title: mouse_neuron_N_neg_18m;N702_i7_10_N504_i5_5

value: NeuN-


title: 2016_05_16_20_43_37_375

status: Public on Jul 18 2025

type: SRA

city: Singapore

first: Wenjing

last: Wang

address: Tahir Foundation Building, MD1 12 Science Drive 2; #13-05; Singapore 117549

country: Singapore

institute: National University of Singapore

description: Library name: RHP3535

library_source: transcriptomic

data_processing:
Raw sequencing data were processed through a standard RNA-seq analysis pipeline. First, fastp was used for quality control and adapter trimming of raw reads. Quality of sequencing data was assessed using MultiQC. The filtered reads were then aligned to the human reference genome hg38 using STAR aligner. Finally, gene expression quantification was performed using featureCounts to obtain read counts for each gene.
Assembly: hg38
Supplementary files format and content: The file contains raw gene or exon counts generated by featureCounts. Each row represents a gene or exon, and each column (starting from the second column) represents a sample.

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was isolated from the snap frozen samples of skeletal muscle biopsies from the subject’s vastus lateralis using NucleoSpin kit. RNA-seq was done on these extracted RNA using HiSeq4000 (Illumina), sequencing up to 80 million bidirectional reads of up to 151 base pairs.
For library construction, replicate sequencing runs from the same sample were prepared in a single library to ensure technical consistency. This means multiple sequencing runs were performed on the same library preparation rather than creating independent libraries for technical replicates.

tag: tissue

value: Skeletal muscle


title: mouse_ESC;N702_i7_9_N502_i5_7

city: Oxford

first: Jingfei

last: Cheng

state: Oxfordshire

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
Raw sequenced reads were demultiplexed using demuxbyname2.sh script from BBMap (version 38.50; https://www.osti.gov/biblio/1241166). Demultiplexed reads were processed with fastp package using default parameters to remove low-quality bases. The trimmed reads were aligned to the reference genome using bwa with default parameters. Reference sequences for mouse genome were downloaded from https://hgdownload.cse.ucsc.edu/goldenpath/mm9/bigZips/; reference sequence for human CD8+ T-cell were downloaded from: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRC h38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_an alysis_set.fna.gz. Uniquely mapped reads were filtered using samtools tools with MAPS>=10. PCR duplicates were called using Picard (2.23.0-Java-11) Mark Duplicates (https://broadinstitute.github.io/picard/). Methylation was called using a custom R script used in our previous project. 10bp at the start or end of reads were excluded for methylation calling. Snakemake pipeline file with detailed steps is provided in the code availability section.
Assembly: MM9 & GRCh38
Supplementary files format and content: bedgraph
Library strategy: scCAPS+

molecule: genomic DNA

organism: Mus musculus

source_name: mESC

extract_protocol:
E14 mouse embryonic stem cells (mES cells) were cultured on gelatin-coated plates in DMEM supplemented with 15% FBS, 2 mM L-glutamine, 1% non-essential amino acids, 1% penicillin/streptavidin, 0.1 mM β-mercaptoethanol, 1,000 units/ml LIF (leukaemia inhibitory factor), 1 μM PD0325901, and 3 μM CHIR99021. The cells were maintained at 37°C and 5% CO2. Before cell sorting, the cells were harvested by centrifugation and passed through a 40 μm cell strainer (Falcon) to achieve single cell suspension.
Optimized TAPS and CAPS+ reactions: For scTAPS, 96 cells were pooled for DNA purification and subjected to mTET1 oxidation as previously described11. A reaction mixture of 50 μl was prepared, comprising 50 mM HEPES buffer (pH 8.0), 100 μM ammonium iron (II) sulfate, 1 mM α-ketoglutarate, 2 mM L-ascorbic acid, 2.5 mM DTT, 1.2 mM ATP, 100 mM NaCl, and 4 μM mTet1CD. The reaction was conducted at 37°C for 80 minutes. Subsequently, 2.0 U of Proteinase K (New England Biolabs) was introduced to the reaction mixture and incubated at 50°C for 1 hour to stop the oxidation process. The oxidized DNA was purified using 1.8x AMPure XP beads, following the provided guidelines. To ensure complete oxidation, a second round of oxidation was performed. The double-oxidized DNA was purified and then underwent borane reduction under optimized conditions and purification using a Zymo column with Oligo Binding Buffer. For scCAPS+, 96 cells were pooled for DNA purification and subjected to a series of chemical reactions to convert 5hmC into 5fC and then to 5caC as previously described with some modifications12. DNA were incubated with 4-acetamido-2,2,6,6- tetramethylpiperidine-1-oxoammonium tetra-fluoroborate (ACT+ BF4-) in a 25 μl solution comprising sodium phosphate buffer at 25°C for 16 hours. The resultant oxidized DNA was purified using 1.8× AMPure XP Beads. then Pinnick oxidation is conducted in a 30 μl reaction mixture containing sodium acetate buffer, NaClO2, and 2- methyl-2-butene at 25°C for 16 hours. The purified product then underwent borane reduction under optimized conditions and purification using a Zymo column with Oligo Binding Buffer.  scTAPS and scCAP+ library construction and sequencing: Individual cells were isolated into a 96-well plate through FACS, each well containing 4 μL of lysis buffer consisting of 16.67mM TAPS-NaOH buffer (pH 8.5, Alfa Aesar, Cat: J63268), 8.33mM MgCl2(Invitrogen), 0.67x NEB buffer 4 (NEB, B7004S), 0.13%  Triton X-100 (sigma, X100-500ML), and 1 μg Qiagen protease. Following centrifugation at 2,000 rpm for 5 minutes, the plates were either preserved at -80°C or progressed to subsequent procedures. Single cell was lysate by incubating at 50°C for 3 h, followed by incubation at 75°C for 30 min, 80°C for 15 min, and a 4°C hold. Tagmentation was performed at 50°C for 15 minutes in a reaction mix consisting of 1x TAPS buffer (10mM TAPS-NaOH, 5mM MgCl2), 6% PEG (polyethylene glycol) 3,350, 1ul 1x preassembled Tn5, and H2O to a total volume of 10 μ. Tn5 was stripped off by adding 1.11 μL of 1.0% SDS (Sodium Dodecyl Sulfate), followed by incubating at room temperature for 5 minutes. Neutralization was performed by adding 1.24 μL of 5.0% NP40 or Triton X-100, followed by incubating at room temperature for 5 minutes. Subsequently, 12.35 μL of 2x Phusion High-Fidelity PCR Master Mix with HF Buffer (Thermo Scientific, F531L) was added, followed by incubating at 72°C for 5 minutes, and a 4°C hold. The 96 reactions were combined into a 50-mL BD tube and supplemented with 2-kb filler DNA (200 ng) and 0.1% spike in DNAs. Following purification, the TAPS or CAPS+ reaction, was employed as mentioned, and the final sequencing library was amplified utilizing the KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit along with index primers from the Nextera XT Index Kit (Illumina, FC-131- 1001). The amplification protocol involved an initial step at 98°C for 45 seconds, followed by 13 cycles (98°C for 10 seconds, 60°C for 15 seconds, and 72°C for 1 minute), then incubation at 72°C for 3 minutes, 4°C hold. The library was subjected to purification and size selected to 500-700bp by 0.5x-0.25x Ampure XP beads. Custom  sequencing primers are used for custom Nova Sequencing (Read 1 Sequencing Primer: GCGATCGAGGACGGCAGATGTGTATAAGAGACAG; Read 2 Sequencing Primer: CACCGTCTCCGCCTCAGATGTGTATAAGAGACAG; Index 1 Sequencing Primer: CTGTCTCTTATACACATCTGAGGCGGAGACGGTG; Index 2 sequencing primer: CTGTCTCTTATACACATCTGCCGTCCTCGATCGC).

tag: cell line

value: mESC

tag: experiment type

value: scCAPS+


title: UMUC3_DMSO1

city: Heidelberg

first: Jonas

last: Koch

address: Im Neuenheimer Feld 580

department: Epigenetics

country: Germany

institute: German Cancer Research Center

description:
Library name: UMUC3_DMSO1
APA_sites_UMUC3_inh.txt

data_processing:
Adaptor sequences were trimmed using Trim Galore (version 0.6.6).
Reads were aligned using HISAT2 (version 2.2.1).
Mapped reads were quantified using featureCounts (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including alternative polyadenylation events in patient and cell line samples.

source_name: Bladder

growth_protocol: T24 cells were cultured in McCoy’s 5A (modified) medium supplemented with 10% FBS and 1% penicillin/streptomycin. UM-UC-3 cells were cultured in DMEM high glucose medium supplemented with 10% FBS and 1% penicillin/streptomycin. Both cell lines were cultivated as adherent monolayers at 37°C in a humidified incubator with a 5% CO2 atmosphere.

extract_protocol:
Total RNA from tissue samples and cell lines were isolated using TRIzol. To remove residual gDNA contaminants, total RNA samples were DNase I-digested and further purified using the RNA Clean & Concentrator-5 kit (Zymo Research).
Libraries for RNA sequencing were prepared by the Genomics and Proteomics Core Facility of the German Cancer Research Center using the Illumina TruSeq Stranded RNA kit.

treatment_protocol: T24 and UM-UC-3 cells were cultured until reaching a confluency of approximately 80%. The cells were then treated for 48h with DMSO or 50 µM of the METTL3 inhibitor STM2457.

value: Bladder

tag: cell type

value: Urothelial carcinoma cell

tag: genotype

value: Wildtype

tag: treatment

value: DMSO


title: mouse_ESC;N702_i7_9_N502_i5_8


title: mouse_neuron_N_neg_18m;N702_i7_10_N504_i5_1

source_name: NeuN-


title: 2016_05_16_23_16_43_347

description: Library name: RHP3558


title: 2016_05_16_19_53_48_315

description: Library name: RHP3500


title: 2016_04_28_16_36_45_877

description: Library name: RHU097


title: mouse_ESC;N702_i7_9_N502_i5_5


title: mouse_ESC;N702_i7_9_N502_i5_6


title: Riboseq,shCONT,rep2

city: Shanghai

first: wei

last: xu

state: China

address: dongan road,131

country: China

institute: Fudan University

description: Library name: Sample8

data_processing:
For RNA-seq, raw FASTQ reads were trimmed using Trim Galore and transcript quantification was performed using Salmon in the quasi-mapping mode. For Ribo-seq, raw FASTQ reads were trimmed using Trim Galore to retain fragments between 20 and 40 base pairs. Ribosomal RNA (rRNA) and transfer RNA (tRNA) sequences were removed using Bowtie2 alignment. The remaining sequences were aligned to the hg38 human genome using STAR and gene expression was quantified using featureCounts
Assembly: hg38
Supplementary files format and content: RNA count matrix at the gene level.
Library strategy: Ribo-Seq

extract_protocol:
For RNA-seq,total RNA was extracted using the RNAprep Pure Cell/Bacteria Kit (TIANGEN; DP430) following the manufacturer’s protocol. For Ribo-seq, cells were treated with a specific lysis buffer containing cycloheximide (50 mg/mL) to obtain the lysate. The concentration of the lysate was measured using a Qubit fluorometer. To digest RNA other than ribosome-protected fragments (RPFs), cell or tissue lysates were treated with the unspecific endoribonuclease RNase I. Monosomes were isolated by size-exclusion chromatography and purification. Both ends of the RPFs were phosphorylated and ligated with 5’ and 3’ adapters, respectively. RNA samples were treated with an rRNA depletion kit (Qiagen; 334387) to minimize rRNA contamination.
For RNA-seq, the extracted RNA was utilized for library construction with the Illumina TruSeq Stranded Total RNA Library Prep Kit. The library was sequenced using paired-end 150-bp reads. For Ribo-seq, the RNA fragments were reverse transcribed and amplified by PCR, followed by library construction using the Multiplex Small RNA Library Prep Set for Illumina (NEB; E7300L). The libraries were subjected to Illumina sequencing with single-end 50bp (SE50) sequencing.

value: control


title: Riboseq,shRPS29,rep2

description: Library name: Sample6

value: RPS29 knockdown


title: Riboseq,shCONT,rep1

description: Library name: Sample7


title: mouse_ESC;N702_i7_9_N502_i5_4


title: Riboseq,shRPS29,rep1

description: Library name: Sample5


title: 2016_05_16_19_34_05_583

description: Library name: RHP3498


title: mouse_ESC;N702_i7_9_N502_i5_3


title: 2016_05_16_19_17_01_373

description: Library name: RHP3496


title: 2016_05_16_19_29_14_833

description: Library name: RHP3497


title: RNAseq,shCONT,rep2

description: Library name: Sample4

data_processing:
For RNA-seq, raw FASTQ reads were trimmed using Trim Galore and transcript quantification was performed using Salmon in the quasi-mapping mode. For Ribo-seq, raw FASTQ reads were trimmed using Trim Galore to retain fragments between 20 and 40 base pairs. Ribosomal RNA (rRNA) and transfer RNA (tRNA) sequences were removed using Bowtie2 alignment. The remaining sequences were aligned to the hg38 human genome using STAR and gene expression was quantified using featureCounts
Assembly: hg38
Supplementary files format and content: RNA count matrix at the gene level.


title: 2016_05_16_19_49_57_716

description: Library name: RHP3501


title: 2016_05_16_19_32_44_128

description: Library name: RHP3495


title: RNAseq,shCONT,rep1

description: Library name: Sample3


title: 2016_05_16_23_19_15_868

description: Library name: RHP3557


title: mouse_ESC;N702_i7_9_N502_i5_1


title: 2016_05_11_18_07_18_439

description: Library name: RHP3453


title: 2016_05_16_19_12_47_537

description: Library name: RHP3494


title: 2016_05_16_18_58_06_631

description: Library name: RHP3492


title: mouse_ESC;N702_i7_8_N502_i5_8


title: 2016_05_16_19_00_54_16

description: Library name: RHP3493


title: RNAseq,shRPS29,rep2

description: Library name: Sample2


title: 2016_05_16_19_44_22_758

description: Library name: RHP3499


title: 2016_04_28_16_12_43_953

description: Library name: RHU096


title: 2016_05_16_18_51_22_708

description: Library name: RHP3491


title: 2016_05_11_17_39_14_990

description: Library name: RHP3450


title: RNAseq,shRPS29,rep1

description: Library name: Sample1


title: mouse_ESC;N702_i7_8_N502_i5_6


title: 2016_04_28_17_48_19_998

description: Library name: RHU105


title: T24_STM2457_2

data_processing:
Adaptor sequences were trimmed using Trim Galore (version 0.6.6).
Reads were aligned using HISAT2 (version 2.2.1).
Mapped reads were quantified using featureCounts (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw counts for each sample.
Supplementary files format and content: tab-delimited text file including alternative polyadenylation events in patient and cell line samples.


title: T24_STM2457_3


title: mouse_ESC;N702_i7_8_N502_i5_7


title: 2016_05_11_17_42_25_313

description: Library name: RHP3449


title: 2016_04_28_17_47_47_294

description: Library name: RHU104


title: T24_STM2457_1


title: 2016_05_11_16_52_25_282

description: Library name: RHP3443


title: mouse_ESC;N702_i7_8_N502_i5_4


title: mouse_ESC;N702_i7_8_N502_i5_5


title: 2016_05_16_18_14_45_538

description: Library name: RHP3486


title: mouse_ESC;N702_i7_9_N502_i5_2


title: T24_DMSO3


title: 2016_05_11_18_30_47_727

description: Library name: RHP3454


title: 2016_05_16_18_26_29_554

description: Library name: RHP3488


title: 2016_05_16_18_32_12_297

description: Library name: RHP3487


title: 2016_05_16_18_09_14_626

description: Library name: RHP3485


title: mouse_ESC;N702_i7_8_N502_i5_3


title: T24_DMSO2


title: mouse_ESC;N702_i7_8_N502_i5_2


title: 2016_05_16_15_49_00_740

description: Library name: RHP3466


title: T24_DMSO1


title: mouse_ESC;N702_i7_8_N502_i5_1


title: 2016_05_16_16_54_05_34

description: Library name: RHP3470


title: 2016_05_16_16_27_38_83

description: Library name: RHP3469


title: 2016_05_16_17_56_20_872

description: Library name: RHP3483


title: mouse_ESC;N702_i7_7_N502_i5_8


title: 2016_05_16_18_08_26_889

description: Library name: RHP3484


title: Tumoral_8

description: Non-muscle-invasive, Ta


title: mouse_ESC;N702_i7_7_N502_i5_7


title: 2016_04_28_14_41_36_84

description: Library name: RHU090


title: mouse_ESC;N702_i7_7_N502_i5_6


title: 2016_04_28_21_47_41_609

description: Library name: RHU091


title: 2016_05_11_16_49_05_664

description: Library name: RHP3444


title: Tumoral_7

description: Non-muscle-invasive, Ta


title: 2016_04_28_14_45_51_929

description: Library name: RHU089


title: mouse_ESC;N702_i7_7_N502_i5_5


title: 2016_05_16_17_37_23_227

description: Library name: RHP3482


title: 2016_05_16_15_56_14_300

description: Library name: RHP3465


title: 2016_05_16_21_38_04_787

description: Library name: RHP3544


title: Tumoral_4

description: Non-muscle-invasive, Ta


title: mouse_ESC;N702_i7_7_N502_i5_4


title: 2016_05_16_21_32_14_437

description: Library name: RHP3543


title: 2016_04_28_14_34_54_126

description: Library name: RHU088


title: mouse_ESC;N702_i7_7_N502_i5_3


title: 2016_05_16_15_29_37_944

description: Library name: RHP3463


title: Tumoral_3

description: Muscle-invasive, T2


title: Tumoral_5

description: Non-muscle-invasive, Ta


title: Tumoral_9

description: Non-muscle-invasive, Ta


title: 2016_05_18_13_45_21_50

description: Library name: RHP3481


title: 2016_05_16_15_32_03_43

description: Library name: RHP3464


title: mouse_ESC;N702_i7_7_N502_i5_2


title: 2016_05_16_22_15_13_752

description: Library name: RHP3548


title: Tumoral_2

description: Muscle-invasive, T2


title: 2016_05_16_15_11_48_308

description: Library name: RHP3462


title: mouse_ESC;N702_i7_7_N502_i5_1


title: Tumoral_6

description: Non-muscle-invasive, Ta


title: 2016_05_16_21_57_28_96

description: Library name: RHP3547


title: mouse_ESC;N702_i7_6_N502_i5_8


title: 2016_05_16_22_59_56_285

description: Library name: RHP3555


title: mouse_ESC;N702_i7_6_N502_i5_7


title: 2016_05_11_16_49_18_593

description: Library name: RHP3440


title: 2016_05_16_23_12_24_585

description: Library name: RHP3556


title: Paratumoral_9


title: Paratumoral_8


title: 2016_05_11_16_23_27_159

description: Library name: RHP3439


title: mouse_ESC;N702_i7_6_N502_i5_6


title: 2016_05_16_21_00_26_706

description: Library name: RHP3538


title: mouse_ESC;N702_i7_6_N502_i5_5


title: 2016_05_16_20_51_34_25

description: Library name: RHP3537


title: 2016_05_16_22_39_23_687

description: Library name: RHP3552


title: 2016_05_16_22_40_54_326

description: Library name: RHP3551


title: mouse_ESC;N702_i7_6_N502_i5_4


title: 2016_05_16_21_18_02_776

description: Library name: RHP3541


title: Paratumoral_6


title: 2016_05_16_21_35_33_708

description: Library name: RHP3542


title: mouse_ESC;N702_i7_6_N502_i5_3


title: 2016_04_28_13_59_15_791

description: Library name: RHU087


title: 2016_05_16_14_53_39_957

description: Library name: RHP3461


title: Paratumoral_5


title: Paratumoral_4


title: Tumoral_1

description: Muscle-invasive, T2


title: 2016_04_28_14_02_38_956

description: Library name: RHU086


title: 2016_04_28_17_11_11_462

description: Library name: RHU102


title: Paratumoral_3


title: mouse_ESC;N702_i7_6_N502_i5_2


title: mouse_ESC;N702_i7_6_N502_i5_1


title: Paratumoral_2


title: 2016_04_28_13_25_26_926

description: Library name: RHU085


title: mouse_ESC;N702_i7_5_N502_i5_8


title: 2016_04_28_13_25_15_06

description: Library name: RHU084


title: 2016_04_28_15_59_55_73

description: Library name: RHU095


title: Paratumoral_1


title: 2016_04_28_15_23_36_476

description: Library name: RHU094


title: Paratumoral_7


title: mouse_ESC;N702_i7_5_N502_i5_7


title: HEK3

data_processing:
Adaptor sequences were trimmed using Trim Galore (version 0.6.6).
Reads were aligned to the genome using STAR (version 2.7.10a) and to the transcriptome using bowtie (version 1.3.0)
Pileup was performed using samtools API pysam (version 1.19).
m6A calling was performed using the so-called GLORI-tools pipeline, which is available on github: https://github.com/liucongcas/GLORI-tools.
Assembly: GRCh38
Supplementary files format and content: tab-separated .csv files providing the detected m6A sites in every GLORI-sequenced sample.

molecule: polyA RNA

source_name: Kidney

growth_protocol: HEK293T cells were cultured in DMEM high glucose medium supplemented with 10% FBS and 1% penicillin/streptomycin. The cells were cultivated as adherent monolayers at 37°C in a humidified incubator with a 5% CO2 atmosphere.

extract_protocol:
Patient tissue samples were homogenized by disruption using the TissueRuptor II (Qiagen). Total RNA from homogenized tissue samples and HEK293T cells was isolated with TRIzol. Small RNA fractions were depleted using the MEGAclear Transcription Clean-Up Kit (Thermo Fisher Scientific). Enrichment of mRNA was performed twice using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific). mRNA was then fragmented by incubation for 3 min at 94 °C using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Fragmented mRNA was then DNase I-treated and purified by the RNA Clean & Concentrator-5 kit (Zymo Research). Fragmented RNA samples were then subjected to the chemical deamination protocol. For RNA protection, 100 – 200 ng of fragmented mRNA supplemented with a synthetic Spike-In RNA oligonucleotide were added into protection buffer (1.32 M Glyoxal solution, 50 % DMSO, prepared in water) and incubated for 30 min at 50 °C in a thermal cycler. The RNA was further stabilized by adding 10 µL of freshly prepared saturated boric acid at RT, followed by incubation for 30 min at 50 °C in a thermal cycler. Protected RNA was then added into 50 µL of freshly prepared deamination buffer (1.5 M NaNO2, 80 mM MES (pH 6.0), 1.76 M Glyoxal solution, prepared in water), and incubated for 8 hours at 16 °C in a thermal cycler. After deamination, RNA was purified by ethanol precipitation ON at – 80 °C. Pelleted RNA was washed twice using 75 % ethanol and air-dried for 5 min at RT. Then, the RNA pellet was resuspended in 50 µL of deprotection buffer (500 mM triethylammonium acetate (pH 8.6), 47.5 % deionized formamide, prepared in water) and incubated for 10 min at 95 °C in a thermal cycler. Deprotected RNA was purified by ethanol precipitation for at least 30 min at – 80 °C. Pelleted RNA was washed twice using 75 % ethanol and air-dried for 5 min at RT. The RNA pellet was then resuspended in 50 µL of water and further purified using the RNA Clean & Concentrator-5 kit (Zymo Research). For sequencing library preparation, a two-step RNA end-repair protocol was pursued. RNA 3’-end dephosphorylation was performed by Antarctic phosphatase (New England Biolabs) treatment in a total reaction volume of 20 µL. The reaction was incubated for 30 min at 37 °C and inactivated for 2 min at 80 °C. Subsequently, RNA 5’-end phosphorylation was performed by T4 Polynucleotide Kinase (New England Biolabs) treatment in a total reaction volume of 50 µL. The reaction was incubated for 30 min at 37 °C, inactivated for 20 min at 65 °C, and purified using the RNA Clean & Concentrator-5 kit (Zymo Research).
The libraries were then prepared using the NEBNext Small RNA Library Prep Set for Illumina in combination with the NEBNext Multiplex Oligos for Illumina (Index Primer Sets 1 and 3) (New England Biolabs). Size selection of the libraries was performed via TBE-PAGE using 8 % TBE polyacrylamide gels (Thermo Fisher Scientific) selecting sequencing competent molecules in a size range of 160 – 250 bp.

value: Kidney

value: human embryonic kidney cells


title: 2016_05_16_22_17_36_662

description: Library name: RHP3550


title: 2016_05_16_21_59_32_901

description: Library name: RHP3546


title: mouse_ESC;N702_i7_5_N502_i5_6


title: 2016_05_16_21_54_35_96

description: Library name: RHP3545


title: HEK2


title: 2016_05_16_22_17_51_922

description: Library name: RHP3549


title: 2016_05_16_16_41_52_417

description: Library name: RHP3472


title: 2016_04_28_17_19_50_455

description: Library name: RHU103


title: 2016_05_16_16_45_29_108

description: Library name: RHP3471


title: HEK1


title: mouse_ESC;N702_i7_5_N502_i5_4


title: 2016_05_16_17_00_59_839

description: Library name: RHP3474


title: Tumoral9

description: Non-muscle-invasive, Ta


title: 2016_05_18_13_58_32_327

description: Library name: RHP3473


title: mouse_ESC;N702_i7_5_N502_i5_3


title: 2016_05_16_17_18_34_289

description: Library name: RHP3478


title: 2016_05_16_17_49_45_376

description: Library name: RHP3479


title: 2016_05_16_17_34_42_92

description: Library name: RHP3477


title: mouse_ESC;N702_i7_5_N502_i5_1


title: mouse_ESC;N702_i7_5_N502_i5_2


title: 2016_05_16_21_11_15_856

description: Library name: RHP3540


title: Tumoral8

description: Non-muscle-invasive, Ta


title: Tumoral7

description: Non-muscle-invasive, Ta


title: Tumoral6

description: Non-muscle-invasive, Ta


title: 2016_05_16_21_12_47_475

description: Library name: RHP3539


title: 2016_05_11_17_16_14_218

description: Library name: RHP3446


title: 2016_05_11_17_18_00_824

description: Library name: RHP3445


title: mouse_ESC;N702_i7_5_N502_i5_5


title: mouse_ESC;N702_i7_4_N502_i5_8


title: Tumoral5

description: Non-muscle-invasive, Ta


title: 2016_04_28_14_00_30_114

description: Library name: RHU083


title: 2016_04_28_13_24_45_801

description: Library name: RHU082


title: mouse_ESC;N702_i7_4_N502_i5_7


title: Tumoral4

description: Non-muscle-invasive, Ta


title: mouse_ESC;N702_i7_4_N502_i5_6


title: Tumoral3

description: Muscle-invasive, T2


title: eMAIT_UDCA, cell, expanded MAIT cells with UDCA,biol rep4

city: Wuhan

first: xiufang

last: weng

address: 13# Hangkong Rd, Wuhan, Hubei

institute: Huazhong University of Science and Technology

data_processing:
Illumina HiSeq platform used for basecalling.
Raw image Data files obtained by Illumina HiSeq are analyzed by CASAVA Base Calling and converted into Raw Data of sequencing sequences，and the results are stored in FASTQ (.fq.gz) file format. The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html).
The clean reads obtained by filtering were compared to the reference sequence.Based on the comparison results, new transcript prediction, differential splicing gene detection, SNP and Indel detection, fusion gene detection and other analyses were performed.
HISAT was used to compare clean reads to reference genes. Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Homo_sapiens.GRCh38.99.chr
Supplementary files format and content: Matrix table with read counts for every gene and every sample

source_name: MAIT cells

extract_protocol:
Total RNAs were extracted from sorted cells using TRIzol Reagent (Invitrogen,cat. NO 15596026 ), following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: MAIT cells

tag: group

value: expanded MAIT cells with UDCA


title: Tumoral2

description: Muscle-invasive, T2


title: 2016_05_16_17_51_10_518

description: Library name: RHP3480


title: eMAIT_UDCA, cell, expanded MAIT cells with UDCA,biol rep3


title: Alk1_ECKO

city: New Haven

first: Mark

last: Robinson

state: CT

address: 300 George St

department: Center of Molecular and Cellular Oncology

country: USA

institute: Yale University

description:
Library name: Alk1_ECKO
10X genomics

library_source: transcriptomic single cell

data_processing:
scRNA sequencing quality assurance was performed using FastQC (version 0.11.9), by looking for the presence of adapters and sequence quality. Genome alignment was mapped to the mouse genome (mm10) using 10x Genomics Cell Ranger pipeline (version 6.1.1), which also included filtering and counting barcodes/UMIs. The resulting filtered feature-barcode matrices were used for downstream analysis
Assembly: Mouse mm10
Supplementary files format and content: matrix files

source_name: Retina

extract_protocol:
Retinas were dissected and dissociated using the Neural Tissue Dissociation kit (P) (Miltenyi Biotec, Cat#130- 092-628), followed by filtration through a 70mm cell strainer. After centrifugation (300g for 3 min), cells were resuspended in PBS supplemented with 2mM EDTA and 0.5% BSA. The single cell suspension was enriched for ECs using CD31 MicroBeads (Miltenyi Biotec, Cat#130-097-418) according to the manufacturer’s instructions. The final single cell suspensions were resuspended in PBS containing 0.04% ultra-pure BSA
scRNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3′ Library Construction Kit V3.1 (CG000204. Generated libraries were sequenced on an Illumina HiSeq4000 for 150bp paired end reads.

value: Retina

value: Endothelial cell enriched

tag: age

value: Alk1f/f Cdh5 CreERT2


title: Alk1_CTL

description:
Library name: Alk1_CTL
10X genomics


title: mouse_ESC;N702_i7_4_N502_i5_4


title: eMAIT_UDCA, cell, expanded MAIT cells with UDCA,biol rep1


title: eMAIT_UDCA, cell, expanded MAIT cells with UDCA,biol rep2


title: Tumoral1

description: Muscle-invasive, T2


title: mouse_ESC;N702_i7_4_N502_i5_3


title: eMAIT_TCDCA, cell, expanded MAIT cells with TCDCA,biol rep4

value: expanded MAIT cells with TCDCA


title: eMAIT_TCDCA, cell, expanded MAIT cells with TCDCA,biol rep3


title: eMAIT_TCDCA, cell, expanded MAIT cells with TCDCA,biol rep2


title: mouse_ESC;N702_i7_4_N502_i5_2


title: Paratumoral8


title: eMAIT_HD, cell, expanded MAIT cells without bile acids,biol rep6

value: expanded MAIT cells without bile acids


title: eMAIT_HD, cell, expanded MAIT cells without bile acids,biol rep5


title: eMAIT_TCDCA, cell, expanded MAIT cells with TCDCA,biol rep1


title: Paratumoral7


title: mouse_ESC;N702_i7_4_N502_i5_1

value: mESC


title: eMAIT_HD, cell, expanded MAIT cells without bile acids,biol rep4


title: mouse_ESC;N702_i7_3_N502_i5_8

value: scCAPS+


title: mouse_ESC;N702_i7_4_N502_i5_5


title: eMAIT_HD, cell, expanded MAIT cells without bile acids,biol rep3


title: eMAIT_HD, cell, expanded MAIT cells without bile acids,biol rep2


title: Paratumoral5

value: Bladder


title: mouse_ESC;N702_i7_3_N502_i5_7


title: mouse_ESC;N702_i7_3_N502_i5_6


title: eMAIT_GUDCA, cell, expanded MAIT cells with GUDCA,biol rep4

value: expanded MAIT cells with GUDCA


title: Paratumoral4


title: mouse_ESC;N702_i7_3_N502_i5_5


title: eMAIT_GUDCA, cell, expanded MAIT cells with GUDCA,biol rep2


title: eMAIT_GUDCA, cell, expanded MAIT cells with GUDCA,biol rep3


title: eMAIT_HD, cell, expanded MAIT cells without bile acids,biol rep1


title: Paratumoral9


title: eMAIT_GUDCA, cell, expanded MAIT cells with GUDCA,biol rep1


title: Paratumoral2


title: eMAIT_GCDCA, cell, expanded MAIT cells with GCDCA,biol rep4

value: expanded MAIT cells with GCDCA


title: mouse_ESC;N702_i7_3_N502_i5_4


title: eMAIT_GCDCA, cell, expanded MAIT cells with GCDCA,biol rep2


title: mouse_ESC;N702_i7_3_N502_i5_3


title: Paratumoral1


title: Paratumoral6


title: eMAIT_DCA, cell, expanded MAIT cells with DCA,biol rep1

value: expanded MAIT cells with DCA


title: human_CD8_T_cell;N701_i7_9_N503_i5_8

data_processing:
Raw sequenced reads were demultiplexed using demuxbyname2.sh script from BBMap (version 38.50; https://www.osti.gov/biblio/1241166). Demultiplexed reads were processed with fastp package using default parameters to remove low-quality bases. The trimmed reads were aligned to the reference genome using bwa with default parameters. Reference sequences for mouse genome were downloaded from https://hgdownload.cse.ucsc.edu/goldenpath/mm9/bigZips/; reference sequence for human CD8+ T-cell were downloaded from: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRC h38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_an alysis_set.fna.gz. Uniquely mapped reads were filtered using samtools tools with MAPS>=10. PCR duplicates were called using Picard (2.23.0-Java-11) Mark Duplicates (https://broadinstitute.github.io/picard/). Methylation was called using a custom R script used in our previous project. 10bp at the start or end of reads were excluded for methylation calling. Snakemake pipeline file with detailed steps is provided in the code availability section.
Assembly: MM9 & GRCh38
Supplementary files format and content: bedgraph
Library strategy: scTAPS

source_name: CD8+ T cell

value: CD8+ T cell

value: scTAPS


title: mouse_ESC;N702_i7_3_N502_i5_2


title: eMAIT_DCA, cell, expanded MAIT cells with DCA,biol rep2


title: mouse_ESC;N702_i7_3_N502_i5_1


title: mouse_ESC;N702_i7_2_N502_i5_8


title: Synph-293

city: Suwon

first: Gwang

last: Lee

address: World cup-ro 206

country: South Korea

institute: Ajou university

data_processing:
FastQC0.11.2 for quality check
Cufflinks version 2.2.1 for sequence assembly

source_name: Stably synphilin-1 overexpressing  HEK293 cells

growth_protocol: Human embryonic kidney 293 cells (HEK293) were obtained from American Type Culture Collection. HEK293 shows neuronal like characteristics as it expresses many proteins that are found in neurons such as neurofilament (NF) subunits NF-L, NF-M, NF-H, and alpha-internexin. Synph-293 cells were constructed to stably overexpress FLAG-tagged synphilin-1 in HEK293 cells. HEK293 cells were cultured in Dulbecco’s high-glucose modified Eagle’s medium (DMEM, HyClone, USA), supplemented with 10 µg/ml streptomycin, 100 U/ml penicillin (Gibco, USA) and 10% fetal bovine serum (Corning, USA). Cells were maintained in a humidified atmosphere of 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated suing TruSeq Stranded Total RNA Library Prep Kit (Illumina, CA, USA). The RNA quality was analyzed by rRNA band integrity on an Agilent RNA 6000 Nano kit (Agilent Technologies, CA, USA).
Following mRNA purification, the RNA was physically fragmented before reverse transcription and cDNA generation. The cDNAs were modified with end-repair, poly (A) addition, and connected with sequencing adapters using the TruSeq RNA sample prep Kit (Illumina, CA, USA). cDNA fragments were purified with BluePippin (Sage Science, MA, USA) and amplified by PCR.
the quality of these cDNA libraries was assessed using the Agilent High Sensitivity DNA Kit (Agilent Technologies, CA, USA). Subsequent cluster amplification of denatured templates was performed and an Illumina HiSeq2500 sequencer (Illumina, CA, USA) was used to perform sequencing.

value: human embryonal kidney cell line

value: untreated

tag: stably overexpressing

value: FLAG-tagged synphilin-1


title: human_CD8_T_cell;N701_i7_9_N503_i5_7


title: human_CD8_T_cell;N701_i7_9_N503_i5_6


title: liver, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep5

city: Kuopio

first: Tiit

last: Örd

address: Neulaniementie 2

country: Finland

institute: A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland

description:
liver_CELDKO_HFD3m_IP_rep5
merged_gene_counts.txt

data_processing:
Fastq files were processed using the nf-core RNA-Seq pipeline (version 1.4.2; https://nf-co.re/rnaseq/).
Assembly: mm10
Supplementary files format and content: raw count matrix (tab-delimited matrix of raw gene counts by sample)

source_name: liver

extract_protocol:
The mice were sacrificed and perfused by cardiac puncture with 10 ml of ice-cold PBS supplemented with 20 U/ml heparin and placed on ice for dissection. Aorta, liver and perigonadal adipose tissue (epididymal in male and periovarial in female) were extracted. Tissue samples were cryogenically pulverized using the Cellcrusher cryo-press cooled with liquid nitrogen. Powdered tissue was mixed with polysome extraction buffer and macrophage-associated RNA was enriched from the tissue lysates by immunoprecipitation with anti-EGFP antibody. The resulting RNA was purified using the Absolutely RNA Nanoprep Kit (Agilent) and quantified using the Bioanalyzer RNA 6000 pico assay (Agilent).
Libraries were prepared using the SMARTer v2 Stranded Total RNA-Seq Pico Kit (Takara Bio).

value: liver

tag: diet

value: 3 months high-fat diet

tag: Sex

value: male


title: HEK293

source_name: HEK293 cells

value: non-expressing control


title: liver, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep6

description:
liver_CELDKO_HFD3m_IP_rep6
merged_gene_counts.txt

value: female


title: liver, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep4

description:
liver_CELDKO_HFD3m_IP_rep4
merged_gene_counts.txt


title: mouse_ESC;N702_i7_2_N502_i5_7


title: eMAIT_GCDCA, cell, expanded MAIT cells with GCDCA,biol rep3

value: MAIT cells


title: Paratumoral3


title: mouse_ESC;N702_i7_2_N502_i5_6

value: mESC


title: liver, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep2

description:
liver_CELDKO_HFD3m_IP_rep2
merged_gene_counts.txt


title: liver, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep3

description:
liver_CELDKO_HFD3m_IP_rep3
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_9_N503_i5_5


title: mouse_ESC;N702_i7_2_N502_i5_5

value: scCAPS+


title: human_CD8_T_cell;N701_i7_9_N503_i5_4


title: eMAIT_GCDCA, cell, expanded MAIT cells with GCDCA,biol rep1


title: human_CD8_T_cell;N701_i7_9_N503_i5_3


title: liver, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep5

description:
liver_CELDKO_HFD1m_IP_rep5
merged_gene_counts.txt

value: 1 month high-fat diet


title: mouse_ESC;N702_i7_2_N502_i5_4


title: liver, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep4

description:
liver_CELDKO_HFD1m_IP_rep4
merged_gene_counts.txt


title: liver, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep3

description:
liver_CELDKO_HFD1m_IP_rep3
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_9_N503_i5_2


title: liver, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep2

description:
liver_CELDKO_HFD1m_IP_rep2
merged_gene_counts.txt


title: mouse_ESC;N702_i7_2_N502_i5_3


title: liver, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep1

description:
liver_CELDKO_HFD1m_IP_rep1
merged_gene_counts.txt


title: liver, LDLR-/- ApoB100/100, chow diet, trap, rep6

description:
liver_CELDKO_chow_IP_rep6
merged_gene_counts.txt

value: chow


title: mouse_ESC;N702_i7_2_N502_i5_2


title: human_CD8_T_cell;N701_i7_8_N503_i5_8


title: liver, LDLR-/- ApoB100/100, chow diet, trap, rep4

description:
liver_CELDKO_chow_IP_rep4
merged_gene_counts.txt


title: mouse_ESC;N702_i7_2_N502_i5_1


title: liver, LDLR-/- ApoB100/100, chow diet, trap, rep3

description:
liver_CELDKO_chow_IP_rep3
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_8_N503_i5_7


title: liver, LDLR-/- ApoB100/100, chow diet, trap, rep2

description:
liver_CELDKO_chow_IP_rep2
merged_gene_counts.txt


title: liver, LDLR-/- ApoB100/100, chow diet, trap, rep1

description:
liver_CELDKO_chow_IP_rep1
merged_gene_counts.txt


title: mouse_ESC;N702_i7_1_N502_i5_8


title: liver, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep6

description:
liver_CELDKO_HFD1m_IP_rep6
merged_gene_counts.txt


title: liver, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep1

description:
liver_CELDKO_HFD3m_IP_rep1
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_8_N503_i5_6


title: mouse_ESC;N702_i7_1_N502_i5_7


title: liver, LDLR+/+ ApoB+/+, chow diet, trap, rep6

description:
liver_CEL_chow_IP_rep6
merged_gene_counts.txt

value: LDLR+/+ ApoB+/+


title: human_CD8_T_cell;N701_i7_8_N503_i5_5


title: liver, LDLR+/+ ApoB+/+, chow diet, trap, rep3

description:
liver_CEL_chow_IP_rep3
merged_gene_counts.txt


title: liver, LDLR+/+ ApoB+/+, chow diet, trap, rep4

description:
liver_CEL_chow_IP_rep4
merged_gene_counts.txt


title: liver, LDLR+/+ ApoB+/+, chow diet, trap, rep5

description:
liver_CEL_chow_IP_rep5
merged_gene_counts.txt


title: mouse_ESC;N702_i7_1_N502_i5_6


title: liver, LDLR+/+ ApoB+/+, chow diet, trap, rep2

description:
liver_CEL_chow_IP_rep2
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_9_N503_i5_1


title: liver, LDLR+/+ ApoB+/+, chow diet, trap, rep1

description:
liver_CEL_chow_IP_rep1
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_8_N503_i5_3


title: mouse_ESC;N702_i7_1_N502_i5_4


title: aorta, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep6

description:
aorta_CELDKO_HFD3m_IP_rep6
merged_gene_counts.txt

source_name: aorta

value: aorta


title: mouse_ESC;N702_i7_1_N502_i5_5


title: liver, LDLR-/- ApoB100/100, chow diet, trap, rep5

description:
liver_CELDKO_chow_IP_rep5
merged_gene_counts.txt


title: aorta, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep5

description:
aorta_CELDKO_HFD3m_IP_rep5
merged_gene_counts.txt


title: mouse_ESC;N702_i7_1_N502_i5_3


title: human_CD8_T_cell;N701_i7_8_N503_i5_2

value: CD8+ T cell


title: aorta, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep4

description:
aorta_CELDKO_HFD3m_IP_rep4
merged_gene_counts.txt


title: aorta, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep2

description:
aorta_CELDKO_HFD3m_IP_rep2
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_7_N503_i5_8

value: scTAPS


title: mouse_ESC;N702_i7_1_N502_i5_2


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep6

description:
aorta_CELDKO_HFD1m_IP_rep6
merged_gene_counts.txt


title: aorta, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep1

description:
aorta_CELDKO_HFD3m_IP_rep1
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_7_N503_i5_7


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep4

description:
aorta_CELDKO_HFD1m_IP_rep4
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_8_N503_i5_4


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep5

description:
aorta_CELDKO_HFD1m_IP_rep5
merged_gene_counts.txt


title: mouse_ESC;N702_i7_1_N502_i5_1


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep3

description:
aorta_CELDKO_HFD1m_IP_rep3
merged_gene_counts.txt


title: mouse_ESC;N702_i7_12_N502_i5_8


title: mouse_ESC;N702_i7_12_N502_i5_7


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep1

description:
aorta_CELDKO_HFD1m_IP_rep1
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_7_N503_i5_5


title: aorta, LDLR-/- ApoB100/100, chow diet, trap, rep6

description:
aorta_CELDKO_chow_IP_rep6
merged_gene_counts.txt


title: aorta, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep2

description:
aorta_CELDKO_HFD1m_IP_rep2
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_7_N503_i5_6


title: mouse_ESC;N702_i7_12_N502_i5_6


title: aorta, LDLR-/- ApoB100/100, chow diet, trap, rep5

description:
aorta_CELDKO_chow_IP_rep5
merged_gene_counts.txt


title: aorta, LDLR-/- ApoB100/100, chow diet, trap, rep4

description:
aorta_CELDKO_chow_IP_rep4
merged_gene_counts.txt


title: mouse_ESC;N702_i7_12_N502_i5_5


title: human_CD8_T_cell;N701_i7_7_N503_i5_3


title: aorta, LDLR-/- ApoB100/100, chow diet, trap, rep3

description:
aorta_CELDKO_chow_IP_rep3
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_7_N503_i5_4


title: aorta, LDLR-/- ApoB100/100, chow diet, trap, rep2

description:
aorta_CELDKO_chow_IP_rep2
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_8_N503_i5_1


title: aorta, LDLR-/- ApoB100/100, chow diet, trap, rep1

description:
aorta_CELDKO_chow_IP_rep1
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_7_N503_i5_2


title: aorta, LDLR+/+ ApoB+/+, chow diet, trap, rep6

description:
aorta_CEL_chow_IP_rep6
merged_gene_counts.txt


title: mouse_ESC;N702_i7_12_N502_i5_3


title: aorta, LDLR+/+ ApoB+/+, chow diet, trap, rep5

description:
aorta_CEL_chow_IP_rep5
merged_gene_counts.txt


title: aorta, LDLR+/+ ApoB+/+, chow diet, trap, rep4

description:
aorta_CEL_chow_IP_rep4
merged_gene_counts.txt


title: mouse_ESC;N702_i7_12_N502_i5_2


title: aorta, LDLR+/+ ApoB+/+, chow diet, trap, rep2

description:
aorta_CEL_chow_IP_rep2
merged_gene_counts.txt


title: mouse_ESC;N702_i7_12_N502_i5_1


title: aorta, LDLR+/+ ApoB+/+, chow diet, trap, rep1

description:
aorta_CEL_chow_IP_rep1
merged_gene_counts.txt


title: aorta, LDLR+/+ ApoB+/+, chow diet, trap, rep3

description:
aorta_CEL_chow_IP_rep3
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_6_N503_i5_7


title: human_CD8_T_cell;N701_i7_6_N503_i5_8


title: adipose, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep5

description:
adipose_CELDKO_HFD3m_IP_rep5
merged_gene_counts.txt

source_name: adipose

value: adipose


title: adipose, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep4

description:
adipose_CELDKO_HFD3m_IP_rep4
merged_gene_counts.txt


title: mouse_ESC;N702_i7_11_N502_i5_7


title: adipose, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep2

description:
adipose_CELDKO_HFD3m_IP_rep2
merged_gene_counts.txt


title: mouse_ESC;N702_i7_11_N502_i5_8


title: mouse_ESC;N702_i7_11_N502_i5_6


title: human_CD8_T_cell;N701_i7_6_N503_i5_5


title: adipose, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep1

description:
adipose_CELDKO_HFD3m_IP_rep1
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_6_N503_i5_4


title: mouse_ESC;N702_i7_12_N502_i5_4


title: adipose, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep5

description:
adipose_CELDKO_HFD1m_IP_rep5
merged_gene_counts.txt


title: adipose, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep3

description:
adipose_CELDKO_HFD3m_IP_rep3
merged_gene_counts.txt


title: adipose, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep6

description:
adipose_CELDKO_HFD1m_IP_rep6
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_6_N503_i5_3


title: human_CD8_T_cell;N701_i7_7_N503_i5_1


title: mouse_ESC;N702_i7_11_N502_i5_4


title: adipose, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep3

description:
adipose_CELDKO_HFD1m_IP_rep3
merged_gene_counts.txt


title: adipose, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep4

description:
adipose_CELDKO_HFD1m_IP_rep4
merged_gene_counts.txt


title: adipose, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep2

description:
adipose_CELDKO_HFD1m_IP_rep2
merged_gene_counts.txt


title: mouse_ESC;N702_i7_11_N502_i5_3


title: human_CD8_T_cell;N701_i7_6_N503_i5_1


title: human_CD8_T_cell;N701_i7_6_N503_i5_6


title: adipose, LDLR-/- ApoB100/100, 1 month high-fat diet, trap, rep1

description:
adipose_CELDKO_HFD1m_IP_rep1
merged_gene_counts.txt


title: mouse_ESC;N702_i7_11_N502_i5_2


title: human_CD8_T_cell;N701_i7_5_N503_i5_8


title: Viral library 12 well rescue

city: London

first: Alexander

last: Becalick

address: 1 Midland Road

institute: The Francis Crick Institute

description:
Library name: RV35
Amplicon of 20 bp continuous rabies barcode

library_source: other

data_processing:
To analyze sequenced libraries, low-quality reads were first removed from raw demultiplexed .fastq files with Trimmomatic 0.36, removing reads with an average PHRED score per base of less than 20 in a 6-base sliding window and removing any reads with a length of less than 101 bp. The sequences flanking the barcode site were then matched to their expected sequences, and any mismatched sequences were discarded to remove frameshifts. Next, the UMI sequences were used to de-duplicate the remaining barcode sequence reads to account for PCR amplification bias. The remaining sequences represented individual species of barcode RNA/DNA found in the viral or plasmid samples. To account for sequencing errors and PCR-induced mutations that may be present in some of these sequences, closely related barcodes were collapsed into their most abundant “parent" sequences using a method adapted from Kebschull et al. First, barcode sequences were aligned to all other barcodes in the library with a maximum hamming distance of 2 using Bowtie2 (2.5.1-GCC-12.3.0). Related sequences were then collapsed onto the barcode with the highest UMI count, summing together all of the counts.
Assembly: CVS-N2c(deltaG)-mCherry Addgene plasmid # 73464
Supplementary files format and content: All processed data files contain two tab separated columns of UMI counts and barcode sequences

molecule: other

organism: Lyssavirus rabies

source_name: HEK293TG packaging

extract_protocol:
For viral libraries, viral genomic RNA was extracted using the Quick DNA/RNA Viral Kit (Zymo Research, D7020) and eluted into 15 μl of RNase-free water. Purified viral barcode RNA was then reverse transcribed using Superscript IV reverse transcriptase (Thermo Fisher Scientific, 18090050) at 50 °C for 10 minutes with 1 μl of 2 μM UMI_P5_Truseq primer (Supplementary Table 1), before heat inactivation at 80 °C for 10 minutes. RNA was subsequently digested with RNase H (New England Biolabs, M0297S) at 37 °C for 20 minutes.
Barcoded library sequencing. The diversity of the barcoded plasmid and viral libraries was quantified using a unique molecular identifier (UMI) tagging approach.  The primer used for reverse transcription (UMI_P5_Truseq, Supplementary Table 1) contained an overhang of 22 bp P5 Truseq for nested adaptor PCR, a 12 bp random UMI sequence and 20 bp of rabies homologous sequence for binding upstream of the barcode. The same UMI-P5-Truseq primer was used to produce UMI-tagged amplicons from the barcoded plasmid libraries in a two-cycle limited PCR reaction. Barcoded plasmid (5 ng) was added to 16 μl Q5 Hot Start High-Fidelity 2X Master Mix (New England Biolabs, M0494S) with 1.25 μl each of UMI_P5_Truseq and P7_universal_reverse primers (Supplementary Table 1) and PCR thermocycled with the following conditions: 98 °C - 3 mins, two cycles of 98 °C - 30 s, 67 °C - 20 s, 72 °C - 30 s, followed by 72 °C - 2 mins and 12 °C hold. The resultant cDNA from the viral samples or amplicons from barcoded plasmids was size-selected and purified using KAPA Pure Beads (Roche, KK8000) in a 1:1 ratio, eluting in 25 μl of RNase-free water. To determine the optimal cycle number for library amplification, the amplification curve inflection point was determined for each sample by qPCR. 2.5 μl of each sample was added to a master mix of 1 μl 2.5X Thiazole Green (Biotium, 40086), 1 μl 2.5X ROX reference dye (Thermo Fisher Scientific, 12223-012), 12.5 μl Q5 Hot Start High-Fidelity 2X Master Mix (New England Biolabs, M0494S), 1.25 μl 10 μM IDT_i7_1 primer (Supplementary Table 1) for plasmid amplicons or P7_universal_reverse for viral single-stranded cDNA, 1.25 μl 10 μM IDT_i5_1 primer and 5.5 μl of molecular grade water. The following thermocycler conditions were used: 98 °C - 3 mins, followed by 40 cycles of 98 °C - 10 s, 68 °C - 20 s, 72 °C - 30 s. Subsequently, the remaining 22.5 μl of each sample was added to a mix of 25 μl Q5 Hot Start High-Fidelity 2X Master Mix, 2.5 μl 10 μM IDT_i7_1-10 primer for plasmid amplicons/P7_universal_reverse for viral single-stranded cDNA, and 2.5 μl 10 μM IDT_i5_1-10 primer. The IDT_i5_X and IDT_i7_X primers each contain 8 bp index sequences derived from the rhAmpSeq index primer set (Integrated DNA Technologies) for dual-index demultiplexing alongside the Illumina P5 and P7 adapter sequences, respectively. Thermocycling conditions for this Illumina adaptor PCR were: 98 °C - 3 mins followed by cycles of 98 °C - 10 s, 68 °C - 20 s, 72 °C - 30 s, then 72 °C - 2 mins. The number of cycles was equal to the qPCR inflection point, less 3 cycles to account for the 10X (∼23) increase in target concentration. For viral amplicons, the P7-indexed adaptor sequences were added in a final PCR step. The UMI-tagged viral amplicons were first gel-purified with a Wizard SV Gel and PCR Clean-Up kit (Promega, A9281) and eluted with 20 μl water. Then, the same PCR mix was used as described above for the barcoded plasmid index PCR, adding the IDT_i7_X primer and the matching IDT_i5_X for each sample. Thermocycling conditions were likewise the same as the Illumina adaptor PCR, but with a fixed number of 3 cycles. The indexed viral and plasmid amplicons were then gel-purified with a Wizard SV Gel and PCR Clean-Up kit (Promega, A9281) and eluted with 25 μl water. The concentration and size distribution of these amplicon libraries were quantified with a High Sensitivity D1000 ScreenTape kit (Agilent, 5067-5584) on an Agilent 2200 TapeStation system. Samples passing QC were sequenced on an Illumina NovaSeq 6000/NovaSeq X using Illumina TruSeq primers for paired-end 100 bp sequencing at a depth of 10-50 million reads per sample.

value: HEK293TG packaging

tag: batch


title: Viral library 2 well rescue

description:
Library name: RV32
Amplicon of 20 bp continuous rabies barcode


title: mouse_ESC;N702_i7_11_N502_i5_1


title: mouse_ESC;N702_i7_10_N502_i5_8


title: Plasmid library 20 bp

description:
Library name: PBC20
Amplicon of 20 bp continuous plasmid barcode

source_name: MegaX DH10B E. coli

value: MegaX DH10B E. coli


title: mouse_ESC;N702_i7_11_N502_i5_5


title: adipose, LDLR-/- ApoB100/100, chow diet, trap, rep6

description:
adipose_CELDKO_chow_IP_rep6
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_5_N503_i5_6


title: adipose, LDLR-/- ApoB100/100, chow diet, trap, rep4

description:
adipose_CELDKO_chow_IP_rep4
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_5_N503_i5_7


title: human_CD8_T_cell;N701_i7_5_N503_i5_5


title: mouse_ESC;N702_i7_10_N502_i5_7


title: adipose, LDLR-/- ApoB100/100, chow diet, trap, rep3

description:
adipose_CELDKO_chow_IP_rep3
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_6_N503_i5_2


title: adipose, LDLR-/- ApoB100/100, chow diet, trap, rep2

description:
adipose_CELDKO_chow_IP_rep2
merged_gene_counts.txt


title: mouse_ESC;N702_i7_10_N502_i5_5


title: human_CD8_T_cell;N701_i7_5_N503_i5_4


title: adipose, LDLR-/- ApoB100/100, chow diet, trap, rep1

description:
adipose_CELDKO_chow_IP_rep1
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_5_N503_i5_3


title: Viral library 10cm plate rescue

description:
Library name: RV2
Amplicon of 20 bp bipartite rabies barcode

source_name: HEK293T packaging

value: HEK293T packaging


title: mouse_ESC;N702_i7_10_N502_i5_4


title: adipose, LDLR+/+ ApoB+/+, chow diet, trap, rep6

description:
adipose_CEL_chow_IP_rep6
merged_gene_counts.txt


title: mouse_ESC;N702_i7_10_N502_i5_3


title: human_CD8_T_cell;N701_i7_5_N503_i5_1


title: adipose, LDLR-/- ApoB100/100, chow diet, trap, rep5

description:
adipose_CELDKO_chow_IP_rep5
merged_gene_counts.txt


title: mouse_ESC;N702_i7_10_N502_i5_2


title: adipose, LDLR+/+ ApoB+/+, chow diet, trap, rep5

description:
adipose_CEL_chow_IP_rep5
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_4_N503_i5_8


title: mouse_ESC;N702_i7_10_N502_i5_6


title: human_CD8_T_cell;N701_i7_4_N503_i5_7


title: adipose, LDLR+/+ ApoB+/+, chow diet, trap, rep3

description:
adipose_CEL_chow_IP_rep3
merged_gene_counts.txt


title: adipose, LDLR+/+ ApoB+/+, chow diet, trap, rep4

description:
adipose_CEL_chow_IP_rep4
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_4_N503_i5_6


title: adipose, LDLR+/+ ApoB+/+, chow diet, trap, rep2

description:
adipose_CEL_chow_IP_rep2
merged_gene_counts.txt


title: HM biol rep 3 (CLASH)

city: Frederick

first: Sharan

last: Malagobadan

address: 1050 Boyles Street, Building 560, Room 11-2

institute: National Institutes of Health

data_processing:
Reads were trimmed for adapter sequence and processed by QuagmiR and bowtie to map the miRNA and target fragments, respectively.
Assembly: Mus musculus custom motif file for miRNA mapping by QuagmiR. Mouse UTR sequence from TargetScan for target mapping by bowtie.
Supplementary files format and content: Tab-delimited text file with gene id, miRNA, full sequence, number of reads, and target fragment sequence of hybrids.

source_name: teratocarcinoma

extract_protocol:
RNA containing miRNA-target hybrid was extracted using TRIzol™ Reagent (Invitrogen, 15596018).
Cross-linking, ligation, and sequencing of hybrids (CLASH) was used to identify miRNA-target RNA interaction sites. In brief, a 10 cm dish of confluent cells was irradiated with UV-C (300 mJ/cm²) to covalently bond RNA-binding proteins to bound nucleic acids. During the subsequent cell lysis, the lysate was treated with Turbo DNase (Invitrogen, AM2238) to remove DNA and RNAse 1 (Thermo Scientific, EN0601) to partially digest the RNA to generate 25-200 nt fragments. Immunoprecipitation of AGO2 proteins was performed using Dynabeads™ Protein G (Invitrogen, 10003D) conjugated with a mouse AGO2 antibody (WAKO, 014-22023) for 4 hours at 4°C. After phosphorylation with T4 PNK (New England Biolabs, M0201), T4 RNA ligase 1 (New England Biolabs, M0204) was used for intermolecular ligation, followed by dephosphorylation and 3' adapter ligation using T4 RNA ligase 2, truncated, K227Q (New England Biolabs, M0351). T4 PNK labeling with 32P of RNA allowed visualization of the AGO2-RNA complexes by SDS-PAGE after transfer to a nitrocellulose membrane. The membrane sections containing protein-RNA complexes were cut and treated with proteinase K (Invitrogen, AM2542) to yield protein-free RNA. The 5' ends were then phosphorylated to prepare the RNA for sequencing library preparation. The final AGO2-CLASH library was sequenced on the Illumina NextSeq 1000 platform using paired-end sequencing.

value: teratocarcinoma

value: Embryonic carcinoma

value: Dicer (HM/-)


title: Urinary Bladder_BBN-induced and SQ-diEG-treated_16 weeks_rep2

type: RNA

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

country: Japan

institute: University of Tsukuba

description: 16W SQ-diEG 2

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, Mouse; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome analysis console software (sheet 2 ). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files) was used. Filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 2 (in linear space) for differentially expressed gene list.
signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4)

label: biotin

source_name: BBN-induced and SQ-diEG-treated urinary bladder at 16W

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

growth_protocol: C57BL/6 mice(6–8 weeks old) were treated with 0.025% N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) to induce bladder cancer.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: Mice were orally administered SQ-diEG or PBS (control) from weeks 0 to 8 or 16, and the mice were sacrificed on the final day of administration and the bladder was collected.

value: Female

tag: strain

value: 6-8 weeks old

value: BBN-induced urinary bladder

value: SQ-diEG

tag: time


title: Urinary Bladder_BBN-induced and SQ-diEG-treated_16 weeks_rep1

description: 16W SQ-diEG 1


title: human_CD8_T_cell;N701_i7_4_N503_i5_5


title: Urinary Bladder_BBN-induced_16 weeks_rep2

description: 16W control 2

source_name: BBN-induced urinary bladder 16W

value: control


title: adipose, LDLR+/+ ApoB+/+, chow diet, trap, rep1

description:
adipose_CEL_chow_IP_rep1
merged_gene_counts.txt

value: chow

value: male


title: DKD_shRNA29

city: Beijing

first: Jingwen

last: Chen

address: 1 XianNongTan Street, Xicheng District

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical （CAMS & PUMC）

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

source_name: kidney

extract_protocol:
RNA was harvest using Trizol,1μg of total RNA was used for the construction of seqencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols.

value: kidney

value: Gcgr shRNA


title: Urinary Bladder_BBN-induced_16 weeks_rep1

description: 16W control 1


title: HM biol rep 2 (CLASH)


title: Urinary Bladder_BBN-induced and SQ-diEG-treated_8 weeks_rep2

description: 8W SQ-diEG 2

source_name: BBN-induced and SQ-diEG-treated urinary bladder 8W


title: Urinary Bladder_BBN-induced_8 weeks_rep2

description: 8W control 2

source_name: BBN-induced urinary bladder at 8W


title: Urinary Bladder_BBN-induced_8 weeks_rep1

description: 8W control 1


title: Urinary Bladder_BBN-induced and SQ-diEG-treated_8 weeks_rep1

description: 8W SQ-diEG 1


title: human_CD8_T_cell;N701_i7_4_N503_i5_4

value: CD8+ T cell

value: scTAPS


title: mouse_ESC;N702_i7_10_N502_i5_1

source_name: mESC

value: mESC

value: scCAPS+


title: HM biol rep 1 (CLASH)


title: DKD_shRNA31


title: human_CD8_T_cell;N701_i7_4_N503_i5_3


title: DKD_shRNA13


title: liver, LDLR-/- ApoB100/100, 3 month high-fat diet, rep5

description:
liver_CELDKO_HFD3m_Input_rep5
merged_gene_counts.txt

extract_protocol:
The mice were sacrificed and perfused by cardiac puncture with 10 ml of ice-cold PBS supplemented with 20 U/ml heparin and placed on ice for dissection. Liver and perigonadal adipose tissue (epididymal in male and periovarial in female) were extracted and used in bulk RNA-Seq library preparation. Tissue samples were cryogenically pulverized using the Cellcrusher cryo-press cooled with liquid nitrogen. Total RNA was isolated and treated with DNase I using the Absolutely RNA Nanoprep Kit (Agilent). RNA was quantified using the Bioanalyzer RNA 6000 pico assay (Agilent).
Bulk RNA-Seq libraries were prepared using the SMARTer v2 Stranded Total RNA-Seq Pico Kit (Takara Bio).

value: liver

value: 3 months high-fat diet


title: DKD_shRNA32


title: WT biol rep 3 (CLASH)

value: teratocarcinoma

value: Embryonic carcinoma

value: Dicer (+/+)


title: liver, LDLR-/- ApoB100/100, 3 month high-fat diet, rep4

description:
liver_CELDKO_HFD3m_Input_rep4
merged_gene_counts.txt


title: DKD_shRNA15


title: human_CD8_T_cell;N701_i7_4_N503_i5_2


title: WT biol rep 2 (CLASH)


title: DKD_shRNA34


title: WT biol rep 1 (CLASH)


title: human_CD8_T_cell;N701_i7_4_N503_i5_1


title: liver, LDLR-/- ApoB100/100, 3 month high-fat diet, rep3

description:
liver_CELDKO_HFD3m_Input_rep3
merged_gene_counts.txt

value: female


title: DKD_shRNA35


title: HM AGO2 IP biol rep 4

data_processing:
Reads were trimmed for adapter sequence and processed by QuagmiR to map and quantify miRNA reads using a custom motif file for mouse miRNA
For total RNA miR-seq data, reads were normalized to spike-in. For AGO2-IP miR-seq, reads were normalized to total miRNA.
Assembly: Mus musculus custom motif file for miRNA quantification by QuagmiR
Supplementary files format and content: Tab-delimited text file with RPM for each group

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018).
Small RNA libraries for miR-seq were generated using the QIAseq miRNA Library Kit (Qiagen, 331502) according to the manufacturer's instructions. For normalization of total RNA samples, 1ul of QIAseq miRNA Library QC Spike-ins (Qiagen, 331535) was added to 500 ng of RNA before library preparation. The library was size-selected and purified on a native 6% (w/v) acrylamide gel and ethanol precipitation, respectively. The library was sequenced on the Illumina Nextseq 1000 platform.

value: Dicer (HM/-)

value: AGO2 immunoprecipitation


title: DKD_Vehicle1

value: Ctr shRNA


title: liver, LDLR-/- ApoB100/100, 3 month high-fat diet, rep6

description:
liver_CELDKO_HFD3m_Input_rep6
merged_gene_counts.txt


title: liver, LDLR-/- ApoB100/100, 3 month high-fat diet, rep2

description:
liver_CELDKO_HFD3m_Input_rep2
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_3_N503_i5_7


title: human_CD8_T_cell;N701_i7_3_N503_i5_6


title: human_CD8_T_cell;N701_i7_3_N503_i5_8


title: liver, LDLR-/- ApoB100/100, 3 month high-fat diet, rep1

description:
liver_CELDKO_HFD3m_Input_rep1
merged_gene_counts.txt


title: DKD_Vehicle19


title: HM AGO2 IP biol rep 3


title: DKD_Vehicle20


title: liver, LDLR-/- ApoB100/100, 1 month high-fat diet, rep6

description:
liver_CELDKO_HFD1m_Input_rep6
merged_gene_counts.txt

value: 1 month high-fat diet


title: liver, LDLR-/- ApoB100/100, 1 month high-fat diet, rep5

description:
liver_CELDKO_HFD1m_Input_rep5
merged_gene_counts.txt

value: male


title: DKD_Vehicle4

value: kidney


title: HM AGO2 IP biol rep 2


title: human_CD8_T_cell;N701_i7_3_N503_i5_5


title: HM AGO2 IP biol rep 1


title: DKD_Vehicle6


title: liver, LDLR-/- ApoB100/100, 1 month high-fat diet, rep4

description:
liver_CELDKO_HFD1m_Input_rep4
merged_gene_counts.txt


title: WT AGO2 IP biol rep 2


title: human_CD8_T_cell;N701_i7_3_N503_i5_4


title: human_CD8_T_cell;N701_i7_3_N503_i5_3


title: liver, LDLR-/- ApoB100/100, 1 month high-fat diet, rep3

description:
liver_CELDKO_HFD1m_Input_rep3
merged_gene_counts.txt


title: DKD_Vehicle8


title: WT AGO2 IP biol rep 1


title: liver, LDLR-/- ApoB100/100, 1 month high-fat diet, rep2

description:
liver_CELDKO_HFD1m_Input_rep2
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_3_N503_i5_2


title: NC_37

value: WT


title: liver, LDLR-/- ApoB100/100, 1 month high-fat diet, rep1

description:
liver_CELDKO_HFD1m_Input_rep1
merged_gene_counts.txt


title: NC_38


title: human_CD8_T_cell;N701_i7_3_N503_i5_1

value: CD8+ T cell


title: liver, LDLR-/- ApoB100/100, chow diet, rep6

description:
liver_CELDKO_chow_Input_rep6
merged_gene_counts.txt

value: chow


title: HM biol rep 5


title: human_CD8_T_cell;N701_i7_2_N503_i5_8

value: scTAPS


title: human_CD8_T_cell;N701_i7_2_N503_i5_7


title: liver, LDLR-/- ApoB100/100, chow diet, rep5

description:
liver_CELDKO_chow_Input_rep5
merged_gene_counts.txt


title: NC_41


title: human_CD8_T_cell;N701_i7_2_N503_i5_6


title: HM biol rep 2


title: liver, LDLR-/- ApoB100/100, chow diet, rep4

description:
liver_CELDKO_chow_Input_rep4
merged_gene_counts.txt


title: Alveolar_macrophages_Ozone-0.8ppm_8046_Rep6

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

data_processing:
Raw reads were trimmed and filtered of adapter contamination using cutadapt (Martin 2011), and further filtered such that at least 90% of bases had a quality score of at least 20 using fastx_toolkit v0.0.14
Reads were then aligned to the reference mouse genome (mm10) and GENCODE vM25 transcript annotations using STAR v2.7.7a, and transcript abundance was estimated using salmon v1.5.2
Differential expression between ozone-exposed vs. filtered air groups was then detected using DESeq2 v1.26.0 in R v3.6.0, using a design that corrected for flow cytometry batch dates. These batch effects were also removed from the VST-normalized expression values using limma v3.42.2. All log2 fold-changes reported were shrunken using ashr 2.2-47
Assembly: mm10
Supplementary files format and content: VST-normalized batch-corrected expression from DESeq2

source_name: Alveolar macrophages

growth_protocol: Female C57BL/6NJ mice were purchased from the Jackson Laboratory and housed in groups of ~3-4/cage under normal 12-hour light/dark cycles with ad libitum food (Envigo 2929) and water on Teklad 7070C bedding (Envigo).

extract_protocol:
Alveolar macrophages from mouse lungs were isolated by flow cytometry using an established protocol (PMID 29671604), followed by RNA extraction using Qiagen RNAEasy kits. RNA quality was assessed by Bioanalyzer.
Library preparation was conducted using the Roche Kapa stranded mRNA library prep kit and sequenced on an Illumina NovaSeq 6000 using paired-end 50bp reads. One mismatch was used in demultiplexing indexes with bcl2fastq ver 2.20.0

treatment_protocol: Mice used were used at an age of 8-11 weeks, and exposed to filtered air (FA) or 0.8 ppm ozone for four hours/day for four consecutive days. Three days later, mice were anesthetized (2 g/kg urethane) and euthanized by inferior vena cava/abdominal aorta exsanguination. Lungs were removed and then processed for flow sorting of alveolar macrophages using a previously published protocol (PMID 29671604). All studies were conducted in compliance with University of North Carolina Institutional Animal Care and Use Committee guidelines in animal facilities approved and accredited by AAALAC.

tag: mouse id

tag: flow sort_batch

value: Female

value: Alveolar macrophages

tag: replicate

value: ozone

tag: rin


title: liver, LDLR-/- ApoB100/100, chow diet, rep3

description:
liver_CELDKO_chow_Input_rep3
merged_gene_counts.txt

tag: tissue

value: liver


title: Alveolar_macrophages_FilteredAir_8045_Rep6

value: filtered air


title: human_CD8_T_cell;N701_i7_2_N503_i5_5

source_name: CD8+ T cell

tag: experiment type


title: HM biol rep 1

value: teratocarcinoma

tag: cell line

tag: cell type

value: Embryonic carcinoma


title: liver, LDLR-/- ApoB100/100, chow diet, rep2

description:
liver_CELDKO_chow_Input_rep2
merged_gene_counts.txt

tag: genotype


title: human_CD8_T_cell;N701_i7_2_N503_i5_4


title: Alveolar_macrophages_Ozone-0.8ppm_8044_Rep5

tag: treatment


title: human_CD8_T_cell;N701_i7_5_N503_i5_2


title: HetKO biol rep 6

value: Dicer (+/-)


title: human_CD8_T_cell;N701_i7_2_N503_i5_3


title: Alveolar_macrophages_FilteredAir_8043_Rep5


title: HM biol rep 6

value: Dicer (HM/-)


title: NC_39


title: HetKO biol rep 5


title: HM biol rep 4


title: human_CD8_T_cell;N701_i7_2_N503_i5_1


title: human_CD8_T_cell;N701_i7_2_N503_i5_2


title: HM biol rep 3


title: HetKO biol rep 4


title: liver, LDLR+/+ ApoB+/+, chow diet, rep6

description:
liver_CEL_chow_Input_rep6
merged_gene_counts.txt

value: LDLR+/+ ApoB+/+

value: female


title: HetKO biol rep 3


title: liver, LDLR+/+ ApoB+/+, chow diet, rep4

description:
liver_CEL_chow_Input_rep4
merged_gene_counts.txt

value: male


title: liver, LDLR+/+ ApoB+/+, chow diet, rep5

description:
liver_CEL_chow_Input_rep5
merged_gene_counts.txt


title: Alveolar_macrophages_Ozone-0.8ppm_8041_Rep3


title: human_CD8_T_cell;N701_i7_1_N503_i5_8


title: Alveolar_macrophages_FilteredAir_8040_Rep4


title: human_CD8_T_cell;N701_i7_1_N503_i5_7


title: Alveolar_macrophages_FilteredAir_8039_Rep3


title: HetKO biol rep 2


title: HetKO biol rep 1


title: liver, LDLR+/+ ApoB+/+, chow diet, rep3

description:
liver_CEL_chow_Input_rep3
merged_gene_counts.txt


title: liver, LDLR+/+ ApoB+/+, chow diet, rep2

description:
liver_CEL_chow_Input_rep2
merged_gene_counts.txt


title: liver, LDLR-/- ApoB100/100, chow diet, rep1

description:
liver_CELDKO_chow_Input_rep1
merged_gene_counts.txt


title: Alveolar_macrophages_Ozone-0.8ppm_8036_Rep2


title: WT biol rep 6

value: Dicer (+/+)


title: human_CD8_T_cell;N701_i7_1_N503_i5_5


title: WT biol rep 5


title: Alveolar_macrophages_FilteredAir_8033_Rep2


title: liver, LDLR+/+ ApoB+/+, chow diet, rep1

description:
liver_CEL_chow_Input_rep1
merged_gene_counts.txt


title: Alveolar_macrophages_Ozone-0.8ppm_8042_Rep4


title: adipose, LDLR-/- ApoB100/100, 3 month high-fat diet, rep6

description:
adipose_CELDKO_HFD3m_Input_rep6
merged_gene_counts.txt

value: adipose

value: 3 months high-fat diet


title: Alveolar_macrophages_FilteredAir_8032_Rep1


title: WT biol rep 4


title: human_CD8_T_cell;N701_i7_1_N503_i5_4

value: CD8+ T cell


title: adipose, LDLR-/- ApoB100/100, 3 month high-fat diet, rep5

description:
adipose_CELDKO_HFD3m_Input_rep5
merged_gene_counts.txt


title: Alveolar_macrophages_Ozone-0.8ppm_8029_Rep1


title: human_CD8_T_cell;N701_i7_1_N503_i5_2

value: scTAPS


title: WT biol rep 2


title: human_CD8_T_cell;N701_i7_1_N503_i5_3


title: human_CD8_T_cell;N701_i7_1_N503_i5_1


title: IMQ-D5, scRNAseq

city: Xiamen

first: Lingjuan

last: Zhang

address: Xiangan South Street

institute: Xiamen University

description: 10x Genomics

data_processing:
The raw sequencing data was demultiplexed and aligned to the reference genome mm10-1.2.0 using Cell Ranger v3.0.2 pipiline(10x Genomics).
The generated raw gene expression matrix was converted into Seurat objects using the R package Seurat v2.0.
To remove doublets and poor-quality cells, we utilized the following procedures to control for cell quality: >200 genes/cell, <5000 genes/cell; >25,000 unique molecular identifiers(UMIs)； and <8% mitochondrial gene expression.
Low quality cells and outliers were discarded, and only ～18,086 viable cells were used for downstream analysis. These included ~10,069 cells – Ctrl; ~8,017 cells – IMQ-D5
Unsupervised clustering and gene expression were visualized with the Seurat 2.0 on R studio, and assignment of cell clusters was based on expression of validated marker genes.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: skin

extract_protocol:
Skin biopsies were minced and digested with collagenase D and DNase1 to isolate single skin cells as previously described (Zhang et al., 2019; Zhang et al., 2021).
Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v 2. cDNA libraries were sequenced on an Illumina Novaseq6000 platform (Illumina).

value: skin

tag: age

value: 2 months old

value: Wild type


title: WT biol rep 3


title: WT biol rep 1


title: Ctrl, scRNAseq

description: 10x Genomics


title: human_CD8_T_cell;N701_i7_1_N503_i5_6


title: adipose, LDLR-/- ApoB100/100, 3 month high-fat diet, rep2

description:
adipose_CELDKO_HFD3m_Input_rep2
merged_gene_counts.txt


title: Mouse sample 34 (WT-ME-V-LCG6365)

city: Pok Fu Lam

first: Peikai

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

description:
WT mouse treat by vehicle from day 25
mouse.n35.COUNTS.txt.gz
mouse.n35.FPKM.txt.gz

data_processing:
The human fastq read-pairs were aligned to human reference genome using the HISAT2 aligner
The mouse fastq read-pairs were aligned to mouse reference genome (mm10) using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The human BAM files were quantified to human gene model by GENCODE (v25) using Cufflinks and HTSeq-count
The mouse BAM files were quantified to mouse gene model by GENCODE (vM11) using Cufflinks and HTSeq-count
Assembly: GRCh38 and mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample for all genes
Supplementary files format and content: tab-delimited text files include raw count values for each Sample for all genes

source_name: Medulla

growth_protocol:
In the human samples, human ES cells were differentiated by Neuron Differentiation Kit (Catalog #08500) and the induced NPCs were cultured using Neurobasal medium.
In the mouse samples, mouse neural precursor cells (mNPCs) were isolated from the various brain tissues of E12.5 mice, and the cells were cultured in DMEM/F12 culture media supplemented with 2% B27, 100 units/mL penicilin, 100ug/mL streptomycin, 20ng/mL epidermal growth factor and 10 ng/mL fibroblast growth factor.

extract_protocol:
RNA extraction from dissociated cells was done by using Ambiion RNA extraction kit (CAT#AM-1560). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ndufs4 wildtype (WT) and knockout (KO) mice were grouped into four groups: WT + V (vehicle), WT + P (pioglitazone), KO + V and KO + P. All mice were treated with equivalent volume (15μl/g) of vehicle or pioglitazone via daily intraperitoneal injection (I.P.) since day 25.

value: Medulla

tag: sequencing batch

value: batch 3

tag: sequencing date

tag: num reads

value: primary brain cells

value: Wild-type

value: vehicle


title: human_CD8_T_cell;N701_i7_12_N503_i5_8

extract_protocol:
E14 mouse embryonic stem cells (mES cells) were cultured on gelatin-coated plates in DMEM supplemented with 15% FBS, 2 mM L-glutamine, 1% non-essential amino acids, 1% penicillin/streptavidin, 0.1 mM β-mercaptoethanol, 1,000 units/ml LIF (leukaemia inhibitory factor), 1 μM PD0325901, and 3 μM CHIR99021. The cells were maintained at 37°C and 5% CO2. Before cell sorting, the cells were harvested by centrifugation and passed through a 40 μm cell strainer (Falcon) to achieve single cell suspension.
Optimized TAPS and CAPS+ reactions: For scTAPS, 96 cells were pooled for DNA purification and subjected to mTET1 oxidation as previously described11. A reaction mixture of 50 μl was prepared, comprising 50 mM HEPES buffer (pH 8.0), 100 μM ammonium iron (II) sulfate, 1 mM α-ketoglutarate, 2 mM L-ascorbic acid, 2.5 mM DTT, 1.2 mM ATP, 100 mM NaCl, and 4 μM mTet1CD. The reaction was conducted at 37°C for 80 minutes. Subsequently, 2.0 U of Proteinase K (New England Biolabs) was introduced to the reaction mixture and incubated at 50°C for 1 hour to stop the oxidation process. The oxidized DNA was purified using 1.8x AMPure XP beads, following the provided guidelines. To ensure complete oxidation, a second round of oxidation was performed. The double-oxidized DNA was purified and then underwent borane reduction under optimized conditions and purification using a Zymo column with Oligo Binding Buffer. For scCAPS+, 96 cells were pooled for DNA purification and subjected to a series of chemical reactions to convert 5hmC into 5fC and then to 5caC as previously described with some modifications12. DNA were incubated with 4-acetamido-2,2,6,6- tetramethylpiperidine-1-oxoammonium tetra-fluoroborate (ACT+ BF4-) in a 25 μl solution comprising sodium phosphate buffer at 25°C for 16 hours. The resultant oxidized DNA was purified using 1.8× AMPure XP Beads. then Pinnick oxidation is conducted in a 30 μl reaction mixture containing sodium acetate buffer, NaClO2, and 2- methyl-2-butene at 25°C for 16 hours. The purified product then underwent borane reduction under optimized conditions and purification using a Zymo column with Oligo Binding Buffer.  scTAPS and scCAP+ library construction and sequencing: Individual cells were isolated into a 96-well plate through FACS, each well containing 4 μL of lysis buffer consisting of 16.67mM TAPS-NaOH buffer (pH 8.5, Alfa Aesar, Cat: J63268), 8.33mM MgCl2(Invitrogen), 0.67x NEB buffer 4 (NEB, B7004S), 0.13%  Triton X-100 (sigma, X100-500ML), and 1 μg Qiagen protease. Following centrifugation at 2,000 rpm for 5 minutes, the plates were either preserved at -80°C or progressed to subsequent procedures. Single cell was lysate by incubating at 50°C for 3 h, followed by incubation at 75°C for 30 min, 80°C for 15 min, and a 4°C hold. Tagmentation was performed at 50°C for 15 minutes in a reaction mix consisting of 1x TAPS buffer (10mM TAPS-NaOH, 5mM MgCl2), 6% PEG (polyethylene glycol) 3,350, 1ul 1x preassembled Tn5, and H2O to a total volume of 10 μ. Tn5 was stripped off by adding 1.11 μL of 1.0% SDS (Sodium Dodecyl Sulfate), followed by incubating at room temperature for 5 minutes. Neutralization was performed by adding 1.24 μL of 5.0% NP40 or Triton X-100, followed by incubating at room temperature for 5 minutes. Subsequently, 12.35 μL of 2x Phusion High-Fidelity PCR Master Mix with HF Buffer (Thermo Scientific, F531L) was added, followed by incubating at 72°C for 5 minutes, and a 4°C hold. The 96 reactions were combined into a 50-mL BD tube and supplemented with 2-kb filler DNA (200 ng) and 0.1% spike in DNAs. Following purification, the TAPS or CAPS+ reaction, was employed as mentioned, and the final sequencing library was amplified utilizing the KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit along with index primers from the Nextera XT Index Kit (Illumina, FC-131- 1001). The amplification protocol involved an initial step at 98°C for 45 seconds, followed by 13 cycles (98°C for 10 seconds, 60°C for 15 seconds, and 72°C for 1 minute), then incubation at 72°C for 3 minutes, 4°C hold. The library was subjected to purification and size selected to 500-700bp by 0.5x-0.25x Ampure XP beads. Custom  sequencing primers are used for custom Nova Sequencing (Read 1 Sequencing Primer: GCGATCGAGGACGGCAGATGTGTATAAGAGACAG; Read 2 Sequencing Primer: CACCGTCTCCGCCTCAGATGTGTATAAGAGACAG; Index 1 Sequencing Primer: CTGTCTCTTATACACATCTGAGGCGGAGACGGTG; Index 2 sequencing primer: CTGTCTCTTATACACATCTGCCGTCCTCGATCGC).


title: adipose, LDLR-/- ApoB100/100, 3 month high-fat diet, trap, rep6

description:
adipose_CELDKO_HFD3m_IP_rep6
merged_gene_counts.txt

tag: diet

tag: Sex


title: SPF mouse ileum, fresh frozen, Sample 2

first: Jeffrey

last: Moffitt

address: 200 Longwood Ave

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital

description: Library name: FF_S2_

data_processing:
To analyze these data, we used tophat (v2.1.1) and cufflinks (v2.2.1) with default parameters, aligning to the mouse genome (GRCm39)
tophat v2.1.1
cufflinks v2.2.1
Assembly: GRCm39
Supplementary files format and content: Tab delimited file containing the gene name, isoform, and FPKM for each transcript

source_name: ileum

growth_protocol: C57BL/6NTac mice were purchased from Taconic Biosciences in SPF condition. The SPF mice were kept at Harvard Medical School’s Warren Alpert Animal Facility. Adult male mice aged between 8-12 weeks were used. All animals were on a 12-hour-light/12-hour-dark cycle with ad libitum access to food and water. All animal experimentation was performed in compliance with NIH guidelines and was approved by the Harvard Medical School Institutional Animal Care and Use Committee (IACUC) protocols.

extract_protocol:
The tissue was then dissolved in TRIzol™ (Thermo 15596026) and RNA extraction was performed by the Direct-zol RNA Miniprep Plus kit (Zymo R2071)
Library preparation and sequencing was performed by the Harvard Medical School Biopolymers Core using the Ribo-Erase kit for rRNA depletion, the KAPA HyperPrep kit for library preparation, and 150-bp paired-end sequencing on an Illumina NextSeq 500.

treatment_protocol: Distal colon tissue was harvested from C57BL/6NTac mice, flushed and rinsed with 4 mM ribonucleoside vanadyl complex (RVC; New England Biolabs S1402S) in 1 x phosphate-buffered saline (PBS; ThermoFisher Scientific AM9625) at 4 C.

value: ileum

tag: strain

value: WT

value: SPF, fresh frozen

tag: batch


title: human_CD8_T_cell;N701_i7_12_N503_i5_7


title: SPF mouse ileum, fresh frozen, Sample 1

description: Library name: FF_S1_


title: Mouse sample 33 (WT-ME-V-9-18-LCG6369)


title: adipose, LDLR-/- ApoB100/100, 1 month high-fat diet, rep6

description:
adipose_CELDKO_HFD1m_Input_rep6
merged_gene_counts.txt

value: 1 month high-fat diet

value: female


title: Mouse sample 32 (WT-ME-P-LCG6366)

description:
WT mouse treat by pioglitazone from day 25
mouse.n35.COUNTS.txt.gz
mouse.n35.FPKM.txt.gz

value: pioglitazone


title: human_CD8_T_cell;N701_i7_12_N503_i5_5


title: human_CD8_T_cell;N701_i7_12_N503_i5_6


title: adipose, LDLR-/- ApoB100/100, 1 month high-fat diet, rep5

description:
adipose_CELDKO_HFD1m_Input_rep5
merged_gene_counts.txt

value: adipose

value: male


title: SPF mouse ileum, processed with 4 mM RVC, Sample 2

description: Library name: 4mm_RVC_S2_

value: SPF, 4 mM RVC


title: Mouse sample 31 (WT-ME-P-9-18-LCG6370)


title: SPF mouse ileum, processed with 4 mM RVC, Sample 1

description: Library name: 4mm_RVC_S1_


title: adipose, LDLR-/- ApoB100/100, 3 month high-fat diet, rep4

description:
adipose_CELDKO_HFD3m_Input_rep4
merged_gene_counts.txt

value: 3 months high-fat diet


title: adipose, LDLR-/- ApoB100/100, 1 month high-fat diet, rep4

description:
adipose_CELDKO_HFD1m_Input_rep4
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_12_N503_i5_4

value: CD8+ T cell

value: scTAPS


title: Mouse sample 30 (S16-31-LCG6375)

description:
Ndufs4 knock out mouse treat by vehicle from day 25
mouse.n35.COUNTS.txt.gz
mouse.n35.FPKM.txt.gz

value: Medulla


title: adipose, LDLR-/- ApoB100/100, 3 month high-fat diet, rep3

description:
adipose_CELDKO_HFD3m_Input_rep3
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_12_N503_i5_3


title: 2 KO

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Cerebral cortex

extract_protocol:
Total RNA was harvested by Trizol reagent.2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

value: Cerebral cortex


title: adipose, LDLR-/- ApoB100/100, 1 month high-fat diet, rep3

description:
adipose_CELDKO_HFD1m_Input_rep3
merged_gene_counts.txt

source_name: adipose


title: human_CD8_T_cell;N701_i7_12_N503_i5_2


title: 1 KO


title: adipose, LDLR-/- ApoB100/100, 3 month high-fat diet, rep1

description:
adipose_CELDKO_HFD3m_Input_rep1
merged_gene_counts.txt


title: Mouse sample 28 (KO-V-LCG6363)

value: batch 3

value: primary brain cells


title: adipose, LDLR-/- ApoB100/100, 1 month high-fat diet, rep2

description:
adipose_CELDKO_HFD1m_Input_rep2
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_12_N503_i5_1


title: Mouse sample 27 (KO-P-LCG6364)

description:
Ndufs4 knock out mouse treat by pioglitazone from day 25
mouse.n35.COUNTS.txt.gz
mouse.n35.FPKM.txt.gz


title: 2 WT


title: adipose, LDLR-/- ApoB100/100, 1 month high-fat diet, rep1

description:
adipose_CELDKO_HFD1m_Input_rep1
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_11_N503_i5_8


title: adipose, LDLR-/- ApoB100/100, chow diet, rep5

description:
adipose_CELDKO_chow_Input_rep5
merged_gene_counts.txt

value: chow


title: human_CD8_T_cell;N701_i7_11_N503_i5_7


title: Mouse sample 26 (KO-ME-V-LCG6367)

value: vehicle


title: 1 WT


title: liver tissue, Apoa1KO ApoeKO 22wks NLD sample 4

city: Milano

first: Stefano

last: Manzini

state: Lombardia

address: via Balzaretti, n. 9

department: DISFEB

country: Italy

institute: Università degli Studi di Milano

description:
73-59-3-l
73-CD_59-3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie-0.12.8, tophat-1.3.2 with parameters --no-novel-juncs, using samtools-0.1.19
Mapped reads were processed with cuffdiff (Trapnell 2012, https://doi.org/10.1038/nprot.2012.016), version 2.0.2, with options --upper-quartile-norm
Assembly: mm10
Supplementary files format and content: tab delimited text with normalized counts

source_name: liver

growth_protocol: double apolipoprotein E and apolipoprotein A-I knockout mice (DKO), or double apolipoprotein E and apolipoprotein A-I knockout mice expressing the human APOA1 gene (DKO/hA1) were fed with either standard laboratory (chow) or high-fat (Western) diet for 22 weeks.

extract_protocol:
Total RNA was isolated from mouse tissues using the NucleoSpin RNA extraction kit according to the manufacturer’s instructions, with on-column DNA digestion. The quality of the mRNA was tested using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) before RNA- seq; samples with RNA integrity number <7.0 were discarded.
RNA samples were processed using the RNA-Seq Sample Prep kit from Illumina (Illumina, Inc, CA). Eight to 9 tagged libraries were loaded on one lane of an Illumina flowcell, and clusters were created using the Illumina Cluster Station (Illumina, Inc, CA).

treatment_protocol: Standard laboratory diet (chow) or high-fat (Western) diet

value: liver

value: Apoa1-/- Apoe-/-

value: Normal laboratory diet, 22 weeks


title: Mouse sample 25 (KO-ME-P-LCG6368)


title: adipose, LDLR-/- ApoB100/100, chow diet, rep4

description:
adipose_CELDKO_chow_Input_rep4
merged_gene_counts.txt


title: liver tissue, Apoa1KO ApoeKO 22wks NLD sample 3

description:
73-57-3-l
73-CD_57-3


title: human_CD8_T_cell;N701_i7_11_N503_i5_6

first: Jingfei

address: Roosevelt Drive

institute: University of Oxford


title: liver tissue, Apoa1KO ApoeKO human APOA1 22wks NLD sample 2

description:
73-57-2-l
73+CD_57-2

value: Apoa1-/- Apoe-/- human APOA1 transgenic


title: Mouse sample 24 (CORWT-P1)

source_name: Cortex

value: Cortex

value: batch 2

value: Wild-type

value: pioglitazone


title: adipose, LDLR-/- ApoB100/100, chow diet, rep3

description:
adipose_CELDKO_chow_Input_rep3
merged_gene_counts.txt

value: adipose

value: female


title: human_CD8_T_cell;N701_i7_11_N503_i5_5

value: CD8+ T cell

value: scTAPS


title: liver tissue, Apoa1KO ApoeKO human APOA1 22wks NLD sample 1

description:
73-57-1-l
73+CD_57-1


title: Mouse sample 22 (HIPWT-V2)

description:
WT mouse treat by vehicle from day 25
mouse.n35.COUNTS.txt.gz
mouse.n35.FPKM.txt.gz

source_name: Hippocampus

value: Hippocampus


title: human_CD8_T_cell;N701_i7_11_N503_i5_4


title: adipose, LDLR-/- ApoB100/100, chow diet, rep2

description:
adipose_CELDKO_chow_Input_rep2
merged_gene_counts.txt

value: male


title: human_CD8_T_cell;N701_i7_11_N503_i5_3


title: adipose, LDLR-/- ApoB100/100, chow diet, rep1

description:
adipose_CELDKO_chow_Input_rep1
merged_gene_counts.txt


title: Mouse sample 21 (MEKO-V)

value: Medulla

value: primary brain cells


title: human_CD8_T_cell;N701_i7_11_N503_i5_2


title: Mouse sample 20 (CORWT-V2)

value: vehicle


title: liver tissue, Apoa1KO ApoeKO human APOA1 22wks WD sample 3

description:
73-49-4-l
73+WD_49-4

value: liver

value: Western diet, 22 weeks


title: adipose, LDLR+/+ ApoB+/+, chow diet, rep6

description:
adipose_CEL_chow_Input_rep6
merged_gene_counts.txt

value: LDLR+/+ ApoB+/+

value: chow


title: human_CD8_T_cell;N701_i7_11_N503_i5_1


title: adipose, LDLR+/+ ApoB+/+, chow diet, rep5

description:
adipose_CEL_chow_Input_rep5
merged_gene_counts.txt


title: liver tissue, Apoa1KO ApoeKO 22wks WD sample 3

description:
73-47-9-l
73-WD_47-9

value: Apoa1-/- Apoe-/-


title: Mouse sample 19 (CORKO-P2)

value: Cortex

value: batch 2


title: Mouse sample 18 (HIPKO-V1)


title: human_CD8_T_cell;N701_i7_10_N503_i5_8


title: adipose, LDLR+/+ ApoB+/+, chow diet, rep4

description:
adipose_CEL_chow_Input_rep4
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_10_N503_i5_7


title: liver tissue, Apoa1KO ApoeKO human APOA1 22wks WD sample 2

description:
73-44-1-l
73+WD_44_1

value: Apoa1-/- Apoe-/- human APOA1 transgenic


title: Mouse sample 17 (MEWT-P)

description:
WT mouse treat by pioglitazone from day 25
mouse.n35.COUNTS.txt.gz
mouse.n35.FPKM.txt.gz

value: Wild-type

value: pioglitazone


title: adipose, LDLR+/+ ApoB+/+, chow diet, rep3

description:
adipose_CEL_chow_Input_rep3
merged_gene_counts.txt

value: adipose

value: female


title: liver tissue, Apoa1KO ApoeKO 22wks WD sample 2

description:
73-43-7-l
73-WD_43-7


title: adipose, LDLR-/- ApoB100/100, chow diet, rep6

description:
adipose_CELDKO_chow_Input_rep6
merged_gene_counts.txt


title: human_CD8_T_cell;N701_i7_10_N503_i5_6

value: CD8+ T cell

value: scTAPS


title: Mouse sample 23 (HIPWT-P1)

value: Hippocampus


title: Mouse sample 16 (CORKO-P1)

value: primary brain cells


title: liver tissue, Apoa1KO ApoeKO 22wks NLD sample 2

description:
73-56-2-l
73-CD_56_2

value: Normal laboratory diet, 22 weeks


title: liver tissue, Apoa1KO ApoeKO human APOA1 22wks WD sample 1

description:
73-41-4-l
73+WD-41_4

value: liver


title: human_CD8_T_cell;N701_i7_10_N503_i5_5


title: liver tissue, Apoa1KO ApoeKO 22wks NLD sample 1

description:
73-54-8-l
73-CD_54-8


title: adipose, LDLR+/+ ApoB+/+, chow diet, rep1

description:
adipose_CEL_chow_Input_rep1
merged_gene_counts.txt

value: male


title: liver tissue, Apoa1KO ApoeKO 22wks WD sample 1

description:
73-41-3-l
73-WD_41-3

value: Western diet, 22 weeks


title: C101

city: Toronto

first: Rachel

middle: D

last: Edgar

state: ON

address: 101 College Street

department: Ajmera Transplant Centre

country: Canada

institute: University Health Network

description: Probe set in Supp

hyb_protocol: Xenium In Situ Protocol

scan_protocol: Xenium In Situ Analyzer

data_processing: Processed slides were scanned by Xenium Analyzer and data were processed with the standard 10x Xenium workflow according to manufacturer’s protocol to generate cell ids and transcript locations.

label: Xenium Human Probe Set

source_name: Liver – Caudate

label_protocol: Human Xenium Multi-Tissue plus 100 liver specific custom markers (Xenium_panel_Human_Multi_Tissue_plus_Liver.csv)

extract_protocol: From 5 livers, 7 FFPE liver sections (one liver sampled three times) were applied to Xenium slides following manufacturers recommended protocols (10x Genomics, Pleasanton, CA, USA)

value: M

tag: structures

value: parenchyma


title: Mouse sample 15 (HIPWT-P2)


title: Mouse sample 14 (CORKO-V2)

description:
Ndufs4 knock out mouse treat by vehicle from day 25
mouse.n35.COUNTS.txt.gz
mouse.n35.FPKM.txt.gz

value: Cortex

value: vehicle


title: human_CD8_T_cell;N701_i7_10_N503_i5_4

last: Cheng


title: human_CD8_T_cell;N701_i7_10_N503_i5_3


title: C95

description: Probe set in Supp

value: F


title: Mouse sample 13 (MEKO-P)

value: Medulla

value: batch 2


title: DEOAA-H1N1-3

city: guangzhou

first: XING

last: HE

state: ( 86 ) CHINA

address: 中山大学南校区生命科学学院A334

institute: 生命科学学院

description: Library name: Sample 12

data_processing:
Adapter sequences were automatically detected and trimmed using TrimGalore v0.6.10 with default parameters.
Clean reads were aligned to the human reference genome (GRCh38) using STAR v2.7.11b in two-pass mode.
Resulting BAM files were sorted using Samtools v1.20.
Gene-level read counts were obtained using the featureCounts function from the Subread package v2.0.6.
Transcripts per million (TPM) values were calculated based on read counts and gene lengths.
Assembly: GRCh38
Supplementary files format and content: Csv file containing Transcripts per million (TPM) values.

source_name: PBMC

growth_protocol: PBMC cells were cultured in 1640 with 1% sodium pyruvate and 10% (vol/vol) fetal bovine serum.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent, and sequencing was conducted by Sangon Biotech. Bioanalyzer (Agilent 2100 Bioanalyzer) was used to assess the quality of samples.
Total RNA was isolated from cells using TRIzol reagent (Invitrogen), and sequencing was performed by Sangon Biotech. Sample quality was assessed using a Bioanalyzer (Agilent 2100 Bioanalyzer). RNA-seq libraries of polyadenylated RNA were prepared using mRNA-seq V2 Library Prep Kit and sequenced on MGISEQ-2000 platform.

treatment_protocol: PBMCs infected with H1N1 in the absence or presence of diethyl-ester OAA.

value: PBMC


title: DEOAA-H1N1-2

address: 中山大学南校区生命科学学院A334

description: Library name: Sample 11


title: human_CD8_T_cell;N701_i7_10_N503_i5_2

city: Oxford


title: DEOAA-H1N1-1

address: 中山大学南校区生命科学学院A334

description: Library name: Sample 10


title: human_CD8_T_cell;N701_i7_10_N503_i5_1


title: Mouse sample 12 (MEWT-V)

value: Wild-type


title: C94_4

description: Probe set in Supp


title: adipose, LDLR+/+ ApoB+/+, chow diet, rep2

description:
adipose_CEL_chow_Input_rep2
merged_gene_counts.txt

value: adipose

value: LDLR+/+ ApoB+/+

value: chow


title: C94_3

description: Probe set in Supp


title: DEOAA-3

address: 中山大学南校区生命科学学院A334

description: Library name: Sample 9

value: DEOAA


title: C94_2

description: Probe set in Supp

value: bile duct hamartoma


title: Human sample 11 (C7-P2)

description:
lost four amino acids on ndufs4 cds
human.n11.COUNTS.txt.gz
human.n11.FPKM.txt.gz

value: ES1 induced NPC

value: no treatment


title: Mouse sample 11 (HIPWT-V1)

value: Hippocampus

value: primary brain cells


title: Mouse sample 10 (CORWT-V1)


title: Human sample 10 (C3-P5)

description:
frame shift mutation
human.n11.COUNTS.txt.gz
human.n11.FPKM.txt.gz


title: DEOAA-2

address: 中山大学南校区生命科学学院A334

description: Library name: Sample 8


title: Mouse sample 9 (HIPKO-P1)

description:
Ndufs4 knock out mouse treat by pioglitazone from day 25
mouse.n35.COUNTS.txt.gz
mouse.n35.FPKM.txt.gz

value: pioglitazone


title: C85

description: Probe set in Supp

value: M

value: parenchyma


title: DEOAA-1

address: 中山大学南校区生命科学学院A334

description: Library name: Sample 7


title: C105

description: Probe set in Supp

source_name: Liver – Right Lobe

value: F


title: Vehicle-H1N1-3

address: 中山大学南校区生命科学学院A334

description: Library name: Sample 6


title: Human sample 8 (C1-1-P5)

description:
Wild-type ES cells induce NPC, passage 5
human.n11.COUNTS.txt.gz
human.n11.FPKM.txt.gz


title: Mouse sample 8 (HIPKO-V2)

value: vehicle


title: Vehicle-H1N1-2

address: 中山大学南校区生命科学学院A334

description: Library name: Sample 5


title: Mouse sample 7 (HIPKO-P2)

value: batch 2


title: Human sample 9 (C7-P5)


title: Human sample 7 (C1-1-P2)

description:
Wild-type ES cells induce NPC, passage 2
human.n11.COUNTS.txt.gz
human.n11.FPKM.txt.gz