title: SDPr08,preoperative SDT,baseline

description: Library name: SDPr08

extract_protocol:
16S rRNA genes of distinct regions (16SV3-V4) were amplified used specific primer with the barcode. All PCR reactions were carried out with 15 µL of Phusion® High-Fidelity PCR Master Mix (New England Biolabs); 0.2µM of forward and reverse primers, and about 10 ng template DNA. Thermal cycling consisted of initial denaturation at 98℃ for 1 min, followed by 30 cycles of denaturation at 98℃ for 10s, annealing at 50℃ for 30 s, and elongation at 72℃ for 30s and 72℃ for 5 min. The PCR products were purified using magnetic bead purification. Samples were mixed in equidensity ratios based on the concentration of PCR products.
After thorough mixing, the PCR products were detected and target bands were recovered. Sequencing libraries were generated and indexes were added. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.


title: Tumor draining lymph node_ATB_EC_GDCA

status: Public on Jun 23 2026

type: SRA

city: Villejuif

first: Miguel

last: Araujo-Voces

state: Île-de-France

address: 114 rue Edouard Vaillant

department: Microbiota and mucosal immunity for cancer immunotherapy

country: France

institute: Gustave Roussy

description: Library name: tdLN_ATB_EC_GDCA

library_source: transcriptomic single cell

data_processing:
Transcriptomic FASTQ files were processed via the standard BD Rhapsody analysis pipeline (BD Biosciences) following the manufacturer's recommendations. Read quality control was performed using recursive substitution error correction (RSEC) and distribution-based error correction (DBEC) algorithms to correct for PCR and sequencing errors. Sample demultiplexing was performed using the Sample Tag Call matrix from the Seven Bridges BD Rhapsody alignment pipeline. A cell was classified as a singlet if the minimum read count of a single sample tag exceeded 75%; multiplets (exceeding the threshold for more than one tag) and undetermined cells were excluded from downstream analysis. Metadata was manually assigned to each sample tag. Filtered gene-expression matrices were processed using Seurat R Package (v5.4.0). Quality control measures were applied to remove debris, damaged cells and doublets (min_genes_per_cell = 600; max_genes_per_cell = 5,000; max_%mitochondrial_reads = 20; max_%ribosomal_reads = 30). Data were normalized using Seurat's log-normalization method. The top 3,000 highly variable genes were identified, and data were scaled regressing out mitochondrial/ribosomal content and total UMI counts. PCA was performed retaining the first 30 principal components. UMAP was generated from these components, followed by neighbor identification and clustering using the Louvain algorithm (resolution = 0.5). Differential expression was performed using FindAllMarkers for manual cell annotation. T cell subsets (CD4/CD8) were resolved using FindSubCluster (resolution = 0.1). Statistical comparisons used Wilcoxon tests with FDR correction.
Assembly: mm10
Supplementary files format and content: Processed single-cell RNA-seq data are provided as a complete Seurat RDS object, including raw and normalized counts, cell-level metadata, clustering results, and dimensionality reductions (e.g., PCA, UMAP).

molecule: polyA RNA

organism: Mus musculus

source_name: lymph node

extract_protocol:
At D11, tdLN (tumor draining lymph node) and tumor were harvested. Excised tumors were cut into small pieces and digested in RPMI medium containing Liberase at 25 mg/ml (Roche) and DNase1 at 150 IU/ml (Roche) for 30 min at 37 °C, and then crushed and filtered twice using 70µm and 30µm cell strainers (Miltenyi Biotec). Lymph nodes were crushed in RPMI medium and subsequently filtered through a 70-µm cell strainer. Tumor cells were enriched using mouse CD45 microbeads from Miltenyi (130-052-30) following the Milteny’s protocol.
Experimental conditions were pooled prior to loading using the BD™ Mouse Single Cell Sample Multiplexing Kit (Cat No: 633793), with 9 and 11 sample barcodes per cartridge, respectively. Libraries were processed according to the BD Rhapsody™ Whole Transcriptome Analysis (WTA) Amplification Kit (Cat No: 633801) and the BD Rhapsody™ Whole Transcriptome Analysis (WTA) Reagent Kit (Cat No: 665915). Libraries were subjected to indexed paired-end sequencing (2×100 bp) on a DNBSEQ-T7 platform (BGI Genomics, Shenzhen, China) with 30% PhiX spike-in control. A total of 1,415 million reads and 2,068 million reads were sequenced for the tumor and lymph node libraries, respectively.

tag: tissue

value: lymph node

tag: Sex

value: female

tag: cell type

value: leukocites

tag: genotype

tag: treatment


title: SDPr06,preoperative SDT,baseline

city: Hangzhou

first: Zhongyu

last: Wu

state: Zhejiang Province

address: 3 East Qingchun Road

department: Sir RunRun Shaw Hospital,School of Medicine

country: China

institute: Zhejiang University

description: Library name: SDPr06

library_source: genomic

data_processing:
Relative abundance: Top 20 taxa of each sample at each taxonomic ranks (Phylum, Class, Order, Family, Genus, Species) were selected to plot the distribution histogram of relative abundance in Perl through SVG function. Alpha and Beta Diversity: For analyzing community diversity, richness, and evenness, alpha diversity was calculated using Shannon and Simpson indices in QIIME2. Beta diversity was performed with Principal Coordinates Analysis (PCoA) and Adonis analysis. Community difference analysis: T-test, and linear discriminant analysis effect size (LEfSe) were conducted to characterize community structure differentiation. Function Prediction: PICRUSt2 (V2.3.0) was applied to predict metagenomic functions based on marker genes. Canonical correspondence analysis (CCA) were used to explore interspecies symbiosis and environmental impacts on community structure, reflecting correlations between environmental factors and genus/species abundance.
Continuous variables were expressed as mean with standard deviation and compared using the Student’s T test. Categorical data, on the other hand, were represented as frequencies and percentages, and comparisons were made using the Pearson χ2 test or the Fisher exact test, depending on suitability. A two-sided p value less than 0.05 was considered statistically significant. All data analyses were conducted using the R software package (version 4.0).
Assembly: 16S rRNA gene reference database(Silva 138.1)
Supplementary files format and content: Processed data are ASV feature count matrix (tab-delimited TSV format). Rows represent individual ASVs, columns correspond to sample IDs, and values denote raw sequencing read counts of each ASV across all fecal samples. Taxonomic classification results assigned against SILVA 138.1 database are also provided in the feature table.
Library strategy: 16S rRNA-seq

molecule: genomic DNA

organism: human feces metagenome

source_name: feces

value: feces


title: DNA from Wilms Tumor 28

type: genomic

city: Caserta

first: Abu

last: Saadat

state: Caserta

address: Via Vivaldi, 43

department: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies

country: Italy

institute: Università degli Studi della Campania Luigi Vanvitelli

description: DNA from Wilms Tumor

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using iSCAN BeadArray reader

data_processing:
R library minfi and ChAMP
processed value definition: Normalized Beta value

label: Cy3 and Cy5

organism: Homo sapiens

source_name: Kidney

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using standard phenol-chloroform-isoamyl alchohol protocol

value: Kidney

value: Male

tag: tissue type

value: Wilms tumor


title: Control 6

city: Hanover

first: Hannah

last: VanBenschoten

state: NH

address: 15 Thayer Dr

department: Thayer School of Engineering

country: USA

institute: Dartmouth College

description:
Library name: Ctrl2_3
Column name in ProcessedData.csv: Ctrl2_3

library_source: transcriptomic

data_processing:
Sequence reads were aligned to GRCm38.97 using STAR Aligner
Read count extraction was performed using ht-seq
Assembly: GRCm38.97
Supplementary files format and content: ProcessedData.csv file includes raw counts for all samples

molecule: total RNA

source_name: eIVFG follicle

extract_protocol:
RNA was extracted using RNA-SPRI beads with 10 µL of cell lysate
RNA libraries for RNA-seq were constructed using Smart-Seq2 protocol

treatment_protocol: Triplicate antral eIVFG follicles per sample were treated with 10 µM Tyrphostin-AG1478 in DMSO and hCG for 4 hours

value: eIVFG follicle

value: Control

tag: batch


title: Tumor draining lymph node_ATB_EC_LCA

description: Library name: tdLN_ATB_EC_LCA


title: SDPr05,preoperative SDT,baseline

description: Library name: SDPr05


title: Control 5

description:
Library name: Ctrl2_2
Column name in ProcessedData.csv: Ctrl2_2


title: SDPr22,preoperative SDT,baseline

description: Library name: SDPr22


title: DNA from Wilms Tumor 30

description: DNA from Wilms Tumor

value: Female


title: Tumor draining lymph node_ATB_EC_DCA

description: Library name: tdLN_ATB_EC_DCA


title: PF+MBV repeat 1

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Library name: Sample 13

data_processing:
The raw sequencing data were filtered using Trimmomatic to remove low-quality reads and adapter sequences.
After preprocessing, the retained reads were aligned to the mouse reference genome (mm10) using the STAR aligner
Assembly: mm10
Supplementary files format and content: TAB for gene count

source_name: liver

extract_protocol:
Total RNA was extracted from liver tissue using RNA-STAT60 (Tel-Test, Ambion, Austin, TX) according to the manufacturer’s instructions. Briefly, samples were homogenized in RNA-STAT60, phase-separated with chloroform, and RNA was precipitated with isopropanol, washed with 75% ethanol, air-dried, and resuspended in RNase-free water. RNA quantity and purity were assessed using a Nanodrop.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: liver

value: PF+MBV


title: Control 4

description:
Library name: Ctrl2_1
Column name in ProcessedData.csv: Ctrl2_1


title: DNA from Wilms Tumor 43

description: DNA from Wilms Tumor


title: Tumor draining lymph node_ATB_EC

description: Library name: tdLN_ATB_EC


title: Control 3

description:
Library name: Ctrl1_3
Column name in ProcessedData.csv: Ctrl1_3


title: DNA from Wilms Tumor 9

description: DNA from Wilms Tumor


title: Intratumoral cd45+ cells_ATB_EC_GDCA

description: Library name: Tumor_ATB_EC_GDCA

source_name: tumor

value: tumor


title: SDPr04,preoperative SDT,baseline

description: Library name: SDPr04


title: SDPr03,preoperative SDT,baseline

description: Library name: SDPr03


title: SDPr02,preoperative SDT,baseline

description: Library name: SDPr02


title: DNA from Wilms Tumor 42

description: DNA from Wilms Tumor


title: Intratumoral cd45+ cells_ATB_EC_LCA

description: Library name: Tumor_ATB_EC_LCA


title: SDPr01,preoperative SDT,baseline

description: Library name: SDPr01


title: Control 1

description:
Library name: Ctrl1_1
Column name in ProcessedData.csv: Ctrl1_1


title: Intratumoral cd45+ cells_ATB_EC_DCA

description: Library name: Tumor_ATB_EC_DCA


title: ILPr45,preoperative ILE,baseline

description: Library name: ILPr45


title: DNA from Wilms Tumor 40

description: DNA from Wilms Tumor


title: Intratumoral cd45+ cells_ATB_EC

description: Library name: Tumor_ATB_EC


title: Bmal1_WT_YAP_input

city: Barcelona

first: Sandra

last: Garcia Mulero

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

description: Library name: Input_Bmal1_WT

data_processing:
ChIP-seq reads were trimmed, adapters were removed and low-quality reads were discarded by using Trimmomatic v.0.36, TRAILING:5, SLIDINGWINDOW:4:5 MINLEN:36
ChIP-seq reads were aligned to the mm10 genome with Burrows-Wheeler aligner v.0.7.12, -n 2 -l 20 -k 1 -t 2.
Aligned reads from the individual biological replicates were merged into one single .bam file, and duplicates were removed using SAMtools v.1.5. Merged/pooled aligned reads were downsampled to 60 million reads. Same downsampling was done for the input DNAs.
Peaks were called using MACS2 v.2.1.1 with the parameters: -q 0.01 –nomodel –extsize 300 -B –SPMR.
Only YAP peaks with a peak score >300 were considered as significant YAP peaks for further analysis
Assembly: mm10
Supplementary files format and content: bed

source_name: epidermis

extract_protocol:
30 million cells were fixed with 1/250 of Gold fixative (C01019027, Diagenode) for 30 minutes, and later a second fixation with 1% methanol-free formaldehyde was performed for 10 minutes. After quenching and cell lysis, nuclear extract was sonicated using a Bioruptor Pico (Diagenode). For IP, 30ug of chromatin were used and incubated with 30 ul of anti-YAP (CS14074, Cell Signaling Technology) with rotation overnight at 4ºC. After immunoprecipitated chromatin was eluted, DNA was purified with the QIAquick PCR Purification Kit (28106, Qiagen).
Libraries were carried out using the NEBNext Ultra DNA Library Prep for Illumina kit (E7370) or the NEBNext® Ultra II DNA Library Prep for Illumina® kit (E7645) using the manufacturer’s protocol. In brief, ChIP-enriched DNA and input DNA were subjected to end repair and the addition of “A” bases to 3’ ends, NEB adapter’s ligation and USER excision. For all purification steps, AgenCourt AMPure XP beads (A63882, Beckman Coulter) were used. Library amplification was performed by PCR using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, E6440, E6442, E6444, E6446). Analysis of final libraries was carried out using either an Agilent Bioanalyzer or Fragment analyzer High Sensitivity assay (5067‐4626 or DNF‐474) to estimate the quantity and check size distribution. Quantification of these final libraries was done by quantitative PCR using the KAPA Library Quantification Kit (KK4835, KapaBiosystems, 07960204001 Roche). Libraries were sequenced 1 x 51 + 10 + 10 base pairs on Illumina’s NextSeq2000. Between 25 and 50 million reads were obtained per sample.

treatment_protocol: Epidermal cells suspensions were obtained from the skin of Bmal1cKO and Bmal1WT adult (18-25 weeks old) mice, that were sacrificed at ZT4.

value: epidermis

value: Bmal1 WT

tag: age

value: adult


title: Bmal1_KO_YAP_input

description: Library name: Input_Bmal1_KO

value: Bmal1 KO


title: ILPr44,preoperative ILE,baseline

description: Library name: ILPr44


title: DNA from Wilms Tumor 39

description: DNA from Wilms Tumor


title: Tumor, 7x19 CAR-T, 4

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

country: Japan

institute: Takeda Pharmaceutical Company Limited

description:
Library name: 7x19.CART_4
10X Genomics

data_processing:
Base calling and making fastq files were performed using software provided with the 10X Genomics Cell Ranger (cellranger mkfastq v4.0).
Count data were calculated from fastq files using software provided with the 10X Genomics Cell Ranger (cellranger count v4.0).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated valuss files and matrix files

source_name: Tumor

growth_protocol: C57BL/6N mice were inoculated with MC38-human CD20 cells for the in vivo study.

extract_protocol:
Single-cell RNA-seq libraries were prepared using CD45+ tumor-infiltrating immune cells. Single-cell libraries were prepared from tumor tissue using the Chromium Single Cell 3' Library Kit v2 (10X Genomics) following the manufacturer’s instructions.
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v4.0.0.

treatment_protocol: CAR-T cells were infused via the tail vein.

value: Tumor

value: Immune cells

value: WT


title: ILPr43,preoperative ILE,baseline

description: Library name: ILPr43

value: feces


title: Bmal1_KO_YAP_ChIP

description: Library name: YAP_Bmal1_KO

tag: antibody

value: anti-YAP (CS14074, Cell Signaling Technology)


title: DNA from Wilms Tumor 33

description: DNA from Wilms Tumor

value: Kidney


title: Tumor, 7x19 CAR-T, 3

description:
Library name: 7x19.CART_3
10X Genomics


title: Bmal1_WT_YAP_ChIP

description: Library name: YAP_Bmal1_WT


title: ILPr42,preoperative ILE,baseline

description: Library name: ILPr42


title: DNA from Wilms Tumor 27

description: DNA from Wilms Tumor

value: Wilms tumor


title: ILPr40,preoperative ILE,baseline

description: Library name: ILPr40


title: Tumor, 7x19 CAR-T, 1

description:
Library name: 7x19.CART_1
10X Genomics


title: ILPr41,preoperative ILE,baseline

description: Library name: ILPr41


title: Tumor, 7x19 CAR-T, 2

description:
Library name: 7x19.CART_2
10X Genomics


title: Bmal1cKO_4

description:
Library name: Bmal1cKO_4
K4_01165A

data_processing:
Adapters from reads were removed using TrimGalore with default parameters.
Reads were aligned to the mm10 version of musmusculus using STAR (v.2.7.10a) with default parameters
Count matrix was generated using the featureCounts function from the Rsubread R package using the Entrez gene annotation
Assembly: mm10 GRCm38.102
Supplementary files format and content: Count matrix in excel format

extract_protocol:
Epidermal cells suspensions were obtained from the skin of Bmal1cKO and Bmal1 WT adult (18-25 weeks old) mice, that were sacrificed at ZT4.
Libraries were prepared using the TruSeq stranded mRNA Library Prep (ref. 20020595, Illumina) according to the manufacturer's protocol, to convert total RNA into a library of template molecules of known strand origin and suitable for subsequent cluster generation and DNA sequencing.  Briefly, 500 ng of total RNA were used for polyA‐mRNA selection using Oligo‐dT beads, and two rounds of purification were performed. During the second elution of the mRNA, this was fragmented under elevated temperature and primed with random hexamers for cDNA synthesis, that was performed using reverse transcriptase (SuperScript II; ref. 18064‐014, Invitrogen). Then, second strand cDNA was synthesized, incorporating dUTP in place of dTTP and generating blunt ended ds cDNA. A single ‘A’ nucleotide was added to the 3’ ends of the blunt fragments (A‐tailing) and immediately afterwards the Truseq adapter was ligated. Finally, PCR selectively enriched those DNA fragments that had adapter molecules on both ends. The PCR was performed using Unique Dual Indexes and the master mix provided with the kit. All purification steps were performed using AgenCourt AMPure XP beads (ref. A63882, Beckman Coulter). Final libraries were analyzed using Bioanalyzer DNA 1000 or Fragment Analyzer Standard Sensitivity (ref. 5067‐1504 or ref. DNF‐473, Agilent) to estimate the quantity and validate the size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit for Illumina (ROX Low) KK4873 (ref. 07960336001, Roche).  Libraries were sequenced 1 X 51+10+10 bp on Illumina's NextSeq2000.

tag: replicate


title: DNA from Wilms Tumor 24

description: DNA from Wilms Tumor

value: Male


title: Bmal1cKO_3

description:
Library name: Bmal1cKO_3
K3_01164A


title: Tumor, conventional CAR-T, 4

description:
Library name: Conv.CART_4
10X Genomics


title: DNA from Wilms Tumor 23

description: DNA from Wilms Tumor


title: ILPr39,preoperative ILE,baseline

description: Library name: ILPr39


title: Bmal1cKO_2

description:
Library name: Bmal1cKO_2
K2_01163A


title: Tumor, conventional CAR-T, 3

description:
Library name: Conv.CART_3
10X Genomics


title: ILPr38,preoperative ILE,baseline

description: Library name: ILPr38


title: Patient 2 Hypercellular zone

city: Beijing

first: Cao

last: Yuchen

address: Thirty-three Badachu Road, Shijingshan District, Beijing, P.R. China

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

description:
Library name: 240807017
GEXSCOPE

data_processing:
Raw sequencing reads were processed using fastQC and fastp for quality control. Poly-A tails and adapter sequences were trimmed using cutadapt. Reads were aligned to the human reference genome GRCh38 (Ensembl release 99) using STAR. Gene expression counts and UMI counts were quantified using FeatureCounts. An expression matrix was generated for downstream analysis. Cell quality control and clustering: Cells were filtered based on: gene counts per cell (200–5000), UMI counts (<30,000), and mitochondrial content (<20–30%). After filtering, 128,678 high-quality cells were retained. Data normalization and scaling were performed using Seurat v3.1.2 (NormalizeData and ScaleData). The top 2000 variable genes were selected for PCA. Batch effects were corrected using Harmony v1.0. Clustering was performed with the Louvain algorithm (resolution = 1.2) in Seurat, followed by UMAP visualization. Downstream analysis: Differentially expressed genes were identified using Seurat FindMarkers (Wilcoxon test, avg_logFC > 0.25, adj. p < 0.05). Cell type annotation was based on canonical markers and SynEcoSys database. Pathway enrichment was performed with clusterProfiler (GO and KEGG). Trajectory analysis used Monocle2/3 and CytoTRACE. Cell-cell interactions were analyzed with CellPhoneDB v2.1.0.
Assembly: GRCh38 (Ensembl release 99)
Supplementary files format and content: Processed data files format and content: Filtered gene expression count matrices in 10x Genomics-compatible Market Exchange (MEX) format: barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene IDs), and matrix.mtx.gz (UMI counts). Additional processed files include Seurat RDS objects containing normalized data, metadata (zone, cluster, cell type), UMAP coordinates, and downstream analysis results (DEGs, pseudotime, cell-cell interactions).
Supplementary files format and content: Processed data files format and content: The processed data include gene expression count matrices (UMI counts) generated from Singleron GEXSCOPE scRNA-seq. Files are provided as:  barcodes.tsv.gz: Cell barcodes features.tsv.gz: Gene features (gene IDs/symbols) matrix.mtx.gz: Sparse UMI count matrix (Matrix Market Exchange format, 10x Genomics compatible)  Additional processed files:  Combined Seurat object files (.rds) containing normalized data, scaled data, PCA, Harmony-corrected embeddings, UMAP coordinates, cluster identities, cell type annotations, and sample/zone metadata (Infiltrating zone vs Hypercellular zone). Tab-delimited files (.tsv.gz) of differentially expressed genes (DEGs), cluster marker genes, and pathway analysis results.

source_name: keloid

growth_protocol: Not applicable. Samples were primary human keloid tissues obtained directly from surgical excision.

extract_protocol:
issue dissociation and single-cell suspension preparation: Keloid samples were preserved in GEXSCOPE tissue preservation solution and transferred to the laboratory under cold conditions. Samples were washed three times with Hanks Balanced Salt Solution (HBSS), cut into 1-2 mm fragments, and digested in 2 ml GEXSCOPE tissue dissociation solution (Singleron Bio, Nanjing, China). After digestion, the mixture was filtered, centrifuged, and the pellet resuspended in PBS. Cell viability and concentration were assessed using trypan blue staining and Countstar Rigel fluorescence cell counter. Single-cell RNA library construction and sequencing: Single-cell suspensions (2×10^5 cells/mL) were loaded onto microwell chips using the Singleron Matrix Single Cell Processing System. scRNA-seq libraries were constructed with GEXSCOPE Single Cell RNA Library Kits (Singleron) following the manufacturer’s protocol. Libraries were sequenced on Illumina NovaSeq 6000 with 150 bp paired-end reads.
Single-cell suspensions (2×10⁵ cells/mL in PBS) were loaded onto microwell chips using the Singleron Matrix® Single Cell Processing System. scRNA-seq libraries were constructed according to the manufacturer’s protocol using the GEXSCOPE® Single Cell RNA Library Kits (Singleron Bio, Nanjing, China). Individual libraries were quantified, diluted to 4 nM, pooled, and sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

treatment_protocol: No treatment was administered. None of the patients had received any topical or intralesional treatment (including corticosteroid injections, 5-fluorouracil, laser therapy, cryotherapy, or radiotherapy) targeting the keloid lesions prior to surgical excision.

value: keloid

value: None of the enrolled patients had received any topical or intralesional treatment (including corticosteroid injections, 7-fluorouracil, laser therapy, cryotherapy, or radiotherapy) targeting the keloid lesions prior to surgical excision


title: Bmal1cKO_1

description:
Library name: Bmal1cKO_1
K1_01162A


title: DNA from Wilms Tumor 18

description: DNA from Wilms Tumor

value: Female


title: Tumor, conventional CAR-T, 2

description:
Library name: Conv.CART_2
10X Genomics


title: ILPr37,preoperative ILE,baseline

description: Library name: ILPr37


title: Bmal1WT_4

description:
Library name: Bmal1WT_4
C4_01161A


title: ILPr36,preoperative ILE,baseline

description: Library name: ILPr36


title: Bmal1WT_3

description:
Library name: Bmal1WT_3
C3_01160A


title: DNA from Wilms Tumor 10

description: DNA from Wilms Tumor


title: DNA from Wilms Tumor 8

description: DNA from Wilms Tumor


title: ILPr34,preoperative ILE,baseline

description: Library name: ILPr34


title: DNA from Wilms Tumor 7

description: DNA from Wilms Tumor


title: Tumor, control, 4

description:
Library name: NT_4
10X Genomics


title: Bmal1WT_2

description:
Library name: Bmal1WT_2
C2_01159A


title: Tumor, control, 3

description:
Library name: NT_3
10X Genomics


title: Bmal1WT_1

description:
Library name: Bmal1WT_1
C1_01158A


title: Tumor, control, 2

description:
Library name: NT_2
10X Genomics


title: ILPr33,preoperative ILE,baseline

description: Library name: ILPr33


title: DNA from Wilms Tumor 6

description: DNA from Wilms Tumor


title: BMAL1_Input

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

department: Biostatistics and bioinformatics Unit

description: Library name: Input_Bmal1

data_processing:
ChIP-seq reads were trimmed, adapters were removed and low-quality reads were discarded by using Trimmomatic v.0.36, TRAILING:5, SLIDINGWINDOW:4:5 MINLEN:36
ChIP-seq reads were aligned to the mm10 genome with Burrows-Wheeler aligner v.0.7.12, -n 2 -l 20 -k 1 -t 2.
Aligned reads from the individual biological replicates were merged into one single .bam file, and duplicates were removed using SAMtools v.1.5. Merged/pooled aligned reads were downsampled to 60 million reads. Same downsampling was done for the input DNAs.
Peaks were called using MACS2 v.2.1.1 with the parameters: -q 0.01 –nomodel –extsize 300 -B –SPMR.
YAP: Only peaks with a peak score >300 were considered as significant YAP peaks for further analysis. p65: Peaks with FDR 0.01 (which is, peak score>20) were considered as significant p65 peaks for further analysis. Bmal1: Only peaks with a peak score >200 were considered as significant BMAL1 peaks for further analysis.
Assembly: mm10
Supplementary files format and content: bed

extract_protocol:
30 million cells were fixed with 1/250 of Gold fixative (C01019027, Diagenode) for 30 minutes, and later a second fixation with 1% methanol-free formaldehyde was performed for 10 minutes. After quenching and cell lysis, nuclear extract was sonicated using a Bioruptor Pico (Diagenode). For IP, 30ug of chromatin were used and incubated with 30 ul of anti-YAP (CS14074, Cell Signaling Technology) with rotation overnight at 4ºC. After immunoprecipitated chromatin was eluted, DNA was purified with the QIAquick PCR Purification Kit (28106, Qiagen).
Libraries were carried out using the NEBNext Ultra DNA Library Prep for Illumina kit (E7370) or the NEBNext® Ultra II DNA Library Prep for Illumina® kit (E7645) using the manufacturer’s protocol. In brief, ChIP-enriched DNA and input DNA were subjected to end repair and the addition of “A” bases to 3’ ends, NEB adapter’s ligation and USER excision. For all purification steps, AgenCourt AMPure XP beads (A63882, Beckman Coulter) were used. Library amplification was performed by PCR using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, E6440, E6442, E6444, E6446). Analysis of final libraries was carried out using either an Agilent Bioanalyzer or Fragment analyzer High Sensitivity assay (5067‐4626 or DNF‐474) to estimate the quantity and check size distribution. Quantification of these final libraries was done by quantitative PCR using the KAPA Library Quantification Kit (KK4835, KapaBiosystems, 07960204001 Roche).

treatment_protocol: Epidermal cells suspensions were obtained from the skin of adult (18-25 weeks old) and aged (80-90 weeks old) mice that were sacrificed at ZT4.

value: Old and young


title: Tumor, control, 1

description:
Library name: NT_1
10X Genomics


title: 8030_Avonex_low_48

type: protein

city: Silver Spring

first: Lakshmi Manasa

middle: Sakuntala

last: Chekka

state: Maryland

address: 10903 New Hampshire Avenue

department: DARS, CDER

institute: U.S. FDA

hyb_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).

data_processing:
https://www.mcgill.ca/genepi/files/genepi/bqc19_jgh_prt_tech_note_0.pdf. R package Biobase and SomaDataIO were used to extract and read the adat files along with the manifest files.
Read out is relative flourescent units (RFU) which is directly proportional to the amount of target protein in the initial sample, as informed by a standard curve generate for each protein-SOMAmer pair. Raw RFU is normalized as described in the data processing step above.

label: 5’ fluorophore, photocleavable linker, and biotin

molecule: protein

source_name: EDTA plasma

growth_protocol: EDTA Plasma from healthy subjects was collected and stored at -80 degrees centigrade.

extract_protocol: EDTA plasma from whole blood

treatment_protocol: Subjects were randomized between IFNβ-1a (7.5 µg) and pegIFNβ-1a (31.25 µg).

tag: drug group

tag: delivery

value: IM

tag: dose

tag: timepoint


title: ILPr32,preoperative ILE,baseline

description: Library name: ILPr32


title: ILPr31,preoperative ILE,baseline

description: Library name: ILPr31


title: Sorted T CD4 naive cells, LC11703, Recovered control

city: Santiago

first: Adolfo

middle: Alexis

last: Rojas-Hidalgo

address: OLIVOS 1007

country: Chile

institute: Universidad de Chile

description:
Library name: LC11703-Naive
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)

data_processing:
Initial data processing used CellRanger v7.1.0 (10x Genomics) for demultiplexing and alignment to human reference genome GRCh38.
Assembly: GRCh38
Supplementary files format and content: Expression matrix files of single-cell RNA sequencing experiments in HDF5 format (.h5)

source_name: PBMCs

extract_protocol:
Whole blood was collected from participants in heparin or EDTA-coated tubes, with processing initiated within four hours of collection. PBMCs were isolated from heparin tubes using Ficoll gradient separation and cryopreserved in cell freezing medium (90% heat-inactivated fetal bovine serum with 10% DMSO) until further use. CD4+ T cells were evaluated using an activation-induced marker (AIM) assay. Briefly, cryopreserved PBMCs were thawed, washed and cultured for 24 hours at 37°C and 5% CO2 with SARS-CoV-2 MPs containing spike and non-spike epitopes (1μg/mL), DMSO (negative control), or staphylococcal enterotoxin B (1μg/mL, positive control). Cells were pre-incubated with anti-human CD40 blocking antibody (0.5μg/mL) for 15 minutes prior to stimulation. Following stimulation, cells were stained with fluorochrome-conjugated antibodies, and CD16 and analyzed on a FACSAria IIu cell sorter (BD Biosciences). CD4+ T cells were classified into naïve (CCR7+CD45RA+), central memory (CCR7+CD45RA−), effector memory (CCR7−CD45RA−), and terminally differentiated effector memory (CCR7−CD45RA+) subsets. AIM+ cells were identified as OX40+41BB+. Three populations (naive, total memory, and AIM+) were sorted for subsequent single-cell RNA sequencing, with viability confirmed before experiments.
For sorted cells, indexed V(D)J, 5' Feature Barcode, and GEX libraries were prepared using the Chromium Next GEM Single Cell 5' v2 Dual Index kit with Feature Barcoding (10x Genomics). Pools of cells of the same subtype from five to seven individuals were obtained following the Cell Multiplexing Oligo Labeling protocol. Libraries were sequenced on Illumina NovaSeq platform.

value: PBMCs

value: T-cell

value: female

tag: severity

value: Severe


title: Old_BMAL1_ChIP

description: Library name: Bmal1_O4

value: epidermis

value: Old


title: 20086-01-08

city: Atlanta

first: Mandakh

last: Bekhbat

state: GA

address: 1365 Clifton Rd NE, Room 5204

department: Psychiatry and Behavioral Sciences

institute: Emory University

description:
Library name: 20086-01-08
10x Genomics

data_processing:
scRNA-Seq reads for gene quantification were analyzed using Seurat 3.1.5 (Stuart et al., 2019) after quality control filtering, alignment to reference genome and normalization to perform unsupervised and supervised analysis (Tran et al., 2016; Raof et al., 2016). Cells were partitioned into clusters based on transcriptome profiles, and batch correction was conducted using Harmony (Korsunsky et al., 2019). Nonlinear dimensional reduction of the sc-transcriptomes was performed with the uniform manifold approximation and projection (UMAP) technique (LJPvd Hinton, 2008). Data were visualized via two-dimensional UMAP plots. Cell type identities of each cluster were determined using automated annotation via SingleR (Aran et al., 2019), and refined using cell-type specific canonical markers.
Assembly: GRCh38
Supplementary files format and content: .rsd file containing Harmony batch-corrected data

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from EDTA whole blood on Histopaque-1077. After washing, cells were counted, and 3-5 million cells were resuspended in sterile freezing media (90% FBS and 10% DMSO). Cells were slowly frozen in an isopropanol-containing cryopreservation vessel at -80C for 24 h then stored in liquid nitrogen.
Final library was constructed using 10X Genomics 3’ GEX v3.1 (10x Genomics) based on manufacturer’s manual. The quality of FL was assessed by High Sensitivity D5000 Tapestation (Agilent Technologies Inc., California, USA) and quantified by Qubit 2.0 DNA HS assay (ThermoFisher, Massachusetts, USA). The average final library size is 400bp with an insert size of about 250bp. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® Hiseq X (Illumina, California, USA) with a read length configuration of 150 PE targeting for 100M total reads per sample (50M in each direction).

value: PBMC

value: Low CRP


title: ILPr30,preoperative ILE,baseline

description: Library name: ILPr30

value: feces


title: 20086-01-09

description:
Library name: 20086-01-09
10x Genomics


title: DNA from Wilms Tumor 29

description: DNA from Wilms Tumor

value: Kidney


title: DNA from Wilms Tumor 41

description: DNA from Wilms Tumor

value: Wilms tumor


title: Young_p65_ChIP

description: Library name: p65_Y4

value: Young


title: DNA from Wilms Tumor 31

description: DNA from Wilms Tumor


title: 20086-01-07

description:
Library name: 20086-01-07
10x Genomics


title: ILPr28,preoperative ILE,baseline

description: Library name: ILPr28


title: Old_p65_ChIP

description: Library name: p65_O4


title: Young_BMAL1_ChIP

description: Library name: Bmal1_Y4


title: DNA from Wilms Tumor 32

description: DNA from Wilms Tumor


title: DNA from Wilms Tumor 26

description: DNA from Wilms Tumor

value: Male


title: Young_p65_input

description: Library name: input_p65_Y4


title: ILPr26,preoperative ILE,baseline

description: Library name: ILPr26


title: ILPr27,preoperative ILE,baseline

description: Library name: ILPr27


title: 20086-01-05

description:
Library name: 20086-01-05
10x Genomics

value: High CRP-Baseline


title: Sorted T CD4 AIM+ cells, LC11373, Recovered control

description:
Library name: LC11373-AIM
Chromium Next GEM Single Cell 5' v2 Dual Index kit (10x Genomics)

value: male

value: Moderate


title: Old_p65_input

description: Library name: input_p65_O4


title: DNA from Wilms Tumor 25

description: DNA from Wilms Tumor

value: Female


title: 20086-01-06

description:
Library name: 20086-01-06
10x Genomics

value: High CRP-Infliximab


title: 20086-01-04

description:
Library name: 20086-01-04
10x Genomics


title: ILPr25,preoperative ILE,baseline

description: Library name: ILPr25


title: ColXIV_WT_YAP_ChIP

description: Library name: Yap_WT

value: 47 weeks old


title: DNA from Wilms Tumor 17

description: DNA from Wilms Tumor


title: DNA from Wilms Tumor 48

description: DNA from Wilms Tumor


title: Control 2

description:
Library name: Ctrl1_2
Column name in ProcessedData.csv: Ctrl1_2

value: eIVFG follicle

value: Control


title: 20086-01-03

description:
Library name: 20086-01-03
10x Genomics


title: DNA from Non neoplastic kidney control 11

description: DNA from Non neoplastic kidney control

value: Non neoplastic kidney control


title: ILPr24,preoperative ILE,baseline

description: Library name: ILPr24


title: 20086-01-02

description:
Library name: 20086-01-02
10x Genomics


title: ColXIV_KO_YAP_ChIP

description: Library name: Yap_KO

value: epidermis


title: ILPr23,preoperative ILE,baseline

description: Library name: ILPr23


title: ColXIV_WT_YAP_input

description: Library name: input_WT


title: DNA from Non neoplastic kidney control 28

description: DNA from Non neoplastic kidney control


title: 8023_Pleg_low_96

scan_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).

value: SC


title: 20086-01-01

description:
Library name: 20086-01-01
10x Genomics

value: PBMC


title: ColXIV_KO_YAP_input

description: Library name: input_KO


title: DNA from Non neoplastic kidney control 30

description: DNA from Non neoplastic kidney control


title: ILPr22,preoperative ILE,baseline

description: Library name: ILPr22

value: feces


title: DNA from Wilms Tumor 19

description: DNA from Wilms Tumor

value: Kidney


title: Total RNA, WI-38 fibroblasts, PDL 57

city: Cambridge

first: Neva

middle: Cherniavsky

last: Durand

state: MA

address: 75 Ames St

institute: Broad Institute

description: Library name: PDL57_totalRNA

data_processing:
Raw fastq reads from total RNA-seq of WI-38 over different PDLs  were mapped with Salmon (Patro et al. 2017) v1.10.1 to the hg38 Salmon Transcriptome index (“salmon_sa_index”). Transcript-level TPM abundances were then aggregated to gene-level abundances in R using the package tximport (Soneson, Love, and Robinson 2015), using as Transcript to Gene mapping the “tx_id” and “gene_id” columns from the EnsDb.Hsapiens.v86 package (Rainer 2017). Mapping from Ensembl Gene IDs to Gene Symbols was performed using a table downloaded from Ensembl BioMart (GRCh38.p13) with ”Gene stable ID” (Ensembl Gene IDs) and ”Gene name” (Gene Symbols), downloaded 3/3/2023.  The Senmayo “score” is the sum of the TPM values of all the Gene Symbols in the list obtained from (Saul et al. 2022) as described above.
Assembly: hg38
Supplementary files format and content: Salmon quantification of transcripts

extract_protocol:
Total RNA was extracted from frozen cell pellets using Trizol following manufacturer’s instructions (Thermo Fisher Scientific, Waltham, MA, USA).
RNA samples were quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) and RNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). rRNA depletion sequencing library was prepared by using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Hilden, Germany). RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs are fragmented for 15 minutes at 94 °C. First strand and second strand cDNA are subsequently synthesized. cDNA fragments are end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were multiplexed and clustered on one lane of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150 Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.

tag: cell line

value: fibroblast


title: Young_YAP_ChIP

description: Library name: YAP_Y4

value: Young


title: ILPr21,preoperative ILE,baseline

description: Library name: ILPr21


title: DNA from Non neoplastic kidney control 43

description: DNA from Non neoplastic kidney control


title: Total RNA, WI-38 fibroblasts, PDL 54

description: Library name: PDL54_totalRNA


title: DNA from Wilms Tumor 16

description: DNA from Wilms Tumor

value: Male

value: Wilms tumor


title: Tumor, conventional CAR-T, 1

description:
Library name: Conv.CART_1
10X Genomics

value: Tumor

value: Immune cells

value: WT


title: DNA from Non neoplastic kidney control 9

description: DNA from Non neoplastic kidney control


title: ILPr19,preoperative ILE,baseline

description: Library name: ILPr19


title: Total RNA, WI-38 fibroblasts, PDL 53.5

description: Library name: PDL535_totalRNA


title: ILPr20,preoperative ILE,baseline

description: Library name: ILPr20


title: Old_YAP_ChIP

description: Library name: YAP_O4

value: Old


title: DNA from Non neoplastic kidney control 42

description: DNA from Non neoplastic kidney control

value: Female


title: ILPr18,preoperative ILE,baseline

description: Library name: ILPr18


title: Old_YAP_input

description: Library name: input_O4


title: DNA from Non neoplastic kidney control 41

description: DNA from Non neoplastic kidney control


title: Young_YAP_input

description: Library name: input_Y4


title: Total RNA, WI-38 fibroblasts, PDL 41

description: Library name: PDL41_totalRNA


title: ILPr35,preoperative ILE,baseline

description: Library name: ILPr35


title: DNA from Non neoplastic kidney control 40

description: DNA from Non neoplastic kidney control


title: Total RNA, WI-38 fibroblasts, PDL 48

description: Library name: PDL48_totalRNA


title: ILPr17,preoperative ILE,baseline

description: Library name: ILPr17


title: Young_H3K4me1_ChIP

description: Library name: K4me1_Y4

data_processing:
ChIP-seq reads were trimmed, adapters were removed and low-quality reads were discarded by using Trimmomatic v.0.36, TRAILING:5, SLIDINGWINDOW:4:5 MINLEN:36
ChIP-seq reads were aligned to the mm10 genome with Burrows-Wheeler aligner v.0.7.12, -n 2 -l 20 -k 1 -t 2.
Aligned reads from the individual biological replicates were merged into one single .bam file, and duplicates were removed using SAMtools v.1.5.
Peaks were called using MACS2 v.2.1.1 with the parameters: -q 0.01 –nomodel –extsize 300 -B –SPMR. Peaks were called against the inputs (input_K4me3_Y and input_K4me3_O) for all ChIPs.
H3K4me3 and H3K27ac: Peaks with FDR 0.01 (which is, peak score>20) were considered as significant H3K4me3 and H3K27ac peaks for further analysis. H3K4me1: Peaks were called against the same input in H3K4me3 ChIP-seq. Peaks with FDR 0.01 (which is, peak score>20) were considered as significant H3K4me1 peaks for further analysis.
Assembly: mm10
Supplementary files format and content: bed

extract_protocol:
20 million cells were fixed with with 1% methanol-free formaldehyde for 10 minutes. After quenching and cell lysis, nuclear extract was sonicated using a Bioruptor Pico (Diagenode). For IP, 20ug of chromatin were used and incubated with 1.6 ul of anti-H3K4me1 (ab8895, Abcam) with rotation overnight at 4ºC. After immunoprecipitated chromatin was eluted, DNA was purified with the QIAquick PCR Purification Kit (28106, Qiagen).
Libraries were carried out using the NEBNext Ultra DNA Library Prep for Illumina kit (E7370) or the NEBNext® Ultra II DNA Library Prep for Illumina® kit (E7645) using the manufacturer’s protocol. In brief, ChIP-enriched DNA and input DNA were subjected to end repair and the addition of “A” bases to 3’ ends, NEB adapter’s ligation and USER excision. For all purification steps, AgenCourt AMPure XP beads (A63882, Beckman Coulter) were used. Library amplification was performed by PCR using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, E6440, E6442, E6444, E6446). Analysis of final libraries was carried out using either an Agilent Bioanalyzer or Fragment analyzer High Sensitivity assay (5067‐4626 or DNF‐474) to estimate the quantity and check size distribution. Quantification of these final libraries was done by quantitative PCR using the KAPA Library Quantification Kit (KK4835, KapaBiosystems, 07960204001 Roche).

tag: condition

value: IP


title: Total RNA, WI-38 fibroblasts, PDL 33

description: Library name: PDL33_totalRNA


title: ILPr16,preoperative ILE,baseline

description: Library name: ILPr16

tag: tissue


title: Old_H3K4me1_ChIP

description: Library name: K4me1_O4


title: DNA from Non neoplastic kidney control 39

description: DNA from Non neoplastic kidney control

tag: Sex


title: ILPr15,preoperative ILE,baseline

description: Library name: ILPr15


title: Total RNA, WI-38 fibroblasts, PDL 21

description: Library name: PDL21_totalRNA

tag: cell type


title: Young_H3K27ac_ChIP

description: Library name: K27Ac_Y4


title: DNA from Non neoplastic kidney control 33

description: DNA from Non neoplastic kidney control


title: [RNA-Seq] Donor_3_ESS

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

description:
Library name: SW9_S45
Donor_3_ESS

data_processing:
Sequenced paired-end 76bp on Illumina HiSeq4000
The paired-end RNA-seq reads were quality assessed using FastQC (v 0.11.3), FastQ Screen (v 0.9.2).
The reads were  quality trimmed with Trimmomatic (v 0.36) and mapped against the reference genome (hg38) using STAR (version 2.7.2b).
Counts per gene were calculated by STAR (version 2.7.2b). using annotation from GENCODE (version32)
Assembly: hg38
Supplementary files format and content: mRNA_raw_counts.tsv: tab-delimited text containing unnormalized gene-level counts

source_name: primary Human Coronary Artery Endothelial Cell

growth_protocol: HCAECs in MV2

extract_protocol:
RNA purification performed using Norgen total RNA plus kit
Illumina TruSeq Stranded mRNA

treatment_protocol: 72 hours culture under flow using parallel plate flow apparatus

value: ESS


title: Old_H3K27ac_ChIP

description: Library name: K27Ac_O4


title: DNA from Non neoplastic kidney control 27

description: DNA from Non neoplastic kidney control

value: Non neoplastic kidney control


title: ILPr14,preoperative ILE,baseline

description: Library name: ILPr14


title: Old_H3K4me3_input_4

description: Library name: input_K4me3_O_4

value: epidermis

value: input


title: DNA from Non neoplastic kidney control 24

description: DNA from Non neoplastic kidney control


title: 8023_Pleg_low_48

label_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).

value: SC


title: [RNA-Seq] Donor_3_LSS

description:
Library name: SW8_S44
Donor_3_LSS

value: primary Human Coronary Artery Endothelial Cell

value: LSS


title: ILPr13,preoperative ILE,baseline

description: Library name: ILPr13

value: feces


title: DNA from Non neoplastic kidney control 23

description: DNA from Non neoplastic kidney control

value: Kidney


title: [RNA-Seq] Donor_2_ESS

description:
Library name: SW6_S42
Donor_2_ESS


title: [RNA-Seq] Donor_3_OSS

description:
Library name: SW7_S43
Donor_3_OSS

value: OSS


title: Old_H3K4me3_input_3

description: Library name: input_K4me3_O_3


title: Old_H3K4me3_input_2

description: Library name: input_K4me3_O_2


title: DNA from Non neoplastic kidney control 19

description: DNA from Non neoplastic kidney control


title: ILPr12,preoperative ILE,baseline

description: Library name: ILPr12


title: [RNA-Seq] Donor_2_LSS

description:
Library name: SW5_S41
Donor_2_LSS


title: Old_H3K4me3_input_1

description: Library name: input_K4me3_O_1


title: DNA from Non neoplastic kidney control 18

description: DNA from Non neoplastic kidney control


title: ILPr09,preoperative ILE,baseline

description: Library name: ILPr09


title: ILPr10,preoperative ILE,baseline

description: Library name: ILPr10


title: [RNA-Seq] Donor_2_OSS

description:
Library name: SW4_S40
Donor_2_OSS


title: DNA from Non neoplastic kidney control 16

description: DNA from Non neoplastic kidney control

value: Male


title: [RNA-Seq] Donor_1_ESS

description:
Library name: SW3_S39
Donor_1_ESS


title: ILPr08,preoperative ILE,baseline

description: Library name: ILPr08


title: Young_H3K4me3_input_4

description: Library name: input_K4me3_Y_4

value: Young


title: ILPr07,preoperative ILE,baseline

description: Library name: ILPr07


title: Young_H3K4me3_input_3

description: Library name: input_K4me3_Y_3


title: Young_H3K4me3_input_2

description: Library name: input_K4me3_Y_2


title: [RNA-Seq] Donor_1_LSS

description:
Library name: SW2_S38
Donor_1_LSS


title: DNA from Non neoplastic kidney control 8

description: DNA from Non neoplastic kidney control


title: ILPr06,preoperative ILE,baseline

description: Library name: ILPr06


title: Young_H3K4me3_input_1

description: Library name: input_K4me3_Y_1


title: ILPr04,preoperative ILE,baseline

description: Library name: ILPr04


title: Donor_3_ESS

description:
Library name: SW9_S9
Donor_3_ESS

data_processing:
Sequenced paired-end 76bp on Illumina HiSeq4000
The R1 RNA-seq reads were quality assessed using FastQC (v 0.11.3), FastQ Screen (v 0.9.2).
The R1 reads were quality trimmed and filtered for length with Cutadapt v1.18 (min length 18nt, max length 26nt), and mapped against the reference genome (hg38) using Bowtie v1.1.1
Counts per gene were calculated using featureCounts with annotation from miRBasev22
Assembly: hg38
Supplementary files format and content: miR_raw_counts.tsv: tab-delimited text containing unnormalized counts for each miRNA

extract_protocol:
RNA purification performed using Norgen total RNA plus kit
NEBNext® Multiplex Small RNA Library Prep Set for Illumina®


title: HD2

city: Wuxi

first: qin

last: chu

address: Department of Respiratory, The Affiliated Wuxi People’s Hospital of Nanjing Medical University

department: Department of Respiratory

description:
Library name: HD2
Human immortalized epidermal cells, control cells treated with TNFα + IFNγ.

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count for each Sample

source_name: Human immortalized epidermal cells

extract_protocol:
Total RNA was extracted from cultured CAFs using TRIzol reagent. Subsequently, small RNA fragments (18-30 nt) were enriched and purified via denaturing polyacrylamide gel electrophoresis to isolate high-quality miRNAs for sequencing.
Purified miRNAs were sequentially ligated to 3' and 5' adapters. The ligated products were reverse-transcribed into cDNA and amplified by PCR. The final cDNA library was purified and validated for quality prior to sequencing.

value: airway epithelial cells

value: Human immortalized epidermal cells

value: control cells treated with TNFα + IFNγ


title: 8019_Avonex_low_144

value: IM


title: ILPr03,preoperative ILE,baseline

description: Library name: ILPr03

data_processing:
Relative abundance: Top 20 taxa of each sample at each taxonomic ranks (Phylum, Class, Order, Family, Genus, Species) were selected to plot the distribution histogram of relative abundance in Perl through SVG function. Alpha and Beta Diversity: For analyzing community diversity, richness, and evenness, alpha diversity was calculated using Shannon and Simpson indices in QIIME2. Beta diversity was performed with Principal Coordinates Analysis (PCoA) and Adonis analysis. Community difference analysis: T-test, and linear discriminant analysis effect size (LEfSe) were conducted to characterize community structure differentiation. Function Prediction: PICRUSt2 (V2.3.0) was applied to predict metagenomic functions based on marker genes. Canonical correspondence analysis (CCA) were used to explore interspecies symbiosis and environmental impacts on community structure, reflecting correlations between environmental factors and genus/species abundance.
Continuous variables were expressed as mean with standard deviation and compared using the Student’s T test. Categorical data, on the other hand, were represented as frequencies and percentages, and comparisons were made using the Pearson χ2 test or the Fisher exact test, depending on suitability. A two-sided p value less than 0.05 was considered statistically significant. All data analyses were conducted using the R software package (version 4.0).
Assembly: 16S rRNA gene reference database(Silva 138.1)
Supplementary files format and content: Processed data are ASV feature count matrix (tab-delimited TSV format). Rows represent individual ASVs, columns correspond to sample IDs, and values denote raw sequencing read counts of each ASV across all fecal samples. Taxonomic classification results assigned against SILVA 138.1 database are also provided in the feature table.
Library strategy: 16S rRNA-seq

extract_protocol:
16S rRNA genes of distinct regions (16SV3-V4) were amplified used specific primer with the barcode. All PCR reactions were carried out with 15 µL of Phusion® High-Fidelity PCR Master Mix (New England Biolabs); 0.2µM of forward and reverse primers, and about 10 ng template DNA. Thermal cycling consisted of initial denaturation at 98℃ for 1 min, followed by 30 cycles of denaturation at 98℃ for 10s, annealing at 50℃ for 30 s, and elongation at 72℃ for 30s and 72℃ for 5 min. The PCR products were purified using magnetic bead purification. Samples were mixed in equidensity ratios based on the concentration of PCR products.
After thorough mixing, the PCR products were detected and target bands were recovered. Sequencing libraries were generated and indexes were added. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.


title: Old_H3K4me3_ChIP_3

description: Library name: K4me3_O_3

value: Old

value: IP


title: Donor_3_LSS

description:
Library name: SW8_S8
Donor_3_LSS


title: DNA from Non neoplastic kidney control 48

description: DNA from Non neoplastic kidney control

data_processing:
R library minfi and ChAMP
processed value definition: Normalized Beta value

extract_protocol: Genomic DNA was extracted using standard phenol-chloroform-isoamyl alchohol protocol

value: Female

value: Non neoplastic kidney control


title: Donor_3_OSS

description:
Library name: SW7_S7
Donor_3_OSS


title: DNA from Non neoplastic kidney control 29

description: DNA from Non neoplastic kidney control


title: Old_H3K4me3_ChIP_2

description: Library name: K4me3_O_2

value: epidermis


title: DNA from Non neoplastic kidney control 31

description: DNA from Non neoplastic kidney control


title: Donor_2_LSS

description:
Library name: SW5_S5
Donor_2_LSS


title: lib25_round2-R2

first: Han

last: Guo

state: Zhejiang

address: Xiasha

department: Aptamer Selection Center

institute: Hangzhou Institute of Medicine, Chinese Academy of Sciences

description:
Library name: lib25_round2-R2
This dataset contains sequencing data from aptamer selection against 24 individual protein targets.

library_source: other

data_processing:
Raw reads were quality-checked using FastQC. Adapter sequences and low-quality bases (Phred score < 20) were trimmed using Cutadapt. Reads shorter than 220 bp after trimming were discarded. Barcode and SELEX primer sequences were removed from the reads using custom scripts. Reads were demultiplexed based on round-specific barcodes. Clean reads were collapsed into unique sequences using fastx-collapser. The abundance of each unique aptamer sequence was counted across all target proteins. Read counts were normalized to reads per million (RPM) across samples.
FASTQ files named with the suffix round1-R5 contain sequencing data of aptamer libraries enriched against each target protein in round 5 of the preliminary screening process (round 1-R5). Each file corresponds to 24 protein targets derived from the same initial random library. We summed the read counts of each unique sequence across all sub-libraries and sorted the results in descending order. Unique sequences with prominent total read counts indicating significant enrichment were retained. The CSV files labeled raw_counts_round1-R5 document the read counts of these selected sequences in each individual sub-library.
FASTQ files named with round2-R2 contain sequencing data of aptamer libraries enriched against each target protein in round 2 of the secondary screening process (round 2-R2). Each file corresponds to 24 protein targets derived from the same top 3000 enriched library. Read counts of the original 3000 unique sequences across all sub-libraries were extracted and compiled into CSV files named raw_read_counts_round2-R2. Fewer than 3000 unique sequences were detected in each file. The missing sequences are likely false positives caused by matrix adsorption during the preliminary screening process, or result from limited sequencing throughput.
Total read counts of the 3000 unique sequences across 24 target-enriched libraries were normalized. For each unique sequence, we calculated the sum of read counts across 24 target libraries, and then computed the relative abundance ratio by dividing the read count of each library by the total read count. All results are presented in CSV files named relative_abundance_ratio_round2-R2. The relative abundance ratio reflect the binding capacity of each unique sequence to different target proteins and characterize sequence binding specificity.
Assembly: Not applicable.
Supplementary files format and content: All processed data are provided as CSV files. Files named with raw_count contain read counts of unique sequences in enriched libraries against each protein target. Files named with relative_abundance_ratio record the relative abundance ratios of corresponding read counts. Lib10, lib13, lib18 and lib25 represent four distinct random ssDNA libraries with different primer regions. Each library was used for aptamer selection against 24 protein targets. In these files, each row corresponds to one unique sequence, and each column represents one protein target. For round1-R5, since sample IDs in FASTQ files do not match protein names in CSV files, a supplementary file named round1-R5_fastq_SampleID_to_csv_Protein_Name_mapping is supplied to clarify the correspondence between sample IDs and protein names. Detailed data processing procedures are described in the Data Processing Steps section.

molecule: other

organism: synthetic construct

source_name: in vitro synthetic nucleic acid library; SELEX aptamer library, no native biological cell/tissue origin

growth_protocol: Not applicable. No biological cells or tissues were used in this study. All experoments were performed in vitro using synthetic oligonucleotide libraries and purified proteins.

extract_protocol:
Nucleotide sequences bound to target proteins were eluted using 100 μL of ddH2O by heating at 95 ℃ for 10 min.
Enriched ssDNA pools from each SELEX round were end-repaired, A-tailed, and ligated with sequencing adapters following standard Illumina library preparation protocols. Barcodes were incorporated for multiplexed sequencing. Libraries were amplified by limited-cycle PCR and purified to remove primer dimers and non-specific products before sequencing.

treatment_protocol: The preliminary screening procedure (round 1-R1 to round 1-R5) was conducted according to the classic magnetic bead-based SELEX process. For each target protein, an initial, artificially synthesized random ssDNA library, comprising approximately 10^15 molecules (1 OD), was employed. These ssDNA libraries were dissolved, denatured at 95 ℃ for 10 min, and cooled to 4 ℃ for 5 min to ensure optimal structural conformation. The prepared libraries were added into the histidine peptide-coupled plate for a 1 h counter selection process to eliminate the nonspecific binding. The supernatant was then transferred to the target protein-coupled plate and incubated for 1 h. To further reduce nonspecific binding through competitive interactions, BSA, HsDNA and histidine peptide were incorporated during the positive selection phase. The concentration of these agents was increased to augment selection pressure in subsequent rounds. Following this, unbound sequences present in the supernatant were discarded, and the plate was washed for four times with 200 μL of DPBS-T. Sequences bound to target proteins were eluted using 100 μL of ddH2O by heating at 95 ℃ for 10 min. The eluted ssDNA was then amplified and collected for the next round of selection. In the secondary screening procedure, the initial libraries comprised the corresponding 3000 sequences (top 3000 sequences). These top3000 sequences were derived from the NGS results of the round 1-R5, representing sequences that were significant enriched in the prior screening. Utilizing chip printing technology, the top 3000 sequences of the four libraries (a total of 12000 sequences) were synthesized in batches. Subsequently, emulsion PCR was performed using the corresponding primers to obtained uniformly amplified initial libraries for the secondary screening. The subsequent steps paralleled those of the preliminary screening.

value: lib25 ssDNA library, round 2 of the secondary screening process


title: DNA from Non neoplastic kidney control 32

description: DNA from Non neoplastic kidney control


title: Young_H3K4me3_ChIP_4

description: Library name: K4me3_Y_4


title: DNA from Non neoplastic kidney control 25

description: DNA from Non neoplastic kidney control


title: lib13_round2-R2

description:
Library name: lib13_round2-R2
This dataset contains sequencing data from aptamer selection against 24 individual protein targets.

value: in vitro synthetic nucleic acid library; SELEX aptamer library, no native biological cell/tissue origin

value: lib13 ssDNA library, round 2 of the secondary screening process


title: Donor_1_LSS

description:
Library name: SW2_S2
Donor_1_LSS

value: primary Human Coronary Artery Endothelial Cell

value: LSS


title: lib10_round2-R2

description:
Library name: lib10_round2-R2
This dataset contains sequencing data from aptamer selection against 24 individual protein targets.

value: lib10 ssDNA library, round 2 of the secondary screening process


title: DNA from Non neoplastic kidney control 17

description: DNA from Non neoplastic kidney control

value: Kidney

value: Male


title: Old_H3K4me3_ChIP_1

description: Library name: K4me3_O_1


title: Donor_1_OSS

description:
Library name: SW1_S1
Donor_1_OSS

value: OSS


title: TH213

status: Public on Jun 22 2026

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

source_name: NoABMRM

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

value: heart biopsy


title: TH214


title: TH211


title: TH210


title: TH209

source_name: ABMRM


title: TH212


title: TH207


title: TH208


title: BK2

institute: The Affiliated Wuxi People’s Hospital of Nanjing Medical University

description:
Library name: BK2
Human airway epithelial cells, TMPRSS4 knockout cells treated with house dust mite (HDM)

source_name: Human airway epithelial cells

value: airway epithelial cells

value: Human airway epithelial cells


title: TH203


title: TH204


title: TH201


title: TH202


title: TH200


title: TH198


title: DNA from Non neoplastic kidney control 26

description: DNA from Non neoplastic kidney control


title: TH197


title: TH196


title: Donor_2_OSS

description:
Library name: SW4_S4
Donor_2_OSS


title: TH195


title: Young_H3K4me3_ChIP_2

description: Library name: K4me3_Y_2

value: Young


title: Young_H3K4me3_ChIP_1

description: Library name: K4me3_Y_1

value: IP


title: TH193


title: TH194


title: TH191


title: TH192


title: TH189


title: TH190


title: Old_H3K4me3_ChIP_4

description: Library name: K4me3_O_4

value: Old


title: ILPr11,preoperative ILE,baseline

description: Library name: ILPr11

source_name: feces

value: feces


title: TH187


title: Whole Blood, 21-3.IP

city: Kunming

first: Ruixia

last: Tang

address: Jiaoling Road 935

institute: Chinese  Academy  of Medical Sciences & Peking Union Medical College

description:
Library name: Sample24
sheet 21-3

data_processing:
Adapter trimming and removal of low-quality reads using cutadapt
Alignment to the reference genome (GCF_003339765.1) using HISAT2
Generation of expression profiles using featureCounts
Differential expression analysis using edgeR
Identification of m6A methylation peaks using MACS
Differential methylation analysis using diffReps
GO, KEGG, and GSEA pathway enrichment analysis using clusterProfiler
Metagene and Motif analysis using MetaPlotR and DREME
Assembly: GCF_003339765.1
Supplementary files format and content: Format: XLSX; Content: m6A MeRIP-seq methylated RNA sites and differential methylation peaks
Library strategy: MeRIP-Seq

organism: Macaca mulatta

source_name: Whole Blood

extract_protocol:
Total RNA was extracted from whole-blood samples using TRIzol reagent (Invitrogen, Catalog No. 10296028CN) per the manufacturer’s protocol. RNA concentration/purity was assessed via NanoDrop 1000 (A260/A280 ≥ 1.8, A260/A230 ≥ 2.0), and integrity via Agilent 2100 Bioanalyzer (RNA Integrity Number (RIN) ≥ 8.0). Only qualified RNA was used for subsequent sequencing.
Total RNA was subjected to ribosomal RNA (rRNA) removal using GenSeq® rRNA Removal Kit (GenSeq, Inc., Shanghai, China). Then, the rRNA- depleted samples were used for library construction with GenSeq® Directional RNA Library Prep Kit (GenSeq, Inc., Shanghai, China) by following manufacturer’s recommendations. The RNA was fragmented into ~300 nt in length. The first-strand cDNA was synthesized from the RNA fragments by reverse transcriptase and random hexamer primers, and the second-strand cDNA was synthesized in 2nd Strand Synthesis Buffer with dUTP Mix. Then, the double stranded cDNA fragments were subjected to end-repair and dA-tailing, followed by adapter ligation. The adapter-ligated DNA samples were PCR amplified and purified to obtain sequencing libraries. Finally, the libraries were sequenced with sequence on the paired-end 150 bp mode.

value: Whole Blood

tag: genotype

value: 21 days

tag: infection

value: MPXV


title: TH185


title: TH186


title: Whole Blood, 21-1.IP

description:
Library name: Sample22
sheet 21-1


title: TH184


title: Whole Blood, 14-3.IP

description:
Library name: Sample21
sheet 14-3

value: 14 days


title: TH182


title: TH181


title: TH183


title: TH180


title: Whole Blood, 14-2.IP

description:
Library name: Sample20
sheet 14-2


title: TH178


title: Donor_1_ESS

description:
Library name: SW3_S3
Donor_1_ESS

value: primary Human Coronary Artery Endothelial Cell

tag: treatment

value: ESS


title: TH179


title: TH176


title: Whole Blood, 07-1.IP

description:
Library name: Sample16
sheet 07-1

value: 07 days


title: Whole Blood, C-3.IP

description:
Library name: Sample15
sheet C-3

value: control


title: TH174


title: TH175


title: Whole Blood, C-2.IP

description:
Library name: Sample14
sheet C-2


title: Whole Blood, C-1.IP

description:
Library name: Sample13
sheet C-1


title: TH173


title: Whole Blood, 21-3.Input

description: Library name: Sample12


title: TH171


title: TH172


title: Whole Blood, 21-2.Input

description: Library name: Sample11


title: Whole Blood, 14-2.Input

description: Library name: Sample8


title: TH167


title: TH170


title: TH168


title: TH166


title: Whole Blood, 14-1.Input

description: Library name: Sample7


title: Whole Blood, 07-3.Input

description: Library name: Sample6


title: TH165


title: TH164


title: Whole Blood, 07-1.Input

description: Library name: Sample4


title: TH163


title: TH162


title: Whole Blood, C-2.Input

description: Library name: Sample2


title: TH161


title: Whole Blood, C-1.Input

description: Library name: Sample1


title: TH159


title: Control_iPSC_derived megakaryocytic differentiation culture, day17

city: Changsha

first: Feifeng

last: Wu

state: Hunan

address: No.139, FuRong Road(Middle)

institute: The Second Xiangya Hospital of Central South University

description:
Library name: Control
whole unsorted day-17 differentiation culture was harvested for RNA extraction

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome GRCh38/hg38 using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Assembly: GRCh38/hg38
Supplementary files format and content: text file containing gene-level raw read counts for all detected genes and all submitted samples. Feature columns include GeneSymbol, EntrezGeneID, Description, and CodingType. Sample count columns are A11 and Control, matching the library names in the SAMPLES section.

source_name: healthy control-derived iPSC line

growth_protocol: Human iPSCs were maintained under feeder-free conditions on Matrigel-coated plates in mTeSR Plus medium and passaged as cell clumps using ReLeSR.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
the libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: Human iPSCs were differentiated toward the megakaryocytic lineage according to the protocol described in the associated manuscript. Cells were collected at day 17 of differentiation for RNA extraction.

value: healthy control-derived iPSC line

value: iPSC-derived megakaryocytic differentiation culture, day17

value: megakaryocytic differentiation for 17 days


title: SLFN14Q93W_iPSC_derived megakaryocytic differentiation culture, day17

description:
Library name: A11
whole unsorted day-17 differentiation culture was harvested for RNA extraction

source_name: patient-derived iPSC

value: patient-derived iPSC

value: SLFN14 p.Q93W heterozygous


title: TH158

value: heart biopsy


title: LS8817, Palbociclib, Biorep C, mH2A1, techrep 3

city: New York

first: Viviana

middle: I.

last: Risca

state: NY

address: 1230 York Ave, Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: The Rockefeller University

description:
Library name: LS8817_PalbociclibC-mH2A1-3
Palbociclib_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&RUN performed on macroH2A1

data_processing:
Cutadapt was used to trim adapters using the following code: cutadapt -a "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC" -a "CTGTCTCTTATACACATCTGACGCTGCCGACGA"  -o "$outfile1" -p "$outfile2" "$infile1" "$infile2". Reads with aligned to hg38 using bowtie2 using the following parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Peaks were called with SEACR software (Meers et al. 2019) with parameters specified to non-normalized and stringent threshold at 0.1 for H3K27ac and 0.01 for macroH2A1. Using bedtools, bam files were converted to bedpe files which were then converted to bedgraph format. Bedgraph files were used as input into SEACR peak caller.
Bedtools intersect was used to keep peaks that were reproducible in at least 2 out of 3 technical replicates before filtering for reproducible peaks across biological replicates. Bedtools merge was then used to generate a non-redundant master peak set across all conditions.
FeatureCounts was used to quantify read pairs overlapping peaks from master peak sets across conditions, with the “count all overlapping features” option enabled.
Assembly: hg38
Supplementary files format and content: files ending in "merged_RPGCnorm.bw" are RPGC normalized bigwig files, merged across both biological replicates.
Supplementary files format and content: mH2A1_0.01.nonredundant.masterpeaks.bed is the master peak set across all samples as a bed file.
Library strategy: CUT&Run

source_name: soft tissue sarcoma

growth_protocol: LS8817 Cells were cultured in DMEM high glucose no glutamine (11960044, Gibco™), supplemented with 9% FBS (10082147, Gibco™), 1% of 100x GlutaMAX™ Supplement (35050061, Gibco™) and 1% of 10,000U/mL penicillin/streptomycin (15140122, Gibco™) and maintained at 37°C and 5% CO2.

extract_protocol:
LS8817 cells were briefly centrifuged followed by resuspension with ConA beads and proceeding with the rest of the CUT&RUN protocol by Epicypher (Version 2.2).
CUT&RUN in approximately 100,000 cells was performed on macroH2A1 (Cat #ab37264, lot #1046297-1, Abcam), 1:100 following an optimized protocol by Epicypher (Version 2.2). NEBNext Ultra II DNA Library Prep Kit for Illumina was used for fragmentation, end repair and dA-tailing, adapter ligation and PCR amplification according to the manufacturer’s instructions. Ampure XP beads were used for post-PCR cleanup. Samples were eluted in IDTE buffer.

treatment_protocol: Cells were passaged at a 1:3 ratio one day before drug treatment and treated with drugs at the specified concentrations, with media changes every 2–3 days until harvest.

value: soft tissue sarcoma

value: liposarcoma

value: TetON FLAG-MDM2

value: day28 1uM palbociclib

tag: batch


title: TH160


title: TH156


title: TH188


title: LS8817, Palbociclib, Biorep C, mH2A1, techrep 2

description:
Library name: LS8817_PalbociclibC-mH2A1-2
Palbociclib_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&RUN performed on macroH2A1


title: Whole Blood, 21-2.IP

description:
Library name: Sample23
sheet 21-2

value: Whole Blood

value: 21 days


title: TH155


title: LS8817, Palbociclib, Biorep C, mH2A1, techrep 1

description:
Library name: LS8817_PalbociclibC-mH2A1-1
Palbociclib_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&RUN performed on macroH2A1


title: TH154


title: Whole Blood, 14-1.IP

description:
Library name: Sample19
sheet 14-1

value: 14 days

value: MPXV


title: Whole Blood, 07-3.IP

description:
Library name: Sample18
sheet 07-3


title: LS8817, Palbociclib, Biorep B, mH2A1, techrep 3

description:
Library name: LS8817_PalbociclibB-mH2A1-3
Palbociclib_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&RUN performed on macroH2A1


title: LS8817, Palbociclib, Biorep B, mH2A1, techrep 2

description:
Library name: LS8817_PalbociclibB-mH2A1-2
Palbociclib_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&RUN performed on macroH2A1


title: TH177


title: TH153


title: Whole Blood, 07-2.IP

description:
Library name: Sample17
sheet 07-2


title: TH157


title: LS8817, Palbociclib, Biorep B, mH2A1, techrep 1

description:
Library name: LS8817_PalbociclibB-mH2A1-1
Palbociclib_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&RUN performed on macroH2A1


title: LS8817, Doxorubicin Biorep C, mH2A1, techrep 1

description:
Library name: LS8817_DoxorubicinC_mH2A1-1
Doxorubicin_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&RUN performed on macroH2A1

value: 100 nM doxorubicin (24 h), harvested on day 14


title: TH152


title: LS8817, Doxorubicin Biorep B, mH2A1, techrep 2

description:
Library name: LS8817_DoxorubicinB_mH2A1-2
Doxorubicin_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&RUN performed on macroH2A1

value: 100 nM doxorubicin (48 h), harvested on day 14


title: TH150


title: LS8817, Doxorubicin Biorep B, mH2A1, techrep 1

description:
Library name: LS8817_DoxorubicinB_mH2A1-1
Doxorubicin_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&RUN performed on macroH2A1


title: TH151


title: TH149


title: LS8817, Doxorubicin Biorep A, mH2A1, techrep 1

description:
Library name: LS8817_DoxorubicinA_mH2A1-1
Doxorubicin_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&RUN performed on macroH2A1


title: TH148


title: LS8817, Doxorubicin Biorep A, mH2A1, techrep 2

description:
Library name: LS8817_DoxorubicinA_mH2A1-2
Doxorubicin_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&RUN performed on macroH2A1


title: TH147


title: LS8817, Cycling Biorep B, mH2A1, techrep 3

description:
Library name: LS8817_CyclingB_mH2A1-3
Cycling_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for Cycling samples with CUT&RUN performed on macroH2A1


title: Whole Blood, 14-3.Input

description: Library name: Sample9


title: Whole Blood, 21-1.Input

description: Library name: Sample10


title: TH169


title: LS8817, Cycling Biorep B, mH2A1, techrep 2

description:
Library name: LS8817_CyclingB_mH2A1-2
Cycling_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for Cycling samples with CUT&RUN performed on macroH2A1


title: TH145


title: LS8817, Cycling Biorep B, mH2A1, techrep 1

description:
Library name: LS8817_CyclingB_mH2A1-1
Cycling_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for Cycling samples with CUT&RUN performed on macroH2A1


title: TH146


title: LS8817, Cycling Biorep A, mH2A1, techrep 3

description:
Library name: LS8817_CyclingA_mH2A1-3
Cycling_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for Cycling samples with CUT&RUN performed on macroH2A1


title: TH144


title: LS8817, Cycling Biorep A, mH2A1, techrep 2

description:
Library name: LS8817_CyclingA_mH2A1-2
Cycling_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for Cycling samples with CUT&RUN performed on macroH2A1


title: LS8817, Cycling Biorep A, mH2A1, techrep 1

description:
Library name: LS8817_CyclingA_mH2A1-1
Cycling_mH2A1_merged_merged_RPGCnorm.bw
RPGC normalized bigwig files, merged across both biological replicates for Cycling samples with CUT&RUN performed on macroH2A1


title: TH142


title: LS8817, day28Palbo, H3K27ac, rep2, techrep 1

description:
Library name: LS8817_day28Palbo_H3K27ac_rep2_3
RPGC normalized bigwig files, merged across both biological replicates for day28 Palbo samples with CUT&Tag performed on H3K27ac
day28_Palbo_K27ac_merged_RPGCnorm.bw

data_processing:
Sequencing data were processed using a modular pipeline implemented in Nextflow (https://github.com/riscalab/NEXDEP-Nextflow_DNA_Epigenomic_Pipeline). Quality control was assessed using FastQC, and reports were aggregated using MultiQC to generate summary metrics across all samples.
Reads were aligned to the reference genome using BWA (Burrows–Wheeler Aligner). SAM files generated from alignment were converted to sorted and indexed BAM files using SAMtools. Alignment statistics, including mapping rates and read counts, were calculated for each sample. Reads overlapping ENCODE blacklist regions were removed. Filtered BAM files were re-indexed prior to downstream analysis.
Peaks were called with SEACR software (Meers et al. 2019) with parameters specified to non-normalized and stringent threshold at 0.1 for H3K27ac and 0.01 for macroH2A1. Using bedtools, bam files were converted to bedpe files which were then converted to bedgraph format. Bedgraph files were used as input into SEACR peak caller.
Bedtools intersect was used to keep peaks that were reproducible in at least 2 out of 3 technical replicates before filtering for reproducible peaks across biological replicates. Bedtools merge was then used to generate a non-redundant master peak set across all conditions.
FeatureCounts was used to quantify read pairs overlapping peaks from master peak sets across conditions, with the “count all overlapping features” option enabled
Assembly: hg38
Supplementary files format and content: files ending in "merged_RPGCnorm.bw" are RPGC normalized bigwig files, merged across both biological replicates.
Library strategy: CUT&Tag

extract_protocol:
LS8817 cells were briefly centrifuged followed by incubation with Nuclear Extraction buffer on ice for 10 minutes. After resuspension in Wash Buffer, nuclei were slow frozen in cryogenic vials with 10% DMSO for storage at –80 °C before resuming the rest of the protocol.
Approximately 100,000 cells were used per sample for overnight incubation with primary H3K27ac antibody (1:100 ab4729). Secondary antibody (1:100 ABIN101961) was incubated for 30 minutes at room temperature followed by addition of in-house pG-Tn5 preloaded with adapters. Phenol chloroform DNA extraction was performed using Qiagen’s Maxtract High Density phase-lock tubes. Libraries were PCR amplified for 12 cycles with Illumina i5 or i7 barcoded primers and Ampure XP beads were used for post-PCR cleanup.


title: TH141


title: TH140


title: TH143


title: LS8817, day28Palbo, H3K27ac, rep2, techrep 2

description:
Library name: LS8817_day28Palbo_H3K27ac_rep2_2
RPGC normalized bigwig files, merged across both biological replicates for day28 Palbo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day28_Palbo_K27ac_merged_RPGCnorm.bw


title: TH139


title: LS8817, day28Palbo, H3K27ac, rep2, techrep 3

description:
Library name: LS8817_day28Palbo_H3K27ac_rep2_4
RPGC normalized bigwig files, merged across both biological replicates for day28 Palbo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day28_Palbo_K27ac_merged_RPGCnorm.bw


title: LS8817, day28Palbo, H3K27ac, rep1, techrep 3

description:
Library name: LS8817_day28Palbo_H3K27ac_rep1_3
RPGC normalized bigwig files, merged across both biological replicates for day28 Palbo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day28_Palbo_K27ac_merged_RPGCnorm.bw


title: Whole Blood, 07-2.Input

description: Library name: Sample5

value: 07 days


title: LS8817, day28Palbo, H3K27ac, rep1, techrep 2

description:
Library name: LS8817_day28Palbo_H3K27ac_rep1_2
RPGC normalized bigwig files, merged across both biological replicates for day28 Palbo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day28_Palbo_K27ac_merged_RPGCnorm.bw


title: TH138


title: TH137


title: TH136


title: LS8817, day14Palbo, H3K27ac, rep2, techrep 3

description:
Library name: LS8817_day14Palbo_H3K27ac_rep2_4
RPGC normalized bigwig files, merged across both biological replicates for day14 Palbo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day14_Palbo_K27ac_merged_RPGCnorm.bw

value: day14 1uM palbociclib


title: LS8817, day14Palbo, H3K27ac, rep2, techrep 2

description:
Library name: LS8817_day14Palbo_H3K27ac_rep2_3
RPGC normalized bigwig files, merged across both biological replicates for day14 Palbo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day14_Palbo_K27ac_merged_RPGCnorm.bw


title: LS8817, day28Palbo, H3K27ac, rep1, techrep 1

description:
Library name: LS8817_day28Palbo_H3K27ac_rep1_1
RPGC normalized bigwig files, merged across both biological replicates for day28 Palbo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day28_Palbo_K27ac_merged_RPGCnorm.bw


title: TH135


title: LS8817, day14Palbo, H3K27ac, rep2, techrep 1

description:
Library name: LS8817_day14Palbo_H3K27ac_rep2_2
RPGC normalized bigwig files, merged across both biological replicates for day14 Palbo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day14_Palbo_K27ac_merged_RPGCnorm.bw


title: TH133


title: Whole Blood, C-3.Input

description: Library name: Sample3

value: control


title: TH132


title: LS8817, day14Palbo, H3K27ac, rep1, techrep 3

description:
Library name: LS8817_day14Palbo_H3K27ac_rep1_3
RPGC normalized bigwig files, merged across both biological replicates for day14 Palbo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day14_Palbo_K27ac_merged_RPGCnorm.bw


title: TH134


title: TH131


title: LS8817, day14Palbo, H3K27ac, rep1, techrep 2

description:
Library name: LS8817_day14Palbo_H3K27ac_rep1_2
RPGC normalized bigwig files, merged across both biological replicates for day14 Palbo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day14_Palbo_K27ac_merged_RPGCnorm.bw


title: LS8817, day14Palbo, H3K27ac, rep1, techrep 1

description:
Library name: LS8817_day14Palbo_H3K27ac_rep1_1
RPGC normalized bigwig files, merged across both biological replicates for day14 Palbo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day14_Palbo_K27ac_merged_RPGCnorm.bw


title: LS8817, day14Doxo, H3K27ac, rep2, techrep 3

description:
Library name: LS8817_day14Doxo_H3K27ac_rep2_4
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day14_Doxo_K27ac_merged_RPGCnorm.bw


title: LS8817, day14Doxo, H3K27ac, rep2, techrep 2

description:
Library name: LS8817_day14Doxo_H3K27ac_rep2_3
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day14_Doxo_K27ac_merged_RPGCnorm.bw


title: TH129


title: LS8817, day14Doxo, H3K27ac, rep2, techrep 1

description:
Library name: LS8817_day14Doxo_H3K27ac_rep2_2
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day14_Doxo_K27ac_merged_RPGCnorm.bw


title: TH127


title: TH130


title: TH125


title: LS8817, day14Doxo, K27ac, rep1, techrep 3

description:
Library name: LS8817_day14Doxo_K27ac_rep1_3
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day14_Doxo_K27ac_merged_RPGCnorm.bw


title: TH126


title: LS8817, day14Doxo, K27ac, rep1, techrep 2

description:
Library name: LS8817_day14Doxo_K27ac_rep1_2
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day14_Doxo_K27ac_merged_RPGCnorm.bw


title: LS8817, day14Doxo, K27ac, rep1, techrep 1

description:
Library name: LS8817_day14Doxo_K27ac_rep1_1
RPGC normalized bigwig files, merged across both biological replicates for day14 Doxo samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
day14_Doxo_K27ac_merged_RPGCnorm.bw


title: LS8817, Cycling, H3K27ac, rep2, techrep 3

description:
Library name: LS8817_Cycling_H3K27ac_rep2_4
RPGC normalized bigwig files, merged across both biological replicates for Cycling samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
Cycling_K27ac_merged_RPGCnorm.bw


title: PDX244_988_20_AZD9833_73L

first: Alba

last: Mas Malavila

address: Saturnino Calleja 11-13

institute: VHIO

description:
Library name: 244_Z1
244_Z1 is a replicate of a sample treated with camizestrant from PDX244
2023-07-18_hg38_PDX244_13_samples_deseq2_normalized_counts.txt

data_processing:
Raw reads were mapped to the human reference genome (Gencode, release 38) and counted at the gene level using STAR version 2.55.3a and parameters '--outSAMunmapped None --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts'.
Differential expression analysis was performed in the R (version 4.0.0)/ Bioconductor environment, using the DESeq2 package version 1.28.1
Assembly: RNA-seq reads were mapped against the human reference genome (Gencode 38) with STAR 2.5.3a using ENCODE parameters.
Supplementary files format and content: DESeq2 normalized counts in txt format

source_name: Breast cancer Patient Derived Xenograft

extract_protocol:
RNeasy Mini Kit (#74106, Qiagen)
KAPA Stranded mRNA-Seq Illumina Platforms Kit (Roche)

value: Breast cancer Patient Derived Xenograft

value: Treated

value: Camizestrant

tag: sensitivity

value: Sensitive


title: TH123

value: heart biopsy


title: TH128


title: LS8817, Cycling, H3K27ac, rep2, techrep 2

description:
Library name: LS8817_Cycling_H3K27ac_rep2_3
RPGC normalized bigwig files, merged across both biological replicates for Cycling samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
Cycling_K27ac_merged_RPGCnorm.bw

value: soft tissue sarcoma

value: liposarcoma


title: TH122


title: irf1_Glucose_R3

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

description: Library name: dirf1_F_Glucose_R3

data_processing:
Processing is automated using the Tail-Tools pipeline, version 1.9 (https://github.com/Monash-RNA-Systems-Biology-Laboratory/tail-tools), and proceeds as follows: Reads are stripped of trailing poly(A) sequences. Reads are aligned using the STAR aligner. Any multi-mapping reads are assigned to one location at random. Counts per gene are produced with UMI deduplication. The UMI sequence can be found at the end of the read names in the FASTQ files. UMIs where the reads had an observed poly(A) tail of length at least 13 are also counted, and the average tail length from these UMIs is calculated. As 3'UTR annotations are not always accurate, reads up to 400 bases down-strand of a gene but not proceeding into another gene on the same strand are counted towards that gene.
Assembly: Candida auris B8441, downloaded 22 June 2020 from candidagenome.org.
Supplementary files format and content: CSV file containing counts of UMIs, counts of UMIs with a tail, and average tail lengths associated with each gene.

organism: Candidozyma auris

source_name: Candida auris cells

growth_protocol: Wild type and 3 transcription factor mutants grown in media containing either glucose or lactate as a carbon source. After 2 days growth on YP+2% Glucose and YP+2% Lactate plates at 30°C, cells were harvested directly from plates, washed in ice-cold ddH2O and pellets were stored at -80°C prior to RNA extraction.

extract_protocol:
Hot Phenol method: 1 ug of DNase treated Total RNA was used as library input.
Beilharz Lab Pooled PAT Seq  method

value: Candida auris cells

value: 470140  background

value: Grown in Glucose media


title: LS8817, Cycling, H3K27ac, rep2, techrep 1

description:
Library name: LS8817_Cycling_H3K27ac_rep2_2
RPGC normalized bigwig files, merged across both biological replicates for Cycling samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
Cycling_K27ac_merged_RPGCnorm.bw

value: TetON FLAG-MDM2


title: LS8817, Cycling, H3K27ac, rep1, techrep 2

description:
Library name: LS8817_Cycling_H3K27ac_rep1_2
RPGC normalized bigwig files, merged across both biological replicates for Cycling samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
Cycling_K27ac_merged_RPGCnorm.bw


title: LS8817, Cycling, H3K27ac, rep1, techrep 3

description:
Library name: LS8817_Cycling_H3K27ac_rep1_3
RPGC normalized bigwig files, merged across both biological replicates for Cycling samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
Cycling_K27ac_merged_RPGCnorm.bw


title: TH121


title: TH120


title: TH118


title: TH124