title: Fa2N4_SEQ_Veh_RSM3

city: Groningen

first: Jingyuan

last: Fu

address: Hanzeplein 1

department: Department of Genetics

country: Netherlands

institute: University Medical Center Groningen

description:
Library name: RNAFa2N4S43
Illumina Sequence A01426

data_processing:
To quantify gene expression levels, featureCounts (v1.5.0-p3) was used. Downstream data analysis was performed in R (v4.3.1). DESeq2 was used to analyze DE genes (utilizing the Wald test) in the conditions versus controls30. The resulting P-values were adjusted using Benjamini and Hochberg’s method to control the false discovery rate (FDR). p ≤ 0.05 was set as the threshold for significant differential gene expression. To generate plots with ggplot2_4.0.0 and gene annotation with org.Hs.eg.db_3.22.0 and AnnotationDbi_1.72.0. Follow-up gene enrichment analysis was performed using the Gene Ontology (GO) Term and MSigDB Hallmarks datasets in iPathwayGuideTM (AdvaitaBio Corporation, https://ipathwayguide.advaitabio.com/)31,32 and with Clusterprofiler33 for the network analysis. To visualize the .csv output from iPathwayGuide, we used ggplot2_4.0.0 in R to create dotplots. Additional visual enhancements in R were applied using scales_1.4.0, tidyselect_1.2.1 and RColorBrewer_1.1-3.
Assembly: ensembl_109_homo_sapiens_grch38_primary
Supplementary files format and content: gene_count.xls containing the normalzied gene counts

source_name: Liver

growth_protocol: Cell culture HepG2 cells (ATCC HB-8065), Manassas, Virginia, USA) were cultured in DMEM with GlutaMAX (10569010, Thermo Fisher Scientific, Waltham, Massachusetts, USA) containing 25 mM glucose and supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% (A5256701, Gibco, Thermo Fisher Scientific) and 1% penicillin-streptomycin (15140122, Thermo Fisher Scientific). Fa2N-4 cells24 were obtained from Tebubio (IFH15, Tebubio, Le Perray-en-Yvelines, France) and cultured on collagen-coated plates (0.02 mg/mL rat tail collagen I (10.9 mg/mL stock, 354249, Corning, New York, USA) diluted in PBS (14190-169, Thermo Scientific). Cells were maintained in Williams E medium with GlutaMax (32551087, Gibco, Thermo Fisher Scientific) containing 11 mM glucose and supplemented with 10% heat-inactivated FBS, 1% penicillin-streptomycin, 20 mU/mL insulin (100 U/mL injection vial, Sanofi, Paris, France) and 100 nM dexamethasone (20 mg/mL stock, 9265331, Centrafarm, The Netherlands). For experiments, HepG2 and Fa2N-4 cells were seeded in 24-well plates at a density of 1.05 x 105 cells/cm² and incubated overnight to reach 60-70% confluence prior to stimulation. Cell line authentication was confirmed by short tandem repeat (STR) profiling (Eurofins Genomics Europe Food/Environment/White Biotech Products & Services GmbH, Eurofins, Luxembourg City, Luxembourg). Cells were tested negative for mycoplasma contamination by PCR.

extract_protocol:
RNA isolation The RNeasy mini kit (74106, Qiagen, Aarhus, Denmark) was used to lyse the cells and isolate the RNA according to the manufacturer's protocol. Samples prepared for RNA sequencing were treated with RNase-free DNase kit (79254, Qiagen).
RNA sequencing RNA quality and quantity were assessed using an Agilent 5400, and all samples had RNA integrity scores above 8. Sequencing was performed at Novogene (Cambridge, UK), which performed non-strand-specific mRNA library preparation with poly (A) enrichment. Sequencing reads were aligned to the genome reference ID ‘ensembl_109_homo_sapiens_grch38_primary’ using HISAT2 (v2.0.5).

treatment_protocol: Induction of MASLD To mimic hepatic steatosis in vitro, HepG2 and Fa2N-4 cells (up to passage 22 and 8, respectively) were stimulated with fructose (D-(−)-Fructose, F0127, Sigma, Merck KGaA) and a 1:2 ratio of palmitic acid and oleic acid (03880 and P9767, Sigma-Aldrich, Merck KGaA). A free fatty acid-BSA complex was prepared by dissolving 10 mM palmitic acid or oleic acid (dissolved in 100% EtOH, dried under gaseous N2) in 10% BSA (A6003, Sigma, Merck KGaA). The solution was adjusted to pH 7.4. An equal volume of BSA was used as a control. Cells were stimulated with 1mM fructose and 600 µM FFA-BSA complex for 48h, unless specified otherwise. Resmetirom (MGL-3196, catalog #NC1772005, Selleckchem, Houston, Texas, USA,) was dissolved in DMSO and was added 24h after the induction of steatosis at 200 µM unless otherwise specified. D-(+)-Glucose (catalog G8644-100ML, Sigma, Merck KGaA) and low-glucose containing DMEM (11885084, Gibco, Thermo Fisher Scientific) were used to modulate glucose concentration in specified experiments.

value: Liver

value: Hepatocyte

value: SEQ Vehicle Resmetirom 3


title: MAR-3.6.2, 24 hrs 415 (3)

status: Public on Mar 15 2026

type: SRA

city: Duarte

first: Le Xuan Truong

last: Nguyen

state: CA

address: 1500 E. Duarte Road

department: Hematology/Bone Marrow T MC

country: USA

institute: City of Hope

description: Library name: 52584_HTB-415 3.6.2 3

library_source: transcriptomic

data_processing:
NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.
Assembly: GRCh38.p14 RNA sequences (Transcriptome)
Supplementary files format and content: comma-delimited csv file includes raw counts for each samples

molecule: total RNA

organism: Homo sapiens

source_name: Bone Marrow Cells

extract_protocol:
RNA was harvested using miRNeasy Mini Kit (Qiagen). DNA digestion was conducted during RNA extraction. 10 ug of total RNA was prepared for the downstream processing for RNA-sequencing.
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep Kit following manufacturer's protocols.

tag: tissue

value: Bone Marrow Cells

tag: cell line

value: Patient-drived primary CD34+CD38- blast

tag: cell type

value: Acute Myeloid Leukemia


title: Penn_F2 donor, male, gestational week 18, non-diseased, outflow tract, ATAC, replicate 2

city: Philadelphia

first: William

last: Gao

state: PA

address: 415 Curie Blvd

department: Genetics

institute: UNIVERSITY OF PENNSYLVANIA

description: Library name: Fetal-OFT-2

library_source: genomic single cell

data_processing:
Processing of these raw data are described in "RNA/internal_datasets" and "ATAC/internal_datasets" of this github repository:  https://github.com/wgao688/Human-cardiac-multiome-analysis. Briefly, the raw FASTQ files were aligned to the hg38 reference genome using STARSolo (v2.7.11a) to produce count matrices for snRNA-seq. These count matrices were then used for downstream analyses (see Github repository and Methods section). For snATAC-seq, cellranger-atac (cellranger-atac-2.1.0) was used to produce fragment files, which were the inputs for downstream processing with SnapATAC2.
Assembly: GRCh38, version 44 (Ensembl 110)
Supplementary files format and content: "Processed data are named GSE290367_integrated_RNA_adata.h5ad.gz" and GSE290367_integrated_RNA_adata.h5ad.gz". These include the aggregated datasets after combining all internal data (denoted as "Penn") with external datasets. This corresponds to the datasets described in Fig. 1a (RNA) and Fig. 2a (ATAC). The processing scripts are located in the "RNA/" and "ATAC/" directories of this github repository: https://github.com/wgao688/Human-cardiac-multiome-analysis"

molecule: genomic DNA

source_name: heart

extract_protocol:
Nuclei isolation from flash frozen human donor hearts
All 19 snRNA-seq libraries were generated using the Dropseq protocol. All 11 snATAC-seq libraries were generated using the 10X Genomics ATAC v1 kit.

value: heart


title: Fa2N4_SEQ_Veh_RSM2

description:
Library name: RNAFa2N4S42
Illumina Sequence A01426

tag: genotype

value: WT

tag: treatment

value: SEQ Vehicle Resmetirom 2

tag: batch


title: Penn_F5 donor, male, gestational week 14, non-diseased, outflow tract, ATAC

description: Library name: Fetal-OFT-14wk


title: Penn_F2 donor, male, gestational week 18, non-diseased, outflow tract, ATAC, replicate 1

description: Library name: Fetal-OFT-1


title: BMDM cells, DMSO, rep2 (TT)

city: Guangzhou

first: dingdang

last: Yu

address: No. 106, Zhongshan 2nd Road, Yuexiu District

country: China

institute: Guangdong Provincial People's Hospital

description:
Library name: DMSO_TT_rep2
Transient transcriptome sequencing (TT-seq)

data_processing:
For ATAC-seq, after trimming the adaptors and low-quality reads with Trim Galore v0.6.6, the remaining reads were align to the mm10 genome using Bowtie 2 v2.3.5.1.
SAMtools v1.11 and Picard v2.23.3 were used to remove low mapping quality reads, mitochondrion DNA and PCR duplicates.
Reads counts adjusted to reads per kilobase per million mapped reads (RPKM) using deeptools v2.5.7.
Assembly: mm10
Supplementary files format and content: bigWig

organism: Mus musculus

source_name: bone marrow

extract_protocol:
For ATAC-seq assays,cells were lysed in ice-cold lysis buffer, followed by resuspending in fragmentation buffer and incubation at 37 ℃ for 30 min. The fragmented DNA products were extracted using ATAC DNA Extract Beads.
ATAC-seq library was performed according to the manual of the Hyperactive ATAC‐Seq Library Prep Kit for Illumina (Vazyme, TD711).

treatment_protocol: 200 nM ATRA or DMO for 24hr

value: bone marrow

value: BMDM

value: macrophage

value: DMSO


title: Fa2N4_SEQ_Veh_RSM1

description:
Library name: RNAFa2N4S41
Illumina Sequence A01426

value: SEQ Vehicle Resmetirom 1


title: Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, ATAC, replicate 1

description: Library name: Fetal-LV-1


title: intestinal MPS EV-A71 1

city: Bunkyo-ku

first: Kazuo

last: Takayama

state: Tokyo

address: Yushima 1-5-45

country: Japan

institute: Institute of Science Tokyo

description: Library name: intestinal MPS EV-A71 1

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 platform with the paired-end mode.
Illumina RTA version 4.12.2 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by cutadapt v4.6. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.7.11a with the GENCODE (release 32, GRCh38.p13) gtf file.
The uniquely and properly mapped reads were used for further analysis. Raw read counts were calculated using htseq-count v2.0.5 with the GENCODE gtf file. Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: ES cell-derived intestinal MPS

extract_protocol:
Total RNA was isolated using ISOGENE (Cat# 319-90211, NIPPON GENE).
Library preparation was performed using an Illumina Stranded mRNA Prep,Ligation Kit (Cat# 20040532, Illumina) according to the manufacturer’s instructions.

treatment_protocol: The human ES cell-derived intestinal MPS was infected with EV-A71 (0.1 multiplicity of infection (MOI)) and cultured for 7 days.

value: ES cell-derived intestinal MPS

value: intestinal MPS

value: wild type

value: EV-A71 infected

tag: time

value: 7 dpi


title: BMDM cells, DMSO, rep1 (TT)

description:
Library name: DMSO_TT_rep1
Transient transcriptome sequencing (TT-seq)


title: BMDM cells, DMSO, rep2 (RNA)

description: Library name: DMSO_RNA_rep2


title: Penn_F5 donor, male, gestational week 14, non-diseased, left and right ventricle, ATAC

description: Library name: Fetal-LRV-14wk


title: Penn_F2 donor, male, gestational week 18, non-diseased, left and right ventricle, ATAC, replicate 1

description: Library name: Fetal-LRV-1


title: BMDM cells, DMSO, rep3 (RNA)

description: Library name: DMSO_RNA_rep3


title: FG214-WT-EN+imidazole

type: protein

city: Boston

first: Stephen

last: Gisselbrecht

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics, Department of Medicine

institute: Brigham and Women's Hospital

hyb_protocol: First, microarrays were double stranded by on-slide primer extension, as described in Berger et al. (Berger et al. Nat Biotechnol. 2006 (PMID 16998473)). The primer extension mixture contains Cy3-conjugated dUTP, to allow for quantification of the relative amount of double stranded DNA on each spot. Double stranded microarrays were pre-wetted in standard phosphate buffered saline (PBS) (10mM PO43-, 137 mM NaCl, 2.7 mMKCl, pH7.4) / 0.01% Triton-X 100 for 5 minutes. PBS / 2% (wt/vol) nonfat dried milk (Sigma) was applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarray was incubated for 1 hour at room temperature. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% (vol/vol) Triton X-100 for 2 min. Proteins were diluted in a 75-μl protein binding mixture containing PBS / 2% (wt/vol) milk or EN (138 mM potassium glutamate, pH 7.2, 12 mM sodium bicarbonate, 0.8 mM magnesium chloride) / 2% (wt/vol) milk, 51.3 ng/μl salmon testes DNA (Sigma), 0.2 μg/μl bovine serum albumin (New England Biolabs), 32.67 micromolar zinc acetate, and, where indicated, 500 mM imidazole. Pre-incubated protein binding mixtures were applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 hour at room temperature. Microarrays were again washed once with PBS/ 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS/ 0.01% (vol/vol) Triton X-100 for 2 minutes. Alexa-488-conjugated mouse monoclonal anti-HA antibody (Invitrogen A-21287) was diluted to 50μg/ml in PBS / 2% (wt/vol) milk and applied to individual chambers of an eight-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 30 minutes at room temperature. Microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each incubation step, microarrays and cover slips were disassembled in a staining dish filled with the first wash solution. All washes were performed in Coplin jars at room temperature on an orbital shaker at 125 rpm. Following each series of washes, microarrays were rinsed in PBS and slowly removed to ensure removal of detergent and uniform drying.

scan_protocol: Cy3 signal was scanned to assess double-stranding efficiency and Alexa488 signal was scanned at multiple photomultiplier tube gain settings on a Molecular Devices GenePix 4400A microarray scanner.

data_processing: The scanned images were analyzed with GenePix software to produce separate .gpr files for each chamber associating background-subtracted median signal intensity at a probe to probe sequence; scans were combined with Masliner and the resulting file was normalized to Cy3 signal and analyzed with the Universal PBM Analysis Suite (Berger et al., Nature Biotechnology 2006) to report Enrichment scores and Median Signal Intensity for each 8-mer in the processed data files.

molecule: protein

organism: Fimbriimonas ginsengisoli

source_name: bacterial expression and purification

label_protocol: Agilent microarrays (AMADID #030236) containing all 10-nt sequences were made double-stranded by primer annealing and on-array extension with Cy3-labelled nucleotides to monitor double-stranding efficiency; HA-tagged proteins were detected with Alexa488-labelled anti-HA antibody.

growth_protocol: Constructs of FG214 wild type and H175I were generated with C-terminal human influenza hemagglutinin (HA) and 6His tags.

extract_protocol: The cells were lysed by sonification, and the lysate was cleared by centrifuging at 10,000 x g for 30 minutes at 4°C. The supernatant was collected and filtered through a 0.2 µm syringe filter. For affinity purification, the protein was loaded onto a 5 mL HisTrap (Cytiva) column preequilibrated with Buffer A. The column was washed with 10 column volumes (CVs) of Buffer A before eluting the protein with buffer B (50mM Tris-HCl pH 8.0, 500 mM NaCl, 500 mM imidazole). The eluate was applied to a Superdex 200 10/300 (Cytiva) column preequilibrated with assay buffer (50 mM sodium phosphate pH 7.0 and 50 mM NaCl).

treatment_protocol: FG214 was recombinantly expressed in BL21(DE3) E. coli (Stratagene) in M9 minimal media plus 1 mM 5-aminolevulinic acid at 16°C overnight. Expression was induced with 1 mM isopropyl β-D-1-thiogalactopyranoside.

value: bacterial


title: Penn_F3 donor, male, gestational week 8, non-diseased, whole heart, ATAC

description: Library name: Fetal-heart-8wk


title: ND15840 donor, female, age 91, non-diseased, right ventricle, replicate 3

description: Library name: ND15840-RV-3rd


title: ND15755 donor, male, age 65, non-diseased, left ventricle, ATAC, replicate 1

description: Library name: LV-NDRI15755_10k


title: No Treatment 415 (3)

description: Library name: 52578_HTB-415 Ctrl 3

value: Bone Marrow Cells


title: BMDM cells, H3K4me3, DMSO, rep2

description: Library name: DMSO_H3K4me3_rep2

library_source: genomic

data_processing:
For ATAC-seq, after trimming the adaptors and low-quality reads with Trim Galore v0.6.6, the remaining reads were align to the mm10 genome using Bowtie 2 v2.3.5.1.
SAMtools v1.11 and Picard v2.23.3 were used to remove low mapping quality reads, mitochondrion DNA and PCR duplicates.
Reads counts adjusted to reads per kilobase per million mapped reads (RPKM) using deeptools v2.5.7.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: Cut&Tag

tag: cut&tag antibody


title: ND15840 donor, female, age 91, non-diseased, right ventricle, replicate 1

description: Library name: ND15840-RV-1st

library_source: transcriptomic single cell

molecule: polyA RNA


title: Fa2N4_SIM_RSM1

description:
Library name: RNAFa2N4S37
Illumina Sequence A01426

value: Liver

value: Hepatocyte

value: SIM Resmetirom 1


title: ND15840 donor, female, age 91, non-diseased, right atrium, replicate 3

description: Library name: ND15840-RA-4th

value: heart


title: mouse_colorectal_organoid_control_biological_replicate_2

city: Beijing

first: Qingtao

last: Meng

address: No.10, West Tou Tiao, Youan Men Wai, Fengtai District

institute: capital Medical University

description:
Library name: RNA_seq_C2
Colorectal organoid derived from a 6–8-week-old female Mus musculus, no treatment, biological replicate 2.

data_processing:
Raw sequencing reads were processed using Trimmomatic (v0.39) to remove adapter sequences and low-quality reads. Clean reads were aligned to the GRCm39 mouse reference genome using HISAT2 (v2.2.1). Gene-level read counts were quantified with featureCounts (Subread v2.0.8).
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text file includes raw read counts for each sample.
Supplementary files format and content: Tab-delimited text file includes FPKM expression values for each sample.

source_name: Colorectal organoids

growth_protocol: Female C57BL/6J mice (6–8 weeks old, 20–22 g)

extract_protocol:
The colon tissue extracted from mice was cut into small sections. Following a wash with PBS, the small tissue fragments underwent digestion with Gentle Cell Dissociation Reagent (GCDR) (100-1077, Stemcell) in a shaking state at 20 rpm for 20 minutes, and the resulting mixture was filtrated through a 70-μm filter. After a subsequent centrifugation, the pellet was resuspended in cold DMEM/F12 medium (C11330500BT, Gibco). The centrifugation and wash were repeated, and the pellet was suspended in IntestiCult organoid growth medium (06005, Stemcell), and an equivalent volume of Matrigel matrix was added. The mixture was poured into a 24-well plate. Finally, 500 μL of IntestiCult organoid growth medium was added. Total RNA was extracted from all samples using TRIzol™ reagent (Invitrogen, Thermo Fisher Scientific).
RNA-Seq experiment was performed by Novogene, employing standard Illumina sequencing procedures for mRNA-seq. Total RNA was used for mRNA enrichment with poly(T) oligo-attached magnetic beads, followed by fragmentation prior to cDNA synthesis. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The resulting cDNA underwent end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification. Library quality and concentration were assessed using a Qubit 2.0 Fluorometer and an Agilent 2100 Bioanalyzer. Quantified libraries will be pooled and sequenced on Illumina platforms (NovaSeq 6000), according to effective library concentration and data amount.

treatment_protocol: Organoids were treated with 10 pM NAP for 48 hours, and control organoids were treated with PBS as vehicle control under identical conditions.

value: Colorectal organoids

value: Control


title: intestinal MPS Mock 2

description: Library name: intestinal MPS Mock 2

value: mock


title: Fa2N4_SIM_Veh_RSM4

description:
Library name: RNAFa2N4S36
Illumina Sequence A01426

value: WT

value: SIM Vehicle Resmetirom 4


title: ND15840 donor, female, age 91, non-diseased, right atrium, replicate 1

description: Library name: ND15840-RA-2nd-run1n2


title: No Treatment 415 (2)

description: Library name: 52577_HTB-415 Ctrl 2

value: Patient-drived primary CD34+CD38- blast

value: Acute Myeloid Leukemia


title: Fa2N4_SEQ_RSM4

description:
Library name: RNAFa2N4S48
Illumina Sequence A01426

value: SEQ Resmetirom 4


title: ND15840 donor, female, age 91, non-diseased, left ventricle, replicate 2

description: Library name: ND15840-LV-2nd-run1n2


title: K1647 donor, male, age 34, non-diseased, left ventricle, ATAC, replicate 1

description: Library name: LV-K1647-run-1


title: Fa2N4_SEQ_RSM3

description:
Library name: RNAFa2N4S47
Illumina Sequence A01426

value: SEQ Resmetirom 3


title: BMDM cells, H3K27ac, ATRA, rep2

description: Library name: ATRA_H3K27ac_rep2

value: bone marrow

value: BMDM

value: macrophage

value: ATRA


title: mouse_colorectal_organoid_control_biological_replicate_1

description:
Library name: RNA_seq_C1
Colorectal organoid derived from a 6–8-week-old female Mus musculus, no treatment, biological replicate 1.


title: K1584 donor, male, age 22, non-diseased, left ventricle, ATAC, replicate 2

description: Library name: LV-K1584-run-2


title: Fa2N4_SIM_Veh_RSM3

description:
Library name: RNAFa2N4S35
Illumina Sequence A01426

value: Liver

value: SIM Vehicle Resmetirom 3


title: K1485 donor, male, age 78, non-diseased, left ventricle, ATAC, replicate 1

description: Library name: LV-K1485-run-1


title: ND15755 donor, male, age 65, non-diseased, right ventricle, replicate 2

description: Library name: ND15755-RV-2nd


title: Fa2N4_SEQ_RSM1

description:
Library name: RNAFa2N4S45
Illumina Sequence A01426

value: Hepatocyte

value: SEQ Resmetirom 1


title: YS_poly

city: Chengdu

first: Xinpu

last: Tang

state: Sichuan

address: Guoxue Alley, Chengdu

institute: West China Hospital

description: Library name: Sample12

data_processing:
CLC Genomics Workbench V11.0.1
Assembly: GRCh38/hg38 for human and GRCm38/mm10 for mouse
Supplementary files format and content: tab-delimited text files containing gene expression matrices.
Supplementary files format and content: The content includes gene identifiers with corresponding FPKM values for each sample

source_name: Skin

extract_protocol:
Trizol-LS(for RNA extraction from liquid)
The library construction protocol in the file is a standard Illumina-compatible method involving mRNA purification from total RNA using poly-T magnetic beads, fragmentation with divalent cations, random hexamer-primed first-strand cDNA synthesis followed by RNaseH degradation and second-strand synthesis, end blunting and adenylation, hairpin adaptor ligation, size selection of 370-420 bp fragments with AMPure XP beads, PCR amplification, and quality assessment via Qubit fluorometry, Agilent 2100 insert size detection, and qRT-PCR effective concentration quantification.

value: Skin

value: Melanoma Cell

value: Polysome  fractions


title: Fa2N4_SIM_Veh_RSM1

description:
Library name: RNAFa2N4S33
Illumina Sequence A01426

value: WT

value: SIM Vehicle Resmetirom 1


title: ND15755 donor, male, age 65, non-diseased, left ventricle, replicate 2

description: Library name: ND15755-LV-2nd-run1234

value: heart


title: YS_mono

description: Library name: Sample11

value: Monosome fractions


title: YS_input

description: Library name: Sample10

value: Polysome input


title: BMDM cells, H3K27ac, ATRA, rep1

description: Library name: ATRA_H3K27ac_rep1


title: ND15840 donor, female, age 91, non-diseased, right ventricle, replicate 2

description: Library name: ND15840-RV-2nd


title: Fa2N4_SEQ_RSM2

description:
Library name: RNAFa2N4S46
Illumina Sequence A01426

value: SEQ Resmetirom 2


title: Fa2N4_MASLD_3

description:
Library name: RNAFa2N4S31
Illumina Sequence A01426

value: MASLD (600 uM FFA) 3


title: Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, ATAC, replicate 2

description: Library name: Fetal-LV-2


title: K1485 donor, male, age 78, non-diseased, left ventricle, ATAC, replicate 2

description: Library name: LV-K1485-run-2


title: Fa2N4_MASLD_2

description:
Library name: RNAFa2N4S30
Illumina Sequence A01426

value: MASLD (600 uM FFA) 2


title: K1783 donor, male, age 69, non-diseased, left ventricle, replicate 3

description: Library name: K1783-LV-RE-FACS


title: YP_mono

description: Library name: Sample8


title: Fa2N4_MASLD_1

description:
Library name: RNAFa2N4S29
Illumina Sequence A01426

value: MASLD (600 uM FFA) 1


title: K1783 donor, male, age 69, non-diseased, left ventricle, replicate 1

description: Library name: K1783-LV-FACS


title: K1488 donor, male, age 81, non-diseased, left ventricle, ATAC, replicate 1

description: Library name: LV-K1488-run-1


title: K1739 donor, male, age 52, non-diseased, left ventricle, replicate 2

description: Library name: K1739-LV-nonFACS


title: YP_input

description: Library name: Sample7


title: Fa2N4_NT_4

description:
Library name: RNAFa2N4S28
Illumina Sequence A01426

value: Negative ctrl (BSA) 4


title: K1739 donor, male, age 52, non-diseased, left ventricle, replicate 1

description: Library name: K1739-LV-FACS


title: BMDM cells, RPB1, ATRA, rep1

description: Library name: ATRA_RPB1_rep1

value: bone marrow

value: BMDM

value: macrophage

value: ATRA


title: BMDM cells, ATRA, rep1 (TT)

description:
Library name: ATRA_TT_rep1
Transient transcriptome sequencing (TT-seq)


title: K1727 donor, male, age 40, non-diseased, left ventricle, replicate 2

description: Library name: K1727-LV-nonFACS


title: Fa2N4_SIM_RSM3

description:
Library name: RNAFa2N4S39
Illumina Sequence A01426

value: Liver

value: Hepatocyte

value: SIM Resmetirom 3


title: Ang II 8

first: Zhiping

last: Liu

state: Guangdong

address: No. 855, East Xingye Avenue

institute: Jinan University

description: Library name: WT_A_8

data_processing:
CLC Genonimcs Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequencing using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost: 3 deletion cost 3: lengh fraction: 0.8 similarity fraction: 0.8)
Read cont extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: aorta

growth_protocol: Mice were euthanized at days 7 and aortas without adventitial tissues after saline or Ang II treatment were collected.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq library Pret Kit following manufacturer's protocols.

treatment_protocol: 8- to 12-week male Apoe-/- mice were infused with saline  (0.9% sodium chloride) or Ang II (1,000 ng/kg/min) by Alzet mini-osmotic pumps (Alzet, Model 2004, Durect Corporation, CA, USA). Seven days after implantation, mice were anesthetized and the aortas without adventitial tissues were collected.

value: aorta

tag: strain

value: Ang II

value: Day 7


title: BMDM cells, ATRA, rep2 (TT)

description:
Library name: ATRA_TT_rep2
Transient transcriptome sequencing (TT-seq)

value: WT


title: Fa2N4_NT_3

description:
Library name: RNAFa2N4S27
Illumina Sequence A01426

value: Negative ctrl (BSA) 3


title: Fa2N4_SIM_RSM4

description:
Library name: RNAFa2N4S40
Illumina Sequence A01426

value: SIM Resmetirom 4


title: K1718 donor, male, age 33, non-diseased, left ventricle, replicate 2

description: Library name: K1718-LV-nonFACS

value: heart


title: K1727 donor, male, age 40, non-diseased, left ventricle, replicate 1

description: Library name: K1727-LV-FACS


title: Ang II 7

description: Library name: WT_A_7


title: ND15840 donor, female, age 91, non-diseased, right atrium, replicate 2

description: Library name: ND15840-RA-3rd


title: Fa2N4_NT_2

description:
Library name: RNAFa2N4S26
Illumina Sequence A01426

value: Negative ctrl (BSA) 2


title: Fa2N4_NT_1

description:
Library name: RNAFa2N4S25
Illumina Sequence A01426

value: Negative ctrl (BSA) 1


title: K1702 donor, male, age 59, non-diseased, left ventricle, replicate 1

description: Library name: K1702-LV-RE-FACS


title: Ang II 6

description: Library name: WT_A_6


title: Ang II 5

description: Library name: WT_A_5


title: K1647 donor, male, age 34, non-diseased, left ventricle, replicate 1

description: Library name: K1647-LV-FACS


title: HepG2_SEQ_RSM3

description:
Library name: RNAHepG2S23
Illumina Sequence A01426

value: SEQ Resmetirom 3


title: HepG2_SEQ_RSM4

description:
Library name: RNAHepG2S24
Illumina Sequence A01426

value: SEQ Resmetirom 4


title: Ang II 3

description: Library name: WT_A_3


title: Fa2N4_SIM_RSM2

description:
Library name: RNAFa2N4S38
Illumina Sequence A01426

value: SIM Resmetirom 2


title: K1617 donor, male, age 64, DCM, left ventricle, replicate 4

description: Library name: K1617-LV-FACS-KAPA


title: HepG2_SEQ_RSM2

description:
Library name: RNAHepG2S22
Illumina Sequence A01426

value: SEQ Resmetirom 2


title: ND15840 donor, female, age 91, non-diseased, left ventricle, replicate 1

description: Library name: ND15840-LV-1st-run1n2


title: K1617 donor, male, age 64, DCM, left ventricle, non-sorted, replicate 2

description: Library name: K1617-LV-2nd


title: Penn_F2 donor, male, gestational week 18, non-diseased, left and right ventricle, ATAC, replicate 2

description: Library name: Fetal-LRV-2


title: ND15840 donor, female, age 91, non-diseased, left ventricle, replicate 3

description: Library name: ND15840-LV-3rd


title: Ang II 2

description: Library name: WT_A_2


title: HepG2_SEQ_RSM1

description:
Library name: RNAHepG2S21
Illumina Sequence A01426

value: SEQ Resmetirom 1


title: K1584 donor, male, age 22, non-diseased, left ventricle, replicate 1

description: Library name: K1584-LV-FACS


title: Fa2N4_SIM_Veh_RSM2

description:
Library name: RNAFa2N4S34
Illumina Sequence A01426

value: Liver

value: SIM Vehicle Resmetirom 2


title: BMDM cells, DMSO, rep1 (ATAC)

description: Library name: DMSO_ATAC_rep1

value: bone marrow

value: BMDM

value: macrophage

value: DMSO


title: HepG2_SEQ_Veh_RSM4

description:
Library name: RNAHepG2S20
Illumina Sequence A01426

value: Hepatocyte

value: WT

value: SEQ Vehicle Resmetirom 4


title: ND15755 donor, male, age 65, non-diseased, atria, replicate 2

description: Library name: ND15755-Atr-3rd

value: heart


title: K1783 donor, male, age 69, non-diseased, left ventricle, replicate 4

description: Library name: K1783-LV-RE-nonFACS


title: YP_poly

description: Library name: Sample9

value: Skin

value: Melanoma Cell

value: Polysome  fractions


title: BMDM cells, DMSO, rep2 (ATAC)

description: Library name: DMSO_ATAC_rep2


title: HepG2_SEQ_Veh_RSM2

description:
Library name: RNAHepG2S18
Illumina Sequence A01426

value: SEQ Vehicle Resmetirom 2


title: Saline 7

description: Library name: WT_S_7

value: aorta

value: Saline

value: Day 7


title: K1570 donor, male, age 73, non-diseased, left ventricle, replicate 2

description: Library name: K1570-LV-nonFACS


title: K1570 donor, male, age 73, non-diseased, left ventricle, replicate 1

description: Library name: K1570-LV-FACS


title: HepG2_SEQ_Veh_RSM1

description:
Library name: RNAHepG2S17
Illumina Sequence A01426

value: Liver

value: SEQ Vehicle Resmetirom 1


title: Saline 6

description: Library name: WT_S_6


title: ND15755 donor, male, age 65, non-diseased, right ventricle, replicate 1

description: Library name: ND15755-RV-1st


title: ND15755 donor, male, age 65, non-diseased, right ventricle, replicate 3

description: Library name: ND15755-RV-3rd


title: Fa2N4_SEQ_Veh_RSM4

description:
Library name: RNAFa2N4S44
Illumina Sequence A01426


title: K1702 donor, male, age 59, non-diseased, left ventricle, replicate 2

description: Library name: K1702-LV-RE-nonFACS


title: HepG2_SIM_RSM4

description:
Library name: RNAHepG2S16
Illumina Sequence A01426

value: SIM Resmetirom 4


title: BMDM cells, ATRA, rep1 (ATAC)

description: Library name: ATRA_ATAC_rep1

value: bone marrow

value: BMDM

value: ATRA


title: K1549 donor, male, age 49, non-diseased, left ventricle, replicate 1

description: Library name: K1549-LV-FACS


title: K1545 donor, male, age 44, non-diseased, left ventricle, replicate 2

description: Library name: K1545-LV-run123


title: Saline 4

description: Library name: WT_S_4


title: K1488 donor, male, age 81, non-diseased, left ventricle, replicate 1

description: Library name: K1488-LV-FACS


title: ND15755 donor, male, age 65, non-diseased, left ventricle, replicate 1

description: Library name: ND15755-LV-1st-run123


title: Saline 3

description: Library name: WT_S_3


title: BMDM cells, ATRA, rep2 (ATAC)

description: Library name: ATRA_ATAC_rep2

value: macrophage


title: K1485 donor, male, age 78, non-diseased, left ventricle, replicate 2

description: Library name: K1485-LV-nonFACS


title: K1622 donor, male, age 56, non-diseased, left ventricle, replicate 1

description: Library name: K1622-LV-FACS


title: K1430 donor, male, age 62, DCM, left ventricle, replicate 3

description: Library name: K1430-LV-FACS


title: Saline 2

description: Library name: WT_S_2


title: Saline 1

description: Library name: WT_S_1


title: K1430 donor, male, age 62, DCM, left ventricle, replicate 4

description: Library name: K1430-LV-FACS-KAPA


title: K1430 donor, male, age 62,  DCM, left ventricle, replicate 2

description: Library name: K1430-LV-2nd


title: HepG2_SIM_Veh_RSM4

description:
Library name: RNAHepG2S12
Illumina Sequence A01426

value: Hepatocyte

value: WT

value: SIM Vehicle Resmetirom 4


title: Fa2N4_MASLD_4

description:
Library name: RNAFa2N4S32
Illumina Sequence A01426

value: MASLD (600 uM FFA) 4


title: K1430 donor, male, age 62, DCM, left ventricle, replicate 1

description: Library name: K1430-LV

value: heart


title: Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 5

description: Library name: Fetal-LV-18wk-e3


title: HepG2_SIM_Veh_RSM3

description:
Library name: RNAHepG2S11
Illumina Sequence A01426

value: SIM Vehicle Resmetirom 3


title: Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 4

description: Library name: Fetal-LV-18wk-e2-run1n2


title: K1617 donor, male, age 64, DCM, left ventricle, non-sorted, replicate 1

description: Library name: K1617-LV


title: Untreated non-SP GL261 cells, Day 6, rep2

city: Singapore

first: Tingting

last: Cui

address: 4 Science Drive 2

department: Department of Diagnostic Radiology

country: Singapore

institute: National University of Singapore

description:
Library name: PC-2
RNA-seq of untreated non-SP GL261 glioblastoma cells treated, replicate 2

data_processing:
Sequence reads were trimmed for adapter sequences and low-quality bases using fastp (v0.22.0) with default parameters.
Trimmed reads were aligned to the Mus musculus reference genome (GRCm39, Ensembl release 110) using HISAT2 (v2.1.0) with default alignment settings.
Gene-level read counts were extracted using featureCounts. Expression levels were normalized as FPKM.
Differentially expressed genes were identified using DESeq2, with significance thresholds of adjusted p-value (padj) < 0.05 and |log2 fold change| > 1.
Assembly: Mus_musculus.GRCm39.110
Supplementary files format and content: tab-delimited text file contains raw read counts for all genes across all samples (rows = genes, columns = samples)
Supplementary files format and content: csv files contain FPKM values for all genes in each individual sample

source_name: brain (glioblastoma)

growth_protocol: non-SP GL261 cells and Hoechst-CD133+ GL261 cells were maintained in DMEM supplemented with 10% fetal bovine serum, 100 U/ml penicillin G and 100 μg/ml streptomycin sulfate at 37 ℃ in 5% CO2.

extract_protocol:
Total RNA from GL261 cells was extracted using TRIzol™ reagent according to the manufacturer’s protocol. The integrity of the extracted RNA was assessed by agarose gel electrophoresis. The RNA concentration was accurately determined using a NanoDrop spectrophotometer.
A high-throughput paired-end RNA sequencing library was prepared following the standard Illumina protocol, and library quality was assessed with a Qubit Fluorometer and an Agilent Bioanalyzer.

treatment_protocol: For the groups treated with hydrogels and cytokine cocktail, lyophilized chiral hydrogels were placed on ice, and Hoechst-CD133+ GL261 cells were added. After incubation on ice for 20 min, the cell-containing hydrogels were obtained and incubated in medium supplemented with cytokine cocktail for 6 days. For the group treated with PBS + cytokine cocktail, Hoechst-CD133+ GL261 cells were cultured in medium supplemented with PBS and cytokine cocktail for 6 days. For the no treatment group, non-SP GL261 cells were cultured under standard conditions without any additional treatment for 6 days. For all group, fresh blank medium was added on days 2 and 4.

value: brain (glioblastoma)

value: GL261 cell

value: glioblastoma cells

value: no treatment


title: K1617 donor, male, age 64, DCM, left ventricle, replicate 3

description: Library name: K1617-LV-FACS


title: Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 3

description: Library name: Fetal_LV_18wk_e1-run1n2


title: HepG2_SIM_Veh_RSM2

description:
Library name: RNAHepG2S10
Illumina Sequence A01426

value: Liver

value: SIM Vehicle Resmetirom 2


title: K1647 donor, male, age 34, non-diseased, left ventricle, replicate 2

description: Library name: K1647-LV-nonFACS


title: Untreated non-SP GL261 cells, Day 6, rep1

description:
Library name: PC-1
RNA-seq of untreated non-SP GL261 glioblastoma cells treated, replicate 1


title: HepG2_SIM_Veh_RSM1

description:
Library name: RNAHepG2S9
Illumina Sequence A01426

value: SIM Vehicle Resmetirom 1


title: Untreated non-SP GL261 cells, Day 6, rep3

description:
Library name: PC-3
RNA-seq of untreated non-SP GL261 glioblastoma cells treated, replicate 3


title: Penn_F2 donor, male, gestational week 18, non-diseased, left and right ventricle, replicate 1

description: Library name: Fetal-LRV-18wk-male1-run1n2


title: K1584 donor, male, age 22, non-diseased, left ventricle, replicate 2

description: Library name: K1584-LV-FACS-e2


title: Hoechst-CD133+ GL261 cells, PBS + cytokine cocktail treament, Day 6, rep2

description:
Library name: NC-2
RNA-seq of Hoechst-CD133+ GL261 glioblastoma cells treated with PBS + cytokine cocktail, replicate 2

value: PBS + cytokine cocktail


title: HepG2_MASLD_4

description:
Library name: RNAHepG2S8
Illumina Sequence A01426


title: Ang II 1

description: Library name: WT_A_1

value: aorta

value: Ang II

value: Day 7


title: Penn_F2 donor, male, gestational week 18, non-diseased, outflow tract (OFT), replicate 2

description: Library name: Fetal-2nd-OFT-2


title: Penn_F1 donor, female, gestational week 18, non-diseased, atria

description: Library name: Fetal-Atria-18wk


title: K1718 donor, male, age 33, non-diseased, left ventricle, replicate 1

description: Library name: K1718-LV-FACS


title: K1622 donor, male, age 56, non-diseased, left ventricle, replicate 2

description: Library name: K1622-LV-run123


title: Ang II 4

description: Library name: WT_A_4


title: Saline 8

description: Library name: WT_S_8

value: Saline


title: K1783 donor, male, age 69, non-diseased, left ventricle, replicate 2

description: Library name: K1783-LV-nonFACS


title: ND15755 donor, male, age 65, non-diseased, atria, replicate 1

description: Library name: ND15755-Atr-1st


title: Penn_F2 donor, male, gestational week 18, non-diseased, left and right ventricle,  non-diseased, replicate 2

description: Library name: Fetal-LRV-18wk-male2-run1n2


title: HepG2_MASLD_3

description:
Library name: RNAHepG2S7
Illumina Sequence A01426

value: Hepatocyte

value: WT

value: MASLD (600 uM FFA) 3


title: Penn_F2 donor, male, gestational week 18, non-diseased, outflow tract (OFT), replicate 1

description: Library name: Fetal-2nd-OFT-1

value: heart


title: K1545 donor, male, age 44, non-diseased, left ventricle, replicate 1

description: Library name: K1545-LV-FACS


title: Hoechst-CD133+ GL261 cells, PBS + cytokine cocktail treament, Day 6, rep1

description:
Library name: NC-1
RNA-seq of Hoechst-CD133+ GL261 glioblastoma cells treated with PBS + cytokine cocktail, replicate 1


title: HepG2_MASLD_2

description:
Library name: RNAHepG2S6
Illumina Sequence A01426

value: MASLD (600 uM FFA) 2


title: Hoechst-CD133+ GL261 cells, LGSNP + cytokine cocktail treament, Day 6, rep3

description:
Library name: LGSNP-3
RNA-seq of Hoechst-CD133+ GL261 glioblastoma cells treated with L-gel@GSNP + cytokine cocktail, replicate 3

value: brain (glioblastoma)

value: L-gel@GSNP + cytokine cocktail


title: Penn_F2 donor, male, gestational week 18, non-diseased, atria, replicate 2

description: Library name: Fetal-2nd-Atria-2


title: HepG2_SIM_RSM3

description:
Library name: RNAHepG2S15
Illumina Sequence A01426

value: SIM Resmetirom 3


title: Penn_F2 donor, male, gestational week 18, non-diseased, atria, replicate 1

description: Library name: Fetal-2nd-Atria-1


title: K1584 donor, male, age 22, non-diseased, left ventricle, replicate 3

description: Library name: K1584-LV-run1n2


title: Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 1

description: Library name: Fetal-1st-LV-0315-1-run1n2


title: K1561 donor, male, age 73, non-diseased, left ventricle

description: Library name: K1561-LV-FACS


title: Hoechst-CD133+ GL261 cells, LGSNP + cytokine cocktail treament, Day 6, rep1

description:
Library name: LGSNP-1
RNA-seq of Hoechst-CD133+ GL261 glioblastoma cells treated with L-gel@GSNP + cytokine cocktail, replicate 1

value: GL261 cell

value: glioblastoma cells


title: HepG2_NT_4

description:
Library name: RNAHepG2S4
Illumina Sequence A01426

value: Liver

value: Negative ctrl (BSA) 4


title: Saline 5

description: Library name: WT_S_5


title: Transcriptome of Episyrphus balteatus, wing replicate 3

city: Baoding

first: He

last: Yuan

address: Dongguan Street, number 437

institute: Hebei Academy of Agriculture and Forestry Sciences

description:
Library name: wing-3
Wing3

data_processing:
The quality assessment of raw data was conducted. Following the removal of adapters and low-quality sequences, clean data were obtained for further analysis. High-quality sequences were assembled into contigs and singletons using Trinity v2.8.5. Subsequently, the initial assembly was optimized and filtered by TransRate v1.0.3. The transcriptome assembly integrity was assessed by BUSCO v3.0.2. The transcripts were blasted against six databases (NR, Swiss-Prot, Pfam, EggCOG, GO, and KEGG databases) to obtain annotation information. Clean reads from each sample were aligned with the assembled reference sequences to generate the mapping results, which were fed to RSEM v1.3.1 for calculating the expression levels of genes and transcripts. The expression levels were measured by transcripts per million. The differential expression of genes among samples was assessed using DESeq2 v1.24.0 with default parameters (|log2FC| > = 1 and padjust < 0.05) relying on the read counts of each sample. Significantly enriched KEGG pathways of differentially expressed genes (DEGs) among different developmental stages and different adult tissues were identified with an padjust < 0.05.
Assembly: no
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Episyrphus balteatus

source_name: wing

extract_protocol:
Total RNA was extracted from each sample using the TransZol kit (Transgen, Beijing) in accordance with the provided instructions. RNA concentration and purity were assessed using Nanodrop 2000, and the integrity of RNA was evaluated by 1% agarose gel electrophoresis. RNA quality number (RQN) was measured using the Agilent 5300. A total of 1 μg of high-quality RNA (OD260/280: 1.8~2.2; RQN > 6.5) was used for cDNA library construction by Shanghai Majorbio Biotech Corporation (Shanghai, China). Each developmental stage or tissue type was used as an independent sample to construct a cDNA library for transcriptome sequencing.
mRNA was isolated from total RNA using oligo(dT) magnetic beads to pair with its polyA tail. Subsequently, mRNA was randomly fragmented into small segments (~300 bp) by adding the fragmentation buffer. Double-stranded cDNA was synthesized utilizing random primers and reverse transcriptase with mRNA as template. Adapters were added to the ends of cDNA, and the resulting products were subjected to PCR amplification. Following purification, the final libraries were quantified using Qubit 4.0. The samples were mixed according to the required ratio, and bridge PCR amplification was conducted on the cBot Cluster Generation System to generate clusters. The final libraries were sequenced on a NovaSeq X Plus platform by Shanghai Majorbio Biotech Corporation (Shanghai, China).

value: wing


title: Transcriptome of Episyrphus balteatus, wing replicate 2

description:
Library name: wing-2
Wing2


title: HepG2_SEQ_Veh_RSM3

description:
Library name: RNAHepG2S19
Illumina Sequence A01426

value: SEQ Vehicle Resmetirom 3


title: HepG2_NT_3

description:
Library name: RNAHepG2S3
Illumina Sequence A01426

value: Negative ctrl (BSA) 3


title: K1488 donor, male, age 81, non-diseased, left ventricle, replicate 2

description: Library name: K1488-LV-nonFACS


title: Transcriptome of Episyrphus balteatus, wing replicate 1

description:
Library name: wing-1
Wing1


title: HepG2_NT_1

description:
Library name: RNAHepG2S1
Illumina Sequence A01426

value: Negative ctrl (BSA) 1


title: Transcriptome of Episyrphus balteatus, leg replicate 1

description:
Library name: leg-1
Leg1

source_name: leg

value: leg


title: HepG2_NT_2

description:
Library name: RNAHepG2S2
Illumina Sequence A01426

value: Hepatocyte

value: Negative ctrl (BSA) 2


title: Hoechst-CD133+ GL261 cells, DNP + cytokine cocktail treament, Day 6, rep2

description:
Library name: DNP-2
RNA-seq of Hoechst-CD133+ GL261 glioblastoma cells treated with D-gel@NP + cytokine cocktail, replicate 2

value: WT

value: D-gel@NP + cytokine cocktail


title: Transcriptome of Episyrphus balteatus,pupa replicate 1

description:
Library name: pupa-Eb-1
P1

source_name: pupa

value: pupa


title: Transcriptome of Episyrphus balteatus, leg replicate 3

description:
Library name: leg-3
Leg3


title: SU-DHL-4 CFLAR knockout untreated_biol rep 2

city: Cologne

first: Alessandro

last: Annibaldi

state: North-Rhine-Westphalia

address: Robert-Koch-Strasse 21

country: Germany

institute: Center for Molecular Medicine Cologne

description: Library name: DHL4_KO_untreated_2

data_processing:
Sequencing reads were mapped to the human reference genome GRCh38 by using STAR.
Transcript quantification was performed using RSEM. The acquired transcriptomic profiles were then compared among different cell lines and their genotypes by applying DESeq2
Differential expression model was built in such way that it measures what effect is brought by the KO genotype for both cell lines separately
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file containing gene counts for each sample

growth_protocol: TMD8 and SU-DHL-4 CFLAR wildtype and knockout cells were cultured in RPMI media (GIBCO). SU-DHL-4 media was supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin/Streptomycin (P/S). TMD8 media was supplemented with 15% FBS, 1% P/S, 1% HEPES, Sodium pyruvate, Non-essential amino acid (100x). Cells were cultured at 37°C in a humified atmosphere with 5% CO2.

extract_protocol:
RNA was extracted using the QuickRNA Kit (ZymoResearch) and 500 ng RNA was used for sequencing
Libraries were prepared using the Illumina® Stranded mRNA® sample preparation Kit. Library preparation started with 500ng total RNA. After poly-A selection (poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature

treatment_protocol: 5*10^6 DLBCL cells were seeded in triplicates and cultured overnight prior to collection

value: B cell

value: knockout

value: untreated


title: K1485 donor, male, age 78, non-diseased, left ventricle, replicate 1

description: Library name: K1485-LV-FACS

value: heart


title: Hoechst-CD133+ GL261 cells, DNP + cytokine cocktail treament, Day 6, rep1

description:
Library name: DNP-1
RNA-seq of Hoechst-CD133+ GL261 glioblastoma cells treated with D-gel@NP + cytokine cocktail, replicate 1

value: brain (glioblastoma)

value: GL261 cell

value: glioblastoma cells


title: Transcriptome of Episyrphus balteatus, leg replicate 2

description:
Library name: leg-2
Leg2


title: Transcriptome of Episyrphus balteatus,proboscis replicate 3

description:
Library name: proboscis-3
M3

source_name: proboscis

value: proboscis


title: HepG2_SIM_RSM1

description:
Library name: RNAHepG2S13
Illumina Sequence A01426

value: Liver

value: SIM Resmetirom 1


title: Transcriptome of Episyrphus balteatus,proboscis replicate 2

description:
Library name: proboscis-2
M2


title: Hoechst-CD133+ GL261 cells, DGSNP + cytokine cocktail treament, Day 6, rep3

description:
Library name: DGSNP-3
RNA-seq of Hoechst-CD133+ GL261 glioblastoma cells treated with D-gel@GSNP + cytokine cocktail, replicate 3

value: D-gel@GSNP + cytokine cocktail


title: Transcriptome of Episyrphus balteatus,pupa replicate 3

description:
Library name: pupa-Eb-3
P3


title: Transcriptome of Episyrphus balteatus,proboscis replicate 1

description:
Library name: proboscis-1
M1


title: K1549 donor, male, age 49, non-diseased, left ventricle, replicate 2

description: Library name: K1549-LV-nonFACS


title: Hoechst-CD133+ GL261 cells, DGSNP + cytokine cocktail treament, Day 6, rep2

description:
Library name: DGSNP-2
RNA-seq of Hoechst-CD133+ GL261 glioblastoma cells treated with D-gel@GSNP + cytokine cocktail, replicate 2


title: Transcriptome of Episyrphus balteatus, head replicate 3

description:
Library name: head-3
Head3

source_name: head

value: head


title: Transcriptome of Episyrphus balteatus, head replicate 2

description:
Library name: head-2
Head2


title: SU-DHL-4 CFLAR knockout untreated_biol rep 1

description: Library name: DHL4_KO_untreated_1


title: mix of four wild-type and four Uhrf1 knockout E8.5 embryos, sublibrary 4, ATAC and DNA methylation

city: New York City

first: Bohan

last: Zhu

state: NY

address: 1425 Madison Ave

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Library name: embryo_TAPS_4

data_processing:
The workflow consists of five main modules: (1) demultiplexing FASTQ files and assigning cell barcode information to each read; (2) adapter trimming and filtering of low-quality reads; (3) read alignment; (4) BAM file processing and quality control; and (5) generation of final gene expression, chromatin accessibility, or methylome profiles. Steps 1 and 2 are identical for sequencing results from multi-omic profiling (scRNA-seq, scATAC-seq, and sc-methyl-seq), whereas steps 3 to 5 are divided into separate branches: ‘a’ transcriptome, ‘b’ methylome, and ‘c’ chromatin accessibility.
Step 1. FASTQ files were generated from base calls using bcl2fastq. Sequencing reads from the Read 2 file were demultiplexed, allowing one mismatch per 8-base barcode across the three rounds of barcoding. Barcode sequences were converted into read identifiers in the format RoundX.xxx (where X denotes the round number and xxx the sequence number) and appended to the header of each read. Step 2. Reads containing adapter sequence were trimmed and the low-quality reads were removed with Trim Galore using default parameters.
Step 3.a (transcriptome). Reads from step 2 were aligned to the mouse reference genome (mm10) with STAR using the following settings: --chimOutType WithinBAM --runThreadN 16 --outFilterMultimapNmax 20 --outFilterScoreMinOverLread 0.3 --outFilterMatchNminOverLread 0.3 --outSAMattributes NH HI AS nM MD --limitOutSJcollapsed 5000000 --outSAMtype BAM Unsorted --limitIObufferSize 400000000 --outReadsUnmapped None --readFilesCommand zcat.   Step 3.b and c (methylome and chromatin accessibility). Trimmed reads were aligned to the mouse reference genome (mm10) with Bismark using default settings (Bismark --non_directional -X 2000).
Step 4.a (transcriptome) STAR mapped reads were first filtered with the -F 256 flag to retain uniquely mapped reads and the primary alignment position of multi-mapped reads. To distinguish RNA reads captured by poly(T) primers (dT) from those captured by random RT primers (N6), we used the ‘PT’ tag (PT=1 for dT and PT=0 for N6). The filtered reads were then annotated to both exons and introns using featureCounts. To speed up processing, only barcode combinations with > 100 reads were retained. Filtered and sorted BAM file was convert to h5 file for the next step.  Step 4.b (methylome) Duplicate reads were identified and removed using deduplicate_bismark with the --barcode option. The first and last 9 bases of each read were marked as unmethylated due to the characteristics of Tn5 transposition. Methylated cytosines in CpG (mCG) or non-CpG (mCH) contexts were then identified using bismark_methylation_extractor.  Step 4.c (chromatin accessibility) Duplicates were removed using Picard. Open chromatin region peaks were called on individual samples using MACS2 peak caller with the following parameters: –nomodel –nolambda –keep-dup -call-summits.
Step 5.a (transcriptome) H5 file from step 4.a was read and processed using Seurat (v5.3.0). Cells with high ambient RNA contamination (score > 0.5) and doublets were identified and removed using DecontX and Doubeltfinder. Quality control filtering excluded cells expressing fewer than 800 genes, more than 7,000 genes, or with >3% mitochondrial transcripts. Expression counts were determined by unique read counts to generate a cell by gene expression matrix, after which mitochondrial genes were removed. The scRNA-seq data were normalized to counts per 10,000 using Seurat. For visualization, the top 3,000 variable genes were projected into two-dimensional space using UMAP.  Step 5.b (methylome) Tab-delimited (ALLC) files containing methylation level for every cytosine position was generated from the BED file in step 4. A matrix of peak methylation ratio by cell was created and used as input matrix for Signac.   Step 5.c (Chromatin accessibility) Fragment counts within peaks were aggregated to generate a cell-by-peak count matrix. A TF-IDF matrix was then computed from this count matrix using truncated singular value decomposition (RunSVD function, Signac). For visualization, UMAP was performed with the Seurat RunUMAP function, using LSI components 2 through 50.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole embryo

extract_protocol:
Uhrf1+/− male and female mice were naturally mated and checked every morning for the appearance of a vaginal plug, the presence of a plug determined the time point E0.5. E8.5 embryos were dissected from the uterus in PBS/FBS and extra-embryonic tissue was removed.The embryos were washed in PBS without Ca2+/Mg2+ and each was put in a 3 cm dish with 1 ml TrypLE, chopped into small pieces, and incubated at 37°C for 20 min. 300 μl serum was added and pipetted up and down until tissue was dissociated in single cells.
Briefly, cells were fixed and permeabilized. For joint measurements of single cell chromatin accessibility, DNA methylation, and expression, cells were first transposed by Tn5 transposase to mark regions of open chromatin. The mRNA was reverse transcribed using a poly(T) primer containing a unique molecular identifier (UMI) and a random primer. Both primers contained a biotin tag. Permeabilized cells were distributed in a 96-well plate to hybridize well-specific barcoded oligonucleotides to transposed chromatin fragments and poly(T) cDNA. Hybridization was repeated three times to expand the barcoding space and ligate cell barcodes to cDNA and chromatin fragments. Reverse crosslinking was performed to release barcoded molecules. cDNA was separated from chromatin using streptavidin beads, and each library was prepared separately for sequencing. Chromatin DNA was purified, gap-filled and oxidized using mTET1, and deaminated with 1 M pyridine borane before amplification. Both DNA and RNA libraries were quantified with KAPA Library Quantification Kit and pooled to 4 nM for sequencing. Libraries were sequenced on the Illumina Nova-seq platform with 150 PE reads (Read 1: 150 cycles, Index 1: 8 cycles, Index 2: 8 cycles, Read 2: 150 cycles). Libraries were sequenced on the Illumina NovaSeq platform, aiming for a minimum coverage of 50,000 reads per single cell.

value: whole embryo

value: mixed samples, wild-type and Uhrf1 knockout

tag: library type

value: ATAC library, with DNA methylation information.


title: Transcriptome of Episyrphus balteatus, head replicate 1

description:
Library name: head-1
Head1


title: Hoechst-CD133+ GL261 cells, DGSNP + cytokine cocktail treament, Day 6, rep1

description:
Library name: DGSNP-1
RNA-seq of Hoechst-CD133+ GL261 glioblastoma cells treated with D-gel@GSNP + cytokine cocktail, replicate 1

value: WT


title: SU-DHL-4 CFLAR wildtype untreated_biol rep 3

description: Library name: DHL4_WT_untreated_3

value: wildtype


title: Transcriptome of Episyrphus balteatus,pupa replicate 2

description:
Library name: pupa-Eb-2
P2

value: pupa


title: Transcriptome of Episyrphus balteatus,larva replicate 2

description:
Library name: larva-Eb-2
L2

source_name: larva

value: larva


title: Penn_F2 donor, male, gestational week 18, non-diseased, left and right ventricle, replicate 4

description: Library name: Fetal-LRV-18wk-male4-run1n2


title: SU-DHL-4 CFLAR wildtype untreated_biol rep 2

description: Library name: DHL4_WT_untreated_2

value: B cell

value: untreated


title: Transcriptome of Episyrphus balteatus,larva replicate 1

description:
Library name: larva-Eb-1
L1


title: Penn_F2 donor, male, gestational week 18, non-diseased, left and right ventricle, replicate 3

description: Library name: Fetal-LRV-18wk-male3-run1n2

value: heart


title: Transcriptome of Episyrphus balteatus,larva replicate 3

description:
Library name: larva-Eb-3
L3


title: HepG2_SIM_RSM2

description:
Library name: RNAHepG2S14
Illumina Sequence A01426

source_name: Liver

value: Hepatocyte

value: SIM Resmetirom 2


title: Hoechst-CD133+ GL261 cells, LGSNP + cytokine cocktail treament, Day 6, rep2

description:
Library name: LGSNP-2
RNA-seq of Hoechst-CD133+ GL261 glioblastoma cells treated with L-gel@GSNP + cytokine cocktail, replicate 2

value: brain (glioblastoma)

value: GL261 cell

value: glioblastoma cells

value: L-gel@GSNP + cytokine cocktail


title: Hoechst-CD133+ GL261 cells, PBS + cytokine cocktail treament, Day 6, rep3

description:
Library name: NC-3
RNA-seq of Hoechst-CD133+ GL261 glioblastoma cells treated with PBS + cytokine cocktail, replicate 3

value: PBS + cytokine cocktail


title: SU-DHL-4 CFLAR wildtype untreated_biol rep 1

description: Library name: DHL4_WT_untreated_1


title: HepG2_MASLD_1

description:
Library name: RNAHepG2S5
Illumina Sequence A01426

value: Liver

value: MASLD (600 uM FFA) 1


title: Transcriptome of Episyrphus balteatus, body replicate 2

description:
Library name: body-2
Body2

source_name: body

value: body


title: Penn_F1 donor, female, gestational week 18, non-diseased, left ventricle, replicate 2

description: Library name: Fetal-1st-LV-0315-2-run1n2

source_name: heart


title: Hoechst-CD133+ GL261 cells, DNP + cytokine cocktail treament, Day 6, rep3

description:
Library name: DNP-3
RNA-seq of Hoechst-CD133+ GL261 glioblastoma cells treated with D-gel@NP + cytokine cocktail, replicate 3

value: WT

value: D-gel@NP + cytokine cocktail


title: TMD8 CFLAR knockout untreated_biol rep 3

description: Library name: TMD8_KO_untreated_3

value: knockout


title: mix of four wild-type and four Uhrf1 knockout E8.5 embryos, sublibrary 3, ATAC and DNA methylation

description: Library name: embryo_TAPS_3

value: whole embryo

value: mixed samples, wild-type and Uhrf1 knockout

value: ATAC library, with DNA methylation information.


title: TMD8 CFLAR knockout untreated_biol rep 2

description: Library name: TMD8_KO_untreated_2

value: B cell

value: untreated


title: Transcriptome of Episyrphus balteatus, body replicate 1

description:
Library name: body-1
Body1


title: mix of four wild-type and four Uhrf1 knockout E8.5 embryos, sublibrary 3, GEX

description: Library name: embryo_RNA_3

value: GEX library


title: Transcriptome of Episyrphus balteatus, egg replicate 2

description:
Library name: egg-Eb-2
Egg2

source_name: egg

value: egg


title: Transcriptome of Episyrphus balteatus, antenna replicate 3

description:
Library name: antenna-3
An_3

source_name: antenna

value: antenna


title: TMD8 CFLAR knockout untreated_biol rep 1

description: Library name: TMD8_KO_untreated_1


title: TMD8 CFLAR wildtype untreated_biol rep 3

description: Library name: TMD8_WT_untreated_3

value: wildtype


title: Transcriptome of Episyrphus balteatus,thorax replicate 2

description:
Library name: thorax-2
Th2

source_name: thorax

value: thorax


title: mix of four wild-type and four Uhrf1 knockout E8.5 embryos, sublibrary 2, ATAC and DNA methylation

description: Library name: embryo_TAPS_2


title: mix of four wild-type and four Uhrf1 knockout E8.5 embryos, sublibrary 4, GEX

description: Library name: embryo_RNA_4


title: Transcriptome of Episyrphus balteatus, body replicate 3

description:
Library name: body-3
Body3


title: Transcriptome of Episyrphus balteatus, antenna replicate 1

description:
Library name: antenna-1
An_1


title: Transcriptome of Episyrphus balteatus,egg replicate 3

description:
Library name: egg-Eb-3
Egg3


title: Transcriptome of Episyrphus balteatus,thorax replicate 3

description:
Library name: thorax-3
Th3


title: Transcriptome of Episyrphus balteatus,thorax replicate 1

description:
Library name: thorax-1
Th1


title: SU-DHL-4 CFLAR knockout untreated_biol rep 3

description: Library name: DHL4_KO_untreated_3


title: mix of four wild-type and four Uhrf1 knockout E8.5 embryos, sublibrary 1, ATAC and DNA methylation

description: Library name: embryo_TAPS_1


title: mix of four wild-type and four Uhrf1 knockout E8.5 embryos, sublibrary 1, GEX

description: Library name: embryo_RNA_1


title: Osteal macrophage not stimulated 3

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

institute: Hokkaido University

description: Library name: Control B

data_processing:
The sequence data of 150 bp × 2 paired ends of 6G bases/sample (3 samples for each condition) were trimmed and mapped via HISAT2 v2.0.5. Reads were counted (FeatureCount v1.55.0-p3) and the number of fragments per 1 million bases of the transcription sequence of each gene was calculated based on the gene and read length. Significance was set up using the Benjamini-Hochberg approach as p <0.05 for false discovery rate (FDR) . The gene ontology and pathway enrichment analyses and GSEA were performed on the differential expression data using NovoMagic online tools (Novogene, Singapore).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone

growth_protocol: The bone tissue was finely cut and digested in 0.25% trypsin at 37°C for 30 minutes, followed by 0.25 U/mL collagenase D at 37°C overnight. Osteal macrophages were then sorted using a Cell Sorter with a specific antibody against F4/80.

extract_protocol:
osteal macrophage RNA was purified using TRIzol Reagent and RNA extraction kit (NucleoSpin®) according to the manufacturere's protocol
The libraries were generated from high-quality RNA (1 μg) of each sample using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) and then subjected for sequencing (Illumina NovaSeq 6000, Illumina, Inc. San Diego, CA, USA). The sequence data of 150 bp × 2 paired ends of 6G bases/sample (3 samples for each condition) were trimmed and mapped via HISAT2 v2.0.5. Reads were counted (FeatureCount v1.55.0-p3) and the number of fragments per 1 million bases of the transcription sequence of each gene was calculated based on the gene and read length. Significance was set up using the Benjamini-Hochberg approach as p <0.05 for false discovery rate (FDR) . The gene ontology and pathway enrichment analyses and GSEA were performed on the differential expression data using NovoMagic online tools (Novogene, Singapore).

treatment_protocol: Colitis was induced by administering 3% DSS in drinking water for 5 days, and osteo-macrophages were isolated after 1 week(DSS1w) and 3 weeks(DSS3w). LPS group was isolated from mice 3 days after administration of LPS 5 mg/kg i.p.

value: bone

value: macrophage


title: ND14, biological rep1

type: RNA

city: Kepala Batas

first: Syahidatulamali

last: Che Shaffi

address: Bandar Putra Bertam

country: Malaysia

institute: Universiti Sains Malaysia

description: Gene expression data from lung organoid for naïve group on day 14

hyb_protocol: This double-stranded cDNA was then amplified by IVT to produce cRNA. IVT generated cRNA was then purified and subjected to 2nd-cycle single stranded cDNA which was later fragmented, labeled, and hybridized to Mouse Gene 2.0 ST Array for 18 hours at 45°C with rotation at 60 rpm.

scan_protocol: Arrays were then washed and stained using the FS450_0002 fluidics protocol and scanned using an Applied Biosystems™ GeneChip™ Scanner 3000 7G.

data_processing: The data were analyzed with Microarray using TAC Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Lung organoid culture from naïve group on day 14

label_protocol: 10ng of total RNA was reverse transcribed to produce first-strand cDNA, which was subsequently used as a template to create double stranded cDNA in in vitro transcription (IVT).

growth_protocol: The 50 × 103 cells from the lung cell were culture according to lung organoid procedure with different groups and lung organoid were harvested in different timepoint.

extract_protocol: The RNA extractiob using the NucleoSpin RNA Plus extraction kit (Macherey Nagel, Germany), following the provided guidelines.

treatment_protocol: To promote the maturation and differentiation of the spheroids into organoids, the medium was changed to a medium containing 2% FBS (instead of 5% in the proliferation medium), with/without ROCK and TGF-β inhibitors

value: Lung organoid


title: Osteal macrophage not stimulated 2

description: Library name: Control A


title: THP-1-Rv-3

first: Yuehan

last: Zhao

address: No. 97, Beiguan Street, Tongzhou District

institute: Beijing Tuberculosis and Thoracic Tumor Research Institute

description:
Library name: THP1-24H-3
THP1-24H-3_FPKM

data_processing:
Base-calling:Raw image files were converted to FASTQ format using Illumina's proprietary software (bcl2fastq, version 2.20). No specific parameters were modified from the default.
Data pre-processing (filtering):Raw reads (FASTQ format) were processed using Seqtk (https://github.com/lh3/seqtk) with the following steps:Removal of adapter sequences.Trimming of 3' ends with base quality below Q20.Discarding reads shorter than 25 nucleotides.Removal of ribosomal RNA reads by mapping to rRNA sequences.
Read alignment:Clean reads were aligned to the human reference genome (GRCh38, downloaded from Ensembl release 83) using HISAT2 (version 2.0.4) with the spliced alignment algorithm. Default parameters were used.
Transcript assembly and abundance estimation:Aligned reads were assembled and quantified using StringTie (version 1.3.0). Gene and lncRNA expression levels were calculated as:Raw counts: Number of fragments mapped to each gene/transcript.FPKM (Fragments Per Kilobase of exon model per Million mapped reads): Normalized expression values.The TMM (trimmed mean of M values) method was applied for normalization across samples.
Differential expression analysis:Differential expression analysis between infected (H37Rv, 24h) and uninfected (control, 0h) groups was performed using the edgeR package in R. The significance thresholds were set as:q-value ≤ 0.05 (adjusted p-value using FDR control)，|Fold-change| ≥ 2 (log2FC ≥ 1 or ≤ -1)。
Assembly: GRCh38
Supplementary files format and content: gene_expression_anno.txt ;Format: Tab-delimited text file ;Content: This file contains the gene expression data for all samples. Rows represent genes, identified by Gene IDs and official gene names. Columns include gene descriptions, genomic loci, and the expression values (FPKM and raw counts) for each of the 8 THP-1 macrophage samples (THP1-0H-1 to THP1-24H-4).

extract_protocol:
Total RNA was extracted using the BeyoZol Animal Tissue Total RNA Extraction Kit (magnetic bead method) following the manufacturer’s instructions. RNA integrity was assessed by calculating the RIN number using an Agilent 5300 system. Qualified total RNA was further purified using the RNAClean XP Kit (Cat# A63987, Beckman Coulter, Inc., Brea, CA, USA) and the RNase-Free DNase Set (Cat# 79254, QIAGEN, Hilden, Germany).
Total RNA was extracted using the BeyoZol Animal Tissue Total RNA Extraction Kit (magnetic bead method). Ribosomal RNA was depleted from total RNA using the HieffNGS® MaxUp Human rRNA Depletion Kit (YEASen, Cat#12257ES24). Sequencing libraries were then constructed using the Dual-mode mRNA Library Prep Kit (YEASen, Cat#12310ES96) following the manufacturer's instructions. The process included RNA fragmentation, first-strand and second-strand cDNA synthesis, end repair, A-tailing, adapter ligation, and PCR enrichment. Library quality was assessed using the Qubit® 2.0 Fluorometer and Agilent 4200 TapeStation.

value: macrophage cell line

value: same


title: THP-1-Rv-4

description:
Library name: THP1-24H-4
THP1-24H-4_FPKM


title: Transcriptome of Episyrphus balteatus, antenna replicate 2

description:
Library name: antenna-2
An_2


title: TMD8 CFLAR wildtype untreated_biol rep 1

description: Library name: TMD8_WT_untreated_1


title: Osteal macrophage stimulated by LPS 3

description: Library name: LPS A


title: mix of four wild-type and four Uhrf1 knockout E8.5 embryos, sublibrary 2, GEX

description: Library name: embryo_RNA_2


title: ND14, biological rep3


title: Transcriptome of Episyrphus balteatus,egg replicate 1

description:
Library name: egg-Eb-1
Egg1


title: TMD8 CFLAR wildtype untreated_biol rep 2

description: Library name: TMD8_WT_untreated_2


title: CSD14, biological rep2

description: Gene expression data from lung organoid for cigarette smoke group on day 14

source_name: Lung organoid culture from cigarette smoke exposure group on day 14


title: Young-NoTension-CTRL-Replicate2

city: Villigen

last: Shivashankar

state: Aargau

address: Forschungsstrasse 111

department: LNB

country: Switzerland

institute: Paul Scherrer Institute

description:
Library name: YNC2
raw_counts_tensionTGFb.csv

data_processing:
Sequence reads were aligned using the STAR sequence alignment tool
Assembly: GRCh38
Supplementary files format and content: csv files include gene raw counts of each sample

growth_protocol: cells were cultured in complete medium consisting of Minimum Essential Medium supplemented with 15% (vol/vol) heat-inactivated fetal bovine serum, 1% nonessential amino acids, 1% GlutaMAX, and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen)
Illumina TruSeq Stranded Total RNA Gold kit was used following manufacturer's protocol

treatment_protocol: Fibroblasts embedded in the 3D collagen gel, with or without tension, were cultured in complete medium for 24 hours, followed by starvation in serum-free medium for 24 hours. Subsequently, cells were treated with 10 ng/mL TGF-β in serum-free medium for an additional 24 hours.

value: primary dermal fibroblast

tag: age

value: young:10 years old

value: no tension without TGFb


title: ND14, biological rep2


title: Young-NoTension-TGFb-Replicate2

description:
Library name: YNT2
raw_counts_tensionTGFb.csv

value: no tesion with TGFb


title: THP-1-Rv-1

description:
Library name: THP1-24H-1
THP1-24H-1_FPKM


title: Osteal macrophage not stimulated 1

description: Library name: Control 2


title: Osteal macrophage stimulated by LPS 1

description: Library name: LPS 1


title: THP-1-1640-3

description:
Library name: THP1-0H-3
THP1-0H-3_FPKM

value: uninfected control


title: THP-1-Rv-2

description:
Library name: THP1-24H-2
THP1-24H-2_FPKM


title: THP-1-1640-4

description:
Library name: THP1-0H-4
THP1-0H-4_FPKM


title: CSD14, biological rep3


title: Osteal macrophage stimulated by LPS 2

description: Library name: LPS 2


title: CSD5, biological rep3

description: Gene expression data from lung organoid for cigarette smoke group on day 5

source_name: Lung organoid culture from cigarette smoke exposure group on day 5


title: Young-Tension-TGFb-Replicate2

description:
Library name: YRT2
raw_counts_tensionTGFb.csv

value: tesion with TGFb


title: Young-Tension-CTRL-Replicate1

description:
Library name: YRC1
raw_counts_tensionTGFb.csv

value: tension without TGFb


title: Young-NoTension-TGFb-Replicate1

description:
Library name: YNT1
raw_counts_tensionTGFb.csv


title: Young-Tension-CTRL-Replicate2

description:
Library name: YRC2
raw_counts_tensionTGFb.csv


title: THP-1-1640-2

description:
Library name: THP1-0H-2
THP1-0H-2_FPKM


title: Young-NoTension-CTRL-Replicate1

description:
Library name: YNC1
raw_counts_tensionTGFb.csv


title: CSD5, biological rep2


title: Old-NoTension-CTRL-Replicate2

description:
Library name: ONC2
raw_counts_tensionTGFb.csv

value: old:75 years old


title: CSD14, biological rep1


title: Young-Tension-TGFb-Replicate1

description:
Library name: YRT1
raw_counts_tensionTGFb.csv


title: Osteal macrophage stimulated by 3%DSS 3weeks 3

description: Library name: DSS 3w_3


title: Osteal macrophage stimulated by 3%DSS 3weeks 1

description: Library name: DSS 3w_1


title: Old-NoTension-TGFb-Replicate1

description:
Library name: ONT1
raw_counts_tensionTGFb.csv


title: peripheral EDTA blood, Norma_17, rep1

city: Moscow

first: Polina

middle: Sergeevna

last: Shlapakova

address: Volokolamskoye Shosse, 80

country: Russia

institute: Research Center of Neurology

description:
Library name: N29
Column name in HTSeq_counts.xlsx: N29

data_processing:
Paired-end reads were aligned to the human reference genome (GRCh38) using the STAR aligner, achieving an average unique alignment rate of 80% per sample
Gene-level read counting was performed with HTSeq in union mode, approximately 55% of total reads were uniquely mapped to annotated genes
Assembly: Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: peripheral EDTA blood

extract_protocol:
Total RNA was extracted from 1.5 mL of whole EDTA blood using the RNeasy Mini Kit (Qiagen, Germany). Residual genomic DNA was removed by treatment with DNase I (Monarch, NEB, USA).
Transcriptomic libraries were prepared from 1,000 ng of total RNA (RIN>8) using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, USA), which includes depletion of cytoplasmic and mitochondrial ribosomal RNA. Libraries were indexed using the IDT for Illumina – TruSeq RNA UD Indexes (Illumina, USA).

value: peripheral EDTA blood

tag: sample group

value: Norma

value: Healthy


title: Osteal macrophage stimulated by 3%DSS 3weeks 2

description: Library name: DSS 3w_2


title: Osteal macrophage stimulated by 3%DSS 1weeks 2

description: Library name: DSS 1w A


title: CSD5, biological rep1


title: Old-NoTension-TGFb-Replicate2

description:
Library name: ONT2
raw_counts_tensionTGFb.csv


title: peripheral EDTA blood, Norma_16, rep1

description:
Library name: N28
Column name in HTSeq_counts.xlsx: N28


title: Young-NoTesion-Replicate2

description:
Library name: YN2
raw_counts_tension.csv

value: no tension


title: Old-Tension-CTRL-Replicate2

description:
Library name: ORC2
raw_counts_tensionTGFb.csv


title: Old-Tension-TGFb-Replicate1

description:
Library name: ORT1
raw_counts_tensionTGFb.csv


title: peripheral EDTA blood, Norma_14, rep1

description:
Library name: N25
Column name in HTSeq_counts.xlsx: N25


title: Osteal macrophage stimulated by 3%DSS 1weeks 3

description: Library name: DSS 1w B

value: bone


title: Young-Tesion-Replicate1

description:
Library name: YR1
raw_counts_tension.csv

value: tension


title: Old-Tension-CTRL-Replicate1

description:
Library name: ORC1
raw_counts_tensionTGFb.csv


title: HKDTR Knockout Diphtheria Toxin Treated

city: Houston

first: Jason

middle: C

last: Mills

state: TX

address: 1 Baylor Plaza

department: Gastroenterology

institute: Baylor College of Medicine

description:
Library name: HKDTR_DT
48 Hours Treatment

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0
Quality control for filtering, normalization, clustering, and differential expression analysis was conducted in Seurat/R (Seurat  v4)
Assembly: mm10
Supplementary files format and content: Tab-separated features.tsv and barcode.tsv files and matrix.mtx files contained in zipped folder

source_name: Gastric Corpus

extract_protocol:
Fresh gastric corpus was harvested and mechanically dissociated in DMEM media+ Collagenase 1A while shaking at  37° for 30 minutes. Tissue was further dissociated chemically in 5-15 minutes at 37° in 0.05% trypsin-EDTA. The single cell suspension was passed through a 30µm filter, quantity and viability assessed with hematocytometer, and submitted to the Single Cell Genomics Core at Baylor College of Medicine in 0.04% BSA 1x PBS.
The single-cell gene expression Library was prepared according to the Chromium Single Cell Gene Expression 3’v3.1 instruction (PN-1000121, PN-1000120, PN-1000213, 10x Genomics). Briefly, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions) where full-length cDNA was synthesized and barcoded for each single cell. Subsequently, the GEMS are broken and cDNA from each single cell is pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR.  The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. The final library was generated by amplification. After passed the quality control, the next-generation sequencing of libraries was performed on NovaSeq 6000 (Illumina).

treatment_protocol: Mice in the HDTAM-treated experimental group received high-dose tamoxifen (5 mg per 20 g body weight) once daily for two days, with tissue harvested 24 hours after the final injection. This time point includes three female mice. Mice in the DT-treated experimental group received diphtheria toxin (225 ng/mouse) once daily for two days, with tissue harvested 24 hours after the final injection. This time point includes three female mice.

value: Gastric Corpus

value: Multiple cell types in gastric corpus

value: Diphtheria Toxin


title: peripheral EDTA blood, Norma_10, rep1

description:
Library name: N19
Column name in HTSeq_counts.xlsx: N19


title: Osteal macrophage stimulated by 3%DSS 1weeks 1

description: Library name: DSS 1w 1

value: macrophage


title: HKDTR Knockout High Dose Tamoxifen Treated

description:
Library name: HKDTR_HDTAM
48 Hours Treatment

value: High Dose Tamoxifen


title: THP-1-1640-1

description:
Library name: THP1-0H-1
THP1-0H-1_FPKM

value: macrophage cell line

value: same


title: peripheral EDTA blood, Norma_12, rep1

description:
Library name: N21
Column name in HTSeq_counts.xlsx: N21


title: peripheral EDTA blood, Norma_18, rep1

description:
Library name: N32
Column name in HTSeq_counts.xlsx: N32


title: Young-Tesion-Replicate2

description:
Library name: YR2
raw_counts_tension.csv

value: primary dermal fibroblast

value: young:10 years old


title: Old-Tension-TGFb-Replicate2

description:
Library name: ORT2
raw_counts_tensionTGFb.csv

value: tesion with TGFb


title: peripheral EDTA blood, Norma_15, rep1

description:
Library name: N27
Column name in HTSeq_counts.xlsx: N27


title: Old-Tesion-Replicate1

description:
Library name: OR1
raw_counts_tension.csv

value: old:75 years old


title: Old-NoTesion-Replicate2

description:
Library name: ON2
raw_counts_tension.csv


title: Young-NoTesion-Replicate1

description:
Library name: YN1
raw_counts_tension.csv


title: Old-Tesion-Replicate2

description:
Library name: OR2
raw_counts_tension.csv


title: peripheral EDTA blood, Norma_11, rep1

description:
Library name: N20
Column name in HTSeq_counts.xlsx: N20

value: peripheral EDTA blood


title: Old-NoTesion-Replicate1

description:
Library name: ON1
raw_counts_tension.csv


title: WildType Control

description:
Library name: WT_Ctrl
No Treatment Control


title: brain_6

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

description: Library name: brain_6

data_processing:
Adaptors and low-quality bases were removed using fastp v0.19.6.
Trimmed reads were aligned to the human reference genome (hg38) using STAR 2.7.1a.
Pre-alignment and post-alignment quality control (QC) reports were generated using MultiQC
Differential expression analysis was conducted using DESeq2 in R.
Pathway enrichment analysis was performed using clusterProfiler.
Assembly: Human reference genome hg38 (Ensembl annotation).
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample (generated from RNA-seq analysis).

source_name: colorectal cancer brain metastasis (FFPE)

extract_protocol:
Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue samples using the High Pure RNA Isolation Kit (Roche) following manufacturer protocols. FFPE blocks were deparaffinized using xylene, followed by ethanol washes and proteinase K digestion before RNA purification using spin columns. RNA quantity and quality were assessed using NanoDrop and Agilent 2100 Bioanalyzer.
RNA libraries were prepared using the NEBNext® ULTRATM II RNA Library Prep Kit (New England BioLabs) according to the manufacturer’s instructions. A total of 1000 ng of RNA was used for fragmentation, cDNA synthesis, adapter ligation, and PCR amplification. Quality and quantity of the libraries were evaluated using Qubit and TapeStation before sequencing.

value: KRAS-Mutant


title: Old-NoTension-CTRL-Replicate1

description:
Library name: ONC1
raw_counts_tensionTGFb.csv

value: no tension without TGFb


title: liver_8

description: Library name: liver_8

source_name: colorectal cancer liver metastasis (FFPE)


title: peripheral EDTA blood, Norma_13, rep1

description:
Library name: N24
Column name in HTSeq_counts.xlsx: N24

value: Norma

value: Healthy


title: liver_6

description: Library name: liver_6

value: colorectal cancer liver metastasis (FFPE)


title: HKDTR Knockout Control

description:
Library name: HKDTR_Ctrl
No Treatment Control

value: Gastric Corpus


title: brain_2

description: Library name: brain_2

value: colorectal cancer brain metastasis (FFPE)


title: peripheral EDTA blood, Norma_7, rep1

description:
Library name: N14
Column name in HTSeq_counts.xlsx: N14


title: brain_1

description: Library name: brain_1


title: CITE-Seq, CD45-positive cells, mRNA data

city: Wuerzburg

first: Julia

last: Krug

email: ag.schmieder@gmail.com, krug_j@ukw.de

state: Bavaria

address: Josef-Schneider-Straße 2

department: Dermatology

institute: University Hospital Wuerzburg

description:
Library name: E6_gene_library
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Raw BCL files were de-multiplexed and corresponding FASTQ files for GEX. libraries were processed with Cellranger version 3.0.1 using the count mode with default parameters and mouse assembly 10 (mm10).
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: Tab-separated file of cell barcodes
Supplementary files format and content: features.tsv.gz: Tab-separated file of gene names and feature name
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange
Library strategy: CITE-seq

source_name: YUMM1.7-derived Melanoma

growth_protocol: Female C57BL/6J eight week old mice with either a floxed Nr3c1 allele (GRf/f) or with an additional Cre recombinase expressed under the Lyz2 promoter (GRf/f-LysMCre) were used for the generation of this data set. The mice were housed under pathogen-free conditions with water and food ad libitum.

extract_protocol:
Two million cells per sample were stained with separate hashtag antibodies and afterwards 8 samples were pooled for each library resulting in two libraries in total. The libraries were subsequently stained with a cocktail of 89 oligo-tagged surface marker antibodies combined with a CD45.2 antibody. After this staining procedure followed sorting for CD45-positive immune cells on a BD FACS Aria II.
Per library, 25,000 CD45-positive cells were processed using 10X Genomics Chromium Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (Dual Index) according to the manufacturer’s instructions.

treatment_protocol: 2,5x 10^5 YUMM1.7 were subcutaneously injected into GRf/f and GRf/f-LysMCre mice. When the tumors were palpable (around seven days post injection), the mice were treated with either anti-PD-1 therapy or isotype control antibody twice per week for additional three weeks (concentrations of therapeutic antibodies 12.5 mg/kg bodyweight). After 28 days post injection of the tumors, the melanoma were extracted and dissociated to single cell suspensions.

value: YUMM1.7-derived Melanoma

value: Mixed (Nr3c1 fl/fl only or LysM-Cre tg/wt+ Nrc3c1 fl/fl)

value: intratumoral CD45+ cells

value: mixed samples (anti-PD-1 antibody, Isotype Control Antibody)

value: mRNA


title: peripheral EDTA blood, Norma_6, rep1

description:
Library name: N11
Column name in HTSeq_counts.xlsx: N11


title: CITE-Seq, CD45-positive cells, ADT data

description:
Library name: E6_citeseq_library
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

library_source: other

value: ADT

tag: adt

value: see feature_reference file for details


title: liver_3

description: Library name: liver_3


title: peripheral EDTA blood, Norma_2, rep1

description:
Library name: N2
Column name in HTSeq_counts.xlsx: N2


title: liver_1

description: Library name: liver_1


title: liver_9

description: Library name: liver_9


title: RNA_67NR_Fusion

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

description:
10x Genomics
RNA_67NR_Fusion

data_processing:
All procedures were made using Cell Ranger software
Assembly: mm10
Supplementary files format and content: h5 files, fragment.tsv and fragment.tsv.tbi files

source_name: primary breast tumor

extract_protocol:
10X Chromium Single Cell Multiome ATAC + Gene Expression
DNA and RNA from indexed cells were extracted from following the 10X Chromium Nuclei Isolation Kitl.
Library preparation follows the 10X Chromium Single Cell Multiome ATAC + Gene Expression protocol.

value: primary breast tumor

value: Murine mammary tumor

value: WGD+

value: In culture

value: Multiome Gene Expression


title: CITE-Seq, CD45+ cells, ADT data

description:
Library name: E5_citeseq_library
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads


title: peripheral EDTA blood, Norma_9, rep1

description:
Library name: N18
Column name in HTSeq_counts.xlsx: N18

value: peripheral EDTA blood

value: Norma


title: liver_2

description: Library name: liver_2

value: colorectal cancer liver metastasis (FFPE)

value: KRAS-Mutant


title: peripheral EDTA blood, Norma_8, rep1

description:
Library name: N15
Column name in HTSeq_counts.xlsx: N15

value: Healthy


title: Mouse 5425-T1, male, infected, 18mpi

city: New York

first: Brad

last: Rosenberg

state: New York

address: 1 Gustave L Levy Pl

department: Microbiology

description:
Library name: m2561_5425-T1
Base comparison, liver m2561

data_processing:
Processed FASTQ files were mapped to the mouse reference genome mm10 (GRCm38) using BWA-MEM.
Local realignment and quality score recalibration was performed using Genome Analysis Toolkit (GATK) according to GATK best practices.
Sample variant calling was performed on tumor samples and normal samples to identify point mutations/single nucleotide variants (SNVs) and small insertions/ deletion (indels).
MuTect (version 1.1.7) was used for SNV calling and SomaticIndelDetector, a tool in GATKv.2.3.9, was used for detecting indel events.
Variants were subsequently annotated using Annovar, and annotations relative to the canonical transcript for each gene (derived from a list of known canonical transcripts obtained from the UCSC genome browser) were reported. Variant allele frequency (VAF) was determined by calculating the fraction of variant reads for a specific out of the total reads at that location.
Assembly: mouse reference genome mm10 (GRCm38)
Supplementary files format and content: Processed data file provided is Mutation Annotation Format (MAF) is a tab-delimited text file/csv with aggregated mutation information from VCF Files.
Library strategy: DNA-Seq

source_name: tumor

extract_protocol:
For the detection of somatic genomic alterations in NrHV-elicited tumors, we extracted genomic DNA from tumor and normal uninfected liver samples and gDNA was enriched for targeted regions using a solution-phase hybridization-based exon capture as previously described (A. Zehir et al. 2017).
M-IMPACT_v2 (mouse version) assay covers more than 600 known cancer driver genes - library preparation and sequencing analysis was performed by the MSKCC Bioinformatics Core.

value: tumor

value: NrHV viral infection


title: liver_7

description: Library name: liver_7


title: liver_4

description: Library name: liver_4


title: liver_10

description: Library name: liver_10


title: peripheral EDTA blood, Norma_5, rep1

description:
Library name: N10
Column name in HTSeq_counts.xlsx: N10


title: Mouse 5475-T1, female, infected, 18mpi

description:
Library name: m2561_5475-T1
Base comparison, liver m2561


title: Mouse 5422-T1, male, infected, 18mpi

description:
Library name: m2561_5422-T1
Base comparison, liver m2561


title: Mouse 5433-T, male, infected, 18mpi

description:
Library name: m2561_5433-T
Base comparison, liver m2561


title: liver_5

description: Library name: liver_5


title: Mouse 5402-T1, female, infected, 18mpi

description:
Library name: m2561_5402-T1
Base comparison, liver m2561


title: brain_7

description: Library name: brain_7

value: colorectal cancer brain metastasis (FFPE)


title: CITE-Seq, CD45-positive cells, Hashtag data

description:
Library name: E6_HTO
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: YUMM1.7-derived Melanoma

value: Mixed (Nr3c1 fl/fl only or LysM-Cre tg/wt+ Nrc3c1 fl/fl)

value: intratumoral CD45+ cells

value: mixed samples (anti-PD-1 antibody, Isotype Control Antibody)

value: HTO

tag: hto


title: ATAC_67NR_Fusion

description:
10x Genomics
ATAC_67NR_Fusion

value: primary breast tumor

value: Murine mammary tumor

value: Multiome ATAC


title: Mouse 5475-T2, female, infected, 18mpi

description:
Library name: m2561_5475-T2
Base comparison, liver m2561


title: CITE-Seq, CD45+ cells, Hashtag data

description:
Library name: E5_HTO
HTO library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads

value: see feature_reference file for details


title: peripheral EDTA blood, Norma_4, rep1

description:
Library name: N5
Column name in HTSeq_counts.xlsx: N5

value: peripheral EDTA blood


title: brain_3

description: Library name: brain_3


title: brain_5

description: Library name: brain_5


title: ATAC_67NR_Parental

description:
10x Genomics
ATAC_67NR_Parental

value: WGD-

value: In culture


title: CITE-Seq, CD45+ cells, mRNA data

description:
Library name: E5_gene_library
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA


title: GEX_TA3_Hauschka_Fusion

description:
10x Genomics
GEX_TA3_Hauschka_Fusion

value: WGD+

value: Multiome Gene Expression


title: F6L

growth_protocol: Primary tumors were induced by injecting cells into mammary fat pads of A/J or NSG mice.

extract_protocol:
Whole tumors were disrupted using micropestles and digested for 1h at 37C on a shaker with digestion medium (2% w/v collagenase IV, 2% w/v hyaluronidase and 2% w/v BSA in DMEM). Cells were filtered through 500 µm meshes, washed with PBS and stored in freezing medium.
Library was prepared following 10X Chromium Single Cell ATAC instruction

value: MFP injection in A/J mice


title: RNA_67NR_Parental

description:
10x Genomics
RNA_67NR_Parental


title: Mouse 5429-T1, male, infected, 18mpi

description:
Library name: m2561_5429-T1
Base comparison, liver m2561

value: tumor

value: NrHV viral infection


title: Mouse 5477-T1, female, infected, 18mpi

description:
Library name: m2561_5477-T1
Base comparison, liver m2561


title: brain_4

description: Library name: brain_4

value: colorectal cancer brain metastasis (FFPE)

value: KRAS-Mutant


title: peripheral EDTA blood, CeAD_17, rep1

description:
Library name: DS32
Column name in HTSeq_counts.xlsx: DS32

value: CeAD

value: 3-month anticoagulation post-dissection


title: ATAC_TA3_Hauschka_Fusion

description:
10x Genomics
ATAC_TA3_Hauschka_Fusion

value: primary breast tumor


title: peripheral EDTA blood, CeAD_19, rep1

description:
Library name: DS34
Column name in HTSeq_counts.xlsx: DS34


title: peripheral EDTA blood, rLDH_11, rep1

description:
Library name: DS26
Column name in HTSeq_counts.xlsx: DS26

value: rLDH

value: Spinal disc surgery:L5-S1 (2 operations)


title: GEX_TA3_Hauschka_Parent

description:
10x Genomics
GEX_TA3_Hauschka_Parent

value: Murine mammary tumor


title: peripheral EDTA blood, Norma_1, rep1

description:
Library name: N1
Column name in HTSeq_counts.xlsx: N1

value: peripheral EDTA blood

value: Norma

value: Healthy


title: Mouse 5423-T1, male, infected, 18mpi

description:
Library name: m2561_5423-T1
Base comparison, liver m2561


title: peripheral EDTA blood, Norma_3, rep1

description:
Library name: N4
Column name in HTSeq_counts.xlsx: N4


title: Mouse 5432-T1, male, infected, 18mpi

description:
Library name: m2561_5432-T1
Base comparison, liver m2561


title: Mouse 5454-T1, male, infected, 18mpi

description:
Library name: m2561_5454-T1
Base comparison, liver m2561


title: Mouse 5470-T1, female, infected, 18mpi

description:
Library name: m2561_5470-T1
Base comparison, liver m2561


title: peripheral EDTA blood, CeAD_16, rep1

description:
Library name: DS31
Column name in HTSeq_counts.xlsx: DS31


title: Mouse 5447, female, mock, 18mpi

description: Library name: cohort18mpi_J2

data_processing:
Read quality was assessed using fastQC (v0.11.9) and reads were trimmed using fastp (v0.23.2)
For quantification of RNA expression, the Salmon (v1.4.0) package was used using the selective-alignment algorithm
Mapped reads to concatenated GRCm39 and B+4 NrHV transcriptome, where NrHV transcriptome was entire RNA genome of the virus (GenBank accession no. KX905133)
TPM normalized abundance output from Salmon read into R using tximport package (v1.18.0)
Assembly: Genome Reference Consortium Mouse Build 39
Supplementary files format and content: Salmon pseudoalignment output in .sf format is a quantification file that includes TPM (relative abundance) values and estimated number of reads mapping to each transcript, quantified for each sample

source_name: normal liver

extract_protocol:
Liver slices previously flash-frozen and pulverized using liquid nitrogen were used for RNA and DNA isolation. Both nucleic acids were isolated from the same liver slice using Allprep Qiagen kit (QIAGEN) following manufacturer’s instructions with addition of RNase inhibitor and DNAseI to the original RNA isolation protocol. Samples were quality checked prior submission to bulk RNAseq. A RIN above 7 was accepted for downstream library preparation and sequencing. Samples that did not reach the criteria for downstream analysis were purified using either RNA mini kit (Zymo) or DNA purification kit (Zymo)
Total RNA previously isolated from livers were submitted to Novogene for bulk RNA sequencing. Samples were enriched for mRNA using polyA selection. Libraries were produced using directional mRNA preparation and submitted to Novaseq PE150, with about 20M depth per sample.

value: normal liver


title: Mouse 2561, female, mock, 18 mo

description:
Library name: m2561
Base comparison, liver m2561

source_name: liver

value: liver


title: Mouse 5441, male, mock, 18mpi

description: Library name: cohort18mpi_J1


title: Mouse 5452-T2, male, infected, 18mpi

description:
Library name: m2561_5452-T2
Base comparison, liver m2561


title: peripheral EDTA blood, CeAD_18, rep1

description:
Library name: DS33
Column name in HTSeq_counts.xlsx: DS33


title: peripheral EDTA blood, CeAD_15, rep1

description:
Library name: DS30
Column name in HTSeq_counts.xlsx: DS30


title: PT_10R

value: WGD-


title: Mouse 2586-T , male, infected, 18 mo

description:
Library name: m2561_2586-T
Base comparison, liver m2561


title: peripheral EDTA blood, CeAD_14, rep1

description:
Library name: DS28
Column name in HTSeq_counts.xlsx: DS28