title: RNA-seq - siTfam - rep1

data_processing:
Illumia bcl2fastq2.17 software was used for basecalling and adapters, reads length shorter than 15 nucleotides and reads with low complexity (< 30%) were removed by FASTP.
Data were aligned to the GRCm38 mouse genome assembly using hisat2 with default setting.
Distribution of aligned reads was calculated according to NCBI with featureCounts.
Genome_build: GRCm38
Supplementary_files_format_and_content: Genes ratio were generated using the utility DESeq2 v3.14.

source_name: OG2 mESCs

growth_protocol: mESCs were initially cultured on 0.2% gelatin-coated plates in N2B27 medium (DMEM/F12 and Neurobasal mixed 1:1, supplemented with 0.5 × N-2, 0.5 × B-27, 1× GlutaMAX, 1× NEAA, 1× sodium pyruvate, 0.1 mM 2-mercaptoethanol, 1,000 U ml-1 LIF, 1 µM PD0325901 and 3 µM CHIR99021) for 24h, then the cells were transferred to differentiation medium [DMEM/F12 and Neurobasal medium mixed 1:1, supplemented with 0.5× N-2, 0.5× B-27, 1× GlutaMAX, 1× NEAA, 1× Sodium Pyruvate, 0.1 mM 2-mercaptoethanol, 12.5 ng ml-1 bFGF, 20 ng ml-1 Activin A, and 1% knockout serum replacement (Gibco)] for another 36h.

extract_protocol:
OG2 mESCs samples, cells were lysed by 1 ml TRI Reagent, followed by adding 200 μl chloroform with robust vortex for 15 s. The mixture was centrifuged at 12,000 g at 4ºC for 15 min, than the RNA was precipitated with isopropanol at -20ºC for 30 min or overnight. And to facilitate precipitation, glycogen (Roche) was added if necessary.
Total RNA, EpiTM mini longRNA-seq kit was used for library preparation. In brief, 10 μl IP RNA and 50 ng input RNA were used for library construction, total RNAs were digested by DNase I to remove residual DNAs, and RNAs were fragmented. Then the first cDNA was synthesized based on SMART (Switching Mechanism At the 5' end of RNA Transcript technology).
OG2 mESCs experiments, followed by two-round of PCR amplifications and purification, the resultant cDNA library was evaluated using Bioptic Qsep100 Analyzer, and diluted to 500 pM for cluster generation and high-throughput sequencing (2 ×150 bp) on NovaSeq 6000 (Illumina).

treatment_protocol: For total RNA extraction of OG2 mESCs，mESCs were initially cultured on 0.2% gelatin-coated plates in N2B27 medium for 24 h, and then were transfected with 50 nM of indicated siRNAs using DharmaFECT 1 siRNA transfection reagent (Dharmacon) according to the manufacturer’s instruction. Meanwhile, the cells were transferred to differentiation medium for another 36 h. Finally, the cells were harvested and lysed with Trizol. Total RNAs were prepared for high-throughput RNA sequencing.

value: Mouse embryonic stem cells

value: (CBA/CaJxC57BL/6J) with 129Sv/Jae female mice

value: Knockdown of Tfam by siRNA transfection


title: CarS2-AKO, S29BAT-4

status: Public on Mar 20 2026

type: SRA

city: Shanghai

first: Xuyun

last: Zhao

state: Shanghai

address: South Chongqing Road

department: Medical school

country: China

institute: Shanghai Jiaotong University

description:
CKO1
raw_counts.text

library_source: transcriptomic

data_processing:
The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05).
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: brown adipose tissue

extract_protocol:
RNA were extracted from brown adipose tissue using  Trizol method.
1 Sample QC
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
2 mRNA Isolation
A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
3 mRNA Fragmentation
The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.
4 cDNA Synthesis
Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA.
5 End Repair, Add A and Adaptor Ligation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.
6 PCR
The PCR reaction system and program are configured and set up to amplify the product.
7 Library QC
The corresponding library quality control protocol will be selected depending upon product requirements.
8 Circularization
Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.
9 Sequencing
Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

tag: tissue

value: brown adipose tissue

tag: genotype

tag: treatment

value: cold tolerance experiment

tag: time


title: High-proliferating Leishmania major infected-single cell#5 , Mouse#4_Right ear [1_B6]

city: Magdeburg

first: Yan

last: Fu

state: Saxony-Anhalt

address: Haus 26, Institut für Molekulare und Klinische Immunologie, Otto-von-Guericke-Universität Magdeburg, Leipziger Str. 44

country: Germany

institute: Otto-von-Guericke-Universität Magdeburg

description:
SmartSeq2
Raw_count_matrix_scRNAseq_20230314.gz

library_source: transcriptomic single cell

data_processing:
Raw fastq files were processed with Cutadapt (v3.7) to remove poly-A tails and adapter sequences introduced during library construction (SMART-seq: AAGCAGTGGTATCAACGCAGAGT & Nextera XT: CTGTCTCTTATACACATCT).
The first 15 bases of each read, bases with Qscore < 20 and reads left with less than 25 bases after trimming were also discarded.
Reads were mapped to a reference genome using STAR with default parameters.
The used reference genome has been built by combining the mouse (GRCm38) and Leishmania major (ASM272v2) genomes as well as spike-ins (ERCC92) and the Kikume Green-Red transcript sequences.
The raw count matrix was generated from the mapping results with featureCounts (Subread, v1.6.3)
Assembly: GRCm38,  ASM272v2, ERCC92
Supplementary files format and content: Tab-separated matrix files

source_name: ear tissue

extract_protocol:
Ears of mice were separated in two sheets (ventral and dorsal) using forceps and enzymatically digested in RPMI 1640 medium containing 1 mg/ml collagenase and 50 ng/ml DNase for 60 min at 600 rpm and 37°C and passed through a 70 μm cell strainer. Cells were centrifuged at 4°C with 300 g for 10 min. Mouse CD45 MicroBeads (Miltenyi Biotec) were used to isolate leukocytes prior to cell surface staining according to manufacturer’s instructions. Afterwards, cells were washed with PBS and FACS buffer before surface staining of cells was done by using surface marker specific antibodies (APC-CD11c and APC-cy7-Ly6c). Samples were blocked with Fc-block using anti-CD16/32 antibody (1:25 in FACS buffer) for 15 min on ice before the antibody staining. Antibodies were applied with a final concentration of 1:200. mKikume G&R Leishmania major infections were analyzed with a FACS ARIA III flow cytometer/sorter. Specifically, mKikumeGreen refers to high-proliferating L. major infected monocytes, while mKikumeRed refers to low-proliferating L. major infected monocytes.
Single cells were sorted into different wells from a 96-well plate (Costar) filled with 4.65 µl of Buffer RLT Plus (Qiagen), 0.25 µl of SUPERase-In RNase-Inhibitor (Invitrogen), and 0.1 µl of ERCC spike-Mix1 (Invitrogen) pre-diluted 1:500000 in RNAse-free water. For cell-population RNAseq, 50-100 cells per subpopulation per sample were sorted into the wells. Sorted cells were immediately frozen and stored at -80 °C. Single-cell libraries were prepared using Smart-seq2 protocol as previous described with minor modifications: Following cDNA amplification, ACTB expression was measured in each cDNA library by qPCR. All cDNA libraries were diluted aiming to an equivalent ct value for ACTB (average = 21.11, SD = 1.05) and were subsequently used as input for a tagmentation-based protocol (Nextera XT, Illumina) using one quarter of the recommended volumes, 10 min for tagmentation at 55°C20. The indexed libraries were quantified using Qubit dsDNA Hs Assay (Life Technologies) and fragment size of libraries was analysed using QIAxcel DNA high resolution Kit (Qiagen) and bioanalyser (Agilent). Libraries were normalized to 2 nM and pooled. Particularly, 218 of single-cell libraries were sequenced for HiSeq 2500 (Illumina).

tag: cell type

value: monocytes

value: ear tissue

tag: strain

tag: age

value: 10 weeks old


title: High-proliferating Leishmania major infected-single cell#2 , Mouse#2_Right ear [1_A9]

department: Institut für Molekulare und Klinische Immunologie


title: VH2

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimed from 3' and 5' until the final base had  a score >30, using Trimmomatic V0.33, discarding reads left with <20bp.
ChIP-seq reads were aligned to the UCSC mm10 genome using HISAT2 version 2.2.1. Only uniquely mapping reads with at most two mismatches were retained.
To create Cut & Tag coverage plots, the locations of the mapped Cut & Tag-Seq reads were extended to 150bp to represent sequenced fragments, renormalized(to reads per million, rpm) and reformatted in the bed file format.
Peaks were called using MACS2 v2.2.7 with the significance fut-off q-value<=.0.01
bed files were generated using the MACS2
Assembly: mm10
Supplementary files format and content: bed
Library strategy: Cut & Tag

molecule: genomic DNA

growth_protocol: Cells were maintained in DMEM growth medium supplemented with 10% fetal bovine serum (FBS) and antibiotics(Penicillin Streptomycin) in humified amosphere with 8% CO2 at 37℃

extract_protocol:
BAC were differentiated and harvested, counted and centrifuged at 600xg for 5 min. 5x104 cells were used for one sample.
experiment was conducted using Commercial Cut & Tag Assay kit (Vazyme, TD903)
Cut&Tag libraries were prepared using CAM from Cut & Tag assay kit (Vazyme, TD903) complemented with  DNA Barcodes  from TruePrep Index Kit (Vazyme, TD-202)

treatment_protocol: Two days after the cells confluenced (disignated day 0), adipogenic differentiation was induced by adding an induction medium (DMEM containing 10% FBS, 0.5 mM IBMX, 125 mM indomethacin, 1 mM dexamethasone, 20 nM insulin and 1 nM T3) until day2. Then Cells were switched to differentiation medium (DMEM, 10% FBS, 20 nM insulin and 1 nM T3), and changed fresh differentiation medium every two days.

tag: cell line

value: BAC-V

value: mouse preadipocyte

value: WT

tag: antibody


title: mitoRICK - Ctrlinput.rep2

city: Guangzhou

first: Jinshuai

last: Sun

address: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Illumia bcl2fastq2.17 software was used for basecalling
Data were aligned to the GRCh38 human genome assembly using hisat2 (v2.1.012) with '--rna-strandness RF'.
Distribution of aligned reads was calculated according to NCBI with featureCounts.
Genome_build: GRCh38 and ERCC
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt file was generated using Samtools and featureCounts script.

organism: Homo sapiens

source_name: HeLa

growth_protocol: HeLa cells were maintained in high-glucose Dulbecco’s modified Eagle’s medium (DMEM, HyClone, SH30022.01) supplemented with 10% fetal bovine serum (FBS, Natocor, SFBE) and 1× nonessential amino acids.

extract_protocol:
For mitoRICK samples samples, cells were lysed by 1 ml TRI Reagent, followed by adding 200 μl chloroform with robust vortex for 15 s. The mixture was centrifuged at 12,000 g at 4ºC for 15 min, than the RNA was precipitated with isopropanol at -20ºC for 30 min or overnight. And to facilitate precipitation, glycogen (Roche) was added if necessary.
For mitoRICK RNA and total RNA, EpiTM mini longRNA-seq kit was used for library preparation. In brief, 10 μl IP RNA and 50 ng input RNA were used for library construction, total RNAs were digested by DNase I to remove residual DNAs, and RNAs were fragmented. Then the first cDNA was synthesized based on SMART (Switching Mechanism At the 5' end of RNA Transcript technology).
For mitoRICK and OG2 mESCs experiments, followed by two-round of PCR amplifications and purification, the resultant cDNA library was evaluated using Bioptic Qsep100 Analyzer, and diluted to 500 pM for cluster generation and high-throughput sequencing (2 ×150 bp) on NovaSeq 6000 (Illumina).

treatment_protocol: For the mitoRICK experiment, 120 mg mitochondrial pellet with or without 0.3 mM EU labelling was weighed Every 100 mg of mitochondrial pellet was resuspended with 1 ml lysis buffer [20 mM Tris-HCl pH 7.5, 500 mM LiCl, and 0.5% lithium-dodecylsulfate (LiDS) supplemented with 1× EDTA-free protease inhibitor cocktail (Roche), 200 U ml-1 RNase inhibitor (Thermo Scientific) and 400 U ml-1 DNase I], and placed on ice for 10 min with occasional upside-down mixing. Lysate was homogenized by passing through a syringe with a narrow needle (29G) for 5 times, centrifuged at 12,000 g at 4ºC for 10 min, and then the supernatant was transferred to a new tube. Diluted the supernatant by adding with ten volumes of the prechilled 50 mM Tris-HCl (pH 7.5), and concentrated the mixture using a 15-ml ultrafiltration tube (molecular weight cutoff: 10 KDa) to a final volume of ≤ 1 mL, then repeated dilution and concentration steps. The final concentrate was used for click reaction as previously described. Briefly, click reaction buffer (containing 100 μM Biotin-PEG3-Azide, 0.5 M CuSO4, 2 mM THPTA, 1 mM aminoguanidine, and 5 mM sodium ascorbate stock) was added to the final concentrate and mixed well, the mixture was placed at room temperature with continuously gentle rotation for 2 h. Then the click reaction was quenched by adding with EDTA at a final concentration of 5 mM at room temperature for 5 min. RNA and protein complexes were precipitated with prechilled methanol at -20ºC for 30 min, and then were washed with methanol twice. Resuspended the pellet with suspending buffer [0.5% sodium dodecyl sulfate (SDS), 1 mM EDTA, 1% Brij-97, 150 mM NaCl, 50 mM triethanolamine supplemented with 200 U ml-1 RNase inhibitor], pipetted up and down to completely dissolve the pellet. Centrifuged the mixture at 4,000 g at 4ºC for 10 min. Subsequently, transferred the supernatant to a new tube and took 1% of the supernatant as input for quality control for Western blot or RNA detection. Next the RNA and protein complexes were incubated with streptavidin agarose beads (Thermo) at 4ºC overnight. Then the RNA-bound agarose beads were collected and washed twice with buffer I (2% SDS in PBS), buffer II (8 M urea and 0.25 M NH4HCO3 in water), buffer III (2.5 M NaCl in PBS) and 50 mM Tris-HCl (pH 7.5) in sequential order for 10 min respectively. The resultant proteins or RNA eluted from the beads were prepared for further RNA extraction.

value: HeLa

value: Derived from cervical cancer cells

value: Uterus; Cervix

value: mitochondria purified from HeLa cells without EU labelling

tag: target

value: total mitochondrial RNA


title: RNA-seq - NC

value: Negative control


title: High-proliferating Leishmania major infected-single cell#4 , Mouse#2_Left ear [1_B4]


title: WT, S29BAT-3

description:
WT3
raw_counts.text


title: mitoRICK - Ctrlinput.rep1


title: CaMPARI-red cells moving condition, batch 1

city: Wako

first: Fumi

last: Kubo

address: 2-1 Hirosawa

department: Center for Brain Science

country: Japan

institute: RIKEN

description:
Library name: Moving1
10x Genomics

data_processing:
Initial preprocessing was performed using the Cell Ranger software suite (version v6.0.1, 10X Genomics) following standard guidelines. ‘‘cellranger count’’ was used to align the reads to a custom reference genome created by combining the improved zebrafish transcriptome annotation file (GTF for v4.3.2) (Lawson et al., 2020) and the FATSA file (GRCz11) with CaMPARI2, using ‘‘cellranger mkref’’. Each biological replicate resulted in 3,000-5,000 estimated number of cells with 3,500-5,000 median unique molecular identifier (UMI) counts per cell. Output from cellranger was loaded into Seurat R package 68 (version 4.1.1) using the Read10X function, with each condition representing different experiment: stationary1, stationary2, moving1, and moving2. The data were stored as Seurat objects, with a minimum threshold of 200 genes per cell and a minimum of 3 cells per gene for inclusion. For quality control, cells with greater than 10% mitochondrial gene expression were excluded from further analysis. Cells were also filtered based on the number of detected genes, retaining those with between 200 and 5000 genes. This quality control was applied uniformly to all datasets. The numbers of cells before and after quality control for each dataset were as follows: stationary1, 3117 cells before QC and 3093 cells after QC; stationary2, 3884 and 3869; moving1, 3735 and 3678; moving2, 4812 and 4804, respectively. Following filtering, the datasets were integrated using the SCTransform function. The datasets for stationary1, stationary2, moving1, and moving2 were stored in a list and processed through the SCTransform function. For each transformed dataset, the 3000 most variable genes were selected as possible integration features using SelectIntegrationFeatures. We then followed the standard integration pipeline, employing PrepSCTIntegration to prepare the data for integration. Integration was performed using the FindIntegrationAnchors function, where stationary1 and stationary2 datasets were used as the reference. Normalization was done using the SCTransform. The resulting integration anchors were used to combine the datasets into a single Seurat object using IntegrateData. To reduce dimensionality, principal component analysis (PCA) was performed using the RunPCA function. Subsequently, UMAP was generated using the first 20 principal components (PCs) to visualize the data in a two dimensional space (RunUMAP). Clustering was performed using the FindNeighbors and FindClusters functions with the PCA reduction and a resolution of 0.8. Marker genes for each cluster were identified using the FindAllMarkers function, selecting only positive markers with a log fold change threshold of 0.25. We annotated clusters based on the expression data of marker genes using the Zebrafish Information Network website (zfin.org).
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Danio rerio

source_name: Brain

extract_protocol:
After photoconversion, larvae were kept at 27.5 degrees for maximally 4 hours until brain dissection. Brain was dissected in ice-cold Neurobasal medium (ThermoFisher Scientific, 21103049) supplemented with B-27 (ThermoFisher Scientific, 17504044). After the eyes were removed from the head, anterior to the habenula and posterior to the otolith was cut away to increase the proportion of pretectal cells. Cell dissociation was performed as previously described with some modifications. Tissues were pooled from 50-60 larvae and digested in 25 U/ml papain, 130 U/ml DNaseI, 2 mM L-cysteine in oxigenated Ames at 37°C for 36 minutes. Every 12 minutes, tissues were triturated by pipetting, followed by a final incubation for 5 minutes. The cell suspension was then passed through a pre-wet 40 µm filter (Falcon, 352340). To stop the digestion, the papain solution was replaced by papain inhibitor solution containing 15 mg/ml ovomucoid and 15 mg/ml BSA. Tissue was gently dissociated by trituration using a broad end tip pipette in the papain inhibitor solution. To wash the cell suspension, cells were pelleted at 300 g for 7 minutes at RT and resuspended in FACS buffer (oxigenated Ames containing 0.25% BSA (Sigma, A4161), 10m M HEPES (Sigma, H0887), 25 U/mL DNase I (Thermofisher, 90083), 5mM MgCl2)). CaMPARI2 red cells were sorted based on green and red fluorescence using SONY Cell Sorter SH800S equipped with 488 nm & 561 nm lasers. First, FACS gates were set after 50,000 recorded events to sort live single-cells. Similar gates were used across experiments. Specifically, a scatter gate was initially set using forward scattering (FSC-A) and back scattering (BSC-A) to select the live cell population. Next, Forward Scatter Area (FSC-A) and Forward Scatter Height (FSC-H) were used to eliminate debris as much as possible and isolate single-cells. Then, CaMPARI2 green and CaMPARI2 red fluorescence were used to collect CaMPARI2 red cells labeled by photoconversion of Tg(elavl3:NLS-CaMPARI2) larvae. The gating was set to include the CaMPARI2 red fluorescent cell population, which was not observed in the Tg(elavl3:NLS-CaMPARI2) control larvae that did not undergo photoconversion. Overall, 60-70% of the population consisted of live single cells, and approximately 8% of those were CaMPARI2 red cells. These cells were sorted using a 100 µm nozzle (20 PSI) and collected to a 2 ml protein LoBind Eppendorf tube filled with 1 ml oxigenated Ames containing 1.0% BSA, 10mM HEPES. A total of 130,000~150,000 CaMPARI2 red cells were collected from 50-60 larvae. After FACS was completed, cell suspension was centrifuged for 5 min at 100 g at RT and the pellet was resuspended in 300 µl of Ames medium/0.5% BSA. This washing step was repeated three times, and finally, the cells were resuspended in 30 μL of Ames/BSA solution. To check cell density and viability, cells were stained with a dead cell stain Trypan Blue (Sigma-Aldrich, T8154) and both live and dead cells were counted using a DIC microscope. Cell density was typically between 300 and 800 cells/µl with a viability rate of over 90%.
Droplet RNA sequencing was performed according to the manufacturer’s instructions with no modifications (10x Genomics Chromium System, Chromium Next GEM Single Cell 3' Reagent Kits v3.1). A single-chromium chip channel was loaded with a cell suspension, aiming to capture 5,000 cells with a doublet rate of <5%. For the “moving” condition, 2 replicates were collected from 2 experiments. For the “stationary” condition, 2 replicates were collected from 2 experiments. cDNA libraries were sequenced on a NovaSeq 6000 (illumina) or DNBSEQ-G400 (MGI Tech) to a depth of ~60,000 reads per cell.

value: Brain


title: CarS2-AKO, S29BAT-5

description:
CKO2
raw_counts.text


title: High-proliferating Leishmania major infected-single cell#3 , Mouse#3_Right ear [1_B10]


title: RNA-seq - siDHX30 - rep1

value: Mouse embryonic stem cells

value: (CBA/CaJxC57BL/6J) with 129Sv/Jae female mice

value: Knockdown of Dhx30 by siRNA transfection


title: Healthy donor, human Monocyte Derived Macrophages, atheroma plaque, DMSO

status: Public on Mar 19 2026

city: Dijon

first: Damien

last: LELEU

address: 36 Rue Félix Vionnois

country: France

institute: CHU Dijon Bourgogne

description: Library name: Donneur-P_ATAC_hg38

data_processing:
Peaks were analysed and visualized using Integrative Genomics Viewer software (IGV). The Fraction of Reads in Peaks (FRiP) scores were above 15 % for the two samples, indicating high signal-to-noise ratios and acceptable data quality for analysis.
Assembly: hg38
Supplementary files format and content: Fraction of Reads in Peaks (FRiP), Peaks, bedgraph

source_name: human blood

growth_protocol: Human Peripheral-blood Monocytes were obtained from buffy coats from male and female healthy anonymous blood donors at the Etablissement Français du Sang (Besançon, France). Mononuclear cells were isolated by Pancoll gradient centrifugation and monocyte negative selection was performed via magnetic activated cell sorting using the Pan Monocyte Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany, Cat#130-117-337) according to the manufacturer’s instructions. Human monocytes were differentiated into macrophages for 6 days with 50 ng/mL of macrophage-colony stimulation factor (CSF1; Miltenyi Biotec, Cat#130-093-963) into RPMI 1640 medium (GIBCO, Fisher Scientific, Strasbourg, France) supplemented with 10% Fetal Bovine Serum (FBS) in 5% CO2 and 37°C.

extract_protocol:
After 48h of treatment with atheroma plaque homogenates with DMSO or with  GSK2033, cells were harvested, stored at -80°C and transfer to Active Motif for tagmentation, library preparation and sequencing.
ATAC-seq analysis were performed by Active Motif company (Waterloo, Belgium) using 1x105 cells per sample.  Filtered reads were aligned to the GRCh38 reference genome. Open chromatin regions were identified with HOMER.

treatment_protocol: On day 6, hMDMs were treated for 48 hours with whole atherosclerotic plaque extracts (1% v/v in cell culture medium) and with 1 µM of GSK2033 (LXR antagonist; Sigma Aldrich, St. Louis, Missouri, USA, Cat#1221277-90-2) or 1µM of dimethylsulfoxyde (DMSO, vehicle control; Sigma Aldrich, St. Louis, Missouri, USA, Cat#D8418)

value: human blood

value: Human Monocyte Derived Macrophages

value: atheroma plaque + DMSO


title: RNA-seq - siDHX30 - rep2


title: Healthy donor, human Monocyte Derived Macrophages, atheroma plaque, GSK

description: Library name: Donneur-PG_ATAC_hg38

value: atheroma plaque + GSK


title: High-proliferating Leishmania major infected-single cell#6 , Mouse#5_Left ear [1_B7]

value: monocytes

value: ear tissue

value: 10 weeks old


title: RNA-seq - siTfam - rep2

value: Knockdown of Tfam by siRNA transfection


title: WT, S29BAT-1

description:
WT1
raw_counts.text

value: brown adipose tissue

value: WT

value: cold tolerance experiment


title: WT, S29BAT-2

description:
WT2
raw_counts.text


title: thm1_like

city: Beijing

first: Lei

last: Gao

state: Beijing

address: East Building of Resources, No. 5 Yiheyuan Road, Haidian District, Beijing

institute: Peking University

description: Library name: T4

data_processing:
Raw sequencing reads were subjected to quality control to remove adaptor contamination, low-quality bases, and reads with excessive ambiguous nucleotides, yielding high-quality clean reads. Clean reads were aligned to the Arabidopsis thaliana reference genome using a standard short-read alignment workflow. Based on the alignment results, single-nucleotide polymorphisms (SNPs) and small insertions/deletions (InDels) were identified and annotated using established variant-calling pipelines.Read filtering and quality control. Raw sequencing reads contained adaptor contamination and low-quality bases and were therefore subjected to stringent quality filtering prior to downstream analyses. Read pairs containing adaptor sequences were removed. For each single-end read within a pair, if the proportion of ambiguous nucleotides (N) exceeded 10% of the read length, the entire read pair was discarded. Similarly, read pairs were removed when more than 50% of bases in either read had a quality score ≤ 5. The remaining high-quality reads were retained as clean reads and used for all subsequent analyses.
Assembly: Arabidopsis thaliana Col-0 genome at Tair 10(https://www.arabidopsis.org/) and Sequnceing genome of WT sample
Supplementary files format and content: Delta_All.index.xls

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
Genomic DNA was extracted from Arabidopsis thaliana leaves using a standard CTAB protocol with minor modifications. Briefly, frozen leaf tissue (~50–100 mg) was ground in liquid nitrogen and incubated in CTAB extraction buffer (2% CTAB, 100 mM Tris-HCl pH 8.0, 20 mM EDTA, 1.4 M NaCl, 1% PVP-40, and 0.2% β-mercaptoethanol) at 65 °C for 30 min. After chloroform:isoamyl alcohol extraction and isopropanol precipitation, DNA was washed with 70% ethanol, air-dried, dissolved in TE, and treated with RNase A
High-quality genomic DNA was sheared to an average fragment size of ~350 bp using a Covaris ultrasonicator. Sequencing libraries were constructed with the TruSeq DNA Library Preparation Kit following the manufacturer’s instructions and using all recommended reagents and consumables. Briefly, fragmented DNA underwent end repair, A-tailing, and adaptor ligation, followed by bead-based purification. Libraries were enriched by limited-cycle PCR amplification, purified, and assessed for size distribution and concentration prior to sequencing.

value: leaf

value: thm1 mutant


title: BM-derived neutrophils + z-IETD-fmk Rep3

city: Messina

first: Concetta

last: Beninati

state: ME

address: Via Consolare Valeria 1

department: Human Pathology

country: Italy

institute: University of Messina

description:
Library name: Lib_SJA_66
Lib_SJA_66

data_processing:
Total RNA sequencing was performed on an Illumina NextSeq2000 instrument usinga NextSeq 2000 P3 flow cell and reagents
Raw sequencing data were uploaded to the Galaxy web platform (https://usegalaxy.org/)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (Galaxy Version 0.39+galaxy2)
Trimmed sequence reads were mapped to GrCM38/mm10 using HISAT2 (Galaxy Version 2.2.1+galaxy1) and annotated with annotate MyIDs (Galaxy Version 3.18.0+galaxy0)
Gene counts (featureCounts,Galaxy Version 2.0.8+galaxy0) were analyzed for differential expression with limma-voom (Galaxy Version 3.58.1+galaxy0)
Comparisons were normalized using a trimmed mean of M values (TMM) and raw p-values were adjusted using Benjamini and Hochberg multiple tests. Adjusted p-values lower than 0.05 were considered significant
Assembly: mm10
Supplementary files format and content: xlsx files include Normalized Counts for each Sample grouped in Neutrophils and Marcrophages
Supplementary files format and content: xlsx files include Differential Gene Expression by limma-voom for each cells line (Neutrophils and Marcrophages)

source_name: Bone Marrow

growth_protocol: Neutrophils and Macrophages cells after isolation from murine bone marrow were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted from TRIzol lysates of 3 x106 cells
Sequencing libraries were prepared using the Illumina Stranded Total RNA Prep Ribo-Zero Plus for stranded total RNA sequencing according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with z-IETD-fmk (50 µM in DPBS) or vehicle (DMSO 0,2%) for 3 h during manteinment  in RPMI supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37°C

value: Bone Marrow

value: Neutrophils

value: z-IETD-fmk 50 µM

value: 3 h


title: BM-derived neutrophils + vehicle Rep4

description:
Library name: Lib_SJA_69
Lib_SJA_69

value: DMSO 0,2%


title: mESCs grown with LIF

city: Vilnius

first: Denis

last: Baronas

address: Saulėtekio al. 7

country: Lithuania

institute: Vilnius University

description:
Library name: mesc
CapSeq experiment performed on Neuro-2a, NIH/3T3, and mESC cell lines, with mESC cells demultiplexed.

data_processing:
To generate cell × gene count matrices, the CapMux snakemake pipeline was run under {run_mode: "bcl", demux_by: "bc1"} and {run_mode: "bcl", demux_by: "index"} execution regimes. Barcode segments were defined as follows: bc1:{start: 32, len: 8}, bc2:{start: 18, len: 10}, bc3:{start: 5,  len: 8}, umi1: {start: 1,  len: 4}, umi2: {start: 40, len: 4}. Reads were aligned to the mouse GRCm39 genome (GENCODE M30).
Assembly: GRCm39
Supplementary files format and content: Matrix files of gene expression raw count data in _matrix.mtx
Supplementary files format and content: Tab separated files of barcodes in _barcodes.tsv
Supplementary files format and content: Tab separated files of genes in _features.tsv
Supplementary files format and content: AnnData files in _adata.h5ad
Supplementary files format and content: Excel files of metadata containing barcode information linked to patient code or condition in _metadata.xlsx

source_name: mESC

growth_protocol: NIH/3T3 (ATCC, CRL-1658) and Neuro-2a (ATCC, CCL-131) cells were grown in Dulbecco's Modified Eagle Medium (DMEM, Gibco, 61965026) supplemented with 10% fetal bovine serum (FBS) and 1X penicillin-streptomycin (PS; Gibco, 15140122). Mouse embryonic stem cells (ATCC, CRL-1821, E14TG2a) were cultivated on dishes coated with 0.15% gelatin in DMEM supplemented with 15% FBS, 1× PS, 0.1 mM sodium pyruvate (Gibco, 11360039), 0.1 mM β-mercaptoethanol (Gibco, 31350010), 1 mM L-alanyl-L-glutamine (Gibco), 1× Non-Essential Amino Acids (Gibco, 11140050), 1×10^3 U/ml mouse leukemia inhibitory factor (Millipore), 3 μM CHIR99021 (Sigma) and 1 μM PD0325901 (Sigma). All cell lines were grown at 5% CO2 and at 37 ºC.

extract_protocol:
Cells were collected at roughly  1×10^6 cells/mL, transferred into 15 mL conical tubes, pelleted by centrifugation (100–300 × g for 5–7 min), and washed twice with ice-cold 1X Dulbecco’s Phosphate-Buffered Saline (DPBS; Gibco 14190144). Cell number and viability were assessed with a hemocytometer using 0.2% trypan blue staining. The cells were then subjected to an additional centrifugation step, the supernatant was discarded, and the cell pellet was resuspended to achieve a final volume corresponding to 3 million cells per milliliter.
Illumina sequencing libraries were prepared for each amplified cDNA aliquot with NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (NEB, cat. no. E7805S) according to the instructions in the manual, with minor changes. In particular, 5-10 ng of amplified cDNA was used for cDNA fragmentation and transferred to a PCR tube. Nuclease-free water was added to reach the final volume on 13 µL. Fragmentation reaction was assembled on ice by adding 3.5 µL of NEBNext® Ultra™ II FS Reaction Buffer followed by 1 µL of NEBNext® Ultra™ II FS Enzyme Mix. Reaction mix was vortexed and spun-down for 3-5 seconds. The fragmentation was performed for 8 minutes at 37 °C, followed by end-repair and dA tailing for 30 min at 65 °C (lid was set at 75 °C). Fragmented cDNA was purified with 0.6X-0.8X double-size selection using SPRIselect beads and eluted in 17.5 µL with nuclease-free water. Then, 1.5 µM ligation adapter was prepared in advance by mixing 1.5 µL of forward ligation primer (100 µM, /5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC; HPLC purification, IDT) and 1.5 µL of reverse ligation primer (/5AmMC6/GCTCTTCCGATCT; HPLC purification, IDT) with 97 µL of water. To anneal oligos, the solution was heated to 95 °C for 2 min (lid at 100 °C) and cooled at room temperature for 5 min. Next, purified fragmented cDNA was mixed with 15 µL of NEBNext® Ultra™ II Ligation Master Mix, 1.25 µL of ligation adapter and 0.5 µL of NEBNext® Ligation Enhancer. Reaction solution was well mixed by pipetting and incubated for 15 min at 20 °C (lid set at 37 °C). The ligation product was diluted to 100 µL with nuclease-free water, followed by a 0.8X SPRI size selection procedure and eluted in 40 µL with nuclease-free water. Finally, the ligation product was amplified by 11-cyles of PCR: 95 ºC for 3 min, 12-cycles [98 ºC for 20 s, 54 ºC for 30 s, 72 ºC for 20 s], and 72 ºC for 60 s. PCR mix was prepared by mixing 20 µL of ligation product, 2.5 µL of forward indexing primer (Table  S25), 2.5 µL of reverse indexing primer (Table S25) and 25 µL of 2X KAPA HiFi HotStart ReadyMix. Amplified sequencing libraries were purified with 0.6X-0.8X double-size selection using SPRIselect beads and eluted in 20 µL with nuclease-free water.

value: mESC


title: Neuro-2a, NIH/3T3, and mESCs mixture

description:
Library name: mixture
CapSeq experiment performed on Neuro-2a, NIH/3T3, and mESC cell lines.

source_name: Neuro-2a, NIH/3T3, and mESC

value: Neuro-2a, NIH/3T3, and mESC


title: M-CSF M + z-IETD-fmk Rep4

description:
Library name: Lib_SJA_61
Lib_SJA_61

value: Macrophages


title: BM-derived neutrophils + vehicle Rep3

description:
Library name: Lib_SJA_68
Lib_SJA_68


title: NIH/3T3 cell line

description:
Library name: nih3t3
CapSeq experiment performed on Neuro-2a, NIH/3T3, and mESC cell lines, with NIH/3T3 cells demultiplexed.


title: BM-derived neutrophils + z-IETD-fmk Rep4

description:
Library name: Lib_SJA_67
Lib_SJA_67


title: BM-derived neutrophils + z-IETD-fmk Rep2

description:
Library name: Lib_SJA_65
Lib_SJA_65


title: M-CSF M + z-IETD-fmk Rep2

description:
Library name: Lib_SJA_59
Lib_SJA_59


title: M-CSF M + vehicle Rep3

description:
Library name: Lib_SJA_56
Lib_SJA_56


title: WTa

description: Library name: WTa


title: High-proliferating Leishmania major infected-single cell#1 , Mouse#2_Left ear [1_A4]

value: monocytes


title: CaMPARI-red cells stationary condition, batch 2

description:
Library name: Stationary2
10x Genomics

value: Brain


title: Sorted CD36 negative cells from B2-3 iPSC-derived airway epithelial cells_rep3

city: Kyoto city

first: Shimpei

last: Gotoh

state: Kyoto prefecture

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Department of clinical application

institute: Kyoto University CiRA

description: Library name: CD36_neg_3

data_processing:
Adapter sequences and low-quality bases were trimmed from the raw reads using cutadapt  ver v4.6 . The trimmed reads were mapped to human reference genome sequences (hg38) plus the reporter (EGFP) sequence using STAR ver 2.7.11a  with the GENCODE  (release 32, GRCh38.p13) gtf file. The raw counts were calculated using htseq-count ver. 2.0.5 with the GENCODE gtf file. Gene expression levels were determined as Transcripts Per Kilobase Million (TPM).
Genes with an average TPM below 0.5 across all samples were excluded from downstream analyses. The resulting expression matrix was log-transformed log2(TPM+1) and normalized via row-wise Z-score scaling.Gene expression patterns were visualized by hierarchical clustering and heatmaps, generated using the heatmap.2 function in R. Hierarchical clustering was conducted using Ward’s method with Euclidean distance (Murtagh and Legendre, 2014). Principal component analysis (PCA) was performed using the top 300 most variable genes across all samples. PCA plots were generated using ggplot2, and each point represents a biological replicate colored by sample ID and shaped by CD36 status. PC1 and PC2 explained 95.3% and 1.75% of the variance, respectively.
Differential gene expression analysis between CD36⁺ and CD36⁻ cell populations was conducted using the Wald test implemented in DESeq2, with Benjamini–Hochberg correction applied for multiple testing (Love et al., 2014; Benjamini and Hochberg, 1995). Genes with |log₂ fold change| > 1 and adjusted p < 0.05 were considered significantly differentially expressed. Volcano plots were generated using the EnhancedVolcano R package.Selected genes of interest, including multiciliogenesis and airway lineage markers, were visualized individually to highlight their expression patterns. Gene Ontology (GO) enrichment analysis was conducted on differentially upregulated genes in CD36⁺ cells using the clusterProfiler R package (Yu et al., 2012). Gene IDs were converted to Entrez IDs via the org.Hs.eg.db database, and enrichment was assessed across three GO categories: Biological Process (BP), Molecular Function (MF), and Cellular Component (CC). Enriched terms were visualized via bar plots and dot plots, and tab-delimited result tables were exported.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files incude count values and TPM for each sample.

source_name: airway epithelium

growth_protocol: CD36-positive and -negative cells were isolated by flow cytometry on day 12 of ALI culture, after CPM-positive cells derived from B2-3 SFTPC-GFP reporter hiPSCs were seeded under ALI conditions. The B2-3 line was generated from the 201B7 hiPSC line, originally established from a healthy donor (Takahashi et al., 2007; Gotoh et al., 2014).

extract_protocol:
Total RNA of CD36-positive and CD36-negative cells was isolated using the RNeasy Micro Kit (Qiagen) following the manufacturer’s instructions. RNA integrity for each sample was assessed using the Agilent 2100 BioAnalyzer, with all samples showing an RNA integrity number (RIN) exceeding 9.5.
For the comparison of CD36-positive and CD36-negative cell populations, 10 ng of total RNA was used for RNA-seq library preparation with the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus (Cat. 20040525) kit according to the manufacturer’s instructions. Sequencing was performed on an illumina NextSeq 2000 platform with the paired-end mode. The fastq files were generated using bcl2fastq-2.20.

value: airway epithelium

value: B2-3 iPSC

value: iPSC-derived airway epithelial cells


title: M-CSF M + z-IETD-fmk Rep1

description:
Library name: Lib_SJA_58
Lib_SJA_58


title: Sorted CD36 positive cells from B2-3 iPSC-derived airway epithelial cells_rep3

description: Library name: CD36_pos_3


title: BM-derived neutrophils + vehicle Rep1

description:
Library name: Lib_SJA_62
Lib_SJA_62


title: Sorted CD36 positive cells from B2-3 iPSC-derived airway epithelial cells_rep2

description: Library name: CD36_pos_2


title: Neuro-2a cell line

description:
Library name: n2a
CapSeq experiment performed on Neuro-2a, NIH/3T3, and mESC cell lines, with Neuro-2a cells demultiplexed.


title: Sorted CD36 positive cells from B2-3 iPSC-derived airway epithelial cells_rep1

description: Library name: CD36_pos_1


title: M-CSF M + z-IETD-fmk Rep3

description:
Library name: Lib_SJA_60
Lib_SJA_60


title: M-CSF M + vehicle Rep4

description:
Library name: Lib_SJA_57
Lib_SJA_57


title: BM-derived neutrophils + z-IETD-fmk Rep1

description:
Library name: Lib_SJA_63
Lib_SJA_63


title: HCC22-088-P5-S2_F_rep

city: Pittsburgh

first: Alexander

middle: Chih-Chieh

last: Chang

state: PA

address: 5051 Centre Ave

country: USA

institute: University of Pittsburgh

description:
Library name: HCC22-088-P5-S2_F_rep
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture

library_source: other

data_processing:
Raw sequencing data was processed using the 10x Genomics Spaceranger pipeline to generate fastq files
Sequences were aligned to the hg38 genome using Spaceranger's default settings
Gene expression of refseq coding genes were quanitfied using Spaceranger's default settings.
Assembly: GrCh38-2020-A
Supplementary files format and content: barcodes.tsv.gz: List of spatial barcodes, each corresponding to a spot on the Visium slide.
Supplementary files format and content: features.tsv.gz: List of gene or protein features, including their unique identifiers and names.
Supplementary files format and content: matrix.mtx.gz: Sparse matrix containing counts of each feature (gene or protein) per barcode (spot).
Supplementary files format and content: aligned_fiducials.jpg: Image of the slide with fiducial markers aligned to aid in spatial registration.
Supplementary files format and content: aligned_tissue_image.jpg: Processed image of the tissue with alignment corrections applied.
Supplementary files format and content: cytassist_image.tiff: High-resolution raw image captured by the CytAssist instrument before alignment.
Supplementary files format and content: detected_tissue_image.jpg: Image showing the detected tissue region on the slide after preprocessing.
Supplementary files format and content: scalefactors_json.json: JSON file containing scale factors for converting between different image resolutions.
Supplementary files format and content: spatial_enrichment.csv: CSV file containing spatial enrichment scores for various features across spots.
Supplementary files format and content: tissue_hires_image.png: High-resolution image of the tissue captured from the slide.
Supplementary files format and content: tissue_lowres_image.png: Lower-resolution version of the tissue image used for visualization and analysis.
Supplementary files format and content: tissue_positions.csv: CSV file mapping spatial barcodes to their corresponding X, Y coordinates in the tissue.
Supplementary files format and content: feature_reference.csv: Reference file containing feature annotations, including gene or protein names and identifiers.
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5-formatted file containing the filtered feature-barcode matrix for gene or protein expression.
Supplementary files format and content: isotype_normalization_factors.csv: CSV file containing normalization factors for isotype control correction in antibody capture data.
Supplementary files format and content: molecule_info.h5: HDF5 file containing detailed molecule-level information, including UMI counts and feature assignments.
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Breast

extract_protocol:
Prior to sectioning, samples were assessed for RNA quality, and all samples had a DV200 score above the minimum threshold (\(\geq30\%\)). Spatial transcriptomic and proteomic libraries were generated with Visium CytAssist for FFPE v2 gene expression kit (10x Genomics: 1000520) with the Human Immune Cell Profiling Panel (10x Genomics: PN-1000607).
Five-micron FFPE sections were placed on Schott Nexterion Hydrogel Coated Slides (Schott North America: 1800434) or Fisherbrand Superfrost Plus Slides (Fisher: 22-037-246) and processed through the 10x CytAssist for FFPE v2 protocol according to the manufacturer’s instructions. Library QC was completed with an Agilent TapeStation 4150. Libraries were normalized and pooled to 2 nM prior to loading on an Illumina NextSeq 2000, using a P3 100 flow cell. The pooled library was loaded at 650 pM, and sequencing was carried out with a 28/10/10/50 bp read structure, targeting 125 million reads per sample for transcriptomic libraries and 25 million reads per sample for proteomic libraries.

value: Breast

value: post primary endocrine therapy


title: M-CSF M + vehicle Rep1

description:
Library name: Lib_SJA_54
Lib_SJA_54


title: Sorted CD36 negative cells from B2-3 iPSC-derived airway epithelial cells_rep1

description: Library name: CD36_neg_1


title: HCC22-088-P4-S2

description:
Library name: HCC22-088-P4-S2
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture


title: HCC22-088-P2-S2

description:
Library name: HCC22-088-P2-S2
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture


title: NRVM, AAV-cTnT-MCS, bio rep 4

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description: Library name: Sample 24

data_processing:
Libraries were sequenced on NovaSeq X Plus using paired-end 150 bp
Reads were mapped to rn6 build of the rat transcriptome using STAR (Dobin et al. 2013).
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Assembly: rn6
Supplementary files format and content: Excel file with differential expression analysis (DESeq2)
Supplementary files format and content: RNA-seq_Wang_2025_NRVM.xlsx

organism: Rattus norvegicus

source_name: Neonatal rat ventricular myocytes

extract_protocol:
RNA was harvested using NucleoSpin RNA kit (Macherey-Nagel). 1.25 ug of total RNA was used for constructio nof sequencign libraries.
RNA libraries for RNA-seq were prepared using KAPA mRNA Hyperprep (mRNA Capture) following manufacturer's protocol.

value: Neonatal rat ventricular myocytes


title: HCC22-088-P1-S1

description:
Library name: HCC22-088-P1-S1
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture

value: pre-treament


title: Sorted CD36 negative cells from B2-3 iPSC-derived airway epithelial cells_rep2

description: Library name: CD36_neg_2


title: BM-derived neutrophils + vehicle Rep2

description:
Library name: Lib_SJA_64
Lib_SJA_64

value: Bone Marrow


title: NRVM, AAV-cTnT-MCS, bio rep 3

description: Library name: Sample 23


title: HCC22-088-P1-S2

description:
Library name: HCC22-088-P1-S2
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture


title: M-CSF M + vehicle Rep2

description:
Library name: Lib_SJA_55
Lib_SJA_55


title: NRVM, AAV-cTnT-MCS, bio rep 1

description: Library name: Sample 21


title: NRVM, AAV-cTnT-Hcn2, bio rep 1

description: Library name: Sample 17


title: HCC22-088-P5-S1

description:
Library name: HCC22-088-P5-S1
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture


title: HCC22-088-P2-S1

description:
Library name: HCC22-088-P2-S1
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture


title: HCC22-088-P4-S2_1i_rep

description:
Library name: HCC22-088-P4-S2_1i_rep
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture


title: NRVM, AAV-cTnT-MCS, bio rep 2

description: Library name: Sample 22


title: HCC22-088-P6-S2_D

description:
Library name: HCC22-088-P6-S2_D
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture


title: HCC22-088-P6-S1

description:
Library name: HCC22-088-P6-S1
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture


title: NRVM, AAV-cTnT-Hcn2, bio rep 2

description: Library name: Sample 18


title: NRVM, AAV-cTnT-TBX18, bio rep 3

description: Library name: Sample 11


title: NRVM, AAV-cTnT-uORF-TBX18, bio rep 1

description: Library name: Sample 13


title: NRVM, AAV-cTnT-uORF-TBX18, bio rep 3

description: Library name: Sample 15


title: NRVM, AAV-cTnT-Hcn2, bio rep 4

description: Library name: Sample 20


title: NRVM, AAV-cTnT-Hcn2, bio rep 3

description: Library name: Sample 19


title: HCC22-088-P4-S1

description:
Library name: HCC22-088-P4-S1
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture


title: NRVM, AAV-cTnT-uORF-TBX18, bio rep 4

description: Library name: Sample 16


title: HCC22-088-P5-S2

description:
Library name: HCC22-088-P5-S2
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture


title: NRVM, AAV-CMV-uORF-TBX18, bio rep 4

description: Library name: Sample 8


title: NRVM, AAV-cTnT-uORF-TBX18, bio rep 2

description: Library name: Sample 14


title: HCC22-088-P3-S1_A

description:
Library name: HCC22-088-P3-S1_A
FFPE Spatial Transcriptomic Sequencing with Visium Antibody Capture


title: NRVM, AAV-cTnT-TBX18, bio rep 4

description: Library name: Sample 12


title: NRVM, AAV-CMV-TBX18, bio rep 2

description: Library name: Sample 2


title: NRVM, AAV-CMV-TBX18, bio rep 1

description: Library name: Sample 1


title: NRVM, AAV-cTnT-TBX18, bio rep 1

description: Library name: Sample 9


title: NRVM, AAV-CMV-uORF-TBX18, bio rep 1

description: Library name: Sample 5


title: NRVM, AAV-cTnT-TBX18, bio rep 2

description: Library name: Sample 10


title: NRVM, AAV-CMV-TBX18, bio rep 3

description: Library name: Sample 3


title: NRVM, AAV-CMV-TBX18, bio rep 4

description: Library name: Sample 4


title: NRVM, AAV-CMV-uORF-TBX18, bio rep 3

description: Library name: Sample 7


title: NRVM, AAV-CMV-uORF-TBX18, bio rep 2

description: Library name: Sample 6


title: HLMC_D4_IL3324h [S16]

city: Solna

first: Elin

last: Rönnberg Höckerlind

address: NKs Bioclinicum J7:30, Visionsgatan 4

department: Medicine (Solna)

country: Sweden

institute: Karolinska Institutet

description:
Library name: S16
The library name represents the column names in the count matrix

data_processing:
Raw data QC, alignment to GRCh38 and gene level read counting steps were performed using the nf-core/rnaseq pipeline at NGI Stockholm, Sweden.
Assembly: GRCh38
Supplementary files format and content: The uploaded processed data represents the count table generated by Salmon within the nf-core pipeline. This file was used for all downstream analysis.

source_name: Lung

growth_protocol: Cells were culture in StemProTM-34 SFM media (Thermo Fisher Scientific) with 2mM L-Glutamine, 1% pen/strep and 100 ng/ml SCF/KITLG.

extract_protocol:
Human lung tissue was cut into small pieces and enzymatically digested for 30 minutes with 0.2 mg/mL DNase I (Sigma-Aldrich, St. Louis, MO, USA) and 0.1 mg/mL Liberase TL (Sigma-Aldrich). Thereafter, the tissue was vigorously cut by scissors and mechanically disrupted by plunging through a syringe. The cells were purified by 30% Percoll centrifugation, and red blood cells were lysed using ACK lysis buffer (Thermo Fisher, Waltham, MA, USA). Mast cells were enriched by magnetic-activated cell sorting (MACS) enrichment using CD117 MicroBead Kit (Miltenyi). RNA was extracted using Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific).
The libraries were prepared at NGI Science for Life Laboratory, Stockholm, Sweden using SMARTer Total Stranded RNA-seq (Takara Bio).

treatment_protocol: Cells were exposed to 10 ng/ml IL-33 (Peprotech, Rocky Hill, NJ, USA) and/or 100 ng/ml IL-2 (Sigma-Aldrich) for various timepoints.

value: Lung

value: HLMC

tag: time point

tag: batch


title: HLMC_D1_IL3324h_IL22h [S17]

description:
Library name: S17
The library name represents the column names in the count matrix


title: HLMC_D2_IL3324h_IL22h [S18]

description:
Library name: S18
The library name represents the column names in the count matrix


title: HLMC_D4_IL3324h_IL22h [S20]

description:
Library name: S20
The library name represents the column names in the count matrix


title: HEK293T, FLAG-DHX29, rep1

city: Kyoto

first: Masanori

last: Yoshinaga

state: Kyoto

address: Yoshida-konoe-cho, Sakyo-ku

department: Graduate School of Medicine

institute: Kyoto University

description: Library name: DMSO_DHX29_0.01unit_rep1

data_processing:
Adapter trimming and quality filtering (fastp, cutadapt v3.7). Demultiplexing by 3′ barcode and UMI extraction (5′ 2nt + 3′ 5nt) using umi_tools v1.1.4. Reads filtered against ncRNAs using STAR v2.7.0a, then aligned to GRCh38 (--alignEndsType Local, --outFilterMultimapNmax 1). PCR duplicates removed by umi_tools v1.1.4. Gene-level counts generated by featureCounts v2.0.3 (--read2pos 5, -s 2).
Assembly: hg38 (GRCh38), Ensembl release 115
Supplementary files format and content: Tab-delimited text file containing gene-level read counts. Columns: gene_id (Ensembl gene ID), count (UMI-deduplicated reads, 5′ end assignment).

growth_protocol: HEK293T cells stably expressing FLAG-DHX29 were cultured in DMEM with 10% FBS, 50 μM 2-mercaptoethanol, 100 μg/ml penicillin/streptomycin, 15 μg/ml blasticidin.

extract_protocol:
Cells were washed with cold-PBS, UV-crosslinked (254 nm, 300 mJ/cm²), and harvested in lysis buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 10 mM DTT, 5 mM MgCl₂, 1% TritonX-100). Lysates were DNase-treated (TurboDNase, 10 min, on ice), clarified (20,000×g, 10 min, 4°C), and digested with RNase I (0.01 units/ml, 37°C, 5 min). After SDS addition (0.1%), lysates were immunoprecipitated with FLAG M2-Protein G Dynabeads (2h, 4°C). Beads were washed, and RNA-protein complexes were dephosphorylated (T4 PNK, 1h, 37°C) and ligated to IR800-conjugated 3′ adapters.  Complexes were eluted, resolved on SuperSep Ace 5-20% gel, and fragments >130 kDa were excised. RNA was extracted by Proteinase K digestion and isopropanol precipitation.
Reverse transcription was performed using SuperScript IV (50°C, 60 min). cDNA fragments (10-200 nt) were size-selected, ligated to 5′ adapter (5′-/5Phos/NNAGATCGAAGGCAGCGCTGTGGAGAAAG/3ddC/-3′), and PCR-amplified (18 cycles, Phusion polymerase). Libraries were sequenced on Illumina NovaSeq X Plus.

treatment_protocol: Cells (5×10^6 per 15 cm dish) were induced with doxycycline (40 ng/ml) for 24 hours.

value: Stablely expressing DOX-inducible FLAG-DHX29

value: DOX 40ng/ml for 24 h


title: HLMC_D2_IL3324h [S14]

description:
Library name: S14
The library name represents the column names in the count matrix


title: HEK293T, FLAG-DHX29, rep2

description: Library name: DMSO_DHX29_0.01unit_rep2


title: HLMC_D1_IL3324h [S13]

description:
Library name: S13
The library name represents the column names in the count matrix


title: HLMC_D3_IL22h [S11]

description:
Library name: S11
The library name represents the column names in the count matrix


title: HLMC_D4_IL22h [S12]

description:
Library name: S12
The library name represents the column names in the count matrix


title: HLMC_D4_IL332h [S8]

description:
Library name: S8
The library name represents the column names in the count matrix


title: HLMC_D3_IL3324h [S15]

description:
Library name: S15
The library name represents the column names in the count matrix


title: HLMC_D4_Control [S4]

description:
Library name: S4
The library name represents the column names in the count matrix

value: Control


title: HLMC_D2_IL332h [S6]

description:
Library name: S6
The library name represents the column names in the count matrix


title: HLMC_D1_IL332h [S5]

description:
Library name: S5
The library name represents the column names in the count matrix


title: HLMC_D3_Control [S3]

description:
Library name: S3
The library name represents the column names in the count matrix


title: HLMC_D2_Control [S2]

description:
Library name: S2
The library name represents the column names in the count matrix


title: HLMC_D3_IL332h [S7]

description:
Library name: S7
The library name represents the column names in the count matrix


title: INPUT_KO_DMSO_Rep11

city: Madison

first: Wei

last: Xu

state: WI

address: 7459 WIMR II

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

description: Library name: INPUT_KO_DMSO_Rep11

data_processing:
ENCODE ChIP-seq pipeline (version 2.1.6) was used to align reads to human genome (hg38), call peaks, and calculate fold-change signals of target over input. Only peaks from Chromosomes 1-22 and X were considered.
Assembly: hg38
Supplementary files format and content: bigWig of ChIP-seq fold-change signals of target over input for each replicates and pooled replicates
Supplementary files format and content: gzipped TSV of ChIP-seq peaks

extract_protocol:
Cells  were fixed with 1% formaldehyde for 14 min,  after quenching and cell lysis. Chromatin was sonicated using a Branson Sonifier 450 with a microtip (40% amplitude, 3 s on, 10 s off, 5 min of total pulse time).
ChIP-seq libraries were constructed using the Ovation Ultralow System V2 1–16 Kit (NuGEN Technologies) according to the manufacturer’s protocol. Briefly, 2ng of ChIP DNA was end-repaired and ligated to specific adaptors. The adapted DNA was purified using Agencourt® Ampure XP Beads (Beckman Coulter, Cat. #A63881), followed by PCR amplification (13 cell cycle for 2ng DNA input). The amplified DNA was purified again with Ampure XP Beads. The quality of the library, including the library size distribution, purity, concentration was assessed at the Sequencing Facility Center of University of Wisconsin-Madison. Qualified libraries were sequenced on an Illumina Novaseq X Plus platform with paired-end reads of 150 bases.

value: human breast cancer

value: BRD8 knockout

value: DMSO

tag: chip antibody


title: H2AZac_WT_NERA_Rep11

description: Library name: H2AZac_WT_NERA_Rep11

value: wide type

value: Neratinib

value: H2A.Z (acetyl K4 + K7 + K11) (abcam, AB232908)


title: H2AZac_WT_DMSO_Rep22

description: Library name: H2AZac_WT_DMSO_Rep22


title: HLMC_D3_IL3324h_IL22h [S19]

description:
Library name: S19
The library name represents the column names in the count matrix


title: HLMC_D1_Control [S1]

description:
Library name: S1
The library name represents the column names in the count matrix


title: HLMC_D2_IL22h [S10]

description:
Library name: S10
The library name represents the column names in the count matrix


title: INPUT_WT_DMSO_Rep11

description: Library name: INPUT_WT_DMSO_Rep11


title: H2AZac_KO_DMSO_Rep22

description: Library name: H2AZac_KO_DMSO_Rep22


title: H2AZac_WT_NERA_Rep22

description: Library name: H2AZac_WT_NERA_Rep22


title: H2AZac_KO_NERA_Rep22

description: Library name: H2AZac_KO_NERA_Rep22


title: H2AZ_WT_NERA_Rep22

description: Library name: H2AZ_WT_NERA_Rep22

value: H2AZ (Thermo, MA5-24666)


title: H2AZac_WT_DMSO_Rep11

description: Library name: H2AZac_WT_DMSO_Rep11


title: H2AZac_KO_NERA_Rep11

description: Library name: H2AZac_KO_NERA_Rep11


title: H2AZ_KO_NERA_Rep22

description: Library name: H2AZ_KO_NERA_Rep22


title: H2AZac_KO_DMSO_Rep11

description: Library name: H2AZac_KO_DMSO_Rep11


title: H2AZ_WT_DMSO_Rep22

description: Library name: H2AZ_WT_DMSO_Rep22


title: HLMC_D1_IL22h [S9]

description:
Library name: S9
The library name represents the column names in the count matrix


title: INPUT_KO_NERA_Rep11

description: Library name: INPUT_KO_NERA_Rep11


title: H2AZ_WT_DMSO_Rep11

description: Library name: H2AZ_WT_DMSO_Rep11


title: H2AZ_WT_NERA_Rep11

description: Library name: H2AZ_WT_NERA_Rep11


title: INPUT_WT_NERA_Rep11

description: Library name: INPUT_WT_NERA_Rep11


title: H2AZ_KO_NERA_Rep11

description: Library name: H2AZ_KO_NERA_Rep11


title: H2AZ_KO_DMSO_Rep22

description: Library name: H2AZ_KO_DMSO_Rep22


title: rice, control, rep3

city: Yangzhou

first: Chongyuan

last: Zhong

address: Hanjiang

institute: Yangzhou University

description: Library name: ZH11_3_2

data_processing:
Fastp V0.20
Quality control of Raw Data was performed using Fastp, with sequencing adapters removed from the reads.
Low-quality reads were trimmed using Fastp.
Assembly: Hisat2 was employed for read alignment using the rice reference genome and annotation files from RGAP with default parameters, and the alignment status of the sequencing reads was subsequently evaluated.
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

organism: Oryza sativa

source_name: culm

extract_protocol:
Total RNA was extracted using a commercial RNA isolation kit.
Total RNA was extracted and qualified.Poly(A) mRNA was isolated and fragmented.First-strand cDNA was synthesized using random hexamers, followed by second-strand cDNA synthesis.After end repair, poly(A) addition, and adapter ligation, the library was purified and amplified by PCR.

value: culm

value: WT


title: rice, TAC4L/TAC4-KO, rep3

description: Library name: DKO_5_2

value: TAC4L/TAC4 knockdown


title: H2AZ_KO_DMSO_Rep11

description: Library name: H2AZ_KO_DMSO_Rep11


title: rice, control, rep2

description: Library name: ZH11_2_2


title: rice, TAC4L/TAC4-KO, rep1

description: Library name: DKO_2_2


title: rice, control, rep1

description: Library name: ZH11_1_2


title: rice, TAC4-KO, rep3

description: Library name: 2KO_5_2

value: TAC4 (LOC_Os02g25230) knockdown


title: rice, TAC4L/TAC4-KO, rep2

description: Library name: DKO_3_2


title: rice, TAC4-KO, rep1

description: Library name: 2KO_3_2


title: rice, TAC4L-KO, rep3

description: Library name: 1KO_4_2

value: TAC4L (LOC_Os04g19140) knockdown


title: rice, TAC4L-KO, rep2

description: Library name: 1KO_3_2


title: rice, TAC4L-KO, rep1

description: Library name: 1KO_2_2


title: rice, TAC4-KO, rep2

description: Library name: 2KO_4_2


title: CUT&Tag DUXR70A OE 24h P300 rep2

city: Shaanxi

first: Qifeng

state: Shaanxi

address: No.3 Taicheng Road, Yangling, Shaanxi, China

institute: Northwest A&F University

description:
Library name: CUT_Tag DUXR70A OE 24h P300 rep2
CUT&Tag DUXR70A OE 24h P300 rep2

data_processing:
Raw sequencing reads were quality controlled using FastQC (v0.11.9)
data processing step: Adapter trimming and quality filtering were performed using Trimmomatic (v0.39) with parameters: ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
Trimmed reads were aligned to the reference genome using Bowtie2 (v2.4.5) with parameters: --end-to-end --very-sensitive --no-mixed
Duplicate reads were removed using Picard MarkDuplicates (v2.25)
Peak calling was performed using SEACR (v1.3) with stringent threshold
Assembly: mm10
Supplementary files format and content: BigWig
Library strategy: CUT&Tag

growth_protocol: Mouse embryonic stem cells were maintained in standard mESC culture medium supplemented with leukemia inhibitory factor (LIF) on gelatin-coated plates under 37°C and 5% CO2 conditions.

extract_protocol:
100,000 live cells were bound to ConA-coated magnetic beads and permeabilized. Cells were incubated with primary antibodies (H3K4me1: CST 5326, H3K4me3: CST 9751, H3K27ac: Active Motif 39034) at 1:100 dilution for 2 hours at room temperature.
CUT&Tag libraries were prepared using the Novoprotein CUT&Tag Kit (N259-YH01). After antibody incubation, cells were incubated with pA-Tn5 adapter complex (1:100) for 1 hour. Tagmentation was activated with MgCl2, followed by DNA extraction and PCR amplification (17 cycles). Libraries were purified with AMPure XP beads.

treatment_protocol: Cells were treated with doxycycline (4 μg/mL) for 24 hours to induce DUX expression. Untreated controls were maintained in parallel.

value: mESCs

value: dox

value: Anti-p300 Cell signaling technology Cat# 54062


title: CUT&Tag mESC P300 rep2

description:
Library name: CUT_Tag mESC P300 rep2
CUT&Tag mESC P300 rep2

value: no


title: CUT&Tag DUX OE 24h P300 rep2

description:
Library name: CUT_Tag DUX OE 24h P300 rep2
CUT&Tag DUX OE 24h P300 rep2


title: CUT&Tag DUX OE 24h P300 rep1

description:
Library name: CUT_Tag DUX OE 24h P300 rep1
CUT&Tag DUX OE 24h P300 rep1


title: CUT&Tag DUXR70A OE 24h P300 rep1

description:
Library name: CUT_Tag DUXR70A OE 24h P300 rep1
CUT&Tag DUXR70A OE 24h P300 rep1


title: CUT&Tag DUXR70A OE 24h CTCF rep2

description:
Library name: CUT_Tag DUXR70A OE 24h CTCF rep2
CUT&Tag DUXR70A OE 24h CTCF rep2

value: Anti-CTCF Cell signaling technology Cat# 3418


title: CUT&Tag mESC CTCF rep2

description:
Library name: CUT_Tag mESC CTCF rep2
CUT&Tag mESC CTCF rep2


title: CUT&Tag DUX OE 24h 1,6hex Flag rep2

description:
Library name: CUT_Tag DUX OE 24h 1,6hex Flag rep2
CUT&Tag DUX OE 24h 1,6hex Flag rep2

value: fibroblast

value: Anti-FLAG Cell signaling technology Cat# 14793


title: CUT&Tag DUXR70A OE 24h Flag rep1

description:
Library name: CUT_Tag DUXR70A OE 24h Flag rep1
CUT&Tag DUXR70A OE 24h Flag rep1


title: CUT&Tag DUX OE 24h CTCF rep2

description:
Library name: CUT_Tag DUX OE 24h CTCF rep2
CUT&Tag DUX OE 24h CTCF rep2


title: CUT&Tag mESC P300 rep1

description:
Library name: CUT_Tag mESC P300 rep1
CUT&Tag mESC P300 rep1


title: CUT&Tag mESC CTCF rep1

description:
Library name: CUT_Tag mESC CTCF rep1
CUT&Tag mESC CTCF rep1


title: ATAC DUXdelta70-80aa OE 24h rep1

description:
Library name: ATAC DUXdelta70-80aa OE 24h rep1
ATAC DUXdelta70-80aa OE 24h rep1

data_processing:
Raw sequencing reads were quality controlled using FastQC (v0.11.9)
data processing step: Adapter trimming and quality filtering were performed using Trimmomatic (v0.39) with parameters: ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
Trimmed reads were aligned to the reference genome using Bowtie2 (v2.4.5) with parameters: --end-to-end --very-sensitive --no-mixed
Duplicate reads were removed using Picard MarkDuplicates (v2.25)
data processing step: Peak calling was performed using MACS2 (v2.2.7.1) with parameters: --nomodel --shift -100 --extsize 200 -q 0.05
Assembly: mm10
Supplementary files format and content: ATAC-seq.bw

extract_protocol:
Cells were harvested and washed with cold PBS. 60,000 cells were used for transposase reaction following the standard ATAC-seq protocol.
ATAC-seq libraries were prepared using the High-Sensitivity Open Chromatin Profile Kit 2.0 (for Illumina®) (Novoprotein-N248) according to manufacturer's instructions. Cells were tagmented with Tn5 transposase, followed by PCR amplification (12 cycles). Libraries were purified and size-selected using AMPure XP beads.

treatment_protocol: Cells were treated with doxycycline (4 μg/mL) for 24 hours to induce DUX expression. Untreated controls were maintained in parallel. The induction condition for RA is 0.53 μM for 48 hours. The induction condition for Plab is 4 nM for 4 days. The control group is treated with DMSO.


title: ATAC DUXR70A OE 24h rep2

description:
Library name: ATAC DUXR70A OE 24h rep2
ATAC DUXR70A OE 24h rep2


title: CUT&Tag DUXR70A OE 24h CTCF rep1

description:
Library name: CUT_Tag DUXR70A OE 24h CTCF rep1
CUT&Tag DUXR70A OE 24h CTCF rep1


title: CUT&Tag DUX OE 24h 1,6hex Flag rep1

description:
Library name: CUT_Tag DUX OE 24h 1,6hex Flag rep1
CUT&Tag DUX OE 24h 1,6hex Flag rep1


title: ATAC DUXR70A OE 24h rep1

description:
Library name: ATAC DUXR70A OE 24h rep1
ATAC DUXR70A OE 24h rep1


title: CUT&Tag DUX OE 24h Flag rep2

description:
Library name: CUT_Tag DUX OE 24h Flag rep2
CUT&Tag DUX OE 24h Flag rep2


title: ATAC DUX OE 24h rep1

description:
Library name: ATAC DUX OE 24h rep1
ATAC DUX OE 24h rep1


title: CUT&Tag DUXR70A OE 24h H3K27ac rep1

description:
Library name: CUT_Tag DUXR70A OE 24h H3K27ac rep1
CUT&Tag DUXR70A OE 24h H3K27ac rep1

value: Anti-H3K27ac Activemotif Cat# 39034


title: CUT&Tag DUXdelta70-80aa OE 24h Flag rep1

description:
Library name: CUT_Tag DUXdelta70-80aa OE 24h Flag rep1
CUT&Tag DUXR70A OE 24h Flag rep2


description:
Library name: CUT_Tag DUXdelta70-80aa OE 24h H3K27ac rep1
CUT&Tag DUXdelta70-80aa OE 24h H3K27ac rep1


title: RNAseq mESC ZSCAN4 OE 24h rep2

description:
Library name: RNAseq mESC ZSCAN4 OE 24h rep2
RNAseq mESC ZSCAN4 OE 24h rep2

data_processing:
data processing step: Raw sequencing reads were quality controlled using FastQC
data processing step: Adapter trimming and quality filtering were performed using Trimmomatic with parameters: ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were aligned to the reference genome using STAR aligner  with default parameters
Gene-level counts were quantified using featureCounts with GTF annotation file
Differential expression analysis was performed using DESeq2 in R
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw read counts for each gene across all samples

extract_protocol:
Total RNA was extracted using Trizol reagent according to manufacturer's instructions. RNA quality was assessed by Agilent Bioanalyzer, and samples with RIN > 8.0 were used for library construction.
RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocol, including polyA selection, fragmentation, cDNA synthesis, and adapter ligation. Libraries were quantified by Qubit and quality checked by Bioanalyzer before sequencing.

value: dox 24h


title: RNAseq DUX KD ZSCAN4 OE rep1

description:
Library name: RNAseq DUX KD ZSCAN4 OE rep1
RNAseq DUX KD ZSCAN4 OE rep1

value: Dux KD


title: RNAseq SE KO DUX OE 24h rep1

description:
Library name: RNAseq SE KO DUX OE 24h rep1
RNAseq SE KO DUX OE 24h rep1

value: SE KO


title: CUT&Tag DUX OE 24h CTCF rep1

description:
Library name: CUT_Tag DUX OE 24h CTCF rep1
CUT&Tag DUX OE 24h CTCF rep1


title: ATAC DUX OE 24h rep2

description:
Library name: ATAC DUX OE 24h rep2
ATAC DUX OE 24h rep2


title: CUT&Tag DUX OE 24h H3K27ac rep1

description:
Library name: CUT_Tag DUX OE 24h H3K27ac rep1
CUT&Tag DUX OE 24h H3K27ac rep1


title: RNAseq mESC ZSCAN4 OE 24h rep1

description:
Library name: RNAseq mESC ZSCAN4 OE 24h rep1
RNAseq mESC ZSCAN4 OE 24h rep1


title: RNAseq SE KO DUX OE 24h rep2

description:
Library name: RNAseq SE KO DUX OE 24h rep2
RNAseq SE KO DUX OE 24h rep2


title: ATAC mESC rep1

description:
Library name: ATAC mESC rep1
ATAC mESC rep1


title: ATAC mESC rep2

description:
Library name: ATAC mESC rep2
ATAC mESC rep2


title: RNAseq DUX KD ZSCAN4 OE rep2

description:
Library name: RNAseq DUX KD ZSCAN4 OE rep2
RNAseq DUX KD ZSCAN4 OE rep2


title: RNAseq DUX KD PlaB 4day rep2

description:
Library name: RNAseq DUX KD PlaB 4day rep2
RNAseq DUX KD PlaB 4day rep2

value: PlaB 4day


title: RNAseq DUX KD PlaB 4day rep1

description:
Library name: RNAseq DUX KD PlaB 4day rep1
RNAseq DUX KD PlaB 4day rep1


title: CUT&Tag DUX OE 24h H3K27ac rep2

description:
Library name: CUT_Tag DUX OE 24h H3K27ac rep2
CUT&Tag DUX OE 24h H3K27ac rep2


title: CUT&Tag DUX OE 24h Flag rep1

description:
Library name: CUT_Tag DUX OE 24h Flag rep1
CUT&Tag DUX OE 24h Flag rep1


title: RNAseq SE KO RA 48h rep2

description:
Library name: RNAseq SE KO RA 48h rep2
RNAseq SE KO RA 48h rep2

value: RA 2day


title: RNAseq SE KO PlaB 4day rep2

description:
Library name: RNAseq SE KO PlaB 4day rep2
RNAseq SE KO PlaB 4day rep2


title: RNAseq DUX KD RA 48h rep1

description:
Library name: RNAseq DUX KD RA 48h rep1
RNAseq DUX KD RA 48h rep1


title: RNAseq DUX OE 24h rep2

description:
Library name: RNAseq DUX OE 24h rep2
RNAseq DUX OE 24h rep2

value: WT


title: RNAseq DUXR70A OE 24h rep2

description:
Library name: RNAseq DUXR70A OE 24h rep2
RNAseq DUXR70A OE 24h rep2


title: RNAseq mESC DMSO rep2

description:
Library name: RNAseq mESC DMSO rep2
RNAseq mESC DMSO rep2

value: DMSO


title: RNAseq mESC RA 48h rep2

description:
Library name: RNAseq mESC RA 48h rep2
RNAseq mESC RA 48h rep2


title: RNAseq mESC DMSO rep1

description:
Library name: RNAseq mESC DMSO rep1
RNAseq mESC DMSO rep1


title: RNAseq SE KO PlaB 4day rep1

description:
Library name: RNAseq SE KO PlaB 4day rep1
RNAseq SE KO PlaB 4day rep1


title: RNAseq DUX KD RA 48h rep2

description:
Library name: RNAseq DUX KD RA 48h rep2
RNAseq DUX KD RA 48h rep2


title: RNAseq mESC rep2

description:
Library name: RNAseq mESC rep2
RNAseq mESC rep2


title: RNAseq mESC RA 48h rep1

description:
Library name: RNAseq mESC RA 48h rep1
RNAseq mESC RA 48h rep1


title: RNAseq mESC PlaB 4day rep1

description:
Library name: RNAseq mESC PlaB 4day rep1
RNAseq mESC PlaB 4day rep1


title: RNAseq mESC PlaB 4day rep2

description:
Library name: RNAseq mESC PlaB 4day rep2
RNAseq mESC PlaB 4day rep2


title: RNAseq mESC rep1

description:
Library name: RNAseq mESC rep1
RNAseq mESC rep1


title: RNAseq DUX OE 24h rep1

description:
Library name: RNAseq DUX OE 24h rep1
RNAseq DUX OE 24h rep1


title: RNAseq SE KO RA 48h rep1

description:
Library name: RNAseq SE KO RA 48h rep1
RNAseq SE KO RA 48h rep1


title: E6.5 Epi,Sp1 ko,H3K4me3,ChIP,rep2

city: chongqing,china

first: xipeng

last: shen

address: yixueyuan road NO.1

department: basic medicine

institute: CQMU

description:
Library name: E65Epi_Sp1_ko_H3K4me3_rep2
E65Epi_Sp1_ko_H3K4me3_merge.bed

data_processing:
After removal of reads with poor quality calls and adapters with Trim Galore (v. 0.4.2) using default parameters, reads from ChIP-seq datasets were mapped to the mouse mm9 reference genome (or human hg19 for datasets generated from Hela cell) using Bowtie2 with the parameters: --t --q --N 1 --L 25. Multiple mapped reads and PCR duplicates were further removed with a javascript (MarkDuplicates.jar). The monoclonal reads were then normalized by calculating the number of RPKM. After validation of the reproducibility, replicates were pooled for downstream analysis.
Assembly: mm9
Supplementary files format and content: All attached processed data were in .bed format.

source_name: E6.5 Epi

growth_protocol: PWK&PhJ male mouses (6-8weeks) were mated with C57BL/6N female mouses (6-8weeks) and the time when the vaginal plug was observed the next day was considered E0.5. The embyos were disserted at E6.5 and E7.5, respectively. Germ layers were seperated using enzyme digestion coupled with mechanical separation.

extract_protocol:
ChIP-seq was performed with minor adjustments to the STAR ChIP-seq protocol. Samples were lysed in a buffer containing 0.5% Tween-20, 0.5% NP-40, and 0.1% SDS, and gently pipetted to release genomic DNA. The mixture was then digested with MNase (Sigma) at 37°C for 5 minutes. Primary antibodies—anti-Pol II RBP1 (BioLegend), anti-Phospho-POLR2A CTD-S2 (Abclonal), anti-SP1(Proteintech), anti-H3K4me3 (Millipore) or anti-H3K27me3 (Abclonal)—were added, followed by incubation at 4°C overnight. Protein A Dynabeads (Thermo Fisher Scientific) were added to the solution and incubated for 3-4 hours. Beads were washed five times with RIPA buffer containing 0.1% protease inhibitor and once with LiCl wash buffer. Elution of DNA fragments was achieved with proteinase K treatment.
The library was constructed using NEB Next® UltraTM II DNA Library Prep Kit according to the operation instruction.

treatment_protocol: C57BL/6N female mouses(5 weeks) were superovulated with PMSG following hCG 48h later. After mating with PWK mouses, PN3 zygotes were colleted in M2 medium the next day. The CRISPR-ZEN methods were used to deliver Cas9-sgRNA complex into zygotes for gene editing. Zygotes were cultured to 2-cell stage in vitro and transferred to E0.5 pseudopregnancy foster mice. Germ layers were seperated as described above. The ExVE of embryos was collected for genotyping.

value: E6.5 Epi

value: Sp1 ko


title: E7.5 Endoderm small size,Sp1 ko,Pol2,ChIP,rep2

description:
Library name: E75_small_End_Sp1_KO_pol2_rep2
E75_small_End_Sp1_KO_pol2_Merge.bed

source_name: E7.5 Endoderm small size

value: E7.5 Endoderm small size


title: E7.5 Endoderm,Pol2,ChIP,rep1

description:
Library name: E75_End_pol2_rep1
E75_End_pol2_merge.bed

source_name: E7.5 Endoderm

value: E7.5 Endoderm


title: HCT116 cells, shPRSS22-1

first: Zijian

last: Kuang

state: Guangdong

address: No. 382, East Outer Ring Road, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou City

institute: South China University of Technology

description:
Library name: Sample4
column name in raw_counts.txt: shPRSS22-1

data_processing:
Raw sequencing reads were trimmed and filtered for short sequences using SOAPnuke (version 1.56) with parameters -l 20 -q 0.4 -n 0.011 -G. Trimmed FASTQ files were analyzed and quality-assessed using FastQC (version 0.12.1). Read alignment to the human reference genome (Gencode GRCh38) was performed using HISAT (version 2.2.1) with default parameters. Bowtie2 (version 2.3.4.3) was employed to map clean data to the reference gene set. Gene expression quantification was performed using RSEM (version 1.3.1), and differential expression analysis was conducted with DESeq2 (version 1.4.5) in R (version 4.3.1). Gene set enrichment analysis was performed using ClusterProfiler (version 4.10.1).
Assembly: Homo_sapiens_9606.NCBI.GCF_000001405.39_GRCh38.p13.v2201
Supplementary files format and content: txt file includes rawcounts, FPKM, TPM for each Sample

growth_protocol: HCT116 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the Trizol Reagent (B610409, Sangon Biotech).
The total RNA was processed using the mRNA enrichment method. mRNA enrichment: mRNA with polyA tails was enriched using magnetic beads coated with Oligo(dT). The obtained RNA was fragmented using fragmentation buffer, followed by reverse transcription with random N6 primers to synthesize cDNA second strands, forming double-stranded DNA. The ends of the synthesized double-stranded DNA were blunted and phosphorylated at the 5' end, while the 3' end formed a sticky end with an protruding "A" base. A bubble-shaped adapter with a protruding "T" at the 3' end was then ligated. The ligation products were amplified by PCR using specific primers. The PCR products were heat-denatured into single strands, and a bridge primer was used to circularize the single-stranded DNA, resulting in single-stranded circular DNA libraries. The constructed libraries underwent quality inspection, and those passing the quality control were subjected to sequencing.

value: Human colorectal cancer cells

value: PRSS22 knockdown


title: E7.5 Endoderm small size,Sp1 ko,Pol2,ChIP,rep1

description:
Library name: E75_small_End_Sp1_KO_pol2_rep1
E75_small_End_Sp1_KO_pol2_Merge.bed


title: HCT116 cells, shCtrl-3

description:
Library name: Sample3
column name in raw_counts.txt: shCtrl-3


title: E6.5 Epi,Sp1 ko,H3K27me3,ChIP,rep2

description:
Library name: E65Epi_Sp1_ko_H3K27me3_rep2
E65Epi_Sp1_ko_H3K27me3_merge.bed


title: E6.5 Epi,Sp1 Ctr,Pol2,ChIP,rep1

description:
Library name: E65Epi_Sp1_Ctr_Pol2_rep1
E65Epi_Sp1_Ctr_Pol2_merge.bed

value: Sp1 Ctr


title: HCT116 cells, shPRSS22-2

description:
Library name: Sample5
column name in raw_counts.txt: shPRSS22-2


title: E6.5 Epi,Sp1 ko,H3K27me3,ChIP,rep1

description:
Library name: E65Epi_Sp1_ko_H3K27me3_rep1
E65Epi_Sp1_ko_H3K27me3_merge.bed


title: HCT116 cells, shCtrl-2

description:
Library name: Sample2
column name in raw_counts.txt: shCtrl-2


title: HCT116 cells, shPRSS22-3

description:
Library name: Sample6
column name in raw_counts.txt: shPRSS22-3


title: E6.5 Epi,Sp1 Ctr,Pol2,ChIP,rep2

description:
Library name: E65Epi_Sp1_Ctr_Pol2_rep2
E65Epi_Sp1_Ctr_Pol2_merge.bed


title: E6.5 Epi,Sp1 ko,H3K4me3,ChIP,rep1

description:
Library name: E65Epi_Sp1_ko_H3K4me3_rep1
E65Epi_Sp1_ko_H3K4me3_merge.bed


title: iPS_tol DC

first: Aiko

last: Hirano

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Inflammation and Immunology, Graduate School of Medical Science

institute: Kyoto Prefectural University of Medicine

description: Library name: Sample2

data_processing:
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software. Trimmed reads were then mapped to the human GRCh38 genome using STAR (version 2.7.2b). Reads on annotated genes were counted using featureCounts (version 1.6.1). FPKM values were calculated from mapped reads by normalizing to total counts and transcript. Differentially expressed genes were detected using the DESeq2 package (version 1.20.0). The list of differentially expressed genes detected by DESeq2 (basemean > 5 and fold-change < 0.25, or basemean > 5 and fold-change > 4) were used for GO enrichment analysis by clusterProfiler package (Yu et al., OMICS 2012, 16:5).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: blood cells

extract_protocol:
iPS-monocytes, iPS-DCs, and iPS-tolDCs were collected in multiple batches, homogenized using ISOGEN II (Nippon Gene, Japan), and stored at -80℃. When the total cell count for each sample reached approximately 1×10⁶ cells, RNA was extracted using ISOGEN II (Nippon Gene) with Ethachinmate (Nippon Gene). The extracted RNA was further purified by removing contaminating DNA using the RNase-Free DNase Set (QIAGEN, Hilden, Germany).
RNA sequence library preparation, sequencing, mapping, gene expression, and gene ontology (GO) enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). Furthermore, we analyzed the obtained data using the RNA-seq Analysis Portal (QIAGEN), including Ingenuity Pathway Analysis. Qualities of total RNA were assessed by Bioanalyzer (Agilent, Santa Clara, CA, USA) to ensure that RIN (RNA integrity number) is over 7.0. Library preparation was performed using the QIAseq UPX 3' Transcriptome Kit (QIAGEN, 333088) and MGIEasy Universal Library Conversion Kit (App-A) (MGI, 1000004155, Shenzhen, China) according to the manufacturer’s instruction. RNA-seq libraries were sequenced using paired end reads (50nt of read1 and 25nt of read2) on a NextSeq 500 instrument (Illumina, San Diego, CA, USA).

value: blood cells

value: iPSC

value: iPS derived tolDC

value: tolDC differentiation


title: iPS_Monocyte

description: Library name: Sample3

value: iPS derived monocytes

value: monocyte differentiation


title: E6.5 Epi,Sp1 Ctr,H3K27me3,ChIP,rep2

description:
Library name: E65Epi_Sp1_Ctr_H3K27me3_rep2
E65Epi_Sp1_Ctr_H3K27me3_merge.bed


title: E6.5 Epi,Sp1 Ctr,H3K4me3,ChIP,rep2

description:
Library name: E65Epi_Sp1_Ctr_H3K4me3_rep2
E65Epi_Sp1_Ctr_H3K4me3_merge.bed


title: RNAseq DUXR70A OE 24h rep1

description:
Library name: RNAseq DUXR70A OE 24h rep1
RNAseq DUXR70A OE 24h rep1

value: mESCs

value: dox 24h


title: Tumor DNA from FFPE tissue of  206467010178_R07C01

type: genomic

city: Rotterdam

first: Bo

last: Deng

address: Dr. Molewaterplein 40

institute: Erasmus MC

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner setting.

data_processing: RnBeads package in R environment (v4.4.2).

label: Cy3 and Cy5

source_name: FFPE glioblastoma DNA

label_protocol: Standard Illumina Protocol.

extract_protocol: Tumor DNA was extracted from FFPE tissue using the QIAamp DNA FFPE Tissue Kit (Qiagen), and the quantity of isolated DNA was assessed with a Qubit 3.0 fluorometer (Invitrogen).

value: FFPE glioblastoma DNA

value: KAE

value: primary

tag: gender

value: Female

tag: treated with tmz

value: Yes

tag: treated with rt

tag: overall survival

tag: status

value: Deceased


title: E6.5 Epi,Sp1 Ctr,H3K4me3,ChIP,rep1

description:
Library name: E65Epi_Sp1_Ctr_H3K4me3_rep1
E65Epi_Sp1_Ctr_H3K4me3_merge.bed

tag: tissue

value: E6.5 Epi

tag: genotype


title: E7.5 Endoderm,Pol2,ChIP,rep2

description:
Library name: E75_End_pol2_rep2
E75_End_pol2_merge.bed

value: E7.5 Endoderm


title: E6.5 Epiblast,Sp1 ko,rep1

description:
Library name: E65Epi_Sp1ko_RNA_rep1
all_gene_knockout_RNA_FPKM.txt

data_processing:
The sequencing reads were processed for quality trimming using the Trim Galore (version 0.6.7), and subsequently aligned to the mouse mm9 reference genome using HISAT2 (version 2.2.1). Gene expression was calculated by StringTie (version 2.2.1) according to the refFlat database.
Assembly: mm9 or hg19
Supplementary files format and content: All attached processed data were listed with gene name and RPKM

source_name: E6.5 Epiblast

extract_protocol:
The RNA-seq library was generated following the Smart-seq2 protocol. Samples were permeabilized in 5 Âµl lysis buffer containing 0.2% Triton X-100 for 30 minutes on ice. After centrifugation, 2 Âµl of the supernatant was transferred to a pre-cooled tube, and reverse transcribed into cDNA.
The library construction was then performed using the One-step DNA Lib Prep Kit for Illumina V2 (Abclonal) according to the manufacturer's instructions.

value: E6.5 Epiblast

value: Sp1 ko


title: iPS_DC

description: Library name: Sample1

value: blood cells

value: iPSC

value: iPS derived DC

value: WT

tag: treatment

value: DC differentiation


title: E6.5 Epiblast,Sp1 Ctr,rep1

description:
Library name: E65Epi_Sp1Ctr_RNA_rep1
all_gene_knockout_RNA_FPKM.txt

value: Sp1 Ctr


title: Tumor DNA from FFPE tissue of  206467010178_R06C01

value: recurrence


title: Tumor DNA from FFPE tissue of  206467110163_R03C01

value: FFPE glioblastoma DNA

value: KAA

value: Male


title: HCT116 cells, shCtrl-1

description:
Library name: Sample1
column name in raw_counts.txt: shCtrl-1

tag: cell type

value: Human colorectal cancer cells


title: Tumor DNA from FFPE tissue of  206467010176_R04C01

value: JAM

value: Yes


title: E6.5 Epiblast,Sp1 ko,rep2

description:
Library name: E65Epi_Sp1ko_RNA_rep2
all_gene_knockout_RNA_FPKM.txt


title: E6.5 Epiblast,Sp1 Ctr,rep2

description:
Library name: E65Epi_Sp1Ctr_RNA_rep2
all_gene_knockout_RNA_FPKM.txt


title: Tumor DNA from FFPE tissue of  206467010143_R08C01

value: JAJ

value: Female

value: Deceased


title: E6.5 Epi,Sp1 Ctr,H3K27me3,ChIP,rep1

description:
Library name: E65Epi_Sp1_Ctr_H3K27me3_rep1
E65Epi_Sp1_Ctr_H3K27me3_merge.bed

value: E6.5 Epi


title: E6.5 Epiblast,SP1,ChIP,rep2

description:
Library name: E65Epi_SP1_rep2
E65Epi_SP1_merge.bed

data_processing:
After removal of reads with poor quality calls and adapters with Trim Galore (v. 0.4.2) using default parameters, reads from ChIP-seq datasets were mapped to the mouse mm9 reference genome (or human hg19 for datasets generated from Hela cell) using Bowtie2 with the parameters: --t --q --N 1 --L 25. Multiple mapped reads and PCR duplicates were further removed with a javascript (MarkDuplicates.jar). The monoclonal reads were then normalized by calculating the number of RPKM. After validation of the reproducibility, replicates were pooled for downstream analysis.
Assembly: mm9 or hg19
Supplementary files format and content: .bed format

value: E6.5 Epiblast


title: Tumor DNA from FFPE tissue of  206467010178_R01C01

value: primary


title: Tumor DNA from FFPE tissue of  206467010178_R08C01

value: HAI

value: Censored


title: E7.5 Epiblast small size,Sp1 ko,Pol2,ChIP,rep1

description: E75Epi_Pol2_Sp1_KO_small_size_Merge.bed.gz

data_processing:
After removal of reads with poor quality calls and adapters with Trim Galore (v. 0.4.2) using default parameters, reads from ChIP-seq datasets were mapped to the mouse mm9 reference genome (or human hg19 for datasets generated from Hela cell) using Bowtie2 with the parameters: --t --q --N 1 --L 25. Multiple mapped reads and PCR duplicates were further removed with a javascript (MarkDuplicates.jar). The monoclonal reads were then normalized by calculating the number of RPKM. After validation of the reproducibility, replicates were pooled for downstream analysis.
Assembly: mm9 or hg19
Supplementary files format and content: All attached processed data were in .bed format.

source_name: E7.5 Epiblast small size

extract_protocol:
ChIP-seq was performed with minor adjustments to the STAR ChIP-seq protocol. Samples were lysed in a buffer containing 0.5% Tween-20, 0.5% NP-40, and 0.1% SDS, and gently pipetted to release genomic DNA. The mixture was then digested with MNase (Sigma) at 37°C for 5 minutes. Primary antibodies-anti-Pol II RBP1 (BioLegend), anti-Phospho-POLR2A CTD-S2 (Abclonal), anti-SP1(Proteintech), anti-H3K4me3 (Millipore) or anti-H3K27me3 (Abclonal)-were added, followed by incubation at 4°C overnight. Protein A Dynabeads (Thermo Fisher Scientific) were added to the solution and incubated for 3-4 hours. Beads were washed five times with RIPA buffer containing 0.1% protease inhibitor and once with LiCl wash buffer. Elution of DNA fragments was achieved with proteinase K treatment.
The library was constructed using NEB Next® UltraTM II DNA Library Prep Kit according to the operation instruction.

value: E7.5 Epiblast small size


title: E6.5 Extra-embryonic ectoderm,Kmt2b Ctr,Pol2,ChIP,rep2

source_name: E6.5 Extra-embryonic ectoderm

value: E6.5 Extra-embryonic ectoderm


title: E6.5 Extra-embryonic ectoderm,Kmt2b Ctr,Pol2,ChIP,rep1


title: Tumor DNA from FFPE tissue of  206467010176_R05C01


title: Tumor DNA from FFPE tissue of  206467110163_R02C01

value: recurrence


title: E6.5 Epiblast,Kmt2b Ctr,Pol2,ChIP,rep1


title: Tumor DNA from FFPE tissue of  206467010171_R01C01

value: FFPE glioblastoma DNA


title: Tumor DNA from FFPE tissue of  206467110163_R05C01

value: HAF


title: E6.5 Epiblast,SP1,ChIP,rep1

description:
Library name: E65Epi_SP1_rep1
E65Epi_SP1_merge.bed


title: Tumor DNA from FFPE tissue of  206467110163_R07C01

value: HAE


title: Tumor DNA from FFPE tissue of  206467110163_R06C01


title: E6.5 Epiblast,Kmt2b Ctr,H3K4me3,ChIP,rep1


title: E6.5 Epiblast,Kmt2b ko,H3K27me3,ChIP,rep1


title: E6.5 Epiblast,Kmt2b ko,H3K4me3,ChIP,rep1


title: E6.5 Epiblast,Kmt2b Ctr,Pol2,ChIP,rep2


title: Tumor DNA from FFPE tissue of  206467010171_R03C01

value: HAC


title: Tumor DNA from FFPE tissue of  206467010171_R02C01


title: Tumor DNA from FFPE tissue of  206467110163_R04C01


title: Tumor DNA from FFPE tissue of  206467110175_R07C01

value: ECK

value: Male


title: E7.5 Epiblast small size,Sp1 ko,Pol2,ChIP,rep2


title: Tumor DNA from FFPE tissue of  206467010171_R05C01

value: ECF

value: Yes


title: E6.5 Epiblast,Eed Ctr,H3K27me3,ChIP,rep1


title: Tumor DNA from FFPE tissue of  206467110175_R06C01

value: Deceased


title: E6.5 Epiblast,Eed ko,H3K27me3,ChIP,rep1


title: E5.5 Epiblast,Pol2,ChIP,rep1

source_name: E5.5 Epiblast

value: E5.5 Epiblast


title: Tumor DNA from FFPE tissue of  206467110157_R01C01

value: ECE


title: E7.5 Endoderm,Sp1 ko,Pol2,ChIP,rep2

data_processing:
After removal of reads with poor quality calls and adapters with Trim Galore (v. 0.4.2) using default parameters, reads from ChIP-seq datasets were mapped to the mouse mm9 reference genome using Bowtie2 with the parameters: --t --q --N 1 --L 25. Multiple mapped reads and PCR duplicates were further removed with a javascript (MarkDuplicates.jar). The monoclonal reads were then normalized by calculating the number of RPKM. After validation of the reproducibility, replicates were pooled for downstream analysis.
Assembly: mm9 or hg19
Supplementary files format and content: All attached processed data were in .bed format.

value: E7.5 Endoderm

value: Sp1 ko


title: Tumor DNA from FFPE tissue of  206467010171_R04C01

value: Female


title: E6.5 Epiblast,Eed ko,H3K4me3,ChIP,rep1

value: E6.5 Epiblast


title: Tumor DNA from FFPE tissue of  206467010178_R04C01

value: EBX

value: Censored


title: E6.5 Epiblast,Total RNA,rep2

data_processing:
The sequencing reads were processed for quality trimming using the Trim Galore (version 0.6.7), and subsequently aligned to the mouse mm9 reference genome using HISAT2 (version 2.2.1). Gene expression was calculated by StringTie (version 2.2.1) according to the refFlat database.
Assembly: mm9
Supplementary files format and content: All attached processed data were listed with gene name and RPKM.

source_name: E6.5 epiblast

extract_protocol:
The RNA-seq library was generated following the Smart-seq2 protocol. Samples were permeabilized in 5 µl lysis buffer containing 0.2% Triton X-100 for 30 minutes on ice. After centrifugation, 2 µl of the supernatant was transferred to a pre-cooled tube, and reverse transcribed into cDNA.
The library construction was then performed using the One-step DNA Lib Prep Kit for Illumina V2 (Abclonal) according to the manufacturer's instructions.

value: E6.5 epiblast


title: E7.5 Endoderm,Sp1 ko,Pol2,ChIP,rep1


title: E7.5 Mesoderm,Sp1 ko,Pol2,ChIP,rep2

source_name: E7.5 Mesoderm

value: E7.5 Mesoderm


title: Tumor DNA from FFPE tissue of  206467010178_R05C01

value: FFPE glioblastoma DNA

value: primary


title: E7.5 Ectoderm,Sp1 ko,Pol2,ChIP,rep1

source_name: E7.5 Ectoderm

value: E7.5 Ectoderm


title: Tumor DNA from FFPE tissue of  206467110163_R08C01

value: recurrence

value: Male


title: E7.5 Ectoderm,Sp1 ko,Pol2,ChIP,rep2


title: E7.5 Endoderm,Sp1 Ctr,Pol2,ChIP,rep2

value: Sp1 Ctr


title: E6.5 Epiblast,Total RNA,rep1


title: Tumor DNA from FFPE tissue of  206467110157_R02C01

value: EBR

value: Yes

value: Deceased


title: E7.5 Mesoderm,Sp1 ko,Pol2,ChIP,rep1


title: Tumor DNA from FFPE tissue of  206467010171_R07C01

value: EBP


title: E7.5 Mesoderm,Sp1 Ctr,Pol2,ChIP,rep2


title: E7.5 Ectoderm,Sp1 Ctr,Pol2,ChIP,rep2


title: Tumor DNA from FFPE tissue of  206467010171_R08C01

value: EBO


title: Tumor DNA from FFPE tissue of  206467110157_R03C01

value: Female


title: Tumor DNA from FFPE tissue of  206467010176_R01C01


title: Tumor DNA from FFPE tissue of  206467110157_R05C01

value: EAZ


title: Tumor DNA from FFPE tissue of  206467110157_R04C01


title: Tumor DNA from FFPE tissue of  206467010143_R05C01

value: EAV


title: E7.5 Mesoderm,Sp1 Ctr,Pol2,ChIP,rep1


title: E7.5 Mesoderm,SP1,ChIP,rep1


title: E7.5 Endoderm,SP1,ChIP,rep3

source_name: E7.6 Endoderm

value: E7.6 Endoderm


title: Tumor DNA from FFPE tissue of  206467010143_R03C01

value: EBM


title: E7.5 Endoderm,Sp1 Ctr,Pol2,ChIP,rep1

value: E7.5 Endoderm


title: Tumor DNA from FFPE tissue of  206467010171_R06C01

value: FFPE glioblastoma DNA

value: Censored


title: Tumor DNA from FFPE tissue of  206467010143_R04C01


title: E7.5 Ectoderm,Sp1 Ctr,Pol2,ChIP,rep1

value: E7.5 Ectoderm


title: Tumor DNA from FFPE tissue of  206467110157_R07C01

value: EAP

value: primary


title: E7.5 Endoderm,SP1,ChIP,rep1


title: Tumor DNA from FFPE tissue of  206467010143_R02C01

value: recurrence

value: Male


title: Tumor DNA from FFPE tissue of  206467010143_R06C01

value: EAN

value: Yes


title: Tumor DNA from FFPE tissue of  206467110157_R06C01

value: Deceased


title: E7.5 Ectoderm,SP1,ChIP,rep2


title: Tumor DNA from FFPE tissue of  206467010143_R07C01


title: E7.5 Ectoderm,SP1,ChIP,rep1


title: E7.5 Mesoderm,SP1,ChIP,rep2

value: E7.5 Mesoderm


title: Tumor DNA from FFPE tissue of  206467110157_R08C01

value: EAI


title: Tumor DNA from FFPE tissue of  206467110176_R01C01


title: E7.5 Mesoderm,Ser2p,ChIP,rep2


title: E7.5 Endoderm,Ser2p,ChIP,rep1


title: Tumor DNA from FFPE tissue of  206467010123_R07C01

value: CDG

value: Female


title: E7.5 Endoderm,SP1,ChIP,rep2


title: E7.5 Extra-embryonic ectoderm,Ser2p,ChIP,rep2

source_name: E7.5 Extra-embryonic ectoderm

value: E7.5 Extra-embryonic ectoderm


title: E7.5 Endoderm,Ser2p,ChIP,rep2


title: Tumor DNA from FFPE tissue of  206467010176_R03C01

value: CBW


title: E7.5 Mesoderm,Ser2p,ChIP,rep1


title: Tumor DNA from FFPE tissue of  206467010176_R02C01


title: Tumor DNA from FFPE tissue of  206467010123_R05C01

value: CDH


title: E6.5 Extra-embryonic ectoderm,Ser2p,ChIP,rep2

value: E6.5 Extra-embryonic ectoderm


title: Tumor DNA from FFPE tissue of  206467010123_R06C01

value: FFPE glioblastoma DNA

value: Censored


title: E7.5 Ectoderm,Ser2p,ChIP,rep1

value: E7.5 Ectoderm


title: Tumor DNA from FFPE tissue of  206467010123_R04C01


title: E7.5 Extra-embryonic ectoderm,Ser2p,ChIP,rep1


title: E6.5 Visceral endoderm,Ser2p,ChIP,rep2

source_name: E6.5 Visceral endoderm

value: E6.5 Visceral endoderm


title: Tumor DNA from FFPE tissue of  206467110176_R02C01

value: CAD

value: recurrence