title: D1-D59

city: Lausanne

first: Andrei Alexandru

last: Mircea

state: Vaud

address: Place du Vallon 18

department: Cardiology Department

country: Switzerland

institute: Centre Hospitalier Universitaire Vaudois

description: Library name: D1-D59

data_processing: For each sample, we used the NIH Biowulf Cluster to conduct library analysis and processing. FastQC (Version 0.11.7) determined the quality control of raw sequencing reads. Libraries with low Phred scores or disproportionate GC plots were removed from further analysis. Samples for the comprehensive study were run on multiple lanes, so before further quantification, the lanes were merged into their corresponding read one and read two bins. After quality analysis, Trimmomatic was used to remove Illumina adapters ligated onto the RNA libraries during library prep.

source_name: adipose and muscle for each sample

extract_protocol: Adipose and cardiac tissue biopsies were dissected from the left ventricular basal anterior region, preserved, and snap-frozen at -20°C. Total RNA was extracted from the frozen samples using QIAzol Lysis Reagent and purified with the Qiagen RNeasy Plus Mini Kit (Qiagen, Santa Clara, California, USA). After extraction, tissue samples were stored at -80◦C. RNA was extracted from each sample and quantified using a fluorometric method (BioAnalyzer TapeStation). All samples had an RNA Integrity Number (RIN) of 9 or higher.Ribo-depleted RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina, San Diego, California, USA). Paired 150 bp reads were sequenced on an Illumina NovaSeq 6000 at the Children’s Hospital Genomics Core, with an average of approximately 200 million paired end reads generated per sample.

value: myocyte/adipocyte


title: HRG1-KO sodium butyrate 3

status: Public on Jun 03 2026

type: SRA

city: Baltimore

first: Iqbal

last: Hamza

state: MD

address: 670 W Baltimore St

department: Pediatrics

country: USA

institute: University of Maryland Baltimore

description: Library name: A12

library_source: transcriptomic

data_processing:
A total of 12 samples were sequenced using Illumina's Novaseq platform (Novogene), with triplicate of each genotype
Paired-end 150 base reads were sequenced and checked by FastQC, version 0.12.1
The reads were aligned to the human reference genome hg38 (UCSC) using STAR alignment (v2.7.11b)
Assembly: hg38
Supplementary files format and content: csv

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow

growth_protocol: K562 WT and HRG1-KO cells were grown on T75 flasks with RPMI supplemented with 10% HI-FBS, 1% Penicilline-Streptamycine-Glutamine, and 1% non-essential amino-acids

extract_protocol:
Cells were collected 6h after the second treatment and washed three times with 1X DPBS. Total RNA was extracted using TRIzol lysis reagent (Invitrogen, #15596018).
Library prepared by Novogene

treatment_protocol: Cells were not treated (control) or treated with 0.75 mM sodium butyrate 24h after being plated, and treated a second time 48h after the first treatment.

tag: tissue

value: bone marrow

tag: cell line

tag: cell type

value: erythroleukemia

tag: genotype

tag: treatment

value: sodium butyrate


title: HRG1-KO sodium butyrate 2

description: Library name: A08


title: NSP1-C3, NSP1 mutant SARS-CoV-2 infected

city: New York

first: Elena

last: Zaslavsky

state: NY

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic single cell

data_processing:
Cell Ranger v7.0.0 pipeline was run on the samples following 10x Genomics guidelines. Seurat v4 was used to perform data processing and analysis.
Assembly: mm10
Supplementary files format and content: Count matrices for cell barcodes in Hierarchical Data Format HDF5.

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
In brief, the freshly collected whole lungs were dissected into single lobes to isolate single cells using a mouse lung dissociation kit (Miltenyi Biotec) and a gentleMACS™ Dissociator (Miltenyi Biotec), and red blood cells were lysed with 1X RBC lysis buffer (eBioscience). Cell suspensions were processed for single-cell sequencing following the protocol for Chromium Next GEM Single Cell 5’ Version 2 (dual index). 10,000 cells were targeted. The transcriptome of each cell was indexed with a pool of 750,000 barcodes by partitioning each cell into Gel beads-in-emulsion (GEMs) combined with a Master Mix containing reverse transcription (RT) reagents and poly(dT) RT primers. The emulsion was generated using Next GEM chips and the Chromium Controller device (10x Genomics). The RT reaction to the generated emulsion produced 10x Barcoded full-length cDNA from poly-adenylated mRNA. This initial cDNA was PCR amplified to produce material for 5’ gene expression sequencing. After PCR amplification, bioanalyzer Quality Control (QC) was performed for all the samples using the Agilent Bioanalyzer High Sensitivity DNA assay in the 2100 expert software (Agilent). All the samples passed the initial QC with a cDNA size 700-1,500 bp.
Amplified full-length cDNA from polyadenylated mRNA was used to generate 5’ gene expression (GEX) libraries. The cDNA was enzymatically fragmented, and size selected to optimize the cDNA amplicon size. P5, P7, i5 and i7 sample indexes, and Illumina R2 sequences (read 2 primer sequences) were added via End Repair, A-tailing, Adaptor ligation and sample index PCR. A second QC was performed for each library before sequencing with an expected library size 500 – 900 bp.

value: Lung


title: m6 Padi6 mutant blastocyst

city: Napoli

first: Francesco

last: Cecere

state: Napoli

address: Via Posillipo 226

department: UOC Ricerca Clinica e Traslazionale

country: Italy

institute: AORN Santobono-Pausilipon

description: Library name: m6

data_processing:
Libraries was adapted and quality-trimmed (Phred score <20) using Trim Galore version 0.4.4. The good quality reads were aligned to the Genome Reference Consortium mouse genome build 39 (GRCm39) with HiSat2 version 2.1.0 in paired-end mode. The data were quantified and analyzed in Rstudio.
Assembly: mm39
Supplementary files format and content: Log normalized counts

source_name: Blastocist

growth_protocol: Blastocysts were cultured in a medium supplemented with 15% FBS in 0.5% gelatin-coated plates and incubated at 37°C in a humidified atmosphere with 5% CO2 for 72 h. Trophoblast outgrowth was evaluated by measuring the area occupied (mm²) using ZEN 3.9 software. To evaluate ICM expansion, blastocysts were further cultured for one week in 2i medium.

extract_protocol:
DNA and RNA were separated using the G&T protocol [59]. Magnetic beads (MyOne C1, Life Technologies) were washed and annealed to oligo dTs and then used to capture polyadenylated mRNA from individual cell lysates. The supernatant containing the DNA was transferred to a new tube, and the beads washed three times in 1× FSS buffer (SuperScript II, Invitrogen), 10 mM DTT, 0.005% Tween-20 (Sigma), and 0.4 U/μl RNasin (Promega) to remove all DNA residues. Each washing solution was added to the DNA tube to maximize recovery.
The mRNA bound to the beads was processed further for cDNA conversion. This involved the resuspension of the beads in 10 μl of reverse transcriptase master mix (100 U of SuperScript II [Invitrogen], 10 U of RNasin [Promega], 1× Superscript II first-strand buffer, 5 mM DTT [Invitrogen], 1 M betaine [Sigma], 9 mM MgCl2 [Invitrogen], 1 μM template-switching oligo [TSO; Eurogentec], 1 mM dNTP mix [Roche]). The mRNA mixture was reverse-transcribed by incubation for 60 min at 42°C followed by 30 min at 50°C and 10 min at 60°C. The cDNA obtained was subjected to PCR amplification by adding 11 μl of 2× KAPA HiFi HotStart ReadyMix and 1 μl of 2 μM ISPCR primer. The amplification was performed in a thermocycler for 3 min at 98°C, followed by 17 cycles of 15 sec at 98°C, 20 sec at 67°C, and 6 min at 72°C, and a final extension step of 5 min at 72°C. The amplified product was purified using Ampure XP beads with a 1:1 ratio and eluted into 20 μl of water. Libraries were prepared from 100–400 pg of cDNA using the Nextera XT kit (Illumina) following the manufacturer's instructions but with one-fifth volumes. All 20 single-blastocyst RNA-seq libraries were pooled together and sequenced on an Illumina NovaSeq X platform to an average depth of 4.2 million reads using paired-end 75-bp read length settings.

value: Blastocist


title: YH-4

city: Taiyuan

first: Zhibo

last: Zhao

address: Shuangtasi. 29

country: China

institute: Shanxi Provincial People's Hospital

description: Library name: YH_4

data_processing:
Raw data (or Raw reads) of fastq format were firstly processed through an in-house pipeline from Shanghai Applied Protein Technology. In this step, remove the adapter sequence and filter out low quality and N ratio is greater than 5% reads to obtain clean reads. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads. FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html), DEGs with |log2FC|>1 and Padj <0.05 were considered to be significantly different expressed genes.
Assembly: GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Kidney

growth_protocol: We cultured the human renal tubular epithelial cell (HK-2) cell line under sterile conditions at 37 °C and 5 % CO2. The culture medium contains MEM, 1 % PS, 10 % fetal bovine serum.

extract_protocol:
Total RNA was extracted from the kidney tissue using TRIzol® Reagent according the manufacturer’s instructions (Magen). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the man-ufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reac-tion Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Tran-scriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapt-er-ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, sequencing was performed with an Illumina Novaseq 6000 /MGISEQ-T7 instrument.

treatment_protocol: For oxidative stress condition, the HK-2 cells were stimulated with hydrogen peroxide (H2O2) at a concentration of 150 μM for 48 hours.

value: Kidney

value: Human kidney-2

value: Yap1 knockdown


title: m5 Padi6 mutant blastocyst

description: Library name: m5


title: M3

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. of Immunology

country: Germany

institute: University Medical Center Mainz

description: Library name: Sample 3

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v24 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files including raw counts, TPM and RPKM. Expression values in manuscript=TPM

source_name: spleen

growth_protocol: Mice were held in IVC cages and killed via CO2 and cervical dislokation.

extract_protocol:
Total RNA was isolated using RNeasy plus micro kit (Qiagen).
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Total RNA (RIN>8) was sent to Novogene (Cambridge, UK) for library preparation and sequencing (PE150) on a NovaSeq 6000 (Illumina).

treatment_protocol: Spleens were isolated and passed through a 70 µm strainer to generate single cells. The splenocytes were stained for fluorescence activated cell sorting and sorted for CD11b positivity.

value: spleen

value: CD11b+ monocytes

value: untreated


title: NSP1-C2, NSP1 mutant SARS-CoV-2 infected


title: HRG1-KO sodium butyrate 1

description: Library name: A04


title: YH-3

description: Library name: YH_3


title: NSP1-C1, NSP1 mutant SARS-CoV-2 infected


title: m4 Padi6 mutant blastocyst

description: Library name: m4


title: YH-2

description: Library name: YH_2


title: WT sodium butyrate 3

description: Library name: A10

value: WT


title: WT sodium butyrate 2

description: Library name: A06


title: YH-1

description: Library name: YH_1


title: m2 Padi6 mutant blastocyst

description: Library name: m2


title: H2O2-4

description: Library name: H2O2_4

value: ShNC


title: m3 Padi6 mutant blastocyst

description: Library name: m3


title: WT sodium butyrate 1

description: Library name: A02


title: Mock-A3, mock infected


title: C2C12, wild-type, no treatment, biol rep 3

city: Berkeley

first: Oscar

last: Whitney

address: 1951 Oxford St

institute: UC Berkeley

description: Library name: c2wt_flag_cntrl_R3.bigWig

library_source: genomic

data_processing:
Nf-core cutandrun pipeline version 3.2.2
Assembly: mm10
Supplementary files format and content: bigWig and narrowPeak files generated by deepTools and seacr
Library strategy: CUT&Run

molecule: genomic DNA

source_name: skeletal muscle

growth_protocol: C2C12 skeletal muscle myoblasts were maintained in DMEM supplemented with 20% fetal bovine serum, penicillin streptomycin in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Fragments were purified using phenol-chloroform DNA extraction
Library preparation was performed using NEBNext Ultra II DNA library Prep kit for Illumina, following manufacturer protocols.

value: skeletal muscle

value: skeletal muscle myoblast

value: Wild-type

value: no treatment


title: HRG1-KO control 3

description: Library name: A11

value: bone marrow

value: control


title: Mock-A4, mock infected


title: H2O2-3

description: Library name: H2O2_3


title: Mock-A1, mock infected


title: Mock-A2, mock infected


title: C2C12, wild-type, no treatment, biol rep 2

description: Library name: c2wt_flag_cntrl_R2.bigWig


title: H2O2-2

description: Library name: H2O2_2


title: HRG1-KO control 2

description: Library name: A07

value: erythroleukemia


title: Aorta, baseline, KO3

city: Augusta

first: Kunzhe

last: Dong

state: GA

address: 1462 Laney Walker Blvd

department: Immunology Center of Georgia

institute: Augusta University

description: KO3, male

data_processing:
Assembly: Ensembl release 101
Sequencing Platform: Illumina NovaSeq6000
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software.
RNA-seq reads were aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes row count values for each Sample

source_name: Aorta

extract_protocol:
Total RNA from the aortic tissues was extracted using TRIzol reagent (Invitrogen).
RNA libraries for RNA-seq were prepared using RiboErase Library Preparation Kit following manufacturer’s protocols.

value: Aorta

tag: Sex

value: male

value: Prdm16 SMC-specific KO

value: Baseline


title: C2C12, wild-type, no treatment, biol rep 1

description: Library name: c2wt_flag_cntrl_R1.bigWig


title: HRG1-KO control 1

description: Library name: A03


title: H2O2-1

description: Library name: H2O2_1

value: Kidney

value: Human kidney-2


title: ShNC-4

description: Library name: ShNC_4

value: Control


title: Aorta, baseline, KO2

description: KO2, male


title: C2C12 cells, endogenously tagged and inducible MyoD1, dox treatment, biol rep 3

description: Library name: b9d1x_dox_flag_R3.bigWig

value: Endogenously 3xF-HaloTagged MyoD1 and additional dox-inducible 3xF-Halo-MyoD1

value: 6 h dox treatment


title: Aorta, baseline, KO1

description: KO1, male


title: WT control 3

description: Library name: A09

value: WT


title: ShNC-3

description: Library name: ShNC_3

value: ShNC


title: C2C12 cells, endogenously tagged and inducible MyoD1, dox treatment, biol rep 2

description: Library name: b9d1x_dox_flag_R2.bigWig

value: skeletal muscle

value: skeletal muscle myoblast


title: WT control 2

description: Library name: A05


title: Aorta, baseline, Ctrl3

description: Ctrl3, male


title: WT control 1

description: Library name: A01


title: Aorta, baseline, Ctrl2

description: Ctrl2, male


title: ShNC-2

description: Library name: ShNC_2


title: C2C12 cells, endogenously tagged and inducible MyoD1, no treatment, biol rep 3

description: Library name: b9d1x_cntrl_flag_R3.bigWig

value: no treatment


title: C2C12 cells, endogenously tagged and inducible MyoD1, dox treatment, biol rep 1

description: Library name: b9d1x_dox_flag_R1.bigWig


title: ShNC-1

description: Library name: ShNC_1


title: Aorta, baseline, Ctrl1

description: Ctrl1, male


title: F9545_Human ABC/PB dataset_BCR

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA92815_vx0151

data_processing:
Sequencing was performed on NovaSeq 6000 or NovaSeq X Plus platform in 28+90, 101+101 or 151+151 base paired-end mode.
Illumina Real Time Analysis RTA3 v3.4.4 or RTA4 v4 software was used for base calling.
Generated reads were input into the cellranger pipeline (cellranger-7.1.0 or 9.0.1, 10x Genomics) for UMI counting for each gene (or tag sequence)-cell (barcode) combination and B cell receptor repertoire profiling.
Assembly: mm10, GRCh38 or GRCm39
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format files including filtered counts data for each gene (or tag sequence) and cell (barcode) combination
Supplementary files format and content: raw_feature_bc_matrix.h5: HDF5 format files including raw counts data for each gene (or tag sequence) and cell (barcode) combination
Supplementary files format and content: airr_rearrangement.tsv : tab-delimited text file including detected clonotypes for each cell (barcode)
Supplementary files format and content: clonotypes.csv : comma-delimited text file including the BCR clonotype information
Library strategy: CITE-seq

source_name: Peripheral blood

extract_protocol:
Sinlge cell droplets were generated by 10x Genomics Chromium Controller. Hashtag oligonucleotides (HTO) or cDNAs with UMIs and a cell barcode were generated at single-cell level in each droplet.
The single cell libraries were prepared following the protocol outlined in the Chromium Next GEM Single Cell 5' Reagent Kits v2 or v3 with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping User Guide.

value: Peripheral blood

tag: library type

value: BCR


title: C2C12 cells, endogenously tagged and inducible MyoD1, no treatment, biol rep 2

description: Library name: b9d1x_cntrl_flag_R2.bigWig


title: HSD, 10days, replicate C

city: MARSEILLE

first: Nathalie

last: Arquier

address: 163 avenue de Luminy

department: Inserm, Aix-Marseille Université

country: France

institute: TAGC U1090

description: column HSD_C in processed data file

data_processing:
Quality scoring was performed with FastQC v0.11.7; Trimming with Sickle v1.33
Assignment of reads to gene features with Subread featureCounts v1.6.1
Alignment with Subread aligner v1.6.1
Differential expression of the reads  was implemented in both DEseq2 v1.20.0 and edgeR v3.22.5 Bioconductor packages in R v3.5.1
Assembly: FlyBase Drosophila melanogaster release 3 (dm3) and reannotation was performed with dm6 for submission
Supplementary files format and content: tab-delimited text file include RPKM values for each sample

organism: Drosophila melanogaster

source_name: heart

growth_protocol: w1118 flies were reared on our ND diet. Crosses of 20 females and 5 males were kept at 25°. Newly emerged females were mated for 2 days. Males were then removed and females were placed in ND, HSD for 10 days. Part of the flies were placed in ND for 7 days then in HFD for the last 3 days. Flies were kept at 23° in an 12 hour-light/dark cycle incubator, 50% humidity. All flies were transferred in fresh tubes every 2 days until dissection.

extract_protocol:
Flies were anesthetized using FlyNap® . 15 hearts per replicate were dissected and put in 300ul TRIzol®  reagent. 30ul of RNAse-free water and 0.2ul of GenElute™ LPA (25ug/ul stock; Sigma Aldrich) were added and samples vortexed. 60ul of Chloroform was added and the volume transferred in Phase Lock Gel™  Heavy (VWR™) after vortexing. Total RNAs, contained in the aqueous phase obtained by centrifugation, were precipitated overnight at -20° in 0.8v/v 2-Propanol. After centrifugation at 4° for  30 minutes, the pellet was carefully washed in 75% EtOH, air dried and dissolved in 8.5ul RNAse-free water. Every sample was quantified using a NanoDrop™. 3 replicates for each diet were prepared for sequencing.
Librairies were prepared according to the specifications of the Illumina® Stranded total RNA prep Ligation with Ribo-Zero Plus" kit .  Librairies quantity and quality were evaluated using the Agilent DNF-474 HS NGS Fragment kit according to the manufacturer's indications.

treatment_protocol: Normal Diet (ND) is composed of 1% w/v agar, 7% w/v dry inactivated yeast, 7% w/v cornmeal and 6% v/v Methyl 4-Hydroxybenzoate (10% w/v in 70% EtOH). High Sugar Diet (HSD) corresponds to ND supplemented with 30% sucrose w/v; High Fat Diet (HFD) is supplemented with 30% coconut oil.

value: heart

tag: gender

value: female

tag: age

value: adult

value: High-sugar diet 10 days


title: F9545_Human ABC/PB dataset_HTO

description: Library name: GA92816_vx0149

library_source: other

molecule: protein

value: HTO

tag: hto

value: TotalSeq-C0251 anti-human Hashtag 1 (ABC); TotalSeq-C0252 anti-human Hashtag 2 (PB)


title: OSC20 cells, sgRNA AMBRA1-2, cisplatin 10uM, rep2

city: Madrid

first: Ana

last: Sastre-Perona

state: Madrid

address: Calle Paseo de la Castellana 261, INGEMM, Laboratorio de Epigenética, Hospital Universitario La Paz

country: Spain

institute: idiPAZ

description:
Library name: Sample8
s54_20_a10_2

data_processing:
Mapping was done using HISAT2
StringTie was used for transcriptome assembly
Deseq was used to identify differentially expressed genes
Assembly: hg38
Supplementary files format and content: tab-delimited tex file includes raw counts for each sample

source_name: Tongue Squamous cell carcinoma

growth_protocol: OSC-20 control or know-out cells were grown in DMEM supplemented with 10% FBS and humidified atmosphenre at 5% CO2 at 37C

extract_protocol:
total RNA was extracted using Trizol and the microprep RNA extraction kit, Zymo
RNA libraries for RNA-seq were prepared using  the llumina® Stranded mRNA Prep and following the manufacture's instructions

treatment_protocol: Cisplatin treatment at 10 micromolar concentration for 24 hours

value: Tongue Squamous cell carcinoma

value: Epithelial

value: sgRNA AMBRA1-2

value: cisplatin 10 micro molar

tag: batch


title: C2C12 cells, endogenously tagged and inducible MyoD1, no treatment, biol rep 1

description: Library name: b9d1x_cntrl_flag_R1.bigWig

value: Endogenously 3xF-HaloTagged MyoD1 and additional dox-inducible 3xF-Halo-MyoD1


title: OSC20 cells, sgRNA AMBRA1-2, cisplatin 10uM, rep1

description:
Library name: Sample7
s50_20_a10_1


title: F9545_Human ABC/PB dataset_GEX

description: Library name: GA92814_vx0149

value: mRNA


title: HSD, 10days, replicate B

description: column HSD_B in processed data file


title: OSC20 cells, sgRNA AMBRA1-2, untreated, rep2

description:
Library name: Sample6
s53_20_a0_2

value: untreated


title: Retina, IL-27, B100_10

city: Miami

first: Ashley

middle: N

last: Zuniga

state: Florida

address: 1501 nw 10th avenue

department: Ophthalmology

institute: University of Miami

description: Library name: B100_10

data_processing:
Single nuclei RNA sequencing (Fastq) files were aligned to mouse transcriptomic reference, with CellRanger (version 9.0.1) to generate filtered count matrices. Filtered count matrices processed with Seurat (v5.2.1) to quality filter single nuclei requiring more than 500 unique molecular identifiers (UMIs), 200 unique features, and less than 5% mitochondrial gene counts. DoubletFinder (v2.0.4) was used to identify doublets, calculating the homotypic doublet proportion estimate with a presumed doublet rate of 8% per sample. Cells called as Doublets were removed before downstream sample integration.
Assembly: Reference-based annotation of snRNA-seq integrated object was conducted with a comprehensive mouse retina single-cell RNA sequencing atlas {Li, 2024 PMID: 38812536}.
Supplementary files format and content: Filtered feature-barcode matrix generated by Cell Ranger (10x Genomics)

molecule: nuclear RNA

source_name: Retina

growth_protocol: rd10 mice were bred in-house and maintained under specific pathogen-free conditions with a 12 h light/12 h dark cycle. Animals had free access to food and water and were monitored in accordance with institutional IACUC protocols.

extract_protocol:
Retinas were removed, flash frozen on dry ice, single nuclei were proced from frozen mouse tissue by Novogene using the Chromium Nuclei Isolation Kit (10x Genomics)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: retinas were intravitreally injected with recombinant IL-27 protein or saline and post-natal day 18.

value: Retina

tag: strain

value: post-natal day 20


title: Multiome, T255,T264_ATAC

city: Seoul

first: Yeji

last: Kim

state: Seoul

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

country: South Korea

institute: The Catholic University of Korea

description:
Library name: T255,T264_sn ATAC
Multiplexed ATAC library (T255 + T264) generated using 10x Genomics.

data_processing:
Barcode processing and gene counting were performed using the count function of the 10x Genomics CellRanger-ARC software v2.0.2 pipeline with GRCh38-2020-A reference genome.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files : filtered_feature_bc_matrix.h5, atac_fragments.tsv
Supplementary files format and content: R object file : T255_RNA.rds, T264_RNA.rds, T255_ATAC.rds, T264_ATAC.rds

molecule: other

extract_protocol:
Nuclei were extracted from frozen human lung tumor tissues using the 10x Single Cell Multiome ATAC + Gene Expression kit (10x Genomics)
Single nuclei suspenstions of T255 and T264 were mixed in equal numbers and subjected to single-nucleus multi-omics sequencing using the 10x Single Cell Multiome ATAC + Gene Expression and Gel Bead kit (10x Genomics). The cell recovery rate was set to 10000 per library, and we followed the manufacturer's instructions with a slight modification. Library was sequenced on an Illumina NovaSeq X Plus as 150 bp paired-end.

value: Lung

value: multiplexed ATAC


title: Multiome, T255,T264_GEX

description:
Library name: T255,T264_snRNA
Multiplexed GEX library (T255 + T264) generated using 10x Genomics.

value: multiplexed mRNA


title: Retina, Saline, B100_6

description: Library name: B100_6

value: Saline


title: HFD, 10days, replicate C

description: column HFD_C in processed data file

value: heart

value: female

value: adult

value: normal diet 7 days + high fat diet 3 days


title: HSD, 10days, replicate A

description: column HSD_A in processed data file

value: High-sugar diet 10 days


title: Retina, IL-27, B100_5

description: Library name: B100_5


title: OSC20 cells, sgRNA AMBRA1-2, untreated, rep1

description:
Library name: Sample5
s49_20_a0_1

value: Tongue Squamous cell carcinoma

value: Epithelial


title: 143B organoids, DX-R, rep3

city: Oviedo

first: Rene

last: Rodriguez

state: Asturias

address: Av. Hospital Universitario s/n

institute: Health Research Institute of Asturias (ISPA)

description:
Library name: O_143BR3
Column name in TPM_nofilt.csv: O143BR3

data_processing:
All sequencing data files were evaluated for quality control and adapters and poor-quality paired-end reads were removed using fastp (v.0.23.4) and these preprocessed reads were pseudoaligned to the GRCh38 human genome and quantified at the transcript-level using the mappingbased mode of the Salmon package (v.1.10.3).
Assembly: GRCh38
Supplementary files format and content: csv file include TPM values for each sample

source_name: 148B organoids

growth_protocol: 143B parental and DX-R organoids were maintained in M2 growth medium in humidified atmosphere with 5% CO2 at 37ºC. M2 growth medium is composed by Advanced Dulbecco’s modified Eagle medium/F-12 (AdDMEM, Gibco, Carlsbad, CA, USA) supplemented with 1 % (v/v) Penicillin-Streptomycin (10,000 U/mL; Gibco), 1 % (v/v) GlutaMAX (Gibco), 1 % (v/v) HEPES buffer solution (1M; Gibco), 10 mM Nicotinamide (Sigma-Aldrich), 1.25 mM N-Acetyl-LCysteine (Sigma-Aldrich), 2 % (v/v) B27 supplement (minus vitamin A, Gibco), 0.05 µg/mL EGF (PeproTech, London, UK), 0.005 µg/mL FGF-2 (PeproTech), 1 µM Forskolin (Bio-Techne), 0.1 µg/mL R-spondin-1 (PeproTech), 3 µM CHIR99021 (Sigma-Aldrich), 0.01 µg/mL FGF-10 (PeproTech), 20 ng/mL IL-6 (PeproTech) and 20 ng/mL IL-8 (PeproTech).

extract_protocol:
Total RNA samples were extracted from triplicated cultures of 143B-PAR and 143B-DXR organoid models using GeneMatrix Universal RNA Purification Kit (EURX, Gdańsk, Poland).
cDNA libraries were prepared by polyA enrichment and checked for quality and quantified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Paired-end sequencing was performed on an Illumina Novaseq X Plus Series (Illumina, San Diego, CA, USA) using 150-base reads (6 Gb per sample).

value: 148B organoids

value: osteosarcoma

value: Doxorubicin Resistant


title: OSC20 cells, sgRNA tomato, cisplatin 10um, rep2

description:
Library name: Sample4
s52_20_t10_2

value: sgRNA control

value: cisplatin 10 micro molar


title: HFD, 10days, replicate B

description: column HFD_B in processed data file


title: Retina, IL-27, B100_4

description: Library name: B100_4

value: Retina

value: post-natal day 20


title: OSC20 cells, sgRNA tomato, cisplatin 10um, rep1

description:
Library name: Sample3
s48_20_t10_1


title: 143B organoids, DX-R, rep2

description:
Library name: O_143BR2
Column name in TPM_nofilt.csv: O143BR2

source_name: 147B organoids

value: 147B organoids


title: HFD, 10days, replicate A

description: column HFD_A in processed data file


title: Retina, Saline, B100_2

description: Library name: B100_2


title: ND, 10days, replicate C

description: column ND_C in processed data file

value: normal diet 10 days


title: 143B organoids, DX-R, rep1

description:
Library name: O_143BR1
Column name in TPM_nofilt.csv: O143BR1

source_name: 146B organoids

value: 146B organoids


title: Retina, Saline, B100_1

description: Library name: B100_1

value: Saline


title: OSC20 cells, sgRNA tomato, untreated, rep2

description:
Library name: Sample2
s51_20_t0_2

value: untreated


title: OSC20 cells, sgRNA tomato, untreated, rep1

description:
Library name: Sample1
s47_20_t0_1


title: 143B organoids, Parental, rep3

description:
Library name: O_143BP3
Column name in TPM_nofilt.csv: O143BP3

source_name: 145B organoids

value: 145B organoids

value: WT


title: Immune cells, H_2

city: Wuhan

first: can

last: Lin

state: Hubei province

address: 237 Luoyu Road

department: School & Hospital of Stomatology

institute: Wuhan University

description: Library name: Sample 4

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the dnbc4tools software v2.1.3.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: MC38 formed tumor tissues

growth_protocol: MC38 cells were grown in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% (v/v) heat-inactivated FBS. Cell cultures were maintained at 37 °C with 5% CO2. 2 x 105 MC38 cells were inoculated in wild-type mice and FOXP3 humanized mice (10 weeks old). The tumor-bearing mice were sacrificed on day 20.

extract_protocol:
Tumors were subjected to single cell isolation. Tumor-infiltrating immune cells were isolated by using Percoll and gradient centrifugation.
Single cells were isolated into oil emulsion droplets with barcoded gel beads and reverse transcriptase mix using the DNBelab C-TaiM 4 (MGI), cDNA was generated within these droplets, then the droplets were dissociated. cDNA was purified. cDNA amplification was performed by PCR using reagents within the DNBelab C High-throughput single-cell RNA library preparation kit V3.0（MGI） Amplified cDNA was purified using SPRIselect magnetic beads (Beckman Coulter) according to the protocol. cDNA was fragmented, end repair and A tailing, the DNAs were ligated to dual Adaptor (DNBelab C Single Cell Library Preparation Sample Labelling Kit S). The ligated products were amplified and purified, quantified (Qubit 4.0) and stored at -80℃ before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to DNBSEQ-T7 system for 150 nt/100 nt paired-end sequencing.

treatment_protocol: No treatment.

value: MC38 formed tumor tissues

value: Immune cells

value: FOXP3 humanized

value: oligo library


title: OSC20 cells,treated cisplatin t7, rep3

description: Library name: Sample9

data_processing:
Sequencing results were analyzed using MAGeCKFlute.
Assembly: lentiCRISPR v2
Supplementary files format and content: merged_counts.txt
Library strategy: CRISPR Screen

growth_protocol: OSC-20 cells infected with the library B were grown in DMEM supplemented with 10% FBS and humidified atmosphenre at 5% CO2 at 37C

extract_protocol:
genomic DNA was extracted using phenol extraction
Libray was constructed amplifiing the sgRNA sequences with the KAPA HiFi Hotstart PCR Kit

treatment_protocol: 2M cells were plated in 10 cm dishes, and collected the day after (t0), 7 days after (t7) or after treatment with 50 micro molar concentration of cisplatin for 7 days.

value: Tongue Squamous cell carcinoma

value: Epithelial

value: treated cisplatin 50 micromolar


title: ND, 10days, replicate B

description: column ND_B in processed data file

value: heart

value: female

value: adult


title: 143B organoids, Parental, rep2

description:
Library name: O_143BP2
Column name in TPM_nofilt.csv: O143BP2

source_name: 144B organoids

value: 144B organoids

value: osteosarcoma


title: Immune cells, W_2

description: Library name: Sample 3


title: ND, 10days, replicate A

description: column ND_A in processed data file

value: normal diet 10 days


title: OSC20 cells,treated cisplatin t7, rep2

description: Library name: Sample8


title: 143B organoids, Parental, rep1

description:
Library name: O_143BP1
Column name in TPM_nofilt.csv: O143BP1

source_name: 143B organoids

value: 143B organoids


title: CTCF CUTRUN  TexIgg_rep2

city: Washington

first: Weiqun

last: Peng

state: District of Columbia

address: Suite 4000 SEH Science & Engineering Hall 800 22nd Street NW

department: Physics

institute: The George Washington University

data_processing:
The sequencing quality of Cut&Run libraries was assessed by FastQC (v0.11.8)(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Low-quality bases and adapters were removed through Trim Galore (v0.6.7)(MAPQ > 20)
Bowtie2 v2.3.4.1 was used to align the sequencing reads to the mm10 mouse genome, and only uniquely mapped reads were retained with PCR duplicates removal using MarkDuplicate from Picard(picard-2.25.5-0)
MACS2( V2.1.1.20160309) as used for calling CTCF peaks, with with the IgG CUT&RUN library used a negative control where stringent criteria of FDR < 0.05 and  --fe-cutoff 4 .
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: Naive P14 TCR transgenic CD8+ T cells

extract_protocol:
Naive P14 TCR transgenic CD8+ T cells, carrying a Tcf7-GFP reporter to mark Tcf1-expressing cells, were adoptively transferred into CD45-disparate recipients and subsequently infected with either LCMV Armstrong or LCMV-Clone 13 to induce acute or chronic viral infection, respectively. On day 8 post-infection in the acute infection model, KLRG1+IL-7Rα- P14 cells were sorted and purified as effector CD8+ T (Teff) cells for CTCF CUT&RUN analysis in live cells along with naive cells. In the chronic infection model, on day 8 post-infection, Tim3+Slamf6-GFP- P14 cells were sorted and purified as effector exhausted CD8+ T (Tex-eff) cells, while Tim3−Slamf6+GFP+ P14 cells were sorted and purified as precursors to stem-like exhausted  CD8+ T (Tex-prec) cells, both for CTCF CUT&RUN analysis. Additionally, WT naive P14 CD8+ T cells were adoptively transferred into CD45-disparate recipients, followed by infection with LCMV-Clone 13. At 72 hours (day 3) post-infection, Tim3+ Tex-eff P14 cells and GFP+ Tim3− Tex-prec P14 cells were sort-purified for CTCF CUT&RUN analysis.
The DNA segments from CTCF Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina HiseqX platform.

value: Naive P14 TCR transgenic CD8+ T cells


title: OSC20 cells,treated cisplatin t7, rep1

description: Library name: Sample7


title: Epicardial Biowire tissue with IRI and epicardial EVs, rep 3

city: Toronto

first: Milica

last: Radisic

state: Ontario

address: 160 College St

country: Canada

institute: University of Toronto

description: Library name: EpiIRISBEV_3

data_processing:
Fastq files from sequencing were cleaned up via Novogene Inc. in-house scripts for adapter trimming, poly-N trimming, and removal of low quality reads to produce data for downstream bioinformatic analyses
Hisat2 v2.0.5 was used to build the index of, and align cleaned reads to, the reference genome (GRCh38).
Mapped reads were counted using featureCounts v1.5.0-p3 then converted to FPKM.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file. Includes raw counts for each sample.

source_name: cardiac

extract_protocol:
Total RNA was isolated from Biowire tissues 15 days after the initial CM/CF seeding (which came 14 days after epicardial cell seeding and 7 days after IRI, when applicable, such that all groups were harvested after the same culture duration) using the PicoPure RNA Isolation Kit (ThermoFisher, KIT0204).
Total RNA was purified using the RNeasy MinElute Cleanup Kit (Qiagen, 74204) according to the manufacturer’s protocol then quantified on an Agilent 5400 Bioanalyzer. For library preparation, mRNA was purified from total RNA using polyT oligo-attached magnetic beads. mRNA was fragmented, random hexamer primers were used for first strand cDNA synthesis, then dTTP for the second strand (non-directional library). This was followed by end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Libraries were quantified using a Qubit and real-time PCR as well as a Bioanalyzer for size distribution, pooled, then sequenced on a NovaSeq X Plus Series sequencer (Illumina) at a read length of 2x150 b.p. and an average depth of 20M reads.

value: cardiac

value: cardiomyocytes, cardiac fibroblasts, epicardial cells

value: IRI + EVs


title: Immune cells, H_1

description: Library name: Sample 2

value: MC38 formed tumor tissues

value: Immune cells

value: cDNA library


title: CTCF CUTRUN  TexIgg_rep1

value: WT


title: Immune cells, W_1

description: Library name: Sample 1


title: Epicardial Biowire tissue with IRI and epicardial EVs, rep 2

description: Library name: EpiIRISBEV_2


title: OSC20 cells, untreated t7, rep3

description: Library name: Sample6

value: Tongue Squamous cell carcinoma

value: Epithelial

value: untreated t7


title: ST2-KO-3

city: Shanghai

first: Jieyuan

last: Xue

address: 280 South Chongqing Road

institute: Shanghai Jiao Tong University

description: Library name: Sample 6

data_processing:
FastQC (Version 0.12.1) was used for quality control of FastQ.gz files.
HISAT2 (Version 2.2.1) was used for alignment against the mouse reference genome (mm39).
Seqtk (Version 1.3) was used to count aligned reads.
Assembly: mm39
Supplementary files format and content: csv file includes raw counts for each sample

source_name: brown adipose tissue

extract_protocol:
RNA were extracted from brown adipose tissue using Trizol method.
RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer's recommendations. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to themanufacturer's instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.

value: brown adipose tissue


title: CTCF CUTRUN  D8_Tex-eff_rep2

description: D8_Tex-eff_merged_treat_pileup_scaled.bw


title: OSC20 cells, untreated t7, rep2

description: Library name: Sample5


title: Epicardial Biowire tissue with IRI and epicardial EVs, rep 1

description: Library name: EpiIRISBEV_1


title: CTCF CUTRUN  D8_Tex-eff_rep1


title: ST2-KO-2

description: Library name: Sample 5


title: OSC20 cells, untreated t7, rep1

description: Library name: Sample4


title: Epicardial Biowire tissue with IRI, rep 3

description: Library name: EpiIRI_3

value: IRI


title: ST2-KO-1

description: Library name: Sample 4


title: OSC20 cells, untreated t0, rep3

description: Library name: Sample3

value: untreated t0


title: Epicardial Biowire tissue with IRI, rep 2

description: Library name: EpiIRI_2


title: WT-3

description: Library name: Sample 3


title: CTCF CUTRUN  D8_Tex-prec_rep2

description: D8_Tex-prec_merged_treat_pileup_scaled.bw


title: CTCF CUTRUN  D8_Tex-prec_rep1


title: OSC20 cells, untreated t0, rep2

description: Library name: Sample2


title: Epicardial Biowire tissue with IRI, rep 1

description: Library name: EpiIRI_1


title: WT-2

description: Library name: Sample 2


title: OSC20 cells, untreated t0, rep1

description: Library name: Sample1


title: CTCF CUTRUN  D3_Tex-eff_rep3

description: D3_Tex-eff_merged_treat_pileup_scaled.bw


title: Biowire tissue without epicardium, rep 3

description: Library name: NoEpi_3

value: cardiomyocytes, cardiac fibroblasts

value: No IRI


title: CTCF CUTRUN  D3_Tex-eff_rep2


title: WT-1

description: Library name: Sample 1


title: patient 29V human aortic valve leaflet tissue, male, diseased

city: La Jolla

first: Talia

last: Baddour

state: California

address: 9500 Gilman Dr.

department: Bioengineering

institute: University of California San Diego

description:
Library name: Patient 29V
Fresh Frozen Spatial Transcriptome sequencing

data_processing:
For single cell RNA sequencing: The Homo Sapiens genome and gene annotations (assembly: GRCh38) were used to align data via the Cell Ranger 8.0.0 (10X Genomics) “count” command to generate expression matrices. Downstream analysis on patient gene expression matrices was performed using the Seurat32 v4.4.0 pipeline in R.  Matrices were filtered from dead cells and cells with high (> 7000) and low (< 200) feature counts. Normalization was performed using Seurat’s SCT transform v.2 which applies a negative binomial regression model to correct for technical artifacts such as sequencing depth variation while maintaining highly variable biological features. The normalized data was then integrated using Pearson’s residuals via the functions PrepSCTIntegration() followed by FindIntegrationAnchors() and IntegrateData() in Seurat. Dimensional reduction was performed on the integrated data set with the RunPCA() and RunUMAP() functions with 30 principal components. Graph-based clustering was performed using k-nearest neighbor FindNeighbors() and transformed into clusters using FindClusters() at a resolution of 0.01 on the data set. Wilcoxon rank sum testing was used to identify differentially expressed genes between different patient groups. For spatial transcriptomics: The sequencing data was aligned to images using SpaceRanger v.3.0.0 (10X Genomics) to generate gene expression matrices for subsequent analysis and processing. Spatial transcriptomics analysis was performed using the Seurat v4.4.0 pipeline in R. Gene expression matrices were initially filtered from high or low feature counts and regions of dead cells. Regions of calcification were confirmed via Von Kossa staining on tissue serial sections. Normalization was performed using Seurat’s SCT transform v.2 and merged our male and female replicates (N = 2) data into a single Seurat object and applied dimensional reduction and principal component analysis on the merged group. Then, male and female groups were integrated for comparison using Pearson residuals, FindIntegrationAnchors(), followed by PrepSCTIntegration(), and IntegrateData(). Graph-based clustering using k-nearest neighbor function FindNeighbors() and transformed into clusters using FindClusters() at a resolution of 0.1 on the entire integrated dataset. Wilcoxon rank-sum testing was used to identify differentially expressed genes between male and female samples.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz; scRNA seq = cell barcodes, spatial = spatial barcodes
Supplementary files format and content: features.tsv.gz; gene IDs
Supplementary files format and content: matrix.mtx.gz; gene expression count data
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: aortic valve leaflet

extract_protocol:
For single cell RNA sequencing: Aortic valve leaflets were excised from the aortic valve by cutting along the valve base and rinsed with Earle’s Balanced Salt Solution (EBSS) (Gibco, Cat. No. 24010043). All 3 leaflets per specimen were cut in half with 3 halves placed on ice for spatial transcriptomics protocols and three halves digested for single cell isolation and sequencing. Tissues were minced in Liberase TM (Sigma-Aldrich, Cat. No. 5401119001) in EBSS at 0.25 WU/mL and digested on an orbital shaker at 175 RPM for 30 mins at 37°C. DNAse I (Sigma Aldrich, Cat. No. DN25) was added to digestion medium at 100 µg/µL to prevent cell aggregation from genomic DNA. After digestion cells were immediately quenched with 10% Fetal Bovine Serum (FBS, Thermo Scientific, Cat. No. 16000069) in Medium 199 (Thermo Fisher Scientific, Cat. No. 11043023). Cells were strained in 3 successive straining steps with 100 µm, 70 µm, and 30 µm strainers and centrifuged at 400 rcf for 10 minutes. The cell pellet was resuspended in red blood cell lysis buffer (Thermo Scientific, Cat. No. 00433357) and rinsed using 10% FBS in media. After a final centrifugation step, cells were resuspended in 200 µL of 10% FBS media and counted using a cell hemacytometer prior to cell encapsulation in gel-beads for single cell RNA sequencing. For spatial transcriptomics: Aortic valve leaflets embedded in OCT medium were cryosectioned at 10 μm in thickness at -20°C. Spatial transcriptomics protocols (10X Genomics) were performed on tissue sections with an RNA Integrity Number (RIN) > 7 measured on the Agilent TapeStation for all samples.
For single cell RNA sequencing: Following the manufacturer’s protocol (Single Cell 3′ v2, 10x Genomics), human aortic valve cells isolated from valve leaflets were suspended in master mix and inserted into a microfluidic chip together with partitioning oil and gel beads to form gel bead-in-emulsions (GEMs). Within each GEM, poly-A RNA from the cell lysate was reverse transcribed into cDNA incorporating an Illumina R1 primer sequence, a Unique Molecular Identifier (UMI), and the 10x barcode. The barcoded cDNA was then purified with Silane DynaBeads, PCR-amplified, and size-selected using SPRIselect reagent. During library assembly, the Illumina R2 primer sequence was added, along with paired-end constructs containing P5 and P7 sequences and a sample index.  For spatial transcriptomics: Spatial gene expression libraries were prepared using the Visium Spatial Gene Expression Kit (10x Genomics) following the manufacturer’s instructions for fresh frozen tissue. Briefly, cryosectioned tissue was placed on Visium Gene Expression Slides, fixed, and stained with hematoxylin and eosin (H&E) for imaging. Permeabilization released mRNA, which hybridized to spatially barcoded capture oligonucleotides on the slide. Reverse transcription generated spatially barcoded cDNA, which was then collected, purified, and amplified by PCR. The amplified cDNA was enzymatically fragmented, end-repaired, A-tailed, and ligated to sequencing adapters containing sample indices. Final libraries were amplified, quantified, and assessed for quality prior to sequencing.

value: aortic valve leaflet

value: male

tag: disease state

value: diseased


title: Biowire tissue without epicardium, rep 2

description: Library name: NoEpi_2

value: cardiac


title: bEnd.3 cells, shNpc1-6

city: Henan

first: Ge

last: Gao

address: Xinxiang

institute: Henan Medical University

description: Library name: shNpc1_6

data_processing:
The obtained raw sequencing data were filtered using SOAPnuke (v1.5.6).
The resulting clean data were then subjected to data analysis, visualization, and mining via the Dr. Tom multi-omics data mining system.
Assembly: Use HIST2 (v2.1.0) software to align clean data to the reference genome. Subsequently, employ Ericscript (v0.5.5) for gene fusion detection and rMATS (v3.2.5) for alternative splicing and differential alternative splicing analysis.
Supplementary files format and content: RNAseq FPKM.xls

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Tiangen). 2 ug of total RNA was used for the construction of sequencing libraries.
During sequencing library preparation, extracted RNA must be denatured at an appropriate temperature to disrupt secondary structures. Subsequently, mRNA is enriched using oligodT magnetic beads. Fragmentation reagent is added to the purified mRNA and incubated at a set temperature to generate short fragments. First-strand cDNA is synthesized by preparing the reverse transcription reaction mixture and incubating under programmed conditions. Subsequently, the corresponding reaction mixture is prepared and incubated to synthesize second-strand cDNA. Prepare the reaction system and set the reaction program to repair the ends of double-stranded cDNA and add an A base to the 3' end. Prepare the adapter ligation reaction system and set the reaction program to ligate the adapter to the cDNA. Prepare the PCR reaction system and amplify the adapter-ligated fragment through cycling. The PCR product is denatured to convert it into single-stranded DNA, which is then circularized under specified conditions within the reaction system to form single-stranded circular DNA (DNBs). After enzymatic digestion of linear DNA molecules, single-stranded circular DNA molecules undergo rolling circle replication to generate DNA nanospheres (DNBs). The resulting DNBs are loaded onto patterned nanoarray chips using high-density DNA nanochip technology and sequenced based on combinatorial probe-anchored synthesis (cPAS) technology.

value: brain-derived endothelial cells

value: Npc1 knockdown


title: CTCF CUTRUN  D3_Tex-eff_rep1

value: Naive P14 TCR transgenic CD8+ T cells


title: CTCF CUTRUN  D3_Tex-prec_rep3

description: D3_Tex-prec_merged_treat_pileup_scaled.bw


title: Biowire tissue without epicardium, rep 1

description: Library name: NoEpi_1


title: patient 23V human aortic valve leaflet tissue, female, diseased

description:
Library name: Patient 23V
Fresh Frozen Spatial Transcriptome sequencing

value: female


title: bEnd.3 cells, shNpc1-5

description: Library name: shNpc1_5


title: Epicardial Biowire tissue, rep 3

description: Library name: Epi_3

value: cardiomyocytes, cardiac fibroblasts, epicardial cells


title: patient 20V human aortic valve leaflet tissue, male, diseased

description:
Library name: Patient 20V
Fresh Frozen Spatial Transcriptome sequencing


title: CTCF CUTRUN  D3_Tex-prec_rep2

value: WT


title: bEnd.3 cells, shNpc1-4

description: Library name: shNpc1_4


title: patient 18V human aortic valve leaflet tissue, female, diseased

description:
Library name: Patient 18V
Fresh Frozen Spatial Transcriptome sequencing


title: Epicardial Biowire tissue, rep 2

description: Library name: Epi_2


title: CTCF CUTRUN  D3_Tex-prec_rep1


title: bEnd.3 cells, shControl-3

description: Library name: Ctrl3


title: Epicardial Biowire tissue, rep 1

description: Library name: Epi_1


title: bEnd.3 cells, shControl-2

description: Library name: Ctrl2


title: patient 27 human aortic valve leaflet cells, female, diseased

description:
Library name: Patient 27
10X Genomics

data_processing:
For single cell RNA sequencing: The Homo Sapiens genome and gene annotations (assembly: GRCh38) were used to align data via the Cell Ranger 8.0.0 (10X Genomics) “count” command to generate expression matrices. Downstream analysis on patient gene expression matrices was performed using the Seurat32 v4.4.0 pipeline in R.  Matrices were filtered from dead cells and cells with high (> 7000) and low (< 200) feature counts. Normalization was performed using Seurat’s SCT transform v.2 which applies a negative binomial regression model to correct for technical artifacts such as sequencing depth variation while maintaining highly variable biological features. The normalized data was then integrated using Pearson’s residuals via the functions PrepSCTIntegration() followed by FindIntegrationAnchors() and IntegrateData() in Seurat. Dimensional reduction was performed on the integrated data set with the RunPCA() and RunUMAP() functions with 30 principal components. Graph-based clustering was performed using k-nearest neighbor FindNeighbors() and transformed into clusters using FindClusters() at a resolution of 0.01 on the data set. Wilcoxon rank sum testing was used to identify differentially expressed genes between different patient groups. For spatial transcriptomics: The sequencing data was aligned to images using SpaceRanger v.3.0.0 (10X Genomics) to generate gene expression matrices for subsequent analysis and processing. Spatial transcriptomics analysis was performed using the Seurat v4.4.0 pipeline in R. Gene expression matrices were initially filtered from high or low feature counts and regions of dead cells. Regions of calcification were confirmed via Von Kossa staining on tissue serial sections. Normalization was performed using Seurat’s SCT transform v.2 and merged our male and female replicates (N = 2) data into a single Seurat object and applied dimensional reduction and principal component analysis on the merged group. Then, male and female groups were integrated for comparison using Pearson residuals, FindIntegrationAnchors(), followed by PrepSCTIntegration(), and IntegrateData(). Graph-based clustering using k-nearest neighbor function FindNeighbors() and transformed into clusters using FindClusters() at a resolution of 0.1 on the entire integrated dataset. Wilcoxon rank-sum testing was used to identify differentially expressed genes between male and female samples.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz; scRNA seq = cell barcodes, spatial = spatial barcodes
Supplementary files format and content: features.tsv.gz; gene IDs
Supplementary files format and content: matrix.mtx.gz; gene expression count data
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots


title: ATAC D8_Tex-eff_rep3

data_processing:
The sequencing quality of ATAC-seq libraries was assessed by FastQC (v0.11.8)(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
ATAC-seq reads were trimmed using Trim Galore (0.6.7) (-q 20 --phred33 --stringency 3 --fastqc --length 30 -e 0.1) to trim low quality sequences and remove adapters.
Bowtie2 v2.3.4.1 was used to align the sequencing reads to the mm10 mouse genome, and only uniquely mapped reads were retained with PCR duplicates removal using MarkDuplicate from Picard(picard-2.25.5-0)
MACS2( V2.1.1.20160309) as used for calling ATAC peaks, with FDR < 0.00001 and  --fe-cutoff 4 .
Assembly: mm10
Supplementary files format and content: bigWig

source_name: splenocytes

extract_protocol:
Naive P14 TCR transgenic CD8+ T cells, carrying a Tcf7-GFP reporter to mark Tcf1-expressing cells, were adoptively transferred into CD45-disparate recipients and subsequently infected with either LCMV Armstrong or LCMV-Clone 13 to induce acute or chronic viral infection, respectively. On day 8 post-infection in the acute infection model, KLRG1+IL-7Rα- P14 cells were sorted and purified as effector CD8+ T (Teff) cells for ATAC-seq analysis along with naive P14 cells.  In the chronic infection model, on day 8 post-infection, Tim3+Slamf6-GFP- P14 cells were sorted and purified as effector exhausted CD8+ T (Tex-eff) cells, while Tim3−Slamf6+GFP+ P14 cells were sorted and purified as precursors to stem-like exhausted CD8+ T (Tex-prec) cells, both for ATAC-seq analysis. Additionally, hCD2-Cre, Rosa26-lsl-GFP, and CTCF wild-type or floxed CD8+ T cells were adoptively transferred into CD45-disparate recipients, followed by infection with LCMV-Clone 13. At 72 hours post-infection, GFP+ Tim3+ Tex-eff P14 cells and GFP+ Tim3− Tex-prec P14 cells from both the WT and CTCF-KO groups were sorted and purified for ATAC-seq analysis.
Sort-purified cells were treated with TN5 transposase to generate tagged DNA fragments. TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries. The resulting libraries were seqeunced with Illumina HiseqX platform.

value: splenocytes


title: patient 23 human aortic valve leaflet cells, female, diseased

description:
Library name: Patient 23
10X Genomics


title: ATAC D8_Tex-eff_rep2


title: THP-1,PMA,rhCTSC,Sivaltat,RSV,3

city: Changsha

first: Xizi

last: Du

address: Xiangya Road 88

institute: Cenrral South University

description: Library name: RSV_CTSC_Siv3

data_processing:
mRNA was purified using magnetic beads with Oligo(dT), fragmented, and reverse transcribed into cDNA. Double-stranded cDNA was end-repaired, A-tailed, and ligated to sequencing adapters, followed by PCR amplification and library quality check.
Assembly: hg38
Supplementary files format and content: CSV
Supplementary files format and content: Gene expression matrix including TPM and raw counts for each gene across all samples, as well as gene annotations (gene ID, symbol, description, KEGG pathway information) and differential expression results between experimental groups.

source_name: peripheral blood

growth_protocol: THP-1 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. A total of 1.5 μg of RNA was used for sequencing library construction.
mRNA sequencing based on a reference genome was performed using the Illumina NovaSeq X Plus platform by Gene Denovo Biotechnology Co., Ltd. (Guangzhou, China).

treatment_protocol: Differentiation of THP-1 monocytes to macrophages was induced by treating the THP-1 cell line (2 × 105 cells/ml) with 200 nM phorbol 12-myristate 13-acetate (PMA)  for 48 h. After PMA stimulation, differentiation was enhanced by removing the PMA-containing medium and then incubating the cells in fresh RPMI 1640 medium (10% FBS, 1% penicillin-streptomycin solution). Recombinant Human Cathepsin C (rhCTSC) and PR3 inhibitor Sivelestatwere incubated with differentiated THP-1 cell for 24h, then cells were infected with RSV (MOI 5) for 24h.

value: peripheral blood

value: monocytic cell line


title: patient 21 human aortic valve leaflet cells, female, diseased

description:
Library name: Patient 21
10X Genomics


title: THP-1,PMA,rhCTSC,Sivaltat,RSV,2

description: Library name: RSV_CTSC_Siv2


title: bEnd.3 cells, shControl-1

description: Library name: Ctrl1


title: ATAC D8_Tex-eff_rep1


title: patient 15 human aortic valve leaflet cells, male, diseased

description:
Library name: Patient 15
10X Genomics


title: Day 6 TAZ uKO pregnant uterus, implantation site, biological replicates 2

city: Bunkyo-ku

first: Shizu

last: Aikawa

state: Tokyo

address: 7-3-1 Hongo

institute: The University of Tokyo

description: Library name: sample4

data_processing:
Raw reads were processed by Cell Ranger with default setting.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5.gz:The filtered feature count matrix generated from Cell Ranger.
Supplementary files format and content: barcodes.tsv.gz: list of list of spatial barcodes (10x Visium)
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coodinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Mouse uterus

extract_protocol:
After reaction with Proteinase K for 30 min, the sections were hybridized with spatial tags on the slides according to manufacturer's protocol.
Following the hybridization with spatial tags, reverse-transcribed in situ according to manufacturer's protocol.

value: Mouse uterus


title: THP-1,PMA,rhCTSC,Sivaltat,RSV,1

description: Library name: RSV_CTSC_Siv1


title: ATAC D8_Tex-prec_rep3


title: Day 6 TAZ uKO pregnant uterus, implantation site, biological replicates 1

description: Library name: sample3


title: ATAC D8_Tex-prec_rep2


title: GSK rep4

city: Melbourne

first: Abdul Waheed

last: Khan

state: Vic

address: 99 Commercial Road

department: Diabetes

country: Australia

institute: Monash University

description: Library name: L14_GSK rep4

data_processing:
Partek flow raw reads underwent trimming with cutadapt (1.12)
Partek flow STAR alignment 2.6.1
Partek gene level quantification to annotation model hg38_ensembl_release103
Assembly: GRCh38
Supplementary files format and content: Partek-flow quantified gene read counts text file with features on rows, samples on columns

source_name: HAEC

growth_protocol: Primary human aortic endothelial cells (HAECs; CC-2535, Lonza, Mt Waverley, Australia) were cultured in EGM-2 medium supplemented with the Endothelial Cell Growth Medium-2 BulletKit (CC-3156 and CC-4176, Lonza) at 37 C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted from HAECs exposed to EndMT-inducing conditions and GSK-126 (5 μM) using TRIzol® Reagent (Invitrogen, Australia) and the Direct-zol™ RNA Miniprep Kit (Zymo Research, USA), following the manufacturer’s protocols
To enrich for mRNA, 1 μg of total RNA was processed using the NEBNext® rRNA Depletion Kit (New England Biolabs, USA). Barcoded libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs)

treatment_protocol: HAECs were stimulated with TNF-α (5 ng/mL) and high glucose (25 mM) ± GSK-126 (5 μM) for 72 hours.

value: HAEC

value: TNFa 5ng/mL, HG 25 mM, GSK126 5uM


title: THP-1,PMA,rhCTSC,RSV,3

description: Library name: RSV_CTSC3


title: GSK rep3

description: Library name: L11_GSK rep3


title: Day 6 control pregnant uterus, implantation site, biological replicates 2

description: Library name: sample2


title: ATAC D8_Tex-prec_rep1


title: THP-1,PMA,rhCTSC,RSV,2

description: Library name: RSV_CTSC2


title: Day 6 control pregnant uterus, implantation site, biological replicates 1

description: Library name: sample1


title: THP-1,PMA,rhCTSC,RSV,1

description: Library name: RSV_CTSC1


title: TNFa rep3

description: Library name: L10_TNFa rep3

value: TNFa 5ng/mL, HG 25 mM


title: ATAC D3_CTCFKO_Tex-eff_rep3

description: D3_CTCF_KO_Tex-eff_merged_treat_pileup_scaled.bw

value: CTCFKO


title: THP-1,PMA,RSV,3

description: Library name: RSV3


title: ATAC D3_CTCFKO_Tex-prec_rep3

description: D3_CTCF_KO_Tex-prec_merged_treat_pileup_scaled.bw


title: TNFa rep2

description: Library name: L6_TNFa rep2


title: Mudskipper spinal cord, C6, scRNA-seq 1

city: Dalseong-gun

first: Tery

last: Yun

state: Daegu

address: 333 Technojungang-daero, Hyeonpung-eup

department: Department of Brain Sciences

institute: DGIST

description: Library name: C6-mudskipper

data_processing:
Raw FASTQ files were processed using Cell Ranger v7.2.0. Fugu reads were mapped to Takifugu rubripes genome (Ensembl release 113). Mudskipper reads were mapped to Periophthalmus magnuspinnatus genome (Ensembl release 113). Chicken reads were mapped to Gallus gallus genome (Ensembl release 113). Empty droplets removed using emptyDrops (FDR ≤ 0.01, DropletUtils v1.26.0). Doublets identified using scDblFinder v1.23.4. Downstream analysis performed in Seurat v5.3.0 with Monocle3 pseudotime and CAME cross-species cell type mapping.
Assembly: Fugu: Takifugu rubripes (Ensembl release 113); Mudskipper: Periophthalmus magnuspinnatus (Ensembl release 113); Chicken: Gallus gallus (Ensembl release 113)
Supplementary files format and content: Tab-separated gzipped files in 10x Genomics sparse matrix format: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene IDs and names), and matrix.mtx.gz (UMI count matrix). Generated by Cell Ranger v7.2.0.

organism: Periophthalmus magnuspinnatus

source_name: spinal cord

growth_protocol: Fugu (Takifugu obscurus) and mudskipper (Periophthalmus magnuspinnatus) were dissected approximately one month post-hatching. Chicken (Gallus gallus) spinal cord was collected at embryonic days 10-11 (Hamburger-Hamilton stage 36-37). All procedures were approved by IACUC of DGIST (Approval No: DGIST-IACUC-23052304-0002).

extract_protocol:
Spinal cord tissue from multiple individuals was pooled per library. Cell dissociation was performed by incubation in pronase solution for 40 min at room temperature, followed by trituration in 100 µL ACSF containing 1% FBS. Volume was adjusted to 3 mL and live cells were enriched by FACS (BD FACSAria III) using propidium iodide (1 µg/mL) exclusion. Cell viability exceeded 80%. Sorted cells were resuspended in 1× DPBS containing 0.04% BSA.
Libraries were prepared using the Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (10x Genomics). Target cell recovery was 1,000-9,000 cells per replicate depending on tissue availability. Reverse transcription was performed using a C1000 Touch Thermal Cycler (Bio-Rad). Libraries were sequenced on an Illumina HiSeq X platform (paired-end 100 bp reads) targeting an average of 20,000 read pairs per cell.

value: spinal cord


title: THP-1,PMA,RSV,2

description: Library name: RSV2


title: ATAC D3_CTCFKO_Tex-eff_rep2


title: GSK 1 rep1

description: Library name: L3_GSK 1 rep1


title: THP-1,PMA,RSV,1

description: Library name: RSV1


title: ATAC D3_CTCFKO_Tex-prec_rep2


title: pEPSCs differentiated in LCDM

city: Nanjing

first: Lihua

last: Zhao

address: #101, Long mian road

institute: Nanjing Medical University

description:
Library name: sample1
10× Genomics

data_processing:
Reads were processed by the Cell Ranger (v7.1.0, 10× Genomics) with Sus scrofa 11.1 genome. Doublets were removed using Scrublet/DoubletFinder. A seurat object (v4.3.0, R v4.0.3) was created (75); filters: genes expressed in <3 cells, cells with 200 to 10,000 genes, cells with ≤20% mitochondrial UMIs. After filtering (14,822 cells retained; median UMI: 24,142; median gene: 2,595), counts were normalized (scale factor 10,000) and log-transformed. Top 2,000 HVGs were identified for integration.
Assembly: Sus scrofa 11.1
Supplementary files format and content: PCA was done using default parameters. Significant PCs were selected via elbow method. Cell clustering used Louvain algorithm, visualized with UMAP. Differential/marker genes were conducted using the ‘findMarkers’ (Wilcoxon’s test: min.pct = 0.1, logfc.threshold = 0.25). Clusters were annotated using SciBet (v1.0); pseudotime analysis used Monocle3 (Qiu et al., 2017).

organism: Sus scrofa

source_name: pEPSCs

extract_protocol:
We lysed captured cells and released RNA was barcoded through reverse-transcription in individual single-cell gel beads in the emulsion (GEMS). In each droplet, complementary DNA (cDNA) was generated and amplified through reverse-transcription on a T100 PCR Thermal Cycler (Bio Rad) at 53 C for 45 min, followed by 85 C for 5 min and a hold at 4 C. Then, cDNA concentration and quality were assessed using Qubit Fluorometer (Thermo Scientific) and bioanalyzer 2100 (Agilent), respectively.
According to the manufacturer’s introduction, scRNA-seq libraries were constructed and sequenced to a depth of  24142 reads per cell on illumina platform by Annoroad Gene Technology Co., Ltd.24142

value: pEPSCs

value: extended pluripotent stem cells

value: differentiated in LCDM medium for 96 hours


title: Control rep1

description: Library name: L1_Control rep1

value: Control


title: THP-1,PMA,PBS,3

description: Library name: PBS3


title: ATAC D3_CTCFKO_Tex-eff_rep1


title: BoMac cells, 475, rep3

city: Yinchuan

first: Gang

address: 489 Helan West Road, Xixia District

institute: ningxia university

data_processing:
Sequence reads were filtered for quality, and adapter sequences were trimmed using a custom Perl script that identifies exact string matches to a user-supplied adapter sequence ratio. Clean data were mapped to the reference genome to calculate the alignment using HISAT2.
Gene expression was represented by fragments per kilobase of exon per million fragments mapped (FPKM). Differential gene transcription analysis was performed using DESeq2 R package (1.16.1) of three biological replicates per condition and genes with 1.5-fold change were selected for further analysis.
Assembly: ARS-UCD1.2
Supplementary files format and content: Excel file contains raw counts for each Sample
Supplementary files format and content: Excel file contains differential expressing gene between BoMacWT and BoMac475

organism: Bos taurus

source_name: BoMac

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen), 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-seq library Prep Kit.

value: BoMac


title: BoMac cells, 475, rep2


title: THP-1,PMA,PBS,2

description: Library name: PBS2


title: PANC-1_KDM5C

city: Jinan, Shandong

first: Shuai

last: Leng

address: 105 Jiefang Road

institute: Central Hospital Affiliated to Shandong First Medical University

description: Library name: Sample 2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Clean reads were mapped to the reference genome using Bowtie2 software. And reads from organelle, mapping quality smaller then 30, PCR duplicated reads all removed. Those high quality mapping reads were subjected to further peak calling.
Macs2 was used to call peaks.
Assembly: hg38
Supplementary files format and content: bw

source_name: Human pancreatic cancer

extract_protocol:
ChIP assays were performed according to the standard crosslinking ChIP protocol with modifications. Briefly, cells were harvested and crosslinker with 1% formaldehyde for 10 min at room temperature. After sonication, immunoprecipitation was performed with antibody. The immunoprecipitated complex was washed, and DNA was extracted and purified by MinElute PCR Purification Kit (QIAGEN, #28006).
The ChIP-Seq library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, #TD501) according to the manufacturer’ s instructions. For ChIP-seq, extracted DNA was ligated to specific adaptors followed by deep sequencing in the Illumina Novaseq 6000 using 150bp paired-end.

value: Human pancreatic cancer

value: Human pancreatic cancer cell line


title: THP-1,PMA,PBS,1

description: Library name: PBS1


title: ATAC D3_WT_Tex-eff_rep3

description: D3_WT_Tex-eff_merged_treat_pileup_scaled.bw

value: WT


title: BoMac cells, 475, rep1


title: PANC-1_Input

description: Library name: Sample 1

value: Input

value: input


title: RNA-seq_AML_OCI3_48h_JIB04_2

city: Houston

first: Margaret

last: Goodell

state: TX

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

description: Library name: AML_OCI3_48h_JIB04_2

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt with the default threshold.
Trimmed sequence reads were aligned to hg38 human reference genome using STAR-2.6.1  with the default settings.
Transcript levels were quantified in term of TPM and count with RSEM.
Tab-delimited text file includes raw counts and FPKM values for each Sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and TPM for each Sample
Supplementary files format and content: tab-delimited text files include only TPM values for each Sample

growth_protocol: AML-OCI3 were cultured in RPMI with 10% FBS and 1% penicillin/streptomycin at 37ºC and 5% CO2

extract_protocol:
RNA was isolated using TRIzol (Invitrogen)
700ng total RNA was used as input for the Illumina TruSeq® Stranded mRNA Library Prep kit (20020594) following the manufacturer’s protocol.

treatment_protocol: AML-OCI3 cells were treated with DMSO or 40nM JIB-04 for 24h and 48h

value: Acute Myeloid Leukemia

tag: time


title: ATAC D3_WT_Tex-prec_rep3

description: D3_WT_Tex-prec_merged_treat_pileup_scaled.bw

value: splenocytes


title: BoMac cells, WT, rep3


title: PANC-1_siKDM5C_3

description: Library name: Sample 9

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: KDM5C knockdown


title: RNA-seq_AML_OCI3_48h_JIB04_1

description: Library name: AML_OCI3_48h_JIB04_1


title: ATAC D3_WT_Tex-eff_rep2


title: PANC-1_siKDM5C_2

description: Library name: Sample 8


title: BoMac cells, WT, rep2


title: RNA-seq_AML_OCI3_48h_DMSO_2

description: Library name: AML_OCI3_48h_DMSO_2

value: DMSO


title: ATAC D3_WT_Tex-prec_rep2


title: BoMac cells, WT, rep1


title: PANC-1_siKDM5C_1

description: Library name: Sample 7


title: RNA-seq_AML_OCI3_48h_DMSO_1

description: Library name: AML_OCI3_48h_DMSO_1


title: f231

city: Chongqing

first: Ziwei

last: Wu

institute: Breast Disease Center, Southwest Hospital, Army Medical University

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method.
RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2  or DEGseq.
Assembly: Reference gene source: Homo_sapiens ; Reference genome version: GRCh38.p13; Reference Genome Source: http://asia.ensembl.org/Homo_sapiens/Info/Index.

source_name: Human breast cancer

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using TRIzol.
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: Human breast cancer

value: TNBC

value: Huaier


title: ATAC D3_WT_Tex-eff_rep1


title: PANC-1_siSIRT6_3

description: Library name: Sample 6

value: SIRT6 knockdown


title: RNA-seq_AML_OCI3_24h_JIB04_2

description: Library name: AML_OCI3_24h_JIB04_2


title: ATAC D3_WT_Tex-prec_rep1


title: e231

address: Southwest Hospital, Army Medical University


title: PANC-1_siSIRT6_2

description: Library name: Sample 5


title: RNA-seq_AML_OCI3_24h_JIB04_1

description: Library name: AML_OCI3_24h_JIB04_1


title: biol rep 2 of undifferentiated sea lamprey gonadal cells from larvae

city: East Lansing

first: Stephanie

middle: Lepp

last: Hickey

state: Michigan

address: 612 Wilson Rd

institute: Michigan State University Bioinformatics Core

description:
Library name: UND2_C00004362
PIPseq™ 3ʹ Single Cell RNA

data_processing:
PIPseeker 3.0.5_Mk6.1
Assembly: kPetMar1.pri, NCBI RefSeq assembly: GCF_010993605.1
Supplementary files format and content: <library>_barcodes.tsv.gz: Tab separated file contaning a list of all unique cell barcodes detected during the single-cell RNA-sequencing analysis. These barcodes correspond to the column indices in the matrix.mtx file.
Supplementary files format and content: <library>_features.tsv.gz: Tab separated file contaning unique gene IDs. Columns 1 and 2 are identical. These features correspond to the row indices in the feature-barcode matrix.
Supplementary files format and content: <library>_matrix.mtx.gz: Matrix Market exchange (MEX) format, contains a sparse matrix representing the number of UMIs (Unique Molecular Identifiers) observed for each gene with each barcode.
Supplementary files format and content: cell_metadata.tsv.gz: Tab separated file containing metadata for each cell included in the study. Columns include barcode, batch, label (cluster number), CellType, TSNE1, TSNE2, fastMNN.corrected expression dimensions 1-50, germ.cluster, germ.broad.CellType, germ.narrow.CellType, germ.Pseudotime, germ.TSNE1, germ.TSNE2, germ.fastMNN.corrected astMNN.corrected expression dimensions 1-50.

organism: Petromyzon marinus

source_name: gonad

growth_protocol: wild-caught, no growth protocol

extract_protocol:
Gonadal tissues were dissociated using Thermo Scientific™ Pierce™ Primary Neuron Isolation Kit (PI88280), live cells were enriched using BD FACS Aria IIu, and cells were captured by PIPseq™ T20 3ʹ Single Cell Capture and Lysis Kit v4.0 and shipped to Fluent BioSciences for sequencing service.
RNA Prep and Library Prep were performed using the PIPseq T20 3ʹ Single Cell RNA kit V4.0

treatment_protocol: wild-caught, no treatment protocol

value: gonad

value: wildtype

value: wild-caught, unknown

value: not determined


title: d231


title: PANC-1_siSIRT6_1

description: Library name: Sample 4

value: Human pancreatic cancer


title: RNA-seq_AML_OCI3_24h_DMSO_2

description: Library name: AML_OCI3_24h_DMSO_2


title: biol rep 1 of undifferentiated sea lamprey gonadal cells from larvae

description:
Library name: UND1_C00004336
PIPseq™ 3ʹ Single Cell RNA


title: c231

value: control


title: PANC-1_Control_3

description: Library name: Sample 3

value: Human pancreatic cancer cell line


title: Mudskipper spinal cord, C7, scRNA-seq 2

description: Library name: C7-mudskipper

value: spinal cord


title: RNA-seq_AML_OCI3_24h_DMSO_1

description: Library name: AML_OCI3_24h_DMSO_1


title: gonadal cells from male transformer (metamorphosed, sex-determined)

description:
Library name: TM_C00004374
PIPseq™ 3ʹ Single Cell RNA

value: Male


title: Control rep3

description: Library name: L9_Control rep3

value: HAEC

value: Control


title: b231


title: PANC-1_Control_2

description: Library name: Sample 2


title: AML_OCI3_48h_JIB04_Input

description: Library name: AML_OCI3_48h_JIB04_Input

data_processing:
ChiP-seq reads were removed adaptor and low-quality reads based on the default threshold using cutadapt.
ChIP-seq reads were aligned to the hg38 genome using Bowtie version 2.3.4. After alignment, samtools was used to perform quality control checks on the alignment BAM files and allowed only the uniquely mapped reads to be retained. Then PCR duplicates were removed by Picard using the MarkDuplicates tool with the parameters “VALIDATION_STRINGENCY = LENIENT REMOVE_DUPLICATES = true” for downstream analyses.
For H3K4me3 and H3K9me3, .narrowPeaks were called using the MACS2 with the significance cut-off p-value 1e-9. For H3K27me3 and H3K36me3, broadpeaks were called using SICER with the parameters “-s hg38 -w 200 -f 150 -fdr 0.01 -g 600 -e 1 --significant_reads”. The peaks were then filtered by the hg38 ENCODE blacklist (https://www.encodeproject.org/files/ENCFF356LFX/).
Signal intensities for each ChIP library were normalized to 1x, and bigwig files were generated from BAM files using deeptools.
Assembly: hg38
Supplementary files format and content: bigwig, narrowPeak and bed (except for input samples)

extract_protocol:
cells were fixed with 1% Formaldehyde for 10 min and further processed using the Covaris truChIP Chromatin Shearing Kit according to Covaris protocol. Chromatin was sheared to 200-500bp fragments using the Covaris M220 Focused-ultrasonicator
Libraries were prepared using the Takara ThruPLEX® DNA-seq 48D Kit (R400675) according to manufacturer instructions.

value: Acute Myeloid Leukemia


title: NpKA_bulbs

city: Trois-Rivières

first: Karen

middle: Cristine

last: Goncalves dos Santos

address: 3351 boul des Forges

department: Departement de Chimie, Biochimie, Physique et Sciences Forensiques

institute: Université du Québec à Trois-Rivières

description:
Library name: SRR5788585
Singh, A. & Desgagné-Penix, I. Transcriptome and metabolome profiling of Narcissus pseudonarcissus ‘King Alfred’ reveal components of Amaryllidaceae alkaloid metabolism. Scientific Reports 7, 17356, doi:10.1038/s41598-017-17724-0 (2017)

data_processing:
Raw data were downloaded from the Sequencing Read Archive (SRA) using sra-toolkit 3.0.9, then quality control was performed using fastp 0.23.4 (mean quality = 20; unqualified percent limit = 30; cut-front window-size = 5; cut-right window size = 4; cut-right mean quality = 15; length required = 50).
Assembly was carried out with Trinity 2.14.0 default parameters, followed by removal of redundant transcripts with CD-HIT-EST 4.8.1 (-c 0.97, -l 200).
Next, detection and removal of contaminant sequences (from viruses, archeobacteria, bacteria, fungi or animals, as well as adaptors) was performed with FCS-adaptor version 0.5.0 and FCS-GX version 0.5.5 on Galaxy Project. Expression quantification was performed using kallisto 0.46.1, with the support scripts align_and_estimate_abundance.pl and abundance_estimates_to_matrix.pl from Trinity. Trinity isoforms with a total read count = 0 were discarded.
Assembly: TSA: DBNIJK000000000
Supplementary files format and content: Narcissus_pseudonarcissus_gene_counts.txt: Read count table, with trinity genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Narcissus_pseudonarcissus_gene_TPM.txt: Transcripts per million table, with trinity genes in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Narcissus_pseudonarcissus_isoform_counts.txt: Read count table, with trinity gene isoforms in the rows and accession numbers of samples in the columns.
Supplementary files format and content: Narcissus_pseudonarcissus_isoform_TPM.txt: Transcripts per million table, with trinity gene isoforms in the rows and accession numbers of samples in the columns.

organism: Narcissus pseudonarcissus

source_name: bulb

growth_protocol: Dormant bulbs

extract_protocol:
CTAB method described by (Singh and Desgagne-Penix 2017)
RNAseq

value: bulb

value: cultivar:King Alfred


title: gonadal cells from female transformer (metamorphosed, sex-determined)

description:
Library name: TF_C00004337
PIPseq™ 3ʹ Single Cell RNA

value: Female


title: a231

value: Human breast cancer

value: TNBC


title: AML_OCI3_48h_DMSO_Input

description: Library name: AML_OCI3_48h_DMSO_Input


title: PANC-1_Control_1

description: Library name: Sample 1


title: f1806

value: Huaier


title: SW480, Tram, 8h, rep3

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

institute: Heidelberg University

description: Library name: Tram_8h_rep3

data_processing:
Alignment to hg38 was performed using STAR v2.5.3a allowing a maximum of 10 mismatches and providing a gtf with exon coordinates of the Gencode Basic V38 transcript set.
Alignments were annotated and summarized at the gene level using featureCounts within the subread package v1.6.3.
Differential expression was tested by pair-wise comparison of each trametinib or CHIR-9901 time-point to its respective DMSO control using the DESeq2 package v1.46.0 with default settings.
Assembly: hg38
Supplementary files format and content: The file RNASeq_SW480_MEKi_DESeq2.csv contains read counts per gene (as determined by a common gene symbol in the Gencode Basic V38 transcript set), normalized read counts as generated by DESeq2 with the median of ratios method (columns ending with _norm), log2 fold-changes (_DESeq2log2FC), standard errors (_DESeq2lfcSE) and corresponding adjusted p-values (_DESeq2padj) for the pair-wise comparisons of the trametinib (Tram) or CHIR-99021 (Chir) time-points to their respective DMSO control.

growth_protocol: SW480 cells were cultured in RPMI 1640 medium (Gibco), supplemented with 10% fetal bovine serum (FBS, Gibco), 1% Glutamax (Gibco), and 1% penicillin/streptomycin (Gibco).

extract_protocol:
RNA was isolated from cultured cells using the peqGOLD Total RNA Kit (VWR), following the manufacturer’s instructions. After lysis in TRK buffer and homogenization, lysates were applied to RNA Mini Columns. DNase I digestion was performed to remove genomic DNA. RNA was washed, eluted with preheated nuclease-free water (70 °C) and stored at −70 °C.
Libraries were prepared at the DKFZ Genomics & Proteomics Core Facility using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and sequenced on a NovaSeq 6000 (Illumina) as paired-end 100 nt long reads.

treatment_protocol: SW480 cells were treated with 100 nM trametinib (Tram), 10 µM CHIR-99021 (Chir) or DMSO for 8 h, 24 h or 72 h.


title: leptomeninges, WT; control, repeat 2

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

description:
Library name: YW82
10X Genomics

data_processing:
snRNA-seq: reads were aligned with the PIPseeker program (Fluent BioSiences, version 3.3.0) or, in the case of the 10/X Genomics data, aligned to a mm10 pre-mRNA index using Cellranger version 3.1.0.. The CellBender program was used to detect empty droplets and remove background (version 0.3.2; Fleming et al., 2023). The SOLO program was used to remove doublets (scVI-tools 1.2.2-post2; Bernstein et al., 2020). Manual curation was used to further remove potentially mixed (doublet) nuclei. The data were normalized using a regularized negative binomial regression algorithm implemented with the SCTransform function (Hafemeister and Satija, 2019). Batch effects were corrected using the Seurat RPCAIntegration function. UMAP dimensional reduction was performed using the R uwot package (https://github.com/jlmelville/uwot) integrated into the Seurat R package (Melville, 2022).  RNA-seq on WT and Tlr4KO bEnd.3 cells: RNA-seq processing and normalization Gene-level count matrices from bEnd.3 cells were analyzed in R (v4.5) with Bioconductor (v3.21).
Assembly: Mouse mm10, mm39
Supplementary files format and content: Tab-separated values files, comma-separated values files, and matrix files.

source_name: leptomeninges

extract_protocol:
For single-nucleus RNA sequencing, leptomeninges were collected as previously described (Wang et al., 2023). In brief, P6 mice were euthanized 24 hours after infection, brains were rapidly removed, and the leptomeninges were dissected into ice-cold Hibernate-A medium. The leptomeninges were frozen at -80 °C. Single nucleus (sn)RNA-seq libraries were preparedusing the PIPseq T20 3’ Single Cell RNA Kit v4.0 PLUS (Fluent BioSiences; Clark et al., 2023). Frozen tissue was suspended in homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH,pH 7.8) supplemented with 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, EDTA free protease inhibitor (Roche 11836 170 001), 0.5% IGEPAL-630, and 40 U/mL Protector RNase Inhibitor (Sigma, 03335402001). Samples were homogenized in a 2 mL Dounce homogenizer,  sing 15 strokes with a loose-fitting pestle followed by 30 strokes with a tight-fitting pestle. The sample was filtered through a 10 μm filter (CellTrix, Sysmex, 04-004-2324), and nuclei were pelleted in Low Retention 1.5 mL microcentrifuge tubes (Thermo Scientific, 3451) for 5 min at 500 x g at 4 °C. Nuclei were washed twice with Nuclei Suspension Buffer (supplied in the Fluent BioSciences kit) supplemented with 1% BSA and 40 U/mL Protector RNase Inhibitor. Nuclei were counted, and ~40,000 nuclei (for the T20 kit) or ~20,000 nuclei (for the T10 kit) were used for library production following the Fluent BioSiences protocol.  RNA-seq on WT and Tlr4KO bEnd.3 cells: libraries and sequencing bEnd.3 mouse brain endothelial cells were cultured in 10-cm tissue culture dishes and grown to confluency under standard conditions (37 C, 5% CO₂). Total RNA was isolated using the Zymo Research RNA purification kit according to the manufacturer’s instructions. Briefly, culture medium was aspirated, cells were rinsed once with ice-cold PBS, and 600 μL of the provided lysis buffer with β-mercaptoethanol was added directly to the dish. The lysate was collected by scraping and transferred to a microcentrifuge tube, briefly mixed, and applied to the Zymo spin column. After binding, the column was washed with the supplied wash buffers, including an on-column DNase I treatment step to remove contaminating genomic DNA, and RNA was eluted in 50 μL of DNase/RNase-free water.
RNA-seq library construction was performed with the Illumina mRNA stranded kit following the manufacturer's protocol, and sequencing was performed on an Illumina NovaSeqX

value: leptomeninges

value: WT


title: AML_OCI3_24h_JIB04_Input

description: Library name: AML_OCI3_24h_JIB04_Input


title: leptomeninges, WT; control, repeat 1

description:
Library name: YW80
10X Genomics


title: e1806


title: SW480, Tram, 72h, rep3

description: Library name: Tram_72h_rep3


title: AML_OCI3_24h_DMSO_Input

description: Library name: AML_OCI3_24h_DMSO_Input


title: PANC-1_SIRT6

description: Library name: Sample 3


title: ATAC D3_CTCFKO_Tex-prec_rep1

city: Washington

first: Weiqun

last: Peng

address: Suite 4000 SEH Science & Engineering Hall 800 22nd Street NW

institute: The George Washington University

value: splenocytes

value: CTCFKO


title: SW480, Tram, 24h, rep3

description: Library name: Tram_24h_rep3


title: d1806


title: AML_OCI3_48h_JIB04_2_H3K36me3

description: Library name: AML_OCI3_48h_JIB04_2_H3K36me3


title: fctx_HET5 snATAC-seq

city: Toronto

first: Paul

middle: M

last: McKeever

state: ON

address: 60 Leonard Ave., 4th floor - 4KD481

department: Tanz CRND

institute: University of Toronto

description:
Library name: ATAC_fctx_HET5
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_HET5_fragments.tsv.gz
fctx_HET5_fragments.tsv.gz.tbi

library_source: genomic single cell

data_processing:
Raw base call files were demultiplexed using Illumina software to generate FASTQ files.
Chromatin accessibility reads were aligned to the mouse reference genome mm10 using BWA within the Cell Ranger ARC pipeline.
FASTQ files were processed using Cell Ranger ARC (10x Genomics) to perform alignment, barcode assignment, and generation of paired gene expression and chromatin accessibility count matrices.
Gene expression reads were aligned to the mouse reference genome mm10 using STAR within the Cell Ranger ARC pipeline.
Chromatin accessibility reads were aligned to the mouse reference genome mm10 using BWA within the Cell Ranger ARC pipeline.
Chromatin accessibility reads were aligned to the mouse reference genome mm10 using BWA within the Cell Ranger ARC pipeline.
Assembly: mm10
Supplementary files format and content: Processed data files include filtered gene expression count matrices, chromatin accessibility peak count matrices, fragment files, and associated cell metadata generated from Cell Ranger ARC and downstream Seurat/Signac analyses.
Supplementary files format and content: Processed files are provided in standard formats including HDF5 (.h5), Matrix Market (.mtx), tab-delimited text (.tsv), and compressed fragment files (.tsv.gz) containing single-nucleus transcriptomic and chromatin accessibility measurements.

source_name: frontal cortex

growth_protocol: C9orf72 wild-type, heterozygous knockout, and homozygous knockout mice were maintained under standard laboratory housing conditions with ad libitum access to food and water on a 12 h light/dark cycle. Brain tissue was collected from approximately 3-month-old animals.

extract_protocol:
Nuclei were isolated from frozen hippocampus and frontal cortex tissue using region-specific nuclei isolation workflows optimized for each brain region. Hippocampal nuclei were isolated using an iodixanol density gradient purification protocol following mechanical homogenization and filtration to enrich for intact nuclei and reduce debris contamination. Frontal cortex nuclei were isolated using the 10x Genomics Nuclei Isolation Kit according to the manufacturer’s protocol. Purified nuclei were counted and assessed prior to loading onto the 10x Genomics Chromium platform. RNA and chromatin accessibility information were simultaneously captured from individual nuclei using the Chromium Single Cell Multiome ATAC + Gene Expression workflow.
Single-nucleus multiomic libraries were generated using the 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression platform according to the manufacturer’s instructions. Briefly, isolated nuclei were subjected to transposition using Tn5 transposase to generate ATAC fragments, followed by GEM generation for simultaneous barcoding of gene expression and chromatin accessibility molecules from individual nuclei. Gene expression and ATAC libraries were amplified separately and sequenced on Illumina NovaSeq 6000 and NovaSeq X Plus instruments.

treatment_protocol: No experimental treatments were applied prior to tissue collection. Hippocampus and frontal cortex tissues were rapidly dissected from frozen brain samples for downstream single-nucleus isolation.

value: frontal cortex

value: C9orf72 heterozygous knockout


title: fctx_HET6 snATAC-seq

description:
Library name: ATAC_fctx_HET6
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_HET6_fragments.tsv.gz
fctx_HET6_fragments.tsv.gz.tbi


title: c1806

value: control


title: AML_OCI3_48h_JIB04_1_H3K36me3

description: Library name: AML_OCI3_48h_JIB04_1_H3K36me3


title: SW480, Tram, 8h, rep2

description: Library name: Tram_8h_rep2


title: fctx_HET7 snATAC-seq

description:
Library name: ATAC_fctx_HET7
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_HET7_fragments.tsv.gz
fctx_HET7_fragments.tsv.gz.tbi


title: b1806


title: SW480, Tram, 72h, rep2

description: Library name: Tram_72h_rep2


title: AML_OCI3_48h_DMSO_2_H3K36me3

description: Library name: AML_OCI3_48h_DMSO_2_H3K36me3

value: DMSO


title: a1806


title: fctx_WT5 snATAC-seq

description:
Library name: ATAC_fctx_WT5
frontal_metadata.tsv.gz
frontal_annotations.tsv.gz
frontal_umap.tsv.gz
frontal_filtered_feature_bc_matrix.h5
frontal_multiome_seurat.rds
fctx_WT5_fragments.tsv.gz
fctx_WT5_fragments.tsv.gz.tbi

value: wild-type


title: AML_OCI3_48h_DMSO_1_H3K36me3

description: Library name: AML_OCI3_48h_DMSO_1_H3K36me3


title: SW480, Tram, 24h, rep2

description: Library name: Tram_24h_rep2