title: Wild-type petal protoplasts, biol rep 2

city: Lyon

first: Marie

last: Monniaux

address: 46 allee d'Italie

institute: ENS de Lyon

description: Library name: wt_biol_rep_2

data_processing:
Read quality was checked with fastqc (0.12.1) and reads were aligned on the P. axillaris v1.6.2 transcriptome. CellRanger Count (7.0.1, 10X Genomics) was used to filter reads, count barcodes and UMIs, and generate the HDF5 matrix. The second WT replicate was split and sequenced in two technical replicates on the same Chromium chip, and read counts were aggregated with the Cell Ranger function aggr. Normalized gene expression, UMAP plots and cluster markers were computed with Seurat 5.1.0.
Assembly: P. axillaris v1.6.2 genome improved by HiC (https://www.dnazoo.org/assemblies/petunia_axillaris)
Supplementary files format and content: .ht5 files = HDF5 matrix output from CellRanger
Supplementary files format and content: .RData files = RData image files containing the Seurat object and associated environment after the full Seurat pipeline
Supplementary files format and content: .rds files = rds R objects containing the Seurat object atfer Harmony integration, for direct usage to explore gene expression

organism: Petunia x hybrida

source_name: petal (tube and limb)

growth_protocol: Plants were grown in a culture room in long day conditions (16h day at 22°C, 8h night at 18°C, 75-Valoya NS12 LED bars, light intensity: 130 μE, 60% humidity).

extract_protocol:
Protoplast isolation was performed in sterile conditions. WT, star and wico corollas (ca. 15, 30 and 30 flowers per replicate, respectively) were briefly soaked in 70% ethanol and in 0.5% bleach for 30’’ then rinsed 3 times with sterile water. Sterile corollas were transferred in a petri dish containing 2 mL of Digestion Mix (0.4% macerozyme R-10, 0.8% Cellulase Onozuka R-10, w/v in TEX Buffer (3.1 g/L Gamborg B5 salts, 500 mg/L MES, 750 mg/L CaCl2*2H2O, 250 mg/L NH4NO3, 136.9 g/L Sucrose, pH 5.7)) and cut in ca. 0.5 cm² pieces, using a new scalpel blade for each corolla to reduce tissue wounding. 10 mL of Digestion Mix were added and digestion was performed for 5 h at 26°C in the dark, with gentle orbital agitation (20 rpm) for the last 15’. After filtration through a 40 µm mesh, the volume was adjusted to 25 mL using 0.4 M Sucrose (492 mOsm.kg-1 H2O) and the mixture was centrifuged for 10’ at 100 g with acceleration 2/9 and deceleration 0/9 with a swing-out rotor. The underlying buffer was removed using a peristaltic pump (Gilson MINIPULS™ Evolution) connected to a sterile Pasteur pipette without perturbing the protoplast layer, at a rate of ca. 100 µL/sec. After adjusting again the volume to 25 mL using 0.4 M Sucrose, the whole process was repeated twice. Protoplast concentration and viability was assessed using a Kova slide and staining with 1% Evans Blue dye solution (w/v in 0.4 M Sucrose).
Protoplast suspensions were adjusted to 345, 480, 590 and 560 cells/µL with Mannitol-BSA (0.44 M Mannitol, 0.1 % BSA (w/v), 498 mOsm.kg-1 H2O) for WT (first replicate), star, wico and WT (second replicate) respectively. Protoplasts were loaded in the 10x Genomics Chromium chip and libraries were prepared using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) kit following manufacturer's instructions.

value: petal (tube and limb)

tag: cultivar

value: Wild-type


title: WT205-50A

status: Public on Nov 26 2025

type: SRA

city: Richland

first: Predictive Phenomics

last: Initiative

state: WA

address: 902 Battelle Boulevard

country: USA

institute: Pacific Northwest National Laboratory

description: Library name: sample 8

library_source: transcriptomic

data_processing:
Rsubread v2.16.1
Assembly: NC007604.1 (16-NOV-2022), NC_007595.1 (16-NOV-2022), NC_004990.1 (29-OCT-2022)
Supplementary files format and content: .csv counts

molecule: total RNA

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: axenic

growth_protocol: Synechococcus elongatus PCC 7942 CscB/SPS strain, engineered to overexpress sucrose phosphate synthase (SPS) and sucrose permease (CscB), was obtained from Dr. Daniel Ducat. Cultures were maintained in BG11 medium supplemented with chloramphenicol (12.5 mg L⁻¹) and kanamycin (25 mg L⁻¹). Standard growth conditions were maintained at 29±2°C with nitrogen gas sparging supplemented with 2% CO₂ under 200 μmol photons m⁻² s⁻¹ illumination from LED lights. Culture mixing was facilitated using PFTE Octagon Spinbar Magnetic Stirring Bars (9.5 mm x 25.4 mm) at 200 r.p.m. Antibiotics were removed prior to experimental procedures. During the experiment, continuous cultivation was performed in 6.5-L New Brunswick Bioflo 310 fermentors (Eppendorf, Inc.) equipped with custom LED photobioreactors. Steady-state cultures (5.5-L) were maintained in turbidostat mode at OD₇₃₀ of 0.08, with constant conditions of 250 rpm agitation, 30°C, and pH 8.0 (controlled by 2 M NaOH or HCl addition). Illumination was provided at 760 μmol photons m⁻² s⁻¹ using 630 and 680 nm narrow-band LED illuminator chips (Marubeni America Corporation). Photosynthetically active radiation (PAR, 400-700 nm) was monitored using three quantum sensors (LI-210SA, LI-COR Biosciences). Initial conditions utilized a baseline sparging rate of 2.04 L min⁻¹ with 98:2 N2/CO2 gas mixture. Oxidative stress was implemented through stepwise increases in O2 content while maintaining constant total gas flow and CO2 concentratio, with corresponding N₂ reduction. Dissolved O₂ was measured using a Clark-type electrode (InPro® 6800Series, Mettler Toledo). Turbidostat operation was maintained by correlating transmitted irradiance measurements with spectrophotometer-verified OD750 values to control medium addition and removal.

extract_protocol:
Total RNA was extracted using RNeasy kit with QiaShredder columns (QIAGEN). Cells were lysed in RLT buffer containing 1% β-mercaptoethanol, homogenized through QiaShredder, then processed following manufacturer's protocol with 70% ethanol addition.
Library construction and sequencing was done by Azenta Life Sciences. Two technical replicates were processed per condition. Samples underwent DNase treatment and rRNA depletion before paired-end sequencing (2x150bp, ~350M reads, ~105GB) with single indexing on Illumina platform.

treatment_protocol: To assess How S. elongatus calibrate response to oxidative stress and to evolve stress-adapted cell-lines the dissolved oxygen (oxidative stress level) was varied in culture by elevating oxygen content in sparged gas phase.  First, oxygen content was increased stepwise from 0 to 78% and RNA-seq samples were collected in order to assess the response of non-adapted S. elongatus PCC 7942 CscB/SPS strain (called WT for short). Highest stress level was followed by long recovery period without oxygen in gas phase maintained under turbidostate mode to select for highest growing cell lines. The cell line selected at the end of no oxygen recovery period was called adapted population 1 (AD1), sample of AD1 was collected for DNA extraction and resequencing. Second, we repeated the oxygen stress campaign by testing oxygen levels from 0% to 93% with collection of RNAseq data for stress response of AD1 population. Highest stress level was followed by long recovery period without oxygen in gas phase maintained under turbidostate mode to select for highest growing cell lines. The cell line selected at the end of no oxygen recovery period was called adapted population 2 (AD2), sample of AD2 was collected for DNA extraction and resequencing.  Third, the oxygen stress campaign was repeated again by increasing the oxygen content from 0 to 99.8% with collection of RNAseq data for stress response of AD2 population. Highest stress level was followed by recovery period without oxygen in gas phase maintained under turbidostate mode to select for highest growing cell lines. The cell line selected at the end of no oxygen recovery period was called adapted population 3 (AD3), sample of AD3 was collected for DNA extraction and resequencing.

tag: cell type

value: axenic

tag: genotype

value: cscB-sps

tag: treatment

value: WT high light 234% O2 air saturation


title: WT205-0A

description: Library name: sample 2

value: WT high light 0% O2 air saturation


title: wico petal protoplasts

country: France

description: Library name: wico

library_source: transcriptomic single cell

molecule: polyA RNA

tag: tissue

value: wico (epidermis wt / mesophyll mutant phdef)


title: Female slide F4 slice A2

type: RNA

city: Mountain View

first: Daniel

last: Berg

state: CA

address: 2005 California Street

institute: Stanford University

description: Resolve Biosciences Molecular Cartography technology was used to spatially resolve distinct cell populations by using 98 specific gene markers in amygdala of mouse brain.

data_processing:
Cell nuclei segmentation masks were obtained using the DAPI channel as input to Cellpose with diameter set to 65 and mask threshold -0.1. This mask was used as prior segmentation information to Baysor (confidence: 0.9; scale: 45; scale_sfd: 50%) to obtain final segmentation counts and cell metadata.
transcript per cell

label: fluorescence

organism: Mus musculus

source_name: amygdala brain tissue

label_protocol: Resolve Biosciences’ Molecular Cartography platform for labeling, hybridization, and imaging with 100-plex combinatorial single molecule fluorescence in-situ hybridization

extract_protocol: Mouse brain was dissected and right hemisphere immersed in OCT with cryo-mold in isopentane dry ice bath and stored at -80.  The frozen brains were sectioned into 10 μm coronal slices on a cryostat at -20°C.

value: amygdala brain tissue

tag: Sex

value: female

tag: bregma coordinate


title: WT100-0A

description: Library name: sample 1

value: WT medium light 0% O2 air saturation


title: ΔlexA ΔsidA_MMC_0_replicate1

city: Bengaluru

first: Anjana

last: Badrinarayanan

state: Karnataka

address: Bellary Road

country: India

institute: National Centre for Biological Sciences

description: Library name: ΔlexA ΔsidA_MMC_0_replicate1

data_processing:
Raw reads for the RNA-seq were obtained as fastq files. BWA was used in order to align the reads to the Caulobacter genome (accession number: NC_011916.1).
The aligned reads in .bam format were converted into a .bed file format using the bamtobed option of Bedtools. Coverage was further calculated using BEDTools. FPKM was further calculated for the samples from the read counts.
Assembly: NC_011916.1
Supplementary files format and content: csv file includes raw counts for all samples
Supplementary files format and content: csv file includes FPKM values for all samples

organism: Caulobacter vibrioides

source_name: Caulobacter crescentus CB15N

growth_protocol: Overnight cultures of Caulobacter grown in PYE media were diluted to 0.025 OD600 and grown for ~3 hours.

extract_protocol:
The samples were then centrifuged at 10000g for 5 minutes following which supernatant was discarded and the pellets were snap frozen and stored at -80°C until further processed. mRNA was isolated from the collected pellets. Pre-heated trizol (65°C) was added to each pellet and cells were lysed using a Thermomixer (65°C, 2000rpm, for 10 minutes). Total RNA was extracted from the lysed cells using the Direct-zol RNA MiniPrep kit. Any DNA contamination was then removed via DNAse treatment and  RNA was purified using RNA Clean & Concentrator-25 kit. Integrity of the total RNA was tested by the Tapestation instrument. Ribosomal RNA was then depleted using the Thermo RiboMinus kit. mRNA was purified using RNA Clean & Concentrator-5 kit and submitted for RNA-seq.
NEBNext Ultra II Directional RNA Library Prep kit was used for library preparation and samples were sequenced via the Illumina NovaSeq 6000 platform.

treatment_protocol: 3 hours post back-dilution, when OD600 reached ~0.1, 0.25 μg/mL MMC damage was introduced in to these cultures. Caulobacter cells were harvested (2mL/sample) for RNA-seq at 0, 20, 40 minutes post damage exposure.

value: exponential phase

value: CB15N; delta-lexA delta-sidA


title: ΔrecA_MMC_0_replicate1

description: Library name: ΔrecA_MMC_0_replicate1

value: CB15N; delta-recA


title: Growth-inhibiting (30%) - Replicate 4

city: Copenhagen

first: Christian

last: Anthon

address: Thorvaldsensvej 57

country: Denmark

institute: University of Copenhagen

description:
S16
CO2-30percent_Lane1-S16_CO2-adaptation

data_processing:
Read filtering with fastp (v0.2)
rRNA removal with SortMeRNA (v4.3.4)
Mapping with bowtie2 (v2.5.2)
Expression quantification with featureCounts (v2.0.6)
Assembly: ASM1948v1
Supplementary files format and content: tab delimited text file with raw expression counts
Supplementary files format and content: compressed fasta file of genome sequence
Supplementary files format and content: tab delimited text file of gene annotations

organism: Picosynechococcus sp. PCC 7002

growth_protocol: A+ medium at 30◦C

extract_protocol:
RNA extraction using PGTX reagent
Library preparation, rRNA depletion, and sequencing performed by Eurofins Germany

treatment_protocol: Variable CO2 aeration at 250micromol m-2s-1 photons at constant pH=7.5

tag: cell line

value: Growth-inhibiting (30%)


title: Growth-inhibiting (30%) - Replicate 3

description:
S15
CO2-30percent_Lane2-S15_CO2-adaptation


title: Wild-type petal protoplasts, biol rep 1

description: Library name: wt_biol_rep_1


title: ΔrecA_MMC_0_replicate2

description: Library name: ΔrecA_MMC_0_replicate2


title: Growth-inhibiting (30%) - Replicate 2

description:
S14
CO2-30percent_Lane1-S14_CO2-adaptation


title: SKL2001

city: Nantong

first: Man

last: Xu

address: No. 19 Qixiu Road

country: China

institute: Nantong University

description: Library name: Sample 2

data_processing:
raw FASTQ reads were first filtered with fastp (v0.22.0) to remove adapters and low-quality sequences, yielding clean data.
Clean reads were aligned to the reference genome with HISAT2 (v2.1.0). Gene-level read counts were quantified by HTSeq (v0.9.1) and normalized to FPKM.
Difference expression of genes was analyzed by DESeq (v1.38.3) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. Heat-map clustering of all DEGs was performed using the R package pheatmap (v1.0.12).
Assembly: GCF_001447785.1_Gekko_japonicus_V1.1_genomic.fna
Supplementary files format and content: txt includes raw counts for each sample

organism: Gekko japonicus

source_name: Blastema

growth_protocol: Blastema cells were maintained in DMEM/F12 containing 10% FBS, 2 mM glutamine  and penicillin-streptomycin-amphotericin solution in  humidified atmosphere with 5% CO2 at 30℃.

extract_protocol:
RNA was harvested using TRIzol Reagent (Vazyme). 1ug of totsl RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following manufacture's protocols.

value: Blastema

value: blastema cells


title: Growth-inhibiting (30%) - Replicate 1

description:
S13
CO2-30percent_Lane2-S13_CO2-adaptation


title: DMSO

description: Library name: Sample 1


title: ΔrecA_MMC_20_replicate2

description: Library name: ΔrecA_MMC_20_replicate2


title: NoSucrose_R1

city: Edinburgh

first: Katherine

last: Bexley

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description:
Library name: S3
col name in processed data S3

data_processing:
Raw sequencing reads were processed using Flexbar to remove Illumina adapters and low-quality bases. Reads less than 18nt or with quality threshold below 30 were discarded.
Trimmed and filtered reads were aligned to the S. cerevisiae transcriptome using Salmon, and the reads mapping to each transcript quantified.  For this, the GTF file alongside fasta files for genes, cDNAs, ncRNA were downloaded from Ensembl using genome version GCF_000146045.2_R64-1-1. These were input to the generateDecoyTranscriptome.sh Salmon script, producing a hybrid fasta containing the decoy sequences from the genome concatenated with the transcriptome. Indices for this decoy-aware transcriptome were then generated using the salmon indexer. The Salmon quant command was used to quantify the processed reads directly against this index.
Processed datasets were normalised in R in counts per million (CPM) and filtered using the edgeR package, applying the TMM method and ‘filterByExp’ function (threshold per sample: CPM > 15; threshold over all samples: CPM > 20)
Assembly: GCF_000146045.2_R64-1-1
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file contains RPM valuess for each sample

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were cultured at 30°C with constant shaking at 200 rpm in 2% synthetic complete (SC) 2% yeast nitrogen base medium supplemented with 2% sucrose. For all experiments, saturated overnight starter cultures were inoculated into fresh media at a starting OD600 of 0.05 and grown to exponential OD (0.45).

extract_protocol:
Cell pellets were re-suspended in TRIzol reagent supplemented with 5 mM DTT final,and lysed using a Fast Prep-24 machine (MP Biomedicals). RNA was cleaned twice with chloroform, treated with DNase I and purified using RNA Clean and Concentrator kit. Libraries were prepared from 500ng of each total-RNA.
Libraries were prepared  using the NEBNEXT Ultra II Directional RNA Library Prep kit (NEB #7760) and the Poly-A mRNA magnetic isolation module (NEB #E7490).  Poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads. Following purification the mRNA was fragmented using divalent cations under elevated temperature and primed with random hexamers. Primed RNA fragments were reverse transcribed into first strand cDNA using reverse transcriptase and random primers. RNA templates were removed and a replacement strand synthesised incorporating dUTP in place of dTTP to generate ds cDNA. The incorporation of dUTP in second strand synthesis quenches the second strand during amplification as the polymerase used in the assay is not incorporated past this nucleotide. AMPure XP beads (Beckman Coulter, #A63881) were then used to separate the ds cDNA from the second strand reaction mix, providing blunt-ended cDNA. A single 'A' nucleotide was added to the 3' ends of the blunt fragments to prevent them from ligating to another during the subsequent adapter ligation reaction, and a corresponding single 'T' nucleotide on the 3' end of the adapter provided a complementary overhang for ligating the adapter to the fragment. Adapter-ligated DNA was then purified with AMPure XP beads before 10 cycles of PCR with unique dual index sequences were used to selectively enrich DNA fragments with adapter sequences and allow multiplexed sequencing. After amplification libraries were purified using AMPure XP beads. Final libraries had an average fragment size of Xbp including index and adapter sequences.

treatment_protocol: Sucrose  grown cells were harvested directly from supplemented media. For NoSucrose, cells were collected by filtration on a nitrocellulose membrane and transferred to fresh medium. This medium contained 2% glycerol and 2% ethanol.

value: WT

value: NoSucrose


title: Optimal growth (8%) - Replicate 4

description:
S12
CO2-8percent_Lane1-S12_CO2-adaptation

value: Optimal growth (8%)


title: CD34_FCD-KO

city: Augusta

first: Sergei

last: Bombin

institute: Augusta University

description:
Library name: Sample #2
10x genomics

data_processing:
Raw sequencing data were processed using Cell Ranger v8.0.0, which aligned reads to the GRCh38-2024-A reference human transcriptome and generated filtered feature-barcode matrices. Downstream analyses were performed in R using the Seurat v5.0.1 package ( Hao et al., 2021). Low-quality cells were excluded based on the following criteria: fewer than 1000 unique molecular identifiers (UMIs), fewer than 500 detected genes (features), counts exceeding the median plus 3 times the median absolute deviation (MAD) for either UMIs or features, or >15% mitochondrial UMI content. Putative doublets were identified and removed using DoubletFinder v2.0.3 (McGinnis et al., 2019). Gene expression normalization and variance stabilization were performed using SCTransform (Hafemeister and Satija, 2019). Samples from different treatment groups were integrated for clustering Seurat's reciprocal principal component analysis (RPCA) approach. Dimensionality reduction and clustering were carried out using RunPCA, FindNeighbors, and FindClusters functions with the first 55 principal components and a clustering resolution parameter set to 0.2. with the clustree v0.5.1 package. Nonlinear dimensionality reduction was performed using t-distributed stochastic neighbor embedding (t-SNE) via the RunTSNE function. Cluster-specific marker genes were identified through differential gene expression analysis using FindAllMarkers with the default Wilcoxon rank-sum test
Assembly: GRCh38
Supplementary files format and content: cellranger filtered matrix

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: CD34+ stem cells purchased from the Fred Hutchinson Cancer Research Center (Seattle, WA) were cultured in a 2-Phase liquid culture system

extract_protocol:
Day 10 cultured CD34 cells were washed with PBS and viability was determined to be more than 95% by MTT assay. The cell differentiation was determined to Giemsa stain and normal maturation with a CD71/CD235a ratio of 95%.
Library was constrcuted by Active Motif using 10x Genomics assay. Briefly, CD34 single-cell GEMs (Gel Beads in Emulsion) were generated on the Chromium Controller, followed by GEM-RT, Dyna Beads cleanup, cDNA amplification and SPRIselect beads cleanup. The Library Bead Kit and Chromium i7 Multiplex Kit was used for generating indexed single-cell libraries for Illumina sequencing. Quality, purity, size and concentrations of cDNA and libraries were determined by Tapestation 2000 (Agilent Technologies, Inc). Libraries were sequenced using the Next-Seq 500 sequencing platform.

value: Peripheral blood

value: erythroid progenitors

value: erythroid


title: Capture Hi-C IGCR1-/- rep2

city: Baltimore

first: Noah

last: Ollikainen

address: 251 Bayview Blvd.

institute: National Institutes of Health

description:
Library name: 2-IGCR1-128-2_S2
Capture Hi-C of Igh locus

library_source: genomic

data_processing:
Capture Hi-C reads were processed using Juicer version 1.6 (parameters -g mm10 -s Arima) to generate .hic files. Duplicate reads and reads with a mapq score below 30 were removed prior to .hic file generation.
Assembly: mm10
Supplementary files format and content: .hic format

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: Pro-B cell lines were grown with complete 1640 RPMI medium (10% fetal bovine serum and 0.05mM 2-Mercaptoethanol)

extract_protocol:
Capture Hi-C was performed using the Arima Hi-C Kit (Arima Genomics, Inc.; Cat # A510008), following the manufacturer’s protocol with strict adherence to the provided instructions. To enrich the Igh locus (chr12: 113,201,001 – 116,030,000 in mm10), SureSelect Target Enrichment probes with 2× tiling density were designed and manufactured by Agilent (Agilent Technologies Inc.). Hi-C libraries were hybridized to probes as specified by the manufacturer (Agilent Technologies Inc., G9916B).
Capture Hi-C libraries were prepared for sequencing using standard protcols. Libraries were sequenced using Illumina NextSeq sequencer to generate paired-end 150-bp reads.

treatment_protocol: No treatment

value: Bone marrow

value: Pro-B cell line

value: No treatment


title: Capture Hi-C IGCR1-/- rep1

description:
Library name: 1-IGCR1-128-1_S1
Capture Hi-C of Igh locus


title: CD34_AAV

description:
Library name: Sample #1
10x genomics


title: star petal protoplasts

description: Library name: star

value: petal (tube and limb)

value: star (epidermis mutant phdef / mesophyll wt)


title: NoSucrose_R2

description:
Library name: S6
col name in processed data S6


title: Huh7_sorafenib_Input

city: Seoul

first: Sunyoung

last: Jang

state: Not required for this country

address: Cheongpa-ro 47-gil 100 (Cheongpa-dong 2ga), Yongsan-gu, Seoul

country: South Korea

institute: Sookmyung Women's University

data_processing:
The reads in ChIP-seq were trimmed of the adapter sequences and low-quality reads using Cutadapt (version 4.1). The reads were then aligned to the human reference genome by Bowtie2 (version 2.4.2), and duplicate reads were removed from the mapped reads using Picard tools. Index generation was performed by Samtools. HOMER (version 4.11) was used to identify target protein binding sites and generate bedGraph files for visualization.
Assembly: hg19
Supplementary files format and content: bedGraph.gz

source_name: Liver

growth_protocol: Hep3B cells were maintained in DMEM containing 10% FBS and 1% penicillin-streptomycin. Huh7 cells were maintained in RPMI containing 10% FBS and 1% penicillin-streptomycin. Cells were grown in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Cells were crosslinked by incubating with 1% formaldehyde (Merck, F8775) for 10 minutes at 37°C, after which the reaction was quenched by adding glycine (final concentration, 0.125 M). Crosslinked cells were scraped out with filtered Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40) supplemented with protease inhibitor (ROCHE, 25530-049) and phenylmethylsulfonyl fluoride (PMSF) (Merck, P7626), then incubated on ice for 10 minutes. Crosslinked cells were subsequently lysed in filtered 1x RIPA buffer (10 mM Tris pH7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-DOC, 1% Triton X-100 ) containing protease inhibitor and PMSF, then sonicated to achieve a chromatin fragment size range of 200-500 bp. The sonicated chromatin was immunoprecipitated with anti-H3K4me3 (Millipore, 17-614), anti-H3K27ac (Abcam, ab4729), anti-pSTAT3 (Cell Signaling, 9145), anti-CTCF (Cell Signaling, 2899), anti-SMC1 (Bethyl Laboratories, A300-055A) and anti-SMC3 (Abcam, ab9263) antibodies, and the resulting ChIP DNA was captured by incubating with protein A and protein G Dynabeads (1:1 mix) at 4°C overnight with rotation. Dynabead protein-antibody complexes were subsequently washed with filtered low-stringency wash buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-DOC, 1% Triton X-100 ), high-stringency wash buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-DOC, 1% Triton X-100, 300 mM NaCl) and LiCl wash buffer (50 mM Tris pH 7.5, 250 mM LiCl, 0.5% NP-40, 0.5% Na-DOC), followed by two washes with 1x PBS. ChIP DNA was reverse-crosslinked and purified for DNA library construction using a MinElute PCR Purification kit (Qiagen, 28004). ChIP-seq libraries were constructed and sequenced using a HiSeq 2500 system and NextSeq 500 (Illumina).

treatment_protocol: Cells were treated with IL-6 (100ng/mL) for 24h. Cells treated with UltraPure distilled water served as control. Cells were also treated with IL-6 (100ng/mL) for 24h and/or sorafenib (10 μM) for 24h. Cells treated with DMSO served as control.

value: Liver

value: Hepatocellular carcinoma tumor

tag: chip antibody

value: none, 100ng/mL IL-6, 10μM sorafenib


title: Optimal growth (8%) - Replicate 2

description:
S10
CO2-8percent_Lane2-S10_CO2-adaptation


title: Optimal growth (8%) - Replicate 3

description:
S11
CO2-8percent_Lane2-S11_CO2-adaptation


title: Sucrose_R1

description:
Library name: S1
col name in processed data S1

value: Sucrose


title: Sucrose_R3

description:
Library name: S7
col name in processed data S7


title: Sucrose_R2

description:
Library name: S4
col name in processed data S4


title: Optimal growth (4%) - Replicate 4

description:
S8
CO2-4percent_Lane2-S8_CO2-adaptation

value: Optimal growth (4%)


title: Hep3B_sorafenib_Input


title: Optimal growth (8%) - Replicate 1

description:
S9
CO2-8percent_Lane2-S9_CO2-adaptation


title: NoSucrose_R3

description:
Library name: S9
col name in processed data S9


title: gamma-delta T cells from healthy donor 3, venetoclax-treated

city: hefei

first: Xing

middle: chi

last: Chen

state: Anhui

address: No. 9, Lujiang Road, Luyang District, Hefei City

institute: University of science and technology of China

description: Library name: Donor3_gamma_deltaT_ven

data_processing:
Raw paired-end FASTQ files were quality-checked and filtered using fastp to remove adapter-containing reads, reads with >0.1% unknown bases, and low-quality reads (reads with >20% bases having quality score <15). The resulting clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 (v2.x) with default parameters. Alignment quality was assessed by overall alignment rate and read distribution. Aligned reads were further mapped to the reference gene set using Bowtie2 (v2.3.4.3), and gene expression quantification was performed with RSEM (v1.3.1) to obtain expected counts and FPKM values. Differential gene expression analysis between conditions (venetoclax-treated vs untreated gamma-delta T cells) was performed using DESeq2 (v1.4.5) with thresholds of FDR ≤ 0.05 (Benjamini–Hochberg correction). Hierarchical clustering and heatmaps were generated with the pheatmap (v1.0.8) R package. Functional enrichment analyses were conducted using GO and KEGG databases, with significance defined as Q ≤ 0.05 using the hypergeometric test (phyper in R).
Assembly: Homo sapiens, GRCh38 (hg38)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files incluse counts and FPKM values for each sample

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were used to derive gamma-delta T cells. αβ T cells were removed using anti-TCRαβ magnetic beads to enrich gamma-delta T cells. Enriched cells were stimulated with zoledronic acid (5 μM) for 72 h to expand Vγ9Vδ2 gamma-delta T cells. Cells were cultured in RPMI-1640 + 10% FBS + IL-2 (100 IU/mL) at 37 °C, 5% CO₂ (optional: +1% penicillin/streptomycin). Medium and IL-2 were replenished every 2–3 days to maintain 0.5–2×10⁶ cells/mL.

extract_protocol:
Total RNA was extracted from PBMC-derived gamma-delta T cells using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer’s protocol. RNA integrity was assessed using an Agilent 2100 Bioanalyzer, and only samples with RIN ≥ 7 were used for library preparation.
mRNA was enriched from total RNA using oligo(dT)-attached magnetic beads. The enriched poly(A) RNA was fragmented using fragmentation buffer, and first-strand cDNA was synthesized with random hexamer primers, followed by second-strand synthesis to obtain double-stranded cDNA. The double-stranded DNA was end-repaired and 5′-phosphorylated, with a 3′-A overhang added. A bubble-shaped adapter with a 3′-T overhang was ligated to the fragments, and ligation products were PCR-amplified with specific primers. The PCR products were denatured into single strands, and single-stranded circular DNA libraries were generated using a bridging primer. Final libraries were quality-checked and sequenced once they passed QC

treatment_protocol: venetoclax(1μM) pretreatment 18h

tag: subject status

value: healthy donor

value: gamma-delta T cell

value: venetoclax (1 μM, 18 h)

tag: batch


title: XND-LC-3

city: Bethesda

first: WeiPing

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

description: LC is low concentration RNA sample.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were normalized by RMA with Partek Genomic Suite 6.6.

label: Biotin

organism: Caenorhabditis elegans

source_name: XND-LC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mRNA is converted to cDNA and amplified using NuGEN pico amplification kit.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: L2-L3 stage whole animals were used as a source for RNA.

tag: strain/background

tag: genotype/variation

value: xnd-1 mutant

tag: developmental stage

value: whole body


title: XND-LC-1

description: LC is low concentration RNA sample.


title: N2-3

description: N2 is the control strain.

value: wild-type


title: XND-HC-1

description: HC is high concentration RNA sample.

source_name: XND-HC


title: N2-2

description: N2 is the control strain.


title: Optimal growth (4%) - Replicate 3

description:
S7
CO2-4percent_Lane1-S7_CO2-adaptation


title: XND-HC-4

description: HC is high concentration RNA sample.


title: Huh7_Input

value: none, 100ng/mL IL-6


title: gamma-delta T cells from healthy donor 3, untreated

description: Library name: Donor3_gamma_deltaT

value: Peripheral blood

value: none; untreated


title: gamma-delta T cells from healthy donor 2, venetoclax-treated

description: Library name: Donor2_gamma_deltaT_ven


title: Air CO2 exposure (0.04%) - Replicate 4

description:
S4
CO2-0-04percent_Lane2-S4_CO2-adaptation

value: Air CO2 exposure (0.04%)


title: Optimal growth (4%) - Replicate 1

description:
S5
CO2-4percent_Lane2-S5_CO2-adaptation


title: ANAPC1P2 KD in OVCAR3 cells Set 3

city: Pune

first: Dr. Sharmila

middle: A

last: Bapat

state: Maharashtra

address: NCCS campus, SPPU, Ganeshkhind road.

institute: National Centre for Cell Science

description: Library name: Sample 3

data_processing:
The paired-end reads are aligned to the reference human genome (hg38). Alignment was performed using STAR (2.4).
The aligned reads are used for estimating expression of the genes. The raw read counts were estimated using FeatureCount (1.5.2). Read count data were normalized using DESeq2.
Assembly: human genome (hg38)
Supplementary files format and content: csv files contain normalized read counts for each sample.

source_name: Ovarian

growth_protocol: OVCAR3_KD and OVCAR3 WT cells were grown in RPMI+10% FBS. All cell lines were maintained in a humidified incubator at 37°C under 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Cat# 74104). 3-4 ug Total RNA was used for the analysis.
A modified NEBNext RNA Ultra II directional protocol is used to prepare the libraries for total RNA sequencing

value: Ovarian

value: Ovarian cancer cells

value: OVCAR3 ANAPC1P2 KD


title: Hep3B_Input

value: Liver

value: Hepatocellular carcinoma tumor


title: ANAPC1P2 KD in OVCAR3 cells Set 1

description: Library name: Sample 1


title: Optimal growth (4%) - Replicate 2

description:
S6
CO2-4percent_Lane1-S6_CO2-adaptation


title: ANAPC1P2 KD in OVCAR3 cells Set 2

description: Library name: Sample 2


title: gamma-delta T cells from healthy donor 2, untreated

description: Library name: Donor2_gamma_deltaT


title: gamma-delta T cells from healthy donor 1, venetoclax-treated

description: Library name: Donor1_gamma_deltaT_ven


title: Air CO2 exposure (0.04%) - Replicate 3

description:
S3
CO2-0-04percent_Lane2-S3_CO2-adaptation


title: Huh7pIL6_sorafenib_H3K27ac

value: H3K27ac (Abcam, ab4729)

value: 100ng/mL IL-6, 10μM sorafenib


title: gamma-delta T cells from healthy donor 1, untreated

description: Library name: Donor1_gamma_deltaT

value: healthy donor


title: rhESC-LYON1-WGS

city: Paris

first: Claire

last: Rougeulle

address: 35 rue Hélène Brion

institute: Université Paris Cité

data_processing:
Reads were trimmed using trim_galore (v0.6.5) with a minimum length of 50 bp.
Reads were then mapped to the rhesus macaque genome (rheMac10) or to the marmoset genome (calJac4) using BWA-MEM 0.7.17 (Li et al 2013) with the default parameters
Aligned reads pre-processing and variant calling were performed by following the Genome Analysis Tool Kit (GATK) Best Practices for short germline variant discovery pipeline.
Variant calling was performed using GATK HaplotypeCaller with --stand-cal-conf=10, Single Nucleotide Variants (SNV) were selected using GATK SelectVariants. The vcf were then filtered with stringent parameters to avoid false positive in SNP calling with VariantFiltration: -FS>60.0 -QD<6.0 -SOR>3.0 -MQ<50.0 -MQRankSum<-12.5 -MQPosRankSum<-8.0  -DP<10.
Assembly: rheMac10, calJac4
Supplementary files format and content: vcf, tab

organism: Macaca mulatta

extract_protocol:
Genomic DNA from 5x10⁶ rhESC and maESC were extracted using the DNeasy Blood and Tissue kit following the manufacturer instructions.
WGS libraries were prepared by the Institut Curie Next Generation Sequencing Core Facility using the KAPA Hyper Prep PCR-free Library Kit according to manufacturer’s instructions and sequenced on an Illumina HiSeq 2500 (PE100)
Whole Genome Sequencing

value: rhesus macaque embryonic stem cell


title: Hep3BpIL6_sorafenib_H3K27ac


title: N2-1

description: N2 is the control strain.


title: Air CO2 exposure (0.04%) - Replicate 2

description:
S2
CO2-0-04percent_Lane2-S2_CO2-adaptation


title: Huh7pIL6_sorafenib_pSTAT3

value: p-STAT3 (Cell Signaling, #9145)


title: rhESC_Primed,IgG,Rep2

data_processing:
Reads were trimmed using trim_galore (v0.6.5) with a minimum length of 50 bp.
Reads were then mapped to the rhesus macaque genome (rheMac10) or to the human genome (hg38) using bowtie 2 (Langmead and Salzberg 2012) with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -L 10 -X 700.
Reads were then deduplicated using MarkDuplicates from picard (v2.23.5) with the following options: --CREATE_INDEX=true --VALIDATION_STRINGENCY=SILENT --REMOVE_DUPLICATES=true --ASSUME_SORTED=true.
BigWig track files were generated with bamCoverage from deeptools (v3.5.0) using the following parameters: --normalizeUsing BPM --binSize 20 --smoothLength 40. normalizeUsing "BPM" --binSize 20 --smoothLength 40.
Assembly: rheMac10, hg38
Supplementary files format and content: bigWig
Library strategy: Cut & Run

extract_protocol:
Digested chromatin was treated with proteinase K and  eluted using phenol chloroform extraction as described in Skene et al.,2017.
High-throughput sequencing libraries were constructed using the TruSeq ChIP Library Preparation Kit according to the manufacturer’s recommendation. Paired-end sequencing was done on the Illumina NovaSeq 6000  with a read length of 100 bp.


title: Huh7nIL6_sorafenib_H3K27ac

value: none, 10μM sorafenib


title: Huh7nIL6_sorafenib_pSTAT3


title: rhESC_Primed,IgG,Rep1


title: 10-IVF_T

city: Jouy-en-Josas

first: Alice

last: Jouneau

address: Domaine de vilvert

institute: INRAE

description: Library name: Sample 10

data_processing:
Single-end sequences (50 to 85 bp, using 50-bp sequencing kits) were generated using Illumina Next-seq 2000 instruments. After trimming Illumina adapter sequences with cutadapt using options -b CTGTCTCTTAT A–minimum-length=1, reads were split in UMI-containing or not with Julia (Bezanson et al, 2017 doi: 10.1137/141000671), trimming 11 bp after the sequence “AAGCAGTGGTATCAACGCAGAGTACGATC” (see the “FLASH-seq” section above). For UMI, reads were further processed in Julia to remove the invariant adapter sequence, extract the identifier, and the UMI/ transcript sequence pairs used to remove duplicates. For our samples, the fraction of unique reads ranged between 69 and 90%. Conventional and UMI reads were mapped to the transcriptome reference genome (Ens113, EquCab3.0) using STAR (v2.7.10b). Tables of counts were generated with featureCounts (v1.6.0). Analysis of differential expression was made using the DESeq2 package (v1.28.1) (Anders & Huber, 2010).
Assembly: Ensembl113 Equus_caballus.EquCab3.0
Supplementary files format and content: FASTQ

organism: Equus caballus

source_name: Embryo

extract_protocol:
Extraction and library preparation were performed in one reaction
Library preparation was made according to Festuccia et al, 2024 (doi: 10.1126/science.adg7325), based on the FLASH-seq method (doi.org/10.1038/s41587-022-01312-3). Embryos were lysed in 5 µl of the a solution containing: 0.1 μl Triton X-100 (10% v/v, Sigma-Aldrich, T8787), 2 μl dNTP mix (25 mM each, ThermoFisher Scientific, R1121), 0.46 μl 5’Bio-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, 100 μM (supplied by IDT), 0.46 μl 5’ Biotin-AGTGGTATCAACGCAGAGTACGATCNNNNNNNNrGrGrG-3′Phospate, 100 μM (supplied by IDT),  0.15 μl recombinant RNase Inhibitor (40 U/μL, ThermoFisher Scientific, AM2684), 0.06 μl Dithiothreitol (DTT, 100 mM; part of the Superscript IV kit, ThermoFisher Scientific, 18091050), 1 μl betaine (5M, Sigma-Aldrich, 61962-50G), 0.45 μl dCTP (100 mM, Sigma-Aldrich, DNTP100), water to 5 μL final. After incubating at 3 min at 72°C in a thermocycler, and transferring on ice,  RT-PCR was performed by adding 20 μl of the following mix to each sample: 1.19 μl Dithiothreitol (DTT, 100 mM; part of the Superscript IV kit, ThermoFisher Scientific, 18091050), 4 μl betaine (5M, Sigma-Aldrich, 61962-50G), 0.23 μl magnesium chloride (1 M, ThermoFisher Scientific, AM9530G), 0.48 μl recombinant RNase Inhibitor (40 U/μl, ThermoFisher Scientific, AM2684), 0.25 μl Superscript IV Reverse Transcriptase (200 U/μl, ThermoFisher Scientific, 18091050), 12.5 μl KAPA HiFi Hot-Start ReadyMix (2x, Roche; cat. KK2502), water to a final volume of 20 μl. Samples were then incubated 60 min at 50°C and 3 min at 90°C. Tubes were then transferred on ice and 0.5μl of a 100 μM solution of amplification primer (TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGAAGCAGTGGTATCAACGCAGAGTACG) were added to each sample. Tubes were then incubated 20 sec at 98°C, 20 sec at 64°C, 6 min at 72°C, followed by 20 cycles of 20 sec 98°C, 20 sec 67°C, 6 min 72°C, adding 12 seconds to the extension time at each amplification cycle. Amplification products were purified using 1x volume of SPRI magnetic beads, and eluted in 15 µl of water. Fragment size distribution was checked on a Genomic DNA Screentpape (Agilent Technologies, 5067-5365/6), with typical lengths ranging from less than 1 kb to more than 10 kb. For tagmentation, each sample was diluted to 150 pg/µl. 2 μl of diluted cDNA was mixed with 2μl of Amplicon Tagment Mix (ATM) and 4 μl of Tagment DNA Buffer (TD) from a Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024), and incubated for 8 min at 55°C. Tn5 was released from DNA by adding 2 μL of Neutralization Buffer (NT), followed by a 5 min RT. Enrichment of UMI containing fragments and subsequent library amplification was performed by adding 13 μL of KAPA HiFi Hot-Start ReadyMix (2x, Roche; cat. KK2502) and 1 µl of 5 µM amplification primer (sequence as above). Tubes were incubated at 72°C for 3 min and 95°C for 30 sec. This was followed by 7 cycles of linear enrichment PCR: 95°C for 10 sec, 61°C for 30 sec, 72°C for 30 sec. Samples were transferred on ice and 4 µl of a 2.5 µM solution of each of the following primers were added on ice: Universal primer, AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, Indexed primer CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG. The 8 Ns represent the Illumina index sequence of choice. Tubes were then subjected to 14 iterations of the cycle: 95°C for 10 sec, 55°C for 30 sec, 72°C for 30 sec. This was followed by 72°C for 5 min. Amplification products were purified using 1x volume of SPRI magnetic beads, eluting in 30 µl water. Fragment size distribution was checked on a DNA Hi Sensitivity D1000 HS Screentape (Agilent Technologies, 5067-5584/5).

value: Embryo

value: IVF


title: Hep3BnIL6_sorafenib_H3K27ac


title: DMM01231

city: Manila

first: Jana Victoria

last: San Pedro

state: Manila

address: 623 Pedro Gil St.

department: Institute of Human Genetics

country: Philippines

hyb_protocol: The samples were processed according to the manufacturer's instructions/protocol using the Affymetrix Human Clariom S Assay providing coverage of 21,448 well-annotated genes, through the use of GeneChip Cartridge Arrays (Affymetrix/Thermo Fisher Scientific).

scan_protocol: The samples were scanned on the GeneChip Scanner 3000 (Affymetrix/Thermo Fisher Scientific).

data_processing: Acquisition of raw gene expression data and initial pre-processing was done via Transcriptome Analysis Console (TAC) version 4.0.1.  All subsequent data processing and integration procedures were performed using R statistical programming language (version 3.5.1) and was done independently for each case-control study (i.e. T2DM, PAD, CAD, Ret, CVD, Neph). To ensure uniformity of raw data pre-processing procedures between the two different platforms for each analysis, raw gene expression values from the Illumina platform were forced to be positive through an offset via the lumi package, subjected to quantile normalization using the preprocessCore package and log-transformed via the Biobase package and R default functions. Collapsing of probes with multiple gene targets and inter-platform normalization (i.e. removal of batch effects and preservation of variance due to affliction through designated “Batch” and “Affliction” parameter values for each sample) were performed using WGCNA and the linear models for microarray data (limma) packages.

source_name: blood

label_protocol: Samples were labelled according to patient ID number and title of study (i.e., in this case, the study is about diabetes mellitus (DM) so for the first patient, the given label was DM00001, the second patient was DM00002, so on and so forth).

extract_protocol: Four (4) mL of whole blood were collected from participants upon recruitment and stored in ethylenediamine tetra acetic acid (EDTA) -containing blood tubes. The blood tubes were kept in ice-cold containers for transport. Within 2 hours of blood collection, peripheral blood mononuclear cells (PBMCs) were isolated from whole blood through Ficoll density gradient centrifugation using Lymphoprep (Stemcell Technologies, Vancouver, Canada). Isolated PBMCs were temporarily stored at -80°C until RNA extraction. Total RNA was extracted from the PBMCs using QIAamp RNA Blood Mini Kit (Qiagen, Hilden, Germany) following manufacturer’s instructions. Quantification and OD260/280 determination of total RNA from PBMCs were performed using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Quality of the total RNA in terms of RNA Integrity Number (RIN) were analyzed on the 2200 TapeStation (Agilent Technologies, Santa Clara, CA) system using the TapeStation RNA analysis kits. RNA samples of good quantity (≥ 50ng/uL) and quality (RIN ≥ 3.5) were stored at -80°C until further use.

tag: age

tag: gender

value: Female

tag: sample group

value: Healthy

tag: comorbidity


title: 9-ICSI_T

description: Library name: Sample 9

value: ICSI


title: rhESC_Primed,CTCF,Rep1

tag: cell type


title: OVCAR3 WT

description: Library name: Sample 4

tag: genotype


title: rhESC_Primed,CTCF,Rep2


title: rhESC_Primed,H3K27ac,Rep2


title: DMM01593


title: Hep3BnIL6_sorafenib_pSTAT3

tag: treatment


title: Huh7nIL6_H3K27ac_rep2

tag: tissue


title: Huh7pIL6_H3K27ac_rep2

value: 100ng/mL IL-6


title: 8-IVF_V

description: Library name: Sample 8


title: DMM01225


title: DMM01236

value: Male


title: DMM01232


title: Air CO2 exposure (0.04%) - Replicate 1

description:
S1
CO2-0-04percent_Lane1-S1_CO2-adaptation

value: Air CO2 exposure (0.04%)


title: 5-ICSI_V

description: Library name: Sample 5


title: 6-IVF_V

description: Library name: Sample 6


title: rhESC_Primed,H3K27ac,Rep1


title: Hep3BpIL6_sorafenib_pSTAT3


title: 4-ICSI_V

description: Library name: Sample 4


title: DMM01028


title: rhESC_Primed,H3K4me1,Rep1


title: 7-IVF_V

description: Library name: Sample 7


title: DMM01027


title: Huh7pIL6_pSTAT3_rep3


title: 3-ICSI_V

description: Library name: Sample 3


title: Hep3BnIL6_H3K27ac_rep2


title: XND-LC-4

description: LC is low concentration RNA sample.

value: xnd-1 mutant

value: whole body


title: rhESC_Primed,H3K4me3,Rep2


title: rhESC_Primed,H3K4me3,Rep1


title: rhES,ATAC

data_processing:
ATAC-seq raw data was processed using the atacseq pipeline (v1.2.1) (https://github.com/nf-core/atacseq/) from nf-core using the default parameters
Adapter trimming using Trim Galore
Reads were aligned using BWA aligner
Duplicates were marked by picard
bigWig tracks were generated by BEDTools.
Assembly: rheMac10
Supplementary files format and content: bigWig

extract_protocol:
DNA was extracted using the MinElute PCR purification kit (QIAGEN).
Transposed DNA were pre-amplified for 5 cycles. The required number of additional cycles for each sample was determined by qPCR as described (Buenrostro et al., 2015). After the final amplification, double-sided bead purification was performed with AMPure XP beads.


title: Huh7pIL6_pSTAT3_rep2

value: Liver

value: Hepatocellular carcinoma tumor


title: 2-IVF_R

description: Library name: Sample 2


title: DMM01047


title: 1-ICSI_R

description: Library name: Sample 1


title: DMM00270

value: DMnoCAD

value: with no CAD


title: Huh7nIL6_pSTAT3_rep3


title: Root,HA2, rep3

city: Yangzhou

first: Yong

address: 88 South Daxue Road

institute: Yangzhou University

description:
Library name: HA2-3
RNA-seq analysis.Transcriptome libraries were constructed and sequenced in PE150 mode using the Illumina NovaSeq6000 platform. The sequencing was performed by Biomarker Technologies. Data analysis was conducted using the Biocloud platform (http://www.biocloud.net/, accessed on 20 January 2025)

data_processing:
The libraries were then sequenced on an Illumina platform to generate paired-end reads. High-quality clean reads were obtained after filtering raw data. Reads with a perfect match or a single mismatch were further analyzed and annotated using the R. rugosa reference genome (https://www.rosaceae.org/). Gene expres sion was quantified using FPKM (fragments per kilobase of transcript per million mapped fragments).
Data analysis was performed using BMKCloud (www.biocloud.net)
Assembly: Rosa rugosa
Supplementary files format and content: The csv file include FPKM values for all Samples

organism: Rosa rugosa

source_name: Root

growth_protocol: R. rugosa plants with uniform growth were selected and cultivated in pots within a greenhouse. Rose plants were watered once a week with Hoagland's nutrient solution, 200 ml per pot, for 37 weeks.

extract_protocol:
RNA was extracted using the RNAprep Pure Plant Kit (Tiangen, Beijing, China) and assessed using the RNA Nano 6000 Assay Kit on the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were prepared using the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) and sequenced on the Illumina NovaSeq 6000 platform by Biomarker Technologies. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was per formed with divalent cations in NEBNext First Strand Synthesis Reaction Buffer (5X). First-strand cDNA synthesis was carried out with random hexamer primers and M-MuLV Reverse Transcriptase, followed by ond strand cDNA synthesis using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease and polymerase activity. cDNA fragments (~240 bp) were purified using the AMPure XP system (Beckman Coulter, Beverly, USA). PCR cation was performed with Phusion High-Fidelity DNA Polymerase, and PCR products were purified again with the AMPure XP system. Library quality was assessed with the Agilent Bioanalyzer 2100 system. Index- coded samples were clustered on a cBot Cluster Generation System with the TruSeq PE Cluster Kit v4-cBot-HS (Illumina).

treatment_protocol: The rose plants were divided into three groups and underwent a sand culture experiment with combined applications of HA and P fertilizer. Rose plants were watered once a week with Hoagland's nutrient solution, 200 ml per pot, for 37 weeks. The composition of Hoagland's nutrient solution is shown in Table S1. The three experimental groups were categorized based on the P content in Hoagland's nutrient solution and the proportion of P replaced by HA. The control group (CK) received 100% P (0.092 g NH4H2PO4). The HA1 group received 60% P + HA (0.0552 g NH4H2PO4 + 0.0368 g HA, equivalent to 40% P). The HA2 group received 40% P + HA (0.0368 g NH4H2PO4 + 0.0552 g HA, equivalent to 60% P).

value: Root

value: Zizhi


title: rhESC_Primed_delHERVK,cHiC,Rep1

description:
rhES_E9.9_ontarget.XIConly.q23.cool
rhES_E9.9_min12000_max48000_step8000_bin4000_score.bw

data_processing:
Sequencing reads from both technical replicates were processed using the HiC-pro pipeline (Servant 2015), including, reads alignement on the human reference genome (hg38, mapping quality > 23) and valid interaction pairs detection. Raw contact matrices were built by binning in genomic windows of 2kb, 4kb, 6kb, 8kb and 10kb, using the allValidPairs2cooler.sh utility. Correlation analysis between the raw contact matrices of both replicates was done using the hicCorrelate package from the HiCExplorer toolbox (Wolff 2020). The 4kb binning was retained for the very good correlation score (R²=0,67) and the contact matrices of both replicates were merged. The raw contact interaction frequencies of the captured region were normalized using the Iterrative Correction approach (Imakaev 2012). Insulation score was computed on the normalized contact matrice using the hicFindTads package (Wolff 2020) with –minDepth 12000 –maxDepth 48000 –step 8000. Viewpoints data were extracted using the chicViewpoint package (Wolff 2020) with default parameters. Chromatin loops were called on ICE normalized contact matrices using the mustache software with default parameters (Ardakany 2020), non-significant loop interactions (FDR p.value < 0,05) were filtered before downstream analysis.
Assembly: rheMac10, panTro6
Supplementary files format and content: cool file containing the raw and the ICE normalized interaction frequency values binned at 4kb
Supplementary files format and content: Bigwig files for insulation score
Library strategy: Capture Hi-C

extract_protocol:
In situ Capture HiC was performed as previously published (Davies 2016) with the following modifications. Cells were crosslinked with 2% formaldehyde. In short, 10x10⁶ cells were lysed on ice in 10 mM Tris-HCL pH8.0, 10 mM NaCl, 0,2% NP40, 1X complete protease inhibitor cocktail (Roche). De-crosslinking was performed in 100 µL 0,5% SDS at 37°C for 1h under agitation (1400 rpm). Nuclei permeabilization was done by adding 50 µL of 10% Triton X-100 and 290µL H2O and incubated for 15 minutes at 37°C and swirling at 1400 rpm. To prepare for digestion, 50µL of 10X DpnII buffer was added and 50µL were taken as an undigested control. At mid day, a first 10µL of DpnII (NEB, 50 000 U/ml) was added and incubated for 4 hours at 37°C, swirling at 1400 rpm. Another 10 µL was added and incubation was carried on overnight. A final 10µL of DpnII  was added the following morning and  left for 4 hours. DpnII was inactivated by heating at 65°C for 20 minutes and 50 µL were taken as an digested-unligated control. Ligation was carried by adding 800 µL of ligation cocktail containing 240U T4 ligase (ThermoScientific 30U/µL), 1X T4 ligase buffer, and incubated overnight at 16°C swirling at 1000 rpm. To prepare for DNA purification, samples and controls were incubated with 150µg of ProteinaseK (Eurobio) for 4 hours ar 65°C. Then, 0,1 vol. of NaAc 3M and 3 vol. of 100% EtOH were added and incubated overnight at -80°C. Precipitated DNA were pelleted by centrifugation, washed with 70% EtOH and finally air dryied. Samples and controls were resuspended in 100 µL and 20 µL H2O respectively and 1 µL of RNAse A (ThermoScientific) was added and incubated at 37°C for 1 hour.  DNA quantities in sample and controls were determined using the Qbit broad range kit (ThermoScientific) and 100 ng of each were loaded on an agarose gel as quality control of the digestion and ligation steps.
Other

value: rhesus macaque embryonic stem cell


title: Root,HA2, rep2

description:
Library name: HA2-2
RNA-seq analysis.Transcriptome libraries were constructed and sequenced in PE150 mode using the Illumina NovaSeq6000 platform. The sequencing was performed by Biomarker Technologies. Data analysis was conducted using the Biocloud platform (http://www.biocloud.net/, accessed on 20 January 2025)


title: rhESC_Primed,cHiC,Rep1

description:
rhES_rep1_ontarget.XIConly.q23.cool
rhES.ontarget.XIConly.q23.cool


title: Hep3BpIL6_H3K27ac_rep2

value: H3K27ac (Abcam, ab4729)


title: Root,HA1,rep3

description:
Library name: HA1-3
RNA-seq analysis.Transcriptome libraries were constructed and sequenced in PE150 mode using the Illumina NovaSeq6000 platform. The sequencing was performed by Biomarker Technologies. Data analysis was conducted using the Biocloud platform (http://www.biocloud.net/, accessed on 20 January 2025)

value: received 60% P + HA, i.e.,0.0552 g NH4H2PO4 + 0.0368 g HA(equivalent to 40% P)


title: rhESC_Primed,cHiC,Rep2

description:
rhES_rep2_ontarget.XIConly.q23.cool
rhES.ontarget.XIConly.q23.cool


title: star IP chromatin, biol rep 2

city: Lyon

first: Marie

description: Library name: Lib_6_04_25_S6

data_processing:
Read quality was assessed with FastQC and MultiQC, and reads were trimmed with fastx-trimmer to remove the first 6 nucleotides on the 5’ end and the last 2 nucleotides on the 3’ end of each read, resulting in 2x68 bp reads. Duplicate reads were removed with a custom  Python script to remove amplification bias. Briefly, replication clusters are first identified as reads having the exact same sequence for the combination of their two mates, then only the best quality read is conserved per cluster. Reads were mapped on the P. axillaris genome (v1.6.2 improved by HiC), which was the most recent version of the genome available at the time data analysis was initiated. Mapping was performed with Bowtie2 (version 2.4.2) with default parameters, and only reads with mapping quality above 20 were kept. The effective genome size was estimated at 9.99e8 with  khmer, with a kmer size of 68.
Peaks were called on the IP and INPUT samples separately with MACS2 with a False Discovery Rate (FDR) threshold at 0.1. The Irreproducible Discovery Rate (IDR) was computed on IP samples to identify reproducible peaks between replicates, and only peaks with an IDR value below 0.1 were kept. Peaks detected in the INPUT sample were removed from the reproducible IP peaks if they overlaped by at least 25 % reciprocally, or if INPUT peaks were included in IP peaks, which was computed with a custom script using a combination of bedtools commands (intersect, window, substract).
Annotation of genes close to peaks was performed with a custom script, and only peaks within 6 kb upstream of the TSS and 6 kb downstream of the TTS were further analyzed. In the cases when a peak was assigned to several possible genes, the gene with the shortest distance to the peak was retained.
Assembly: P. axillaris v1.6.2 genome improved by HiC (https://www.dnazoo.org/assemblies/petunia_axillaris)
Supplementary files format and content: bam files = binary alignment maps for individual libraries
Supplementary files format and content: bed files = bedgraph files with final peaks annotated after replicate intersection and INPUT intersection

extract_protocol:
Chromatin immunoprecipitation on two biological replicates for WT, star and wico petals at stage 8 was performed as follows: petals were flash-frozen and ground in liquid nitrogen, and ground tissue was resuspended into 10 mL fixation buffer (10 mM Hepes pH7.6, 0.5 M sucrose, 5 mM KCl, 5 mM MgCl2, 5 mM EDTA pH8, Complete Protease Inhibitor Cocktail (Merck), 14 mM 2-mercaptoethanol) and a double cross-linking was performed at room temperature (1 hour with disuccinimidyl glutarate at 2.5 mM with gentle shaking, and 5 minutes with formaldehyde 1% (v/v)). Cross-linking was stopped by adding glycine at 200 mM and samples were put directly on ice. Cells were lysed with a 40 mL-Dounce tissue grinder, Triton X-100 was added at 0.6% (w/v) and the lysate was filtered subsequently through 100 µm and 40 µm nylon meshes to recover nuclei. Nuclei were pelleted for 10 minutes at 3,000 g at 4°C, and the pellet was resuspended in 300 µL of cold nuclear isolation buffer (i.e. fixation buffer without 2-mercaptoethanol), carefully deposited on 600 µL of a 15% Percoll solution (15 % (v/v) Percoll, 10 mM Hepes pH8, 0.5 M sucrose, 5 mM KCl, 5 mM MgCl2, 5 mM EDTA pH8) and centrifuged for 5 minutes at 2,000 g at 4°C. The pellet was resuspended into 900 µL of cold nuclear lysis buffer (50 mM Tris-HCl pH7.5, 0.1% (w/v) SDS, 10 mM EDTA pH8) to lyse the nuclei, and chromatin was sonicated twice for 15 minutes with a Covaris S220 sonicator (peak power 105, Duty factor 5, Cycles/Burst 200 for 900s). For each sample, 25 µL of magnetic protein-A Dynabeads and 25 µL of magnetic protein-G Dynabeads (Invitrogen) were washed twice with 100 µL of cold ChIP dilution buffer (15 mM Tris-HCl pH7.5, 150 mM NaCl, 1% (w/v) Triton X-100, 1 mM EDTA pH8) using a magnetic rack. Beads were mixed with 2.5 µg of anti-PhDEF antibody and 1.8 mL of cold ChIP dilution buffer, and incubated for 2 hours at 4°C on a rotating wheel. Sonicated chromatin was centrifuged for 5 minutes at 15,000 g at 15°C, and 25 µL of supernatant (for wt samples) or 100 µL of supernatant (for star and wico samples) was added to the mix of beads and antibody, and incubated overnight at 4°C on a rotating wheel. Beads were washed twice (one quick wash and one long wash with 15 minutes incubation on a rotating wheel) with each of the following buffers: low salt wash buffer (0.1% (w/v) SDS, 1% (w/v) Triton X-100, 2 mM EDTA pH8, 20 mM Tris-HCl pH8, 150 mM NaCl), high salt wash buffer (0.1% (w/v) SDS, 1% (w/v) Triton X-100, 2 mM EDTA pH8, 20 mM Tris-HCl pH8, 500 mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% (v/v) NP40/Igepal,1% (w/v) deoxycholate, 1 mM EDTA pH8, 20 mM Tris-HCl pH8) and TE buffer. Elution was performed twice with 250 µL of elution buffer (0.1 M NaHCO3, 1% (w/v) SDS) at 65°C. IP and input samples were decrosslinked overnight at 65°C by adding NaCl at 200 mM, then incubating for 2 h at 42°C with 20 µg proteinase K in 10 mM EDTA pH8 and 40 mM Tris-HCl pH6.5. DNA was purified with phenol:chloroform:isoamyl alcohol (25:24:1) followed by chloroform:isoamyl alcohol (24:1), precipitated with ethanol at -20°C and the pellet was washed with ethanol 70 %. The dry pellet was recovered in 50 µL TE.
The quality of IP and INPUT samples was assessed with Tapestation 4150 HS D5000 (Agilent). Libraries were prepared with MicroPlex Library Preparation Kit v3 (Diagenode) and around 1 ng of each library was PCR-amplified (12 cycles), following Diagenode's recommendations. Libraries were analyzed Tapestation 4150 HS D5000 and quantified with Qubit 4.0 with the Qubit dsDNA HS Assay Kit (Thermofisher), then mixed at equimolar ratio for sequencing with an Illumina NextSeq 500 (paired-end, 2x76 bp, dual indexing).

value: petal (tube and limb)

value: cultivar R27

value: star (epidermis mutant phdef / mesophyll wt)


title: star IP chromatin, biol rep 1

description: Library name: Lib_5_04_25_S5


title: Huh7nIL6_pSTAT3_rep1

value: p-STAT3 (Cell Signaling, #9145)


title: Hep3BpIL6_pSTAT3_rep3

value: 100ng/mL IL-6


title: Root,HA2, rep1

description:
Library name: HA2-1
RNA-seq analysis.Transcriptome libraries were constructed and sequenced in PE150 mode using the Illumina NovaSeq6000 platform. The sequencing was performed by Biomarker Technologies. Data analysis was conducted using the Biocloud platform (http://www.biocloud.net/, accessed on 20 January 2025)


title: Huh7pIL6_pSTAT3_rep1


title: DMM00834

value: Female

value: DMCAD

value: with CAD


title: DMM01311


title: DMM00095


title: Subcutaneous tumor 3, CAR-iNEV treated group

city: Chicago

first: Hao

last: Zhang

address: 1101 E. 58th Street, Chicago

institute: University of Chicago

description: Library name: Sample 6

data_processing:
Raw data is processed using the 10x Genomics official analysis software Cell Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) for data filtering, genome alignment, transcript quantification, and cell identification, ultimately generating a gene expression matrix for individual cells. Subsequent analysis employs Seurat (https://satijalab.org/seurat/) to perform further cell filtering, normalization of cellular expression quantification, classification of cell subpopulations, differential expression analysis across subpopulations, and screening of marker genes. When the species is human or mouse, SingleR is utilized to preliminarily annotate cell types and perform single-cell data mining on the sequenced cluster cell groups.
Assembly: GRCh38
Supplementary files format and content: TAR archive containing 10X Genomics files.

source_name: Subcutaneous tumor

extract_protocol:
The experimental workflow begins with cell quality control, where the cell suspension is adjusted to an optimal concentration of 700–1,200 cells/μL and rigorously assessed for viability (>80%), minimal debris (<10%), and absence of clumping or contamination. For 10X barcoding and cDNA synthesis, cells are combined with oligonucleotide-loaded gel beads (containing 16-bp cell barcodes, 12-bp UMIs, and poly-dT primers) and encapsulated into GEMs (Gel Beads-in-Emulsion) via a microfluidic system. Within each GEM, cells are lysed, mRNA is reverse-transcribed into barcoded cDNA, and droplets are subsequently broken to pool the cDNA for amplification.
The amplified cDNA is enzymatically fragmented into 200–300 bp segments, ligated with Illumina adapters (P5/P7), and size-selected to construct the sequencing library. Finally, paired-end sequencing (2×150 bp) is performed on Illumina platforms (e.g., NovaSeq 6000) targeting a depth of 25,000 reads per cell, followed by data preprocessing using Cell Ranger for demultiplexing, genome alignment, and generation of a gene-cell expression matrix. This integrated workflow ensures high sensitivity (UMI-based quantification), scalability (up to 80,000 cells per run), and compatibility with multiomic or spatial transcriptomics extensions.

value: Subcutaneous tumor

value: tissue


title: Huh7nIL6_pSTAT3_rep2

value: Liver

value: Hepatocellular carcinoma tumor


title: Hep3BpIL6_pSTAT3_rep1


title: Hep3BpIL6_pSTAT3_rep2


title: DMM01373


title: rhESC_Primed,H3K4me1,Rep2


title: Subcutaneous tumor 1, CAR-iNEV treated group

description: Library name: Sample 4


title: Root,HA1,rep1

description:
Library name: HA1-1
RNA-seq analysis.Transcriptome libraries were constructed and sequenced in PE150 mode using the Illumina NovaSeq6000 platform. The sequencing was performed by Biomarker Technologies. Data analysis was conducted using the Biocloud platform (http://www.biocloud.net/, accessed on 20 January 2025)

value: Root


title: wico IP chromatin, biol rep 1

address: 46 allee d'Italie

institute: ENS de Lyon

description: Library name: Lib_3_04_25_S3

value: wico (epidermis wt / mesophyll mutant phdef)


title: Root,CK, rep3

description:
Library name: CK3
RNA-seq analysis.Transcriptome libraries were constructed and sequenced in PE150 mode using the Illumina NovaSeq6000 platform. The sequencing was performed by Biomarker Technologies. Data analysis was conducted using the Biocloud platform (http://www.biocloud.net/, accessed on 20 January 2025)

value: Zizhi


title: Subcutaneous tumor 3, control group

description: Library name: Sample 3

value: CAR-Ctrl


title: Wild-type IP chromatin, biol rep 2

description: Library name: Lib_2_04_25_S2

value: Wild-type


title: Subcutaneous tumor 2, CAR-iNEV treated group

description: Library name: Sample 5


title: Hep3BnIL6_pSTAT3_rep2


title: Wild-type INPUT chromatin

description: Library name: Lib_7_04_25_S7

value: petal (tube and limb)


title: Root,HA1,rep2

description:
Library name: HA1-2
RNA-seq analysis.Transcriptome libraries were constructed and sequenced in PE150 mode using the Illumina NovaSeq6000 platform. The sequencing was performed by Biomarker Technologies. Data analysis was conducted using the Biocloud platform (http://www.biocloud.net/, accessed on 20 January 2025)

value: received 60% P + HA, i.e.,0.0552 g NH4H2PO4 + 0.0368 g HA(equivalent to 40% P)


title: wico IP chromatin, biol rep 2

description: Library name: Lib_4_04_25_S4

value: cultivar R27


title: Subcutaneous tumor 1, control group

description: Library name: Sample 1


title: Wild-type THP-1 cells, infection with VSV for 8 h, 2

status: Public on Nov 25 2025

city: Wuhan

first: Hongyan

last: Deng

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description: Library name: WT_VSV2

data_processing:
Fastp version 0.21.0 (https://github.com/OpenGene/fastp) was used to perform basic statistics on the quality of the raw reads. The data processing steps were as follows: discard a paired reads if either one read contains adapter contamination; discard a paired reads if more than 10% of bases are uncertain in either read; discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
The clean reads were mapped to the mouse reference genome (http://ftp.ensembl.org/pub/current_fasta/mus_musculus/) using Star version 2.7.9a (https://github.com/alexdobin/STAR).
RSEM version 1.3.3 (https://github.com/deweylab/RSEM) was used to calculate read counts of genes and transcripts.
Assembly: Hg38
Supplementary files format and content: excel file includes FPKM values for each Sample

source_name: THP-1 cells

growth_protocol: IRF3-deficient or wild-type H1299 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (VivaCell) supplemented with 10% fetal bovine serum (FBS) (VivaCell). THP-1 cells (originally obtained from ATCC) were cultured in RPMI 1640 medium (VivaCell) supplemented with 10% FBS. All cells were grown at 37 °C in a humidified atmosphere incubator containing 5% CO2.

extract_protocol:
Total RNAs were extracted using RNAiso Plus (TaKaRa Bio),and then purified using the RNeasy Mini Kit (QIAGEN, 74104).
Sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, #E7530L) according to the manufacturer’s protocol. Qualified libraries were pooled and sequenced on Illumina NovaSeq platforms using PE150 strategy at Wuhan Benagen Technology Co., Ltd. (Wuhan, China).

treatment_protocol: THP-1 cells infected without or with VSV or HSV-1 for 8 hours. IRF3-deficient or wild-type H1299 cells under normoxia (21% O2) or hypoxia (1% O2) for 24 hours.

value: THP-1 cells

value: monocytes

value: infection with VSV for 8 h


title: Subcutaneous tumor 2, control group

description: Library name: Sample 2


title: Root,CK, rep2

description:
Library name: CK2
RNA-seq analysis.Transcriptome libraries were constructed and sequenced in PE150 mode using the Illumina NovaSeq6000 platform. The sequencing was performed by Biomarker Technologies. Data analysis was conducted using the Biocloud platform (http://www.biocloud.net/, accessed on 20 January 2025)


title: Wild-type IP chromatin, biol rep 1

last: Monniaux

description: Library name: Lib_1_04_25_S1


title: Wild-type THP-1 cells, infection with HSV-1 for 8 h, 1

description: Library name: WT_HSV1

value: infection with HSV-1 for 8 h


title: Wild-type THP-1 cells, infection with HSV-1 for 8 h, 2

description: Library name: WT_HSV2


title: Wild-type THP-1 cells, infection with HSV-1 for 8 h, 3

description: Library name: WT_HSV3


title: Wild-type THP-1 cells, infection with VSV for 8 h, 1

description: Library name: WT_VSV1


title: Hep3BnIL6_pSTAT3_rep1

value: p-STAT3 (Cell Signaling, #9145)


title: IRF3-deficient H1299 cells, Hypoxia 24 h, 2

description: Library name: IRF3-KO-HYP2

source_name: H1299 cells

value: H1299 cells

value: non-small cell lung cancer cells

value: hypoxia 24 h


title: IRF3-deficient H1299 cells, Hypoxia 24 h, 3

description: Library name: IRF3-KO-HYP3


title: Hep3BnIL6_pSTAT3_rep3

value: Liver

value: Hepatocellular carcinoma tumor


title: IRF3-deficient H1299 cells, Hypoxia 24 h, 1

description: Library name: IRF3-KO-HYP1


title: Wild-type THP-1 cells, 1

description: Library name: WT_con1

value: control


title: Wild-type H1299 cells, hypoxia 24 h, 3

description: Library name: IRF3-WT-HYP3


title: Wild-type H1299 cells, hypoxia 24 h, 2

description: Library name: IRF3-WT-HYP2


title: Root,CK, rep1

description:
Library name: CK1
RNA-seq analysis.Transcriptome libraries were constructed and sequenced in PE150 mode using the Illumina NovaSeq6000 platform. The sequencing was performed by Biomarker Technologies. Data analysis was conducted using the Biocloud platform (http://www.biocloud.net/, accessed on 20 January 2025)

value: Root

value: Zizhi


title: Wild-type H1299 cells, hypoxia 24 h, 1

description: Library name: IRF3-WT-HYP1

value: Wild-type


title: Wild-type H1299 cells, normoxia 24 h, 3

description: Library name: IRF3-WT-NOR3

value: normoxia 24 h


title: Wild-type H1299 cells, normoxia 24 h, 2

description: Library name: IRF3-WT-NOR2


title: IRF3-deficient H1299 cells, normoxia 24 h, 1

description: Library name: IRF3-KO-NOR1


title: IRF3-deficient H1299 cells, normoxia 24 h, 2

description: Library name: IRF3-KO-NOR2


title: Wild-type H1299 cells, normoxia 24 h, 1

description: Library name: IRF3-WT-NOR1


title: Wild-type THP-1 cells, infection with VSV for 8 h, 3

description: Library name: WT_VSV3


title: Wild-type THP-1 cells, 2

description: Library name: WT_con2


title: M2

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description: Library name: Sample 26

data_processing:
RNA-seq reads were aligned to the human reference genome (hg38) using STAR (v2.7.1a). For each sample, a BAM file was generated containing both mapped and unmapped reads across splice junctions. Secondary alignments and multi-mapped reads were removed using in-house scripts, and only uniquely mapped reads were retained for downstream analyses. GENCODE annotation for hg38 (version 32) was used for reference-guided alignment and downstream quantification. Gene-level expression was quantified using featureCounts (v2.0.1) , based on protein-coding genes from the annotation files.
Assembly: Hg38
Supplementary files format and content: gene_count

source_name: renal mesangial

extract_protocol:
hRMCs (lots 12445, 17544, and 20018) were treated in quadruplicate wells in 6-well plates withvehicle, 25 ng/ml IL-1b, or 25 ng/ml IL-1b +20 nM eliglustat for 24, 48, or 72 hrs. Media was collected for ELISAs and GSL quantification, cell viability was measured by the alamar blue assay, and cells scraped into DPBS and replicate wells combined. The cell suspension was split into two tubes, centrifuged, and DPBS removed. Half the cells were used for GSL quantification, and the other half were used for RNA isolation.
RNA was isolated using RNeasy kit with QiaShredders, resuspended in RNase free water and the concentration and quality assessed by Nanodrop. A total of 2 μg RNA per sample was shipped to Novagene for library preparation and sequencing after passing their quality control (QC) checks.

value: renal mesangial


title: RUNX1-expressing 293T

city: Yokohama

first: Shiori

last: Maeda

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description: Library name: Sample 2

data_processing:
Adapter Trimming
Quality control using prinseq, FastQC
Bismark mapping, duplicate removal
Methylation call, methylation level comparison using methylkit
Assembly: hg38
Supplementary files format and content: bedGraph

extract_protocol:
Genomic DNA was extracted from the 293T cells by using a NucleoSpin Tissue Kit.
Library was constructed by Zymo Research Zymo-Seq RRBS Library Kit.

value: Human embrionic kideney


title: Wild-type THP-1 cells, 3

description: Library name: WT_con3

value: THP-1 cells


title: RUNX11-299–SPI11-102-expressing 293T

description: Library name: Sample 3


title: Mock-infected 293T

description: Library name: Sample 1


title: M1

description: Library name: Sample 25


title: L3

description: Library name: Sample 24


title: L1

description: Library name: Sample 22


title: L2

description: Library name: Sample 23


title: K2

description: Library name: Sample 20


title: M3

description: Library name: Sample 27


title: J3

description: Library name: Sample 18


title: K3

description: Library name: Sample 21


title: I3

description: Library name: Sample 15


title: I2

description: Library name: Sample 14


title: J2

description: Library name: Sample 17


title: J1

description: Library name: Sample 16


title: H3

description: Library name: Sample 12


title: I1

description: Library name: Sample 13


title: H2

description: Library name: Sample 11


title: IRF3-deficient H1299 cells, normoxia 24 h, 3

description: Library name: IRF3-KO-NOR3


title: G2

description: Library name: Sample 8


title: F1

description: Library name: Sample 4


title: G1

description: Library name: Sample 7


title: F3

description: Library name: Sample 6


title: E3

description: Library name: Sample 3


title: F2

description: Library name: Sample 5


title: E2

description: Library name: Sample 2


title: K1

description: Library name: Sample 19


title: RNAseq_LOS_#5

city: Columbia

first: Rocío

middle: Melissa

last: Rivera

state: MO

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: University of Missouri, Columbia

data_processing:
All read data was assessed for quality with FastQC 0.11.7 and low-quality bases (Phred scores ≤ 20) were trimmed using the dynamictrim function of SolexaQA++ 3.1.7.1. Reads less than 60 bases in length were removed using SolexaQA++ LengthSort. Known splice sites were extracted from the gtf file of each reference genome using the Python script hisat2_extract_splice_sites.py. Hisat2 2.1.0 was used to establish a genome index with the hisat2-build and also to align the quality trimmed reads to the reference genome with the following adjusted parameters: --mp 6,6; –score-min L,0,-0.2; known-splicesite-infile. Sam files were converted to bam files and coordinate-sorted using Samtools 1.8. Then, Stringtie 2.1.4 was used with the sorted bam files to assemble transcriptomes for each sample. Stringtie merge was used to combine the assembled transcripts from all samples into a reference assembly. Assembled transcripts were extracted using the gffread module in cufflinks 2.2.1. An index was built for the merged transcriptome and reads were quantified using Salmon 0.11.1. IsoformSwitchAnalyeR 1.17.04 was used to rescue stringtie annotations and generate a gene count matrix.
To assign allele specificity for total RNA-seq reads in bovine, variants were called from the aligned data according to GATK’s Best Practices for Calling Variants in RNA-seq data. Duplicate reads were removed and read groups were assigned using Picard 2.22.4. A dictionary was created for the reference genome using GATK’s CreateSequenceDictionary. GATK SplitNCigarReads was used to hard clip sequences extending into intronic regions and GATK BaseRecalibrator to recalibrate base quality scores. Then, HaplotypeCaller was run on calibrated data and called variants were filtered with adjusted parameters (AB < 0.2 & MQ0 > 50). Variants that were shared between genomic and RNA-seq data for each sample were kept. Variants that were heterozygous in the fetus and homozygous in the bull were used to assign alleles. A variant annotation file was created using the annotate function of bcftools 1.8 and gene annotations were added using custom scripts. Custom R scripts were used to retrieve maternal and paternal allele depth read counts from VCF files in order to quantify allele-specific expressions. Genes with reads covering at least one informative SNP (can be used to assign alleles) in all samples were included for analyses. The raw allelic read counts for each gene in each sample were further used to calculate allelic ratios and multiplied by the total (non-allelic) gene read counts. This step was included since only ~20% of the informative SNPs were shared by all samples and the raw allelic read counts for genes would be largely affected by the total informative SNP number in each sample. The allelic ratio adjusted gene read counts were used in downstream statistical analyses.
Statistical analyses were conducted using R package edgeR 3.36.0 to identify differentially expressed genes (DEGs) between groups. Parameters used include ‘method = "TMM"’ for calcNormFactors function and ‘robust = TRUE’ for glmFit function. FDR was controlled at 0.05 for significance.
Assembly: ARS-UCD1.2
Supplementary files format and content: Total and allelic gene read count in plain text format.

organism: Bos indicus x Bos taurus

source_name: skin fibroblast primary cell

growth_protocol: Day 105 Bos taurus indicus (B. t. indicus; Brahman breed) x Bos taurus taurus (B. t. taurus; Angus breed) F1 hybrid fetuses were generated by our laboratory in 2019 (PMID: 35542046) and used as tissue donors. Fetal skins were collected to establish fibroblast primary cell line using protocol adapted from a publication (PMID: 24198123). Fibroblast cells were cultured in bovine embryonic fibroblast medium (89% (v/v) DMEM (Gibco, 11885084), 10% (v/v) fetal bovine serum (Atlanta Biologicalsa, S11150H), and 1% (v/v) Antibiotic-antimycotic (Gibco, 15240062)) at 38.5°C with 5% CO2.

extract_protocol:
Total RNA was isolated from bovine fibroblast cells using TRIzol™ Reagent (Invitrogen, 15596026) following the manufacturer’s instructions. The concentration of RNA was measured by using a NanoDrop® ND-1000 Spectrophotometer. RNA samples were stored at -80°C.
Total RNA-seq for fibroblast cells was conducted by CD Genomics. Information on library preparation and sequencing obtained from the company is as follows: The first step involves the removal of ribosomal RNA using RiboZero kit (Illumina). Subsequently, the RNA is fragmented into small pieces using divalent cations under elevated temperatures. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are purified and enriched with PCR to create the final cDNA library. This results in libraries with inserts ranging in size from 120–200 bp with a median size of 150 bp. Equimolar pooling of libraries was performed based on QC values and sequenced on Novaseq6000 sequencer (Illumina) with a read length configuration of 150 PE for 33M PE reads per sample (33M in each direction).

treatment_protocol: For bovine fetuses, artificial insemination was used to generate the control group and assisted reproductive technologies (ART) were used to generate the ART group (PMID: 35732675). The large offspring syndrome (LOS) group was defined as individuals from the ART group with body weight greater than 97th centile of controls.

tag: original fetal_id

value: skin fibroblast primary cell

value: D105 fetus

tag: conception method

value: Assisted reproductive technology

tag: disease status

value: LOS

tag: Sex

value: Male


title: NLS-madID

first: Sebastian

last: Baumgarten

address: 25, Rue du Dr. Roux

department: Parasites and Insect Vectors

institute: Institut Pasteur

description: Library name: NLS-madID

data_processing:
Raw pod5 files were merged using pod5 ‘merge’. Basecalling and mapping to the unmasked reference genome of P. falciparum was performed in a single step using dorado basecaller (v0.8.2) and minimap2, respectively, using options ‘--emit-moves --emit-sam --kit-name SQK-NBD114-96 --reference PlasmoDB-64_Pfalciparum3D7_Genome.fasta sup@v5.0.0‘. Model ’dna_r10.4.1_e8.2_400bps_sup@v5.0.0’ was used for base calling. Individual samples were demultiplexed using dorado ‘demux’ (v0.8.2) and alignments with a MAPQ score >= 60 were filtered using samtoos ‘view’ (option -q 60). For each sample (i.e. gDNA, NLS-madID and Sir2a-madID), raw signal alignments were performed using uncalled4 ‘align’ with model 'dna_r10.4.1_400bps_9mer'. For each genomic position and sample, the normalized mean read signal current was calculated using uncalled4 ‘refstats’ with options ‘--stats mean --layers dtw.current’. Genomic positions with a normalized mean read signal current difference >= 2 between NLS-madID vs gDNA (i.e. ‘madID’ and Sir2a-madID vs gDNA (i.e. ‘Sir2a-madID’) were retained as putatively modified sites and the number of modified sites averaged per bin. The number of modified sites was further normalized to the AT content of each bin.
Assembly: PlasmoDB v64
Supplementary files format and content: Bedgraph files with 6mA densities in bins of 10bp and 1000bp normalized to the AT content of each bin

organism: Plasmodium falciparum

source_name: NLS-madID

growth_protocol: For NLS-madID, cells were synchronized by plasmion/sorbitol to a 6h window. To dimerize and activate the Cre recombinase, rapamacin was added (200nM final concentration) after the sorbitol, and cells were collected at 40 h.p.i. Successful excision of the yDHODH locus was confirmed by PCR. For Sir2a-madID, the cell line was synchronized by plasmion/sorbitol to a 6h window and collected at 40 h.p.i. Red blood cells were lysed with 0.075% saponin in DPBS at 37°C. The parasite cell pellet was washed twice with ice-cold DPBS, snap-frozen and stored at -80°C.

extract_protocol:
gDNA was extracted using the Qiagen DNeasy Blood & Tissue Kit (#69504). gDNA was purified by treatment with RNase A (0.2 mg/mL final concentration) for 2h at 37°C, followed by a 2 h incubation at 55°C with proteinase K (0.2 mg/mL final concentration). The obtained gDNA was further purified by phenol/chloroform extraction and ethanol precipitation.
Libraries were prepared using the native barcoding SQK-NBD114.96 kit using the recommendations for long gDNA fragments. Sequencing was performed using a MinION flow cell (R10.4.1) on a MinION sequencer.

tag: cell line

value: NLS-madID


title: RNAseq_LOS_#4


title: Sir2a-madID

description: Library name: Sir2a-madID


title: RNAseq_LOS_#3

value: Female


title: RNAseq_LOS_#6


title: RNAseq_LOS_#1


title: RNAseq_LOS_#2


title: RNAseq_CON_B_#5

value: Artificial insemination

value: Healthy


title: H1

description: Library name: Sample 10


title: Nvs2

city: Changsha

first: Zhou

last: jian

address: renming road

institute: The Second Xiangya Hospital

description:
Library name: sample 5
control group, replicate biosample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts and fpkm for each sample

source_name: Skin

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: Skin

value: HaCaT

value: Keratinocyte

value: control


title: Nvs1

description:
Library name: sample 4
control group, replicate biosample 1


title: mod2

description:
Library name: sample 2
UV-induced group, replicate biosample 2

value: UV-induced


title: mod1

description:
Library name: sample 1
UV-induced group, replicate biosample 1


title: Nvs3

description:
Library name: sample 6
control group, replicate biosample 3


title: mod3

description:
Library name: sample 3
UV-induced group, replicate biosample 3


title: G3

description: Library name: Sample 9

value: renal mesangial


title: RNAseq_CON_B_#3


title: RNAseq_CON_B_#2


title: U2OS_CC_PARGi_R2

city: Oxford

first: Callum

last: Henfrey

address: Sir William Dunn School of Pathology, South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

description:
Library name: U2OS_CC_PARGi_R2
RNA-seq U2OS cells, PARGi treated, replicate 2

data_processing:
Adapters were trimmed with Cutadapt v1.18
Removal of rRNA reads and mapping to the hg38 genome were performed with STAR v2.7.3a
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.9
Differential gene expression analysis was performed with the outputs from STAR --quantMode GeneCounts using DESeq2 v3.12
Bigwig files were generated with the Deeptools2 v3.4.2 bamCoverage tool
Assembly: hg38
Supplementary files format and content: bigwig

growth_protocol: DMEM (Sigma) supplemented with 10% FBS (Gibco) and penicillin-streptomycin (100 U/mL, Gibco)

extract_protocol:
RNA was extracted using Direct-zol RNA MiniPrep Plus kit (Zymo Research) according to the manufacturer’s instructions. The quality of the RNA was measured spectrophotometrically using NanoDrop 2000c (Thermo Scientific) and quality was analysed by RNA ScreenTape Assay and 4200 TapeStation System (Agilent).
For RNA-seq, libraries were prepared using Illumina's TruSeq Stranded Total RNA library Preparation Kit according to Illumina's instructions

treatment_protocol: DMSO or 25µM PARGi inhibitor (PDD00017273, Sigma) for 4 days

value: PARGi


title: U2OS_CC_DMSO_R3

description:
Library name: U2OS_CC_DMSO_R3
RNA-seq U2OS cells, DMSO treated, replicate 3

value: DMSO


title: U2OS_CC_PARGi_R3

description:
Library name: U2OS_CC_PARGi_R3
RNA-seq U2OS cells, PARGi treated, replicate 3


title: RNAseq_CON_B_#1

value: skin fibroblast primary cell


title: U2OS_CC_PARGi_R1

description:
Library name: U2OS_CC_PARGi_R1
RNA-seq U2OS cells, PARGi treated, replicate 1


title: E1

description: Library name: Sample 1


title: WGBS_LOS_#5

data_processing:
For WGBS data, raw sequencing reads were deduplicated using the clumpify function of BBMap 38.90 and trimmed for adapter sequences and low quality bases using trimmomatic 0.39 with parameters ‘ILLUMINACLIP:adapter_seq:2:30:10:1:true LEADING:20 TRAILING:20 AVGQUAL:20 MAXINFO:0:0.5’. Trimmed reads were aligned to the corresponding reference genome using BSBolt 1.5.0 with default setting. Trimmed reads were also aligned to lambda phage genome to determine bisulfite conversion rates. Samtools 1.13 was used to convert, sort, filter, and index bam files. MarkDuplicates function of picard 2.25.5 was used with parameter ‘--OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500’ to further remove duplicated reads after alignment. CpG methylation information was extracted from the bam files using the function CallMethylation of BSBolt with parameter ‘-CG -min 1 -BQ 20’. For each sample, CpG methylation at C/T SNPs detected in their corresponding Hi-C data were excluded for sense strand reads, and CpG methylation at G/A SNPs were excluded for antisense strand reads. For bovine samples, SNPs identified from Hi-C dataset were also used to assign alleles for WGBS reads using custom Perl scripts. C/T SNPs (based on sense strand sequence) were only applied for antisense strand reads, and G/A SNPs were only applied for sense strand reads. Other types of SNP were applied for both strands. Reads that cover multiple SNPs and have conflicting allele assignments were excluded. For both overall and allele-specific comparisons, statistical analyses were conducted using R package hummingbird with parameter ‘minCpGs = 10, minLength = 100, maxGap = 300’ to identify differentially methylated regions (DMRs) between groups. DMRs with at least 15% difference in methylation level (both gain and loss of methylation) and at least 4 mean read coverage at CpG sites in all the samples were reported. For allele-specific analyses, the read coverage filtering was not applied since only about 20% of the usable SNPs are shared by all the sample. The sex chromosomes were excluded from analyses to circumvent confounding created by X chromosome inactivation.
Assembly: ARS-UCD1.2
Supplementary files format and content: Read coverage and DNA methylation percentage for CpG sites in BEDGRAPH format.

extract_protocol:
Bovine fibroblast cells were lysed in lysis buffer (0.05 M Tris-HCl (pH 8.0), 0.1 M EDTA, and 0.5% (w/v) SDS) with proteinase K (Fisher BioReagents, BP1700) at 55°C for four hours. Genomic DNA was extracted with Phenol:Chloroform:Isoamyl Alcohol (SIGMA, P3803) following the manufacturer’s instructions. The concentration of DNA was measured by using a NanoDrop® ND-1000 Spectrophotometer and DNA integrity was confirmed by electrophoresis on a 0.7% agarose gel. Genomic DNA samples were stored at -20°C.
WGBS for fibroblast cells was conducted by CD Genomics (Shirley, NY, USA). Information on library preparation and sequencing obtained from the company is as follows: Genomic DNA was fragmented by sonication to a mean size of approximately 200-400 bp. Fragmented DNA was end-repaired, 5'-phosphorylated, 3'-dA-tailed and then ligated to methylated adapters. The methylated adapter-ligated DNAs were purified using 0.8× Agencourt AMPure XP magnetic beads and subjected to bisulfite conversion by ZYMO EZ DNA Methylation-Gold Kit (Zymo Research). The converted DNAs then have the addition of 8-bp index primers to create the final cDNA library. Equimolar pooling of libraries was performed based on QC values and sequenced on Novaseq6000 sequencer (Illumina) with a read length configuration of 150 PE for 300M PE reads per sample (300M in each direction). 0.1-1% lambda DNA were added during the library preparation to monitor bisulfite conversion rate.

value: D105 fetus


title: U2OS_CC_DMSO_R2

description:
Library name: U2OS_CC_DMSO_R2
RNA-seq U2OS cells, DMSO treated, replicate 2


title: 20MSTO-TAZ-2

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description:
Library name: 20221014_MSTO-TAZ-2_AH10424_S110
Column name in Star_Gene_Counts.csv: 20MSTO-TAZ-2

data_processing:
RNA-seq analysis using the VIPER snakemake pipeline
Differential gene expression testing was performed by DESeq2 (v1.22.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited gene count files

growth_protocol: MSTO-211H cells were maintained in RPMI supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2  at 37oC

extract_protocol:
Total RNAs were extracted and purified using the RNeasy Mini Kit (Qiagen; 74106). rRNA depletion was performed from 100ng of purified RNA using QIAseq FastSelect rRNA HMR reagents
Libraries were prepared using Roche Kapa Biosystems RNA HyperPrep sample preparation kits on a Beckman Coulter Biomek i7. Finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance. The final pool was sequenced with paired-end 150 bp reads on an Illumina NovaSeq 6000 at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

treatment_protocol: MSTO-211H malignant pleural mesothelioma cells were transiently transfected with Cas9 and either an sgRNA control guide (sgCTRL) or a guide targeting EZH2 (EZH2-KO). sgCTRL and EZH2-KO cells were treated with DMSO or a TEAD inhibitor, MYF-03-69 for 24h.

value: Malignant Pleural Mesothelioma

value: Tazemetotstat


title: U2OS_CC_DMSO_R1

description:
Library name: U2OS_CC_DMSO_R1
RNA-seq U2OS cells, DMSO treated, replicate 1


title: 20MSTO-TAZposTEAD-2

description:
Library name: 20221014_MSTO-TAZposTEAD-2_AH10424_S112
Column name in Star_Gene_Counts.csv: 20MSTO-TAZposTEAD-2

value: Tazemetotstat+MYF-03-69 (TEADi)


title: WGBS_LOS_#2

value: Assisted reproductive technology

value: LOS


title: WGBS_LOS_#3

value: Female


title: 20MSTO-TAZposTEAD-1

description:
Library name: 20221014_MSTO-TAZposTEAD-1_AH10424_S111
Column name in Star_Gene_Counts.csv: 20MSTO-TAZposTEAD-1


title: 20MSTO-TAZ-1

description:
Library name: 20221014_MSTO-TAZ-1_AH10424_S109
Column name in Star_Gene_Counts.csv: 20MSTO-TAZ-1


title: WGBS_LOS_#1


title: RNAseq_CON_B_#4

value: Artificial insemination

value: Healthy

value: Male


title: 20MSTO-EZH2-KO-TEAD-1

description:
Library name: 20221014_MSTO-EZH2-KO-TEAD-1_AH10424_S114
Column name in Star_Gene_Counts.csv: 20MSTO-EZH2-KO-TEAD-1


title: 20MSTO-DMSO-2

description:
Library name: 20221014_MSTO-DMSO-2_AH10424_S108
Column name in Star_Gene_Counts.csv: 20MSTO-DMSO-2


title: 20MSTO-EZH2-KO-DMSO-2

description:
Library name: 20221014_MSTO-EZH2-KO-DMSO-2_AH10424_S118
Column name in Star_Gene_Counts.csv: 20MSTO-EZH2-KO-DMSO-2


title: WGBS_CON_B_#1


title: 20MSTO-DMSO-1

description:
Library name: 20221014_MSTO-DMSO-1_AH10424_S107
Column name in Star_Gene_Counts.csv: 20MSTO-DMSO-1


title: WGBS_CON_B_#2


title: WGBS_CON_B_#5


title: 20MSTO-EZH2-KO-DMSO-1

description:
Library name: 20221014_MSTO-EZH2-KO-DMSO-1_AH10424_S117
Column name in Star_Gene_Counts.csv: 20MSTO-EZH2-KO-DMSO-1


title: WGBS_LOS_#6


title: WGBS_CON_B_#4