title: Spheroid-IVA-2

city: Shanghai

last: Li

state: 279 Zhouzhu RD, Pudong New District

address: Zhou

institute: Shanghai University of Medicine and Health Sciences

description:
Library name: sample14
Spheroid iva-readcount.txt

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 . After that, Ericscript (v0.5.5) and rMATS (V4.1.2)  were used to detect fusion genes and differential splicing genes (DSGs), respectively
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included
Expression level of gene was calculated by RSEM (v1.3.1). The heatmap was drawn by pheatmap (v1.0.12) according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.34.0) [8] (or DEGseq （v1.48.0） or PoissonDis )with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw gene counts for each sample

source_name: Human liver spheroid

extract_protocol:
Total RNA was extracted with RNeasy Micro Kit（QIAGEN，Germany） following the manufacturer’s instructions.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Then First-strand cDNA is generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized double strand cDNA is subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the reaction system for adaptor ligation configured to ligate adaptors with the cDNAs, and finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded cyclized DNA products. Any uncyclized single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and PE 150 bases reads are generated on T7 platform (BGI-Shenzhen, China).

value: Human liver spheroid

value: NASH donor


title: Whole_Blood_Severe_44

status: Public on Jun 18 2025

type: RNA

city: Amsterdam

first: Cosimo

last: Cristella

address: Meibergdreef 9

department: Medical microbiology and infection prevention

country: Netherlands

institute: Amsterdam University Medical Centers

description: Whole blood gene expression of critically ill Sars-CoV2 infected patients

hyb_protocol: Hybridization, wash and staining was performed using the GeneTitan™ Hybridization, Wash, and Stain Kit for WT Array Plates (Termofisher, Applied Biosystems™)

scan_protocol: Arrays were scanned using the GeneTitan instrument (Termofisher, Applied Biosystems™)

data_processing: The BrainArray (version 25) custom Chip Description File (CDF) was used to re-map probesets on the arrays based on the latest genome and transcriptome information (Dai et al., 2005). Probesets normalization was achieved by Robust Multi-array Average (RMA) function implemented in the Affy R package.

label: Biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Total RNA was used as input for the amplification and labelling of samples using the Clariom™ S Assay HT, human (Thermofisher, Applied Biosystems™)

extract_protocol: Total RNA was extracted by TempusTM Spin RNA isolation kit following manufacturer guidelines. Samples were concentrated by speedVac or diluted with nuclease-free water in order to ensure a normalised concentration of 33ng/ul in a 20ul volume.

treatment_protocol: DNase treatment using PureLink DNase Set

tag: tissue

value: Whole blood

tag: age

tag: gender

value: Male

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: LIU-LSC-1, epithelium, PRMT1 knockdown, rep 3

type: SRA

city: HeFei

first: Liu

last: Shixian

address: No. 81 Meishan Road

country: China

institute: Anhui Medical University

library_source: transcriptomic

data_processing:
Cutadapt was used to filter out unqualified sequences (sequencing adapters, low-quality sequences, etc.) from the raw data
Hisat2 was used for reference genome alignment
StringTie was ued to reconstruct transcripts and calculate the expressions of all genes in each sample
Assembly: hg18
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

molecule: polyA RNA

source_name: epithelium

extract_protocol:
RNA was extracted and purified using TRIzol (Thermo Fisher, 15596018). A concentration>50ng/µL, RIN value>7.0, and total RNA>1µg are sufficient for downstream experiments. Use oligo (dT) magnetic beads (Dynabeads Oligo (dT), cat. 25-61005, Thermo Fisher, USA) to specifically capture mRNA containing PolyA (polyadenylation) through two rounds of purification. The captured mRNA was fragmented using the NEBNextR Magnesium RNA Fragmentation Module (cat. E6150S, USA) under high temperature conditions at 94 ℃ for 5-7 minutes.
cDNA was synthesized using Invitrogen SuperScriptTM II Reverse Transcriptase (cat. 1896649, CA, USA), and E Escherichia coli DNA polymerase I (NEB, cat. m0209, USA) and RNase H (NEB, cat. m0297, USA) were subjected to double stranded synthesis. The double stranded DNA was digested using UDG enzyme (NEB, cat. m0280, MA, US), and a library with fragment size of 300bp ± 50bp was formed by PCR (chain specific library)

value: epithelium

tag: cell line

tag: cell type

value: head and neck squamous cell carcinoma cells


title: Whole_Blood_Severe_53

value: Thrombotic


title: epithelium, HA-PBX2, rep 2

library_source: genomic

data_processing:
Cutadapt was used to filter out unqualified sequences (sequencing adapters, low-quality sequences, etc.) from the raw data
Assembly: hg18
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
Initially, sample preprocessing involved the conversion of samples into cell suspensions, followed by cell collection and enumeration. Subsequent steps included cell washing, primary antibody binding, and subsequent addition of secondary antibodies. Following secondary antibody binding, the product underwent washing and interaction with ChiTagTM transposase.
Sequencing of the library was conducted on the Illumina platform. For qualified libraries, NaOH was utilized to denature the library into single strands. The denatured library was diluted to a specific concentration based on the expected data volume and then introduced to the FlowCell. Hybridization of the denatured and diluted library with adapters on the FlowCell was followed by bridge PCR amplification on the cBot cluster generation platform, culminating in sequencing on the designated platform.

tag: group


title: LIU-LSC-1, epithelium, PRMT1 knockdown, rep 2


title: Whole_Blood_Severe_48


title: Whole_Blood_Severe_47


title: Spheroid-IVA-1

description:
Library name: sample13
Spheroid iva-readcount.txt

tag: disease state


title: Whole_Blood_Severe_50

value: Female


title: Whole_Blood_Severe_46


title: Whole_Blood_Severe_54


title: Whole_Blood_Severe_52


title: Whole_Blood_Severe_51


title: LIU-LSC-1, epithelium, control, rep 3


title: Whole_Blood_Severe_43


title: Whole_Blood_Severe_49


title: Whole_Blood_Severe_36


title: Whole_Blood_Severe_42


title: LIU-LSC-1, epithelium, PRMT1 knockdown, rep 1


title: Whole_Blood_Severe_33


title: Whole_Blood_Severe_40


title: Whole_Blood_Severe_32


title: Whole_Blood_Severe_41


title: Whole_Blood_Severe_38


title: Whole_Blood_Severe_37


title: Whole_Blood_Severe_39


title: Spheroid-NASH-2

description:
Library name: sample12
Spheroid iva-readcount.txt


title: Whole_Blood_Severe_35


title: LIU-LSC-1, epithelium, control, rep 2


title: Spheroid-NASH-1

description:
Library name: sample11
Spheroid iva-readcount.txt


title: LIU-LSC-1, epithelium, control, rep 1


title: Spheroid-CTRL-2

description:
Library name: sample10
Spheroid iva-readcount.txt


title: Whole_Blood_Severe_31


title: Whole_Blood_Severe_30


title: Spheroid-CTRL-1

description:
Library name: sample9
Spheroid iva-readcount.txt


title: FP_PLVX_80_Rep4

city: Guadalajara

first: Adriana

middle: del Carmen

last: Aguilar Lemarroy

state: Jalisco

address: Sierra Mojada #800, Colonia Independencia

department: División de Inmunología

country: Mexico

institute: Centro de Investigación Biomédica de Occidente

data_processing:
The execution of the bioinformatics pipeline analysis was carried out as follow: R (ver. 4.4.1), RStudio (2024.09.0+375) and Galaxy (https://www.usegalaxy.org accessed on 05 September 2024) open-source platforms were used to analyze the Illumina raw data
The Quality Control was conducted through the FastQC tool (v0.74+galaxy0).
Afterward, all the reads were processed by the Rsubread package (v2.14.2); at that point, the reads were trimmed and aligned to the Human Genome Reference (GRCh38.p13 v46).
The obtained output was the BAM files, of which the number of reads was counted by the FeatureCounts tool (v2.0.3).
At the final step, the Differential Expression Analysis was settled by the DESeq2 package for R (v1.42. 0). The differential gene expression measurements were normalized by DESeq2's median of ratios (median of ratio of gene counts relative to geometric mean per gene) method.
Assembly: All reads were mapped and aligned to the Human Reference Genome GRCh38.p13v46 using the Rsubread package (Ver. 2.14.2) with the align function.
Supplementary files format and content: Tab-delimited text file includes normalized counts for each sample.

source_name: Dermal-Connective

growth_protocol: Fibroblast models were cultivated in Dulbecco's Modified Eagle Medium (DMEM) supplemented with GlutaMAX™ (584 mg/L), sodium pyruvate (110 mg/L), D-glucose (1 g/L) (Cat. No. 10567-014 Gibco, Thermo Fisher Scientific, Waltham, MA, USA), penicillin (100 U/mL), streptomycin (100 μg/mL), and 10% fetal bovine serum. Cell cultures were incubated at 37°C in a humidity atmosphere with 5% CO2.

extract_protocol:
Treated cell lines were seeded in 100 mm tissue culture dishes (Corning, NY, USA, Cat. 430167) at a density of 3x106 and incubated under previous conditions overnight. Subsequently,  the cells were harvested for RNA extraction using the column-based extraction and purification system Zymo Quick-RNA MiniPrep (Zymo Research Corp., Irvine, CA, USA) following manufacturer's instructions. The obtained RNA was quantified by absorbance at 260/280 nm and stored at -80°C until further use.
First, total RNA is fragmented into 150 pb segmentes. Second, Reverse transcription is achive to obtain cDNA. Third, ligation of adapters at the ends.

treatment_protocol: Cells were transduced with lentiviral vectors (MOI 5) to induce the constitutive expression of E6/E7 HPV80 genes, aftermath cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence for some passages before functional tests and total RNA extraction. Cells were selected by adding puromicine (0.3 micrograms/mL) to culture medium during 2 weeks

value: Dermal-Connective

value: Primary skin fibroblast

tag: treatment

value: pLVX_E6/E7 HPV80


title: Whole_Blood_Severe_29


title: FP_PLVX_80_Rep3


title: Whole_Blood_Severe_27


title: Whole_Blood_Severe_28


title: 55SC-IVA-2

description:
Library name: sample8
hHSC iva-readcount.txt

source_name: Primary hepatic stellate cells

value: Primary hepatic stellate cells


title: GLA-KO+siRNA-HLNP hiPSC-PC_2

city: Seoul

first: Yoo Jin

last: Shin

address: 222, Banpo-daero, Seocho-gu,

department: Transplantation Research Center

country: South Korea

institute: College of Medicine, The Catholic University of Korea

data_processing:
Illumina bcl2fastq (v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastp), then mapped to GRCh38 (NCBI) whole genome using STAR.
Read count extraction using HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: GLA-KO hiPSC-PC

growth_protocol: iPSC-ECs were maintained in STEMdiff™ Endothelial Expansion Medium. iPSC-PCs were cultured in DMEM/F12 containing Glutamax and 1X B27, supplemented with 100 ng/ml BMP7, 100 ng/ml Activin A, 50 ng/ml VEGF, 3 μM CHIR99021, and 0.1 μM RA. All cell types were cultured in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.

treatment_protocol: hiPSC-ECs and hiPSC-PCs were treated with 20 μg/mL of A4GALT siRNA-HLNP for 24 hours.

value: GLA-KO hiPSC-PC

value: iPSC-derived podocyte

tag: genotype

value: GLA-knock out

value: A4GALT siRNA-HLNP


title: FP_PLVX_80_Rep2


title: 55SC-IVA-1

description:
Library name: sample7
hHSC iva-readcount.txt


title: FB_PLVX_80_Rep1


title: 55SC-CTRL-2

description:
Library name: sample6
hHSC iva-readcount.txt


title: FB_PLVX_6

value: pLVX-Puro


title: 55SC-CTRL-1

description:
Library name: sample5
hHSC iva-readcount.txt


title: FB_PLVX_5


title: Whole_Blood_Severe_22


title: Whole_Blood_Severe_24


title: FB_PLVX_3


title: 00SC-IVA-2

description:
Library name: sample4
hHSC iva-readcount.txt

value: NAFL donor


title: Whole_Blood_Severe_19


title: Whole_Blood_Severe_21


title: FB_PLVX_4


title: 00SC-IVA-1

description:
Library name: sample3
hHSC iva-readcount.txt


title: FB_PLVX_2


title: Whole_Blood_Severe_20


title: Whole_Blood_Severe_26


title: 00SC-CTRL-1

description:
Library name: sample1
hHSC iva-readcount.txt


title: Whole_Blood_Severe_17


title: FB_PLVX_1


title: Whole_Blood_Severe_18


title: Whole_Blood_Severe_14


title: Whole_Blood_Severe_15


title: Whole_Blood_Severe_25


title: Whole_Blood_Severe_16


title: 00SC-CTRL-2

description:
Library name: sample2
hHSC iva-readcount.txt


city: Beijing

first: Yao

last: Lv

state: Beijing

address: No. 7 Science Park Road, Zhongguancun Life Science Park, Changping District,   Beijing 102206, P.R. China

institute: National Institute of Biological Sciences,Beijing

description:
Library name: Lung epi IL-33KO mice LSL2
IL-33 KO mouse lung epithelial cells, seq2 LSL2, 6h

data_processing:
Raw sequencing data were processed using Fastp (version 0.19.7) to remove adaptors and low-quality reads according to the following criteria: (1) paired reads were discarded if either read contained adapter contamination; (2) paired reads were discarded if more than 10% of bases were uncertain in either read; (3) paired reads were discarded if the proportion of low-quality bases (Phred quality < 5) exceeded 50% in either read.
Filtered reads were then aligned to the mouse reference genome (mm10) or the human reference genome (hg19) using HISAT2 (v2.2.1)
The resulting SAM files were converted to sorted BAM files using Samtools
Gene annotations were based on the GENCODE mouse release M25 and GENCODE human release 19 comprehensive gene annotation files.Rawcounts were extracted with featureCounts (v2.0.2)
Read count normalization and differential gene expression analysis were performed using DESeq2 (v1.36.0) in the R environment (v4.2.2)
Assembly: mm10, hg19
Supplementary files format and content: format:txt, content:raw counts of each sample in the experiment

organism: Mus musculus

source_name: lung

growth_protocol: Mice were bred and maintained in the animal facility under specific pathogen-free conditions.Cells were cultured in RPMI 1640 medium (Gibco) supplemented with 10% heat-inactivated FBS (GEMINI Cat 900-108), 100 U/ml penicillin, and 100 μg/ml streptomycin (Gibco), and were maintained in a humidified incubator at 37 °C with 5% CO2.

extract_protocol:
RNAprep Pure Cell/Bacteria Kit (TIANGEN, Cat: DP430)
RNA-seq libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) following manufacturer’s protocols.

value: lung

value: lung epithelial cell

value: IL-33 KO


title: Whole_Blood_Severe_10

value: Whole blood

value: Male


title: Whole_Blood_Severe_13

value: Thrombotic


title: Whole_Blood_Severe_7


title: Whole_Blood_Severe_9


title: HGU-053, HC

city: Pohang

first: Sarah

last: Kim

address: 558, Handong-ro, Buk-gu

institute: Handong Global University

data_processing:
In this study, we processed the Fastq files using Trimmomatic (version 0.39) to clip sequence adapters and trim reads based on quality metrics. Subsequently, we aligned the sequencing reads to the human GRCh38 genome reference using HISAT2 (version 2.1.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: blood

extract_protocol:
RNA extraction from stored platelet samples was performed using the miRVana RNA isolation kit
The SMART-Seq v4 Ultra Low Input RNA Kit was employed for the cDNA synthesis and amplification process. The amplified cDNA samples underwent shearing via sonication and were subsequently labeled with index barcodes suitable for Illumina sequencing using the Truseq Nano DNA Sample Prep Kit platform.

value: blood


description:
Library name: Lung epi IL-33KO mice LSL1
IL-33 KO mouse lung epithelial cells, seq2 LSL1, 6h


title: Whole_Blood_Severe_8


title: Whole_Blood_Severe_4


title: HGU-022, HC


description:
Library name: Lung epi IL-33KO mice PlyA2EryB2
IL-33 KO mouse lung epithelial cells, seq2 PlyA2EryB2, 6h


description:
Library name: Lung epi IL-33KO mice PlyA2EryB1
IL-33 KO mouse lung epithelial cells, seq2 PlyA2EryB1, 6h


title: Whole_Blood_Severe_11

description: Whole blood gene expression of critically ill Sars-CoV2 infected patients


title: HGU-019, HC


title: Whole_Blood_Severe_6


description:
Library name: Lung epi IL-33KO mice Lysenin2
IL-33 KO mouse lung epithelial cells, seq2 Lysenin2, 6h


title: Whole_Blood_Severe_2


title: Whole_Blood_Severe_5

value: Female


title: Whole_Blood_Severe_34


title: HGU-016, HC


title: Whole_Blood_Severe_57


title: Whole_Blood_Severe_23


title: Whole_Blood_Severe_45


description:
Library name: Lung epi IL-33KO mice Mock2_2
IL-33 KO mouse lung epithelial cells, seq2 DPBS ctrl2, 6h


title: SNUH-211, OC


title: SNUH-215, EC


description:
Library name: Lung epi IL-33KO mice Lysenin1
IL-33 KO mouse lung epithelial cells, seq2 Lysenin1, 6h


title: Whole_Blood_Severe_12


title: HGU-021, HC


description:
Library name: Lung epi IL-33KO mice Mock2_1
IL-33 KO mouse lung epithelial cells, seq2 DPBS ctrl1, 6h


title: SNUH-208, OC


description:
Library name: Lung epi LSL2
mouse lung epithelial cells, seq4 LSL2, 6h

value: WT


description:
Library name: Lung epi LSL1
mouse lung epithelial cells, seq4 LSL1, 6h


title: SNUH-207, EC


description:
Library name: Lung epi PlyA2EryB2
mouse lung epithelial cells, seq4 PlyA2EryB2, 6h


title: Whole_Blood_Severe_1


title: Whole_Blood_Control_53

description: Whole blood gene expression of convalescent patients from diverse viral infections


title: Whole_Blood_Severe_58


title: Whole_Blood_Control_13


title: Whole_Blood_Control_14


title: Whole_Blood_Severe_55


title: Whole_Blood_Control_16


title: Whole_Blood_Control_28


title: SNUH-202, OC


title: Whole_Blood_Control_57


title: Whole_Blood_Control_51


title: Whole_Blood_Control_42


description:
Library name: Lung epi PlyA2EryB1
mouse lung epithelial cells, seq4 PlyA2EryB1, 6h


title: SNUH-209, EC


title: Whole_Blood_Control_58


description:
Library name: Lung epi Lysenin2
mouse lung epithelial cells, seq4 Lysenin2, 6h


title: SNUH-200, EC


title: Whole_Blood_Control_20


title: TLR5 KO-MCD-5

city: Hwasun-gun, Jeollanam-do

first: Dong-Hyun

state: Not Applicable

address: 264, Seoyang-ro, Hwasun-eup,

institute: Medispan

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10(UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: LIVER

value: LIVER

value: Toll-like receptor 5 knockout (TLR14 KO)

value: methionine-choline deficient (MCD) diet


title: Whole_Blood_Severe_56


title: Whole_Blood_Control_11


title: SNUH-192, EC


title: TLR5 KO-MCD-4

value: Toll-like receptor 5 knockout (TLR13 KO)


title: Whole_Blood_Control_19


description:
Library name: Lung epi Mock4_2
mouse lung epithelial cells, seq4 DPBS ctrl2, 6h


title: Whole_Blood_Control_31


title: SNUH-188, EC


title: Whole_Blood_Control_29


title: SNUH-201, EC


title: Whole_Blood_Control_8


description:
Library name: Lung epi Mock4_1
mouse lung epithelial cells, seq4 DPBS ctrl1, 6h


title: TLR5 KO-MCD-3

value: Toll-like receptor 5 knockout (TLR12 KO)


description:
Library name: Lung epi Rag2gcdKO mice Aeg-S/L2
Rag2gcdKO mouse lung epithelial cells, Aeg-S/L_2, 6h


title: SNUH-185, OC


title: TLR5 KO-MCD-1

value: Toll-like receptor 5 knockout (TLR10 KO)


title: TLR5 KO-MCD-2

value: Toll-like receptor 5 knockout (TLR11 KO)


title: SNUH-182, EC


description:
Library name: Lung epi Rag2gcdKO mice Aeg-S/L1
Rag2gcdKO mouse lung epithelial cells, Aeg-S/L_1, 6h


title: TLR5 KO-ND-5

value: Toll-like receptor 5 knockout (TLR9 KO)

value: normal diet


title: SNUH-174, OC


description:
Library name: Lung epi Lysenin1
mouse lung epithelial cells, seq4 Lysenin1, 6h

value: lung

value: lung epithelial cell


title: SNUH-172, EC


description:
Library name: Lung epi Rag2gcdKO mice Mock2
Rag2gcdKO mouse lung epithelial cells, DPBS ctrl2, 6h


title: TLR5 KO-ND-4

value: Toll-like receptor 5 knockout (TLR8 KO)


title: Whole_Blood_Control_23

value: Whole blood

value: Male


title: Whole_Blood_Control_1


title: Whole_Blood_Control_37


title: Whole_Blood_Control_6


title: Whole_Blood_Control_47


title: SNUH-169, OC

value: blood


title: TLR5 KO-ND-3

value: Toll-like receptor 5 knockout (TLR7 KO)


title: SNUH-166, OC


title: TLR5 KO-ND-2

value: Toll-like receptor 5 knockout (TLR6 KO)


description:
Library name: Lung epi IL-33KO mice Aeg-S/L1
IL-33 KO mouse lung epithelial cells, seq1 Aeg-S/L_1, 6h

value: IL-33 KO


title: SNUH-165, Benign


description:
Library name: Lung epi IL-33KO mice Aeg-S/L2
IL-33 KO mouse lung epithelial cells, seq1 Aeg-S/L_2, 6h


description:
Library name: Lung epi IL-33KO mice ALT2
IL-33 KO mouse lung epithelial cells, seq1 ALT2, 6h


title: SNUH-163, EC


title: WT-MCD-5

value: LIVER

value: wild-type


title: TLR5 KO-ND-1

value: Toll-like receptor 5 knockout (TLR5 KO)


description:
Library name: Lung epi IL-33KO mice ALT1
IL-33 KO mouse lung epithelial cells, seq1 ALT1, 6h


title: SNUH-162, EC


title: WT-MCD-4

value: methionine-choline deficient (MCD) diet


title: Whole_Blood_Control_41

value: Female


description:
Library name: Lung epi IL-33KO mice Mock1_2
IL-33 KO mouse lung epithelial cells, seq1 DPBS ctrl2, 6h


description:
Library name: Lung epi Rag2gcdKO mice Mock1
Rag2gcdKO mouse lung epithelial cells, DPBS ctrl1, 6h


title: SNUH-161, EC


title: WT-MCD-3


description:
Library name: Lung epi IL-33KO mice Mock1_1
IL-33 KO mouse lung epithelial cells, seq1 DPBS ctrl1, 6h


title: Whole_Blood_Control_21


title: SNUH-160, EC


title: Whole_Blood_Control_24


title: WT-MCD-2


title: M18-Old

city: New Haven

first: Jessica

middle: Yuki

last: Kasamoto

state: CT

address: 300 George Street

department: Computational Biology and Bioinformatics

country: USA

institute: Yale University

description:
Library name: M18
Old (20 months)

data_processing:
Samples were sequenced using 100bp paired-end sequencing on a NovaSeq 6000 (Illumina) according to the manufacturer’s protocols targeting 100+ M read pairs/sample.
Reads were aligned to Mus Musculus reference genome assembly GRCm39 using STAR/2.7.9a. Transcript feature counts were obtained using Subread’s featureCounts function.
Raw counts for our dataset was normalized to Transcripts Per Million (TPM) as previously described (González et al., 2025; Schaum et al., 2020; Stoeger et al., 2022).
Assembly: mm10
Supplementary files format and content: Transcripts Per Million (TPM) for each Sample

source_name: Liver

growth_protocol: Male C57BL/6J mice aged 6 months (young) and 21 months (old) were obtained from The Jackson Laboratory (stock number: 000664).

extract_protocol:
RNA was extracted according to the manufacturer’s protocols for each kit. For RNA isolation, the optional on-column DNase digestion step (Qiagen, 79254) was included for all samples. RNA was extracted using either the AllPrep DNA/RNA Mini Kit (Qiagen, 80204; samples M1, M5, M7, M8, M9, M10, M13, and M18) or the RNeasy Mini Kit (Qiagen, 74104; samples M2, M3, M4, M6, M11, M12, M14, M15, M16, and M17).
The Yale Center for Genome Analysis performed the following steps. RNA quality was estimated with A260/A280 and A260/A230 nanodrop ratios, and RNA integrity was evaluated using an Agilent Bioanalyzer gel. rRNA depletion, cDNA synthesis, and library preparation were done with the Kapa RNA HyperPrep Kit with RiboErase (KR1351).

treatment_protocol: Frozen liver tissues collected immediately following hyperinsulinemic-euglycemic clamp and used for RNA extraction

value: Liver

tag: metaboliccageid

tag: agecategory

value: Old

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: vo2 perkg_dark

tag: vco2 perkg_dark

tag: ee perkg_dark

tag: feed g_perkg_dark

tag: feed kcal_perkg_dark

tag: drink perkg_dark

tag: rer dark

tag: activitycounts dark

tag: vo2 perlbm_dark

tag: vco2 perlbm_dark

tag: ee perlbm_dark

tag: feed g_perlbm_dark

tag: feed kcal_perlbm_dark


title: SNUH-156, Benign

tag: tissue


title: Whole_Blood_Control_27

tag: age

tag: gender

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: WT-MCD-1

tag: genotype

tag: treatment


title: M17-Old

description:
Library name: M17
Old (20 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: vo2 perkg_dark

tag: vco2 perkg_dark

tag: ee perkg_dark

tag: feed g_perkg_dark

tag: feed kcal_perkg_dark

tag: drink perkg_dark

tag: rer dark


title: SNUH-154, EC

tag: tissue


title: WT-ND-5

tag: genotype

tag: treatment

value: normal diet


title: Whole_Blood_Control_52

tag: age

tag: gender

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: Whole_Blood_Control_45


title: WT-ND-4


title: Whole_Blood_Control_36


title: SNUH-149, EC


title: M16-Old

description:
Library name: M16
Old (20 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: vo2 perkg_dark

tag: activitycounts dark

tag: vo2 perlbm_dark

tag: vco2 perlbm_dark

tag: ee perlbm_dark

tag: feed g_perlbm_dark

tag: feed kcal_perlbm_dark


title: SNUH-148, OC

tag: tissue


title: Whole_Blood_Control_12

tag: age

tag: gender

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: WT-ND-3

tag: genotype

tag: treatment


title: M14-Old

description:
Library name: M14
Old (20 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: vo2 perkg_dark

tag: vco2 perkg_dark

tag: ee perkg_dark

tag: feed g_perkg_dark

tag: feed kcal_perkg_dark

tag: drink perkg_dark

tag: rer dark


title: Whole_Blood_Control_33

tag: tissue

tag: age

tag: gender

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: Whole_Blood_Control_2


title: WT-ND-2

tag: genotype

tag: treatment


title: SNUH-082, HC


title: M9-Old

description:
Library name: M9
Old (20 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: vo2 perkg_dark

tag: activitycounts dark

tag: vo2 perlbm_dark

tag: vco2 perlbm_dark

tag: ee perlbm_dark

tag: feed g_perlbm_dark

tag: feed kcal_perlbm_dark


title: M8-Old

description:
Library name: M8
Old (20 months)

tag: tissue

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: vco2 perkg_dark

tag: ee perkg_dark

tag: feed g_perkg_dark

tag: feed kcal_perkg_dark

tag: drink perkg_dark

tag: rer dark


title: Whole_Blood_Control_15

tag: tissue

tag: age

tag: gender

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: SNUH-084, HC


title: Valves, KO, Day 14, Replicate 2

city: Philadelphia

first: Mark

last: Kahn

state: PA

address: 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were performed using CellRanger.
Quality control filtering and clustering performed with Seurat.
Assembly: mm10
Supplementary files format and content: ValveData.rds

source_name: Tricuspid valve

extract_protocol:
Mice were perfused with cold sterile PBS and tricuspid valves were manually dissected out of the heart. Valves were incubated with Collagenase, Dispase, and Dnase at 37C for 15 minute intervals to generate a single cell suspension. B59
Library preparation was performed according to the manufacter's instructions (10X Genomics, sc 3' v3.2)

value: Tricuspid valve

tag: genotype

tag: treatment

value: Tamoxifen gavage

tag: time

value: Day 14


title: Whole_Blood_Control_35

value: Whole blood


title: SNUH-079, HC


title: M7-Old

description:
Library name: M7
Old (20 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: vo2 perkg_dark

tag: vco2 perkg_dark

tag: activitycounts dark

tag: vo2 perlbm_dark

tag: vco2 perlbm_dark

tag: ee perlbm_dark

tag: feed g_perlbm_dark

tag: feed kcal_perlbm_dark


title: Valves, KO, Day 14, Replicate 1

tag: tissue

tag: genotype

tag: treatment

tag: time


title: M15-Old

description:
Library name: M15
Old (20 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee perkg_dark

tag: feed g_perkg_dark

tag: feed kcal_perkg_dark

tag: drink perkg_dark

tag: rer dark


title: M6-Old

description:
Library name: M6
Old (20 months)

tag: tissue

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: vo2 perkg_dark

tag: vco2 perkg_dark

tag: activitycounts dark

tag: vo2 perlbm_dark

tag: vco2 perlbm_dark

tag: ee perlbm_dark

tag: feed g_perlbm_dark

tag: feed kcal_perlbm_dark


title: Whole_Blood_Control_46

tag: tissue

tag: age

tag: gender

value: Male

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: M5-Old

description:
Library name: M5
Old (20 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: ee perkg_dark

tag: feed g_perkg_dark

tag: feed kcal_perkg_dark

tag: drink perkg_dark

tag: rer dark


title: Valves, Control, Day 14, Replicate 2

tag: tissue

tag: genotype

tag: treatment

tag: time


title: SNUH-029, Benign

value: blood


title: SNUH-050, OC


title: Valves, Control, Day 14, Replicate 1


title: M13-Young

description:
Library name: M13
Young (6 months)

tag: metaboliccageid

tag: agecategory

value: Young

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: vo2 perkg_dark

tag: vco2 perkg_dark

tag: activitycounts dark

tag: vo2 perlbm_dark

tag: vco2 perlbm_dark

tag: ee perlbm_dark

tag: feed g_perlbm_dark

tag: feed kcal_perlbm_dark


title: Whole_Blood_Control_25

tag: tissue

tag: age

tag: gender

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: M12-Young

description:
Library name: M12
Young (6 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: ee perkg_dark

tag: feed g_perkg_dark

tag: feed kcal_perkg_dark

tag: drink perkg_dark

tag: rer dark


title: Valves, KO, Day 7, Replicate 2

tag: tissue

tag: genotype

tag: treatment

tag: time

value: Day 7


title: Whole_Blood_Control_10

tag: age

tag: gender

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: WT-ND-1


title: Whole_Blood_Control_4


title: Whole_Blood_Control_54


title: SNUH-013, Benign


title: SNUH-077, HC


title: M11-Young

description:
Library name: M11
Young (6 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: vo2 perkg_dark

tag: vco2 perkg_dark

tag: activitycounts dark

tag: vo2 perlbm_dark

tag: vco2 perlbm_dark

tag: ee perlbm_dark

tag: feed g_perlbm_dark

tag: feed kcal_perlbm_dark


title: Whole_Blood_Control_49

tag: tissue

tag: age

tag: gender

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: Valves, KO, Day 7, Replicate 1

tag: genotype

tag: treatment

tag: time


title: SNUH-012, Benign


title: M10-Young

description:
Library name: M10
Young (6 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: vo2 perkg_dark

tag: vco2 perkg_dark

tag: ee perkg_dark

tag: feed g_perkg_dark

tag: feed kcal_perkg_dark

tag: drink perkg_dark

tag: rer dark

tag: activitycounts dark


title: Valves, Control, Day 7, Replicate 1

tag: tissue

tag: genotype

tag: treatment

tag: time


title: Valves, Control, Day 7, Replicate 2


title: M4-Young

description:
Library name: M4
Young (6 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: vo2 perlbm_dark

tag: vco2 perlbm_dark

tag: ee perlbm_dark

tag: feed g_perlbm_dark

tag: feed kcal_perlbm_dark


title: Valves, KO, Day 4, Replicate 2

tag: tissue

tag: genotype

tag: treatment

tag: time

value: Day 4


title: Whole_Blood_Control_34

tag: age

tag: gender

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: SNUH-142, OC


title: Whole_Blood_Control_48


title: M3-Young

description:
Library name: M3
Young (6 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: vo2 perkg_dark

tag: vco2 perkg_dark

tag: ee perkg_dark

tag: feed g_perkg_dark

tag: feed kcal_perkg_dark

tag: drink perkg_dark

tag: rer dark

tag: activitycounts dark


title: Whole_Blood_Control_40

tag: tissue

tag: age

tag: gender

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: SNUH-138, EC


title: SNUH-018, Benign


title: M2-Young

description:
Library name: M2
Young (6 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: vo2 perlbm_dark

tag: vco2 perlbm_dark

tag: ee perlbm_dark

tag: feed g_perlbm_dark

tag: feed kcal_perlbm_dark


title: Whole_Blood_Control_56

tag: tissue

tag: age

tag: gender

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: Valves, KO, Day 4, Replicate 1

tag: genotype

tag: treatment

tag: time


title: SNUH-137, OC


title: M1-Young

description:
Library name: M1
Young (6 months)

tag: metaboliccageid

tag: agecategory

tag: isold

tag: age wks

tag: age months

tag: dob plusminus1day

tag: dosactifice

tag: weight clamp

tag: egp basal

tag: egp clamp

tag: egp suppression

tag: glycerol basal

tag: glycerol clamp

tag: glycerol suppression

tag: insulin basal

tag: insulin clamp

tag: glucose ssgir

tag: liver glycogen

tag: liver citratesynthase

tag: liver percentpyruvate2citrate

tag: liver pyruvatedehydrogenase

tag: liver fattyacidoxidation

tag: liver pyruvatecarboxylase

tag: liver percentegp2tca

tag: weight mcage_in

tag: weight mcage_out

tag: fat g

tag: leanmass g

tag: fat percent

tag: leanmass percent

tag: vo2 perkg_light.dark

tag: vco2 perkg_light.dark

tag: ee perkg_light.dark

tag: feed g_perkg_light.dark

tag: feed kcal_perkg_light.dark

tag: drink perkg_light.dark

tag: rer light.dark

tag: activitycounts light.dark

tag: vo2 perlbm_light.dark

tag: vco2 perlbm_light.dark

tag: ee perlbm_light.dark

tag: feed g_perlbm_light.dark

tag: feed kcal_perlbm_light.dark

tag: drink perlbm_light.dark

tag: vo2 wb_light.dark

tag: vco2 wb_light.dark

tag: ee wb_light.dark

tag: feed g_wb_light.dark

tag: feed kcal_wb_light.dark

tag: drink wb_light.dark

tag: vo2 perkg_light

tag: vco2 perkg_light

tag: ee perkg_light

tag: feed g_perkg_light

tag: feed kcal_perkg_light

tag: drink perkg_light

tag: rer light

tag: activitycounts light

tag: vo2 perlbm_light

tag: vco2 perlbm_light

tag: ee perlbm_light

tag: feed g_perlbm_light

tag: feed kcal_perlbm_light

tag: drink perlbm_light

tag: vo2 wb_light

tag: vco2 wb_light

tag: ee wb_light

tag: feed g_wb_light

tag: feed kcal_wb_light

tag: drink wb_light

tag: vo2 perkg_dark

tag: vco2 perkg_dark

tag: ee perkg_dark

tag: feed g_perkg_dark

tag: feed kcal_perkg_dark

tag: drink perkg_dark

tag: rer dark

tag: activitycounts dark


title: Valves, Control, Day 4, Replicate 2

tag: tissue

tag: genotype

tag: treatment

tag: time


title: Whole_Blood_Control_55

tag: age

tag: gender

tag: cardiovascular disease

tag: pulmonary disease

tag: metabolic disease

tag: matching factor

tag: status


title: Whole_Blood_Control_50


title: SNUH-127, OC


title: Valves, Control, Day 4, Replicate 1


title: SNUH-126, OC


title: Mouse macrophage, MNP 2

first: Koung-Min

last: Park

address: 5-26, Sinchon-ro 4-gil

institute: Yonsei university college of medicine

description: Library name: MP_2

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: bone marrow

growth_protocol: Bone marrow (BM) was isolated from the tibia and femur of C57BL/6 mice by flushing. The isolated BM precursors were cultured at 37°C with 5% CO2 in Dulbecco's Modified Eagle Medium (DMEM) supplemented with mouse macrophage colony-stimulating factor (25 ng/ml), 10% fetal bovine serum, and 1% penicillin/streptomycin/amphotericin B (PSA) for four days to differentiate into BMDMs.

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

treatment_protocol: BMDMs (1 × 10⁶ cells/ml) were plated in six-well plates and treated with or without polystyrene MNPs (50 µg) at 37°C with 5% CO2 for 24 h.

value: bone marrow

tag: cell type

value: macrophage

value: polystyrene micro- and nanoplastic


title: Mouse macrophage, MNP 3

description: Library name: MP_3


title: SNUH-141, EC


title: Whole_Blood_Control_44


title: Whole_Blood_Control_43


title: Mouse macrophage, MNP 1

description: Library name: MP_1


title: SNUH-119, OC


title: Mouse macrophage, Control 3

description: Library name: CTL_3


title: SNUH-110, EC


title: Whole_Blood_Control_32


title: Mouse macrophage, Control 2

description: Library name: CTL_2


title: SNUH-108, EC


title: Whole_Blood_Control_5


title: renal tissue, sham-2, Day14

first: Kaiting

last: Zhuang

address: 28 Fuxing Road, Haidian District

institute: 1st Medical Center of Chinese PLA General Hospital

description: Library name: 15_1,15_2

data_processing:
trimadap was used to remove connectors, seqtk trimfq v1.0 was used to remove low quality, lengthsort.pl was used to remove short fragments, bowtie2 v2.2.6 was used to remove rRNA, and fastQC v0.10.1 was used to evaluate reads quality. mapping was performed using hisat2 v2.0.4. samtools v1.9 and sambamba v0.6.4 were used for sam and bam file processing. stringtie v1.3.3b was used for gene expression quantification and edgeR v3.2.0 was used for differential gene analysis.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: renal

extract_protocol:
Total RNA was extracted using the MJzol Animal RNA Isolation Kit (Majorivd) following the standard operating procedures provided by the manufacturer. The RNA was then purified using the RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN). RNA integrity was assessed using the Agilent 2100 Bioanalyzer/Agilent 4200 TapeStation (Agilent technologies), and the total RNA quantity and purity were determined using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and NanoDrop ND-2000 Spectrophotometer (Thermo Fisher Scientific).
The purified Total RNA was subjected to mRNA isolation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3' end A-tailing, adapter ligation, and enrichment to construct the mRNA sequencing library. The library concentration was detected using the Qubit 2.0 Fluorometer (Thermo Fisher Scientific), and the fragment distribution of the library was analyzed by the Agilent 4200 TapeStation (Agilent Technologies).

value: renal

value: renal tissue cell

value: WT

value: sham


title: Whole_Blood_Control_7


title: renal tissue, sham-1, Day14

description: Library name: 14_1,14_2


title: SNUH-091, EC


title: Mouse macrophage, Control 1

description: Library name: CTL_1


title: SNUH-098, OC


title: Whole_Blood_Control_17


title: SNUH-083, HC


title: SNUH-090, EC


title: Whole_Blood_Control_30

value: Female


title: Whole_Blood_Control_26


title: renal tissue, uIRI+MSCs transplantation-2, Day14

description: Library name: 11_1,11_2

value: uIRI+MSCs tranplantation


title: renal tissue, uIRI+MSCs transplantation-1, Day14

description: Library name: 5_1, 5_2


title: R12 216 hours of growth biological replicate B

city: Seattle

first: Alex

middle: V

last: Carr

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
FASTQC: default parameters
Trimmomatic: quality score of 20
Kallisto: quant function with default parameters
Assembly: Rhodanobacter sp. FW510-R12 (NCBI BioProject PRJNA255897) and Acidovorax sp. GW101-3H11 (NCBI BioProject PRJNA314893)
Supplementary files format and content: tsv containing transcript counts across both species

organism: Rhodanobacter sp.

source_name: Rhodanobacter sp. FW510-R12

growth_protocol: From freezer stocks, cells were plated on R2A agar and incubated at 30 °C. Following growth of isolated colonies, colonies were picked and used for inoculation of R2A liquid medium cultures. Liquid R2A cultures were incubated at 30°C with shaking at 100 rpm. Following overnight growth, optical density at 600 nm (OD600) was measured and cell density was normalized to using R2A liquid medium if necessary. With starting cultures at ~0.5 OD600 units, 100 uL of Rhodanobacter sp. FW510-R12 (R12) and 100 uL of Acidovorax GW101-3H11 (3H11) were inoculated into a NO3 reduction medium to establish co-cultures. For pure cultures 200 uL of either strain was utilized to normalize starting cell densities. Initial cell densities were normalized to ∼0.01 OD600 units across all experiments and conditions.

extract_protocol:
Cell pellets were harvested by centrifugation at 4,000 × g and flash frozen in liquid N2. Total RNA was extracted using the MasterPure™ Complete DNA and RNA Purification Kit from Epicentre. All samples were treated with Invitrogen TURBO DNA-Free kit to remove DNA contamination. The Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Illumina) was used for rRNA depletion and library preparation.
The Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (Illumina) was used for rRNA depletion and library preparation.

value: Rhodanobacter sp. FW510-R12

value: Anearobic denitrification media:20 mM Acetate, 10 mM Nitrate


title: SNUH-109, OC


title: Whole_Blood_Control_38

value: Whole blood


title: SNUH-081, HC


title: R12 216 hours of growth biological replicate A


title: SNUH-080, HC


title: renal tissue, uIRI-3, Day14

description: Library name: 9_1,9_2

value: uIRI


title: R12 119 hours of growth biological replicate C


title: Whole_Blood_Control_22


title: SNUH-075, HC

value: blood


title: Whole_Blood_Control_18

value: Male


title: renal tissue, uIRI-2, Day14

description: Library name: 2_1,2_2


title: renal tissue, uIRI-1, Day14

description: Library name: 1_1,1_2


title: R12 119 hours of growth biological replicate B


title: renal tissue, uIRI+MSCs transplantation-3, Day14

description: Library name: 13_1,13_2


title: SNUH-074, HC


title: SNUH-073, HC


title: R12 119 hours of growth biological replicate A


title: R12 216 hours of growth biological replicate C


title: FAC-sorted cells, DNMT1 knockout, rep 2

city: Aachen

first: Geraldine

last: Zimmer-Bensch

address: Worringerweg 3

department: Neuroepigenetics

country: Germany

institute: RWTH Aachen University

description: Library name: Sst_KO_2_EM

data_processing:
FASTQ files were generated using bcl2fastq (Illumina, U.S.A.). To facilitate reproducible analysis, samples were processed using the publicly available nf-core/methylseq pipeline version 2.6.010  implemented in Nextflow 23.10.0 with the minimal command. Briefly, FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc ) and Trimmomatic were utilized to perform a quality control, and clean reads were aligned to the reference genome using Bismark to identify methylated cytosines.
Assembly: mm10
Supplementary files format and content: BedGraph files containing the chromosomal locations of individual CpG sites and the corresponding ß values
Library strategy: EM-seq

source_name: Basal telencephalon

extract_protocol:
The basal telencephalons  were collected in cold HBSS (w/ phenol red, w/o calcium, w/o magnesium)/0.65% D-glucose; 4 µg/µL (600 U) of DNAse I (AppliChem GmbH, Germany). After treatment with 0.04% trypsin for 17 min at 37 °C, HBSS was replaced by DMEM with additional L-glutamine and 4.5 g/L D-glucose, 10% FBS and 1% P/S to stop the trypsinization. Subsequently, the cells were pelletized, resuspended and triturated in cold HBSS (w/o phenol red, w/o calcium, w/o magnesium)/0.65% D-glucose, before being filtered through a nylon gauze (pore size 140 µm, Merck, U.S.A.) for FACS. Respective parameters for the procedure using a BD FACS Aria Fusion (BD Biosciences, U.S.A) were defined as follows: 5-laser (FCS, SSC, PE, BV421), 18-color (3-6-2-4-3). TdTomato-positive cells were collected in 100 µL of cold HBSS (w/o phenol red, w/o calcium, w/o magnesium)/0.65% D-glucose for methyl-seq. Samples were mixed by inversion and stored at -80°C until processing. DNA was isolated from at least 50.000 pooled cells per sample using the PureLink genomic DNA Mini Kit (Thermo Fisher Scientic, U.S.A.). Per genotype, the samples were initially pooled by volume (200 uL each), supplemented with lysis buffer provided in the kit and incubated with 2 µL proteinase K (Thermo Fisher Scientific, U.S.A.) at 55°C for 10 min. DNA was precipitated with 100% ethanol. Samples were bound to one column per genotype each, washed as instructed, briefly dried and eluted with 35 µL Tris-EDTA (TE) buffer.
Libraries were generated using the Enzymatic Methyl-seq kit for Illumina (#E7120, New England Biolabs, U.S.A.). After enzymatic shearing for 25 min at 37°C with the NEBNext UltraShear enzyme and buffer, followed by an inactivation at 65°C for 15 min, 5-methylcytosines were oxidized by TET2 after adaptor ligation. Samples were denatured with formamide and deaminated with APOBEC. Libraries were subjected to 7 cycles of upscale PCR (98°C for 10 s, 62°C for 30 s, and 65°C for 60 s). Library concentrations were determined with a QubitTM 4 fluorometer and the 1x dsDNA HS reagent (Thermo Fisher Scientific, U.S.A.). All recommended clean-up steps were performed with magnetic AMPure XP beads (Beckman Coulter, U.S.A.). Library size was assessed on a Tape Station 4200 using the DNA D5000 kit (Agilent Technologies, U.S.A.). Concentrations were determined with a QubitTM 4 fluorometer and the 1x dsDNA HS reagent (Thermo Fisher Scientific, U.S.A.). Libraries were diluted, equimolarly pooled, denatured, and clustered onto an Illumina NextSeq 500/550 Mid Output Kit v2.5 (300 cycles) flow cell (Illumina, U.S.A.). The 1% PhiX control library was spiked in to improve base calling accuracy. Paired-end sequencing was performed with 151 cycles.

value: Basal telencephalon

value: Sst interneuron

value: Sst-Cre/tdTomato/Dnmt1 loxP2


title: R12 95 hours of growth biological replicate C


title: SNUH-072, HC


title: FAC-sorted cells, DNMT1 knockout, rep 1

description: Library name: Sst_KO_1_EM


title: R12 95 hours of growth biological replicate B


title: SNUH-076, HC


title: SNUH-071, HC


title: SNUH-069, EC


title: FAC-sorted cells, DNMT1 control, rep 2

description: Library name: Sst_WT_2_EM

value: Sst-Cre/tdTomato


title: R12 95 hours of growth biological replicate A


title: FAC-sorted cells, DNMT1 control, rep 1

description: Library name: Sst_WT_1_EM


title: R12 77 hours of growth biological replicate C


title: Control_2

description:
Library name: WT2
Contains data from two sublibraries

data_processing:
The sequencing dataset was processed using Trailmaker (https://app.trailmaker.parsebiosciences.com/; Parse Biosciences, 2024) to generate unfiltered count matrices which were used for downstream analyses using the Seurat package for R (R 4.4.1, Seurat 5.0.1.9001).
Assembly: mm39
Supplementary files format and content: Unfiltered count matrices, all genes, cell metadata

molecule: nuclear RNA

source_name: Brain

extract_protocol:
The medial neocortices from E16.5 Sst-Cre/tdTomato and Sst-Cre/tdTomato/Dnmt1 loxP2 mice were dissected. The samples were snap-frozen on dry ice and stored at -80 °C until library preparation to ensure RNA integrity was maintained while the genotype and the sex of each sample could be verified for a bias-free transcriptomic analysis. Consequently, single-nucleus RNA sequencing (snRNA-seq) was selected over scRNA-seq to accommodate the processing of frozen samples. The nuclei were extracted from the frozen tissue by discontinuous sucrose gradient ultracentrifugation. Briefly, the tissue was homogenized in 1 ml of lysis buffer (0.32 M sucrose, 10 mM Tris-HCl (pH 8.0), 5 mM CaCl2, 3 mM Mg acetate, 1 mM dithiothreitol (DTT), 0.1 mM EDTA, 0.1% Triton X-100, 50 U/ml RNase inhibitors (#M0314S, New England Biolabs, U.S.A.)) using a 2-ml glass Dounce homogenizer on ice and stroking 25 times with pestle A followed by 100 strokes with pestle B. The homogenates were transferred to 5-ml ultracentrifuge tubes (#344057, Beckman Coulter) and under-layered with 3 ml of sucrose cushion (1.8 M sucrose, 10 mM Tris-HCl (pH 8.0), 3 mM Mg acetate, 1 mM DTT, 50 U/ml RNase inhibitors). The samples were loaded onto a Sw 55 Ti rotor and centrifuged for 1 h at 4 °C and 28,300 rpm (97,500x g). The nuclei pellets were resuspended in 150 µl of cold 1% BSA in PBS and immediately fixed using the Evercode™ Nuclei Fixation kit (Parse Biosciences, U.S.A.) following the manufacturer’s guidelines. The fixed nuclei were stored at  80 °C until library preparation.
The snRNA-seq libraries were generated with the Evercode™ WT kit (Parse Biosciences, U.S.A.). The quality check of the cDNA and the final libraries was performed using the High Sensitivity D5000 and D1000 ScreenTape kits (Agilent Technologies, U.S.A.). Libraries were equimolarly pooled and sequenced in conjunction with 5% PhiX control library on an Illumina NovaSeq machine in paired-end mode using the S2 Reagent Kit v1.5 (200 cycles) (Illumina, U.S.A.).

value: Brain

tag: batch


title: SNUH-066, EC


title: Control_1

description:
Library name: WT1
Contains data from eight sublibraries


title: R12 77 hours of growth biological replicate B


title: SNUH-065, Benign


title: R12 77 hours of growth biological replicate A


title: 3H11-R12 co-culture 142 hours of growth biological replicate C

organism:
Acidovorax sp.
Rhodanobacter sp.

source_name: Acidovorax sp. GW101-3H11 + Rhodanobacter sp. FW510-R12


title: SNUH-057, EC


title: Dnmt1_Knockout_2

description:
Library name: KO2
Contains data from eight sublibraries


title: 3H11-R12 co-culture 142 hours of growth biological replicate B

value: Acidovorax sp. GW101-3H11 + Rhodanobacter sp. FW510-R12


title: pancreatic islet

city: Paris 15

first: Lamine

last: TOURE

address: 160 Rue de Vaugirad

country: France

institute: INEM

description:
Library name: Sample1 Ide-/-, Sample2 Ide+/+
Rhapsody

data_processing:
Sequencing libraries for single-cell transcriptomic analysis were prepared using the BD Rhapsody Whole Transcriptome Analysis (WTA) Pipeline version 2.0. The resulting FASTQ files were uploaded to the Seven Bridges platform via the command-line interface (CLI) provided by BD. Quality control of the FASTQ files was performed using FastQC CWL 1.0 to ensure high read quality. The BD Rhapsody™ Sequence Analysis Pipeline was then used to process the sequencing data. This pipeline aligned the FASTQ reads to the mouse reference genome GRCm39, using the RhapRef_Mouse_WTA_2023-02.tar.gz archive provided by BD, along with Gencode M31 for transcript annotation and quantification. Downstream analysis was conducted in R version 4.4.1 using the Seurat package version 5.1.0, including cell and gene filtering, clustering, and differential gene expression analysis.
Supplementary files format and content: BD Rhapsody WTA analysis output
Assembly: GRCm39
Supplementary files format and content: Seraut Object

source_name: islet cells

extract_protocol:
Islets were isolated from the pancreas of 3 Ide-/- and 3 Ide+/+ C57BL/6 mice. Ice-cold collagenase P (Roche; 0.76 mg/ml in HBSS) was injected through a catheter introduced into the pancreatic duct (2 mL/mouse). The instilled pancreas was excised and digested for 10 min at 37 °C, digestion was stopped by addition of cold HBSS containing 10% heat inactivated FCS. The islets were handpicked under the microscope and dissociated into single cell suspensions by incubation in 100 mL of Accutase (Thermofisher) at 37°C and 5% CO2 for 15 min. The reaction was blocked with 1mL HBSS/10% FCS and the cells were filtered through a 40 mm cell strainer (Corning) and centrifuged at 300 x g for 5 min. The cells were resuspended in 100 mL of cold Sample Buffer (BD Rhapsody) and stained with the viability markers, Calcein AM (Thermo Fisher Scientific) and Draq7 (BD Bioscience) according to the BD Rhapsody Single Cell Analysis protocol. The cell concentration and viability were determined with BD Rhapsody Scanner. Cell barcoding was performed using Custom BD Single Cell Sample Multiplexing Kit (N°626545) after pooling the same number of cells for each genotype.
Cell capture and cDNA library amplification were carried out using the BD Rhapsody Enhanced (N°66487), cartridge Reagent Kit (No. 633733) and the BD Rhapsody cDNA Kit (N°633773), respectively, according to the manufacturer’s instructions. The DNA library, from 14755 single cells captured in a single run with 4 pooled barcoded samples, was constructed using the BD Rhapsody Whole Transcriptome Analysis (WTA) Pipeline version 2 (N°633801). The Illumina primer R1 was added to the library. The single cell library was quantified by Qubit 4 Fluorometer (Thermofischer), and by capillary electrophoresis using Fragment Analyzer (Agilent Technologies). The sequencing was performed on a NovaSeq 6000 system (Illumina) with 3% control PhiX library (Illumina) on a Flow Cell NovaSeq S1 100cycles to generate ~1500 millions paired-end reads (51 bases + 71 bases).  The generated FASTQ files were uploaded to the SevenBridges platform using the command-line interface (CLI) provided by BD.

value: islet cells


title: SNUH-055, EC


title: SNUH-048, EC


title: 3H11-R12 co-culture 142 hours of growth biological replicate A


title: 3H11-R12 co-culture 95 hours of growth biological replicate C


title: 3H11-R12 co-culture 95 hours of growth biological replicate B


title: SNUH-047, Benign


title: SNUH-043, EC


title: SNUH-068, Benign


title: 3H11-R12 co-culture 95 hours of growth biological replicate A


title: SNUH-038, Benign


title: Sample_MEPC_DSS

city: hangzhou

first: Yumeng

last: Pei

state: zhejiang

address: Xihu district Zhuan Tang street

institute: Zhejiang university

description:
Library name: Sample_MEPC
10X Genomic

data_processing:
The estimated number of cells is 27513, fraction reads in cells is 92.3%, median genes per cell is 1366, and the median UMI counts per cell is 5159. Quality control of the raw data was performed to remove low-quality cells based on the following criteria: 1) < 200 gene expressed; 2) < 99 unique molecular identifiers (UMIs); 3) > 25% UMIs derived from mitochondrial genome. Subsequent analysis was performed using the R package Seurat. The integrated genes underwent principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP) analysis. Cells were clustered together based on common features, and clusters were annotated using the expressions of canonical markers of particular cell types. Pseudotime calculations were conducted using Monocle 2, with stem cell as the origin of differentiation. ‘AddModuleScore’ function implanted in Seurat R package was utilized to perform calculation of signature scores. Genes included in the calculation of scores for stem cells were Lgr5, Ube3c, Mki67, and Myc; genes for absorptive lineage were Arg2, Apoa4, Aldob and Hes1; genes for secretory cells were Dll1, Muc2, Ang4, and Pou2f3.
Assembly: Mouse mm10
Supplementary files format and content: fastq

source_name: intestine

extract_protocol:
Crypts isolated from mouse intestine were incubated with TrypLE Express (Gibco, 12605010) at 37°C for 60 s. The single cell suspension was passed through a 40-μm filter. The cells were stained with EpCAM (Thermofisher, 14-5791-81) and 7-AAD (BD Biosciences, 559925), and sorted by FACS to enrich 7-AAD-EpCAM+ intestinal epithelial cells.
Single-cell RNA sequencing (scRNA-seq) libraries were constructed using the 10 × Genomics single cell 3′ Library and Gel Bead Kit V3 (10 × Genomics, 1000075) following the manufacturer’s instructions. The cell suspension (300–600 live cells per mL as determined by Count Star) was loaded onto a Chromium single cell controller (10X Genomics) to generate single-cell gel beads in the emulsion (GEMs). Reverse transcription was performed on a PCR Thermal Cycler (Takara) programed at 53°C for 45 min, followed by 85°C for 5 min to terminate reaction. The cDNA library was generated, amplified, and assessed for quality control using the Agilent 4200. The scRNA-seq was carried out on the Illumina Novaseq6000 sequencer.

value: intestine

value: epithelial cells

value: DSS


title: Neuronal cells after SP treatment 3

city: Guangzhou

first: Huasong

last: Zhang

state: Guangdong

address: 63 Duobao Road, Liwan District, Guangzhou

institute: The Third Affiliated Hospital, Guangzhou Medical University

description: Library name: SP3

data_processing:
Beginning from raw data of double-trim RNA sequencing on mouse samples, we used fastp software1 (https://github.com/OpenGene/fastp) to carry out data-cleaning workflow. Fastp is a tool providing fast all-in-one preprocessing for FastQ files, so all parameters were kept as default to preprocess the raw data, including (but not restricted to) striping adaptors, filtering out low-quality reads, correcting mismatched base pairs and  trimming poly G ends.
After pre-processing, the RNAseq data was delivered to salmon tool (https://salmon.readthedocs.io/en/latest/salmon.html) to generate gene expression matrix. In detail, reads were aligned to GRCm9 (http://asia.ensembl.org/Mus_musculus/Info/Index) gene annotation file downloaded from Ensemble web service.
After filtering off genes that exhibited raw counts of 0 in each sample, raw counts of gene symbol along all mouse samples were generated.
In parallel, we generated another gene expression matrix by the popular STAR tool  (https://github.com/alexdobin/STAR) for one randomly selected sample, and the significant linear co-relationship of all gene expressions respectively calculated by STAR7 and salmon in this sample confirmed the reliability of the gene expression matrix generated by alignment-free method.
Assembly: After pre-processing, the RNAseq data was delivered to salmon tool to generate gene expression matrix. In detail, reads were aligned to GRCm9 (http://asia.ensembl.org/Mus_musculus/Info/Index) gene annotation file downloaded from Ensemble web service.
Supplementary files format and content: “raw_counts.csv” is the comma-seperated matrix of gene raw counts of all the sample mouse. The rows are gene symbols and the columns are sample IDs.
Supplementary files format and content: “FPKM_normalized.csv” is the comma-seperated matrix of gene FPKM-normalized abundance of all the sample mouse. The rows are gene ensembl IDs and the columns are sample IDs.

source_name: Hippocampal tissue

growth_protocol: C57BL/6J male mice were randomly assigned into six groups, namely the control group (NC), the Sodium phenylbutyrate (SP) group, the Rotenone (ROT) group, the ROT+SP group, the Meclofenoxate-hydrochloride (MH) group, and the ROT+MH group. The mice in the NC group received dimethylsulfoxide (DMSO) (olive oil only); the mice in the SP group were treated with SP (300 mg/kg bw/d; intraperitoneal [i.p.]) for 4 consecutive weeks; the mice in the ROT group were given rotenone (1 μg/g bw/d; i.p.) for 3 consecutive weeks; the mice in the ROT+SP group received SP prophylaxis (300 μg/g bw/d; i.p.) for 1 week followed by ROT (1 μg/g bw/d, i.p.) from 1 week onwards for the next 3 consecutive weeks; the mice in the MH group were administered with MH (50  μg/g bw/d; i.p.) for 4 consecutive weeks; the mice in the ROT+MH group received MH prophylaxis (50 μg/g bw/d; i.p.) for 1 week followed by ROT challenge (1 μg/g bw/d, i.p.) from 1 week onwards for the next 3 weeks.

extract_protocol:
Total RNA was extracted from tissue or cell samples using a standardized RNA extraction kit, following the manufacturer’s instructions. Briefly, samples were lysed and homogenized in a denaturing buffer to inactivate RNases. RNA was separated from DNA and proteins through phase separation using acid-phenol:chloroform, followed by RNA precipitation with isopropanol. The RNA pellet was washed with 75% ethanol and dissolved in RNase-free water. The quantity and purity of RNA were measured using a NanoDrop spectrophotometer (OD260/280 and OD260/230 ratios), and RNA integrity was assessed using the Agilent 2100 Bioanalyzer. Only high-quality RNA samples (RIN ≥ 7.0) were used for downstream library construction.
Total RNA was extracted using a standardized protocol and assessed for integrity and concentration with the Agilent 2100 Bioanalyzer. mRNA was enriched either by poly(A) selection with Oligo(dT) magnetic beads or by rRNA depletion. Fragmentation of mRNA was performed in NEB Fragmentation Buffer. First-strand cDNA synthesis was conducted using random hexamer primers and M-MuLV reverse transcriptase, followed by second-strand synthesis with either dNTPs (standard libraries) or dUTP substitution (strand-specific libraries). After end repair, A-tailing, and adapter ligation, size selection (250–300 bp) was carried out using AMPure XP beads. Strand-specific libraries underwent USER enzyme digestion prior to PCR amplification. Libraries were quantified by Qubit 2.0 and qRT-PCR, and insert sizes were assessed using the Agilent 2100 Bioanalyzer. Qualified libraries (effective concentration >2 nM) were pooled and sequenced on an Illumina platform using sequencing-by-synthesis technology. Library preparation was performed using the NEBNext® Ultra™ RNA Library Prep Kit or the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®.

treatment_protocol: The mice in the MH group were administered with MH (50  μg/g bw/d; i.p.) for 4 consecutive weeks; the mice in the ROT+MH group received MH prophylaxis (50 μg/g bw/d; i.p.) for 1 week followed by ROT challenge (1 μg/g bw/d, i.p.) from 1 week onwards for the next 3 weeks.

value: Hippocampal tissue

tag: cell line

value: Neuronal cells

value: WT

value: Neuronal cells after SP treatment 3


title: Neuronal cells after SP treatment 2

description: Library name: SP2

value: Neuronal cells after SP treatment 2


title: SNUH-037, OC

value: blood


title: Neuronal cells after SP treatment 1

description: Library name: SP1

value: Neuronal cells after SP treatment 1


title: 3H11-R12 co-culture 71 hours of growth biological replicate C

value: Anearobic denitrification media:20 mM Acetate, 10 mM Nitrate


title: Sample_WTEPC_DSS

description:
Library name: Sample_WTEPC
10X Genomic


title: 3H11-R12 co-culture 71 hours of growth biological replicate B


title: Neuronal cells after ROT-SP treatment 5

description: Library name: ROT_SP5

value: Neuronal cells after ROT-SP treatment 5


title: Dnmt1_Knockout_1

description:
Library name: KO1
Contains data from eight sublibraries

value: Sst-Cre/tdTomato/Dnmt1 loxP2


title: 3H11-R12 co-culture 71 hours of growth biological replicate A


title: SNUH-036, Benign


title: 3H11-R12 co-culture 53 hours of growth biological replicate C


title: Neuronal cells after ROT-SP treatment 4

description: Library name: ROT_SP4

value: Neuronal cells after ROT-SP treatment 4


title: SNUH-030, Benign


title: SNUH-034, Benign


title: 3H11-R12 co-culture 53 hours of growth biological replicate B


title: Neuronal cells after ROT-SP treatment 2

description: Library name: ROT_SP2

value: Neuronal cells after ROT-SP treatment 2


title: SNUH-027, OC


title: 3H11-R12 co-culture 42 hours of growth biological replicate C

value: Acidovorax sp. GW101-3H11 + Rhodanobacter sp. FW510-R12


title: 3H11-R12 co-culture 53 hours of growth biological replicate A


title: SNUH-026, Benign


title: SNUH-031, Benign


title: Neuronal cells after ROT-SP treatment 3

description: Library name: ROT_SP3

value: Neuronal cells after ROT-SP treatment 3


title: 3H11-R12 co-culture 42 hours of growth biological replicate B


title: Neuronal cells after ROT-MH treatment 3

description: Library name: ROT_MH3

value: Neuronal cells after ROT-MH treatment 3


title: SNUH-024, Benign


title: Neuronal cells after ROT-MH treatment 1

description: Library name: ROT_MH1

value: Neuronal cells after ROT-MH treatment 1


title: SNUH-022, Benign


title: Neuronal cells after ROT-MH treatment 2

description: Library name: ROT_MH2

value: Neuronal cells after ROT-MH treatment 2


title: Neuronal cells after ROT treatment 5

description: Library name: ROT5

value: Hippocampal tissue

value: Neuronal cells after ROT treatment 5


title: SNUH-021, Benign


title: 3H11-R12 co-culture 42 hours of growth biological replicate A


title: Liver, NC/WD, rep5

city: Ghent

first: Yannick

last: Gansemans

address: Ottergemsesteenweg 460

department: Pharmaceutical Sciences

country: Belgium

institute: Ghent University

description: Library name: AH01-29

data_processing:
Raw read QC was done using FastQC (v0.11.9)
Adapter and quality trimming was done using cutadapt (v3.5)
Mapping of the trimmed reads on the reference genome was done using STAR (v2.7.9a)
UMI-based removal of mapped PCR duplicates was done using umi_tools (v1.1.2)
Expression quantification was done using rsem-calculate-expression (RSEM v1.3.3)
Assembly: Mus musculus GRCm39 (Ensembl release 104)
Supplementary files format and content: all_samples_rsem_gene_counts.tsv: raw expression count table in tab separated format, with genes as rows and samples as columns

source_name: liver

extract_protocol:
RNA was extracted using the Aurum Total RNA Mini Kit (Bio-rad Laboratories)
QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

value: liver

value: NC/WD


title: Neuronal cells after ROT treatment 4

description: Library name: ROT4

value: Neuronal cells

value: WT

value: Neuronal cells after ROT treatment 4


title: SNUH-019, Benign

value: blood


title: Liver, Multigenerational WD without fibrosis, rep5

description: Library name: AH01-26

value: Multigenerational WD without fibrosis


title: Liver, NC/NC, rep5

description: Library name: AH01-27

value: NC/NC


title: Liver, Multigenerational WD with fibrosis, rep3

description: Library name: AH01-25

value: Multigenerational WD with fibrosis


title: Neuronal cells after ROT treatment 3

description: Library name: ROT3

value: Neuronal cells after ROT treatment 3


title: SNUH-016, EC


title: Liver, Multigenerational WD without fibrosis, rep4

description: Library name: AH01-20


title: Neuronal cells after ROT-SP treatment 1

description: Library name: ROT_SP1

value: Neuronal cells after ROT-SP treatment 1


title: Neuronal cells after ROT treatment 2

description: Library name: ROT2

value: Neuronal cells after ROT treatment 2


title: Neuronal cells after ROT treatment 1

description: Library name: ROT1

value: Neuronal cells after ROT treatment 1


title: Liver, Multigenerational WD with fibrosis, rep2

description: Library name: AH01-19


title: SNUH-005, Benign


title: SNUH-004, Benign


title: Liver, Multigenerational WD without fibrosis, rep3

description: Library name: AH01-18


title: Neuronal cells 5

description: Library name: NC5

value: Neuronal cells 5


title: CaB34 CF, rep3

city: Toronto

last: Wright

state: Ontario

address: 2075 Bayview Ave

country: Canada

institute: Sunnybrook Research Institute

data_processing:
Transformed to sequenced reads by CASAVA base recognition. Data cleaned by removing reads containing adapter, ploy-N, and low quality reads.
Mapped to reference genome using HISAT2 v2.0.5, then featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: hg38
Supplementary files format and content: .xls file contains raw counts for each sample

source_name: Prostate

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini kit
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: Prostate

value: Prostate Cancer


title: Neuronal cells 4

description: Library name: NC4

value: Hippocampal tissue

value: Neuronal cells 4


title: Liver, Multigenerational WD without fibrosis, rep2

description: Library name: AH01-17

value: liver


title: CaB34 CF, rep2


title: Liver, Multigenerational WD without fibrosis, rep1

description: Library name: AH01-13


title: Neuronal cells 2

description: Library name: NC2

value: Neuronal cells

value: Neuronal cells 2


title: CaB34 Parental, rep3


title: SNUH-017, Benign


title: Liver, NC/WD, rep4

description: Library name: AH01-12

value: NC/WD


title: CaB34 CF, rep1


title: CaB34 Parental, rep2


title: Neuronal cells 1

description: Library name: NC1

value: WT

value: Neuronal cells 1


title: Neuronal cells after MH treatment 6

description: Library name: MH6

value: Neuronal cells after MH treatment 6


title: Liver, NC/WD, rep3

description: Library name: AH01-11


title: Neuronal cells after MH treatment 5

description: Library name: MH5

value: Neuronal cells after MH treatment 5


title: Liver, NC/WD, rep2

description: Library name: AH01-9


title: CaB34 Parental, rep1