRBS Methyl-Seq


title: Embryonal carcinoma 02

value: 12 years


title: 101447, 2 Kidney,OxBS (DNA Oxidation)

description:
Library name: P1278_6oxBS_2K
Ovation RRBS Methyl-Seq


title: Yolk sac tumor 03

value: 14 years


title: B_137

value: Mammary gland


title: 101447, 2 Kidney,Mock (Bisulfite conversion RRBS)

description:
Library name: P1278_6mock_2K
Ovation RRBS Methyl-Seq


title: AP92928

description: High-plane of nutrition

value: Holstein-Friesian

value: High


title: NOS3 overexpression with calcium biol rep 4

city: Cleveland

first: Joseph

middle: C.

last: Schindler

state: OH

address: 10900 Euclid Ave.

department: Biochemistry

institute: Case Western Reserve University

description: Library name: NOS3_Ca_d

data_processing:
QC filtering using TrimGalore! v0.4.2 (Babraham Bioinformatics), a wrapper script for FastQC and cutadapt. Reads passing QC and with adapter sequences trimmed were aligned to the human GRCh38 reference genome using STAR aligner v2.7.98 with GENCODE annotations. Aligned reads were analyzed for differential expression using Cufflinks v2.2.19 and expression values were reported as fragment counts per kilobase of exon per million fragments mapped (FPKM)
Assembly: GRCh38
Supplementary files format and content: xlsx file contains a matrix of FPKM values for each aligned transcript

extract_protocol:
24h after treatment, total RNA was purified using TRIzol reagent
NEBNext Ultra II RNA kit- incl. QC of total RNA and Qubit, Fragment Analyzer, and qPCR of final libraries

treatment_protocol: 6-well plates of cells at ~70% confluency were transfected with 2.5 µg of DNA for empty vector or NOS overexpression plasmids with Lipofectamine3000. 8h prior to harvest, cells were treated with 5µM calcium ionophore (A23187).


title: stress_testis_rep3

city: Shanghai

first: Xiaoguo

last: Zheng

address: 145 Guangyuan Road

institute: Shanghai Jiaotong University

data_processing:
The raw data were trimmed and subjected to quality control. Then, the clean reads were separately aligned to the reference genome (mm39). The expression level of each transcript was calculated using the fragments per kilobase of exon per million mapped reads (FPKM) method. Differentially expressed genes between two samples were identified based on a cutoff P value for per-gene variance less than 0.05 with conservative Bonferroni correction and Foldchange more than 2. Protein and Protein interaction analysis was performed in the web: https://string-db.org/. GO and KEGG analysis were analyzed with the R package clusterProfiler.
Assembly: mm39
Supplementary files format and content: tab-delimited text file include raw counts, TPM and FPKM valuse for each sample

source_name: testis

extract_protocol:
Total RNA was extracted from the liver, hippocampus and testis of control and CRS-treated mice using RNeasy Plus Universal Kits (Qiagen, Germany) according to the manufacturer’s instructions. The concentration and quality of the total RNA were determined with a NanoDrop 2000 (Thermo Fisher Scientific, USA.) and a 2100 Bioanalyzer (Agilent, USA).
A total of 5 μg of high-quality RNA was used to construct each sequencing library. The mRNA-seq libraries were prepared with a TruSeq Stranded Total RNA Preparation Kit (Illumina, CA) according to the manufacturer’s instructions. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to the Illumina protocol.

value: testis

value: chronic restraint stress


title: AP93744

description: High-plane of nutrition


title: AP93760

description: High-plane of nutrition


title: AP81983

description: High-plane of nutrition


title: Yolk sac tumor 02

value: 02 years


title: Yolk sac tumor 01

value: Yolk sac tumor

value: F

value: 13 years


title: NOS3 overexpression with calcium biol rep 3

description: Library name: NOS3_Ca_c


title: 101432, 2 Kidney,OxBS (DNA Oxidation)

description:
Library name: P1278_5oxBS_2K
Ovation RRBS Methyl-Seq


title: 101432, 2 Kidney,Mock (Bisulfite conversion RRBS)

description:
Library name: P1278_5mock_2K
Ovation RRBS Methyl-Seq


title: B_91

value: Female


title: stress_testis_rep2


title: NOS3 overexpression with calcium biol rep 2

description: Library name: NOS3_Ca_b


title: stress_testis_rep1


title: AP77860

description: High-plane of nutrition


title: AP47858

description: High-plane of nutrition


title: B_50

value: Poodle


title: stress_liver_rep3

value: liver


title: AP42931

description: High-plane of nutrition

value: anterior pituitary


title: stress_liver_rep2


title: 100595, 2 Kidney,OxBS (DNA Oxidation)

description:
Library name: P1278_4oxBS_2K
Ovation RRBS Methyl-Seq


title: 100595, 2 Kidney,Mock (Bisulfite conversion RRBS)

description:
Library name: P1278_4mock_2K
Ovation RRBS Methyl-Seq


title: NOS1 overexpression with calcium biol rep 4

description: Library name: NOS1_Ca_d


title: AP37840

description: High-plane of nutrition


title: NOS1 overexpression with calcium biol rep 3

description: Library name: NOS1_Ca_c


title: 100254, 2 Kidney,OxBS (DNA Oxidation)

description:
Library name: P1278_3oxBS_2K
Ovation RRBS Methyl-Seq


title: NOS1 overexpression with calcium biol rep 2

description: Library name: NOS1_Ca_b


title: AP37824

description: High-plane of nutrition


title: 100254, 2 Kidney,Mock (Bisulfite conversion RRBS)

description:
Library name: P1278_3mock_2K
Ovation RRBS Methyl-Seq


title: stress_brain_rep3

source_name: brain

value: brain


title: AP31979

description: High-plane of nutrition


title: NOS1 overexpression with calcium biol rep 1

description: Library name: NOS1_Ca_a


title: 100241, 2 Kidney,OxBS (DNA Oxidation)

description:
Library name: P1278_2oxBS_2K
Ovation RRBS Methyl-Seq

value: Kidney


title: AP27864

description: High-plane of nutrition


title: stress_brain_rep2


title: Empty Vector with calcium biol rep 4

description: Library name: EV_Ca_d


title: 100241, 2 Kidney,Mock (Bisulfite conversion RRBS)

description:
Library name: P1278_2mock_2K
Ovation RRBS Methyl-Seq


title: Empty Vector with calcium biol rep 3

description: Library name: EV_Ca_c


title: AP27848

description: High-plane of nutrition


title: 100235, 2 Kidney,OxBS (DNA Oxidation)

description:
Library name: P1278_1oxBS_2K
Ovation RRBS Methyl-Seq


title: Empty Vector with calcium biol rep 2

description: Library name: EV_Ca_b


title: NOS3 overexpression with calcium biol rep 1

description: Library name: NOS3_Ca_a


title: control_testis_rep3

value: control


title: 100235, 2 Kidney,Mock (Bisulfite conversion RRBS)

description:
Library name: P1278_1mock_2K
Ovation RRBS Methyl-Seq


title: AP27823

description: High-plane of nutrition


title: control_testis_rep2


title: AP17855

description: High-plane of nutrition


title: stress_liver_rep1


title: control_testis_rep1


title: AP13745

description: High-plane of nutrition


title: Gedatolisib-treated mouse 737

city: Houston

first: Kelli

last: McCord

state: TX

address: 1 Baylor Plz

institute: Baylor College of Medicine

description: 10X Genomics 5K in situ spatial transcriptomics

hyb_protocol: Probes from the predesigned  Xenium Prime 5K Human Pan-Tissue and Pathways Panel, consisting of 5001 genes as well as an additional 45 custom gene panel containing key human and mouse probes were used for gene detection.

scan_protocol: Samples were run on Xenium Analyzer using intrument software version 3.1.0.0 and analysis version xenium-3.1.0.4

source_name: humanized mouse tumor resected from tongue

label_protocol: Randomly selected mice were assigned numbers and different treatments

growth_protocol: Immediately following tumor resection, tumor samples were embedded in optimal cutting temperature (OCT) compound and flash frozen in a dry ice/isopentane bath before being stored in the vapor phase of liquid nitrogen.

extract_protocol: Xenium slides were prepared following the Xenium Prime In Situ Gene expression with optional cell segmentation staining user guide (CG000760) and Xenium analyzer user guide (CG000584)

treatment_protocol: For each tumor sample, 10 µm sections were mounted onto Xenium slides and stored at -80ºC for under one week prior to initiating the Xenium experiment.

value: Gedatolisib


title: Empty Vector with calcium biol rep 1

description: Library name: EV_Ca_a


title: Untreated biol rep 4

description: Library name: untreated_d

treatment_protocol: 6-well plates of cells at ~70% confluency were transfected with 2.5 µg of DNA for empty vector or NOS overexpression plasmids with Lipofectamine3000; or treated with 1000 µM or 100 µM of GSNO or DETA NONOate

value: Untreated


title: control_liver_rep3

source_name: liver


title: Gedatolisib-treated mouse 735

data_processing: Samples were run on Xenium Analyzer using intrument software version 3.1.0.0 and analysis version xenium-3.1.0.4


title: 981

source_name: Skeletal muscle

growth_protocol: Angus X Holstein-Friesian heifer calves were fed differentially either a High plane of nutrition (n=10) or a Moderate plane of nutrition (n=10)  from 2-21 weeks of age. Calves on the High plane of nutrition were expected to grow at 1.2 kg/day, with the Moderate plane of nutrition expected to gain 0.5 kg/day.

extract_protocol:
RNA was  precipitated and purified from skeletal muscle samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
cDNA libraries were prepared from high quality RNA  using the Illumina TruSeq stranded RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

treatment_protocol: Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates during the calf phase. During the subsequent post-weaning phase this group were then offered concentrates ad libitum and hay to appetite. During the calf phase the Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 1 kg of concentrates, subsequently receiving 1kg of concentrates and hay to appetite during the post-weaning phase. The calf phase lasted for 8 weeks and was followed by the post-weaning phase which lasted for 11 weeks.

value: Skeletal muscle

value: Holstein-Friesian X Angus

value: Moderate-plane of nutrition


title: control_liver_rep2


title: 3622


title: Gedatolisib-treated mouse 734


title: Untreated biol rep 2

description: Library name: untreated_b


title: Gedatolisib-treated mouse 732


title: 2570

value: High-plane of nutrition


title: stress_brain_rep1

value: chronic restraint stress


title: Untreated biol rep 1

description: Library name: untreated_a


title: Untreated biol rep 3

description: Library name: untreated_c


title: 2551


title: Control mouse 738

value: Saline


title: GSNO 100 µM biol rep 3

description: Library name: GSNO100c

value: GSNO 100 µM


title: control_brain_rep2


title: control_brain_rep3


title: Control mouse 736


title: 2537


title: GSNO 100 µM biol rep 4

description: Library name: GSNO100d


title: Control mouse 733


title: GSNO 100 µM biol rep 2

description: Library name: GSNO100b


title: control_brain_rep1


title: BAT cell line, shEtv4, +FSK, rep4

city: Berkeley

first: Pengya

last: Xue

state: CA

address: Morgan hall, 220

institute: UC Berkeley

description:
Normalized_counts(FPKM).txt
shE4FSK_4_CKDL230021177-1A_HJLC7BBXX_L6

data_processing:
raw data was trimmed adaptor and filtered with quality>35
data was aligned to mm10
peak was called by macs2
bigwig file generated by bamboverage
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: tab delimited text file including RPKM value for each sample

source_name: BAT cell line

growth_protocol: mouse was hosted in UCB facility while cell was mainteined in DMEM with 10% FBS and antibiotics.

extract_protocol:
DNA was purified use zymo pure DNA kit
KAPA pure kit was used for cut&run library

treatment_protocol: cell was treated with FSK for 4 hours before collection

value: BAT cell line

value: Etv4 knockdown

value: FSK


title: 2532


title: GSNO 100 µM biol rep 1

description: Library name: GSNO100a


title: Control mouse 731

value: Female


title: BAT cell line, shEtv4, +FSK, rep3

description:
Normalized_counts(FPKM).txt
shE4FSK_3_CKDL230021177-1A_HJLC7BBXX_L6


title: Kidney, LOY + ABT263, Animal 18

city: Charlottesville

first: Nicholas

middle: W

last: Chavkin

address: 415 Lane Road

institute: University of Virginia

description:
Library name: KLA18
Kidney_CTvsABT_RNAseq.csv

data_processing:
Raw sequencing data was aligned to the murine mm10 reference genome .
Assembly: mm10
Supplementary files format and content: csv containing raw counts of genes per sample

source_name: kidney

extract_protocol:
Total RNA from kidneys was extracted and purified using QIAzol reagent (QIAGEN, #79306) and RNeasy Mini QIAcube Kit (Qiagen, #74116).
Purified RNA was submitted to Novogene (Sacramento, CA, USA) for RNA sequencing for total RNA library preparation and subsequent Illumina NovaSeq X sequencing.

value: kidney

value: LOY


title: GSNO 1000 µM biol rep 4

description: Library name: GSNO1000d

value: GSNO 1000 µM


title: 2528


title: BAT cell line, shEtv4, +FSK, rep2

description:
Normalized_counts(FPKM).txt
shE4FSK_2_CKDL230021177-1A_HJLC7BBXX_L6


title: control_liver_rep1

value: liver

value: control


title: 2346


title: Kidney, LOY + ABT263, Animal 17

description:
Library name: KLA17
Kidney_CTvsABT_RNAseq.csv


title: GSNO 1000 µM biol rep 3

description: Library name: GSNO1000c


title: Kidney, LOY + ABT263, Animal 16

description:
Library name: KLA16
Kidney_CTvsABT_RNAseq.csv


title: Kidney, LOY + ABT263, Animal 15

description:
Library name: KLA15
Kidney_CTvsABT_RNAseq.csv


title: 2120


title: BAT cell line, shEtv4, -FSK, rep4

description:
Normalized_counts(FPKM).txt
shE4_4_CKDL230021177-1A_HJLC7BBXX_L6


title: 1707


title: GSNO 1000 µM biol rep 1

description: Library name: GSNO1000a


title: Kidney, LOY + Control, Animal 10

description:
Library name: KLC10
Kidney_CTvsABT_RNAseq.csv

value: Control


title: 1690

value: Skeletal muscle


title: BAT cell line, shEtv4, -FSK, rep3

description:
Normalized_counts(FPKM).txt
shE4_3_CKDL230021177-1A_HJLC7BBXX_L6


title: 2535

value: Holstein-Friesian X Angus


title: DETA 100 µM biol rep 4

description: Library name: DETA100d

value: DETA 100 µM


title: Kidney, LOY + Control, Animal 09

description:
Library name: KLC09
Kidney_CTvsABT_RNAseq.csv


title: BAT cell line, shEtv4, -FSK, rep2

description:
Normalized_counts(FPKM).txt
shE4_2_CKDL230021177-1A_HJLC7BBXX_L6


title: 1689

value: Moderate-plane of nutrition


title: Kidney, LOY + Control, Animal 08

description:
Library name: KLC08
Kidney_CTvsABT_RNAseq.csv


title: 1531

value: High-plane of nutrition


title: Kidney, LOY + Control, Animal 06

description:
Library name: KLC06
Kidney_CTvsABT_RNAseq.csv


title: DETA 100 µM biol rep 2

description: Library name: DETA100b


title: BAT cell line, shScr, +FSK, rep4

description:
Normalized_counts(FPKM).txt
shScrFSK_4_CKDL230021177-1A_HJLC7BBXX_L6

value: wild type


title: 1392


title: Kidney, LOY, Animal 18

description:
Library name: KL18
Kidney_CTvsLOY_RNAseq.csv


title: DETA 100 µM biol rep 1

description: Library name: DETA100a


title: BAT cell line, shEtv4, +FSK, rep1

description:
Normalized_counts(FPKM).txt
shE4FSK_1_CKDL230021177-1A_HJLC7BBXX_L6


title: BAT cell line, shScr, +FSK, rep3

description:
Normalized_counts(FPKM).txt
shScrFSK_3_CKDL230021177-1A_HJLC7BBXX_L6


title: Kidney, LOY, Animal 14

description:
Library name: KL14
Kidney_CTvsLOY_RNAseq.csv


title: 1388


title: GSNO 1000 µM biol rep 2

description: Library name: GSNO1000b


title: BAT cell line, shScr, +FSK, rep2

description:
Normalized_counts(FPKM).txt
shScrFSK_2_CKDL230021177-1A_HJLC7BBXX_L6


title: DETA 1000 µM biol rep 4

description: Library name: DETA1000d

value: DETA 1000 µM


title: 1360


title: Kidney, LOY, Animal 10

description:
Library name: KL10
Kidney_CTvsLOY_RNAseq.csv


title: DETA 1000 µM biol rep 3

description: Library name: DETA1000c


title: 1089


title: BAT cell line, shScr, +FSK, rep1

description:
Normalized_counts(FPKM).txt
shScrFSK_1_CKDL230021177-1A_HJLC7BBXX_L6

value: BAT cell line


title: DETA 1000 µM biol rep 2

description: Library name: DETA1000b


title: Kidney, LOY, Animal 09

description:
Library name: KL09
Kidney_CTvsLOY_RNAseq.csv


title: 1057


title: DETA 1000 µM biol rep 1

description: Library name: DETA1000a


title: DETA 100 µM biol rep 3

description: Library name: DETA100c


title: BAT cell line, shScr, -FSK, rep4

description:
Normalized_counts(FPKM).txt
shScr_4_CKDL230021177-1A_HJLC7BBXX_L6


title: BAT cell line, shEtv4, -FSK, rep1

description:
Normalized_counts(FPKM).txt
shE4_1_CKDL230021177-1A_HJLC7BBXX_L6

value: Etv4 knockdown


title: BAT cell line, shScr, -FSK, rep3

description:
Normalized_counts(FPKM).txt
shScr_3_CKDL230021177-1A_HJLC7BBXX_L6


title: 1050


title: BAT cell line, shScr, -FSK, rep2

description:
Normalized_counts(FPKM).txt
shScr_2_CKDL230021177-1A_HJLC7BBXX_L6


title: NOS3 overexpression biol rep 3

description: Library name: NOS3c

value: NOS3 overexpression


title: Dairy cow 10, visceral adipose tissue (VAT), control group

city: Lexington

first: Shavahn

middle: C

last: Loux

state: KY

address: 1400 Nicholasville

department: Veterinary Science

institute: University of Kentucky

data_processing:
FASTQ reads were trimmed for quality and adapters with TrimGalore 0.4.3 and mapped to bovine genome ARS-UCD1.2 with STAR-2.7.2a (Dobin et al., 2012) in the two-pass mode, quantMode GeneCounts including the following specifications (--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignEndsType Local --chimOutType WithinBAM --twopassMode Basic --twopass1readsN -1). Annotation was performed using Ensembl v106.  Normalization of expression values was performed using gene length corrected trimmed mean of M-values (GeTMM) (Smid et al., 2018). Differentially expressed genes were identified One-Way ANOVA between VAT and SAT samples based upon a robust Benjamini-Hochberg corrected false discovery rate (FDR) P value < 0.05 (JMP 14 Pro).
Assembly: ARS-UCD1.2
Supplementary files format and content: xls

source_name: Adipose tissue

extract_protocol:
Adipose tissue total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) reagent in combination with the RNeasy Plus Mini Kit and RNAase-free DNAase set (Qiagen, Hilden, Germany), following the manufacturer’s instructions with some modifications. Briefly, around 200 mg of adipose tissue were immersed in a 2-mL RNase-free O-ring tube containing 1 mL of Trizol and ten 3 mm high impact zirconium beads (Benchmark Scientific Inc, Sayreville, NJ, USA). Tissue was homogenized using a beadblaster (Benchmark Scientific Inc, Sayreville, NJ, USA). After homogenization, sample was centrifuged at 12,000 × g for 10 min at 4°C, and a pink middle layer fluid was collected into a new 2-mL RNase-free microtube. Then, 200 µL of Phenol:chloroform (Invitrogen, Carlsbad, CA) at 4°C were added to the sample in order to isolate the RNA from the organic phase. After centrifugation at 12,000 × g for 15 min at 4°C, the clear upper phase was transferred into a new 2-mL RNase-free microtube containing 700 µL of 70% ethanol. The total RNA was purified using RNeasy Plus Mini Kit and eluted in 30 µL of RNase-free water.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). 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. PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: Adipose tissue

value: Non ketotic


title: BAT cell line, shScr, -FSK, rep1

description:
Normalized_counts(FPKM).txt
shScr_1_CKDL230021177-1A_HJLC7BBXX_L6


title: Kidney, Control, Animal 17

description:
Library name: KC17
Kidney_CTvsLOY_RNAseq.csv

value: kidney


title: Dairy cow 10, subcutaneous adipose tissue (SAT), control group


title: NOS3 overexpression biol rep 2

description: Library name: NOS3b


title: Kidney, Control, Animal 16

description:
Library name: KC16
Kidney_CTvsLOY_RNAseq.csv


title: NOS3 overexpression biol rep 1

description: Library name: NOS3a


title: BAT cell line, CRISPRi shEtv4, rep2, ATAC-seq

value: CRISPRi shEtv4


title: Kidney, Control, Animal 13

description:
Library name: KC13
Kidney_CTvsLOY_RNAseq.csv


title: Dairy cow 9, subcutaneous adipose tissue (SAT), ketosis group

value: Subclinical ketosis


title: BAT cell line, CRISPRi shScr, rep2, ATAC-seq

value: CRISPRi shScr


title: NOS2 overexpression biol rep 4

description: Library name: NOS2d

value: NOS2 overexpression


title: Dairy cow 8, visceral adipose tissue (VAT), control group


title: Kidney, Control, Animal 12

description:
Library name: KC12
Kidney_CTvsLOY_RNAseq.csv

value: Control


title: NOS2 overexpression biol rep 3

description: Library name: NOS2c


title: NOS2 overexpression biol rep 2

description: Library name: NOS2b


title: NOS3 overexpression biol rep 4

description: Library name: NOS3d


title: BAT cell line, CRISPRi g(-12kb)-3, rep2, ATAC-seq

value: CRISPRi g(-12kb)-3


title: Kidney, Control, Animal 03

description:
Library name: KC03
Kidney_CTvsLOY_RNAseq.csv


title: Kidney, LOY, Animal 05

description:
Library name: KL05
Kidney_CTvsLOY_RNAseq.csv

value: LOY


title: BAT cell line, CRISPRi shScr, rep1, ATAC-seq


title: NOS2 overexpression biol rep 1

description: Library name: NOS2a


title: Dairy cow 7, visceral adipose tissue (VAT), ketosis group


title: BAT cell line, CRISPRi g(-12kb)-3, rep1, ATAC-seq


title: Dairy cow 9, visceral adipose tissue (VAT), ketosis group


title: NOS1 overexpression biol rep 4

description: Library name: NOS1d

value: NOS1 overexpression


title: BAT cell line, CRISPRi g(-12kb)-2, rep2, ATAC-seq

value: CRISPRi g(-12kb)-2


title: Dairy cow 6, visceral adipose tissue (VAT), control group


title: Dairy cow 7, subcutaneous adipose tissue (SAT), ketosis group


title: BAT cell line, CRISPRi shEtv4, rep1, ATAC-seq


title: Kidney, LOY, Animal 08

description:
Library name: KL08
Kidney_CTvsLOY_RNAseq.csv


title: NOS1 overexpression biol rep 3

description: Library name: NOS1c


title: BAT cell line, CRISPRi g(-12kb)-2, rep1, ATAC-seq


title: NICD dorsal forebrain progenitor cells, E17.5, RNA-seq, Sample 1

city: Aurora

first: Santos

middle: J

last: Franco

state: CO

department: Pediatrics

institute: University of Colorado Anschutz Medical Campus

description:
Library name: NICD E17.5 RNA-seq Sample 1
column name in rnaseq_e17_raw_counts.tsv: NICD_e17_1

data_processing:
The nf-core RNA-seq pipeline (v 3.14.0)  was used for data preprocessing and analysis with default parameters.
STAR was specified in the nf-core pipeline for alignment to the GRCm38 mouse genome
Salmon was specified for transcript quantification based on STAR alignments
Assembly: mm10
Supplementary files format and content: tsv file includes gene level raw counts for each sample

source_name: dorsal forebrain neural progenitor cells

extract_protocol:
Dorsal forebrain neural progenitor cells were isolated from embryonic mouse brains via magnetic-activated cell sorting (MACS) using Prominin-1 (Prom1) as the cell surface marker. Total RNA was extracted from the isolated cells using the Zymo Quick-RNA Microprep Kit (Zymo Research) following the manufacturer’s protocol
Libraries were prepared using SMARTer Stranded Total RNA-seq Kit

value: Emx1-Cre; LSL-NICD


title: Dairy cow 6, subcutaneous adipose tissue (SAT), control group


title: NOS1 overexpression biol rep 2

description: Library name: NOS1b


title: Kidney, Control, Animal 11

description:
Library name: KC11
Kidney_CTvsLOY_RNAseq.csv


title: Dairy cow 8, subcutaneous adipose tissue (SAT), control group


title: CTRL dorsal forebrain progenitor cells, E17.5, RNA-seq, Sample 3

description:
Library name: CTRL E17.5 RNA-seq Sample 3
column name in rnaseq_e17_raw_counts.tsv: CTRL_e17_1

value: dorsal forebrain neural progenitor cells

value: Emx1-Cre Control


title: BAT cell line, CRISPRi g(-12kb)-1, rep2, ATAC-seq

value: BAT cell line

value: CRISPRi g(-12kb)-1


title: NOS1 overexpression biol rep 1

description: Library name: NOS1a


title: Dairy cow 5, visceral adipose tissue (VAT), ketosis group

value: Adipose tissue


title: Dairy cow 5, subcutaneous adipose tissue (SAT), ketosis group


title: CTRL dorsal forebrain progenitor cells, E17.5, RNA-seq, Sample 1

description:
Library name: CTRL E17.5 RNA-seq Sample 1
column name in rnaseq_e17_raw_counts.tsv: CTRL_e17_1


title: CTRL dorsal forebrain progenitor cells, E17.5, RNA-seq, Sample 2

description:
Library name: CTRL E17.5 RNA-seq Sample 2
column name in rnaseq_e17_raw_counts.tsv: CTRL_e17_2


title: BAT cell line, CRISPRi gScr, rep2, ATAC-seq

value: CRISPRi gScr


title: BAT cell line, CRISPRi g(-12kb)-1, rep1, ATAC-seq


title: Empty Vector biol rep 4

description: Library name: EVd

value: Empty Vector


title: NICD dorsal forebrain progenitor cells, E17.5, RNA-seq, Sample 3

description:
Library name: NICD E17.5 RNA-seq Sample 3
column name in rnaseq_e17_raw_counts.tsv: NICD_e17_1


title: Empty Vector biol rep 3

description: Library name: EVc


title: NICD dorsal forebrain progenitor cells, E16.5, RNA-seq, Sample 3

description:
Library name: NICD E16.5 RNA-seq Sample 3
column name in rnaseq_e16_raw_counts.tsv: NICD3


title: NICD dorsal forebrain progenitor cells, E17.5, RNA-seq, Sample 2

description:
Library name: NICD E17.5 RNA-seq Sample 2
column name in rnaseq_e17_raw_counts.tsv: NICD_e17_1


title: Dairy cow 4, visceral adipose tissue (VAT), control group

value: Non ketotic


title: BAT cell line, CRISPRi gScr, rep1, ATAC-seq


title: NICD dorsal forebrain progenitor cells, E16.5, RNA-seq,  Sample 2

description:
Library name: NICD E16.5 RNA-seq Sample 2
column name in rnaseq_e16_raw_counts.tsv: NICD2


title: Empty Vector biol rep 2

description: Library name: EVb


title: BAT H3K27me3 4ºC, CUT&RUN

data_processing:
library strategy: CUT&RUN
raw data was trimmed adaptor and filtered with quality>35
data was aligned to mm10
peak was called by macs2
bigwig file generated by bamboverage
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: tab delimited text file including RPKM value for each sample

source_name: Brown adipose tissue

value: Brown adipose tissue

value: wild type


title: Dairy cow 3, visceral adipose tissue (VAT), control group


title: Dairy cow 4, subcutaneous adipose tissue (SAT), control group


title: BAT H3K27me3 30ºC, CUT&RUN


title: NICD dorsal forebrain progenitor cells, E16.5, RNA-seq, Sample 1

description:
Library name: NICD E16.5 RNA-seq Sample 1
column name in rnaseq_e16_raw_counts.tsv: NICD1


title: Empty Vector biol rep 1

description: Library name: EVa


title: CTRL dorsal forebrain progenitor cells, E16.5, RNA-seq, Sample 3

description:
Library name: CTRL E16.5 RNA-seq Sample 3
column name in rnaseq_e16_raw_counts.tsv: CTRL3


title: BAT H3K27ac 4ºC, CUT&RUN


title: Dairy cow 2, visceral adipose tissue (VAT), ketosis group

value: Subclinical ketosis


title: Dairy cow 3, subcutaneous adipose tissue (SAT), control group


title: HAP1_1000C_2

city: Oslo

first: Adnan

last: Hashim

state: Oslo

address: NCMM - Forskningsparken, House 1, 3rd Floor - Gaustadalléen 21

department: NCMM (Centre for Molecular Medicine Norway)

country: Norway

institute: UiO (University of Oslo)

description:
Library name: HAP1_1000C_2
1000 cels

data_processing:
Raw sequencing data quality was assessed using FastQC (v0.11.9). Adapter trimming and quality filtering were performed using Trim Galore (v0.6.7). Paired-end reads were processed simultaneously, and poor-quality bases and adapter sequences were removed from both reads.FastQC was run on the trimmed reads to verify the improvement in sequence quality.
The trimmed reads were aligned to the reference genome using HISAT2 (v2.2.1). The resulting SAM files were converted to BAM format, sorted by genomic coordinates, and indexed using SAMtools (v1.16.1).
Gene-level quantification was performed using the featureCounts function from the Subread package (v2.0.6). The resulting count matrix was then used for differential expression analysis using DESeq2 (v1.44.0) in R to compare gene expression levels between different experimental conditions.
Assembly: hg38
Supplementary files format and content: txt

growth_protocol: HAP1 cells were cultured in IMDM medium (Gibco) supplemented with 5% fetal bovine serum (Sigma-Aldrich), 1% l-glutamine (200 mM, Sigma-Aldrich) and 1% Penicillin (10,000 U/mL) Streptomycin (10,000 µg/mL) (Gibco) at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from biological replicates of 1, 10, 100 and 1000 sorted HAP1 cells. For each sample, cells were sorted with single cell precision using BD FACSAria IIu into a 60 µl mixture containing 1 part PBS and 2 parts NAxtra LYSIS BUFFER (Lybe Scientific) and combined with a 80 µl mixture of 4 µl NAxtra MAGNETIC BEADS (Lybe Scientific) in isopropanol. Following mixing and magnetization, the beads were washed on magnet with 150 µl absolute ethanol, dried for 2 min and resuspended in 15 µl nuclease-free water. Samples were DNase-treated by 10 min incubation with 0.4 µl RNase-Free DNase (QIAGEN), 2 µl Buffer RDD (QIAGEN) and nuclease-free water to a final volume of 20 µl. Nuclease-treated samples were combined with 40 µl NAxtra LYSIS BUFFER (Lybe Scientific), followed by 80 µl isopropanol. Following mixing and magnetization, the beads were washed on magnet, once with 150 µl isopropanol, and twice with 150 µl 80% ethanol, then dried for 2 min and resuspended in 8 µl nuclease-free water. Following mixing and magnetization, eluates were collected and stored at -80°C.
The SMART-Seq® Stranded Kit (Takara) was used to generate dual index libraries according to manufacturer's instructions.

value: WT


title: BAT H3K27ac 30ºC, CUT&RUN


title: HAP1_1000C_1

description:
Library name: HAP1_1000C_1
1000 cells


title: CTRL dorsal forebrain progenitor cells, E16.5, RNA-seq, Sample 2

description:
Library name: CTRL E16.5 RNA-seq Sample 2
column name in rnaseq_e16_raw_counts.tsv: CTRL2


title: Dairy cow 2, subcutaneous adipose tissue (SAT), ketosis group


title: HAP1_100C_2

description:
Library name: HAP1_100C_2
100 cells


title: iWAT CTCF, CUT&RUN

source_name: iWAT

value: iWAT


title: CTRL dorsal forebrain progenitor cells, E16.5, RNA-seq, Sample 1

description:
Library name: CTRL E16.5 RNA-seq Sample 1
column name in rnaseq_e16_raw_counts.tsv: CTRL1


title: Dairy cow 1, visceral adipose tissue (VAT), ketosis group


title: NICD dorsal forebrain progenitor cells, E16.5,  ATAC-seq, Sample 3

description: Library name: NICD E16.5  ATAC-seq Sample 3

data_processing:
The nf-core ATAC-seq pipeline (v 2.1.2) was used for data preprocessing and alignment to the GRCm38 mouse genome with default parameters.
Reads mapped to the mitochondrial genome were removed. Bam files resulting from BWA alignment in the nf-core pipeline were filtered for fragments less than 100 bp in length using sambamba (v 0.8.2)
Salmon was specified for transcript quantification based on STAR alignments
Newly filtered bam files were then indexed using SAMtools (v 1.16.1) and used to generate bigwig files with Deeptools (v 3.3.0)
Peaks were called using MACS2 (2.1.1.20160309) with the following parameters: -f BAMPE, --keep-dup all, -g mm, --call-summits.
Assembly: mm10
Supplementary files format and content: bigwig files contain normalized read coverage across the genome for each sample
Supplementary files format and content: narrowPeak files contain genomic coordinates of called peaks

extract_protocol:
The Zymo-Seq ATAC library kit was used for both extraction and library construction. Dorsal forebrain neural progenitor cells were isolated from embryonic mouse brains via magnetic-activated cell sorting (MACS) using Prominin-1 (Prom1) as the cell surface marker. Isolated cells were lysed to release nuclei, and transposition was performed to fragment chromatin while tagging accessible DNA regions with sequencing adapters.
ATAC-seq libraries were prepared using the Zymo-Seq ATAC Library Kit (Zymo Research) following the manufacturer's instructions.
Transposed DNA fragments were purified, PCR-amplified to incorporate indexed adapters, and size-selected to enrich for fragments representing accessible chromatin. Final libraries were assessed for quality and quantified before sequencing.


title: BAT CTCF, CUT&RUN


title: Dairy cow 1, subcutaneous adipose tissue (SAT), ketosis group


title: HAP1_10C_2

description:
Library name: HAP1_10C_2
10 cells


title: HAP1_100C_1

description:
Library name: HAP1_100C_1
100 cells


title: iWAT 4ºC, ATAC-seq


title: Monensin, biol rep 2

city: Warsaw

first: Beata

last: Pyrzynska

state: Mazowieckie

address: Zwirki i Wigury 61

institute: Medical University of Warsaw

description: Library name: Sample 4

data_processing:
sequencing with HiSeq XTen platform in a PE 2x150bp format, with at least 10 million reads
Assembly: The reference genome was UCSC hg19; the BamStats summary method, Isis analysis software (version 2.6.25.19), BEDTools (version 2.17.0), Picard (version 1.128), and DESeq2 (version 1.6.3) were used
Supplementary files format and content: normalized read counts

source_name: Raji

growth_protocol: Raji cells were maintained in RPMI medium supplemented with 10% FBS and antibiotics (pen/strep) with 5% CO2 at 37C

extract_protocol:
RNA extraction using High Pure RNA Isolation Kit (Roche)
libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library kit (Illumina)

treatment_protocol: Treatment with either monensin (0.1 uM) or control vehicle for 18 hours

value: Raji

value: Monensin (0.1 uM)


title: NICD dorsal forebrain progenitor cells, E16.5,  ATAC-seq, Sample 2

description: Library name: NICD E16.5  ATAC-seq Sample 2


title: iWAT 30ºC, ATAC-seq


title: HAP1_10C_1

description:
Library name: HAP1_10C_1
10 cells


title: BAT 4ºC, ATAC-seq


title: CTRL dorsal forebrain progenitor cells, E16.5, ATAC-seq, Sample 3

description: Library name: CTRL E16.5  ATAC-seq Sample 3


title: Monensin, biol rep 1

description: Library name: Sample 3


title: BAT 30ºC, ATAC-seq


title: HAP1_SC_3

description:
Library name: HAP1_SC_3
Single cell


title: Control, biol rep 1

description: Library name: Sample 1

value: Vehicle


title: [GK cells] {[GF-1] [4]

status: Public on Jul 08 2025

city: Chestnut Hill

first: Aurelien

last: CHUARD

state: MA

address: 140 Commonwealth Ave, Higgins Hall, Altindis Lab

department: Biology

institute: Boston College

description: Library name: [IGF4]

data_processing:
Transcriptomic datasets generated from the sequencing were trimmed for low quality reads and adaptor contamination was removed using TrimGalore
Trimmed reads were assembled using Trinity de novo assembly tool (version v2.15.1)59. Coding regions for the assembly were identified using TransDecoder
The identified 65,169 contigs were annotated to identify known genes using Blast2Go61. Counts of reads mapping to the assembled cds in each sample were estimated using the Trinity tool (align_and_estimate_abundance.pl.) These read counts were used to estimate the differential transcript expression using DESeq2
Assembly: UNPE01001373.1
Supplementary files format and content: Excel table representing differentially expressed transcripts included analysis were subject to a false discovery rate (FDR) of ≤ 0.01 and a fold change (FC) of ≥ 1.5

organism: Epinephelus coioides

growth_protocol: Grouper Kidney (GK) cells were maintained in Leibovitz-15 medium (L-15) containing 10% Fetal Bovine Serum (ThermoFisher #A5256801), 1% L-Glutamine (Sigma-Aldrich #G3126), and 1% Penicillin-Streptomycin (Sigma-Aldrich #P4333) at 28°C without CO2.

extract_protocol:
Total RNA were extracted using the RNeasy Plus Mini Kit (Qiagen #74134)
cDNA libraries were prepared using the KAPA C HyperPrep Kit (Roche)

treatment_protocol: GK cells that were serum-starved for 12 hours, followed by 6 hours of stimulation with respective ligands (100 nM) or infection with GIV (MOI 1) for 18 hours

value: Kidney

value: Grouper Kidney (GK)

value: Fibroblasts


title: [GK cells] [IGF-1] [2]

description: Library name: [IGF2]


title: HAP1_SC_2

description:
Library name: HAP1_SC_2
Single cell


title: [GK cells] [IGF-1] [3]

description: Library name: [IGF3]


title: [GK cells] [IGF-1] [1]

description: Library name: [IGF1]


title: [GK cells] [GIV Infection] [3]

description: Library name: [GIV3]


title: [GK cells] [GIV Infection] [2]

description: Library name: [GIV2]


title: CTRL dorsal forebrain progenitor cells, E16.5,  ATAC-seq, Sample 1

description: Library name: CTRL E16.5 ATAC-seq Sample 1

value: dorsal forebrain neural progenitor cells

value: Emx1-Cre Control


title: [GK cells] [GIV-scVILP] [2]

description: Library name: [GIV-scVILP2]


title: [GK cells] [GIV-scVILP] [1]

description: Library name: [GIV-scVILP1]


title: NICD dorsal forebrain progenitor cells, E16.5,  ATAC-seq, Sample 1

description: Library name: NICD E16.5  ATAC-seq Sample 1

value: Emx1-Cre; LSL-NICD


title: Control, biol rep 2

description: Library name: Sample 2


title: [GK cells] [GIV-scVILP] [3]

description: Library name: [GIV-scVILP3]


title: PCC1/PHCF-Gel group rep3

first: Yali

last: Zhou

state: Shanghai

address: No. 100 Haining Road

department: Shanghai General Hospital, School of Medicine

institute: Shanghai Jiao Tong University

description: Library name: PCC-3A

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include genecount and FPKM values for each Sample

source_name: retina

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: retina

tag: group

value: PCC1/PHCF Gel


title: PCC1/PHCF-Gel group rep1

description: Library name: PCC-1A

tag: tissue


title: HAP1_SC_1

description:
Library name: HAP1_SC_1
Single cell


title: [GK cells] [GIV Infection] [1]

description: Library name: [GIV1]


title: [GK cells] [GIV-scVILP] [4]

description: Library name: [GIV-scVILP4]


title: PCC1/PHCF-Gel group rep2

description: Library name: PCC-2A


title: CTRL dorsal forebrain progenitor cells, E16.5,  ATAC-seq, Sample 2

description: Library name: CTRL E16.5  ATAC-seq Sample 2


title: [GK cells] [GIV Infection] [4]

description: Library name: [GIV4]


title: PBS group rep1

description: Library name: OIR-1A

value: PBS


title: Normoxic group rep3

description: Library name: WT-3A

value: Normoxic


title: Normoxic group rep2

description: Library name: WT-2A


title: Normoxic group rep1

description: Library name: WT-1A


title: SRG rat skin: DHT+  FeCl₃, replicate 3

city: Los Angeles

first: Bo

last: Tao

address: 675 Charles E Young Drive

department: Cardiology

institute: University of California Los Angeles

description: Library name: SRG-3

data_processing:
Bulk RNA-seq data were processed using STAR (v2.7.10a) for alignment to the Rattus norvegicus reference genome (Rnor_6.0).  ScRNA-seq data were processed using Cell Ranger (v7.1.0) for demultiplexing and counting.
Gene counts were generated using featureCounts v2.0.3.
Assembly: Rattus norvegicus Rnor_6.0 (Ensembl release 107).
Supplementary files format and content: Bulk RNA-seq: Gene-level expression matrices in CSV format. Rows represent Ensembl gene IDs for Rattus norvegicus; columns represent individual samples. Values represent log2-transformed normalized expression from DESeq2 (using rlog transformation). File names: PBS_CPA_expression.csv, WT_SRG_expression.csv, main_groups_expression.csv, WT_SRG_expression.csv, LPS_DHT_LPS_expression.csv. ScRNA-seq:HDF5 (.h5) format expression matrix file. The file contains gene-by-cell expression count matrix for Rattus norvegicus skin tissue, generated using Cell Ranger (or Seurat/Scanpy). Rows are genes, columns are cell barcodes. Values are raw or normalized counts depending on processing step.

source_name: SRG rat,  DHT + FeCl₃

growth_protocol: Sprague-Dawley rats were housed in a temperature- and humidity-controlled facility with a 12 h light/dark cycle and ad libitum access to food and water.

extract_protocol:
For bulk RNA-seq: Total RNA was extracted from skin tissue using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. For scRNA-seq: Cell pellets were obtained from dissociated skin tissue using enzymatic digestion, followed by centrifugation. Cell pellets were directly used for RNA extraction or single-cell library preparation.
For bulk RNA-seq, RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB), following polyA enrichment or rRNA depletion. For scRNA-seq, chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) were used.

treatment_protocol: (1)Sprague-Dawley(SD) Rats were given vehicle (p.o.) + FeCl₃ (s.c.), DHT (p.o.) + FeCl₃ (s.c.), DHT (p.o.) + LPS (s.c.). (2) SD Rats and SRG rats were given DHT (p.o.) + FeCl₃ (s.c.). (3) SD Rats were given DHT (p.o.) + FeCl₃ (s.c.) with PBS/CPA/IgG/IL-17a treatments, as described in the Methods section.

value: skin

value: SRG

value: DHT (p.o.) + FeCl₃ (s.c.)


title: WT rat skin: DHT+  FeCl₃, replicate 4

description: Library name: WT-4

source_name: WT rat,  DHT + FeCl₃

value: wiid type


title: Rat skin: DHT+  LPS, replicate 2

description: Library name: DHT_LPS-2

value: DHT (p.o.) + LPS (s.c.)


title: SRG rat skin: DHT+  FeCl₃, replicate 2

description: Library name: SRG-2


title: PBS group rep3

description: Library name: OIR-3A


title: Rat skin: DHT+ H₂O, replicate 2

description: Library name: DHT_H2O-2

source_name: WT rat, DHT + H₂O

value: DHT (p.o.) + H₂O (s.c.)


title: Rat skin: DHT+  LPS, replicate 3

description: Library name: DHT_LPS-3


title: Rat skin: DHT+ H₂O, replicate 1

description: Library name: DHT_H2O-1


title: SRG rat skin: DHT+  FeCl₃, replicate 4

description: Library name: SRG-4


title: Rat skin: vehicle + H₂O, replicate 3

description: Library name: H2O-3

source_name: WT rat, vehicle + H₂O

value: vehicle (p.o.) + H₂O (s.c.)


title: Rat skin: DHT+  FeCl₃, replicate 1

description: Library name: DHT_FeCl3-1


title: Rat skin: DHT+  LPS, replicate 1

description: Library name: DHT_LPS-1


title: Rat skin: DHT+ H₂O, replicate 3

description: Library name: DHT_H2O-3


title: WT rat skin: DHT+  FeCl₃, replicate 2

description: Library name: WT-2


title: SRG rat skin: DHT+  FeCl₃, replicate 1

description: Library name: SRG-1


title: Rat skin: vehicle+ LPS, replicate 1

description: Library name: LPS-1

value: vehicle (p.o.) + LPS (s.c.)


title: Rat skin: vehicle + FeCl₃, replicate 1

description: Library name: FeCl3-1

source_name: WT rat, vehicle + FeCl₃

value: vehicle (p.o.) + FeCl₃ (s.c.)


title: PBS group rep2

description: Library name: OIR-2A


title: Rat skin: vehicle + FeCl₃, replicate 2

description: Library name: FeCl3-2


title: WT rat skin: DHT+  FeCl₃, replicate 1

description: Library name: WT-1


title: Rat skin: vehicle+ LPS, replicate 3

description: Library name: LPS-3


title: IRISeq, mouse brain [ST]

city: New York

first: Zehao

last: Zhang

state: NY

address: 1230 York Ave, The Rockefeller University

institute: The Rockefeller University

data_processing:
cDNA data processing: Initial Data Preparation: After the sequencing process, the data is obtained in the form of two sets of FASTQ files: R1 and R2. R1 FASTQ files contain the barcode sequences for receiver bead along with their associated Unique Molecular Identifiers (UMIs). R2 FASTQ files contain the tagmented cDNA sequences. Barcode Mapping and Tagging: The barcode sequences from R1 are mapped to a whitelist of bead barcodes with a tolerance of 1 base pair error. The identified bead barcode is then added as an identifier (ID) for the corresponding sequences in R2. Read2 File Generation and PolyA Trimming: New Read2 files are generated where the name of each sequence in R2 contains the corresponding Read1 barcode. Additionally, any PolyA tails present at the end of the sequences are trimmed to ensure accurate mapping and analysis. Read Mapping to Genome: The filtered and trimmed reads are then mapped to the reference genome using a tool such as STAR(25) (Spliced Transcripts Alignment to a Reference). This step involves aligning the sequences from R2 to the genomic sequences to identify their locations and potential splice sites. Duplicate Removal: After mapping, duplicate reads are identified and removed to eliminate redundant data and ensure accuracy in downstream analysis. This process generates new SAM (Sequence Alignment/Map) files containing the mapped reads with duplicates removed. Gene Count Matrices Generation: From the processed SAM files, gene count matrices are generated for each associated receiver bead. This involves counting the number of reads aligned to each gene for every receiver bead, providing quantitative information about gene expression levels. Beads Connections processing Initial Data Preparation: Following the sequencing process, data from two beads, namely receiver bead and sending beads, are obtained. Each bead connection includes unique molecular identifiers (UMIs) which help in identifying and quantifying individual connection molecules. Additionally, there are two types of reads: R1, which contains the barcode for receiver beads, and R2, which contains the barcodes for receiver beads. The reads are mapped to a whitelist of barcodes with 1 base pair error, including the UMI sequence. Duplicated reads are then filtered, and a csv file is generated with receiver bead, UMI, and sending bead barcode, where each line represents a unique molecular connection between receiver and sending beads. Assembly: STAR_hg19_mm10_RNAseq Supplementary files format and content: Please check below. Annotation column has content description as well.
Assembly: mm39
Supplementary files format and content: IRISeq_gene_count.txt - gene count sparse matrix file
Supplementary files format and content: IRISeq_df_cell.txt - cell annotation csv file
Supplementary files format and content: IRISeq_df_gene.txt - gene annotation csv file
Library strategy: Spatial Transcriptomics

molecule: cytoplasmic RNA

source_name: brain

extract_protocol:
10 um thick mouse brains were cryosectioned, and RNA was hybridized to a barcoded hydrogel bead based array Barcoded beads have a PCR handle, and Template Switching Oligo was utilized to amplify bound nucleic acid molecules.
To capture RNA from tissues, a beads array is generated by mixing ~5 ul of receiver beads and sender beads in 6XSSC buffer in a 1:3 ratio, respectively. Then gel beads are monolayered into a square shape utilizing a gasket barrier of the desired shape and size, and semi-dried for a few minutes until their stabilization on the glass is observed, and no movement is observed. Then, 10-um thick tissue sections are placed on the beads array, and RNA hybridization is performed for ~13 minutes without additional buffer addition to prevent array disturbance. Next, photocleavage of sender beads is performed for ~2 minutes in a UV device (alpha thera AT8001). Library preparation follows protocols40, with slight modifications. Following second strand synthesis, cDNA was released from receiver beads utilizing 0.1 N NaOH and quenched with 1 M Tris-HCl pH 7.0, followed by 1X Ampure beads purification following manufacturer recommendations. cDNA amplification followed protocols40 utilizing SMRT primer and Truseq_Read1. Amplified cDNA tagmentation is adapted from (21). For receiver beads-sender beads DNA interactions library preparation, after collecting supernatant for cDNA library preparation, beads were washed with TE-TW buffer adapted from protocols40, and then resuspended in ~25 ul of H2O. Then, DNA connections between sender and receiver beads were amplified by performing on-bead PCR and utilizing the NEBnext master mix.  0.25 uM of P5_Truseq_Read1 primers and Truseq_Read2 indexed sequencing primers were utilized for PCR.  After PCR, perform gel extraction of the connections band which should be approximately ~250 bp in size.

value: brain

value: multiplexed sample:Caloric restriction and Ad libitum


title: Rat skin: DHT+  FeCl₃, replicate 2

description: Library name: DHT_FeCl3-2


title: Rat skin: DHT+  FeCl₃, replicate 3

description: Library name: DHT_FeCl3-3


title: Rat skin: vehicle + FeCl₃, replicate 3

description: Library name: FeCl3-3


title: WT rat skin: DHT+  FeCl₃, replicate 3

description: Library name: WT-3


title: Mv4;11 12hrs PMR 1uM n3

city: Canberra

first: Zaka

last: Yuen

address: Australian National University, Canberra ACT 2601

institute: Australian National University

description:
Library name: Sample_48_S48_R1_001
counts_pol1.txt
info_pol1.txt

data_processing:
Transcript abundance was quantified using Salmon (v1.5.2) in quasi-mapping mode against the GENCODE v37 human transcriptome (GRCh38.p13).
Transcript-level quantification estimates were summarized to the gene level using tximport in R.
Gene-level counts were normalized using the “lengthScaledTPM” method and used for downstream differential expression analysis in DESeq2.
Assembly: GRCh38.p13 (GENCODE v37)
Supplementary files format and content: Two TSV files contain gene-level count matrices generated by tximport. For KG-1 samples, counts_pol1_batch2_trimmed.txt includes 32 high-quality samples from batch 2 (n=4 per condition), with sample details provided in info_pol1_batch2.txt. For Mv4;11 samples, counts_pol1.txt includes all 48 samples from batch 1 (n=3 per condition), from which 24 Mv4;11 samples were used, as detailed in info_pol1.txt. In both files, column names match the sample IDs (with _R1_001 removed).

source_name: Cell line

growth_protocol: KG-1 and Mv4;11 AML cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 1% penicillin/streptomycin, and maintained at 37 °C in 5% CO₂.

extract_protocol:
Total RNA was extracted using the Nucleospin RNA kit (Macherey-Nagel, 740955.250) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep Kit. Libraries were pooled and sequenced by the Biomolecular Resource Facility (BRF) at the Australian National University.

treatment_protocol: Cells were treated with 1 µM PMR-116, 1 µM CX-5461, or vehicle control (50 mM citric acid, 50 mM NaH₂PO₄) for 3 or 12 hours.

value: Cell line

value: AML cells


title: Rat skin: vehicle+ LPS, replicate 2

description: Library name: LPS-2


title: Rat skin: vehicle + H₂O, replicate 2

description: Library name: H2O-2


title: Mv4;11 12hrs PMR Veh n3

description:
Library name: Sample_47_S47_R1_001
counts_pol1.txt
info_pol1.txt

value: vehicle (PMR-116)


title: Rat skin: vehicle+ H₂O, replicate 1

description: Library name: H2O-1


title: Mv4;11 12hrs PMR 1uM n2

description:
Library name: Sample_46_S46_R1_001
counts_pol1.txt
info_pol1.txt


title: Mv4;11 12hrs PMR Veh n2

description:
Library name: Sample_45_S45_R1_001
counts_pol1.txt
info_pol1.txt


title: Mv4;11 12hrs PMR Veh n1

description:
Library name: Sample_43_S43_R1_001
counts_pol1.txt
info_pol1.txt


title: Mv4;11 12hrs CX Veh n2

description:
Library name: Sample_39_S39_R1_001
counts_pol1.txt
info_pol1.txt

value: vehicle (CX-5461)