title: genomic DNA from control-siRNA treated HaCaT cells 1

source_name: control-siRNA treated HaCaT cells 1

value: control


title: jmjd-3.1(gk384) adult day 2 animals on cbp-1 RNAi, fasted for 24 hours, Replicate 4

status: Public on Feb 26 2026

type: SRA

city: Boston

first: Fasih

middle: Mubtasim

last: Ahsan

state: MA

address: 185 Cambridge Street, CPZN 6500

department: Center for Genomic Medicine

country: USA

institute: Massachusetts General Hospital

description: Library name: YZ16

library_source: transcriptomic

data_processing:
Fastq read quality control, adapter trimming, quality score filtering, and quasi-alignment were all performed using custom UNIX/Bash shell scripts on the Mass General Brigham ERISTwo Scientific Computing CentOS 7 Linux Cluster. Reads were analyzed for quality control using FastQC v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and MultiQC v1.19. Reads were then filtered for Illumina adapter contamination, truncated short reads or low-quality base calls using BBDuk (BBTools). The subsequently trimmed and cleaned reads were then quasi-aligned to the Caenorhabditis elegans reference transcriptome annotation (WBcel235, Ensembl Release 105) using Salmon v1.9.0, correcting for GC content and sequencing bias using the command parameters ‘--gcBias’ and ‘--seqBias’. All statistical analyses and visualizations were generated using the R v4.3.2 (www.r-project.org) Bioconductor v3.18 statistical environment on a local machine through Jupyter Notebook v6.4.10 (https://jupyter.org). Quasi-aligned transcript quantification files for each sample were collapsed into gene-level count matrices using R package tximport v1.30.0.
Paired differential expression was calculated using R package DESeq2 v1.42.1x with a design formula of ‘∼ Genotype_Treatment’. Genes were considered differentially expressed with a Benjamini-Hochberg False Discovery Rate (FDR) corrected P value < 0.05 and an absolute log2 transformed fold change of 1. Metabolism gene set variation analysis (GSVA) was performed using R package GSVA v1.50.1 using metabolic gene sets extracted from WormPaths. Heatmaps were generated using R package pheatmap v1.0.12, using row-scaled z scores generated from DESeq2 variance stabilized count transformation. Gene set overrepresentation analyses for genes identified as differentially expressed (with thresholds set as indicated above) were performed using R package clusterProfiler v4.12.3 for GO Molecular Function and Reactome-based pathway annotations. Venn diagram overlaps between differentially expressed genes in this study, npp-16 overexpression studies, and cbp-1/cco-1 knockdown/target studies were performed using ggvenn v0.1.10. Volcano plots were generated using ggplot2 v3.5.0. Visualizations were post-edited for font, sizing, and appearance using Adobe Illustrator and the Adobe Creative Cloud Suite. All custom bash scripts, Jupyter Notebook files, and processed fastq and transcript count files used in these analyses will be provided upon reasonable request by the corresponding author.
Assembly: ce11/WBcel235 (Ensembl Release 105)
Supplementary files format and content: Raw gene-level collapsed read counts for all 16 samples in matrix format (rows are samples, columns are WormBase Gene ID). Values represent raw read counts collapsed for each transcript from the WBcel235 (Ensembl Release 105) assembly to gene-level estimates using Salmon. 12 samples total (4 N2+EV AL, 4 N2+EV Fasted, 4 jmjd-3.1(-)+cbp-1 RNAi AL, 4 jmjd-3.1(-)+cbp-1 RNAi Fasted).
Supplementary files format and content: Salmon output generated quant.sf files are included for each sample. These files include (1) the transcript Wormbase Sequence ID, (2) the transcript length, (3) the effective length averaged for each gene-level, (4) the normalized transcript per million (TPM) abundance, and (5) the raw number of reads binned per transcript.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: Whole organism lysate

growth_protocol: C. elegans wild-type (N2 - Bristol) and H3K27ac(-) nematodes were grown and maintained at 20°C on Nematode Growth Media (NGM) seeded with Escherichia coli OP50-1 as previously described (Soukas et al., 2009). Animals were synchronized by hypochlorite bleach treatment of a population of gravid adults. Animals were collected in M9 medium, centrifuged at 4400 rpm for 1 minute and resuspended in 6 mL 1.3% bleach, 250 mM NaOH for 1 minute of vigorous shaking. Bleach solution exposure and shaking step was repeated after one wash in M9. After second bleach step, pellet was resuspended in minimal M9 by gentle pipetting, and washed in M9 four times. Eggs were resuspended in 12 mL M9, and solution was left to rotate overnight for 23 hours at 20°C. Animals were then dropped onto NGM RNAi plates supplemented with IPTG and Carbenicillin, and seeded with E. coli bearing EV or cbp-1 RNAi plasmids. Animals were grown to D1, and subsequently transferred to NGM RNAi plates supplemented with full E. coli RNAi food source (ad libitum) or fasted for 24 hours prior to harvest.

extract_protocol:
All RNA-sequencing data pro-processing, quantification, and statistical testing was performed as previously described. Briefly, ~1000 synchronized D1 WT and H3K27ac(-) nematodes were fed ad libitum or fasted for 24 hours and subsequently collected into 500 μl RNAzol (Sigma- Aldrich, Cat# R4533) after 3x washing for total RNA extraction in biologically independent quadruplicates (16 total samples). The total RNA was extracted, and the genomic DNA was removed using the Direct-zol RNA Miniprep Plus Kit (ZYMO research, Cat# R2072) following the manufacturer’s instructions. The extracted total RNA was evaluated for quality control using a NanoDrop One C Microvolume UV-Vis Spectrophotometer (Thermo Fisher Scientific), with an A260/A280 > 1.98 and an A260/A230 > 1.85. Samples were sent to Azenta (Genewiz) for additional quality control, library preparation, and mRNA sequencing. Samples were first validated for RNA integrity with a RIN score > 8.5 and DV200 > 50 using an RNA Tapestation 4200 (Agilent).
Illumina library preparation was performed using polyA selection for mRNA species. Approximately 17.5 - 30 million paired-end 150bp reads were generated per sample, with > 90% of bases passing a Phred quality score Q30.

treatment_protocol: Nematodes were synchronized as described in the growth protocol and plated onto 10 cm OP50-1 NGM agar plates from L1 of development to adult day 1 stage. Four independent biological replicate experiments were performed, using independently synchronized animals, OP50-1 seeded cultures, and prepared NGM agar plates for each experiment.

tag: tissue

value: Whole organism lysate

tag: genotype

tag: treatment

value: Treated from L1 to D2 with cbp-1 RNAi, fasted from D1 to D2.

tag: batch


title: jmjd-3.1(gk384) adult day 2 animals on cbp-1 RNAi, treated ad libitum for 24 hours, Replicate 4

description: Library name: YZ12

value: Treated from L1 to D2 with cbp-1 RNAi, treated from D1 to D2 with ad libitum feeding.


title: genomic DNA from control-siRNA treated HaCaT cells 2

type: genomic

city: Xi'an

first: Qinqin

last: Meng

state: Shaanxi

address: No.157 Xi Wu Road

department: Department of Dermatology

country: China

institute: The Second Affiliated Hospital of Xi’an Jiaotong University

hyb_protocol: The genomic DNA underwent bisulfite conversion and the bisulfite modified DNA was then whole-genome amplified, fragmented by an enzymatic process and hybridized to the HumanMethylatio850 BeadChip by the manufacturer

scan_protocol: Scanning and imaging Beadchip with iScan

data_processing:
R-package minifi (V1.30.0)
Average Beta
Unmethylated and methylated signal intensities

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: control-siRNA treated HaCaT cells 2

label_protocol: Standard Illumina Protocol

extract_protocol: genome DNA was extracted and purified from HaCaT cells using Qiagen DNeasy Blood and Tissue Kit according to standard instructions


title: jmjd-3.1(gk384) adult day 2 animals on cbp-1 RNAi, fasted for 24 hours, Replicate 1

description: Library name: YZ13


title: jmjd-3.1(gk384) adult day 2 animals on cbp-1 RNAi, treated ad libitum for 24 hours, Replicate 2

description: Library name: YZ10


title: jmjd-3.1(gk384) adult day 2 animals on cbp-1 RNAi, fasted for 24 hours, Replicate 3

description: Library name: YZ15


title: N2 wildtype adult day 2 animals on EV RNAi, fasted for 24 hours, Replicate 4

description: Library name: YZ8

value: N2 (Bristol)

value: Treated from L1 to D2 with EV RNAi, fasted from D1 to D2.


title: N2 wildtype adult day 2 animals on EV RNAi, fasted for 24 hours, Replicate 1

description: Library name: YZ5


title: N2 wildtype adult day 2 animals on EV RNAi, fasted for 24 hours, Replicate 2

description: Library name: YZ6


title: jmjd-3.1(gk384) adult day 2 animals on cbp-1 RNAi, treated ad libitum for 24 hours, Replicate 3

description: Library name: YZ11


title: N2 wildtype adult day 2 animals on EV RNAi, treated ad libitum for 24 hours, Replicate 3

description: Library name: YZ3

value: Treated from L1 to D2 with EV RNAi, treated from D1 to D2 with ad libitum feeding.


title: N2 wildtype adult day 2 animals on EV RNAi, treated ad libitum for 24 hours, Replicate 4

description: Library name: YZ4


title: jmjd-3.1(gk384) adult day 2 animals on cbp-1 RNAi, fasted for 24 hours, Replicate 2

description: Library name: YZ14


title: N2 wildtype adult day 2 animals on EV RNAi, fasted for 24 hours, Replicate 3

description: Library name: YZ7


title: N2 wildtype adult day 2 animals on EV RNAi, treated ad libitum for 24 hours, Replicate 2

description: Library name: YZ2


title: N2 wildtype adult day 2 animals on EV RNAi, treated ad libitum for 24 hours, Replicate 1

description: Library name: YZ1


title: cn_ppi_koB_rox1d3_rep2

city: Planegg-Martinsried

first: Fotios

last: Gkountromichos

address: Großhaderner Strasse 9

department: Molecular Biology

country: Germany

institute: Biomedical Center, Ludwig-Maximilians-Universität München

description: Library name: cn_ppi_koB_rox1d3_rep2

library_source: genomic

data_processing:
Paired-end CUT&RUN and ChIP-MNase sequencing reads were aligned to the Drosophila melanogaster dm6 reference genome (UCSC) using Bowtie2 (v2.2.9, --local --very-sensitive-local --no-unal --no-mixed --no-discordant)( Maximum fragment sizes were set to 700 bp for CUT&RUN and 1000 bp for ChIP-MNase to accommodate the distinct fragment size distributions of each method. SAM files were converted to BAM format retaining high-quality alignments (samtools v1.22.1, samtools view -q 2), name-sorted, and converted to BED format using BEDtools (v2.31.1) bamToBed to extract fragment coordinates. CUT&RUN data were normalized to total read counts. Scaling factors were calculated as 106 divided by the total number of filtered reads per sample (excluding secondary, supplementary, and unmapped reads, and reads with mapping quality < 30). Normalized coverage tracks were generated using deepTools2 (v3.5.0) bamCoverage at 10 bp resolution with target-specific smoothing (20 bp for MSL2/PPI; 80 bp for H4K16ac/IgG). Pairwise target-to-control comparisons were computed using bamCompare to generate ratio tracks with a pseudocount of 1. Pre-immune serum (PPI) and rabbit IgG were used as negative controls for the targets MSL2 and H4K16ac respectively. For ChIP-MNase data, spike-in normalization was performed using reads aligned to the Drosophila virilis droVir3 genome. Scaling factors were calculated as 106 divided by the spike-in read count for each sample. Normalized to Input coverage tracks were generated using BEDtools (v2.31.1) genomecov and converted to bigWig format using bedGraphToBigWig (UCSC utilities, 3.4.1).
DCC binding sites were identified from CUT&RUN data derived from wild-type cells using a window-based differential binding approach implemented in the csaw R/Bioconductor package (v1.42.0). Read counts were TMM-normalized (edgeR, v4.6.3) and dispersions were estimated robustly. Differential binding between target and negative control was assessed using quasi-likelihood F-tests. Significance thresholds were FDR ≤ 0.01 and |log2FC| ≥ 2 for MSL2, and FDR ≤ 0.05 and |log2FC| ≥ 1 for H4K16ac.  Significant windows were merged within 50 bp to define MSL2 CUT&RUN csaw sites (MCCS) and H4K16ac CUT&RUN csaw sites (HCCS). Significant windows passing all filters were merged into contiguous binding regions using GenomicRanges package (v1.60.0)(Lawrence et al., 2013) with a maximum gap of 50 bp. Merged regions were annotated to genomic features using the ChIPseeker package (v1.44.0)with TxDb.Dmelanogaster.UCSC.dm6.ensGene (v3.12.0), defining promoters as 1 kb upstream from the TSS.
Assembly: Drosophila melanogaster dm6
Supplementary files format and content: Normalized coverage tracks in bigwig format. Bedgraph files with coordinates from csaw analysis of CUT&RUN data, MCCS, HCCS.
Library strategy: CUT&Run

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: Drosophila melanogaster S2 cells  were cultured at 26 °C in Schneider’s medium supplemented with 10% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
CUT&RUN was performed as described previously (Eggers et al., 2023; Meers et al., 2019).
Libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Strand-specific RNA-seq libraries were prepared from 100 ng of DNase-treated total RNA using the QIAseq FastSelect RNA Library Kit (Qiagen, Cat. No. 334302).

treatment_protocol: Stable transgenic lines expressing roX variants were generated by transfection of roX2 knock out S2 cells (KO-B) using Effectene transfection reagent (Qiagen, Cat. No. 301425) according to the manufacturer. Cells were maintained under blasticidin selection and monitored for transgene expression for 3–4 weeks, then taken out of selection and passaged several times before use in experiments.

tag: cell line

value: S2 cells

value: stable expression of roX1D3


title: cn_ppi_wt_rep3

description: Library name: cn_ppi_wt_rep3

value: wild-type


title: cn_ppi_wt_rep2

description: Library name: cn_ppi_wt_rep2


title: cn_ppi_wt_rep1

description: Library name: cn_ppi_wt_rep1


title: jmjd-3.1(gk384) adult day 2 animals on cbp-1 RNAi, treated ad libitum for 24 hours, Replicate 1

description: Library name: YZ9


title: Dataset 4: NMU-treated rat tumor #7 (Spatial)

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

description:
Fresh frozen spatial transcriptomics
Sample 6RC

data_processing:
The sequenced reads were processed via the 10X Space Ranger to obtain FASTQ files.
The sequences were aligned to the rat reference genome Rn6 to generate gene expression counts using the default settings.
Expression level of the rat coding genes were quantified in Space Ranger and downstream analyses including cell filtering, integration, clustering and UMAP were performed in R
Assembly: Rn6 (Dataset 4)
Supplementary files format and content: barcodes.tsv.gz (spatial barcodes), features.tsv.gz (gene IDs), matrix.mtx.gz (gene expression count matrix)
Supplementary files format and content: aligned_fiducials.jpg (frame alignment), detected_tissue_image.jpg (image of tissue and spots), scalefactors_json.json (scale factors in json format), tissue_hires_image.png (high res.), tissue_lowres_image.png (low-res), tissue_positions_list.csv (spatial barcodes and spot coordinates)
Library strategy: Visium Spatial Transcriptomics

organism: Rattus norvegicus

source_name: Rat breast tumor tissues

extract_protocol:
Mammary tissues and tumor tissues were embedded as fresh frozen blocks and cryosectioned as serial sections with 10um thickness under Rnase-free condition.
For dataset 4, cell and library construction were performed via the 10X Visium 3' Spatial Gene Expression Slides and Reagent Kits with Dual Index (PN-1000184) allowing 5000 gene expression per spot, according to manufacturer's instruction.

treatment_protocol: For dataset 4, tumor induction in Sprague-Dawley rats was performed via two injection of N-Nitroso-N-Methylurea(NMU, 50mg/kg, 7 days apart). Tumor volumes were measured daily following first detection of palpable tumors in the mammary areas. Selected tumors were frozen fresh and spatial transcriptomics was performed subsequently.

value: Breast tumor

tag: strain

value: Hsd:Sprague-Dawley SD

tag: Sex

value: Female

value: N-Nitroso-N-MethylUrea (NMU, 50mg/kg, twice, dissolved in pH6 ddH2O


title: Dataset 4: NMU-treated rat tumor #5 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 5NC


title: cn_ppi_koB_rep3

description: Library name: cn_ppi_koB_rep3


title: Dataset 4: NMU-treated rat tumor #6 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 5RA


title: Dataset 4: NMU-treated rat tumor #8 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 6LD


title: Dataset 4: NMU-treated rat tumor #4 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 4RC


title: cn_ppi_koB_rox1d3_rep1

description: Library name: cn_ppi_koB_rox1d3_rep1


title: cn_ppi_koB_a3b0_rep1

description: Library name: cn_ppi_koB_a3b0_rep1

value: stable expression of A3B0


title: cn_ppi_koB_res_rep2

description: Library name: cn_ppi_koB_res_rep2

value: stable expression of roX2-FL


title: Dataset 4: NMU-treated rat mammary gland #7 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 5L

source_name: Rat breast tissues

value: Microlesions


title: Dataset 4: NMU-treated rat mammary gland #5 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 4NMFPC


title: cn_ppi_koB_a0b0_rep1

description: Library name: cn_ppi_koB_a0b0_rep1

value: stable expression of A0B0


title: cn_ppi_koB_a0b0_rep2

description: Library name: cn_ppi_koB_a0b0_rep2


title: cn_ppi_koB_rep2

description: Library name: cn_ppi_koB_rep2


title: cn_ppi_koB_rep1

description: Library name: cn_ppi_koB_rep1


title: cn_ppi_koB_mini_rep1

description: Library name: cn_ppi_koB_mini_rep1

value: stable expression of miniroX


title: Dataset 4: NMU-treated rat tumor  #1 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 3NC


title: Dataset 4: NMU-treated rat mammary gland #8 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 6N


title: cn_ppi_koA_rep3

description: Library name: cn_ppi_koA_rep3


title: Dataset 4: NMU-treated rat tumor #2 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 3LB


title: cn_msl2_wt_rep2

description: Library name: cn_msl2_wt_rep2


title: Dataset 4: NMU-treated rat mammary gland #6 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 4LMFPC


title: Dataset 4: NMU-treated rat tumor #3 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 4RA


title: Dataset 4: NMU-treated rat mammary gland #1 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 1LMFPC


title: cn_ppi_koB_res_rep1

description: Library name: cn_ppi_koB_res_rep1


title: Dataset 4: NMU-treated rat mammary gland #3 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 2LMFPC


title: cn_ppi_koB_mini_rep2

description: Library name: cn_ppi_koB_mini_rep2


title: cn_ppi_koB_a3b0_rep2

description: Library name: cn_ppi_koB_a3b0_rep2


title: Dataset 4: Untreated rat mammary gland #3 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 7R

value: Normal mammary tissues

value: ddH2O (pH6)


title: Dataset 4: NMU-treated rat mammary gland #2 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 2NMFPC


title: Dataset 4: Untreated rat mammary gland #1 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 1NMFPC


title: NCI-H446 VC 5wk tumor 2

city: Irvine

first: Claudia

last: Benavente

state: CA

address: 839 Health Sciences Road, Sprague Hall B200

institute: University of California, Irvine

description:
Library name: Sample 12
Column name in processed_human_counts.xlsx matche with sample title

data_processing:
All data processing steps were conducted on Galaxy platform. Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic. Trimmed sequence reads were mapped to hg38 for human and mm10 for mouse samples using HISAT2. Read count extraction and normalization were performed using featurecounts/Kallistro counts.
Assembly: hg38 for human, mm10 for mouse
Supplementary files format and content: txt or xls files include raw counts for each sample

source_name: small cell lung cancer

extract_protocol:
Total RNA from homogenized tumors was isolated using RNeasy Mini Kit (Qiagen). After quality check with Agilent BioAnalyzer and Qubit, 1 µg RNA per sample was used for poly(A) mRNA isolation.
cDNA libraries were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina, following manufacturer instructions. Barcode-indexed libraries were purified with AMPure XP beads (Beckman Coulter) and checked for library quality using Agilent BioAnalyzer DNA Chip and quantified using KAPA qPCR.

value: small cell lung cancer

value: VC


title: cn_ppi_koA_rep1

description: Library name: cn_ppi_koA_rep1


title: cn_msl2_koB_rox1d3_rep1

description: Library name: cn_msl2_koB_rox1d3_rep1


title: cn_msl2_wt_rep1

description: Library name: cn_msl2_wt_rep1


title: Dataset 4: Untreated rat mammary gland #2 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 1RMFPC


title: Dataset 4: NMU-treated rat mammary gland #4 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 3RMFPC


title: cn_msl2_koB_rox1d3_rep2

description: Library name: cn_msl2_koB_rox1d3_rep2


title: GNAQ+, tp53 -/-, ptena -/-, ptenb -/- skin tumor from a 4-6 month old AB wildtype zebrafish, replicate

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: CBRB, 5269, 285 Newton Road

department: Surgery

institute: University of Iowa

description:
Library name: WT_Skin_Tumor
10x Genomics

library_source: transcriptomic single cell

data_processing:
The scRNA-seq reads were then mapped to custom GRCz11/danRer11 reference genome using Cell Ranger v.5.0.1 (cellranger count function), and Seurat was used for further analysis. Cells with unique RNA feature counts less than 200 and more than 5% (15% for CK8) mitochondrial contamination were removed from further processing. UMAP was generated using Seurat RunUMAP function with default settings by PCA reduction with dims 1:30, followed by FindNeighbors with dims 1:30 and FindClusters with a resolution of 0.4. Differential gene expression was then calculated by FindMarkers and FindAllMarkers with thresholds for percentage of cells between conditions. Adjusted p-value < 0.05 was used as the threshold for statistically significant difference.
Assembly: A custom reference genome including GNAQQ209L and GFP transgenes was constructed using Cell Ranger (cellranger mkref function).
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: skin

extract_protocol:
Zebrafish eyes or skin were harvested with and without tumors from 4-6 month old AB wildtype and casper (mitfa -/-, mpv17 -/-) zebrafish. Tissues were made into single cell suspension using collagenase/hyaluronidase and trypsin and prepared according to 10X Genomics cell preparation guidelines. Approximately, 10,000 cells were loaded per channel to generate single-cell gel beads-in-emulsion (GEMs).
Single-cell RNA-Seq libraries were prepared with Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (#1000128, 10X Genomics), Chromium Next GEM Chip G Single Cell Kit (#1000127, 10X Genomics), and Chromium i7 Multiplex Kit (#120262, 10X Genomics). Libraries were sequenced on an Illumina HiSeq 6000 with 150 bp paired-end reads in the genomics core at University of Iowa (Iowa City, IA).

value: skin

tag: developmental stage

value: adult

tag: cell type

value: fibroblasts, skin cells, melanocytes

value: AB wildtype

value: injected with oncogenic plasmids


title: cn_msl2_wt_rep3

description: Library name: cn_msl2_wt_rep3

value: S2 cells

value: wild-type


title: Dataset 4: Untreated rat mammary gland #4 (Spatial)

description:
Fresh frozen spatial transcriptomics
Sample 7L

value: Hsd:Sprague-Dawley SD

value: Female


title: Uninjected eyes from four 4-6 month old AB wildtype zebrafish (sibling matched with WT eye tumors)

description:
Library name: Eye_controls_uninj
10x Genomics

source_name: eye

value: eye

value: melanocytes, retina, sclera, fibroblasts, immune cells

value: control (uninjected)


title: Uveal melanoma in a singular eye from a 4-6 month old AB wildtype zebrafish

description:
Library name: CK8
10x Genomics


title: GNAQ+, tp53 -/-, ptena -/-, ptenb -/- skin tumor from a 4-6 month old AB wildtype zebrafish

description:
Library name: CK6
10x Genomics


title: Uninjected skin from a 4-6 month old AB wildtype zebrafish (paired with CK6)

description:
Library name: CK5
10x Genomics


title: cn_msl2_koB_res_rep1

description: Library name: cn_msl2_koB_res_rep1

value: stable expression of roX2-FL


title: cn_msl2_koB_a3b0_rep1

description: Library name: cn_msl2_koB_a3b0_rep1

value: stable expression of A3B0


title: cn_msl2_koB_res_rep2

description: Library name: cn_msl2_koB_res_rep2


title: Uveal Melanoma in two eyes from two 4-6 month old AB wildtype zebrafish

description:
Library name: WT_Eye_Tumors
10x Genomics


title: Uninjected skin from a 4-6 month old AB wildtype zebrafish, replicate (paired with WT Skin Tumor)

description:
Library name: WT_Skin_normal
10x Genomics


title: cn_msl2_koB_rep3

description: Library name: cn_msl2_koB_rep3


title: Mock injected eyes from three 4-6 month old AB wildtype zebrafish (sibling matched with WT eye tumors)

description:
Library name: Eyes_poked
10x Genomics

value: control (mock injected)


title: Uninjected eyes from two 4-6 month old AB wildztype zebrafish (paired with WT eye tumors)

description:
Library name: Eye_controls_uninj_paired
10x Genomics


title: cn_msl2_koB_rep1

description: Library name: cn_msl2_koB_rep1


title: cn_msl2_koB_rep2

description: Library name: cn_msl2_koB_rep2


title: cn_msl2_koB_mini_rep2

description: Library name: cn_msl2_koB_mini_rep2

value: stable expression of miniroX


title: cn_msl2_koB_mini_rep1

description: Library name: cn_msl2_koB_mini_rep1


title: cn_msl2_koB_a3b0_rep2

description: Library name: cn_msl2_koB_a3b0_rep2


title: Uninjected eyes from three 4-6 month old casper (mitfa -/-, mpv17 -/-) zebrafish (paired with CK2)

description:
Library name: CK1
10x Genomics

value: melanocyte precursors, retina, sclera, fibroblasts, immune cells

value: casper (mitfa -/-, mpv17 -/-)


title: cn_msl2_koB_a0b0_rep1

description: Library name: cn_msl2_koB_a0b0_rep1

value: stable expression of A0B0


title: Uveal melanoma in a singular eye from three 4-6 month old casper (mitfa -/-, mpv17 -/-) zebrafish

description:
Library name: CK2
10x Genomics

value: adult


title: cn_msl2_koA_rep3

description: Library name: cn_msl2_koA_rep3


title: YOUNG2 [ChIP-Seq]

city: changzhi

first: pu

last: wang

address: jiefang road163

institute: changzhi medical college

description: Library name: YOUNG-2_sequence_1.fastq

data_processing:
The UCSC table browser (http://genome.ucsc.edu/cgibin) was employed to download genomic annotation data. To elaborate, BedTools multicov and BedTools groupby were utilized to count the number of reads mapped to each repetitive element. RepeatMasker open-4.0.5 (http://repeatmasker.org) was utilized for this purpose. A normalized mapping ratio was subsequently calculated by dividing the number of reads mapped to a specific repetitive element by the number of reads in the nuclear genome containing the specific repetitive element.2.7 Characterisation of the eccDNA fragment junction site To acquire 10 bp upstream and downstream DNA sequences of each junction site of the eccDNA, Bedtools 2.29.2 was employed. A mean mononucleotide frequency for each base was subsequently calculated using Homer Tools. The motif signature of the eccDNA fragment junction site was visualized using the R package ggseqlogo-0.1
Assembly: mm10
Supplementary files format and content: raw, .gz

organism: Mus

source_name: LIVER

extract_protocol:
Total DNA extraction from liver tissues was performed via column centrifugation, utilizing a technique developed by BEYOTIME.
Ten micrograms of the total DNA was then subjected to a 25-unit Plasmid-Safe Dnase (Epicenter) treatment at a sustained temperature of 37°C for a 24-hour period, with the intention of eliminating linear DNA sections. Ensuing the inactivation of Plasmid-Safe DNAse, MSSI enzyme (Thermo Fisher Scientific) was introduced to eradicate mitochondrial DNA. EccDNA was subsequently recuperated via the Plasmid Recovery Kit (TIANGEN) and eluted through a 30-μl RNase-free water medium. A 50% (14 μl) fraction of the resultant eccDNA was then exposed to a 16-hour RCA reaction at 30°C.Roughly 500 ng of the amplified DNA underwent sonication, facilitated by a Covaris LE220, to generate a median fragment size of 400-bp. Further, 50 ng of the resultant fragmented DNA was employed for library construction, utilizing the MGIEasy DNA Library Preparation Kit produced by MGI-BGI, China. The quality and length distribution of each library were subsequently analyzed using an Agilent Bioanalyzer 2100 procured from Agilent. The sequencing phase was executed utilizing the MGISeq-2000 platform (supplied by Cloudseq, Shanghai, China) incorporating PE150 DNA libraries. The next phase of the study entailed the identification of eccDNA. To detect eccDNA in PE150 high-throughput sequencing data, we utilized Circle-Map (version 1.1.4) software (https://github.com/iprada/Circle-Map). Initially, a BWA-MEM alignment of sequencing reads was conducted against the mouse reference genome (mm10 genome download from UCSC). Subsequently, circular reads were extracted from two BAM files by sorting them based on their read names and coordinates. The coordinates of each eccDNA were then calculated from the aforementioned files.

value: LIVER


title: AGE1 [ChIP-Seq]

description: Library name: AGE-1_sequence_1.fastq


title: cn_msl2_koA_rep2

description: Library name: cn_msl2_koA_rep2


title: cn_msl2_koB_a0b0_rep2

description: Library name: cn_msl2_koB_a0b0_rep2


title: dpSTR_Hela_RNH_WT_gDNA_Rep3

city: La Jolla

first: Alon

last: Goren

address: 9500 Gilman Drive

institute: University of California San Diego

description:
Library name: dpSTR_Hela_RNH_WT_gDNA_Rep3
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.

data_processing:
The FASTQ reads from the MPRA library were first subjected to quality control and adaptor trimming using Cutadapt, ensuring that low-quality bases and residual adaptor sequences were removed.
Following this preprocessing step, the cleaned reads were aligned to the appropriate variant reference library using BWA (Burrows-Wheeler Aligner), allowing accurate mapping of reads to their corresponding designed variants.
After alignment, read counts were computed for each variant to quantify their abundance in the library, forming the basis for downstream expression analysis.
Assembly: hg38
Supplementary files format and content: A tab-delimited text file or CSV containing raw read counts for each variant in each sample.
Supplementary files format and content: A barcode-to-variant association table should be provided in TSV format.

source_name: HeLa

growth_protocol: HEK293T cells were cultured in DMEM, high glucose, supplemented with 10% heat inactivated fetal bovine serum (FBS-HI) and 2 mM L-Glutamine in humidified incubator with 5% CO2 at 37 ºC. HeLa S3 cells were cultured in DMEM, high glucose, pyruvate supplemented with 10% heat inactivated fetal bovine serum (FBS-HI) and 2 mM L-Glutamine in humidified incubator with 5% CO2 at 37 ºC.

extract_protocol:
After 40-42 hours post-transfection, RNA and DNA were harvested using the AllPrep DNA/RNA mini Kit (Qiagen, 80204).
RNA was converted to cDNA using Superscript  Libraries were prepared using two rounds of PCR to attach Illumina barcodes and adaptors. Libraries were amplified using XX cycles on the thermocycler.

treatment_protocol: Cells were transfected using Lipofectamine 3000 to deliver the expression plasmid.

value: HeLa

value: cervical epithelial

value: Untreated


title: cn_ppi_koA_rep2

description: Library name: cn_ppi_koA_rep2

value: S2 cells


title: YOUNG1 [ChIP-Seq]

description: Library name: YOUNG-1_sequence_1.fastq


title: dpSTR_Hela_RNH_WT_gDNA_Rep1

description:
Library name: dpSTR_Hela_RNH_WT_gDNA_Rep1
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.


title: cn_igg_wt_rep2

description: Library name: cn_igg_wt_rep2

value: wild-type


title: cn_igg_wt_rep3

description: Library name: cn_igg_wt_rep3


title: dpSTR_Hela_RNH_WT_gDNA_Rep2

description:
Library name: dpSTR_Hela_RNH_WT_gDNA_Rep2
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.


title: dpSTR_Hela_RNH_WT_cDNA_Rep3

description:
Library name: dpSTR_Hela_RNH_WT_cDNA_Rep3
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: K562_CHX_rep2

city: Worcester

first: Athma

middle: A

last: pai

address: 55 Lake Avenue North

department: RNA Therapeutics Institute

institute: UMass Chan Medical School

description: Library name: K5CHX2

data_processing:
Adapters were trimmed and removed from reads with trimmomatic v0.32. Adapter removal was verified by running fastqc v0.11.565 on trimmed fastqc files. Overlapping read-mates were merged with PEAR v0.9.1166 and merged overlapping read-mates, non-overlapping read 1 and non-overlapping read 2 for each sample were pooled into a single fastq file per library. Fastq files for cell lines were subsampling to 112.67M reads to match the depth of the library with the lowest sequencing depth  using seqtk v1.3. Fastq files for K562 transcriptional noise experiments were subsampled to 33.1M reads to match the depth of library with the lowest sequencing depth.
Subsampled reads were mapped to GRCH38 genome by STAR v2.7.0e69 using default parameters with the following modifications or additions: --outSAMattributes All --outSJfilterOverhangMin 40 12 12 12 --outSJfilterCountUniqueMin 1 1 1 1 --alignIntronMin 100 --alignIntronMax 250000 --limitOutSJcollapsed 2000000 --outSJfilterDistToOtherSJmin 20 0 10 10 --alignSJstitchMismatchNmax 2 2 2 2
Assembly: Grch38
Supplementary files format and content: Sj.out.tab  output from STAR

molecule: polyA RNA

growth_protocol: K562 cells were grown in IMDM supplemented with 10% FBS. KNS60 cells were grown in DMEM supplemented with 5% FBS. AM38 cells were grown in EMEM supplemented with 20% FBS. HepG2 cells were grown in DMEM supplemented with 10% FBS. SH-SY5Y cells were grown in DMEM:F12 supplemented with 10% FBS. All cell lines were maintained at 37°C and 5% CO2 until 70% confluent.

extract_protocol:
Nuclear extraction: Nuclear isolation from total cells was performed following a previously established protocol(Nabbi and Riabowol 2015). Briefly, trypsinized cells were pelleted, washed with ice cold 1X PBS, and resuspended in ice cold Nuclear Isolation Buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2, 0.3% NP40, Roche EDTA-free protease inhibitor (Millipore Sigma, 11836153001), Sigma PhosSTOP phosphatase inhibitor (Millipore Sigma, 4906845001). The suspension was briefly centrifuged again to pellet the nuclei. The supernatant was removed (cytoplasmic fraction) and the pellet was resuspended in ice cold Nuclear Isolation Buffer. The suspension was centrifuged at 10,000 RCF and supernatant removed. The nuclear pellet was resuspended in TRIzol (Invitrogen, 15596018) before RNA isolation. Nascent RNA isolation from nuclei: Cells were incubated with 1mM 4-thiouridine (Sigma, T4509), dissolved in wter, for 8 minutes and spun down to pellet cells. The pellet was resuspended in Trizol and flash frozen in liquid nitrogen. After nuclear isolation and RNA isolation and described below, 4sU pulldowns were performed using MTSEA biotin-XX (VWR, 89139-636) 4sU-containing (nascent) transcripts were purified following previously established protocols(Garibaldi et al. 2017; Duffy and Simon 2016).  RNA was extracted from whole cells or nuclear pellets using TRIzol reagent to separate the aqueous RNA phase from the DNA and protein phases. The aqueous RNA phase was carried forward into column purification using a Zymo-25 RNA Clean & Concentrator kit (Zymo, R1018)
Library preparation for polyA RNA, CHX-treated, NMDi14-treated, and DMSO-treated samples was performed using the KAPA Stranded mRNA-Seq Kit for Illumina Platforms (KK8421). Library preparation for the nuclear and 4sU-labeled samples was performed using Kapa Biosystems KAPA RNA HyperPrep Kit with RiboErase (KK8561). Libraries were sequenced commercially at Novogene using an Illumina Novaseq 6000,  Illumina Nextseq 2000. SIRV libraries were made with both KAPA Stranded mRNA-Seq Kit and KAPA RNA HyperPrep Kit and sequenced on Illumina NextSeq 500

treatment_protocol: For 4sU labelleing experiments, K562 and KNS60 cells were labelled with either 500uM  or 1mM 4sU (Sigma, T4509) for 8 mins, whereas AM38, SY5Y and HepG2 cells were labelled with 1mM 4SU for 8 mins. For cychoheximide experiments, K562 or KNS60 cells were treated 50ug/mL cycloheximide (CHX) (Sigma, C7698) resuspended in DMSO for 3 hours (or only DMSO as a control). For NMDi14 experiments, K562 and KNS60 cells were  treated with 50uM NMDi14 (Sigma, SML1538) resuspended in DMSO for 6 hours. For transcriptional noise experiments, K562 cells were treated with 10uM 5-Iodo-2’-deoxyuridine (IdU) resuspended in DMSO for 24 hours and media containing 1mM 4sU (Sigma, T4509) was added during the last 8 minutes for subsequent nuclear isolation and nascent mRNA enrichment, as described below. Control cells were treated with equivalent amounts of DMSO without CHX, NMDi14, or IdU for 3, 6, and 24 hours, respectively. Uridine treatment: Control cells were treated 1mM uridine (ChemGenes, RP-1186) dissolved in water for 8 minutes or with 1mM 4sU for 24 hours. For synthetic SIRV: Synthetic Spike-In RNA Variant (SIRV-Set1; Lexogen 025.03 & SIRV-Set4: Lexogen 141.01) were pooled before library prep

value: chronic myeloid leukemia

value: WT

value: 50 ug/ml cycloheximide, 3 hour


title: dpSTR_Hela_RNH_WT_cDNA_Rep1

description:
Library name: dpSTR_Hela_RNH_WT_cDNA_Rep1
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: cn_igg_wt_rep1

description: Library name: cn_igg_wt_rep1


title: AGE2 [ChIP-Seq]

description: Library name: AGE-2_sequence_2.fastq


title: cn_igg_koB_rox1d3_rep2

description: Library name: cn_igg_koB_rox1d3_rep2

value: stable expression of roX1D3


title: cn_igg_koB_rox1d3_rep1

description: Library name: cn_igg_koB_rox1d3_rep1


title: hSTR2_HEK293T_gDNA_Rep3

description:
Library name: hSTR2_HEK293T_gDNA_Rep3
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.

value: embryonic kidney epithelial


title: hSTR2_HEK293T_gDNA_Rep2

description:
Library name: hSTR2_HEK293T_gDNA_Rep2
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.


title: cn_igg_koB_res_rep2

description: Library name: cn_igg_koB_res_rep2

value: stable expression of roX2-FL


title: dpSTR_Hela_RNH_WT_cDNA_Rep2

description:
Library name: dpSTR_Hela_RNH_WT_cDNA_Rep2
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: cn_igg_koB_res_rep1

description: Library name: cn_igg_koB_res_rep1


title: hSTR2_HEK293T_cDNA_Rep3

description:
Library name: hSTR2_HEK293T_cDNA_Rep3
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: hSTR2_HEK293T_cDNA_Rep2

description:
Library name: hSTR2_HEK293T_cDNA_Rep2
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: MATEX_1_MC38_D14_CD64DTR_CD45pos_CD64pos

city: Geneva

first: Zoe

last: Fusilier

address: Michel servet 1

country: Switzerland

institute: UNIGE

description:
Library name: Sample 7
MC38sc tumors (day 14 pi) from CD64 WT/WT mice

data_processing:
Batch #1 and DAPI-CD45- from batch #2 were sequenced at 50,000 reads / cell, DAPI-CD45+CD64+, DAPI- CD45+CD64- from batch #2 were sequenced at 100,000 reads / cell. . Sequencing was performed on a Novaseq 6000
cellranger-6.0.0 and cellranger-7.1.0
Assembly: mouse mm10
Supplementary files format and content: Tab separated values and matrix files

organism: Mus musculus

source_name: MC38 sc D14

extract_protocol:
MC38 tumors from CD64DTR and CD64WT were harvested at day 14 d.p.i., digested in Liberase TL 0,25mg/ml (Roche, #5401020001) DNAse 0,5mg/ml (Sigma, DN25-100MG) in CO2 independent medium (Gibco, 18045088) using GentleMacs Octo dissociator pre-set program (37C_m_TDK1, 41min at 37° under agitation). Cells were filtered on a 100 µm cell strainer and red blood cells were lysed using red blood cells lysis buffer 1X (Biolegend, 420301) diluted in water. After centrifugation (5min, 1500rpm), cells were incubated 10 min with Fcblock solution diluted in FACS buffer (BD, 553142, 1:100) and stained either with (1) DAPI (Invitrogen, 11534886, 1:10000) for the first experiment (batch #1), or (2) with DAPI, anti-CD45 APC-Cy7 (BD, 557659, 1:200) and anti-CD64 APC (Biolegend,139306, 1:200) (for the second experiment (batch #2) diluted in FACS buffer (PBS 1X, 0,5%BSA, 2mM EDTA). For batch#1, DAPI- cells were sorted while for batch#2, DAPI-CD45-, DAPI-CD45+CD64+, DAPI- CD45+CD64- populations were sorted separately. For batch #1, 15 000 cells form CD64WT and CD64DTR tumors were loaded. For Batch #2, 10000 cells form CD64WT and CD64DTR tumors were loaded.
Library was performed following 10x Genomics instructions (Single Cell 3’ V3.1 Next-GEM kit protocol).

value: MC38 sc D14

value: CD64-hDTR KI/WT

value: DT


title: hSTR2_HEK293T_gDNA_Rep1

description:
Library name: hSTR2_HEK293T_gDNA_Rep1
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.


title: MATEX_1_MC38_D14_CD64DTR_CD45pos_CD64neg

description:
Library name: Sample 8
MC38sc tumors (day 14 pi) from CD64 WT/WT mice


title: cn_igg_koB_rep2

description: Library name: cn_igg_koB_rep2


title: cn_igg_koB_rep3

description: Library name: cn_igg_koB_rep3


title: cn_msl2_koA_rep1

description: Library name: cn_msl2_koA_rep1


title: MATEX_1_MC38_D14_WT_CD45pos_CD64neg

description:
Library name: Sample 5
MC38sc tumors (day 14 pi) from CD64 WT/WT mice

value: CD64-hDTR WT/WT


title: p300 degrader 27-treated, replicate 3

city: South San Francisco

first: Anlu

last: Chen

address: 1000 Gateway Blvd

department: Quantitative Medicine & Genomics

institute: AbbVie Inc

description: Library name: Sample7

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides of poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the human reference genome (GRCh38) available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. Mapping .bam files were used to generate hit counts for genes and exons. Unique gene hit counts were calculated using feature Counts from the Subread package v.1.5.2. Unique reads within exon regions were counted and used in downstream analysis.
Read counts were normalized to adjust for various factors, such as variations of sequencing yield between samples (software package DESeq2 v.1.16.1). Sample similarities were assessed by heatmap and principal component analysis.
Assembly: The trimmed reads were mapped to the human reference genome (GRCh38) available on ENSEMBL using the STAR aligner v.2.5.2b.
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: NCI-H929 (CRL-3580) cells were cultured in RPMI 1640 medium (22400-089, Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated FBS (A5256801, Gibco), 100 U ml-1 of penicillin and 100 µg ml-1 of streptomycin (penicillin-streptomycin, 15140122, Thermo Fisher Scientific) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the Qiagen QIAsymphony RNA kit following the manufacturer’s instructions (Qiagen, Hilden, Germany). RNA samples were quantified using a Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), and RNA integrity was checked using an Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using the manufacturer's instructions (NEB, Ipswich, MA, USA).

value: myeloma cell line

value: p300 degrader 27


title: hSTR2_HEK293T_cDNA_Rep1

description:
Library name: hSTR2_HEK293T_cDNA_Rep1
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: p300 degrader 27-treated, replicate 4

description: Library name: Sample8


title: p300 degrader 27-treated, replicate 2

description: Library name: Sample6


title: MATEX_1_MC38_D14_CD64DTR_CD45neg

description:
Library name: Sample 6
MC38sc tumors (day 14 pi) from CD64 WT/WT mice


title: cn_igg_koB_mini_rep2

description: Library name: cn_igg_koB_mini_rep2

value: stable expression of miniroX


title: cn_igg_koB_rep1

description: Library name: cn_igg_koB_rep1


title: p300 degrader 27-treated, replicate 1

description: Library name: Sample5


title: DMSO-treated, replicate 2

description: Library name: Sample2

value: DMSO


title: DMSO-treated, replicate 4

description: Library name: Sample4


title: cn_igg_koB_mini_rep1

description: Library name: cn_igg_koB_mini_rep1


title: DMSO-treated, replicate 3

description: Library name: Sample3


title: cn_igg_koB_a3b0_rep2

description: Library name: cn_igg_koB_a3b0_rep2

value: stable expression of A3B0


title: DMSO-treated, replicate 1

description: Library name: Sample1


title: MATEX_1_MC38_D14_WT_CD45pos_CD64pos

description:
Library name: Sample 4
MC38sc tumors (day 14 pi) from CD64 WT/WT mice


title: p300 KO, replicate 4

description: Library name: Sample16


title: NTC, replicate 4

description: Library name: Sample12

value: NTC


title: p300 KO, replicate 2

description: Library name: Sample14


title: MATEX_1_MC38_D14_WT

description:
Library name: Sample 1
MC38sc tumors (day 14 pi) from CD64 WT/WT mice

value: DAPI-


title: NTC, replicate 3

description: Library name: Sample11


title: MATEX_1_MC38_D14_CD64DTR

description:
Library name: Sample 2
MC38sc tumors (day 14 pi) from CD64 WT/WT mice


title: p300 KO, replicate 1

description: Library name: Sample13


title: p300 KO, replicate 3

description: Library name: Sample15


title: cn_igg_koB_a0b0_rep2

description: Library name: cn_igg_koB_a0b0_rep2

value: S2 cells

value: stable expression of A0B0


title: MATEX_1_MC38_D14_WT_CD45neg

description:
Library name: Sample 3
MC38sc tumors (day 14 pi) from CD64 WT/WT mice


title: NTC, replicate 2

description: Library name: Sample10


title: Lung, KO-2

city: DALLAS

last: YAN

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description:
Library name: KO-2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were done using CellRanger 7 software (10x Genomics)
Assembly: mouse reference mm10 2020-A
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Lung

extract_protocol:
Lung tissue from 10-month-old wild-type and Parp7–/– mice (n = 2 per genotype) were isolated at death, snap-frozen in liquid nitrogen, and stored at -80°C. Nuclei were prepared from frozen tissue by cutting lung into ~5 mm pieces, injecting lung pieces with 1 mL Nuclei EZ Lysis Buffer (#NUC101; Sigma-Aldrich) supplemented with 1x protease inhibitor (589279100; Roche), 200 U/mL Protector RNase Inhibitor (#3335399001; Sigma-Aldrich), and 200 U/mL SUPERaseIN (AM2696; ThermoFisher). Lung tissue was further minced with an additional 1 mL of supplemented Nuclei EZ Lysis Buffer and then transferred to a GentleMACS C tube. GentleMACS program m_lung_01.01 was run followed by m_lung_02.01 for 20 seconds. Lysate was briefly spun down at 750 xg for 2 min. to spin down the foam. Lysate was passed through a 40 μm strainer and rinsed with PBS supplemented with 0.04% BSA (AM2616; ThermoFisher), 200 U/mL Protector RNase Inhibitor, and 200 U/mL SUPERaseIN. Nuclei were spun down at 1000 xg for 5 min. at 4°C followed by another wash. Nuclei were resuspended in 1 mL supplemented PBS and passed through a 40 μm Flowmi Cell Strainer (BAH136800040) twice. Nuclei were counted with a hemocytometer and diluted to 700-1200 nuclei/μL.
Single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 5’ Reagent Kits (10x Genomics) according to the manufacturer’s protocol.

value: Lung

tag: age

value: 10 months

value: Female


title: Lung, WT-2

description:
Library name: WT-2
10x Genomics


title: cn_igg_koA_rep3_

description: Library name: cn_igg_koA_rep3_


title: Lung, WT-1

description:
Library name: WT-1
10x Genomics


title: Lung, KO-1

description:
Library name: KO-1
10x Genomics

value: Male


title: I3

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

institute: Zhejiang University

description: Library name: I3

data_processing:
Adaptors and low-quality reads were removed using Trim Galore (v0.6.7) with the parameters ‘-q 20’. Then the remaining reads were aligned to the human reference genome (hg19) using STAR (v2.7.6a).
Expression counts were generated using featureCounts (v2.0.1). Differentially expressed gene were identified by R package DESeq2 (v1.44.0) with the criteria of  "p.value < 0.05 and |log2FC| >= 1".
clusterProfiler (v4.12.3) was used to perform Gene Ontology (GO) analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Human Skeletal Stem Cells

extract_protocol:
hSSCs were seeded into 96 well plates at 3000 cells per well onto Active Wnt3a platform or Inactive Wnt3a platform with 100 μl hSSC basal medium and cultured for 24h to allow cells to attach. After 24h, media was replaced with osteogenic media and cells were cultured for 48h.
RNA was extracted and purified using a commercial kit (Nucleospin RNA XS, Macherey-Nagel) according to the manufacturer’s recommendation. 30 wells were pooled to obtain enough material and counted as 1 biological replicate (n=3 per group). Samples were sequenced using the NovaSeq6000 instrument (Illumina).

value: Human Skeletal Stem Cells

value: WT

value: Inactive Wnt3a platform


title: I1

description: Library name: I1


title: cn_igg_koB_a3b0_rep1

description: Library name: cn_igg_koB_a3b0_rep1


title: cn_igg_koA_rep2

description: Library name: cn_igg_koA_rep2


title: cn_igg_koB_a0b0_rep1

description: Library name: cn_igg_koB_a0b0_rep1


title: I2

description: Library name: I2


title: AT2_RFP_wt_flu_4

city: Shanghai

first: pei

last: wu

address: 393 Middle Huaxia Road

institute: ShanghaiTech University

description: Library name: wt_flu_4

data_processing:
The raw paired end reads were trimmed and quality controlled by Skewer with default parameters
hisat2  software was used to compare the preprocessed sequecnces with the reference genome sequences of sequenced species
featurecounts was used to count the original sequence of known genes
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

source_name: lung

extract_protocol:
RNA was harvested using Direct-zolTM RNA MicroPrep（Zymo research), 2ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Kit following manufacture's protocols

treatment_protocol: CD45-Epcam+Integrin RFP+β4- cells from 3 mice each group (flu D14) were sorted by FACS. RNA was harvested using EastepTM Super Total RNA extraction kit（Promega), 2ug of total RNA was used for the construction of sequencing libraries

value: lung

value: RFP+AT2 cells

value: flu D14


title: NTC, replicate 1

description: Library name: Sample9

value: myeloma cell line


title: AT2_RFP_wt_flu_3

description: Library name: wt_flu_3


title: cn_h4k16ac_wt_rep3

description: Library name: cn_h4k16ac_wt_rep3


title: K27_I3_L1

description: Library name: K27_I3_L1

data_processing:
Adaptors and low-quality reads were removed using Trim Galore (v0.6.7) with the parameters ‘-q 20 –paired’. Then filtered reads were uniquely mapped to the human reference genome (hg19) using Bowtie2 (v2.3.5.1). The output SAM files were converted to sorted BAM files using SAMtools (v1.9).
For visualizing enrichment signals, normalizing mapped reads, and calculating the coverage of features across the genome, BEDtools12 (v2.26.0) and bedGraphToBigWig (v4) were used with the following parameters ‘–scale 1e7/(the total number of mapped reads)’. Normalized signals were visualized in Integrative Genomics Viewer (IGV) (v2.15.2).
Assembly: hg19
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag

extract_protocol:
hSSCs were seeded into 96 well plates at 3000 cells per well onto Active Wnt3a platform or Inactive Wnt3a platform with 100 μl hSSC basal medium and cultured for 24h to allow cells to attach. After 24h, media was replaced with osteogenic media and cells were cultured for 48h. Cells were washed twice with PBS and trypsinized (Trypsin EDTA 0.05%) for 3min at 37C. 15 wells were pooled to obtain enough cells and counted as 1 biological replicate (n=3 per group).
Samples were then processed for Cut&Tag using a commercial kit (Active Motif, CUT&Tag-IT Assay Kit Anti-Rabbit) according to the manufacturer’s recommendation. Antibodies used: anti-H3K14ac (Abcam, Ab52946), anti-H3K27me3 (Invitrogen, MA5-11198). Sample quality was assessed using the Fragment Analyzer 5200 (Agilent, software version: 3.1.0.12). Samples were sequenced using the NovaSeq6000 instrument (Illumina), 50 million reads per library.

tag: chip antibody

value: anti-H3K27me3 (Invitrogen, MA5-11198)


title: A3

description: Library name: A3

value: Active Wnt3a platform


title: cn_igg_koA_rep1

description: Library name: cn_igg_koA_rep1


title: AT2_RFP_wt_flu_2

description: Library name: wt_flu_2


title: AT2_RFP_wt_flu_1

description: Library name: wt_flu_1


title: A1

description: Library name: A1


title: A2

description: Library name: A2


title: cn_h4k16ac_wt_rep1

description: Library name: cn_h4k16ac_wt_rep1


title: K14_I3_L1

description: Library name: K14_I3_L1

value: anti-H3K14ac (Abcam, Ab52946)


title: cn_h4k16ac_wt_rep2

description: Library name: cn_h4k16ac_wt_rep2


title: K27_I1_L1

description: Library name: K27_I1_L1


title: AT2_RFP_u30_flu_6

description: Library name: u30_flu_6


title: K27_I2_L1

description: Library name: K27_I2_L1


title: K27_A2_L1

description: Library name: K27_A2_L1


title: K27_A3_L1

description: Library name: K27_A3_L1


title: K27_A1_L1

description: Library name: K27_A1_L1


title: AT2_RFP_u30_flu_4

description: Library name: u30_flu_4


title: cn_h4k16ac_koB_rox1d3_rep2

description: Library name: cn_h4k16ac_koB_rox1d3_rep2

value: stable expression of roX1D3


title: K14_I1_L1

description: Library name: K14_I1_L1


title: AT2_RFP_u30_flu_5

description: Library name: u30_flu_5


title: cn_h4k16ac_koB_res_rep1

description: Library name: cn_h4k16ac_koB_res_rep1

value: S2 cells

value: stable expression of roX2-FL


title: cn_h4k16ac_koB_res_rep2

description: Library name: cn_h4k16ac_koB_res_rep2


title: K14_I2_L1

description: Library name: K14_I2_L1


title: AT2_RFP_u30_flu_3

description: Library name: u30_flu_3


title: K14_A2_L1

description: Library name: K14_A2_L1


title: AT2_RFP_u30_bleo_5

description: Library name: S19

data_processing:
The raw paired end reads were trimmed and quality controlled by Skewer with default parameters
hisat2 software was used to compare the preprocessed sequecnces with the reference genome sequences of sequenced species
Featurecounts was used to count the original sequence of known genes
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

extract_protocol:
CD45-Epcam+Integrin RFP+β4- cells from 3 mice each group (saline, bleo D14) were sorted by FACS. RNA was harvested using EastepTM Super Total RNA extraction kit（Promega), 2ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Kit following manufacture's protocols

value: Bleo D14


title: K14_A3_L1

description: Library name: K14_A3_L1


title: K14_A1_L1

description: Library name: K14_A1_L1


title: ATACseqA5

description: Library name: ATACseqA5

data_processing:
Adaptors and low-quality reads were removed using Trim Galore (v0.6.4) with the parameters ‘-q 20 –paired’. Then filtered reads were uniquely mapped to the human reference genome (hg19) using Bowtie2 (v2.3.5.1). PCR duplicates were removed by GATK4 (v4.1.4.0) with the parameter ‘--REMOVE_DUPLICATES =true’. MACS2 (v2.2.6) was used to call narrow peaks for ATAC-seq.
For visualizing epigenomic signals, normalizing mapped reads, and calculating the coverage of features across the genome, BEDtools (v2.92.2) and bedGraphToBigWig approach (v4) were used. deepTools (v3.4.3) was used to draw heatmaps by function computeMatrix and plotHeatmap.
For downstream differential peaks analysis, multiBigwigSummary in deepTools was used to count average signals over each region. Differential regions analysis was performed by limma (v3.42.2) with normalized signals.
clusterProfiler (v3.14.3) was used for peak distribution analysis, peak annotation and GO analysis.
Assembly: hg19
Supplementary files format and content: bigWig files

extract_protocol:
hSSCs were seeded into 96 well plates at 3000 cells per well onto Active Wnt3a platform or Inactive Wnt3a platform with 100 μl hSSC basal medium and cultured for 24h to allow cells to attach. After 24h, media was replaced with osteogenic media and cells were cultured for 48h. Cells were washed twice with PBS and trypsinized (Trypsin EDTA 0.05%) for 3min at 37C. 18 wells were pooled to obtain enough cells and counted as 1 biological replicate (n=4 per group). Samples were then processed for ATAC-seq using a commercial kit (Active Motif, ATAC-Seq Kit) according to the manufacturer’s recommendation. Sample quality was assessed using the Fragment Analyzer 5200 (Agilent, software version: 3.1.0.12).
Sequencing of the libraries generated was done on an Aviti sequencer (Element Biosciences), 50 million reads per library.


title: ATACseqI1

description: Library name: ATACseqI1


title: ATACseqI4

description: Library name: ATACseqI4


title: cn_h4k16ac_koB_rep1

description: Library name: cn_h4k16ac_koB_rep1


title: AT2_RFP_u30_bleo_2

description: Library name: S16


title: ATACseqI3

description: Library name: ATACseqI3


title: cn_h4k16ac_koB_rep2

description: Library name: cn_h4k16ac_koB_rep2


title: cn_h4k16ac_koB_rox1d3_rep1

description: Library name: cn_h4k16ac_koB_rox1d3_rep1


title: ATACseqA3

description: Library name: ATACseqA3


title: AT2_RFP_u30_bleo_1

description: Library name: S15


title: ATACseqI2

description: Library name: ATACseqI2


title: AT2_RFP_u30_bleo_4

description: Library name: S18


title: LY18_NGFR_3

city: Amsterdam

first: Linda

last: Gijsbers

address: Meibergdreef 9

department: Pathology

country: Netherlands

institute: Amsterdam UMC - location AMC

description: Library name: Sample 12

data_processing:
Processing in Galaxy (https://usegalaxy.org).
Sequence reads were checked for quality and subsequenly trimmed using Trim Galore and aligned by HISAT2 to hg38. Counts per gene were collected using Featurecounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes counts for each sample

source_name: B-cell lymphoma

growth_protocol: Cell clones were maintained in IMDM supplemented with 10% or 20% heat inactivated FBS or human serum, 2 mM L-glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
Total RNA was harvested using Trizol extraction followed by purification using RNase minikit (Qiagen). 1 ug of RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA library kit.

value: B-cell lymphoma

value: GCB-type DLBCL

value: NGFR

value: NGFR control


title: cn_h4k16ac_koB_rep3

description: Library name: cn_h4k16ac_koB_rep3


title: cn_h4k16ac_koB_mini_rep1

description: Library name: cn_h4k16ac_koB_mini_rep1

value: stable expression of miniroX


title: AT2_RFP_u30_bleo_3

description: Library name: S17


title: AT2_RFP_u30_saline_3

description: Library name: S14

value: saline D14


title: ATACseqA4

description: Library name: ATACseqA4

value: Human Skeletal Stem Cells

value: WT


title: cn_h4k16ac_koB_a3b0_rep2

description: Library name: cn_h4k16ac_koB_a3b0_rep2

value: stable expression of A3B0


title: LY18_AID-ER_3

description: Library name: Sample 9

value: AID-ER

value: AID overexpression


title: LY18_AID-ER_2

description: Library name: Sample 8


title: LY18_NGFR_1

description: Library name: Sample 10


title: LY18_NGFR_2

description: Library name: Sample 11


title: cn_h4k16ac_koB_a3b0_rep1

description: Library name: cn_h4k16ac_koB_a3b0_rep1


title: AT2_RFP_u30_saline_1

description: Library name: S12

value: lung

value: RFP+AT2 cells


title: ATACseqA1

description: Library name: ATACseqA1

value: Active Wnt3a platform


title: SUDHL6_NGFR_3

description: Library name: Sample 6


title: cn_h4k16ac_koB_mini_rep2

description: Library name: cn_h4k16ac_koB_mini_rep2

value: S2 cells


title: SUDHL6_AID-ER_3

description: Library name: Sample 3


title: AT2_RFP_u30_saline_2

description: Library name: S13


title: cn_h4k16ac_koB_a0b0_rep2

description: Library name: cn_h4k16ac_koB_a0b0_rep2

value: stable expression of A0B0


title: AT2_RFP_wt_bleo_4

description: Library name: S8

value: Bleo D14


title: LY18_AID-ER_1

description: Library name: Sample 7

value: B-cell lymphoma


title: SUDHL6_NGFR_1

description: Library name: Sample 4

value: GCB-type DLBCL


title: SUDHL6_NGFR_2

description: Library name: Sample 5

value: NGFR


title: cn_h4k16ac_koB_a0b0_rep1

description: Library name: cn_h4k16ac_koB_a0b0_rep1


title: cn_h4k16ac_koA_rep3

description: Library name: cn_h4k16ac_koA_rep3


title: SUDHL6_AID-ER_1

description: Library name: Sample 1


title: TMD8_5.A_AID-ER

description: Library name: Sample 8

value: ABC-type DLBCL


title: AT2_RFP_wt_bleo_5

description: Library name: S9


title: cn_h4k16ac_koA_rep1

description: Library name: cn_h4k16ac_koA_rep1


title: AT2_RFP_wt_bleo_3

description: Library name: S7


title: TMD8_6.N_NGFR

description: Library name: Sample 12

value: NGFR control


title: HBL1_5.N_NGFR

description: Library name: Sample 5


title: cn_h4k16ac_koA_rep2

description: Library name: cn_h4k16ac_koA_rep2


title: TMD8_4.N_NGFR

description: Library name: Sample 10


title: HBL1_4.N_NGFR

description: Library name: Sample 4


title: wt_rep5

description: Library name: FG3701

data_processing:
Raw paired-end sequencing reads were processed using the snakePipes (v3.2.0) noncoding RNA-seq workflow (63). Adapter sequences were trimmed using cutadapt via Trim Galore (v4.6/0.6.10). Quality control was performed using FastQC (v0.12.1)(64) and summarized with MultiQC (1.25)(65). Trimmed reads were aligned to the Drosophila melanogaster dm6 reference genome using STAR (v2.7.10b)(66) with parameters optimized for multi-mapping reads (--outFilterMultimapNmax 1000 --outFilterMismatchNoverLmax 0.1 --outSAMstrandField intronMotif). Gene-level read counts were quantified using the Ensembl gene annotation (release 96).
Assembly: Drosophila melanogaster dm6
Supplementary files format and content: Raw counts in tab-delimited file (.tsv), with gene IDs as row names, samples as columns

extract_protocol:
Total RNA was isolated from S2 cells using the RNeasy Mini Kit (Qiagen, Cat. No. 74106) according to the manufacturer's instructions.
Strand-specific RNA-seq libraries were prepared from 100 ng of DNase-treated total RNA using the QIAseq FastSelect RNA Library Kit (Qiagen, Cat. No. 334302).

value: wild-type


title: TMD8_6.A_AID-ER

description: Library name: Sample 9


title: AT2_RFP_wt_bleo_2

description: Library name: S5


title: wt_rep4

description: Library name: FG3207


title: HBL1_6.N_NGFR

description: Library name: Sample 6


title: SUDHL6_AID-ER_2

description: Library name: Sample 2


title: AT2_RFP_wt_bleo_1

description: Library name: S4


title: wt_rep6

description: Library name: FG3702


title: TMD8_4.A_AID-ER

description: Library name: Sample 7


title: TMD8_5.N_NGFR

description: Library name: Sample 11


title: AT2_RFP_wt_saline_2

description: Library name: S2

value: saline D14


title: AT2_RFP_wt_saline_1

description: Library name: S1


title: AT2_RFP_wt_saline_3

description: Library name: S3


title: LY10_NT_cl.3

description: Library name: Sample 18

value: NT

value: NT control


title: HBL1_5.A_AID-ER

description: Library name: Sample 2

value: AID-ER


title: LY10_NT_cl.1

description: Library name: Sample 16


title: HBL1_6.A_AID-ER

description: Library name: Sample 3

value: AID overexpression


title: LY10_AID_cl.6

description: Library name: Sample 15

value: AID KO

value: AID knockout


title: koB_res_rep1

description: Library name: FG3703

value: stable expression of roX2-FL


title: HBL1_4.A_AID-ER

description: Library name: Sample 1


title: TMD8_NT_cl.1

description: Library name: Sample 10


title: wt_rep2

description: Library name: FG3203

value: S2 cells


title: LY10_AID_cl.4

description: Library name: Sample 13


title: TMD8_AID_cl.5

description: Library name: Sample 9


title: koB_rep4

description: Library name: FG3208


title: koB_res_rep2

description: Library name: FG3704


title: TMD8_AID_cl.4

description: Library name: Sample 8


title: wt_rep1

description: Library name: FG3201


title: wt_rep3

description: Library name: FG3205


title: LY10_AID_cl.5

description: Library name: Sample 14


title: TMD8_AID_cl.6

description: Library name: Sample 7


title: koB_rep3

description: Library name: FG3206


title: TMD8_NT_cl.2

description: Library name: Sample 11


title: TRU TKO tumor 3

description: Library name: Sample 28

value: small cell lung cancer

value: Tp53/Rb1/Uhrf1 TKO


title: TMD8_NT_cl.3

description: Library name: Sample 12

value: B-cell lymphoma


title: HBL1_NT_cl.1

description: Library name: Sample 4


title: TRU TKO tumor 5

description: Library name: Sample 30


title: koB_rep2

description: Library name: FG3204


title: LY10_NT_cl.2

description: Library name: Sample 17


title: TRU TKO tumor 4

description: Library name: Sample 29


title: HBL1_NT_cl.2

description: Library name: Sample 5


title: TRU TKO tumor 1

description: Library name: Sample 26


title: dpSTR_Hela_RNH_KD_gDNA_Rep3

description:
Library name: dpSTR_Hela_RNH_KD_gDNA_Rep3
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.

value: HeLa

value: cervical epithelial

value: RNASEH1 KD


title: HBL1_NT_cl.3

description: Library name: Sample 6

value: ABC-type DLBCL


title: HBL1_AID_cl.5

description: Library name: Sample 2


title: koA_rep4

description: Library name: FG3708


title: TRU TKO tumor 2

description: Library name: Sample 27


title: koB_rep1

description: Library name: FG3202


title: dpSTR_Hela_RNH_KD_gDNA_Rep1

description:
Library name: dpSTR_Hela_RNH_KD_gDNA_Rep1
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.


title: HBL1_AID_cl.4

description: Library name: Sample 1


title: TR DKO tumor 5

description: Library name: Sample 25

value: Tp53/Rb1 DKO


title: dpSTR_Hela_RNH_KD_gDNA_Rep2

description:
Library name: dpSTR_Hela_RNH_KD_gDNA_Rep2
Library prepared from gDNA by PCR amplification of barcodes with MPRA plasmid adaptors. Sequencing measures input plasmid abundance for normalization.


title: HBL1_AID_cl.6

description: Library name: Sample 3


title: dpSTR_Hela_RNH_KD_cDNA_Rep3

description:
Library name: dpSTR_Hela_RNH_KD_cDNA_Rep3
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.


title: TR DKO tumor 3

description: Library name: Sample 23


title: koA_rep1

description: Library name: FG3705


title: SIRV_mRNA_rep1

description: Library name: SIRV_mRNA_kit_rep_1

organism: synthetic construct

source_name: SIRV

value: SIRV

value: synthetic RNA

value: WT

value: untreated


title: TR DKO tumor 4

description: Library name: Sample 24


title: TR DKO tumor 1

description: Library name: Sample 21


title: SIRV_mRNA_rep2

description: Library name: SIRV_mRNA_kit_rep_2


title: SIRV_total_rep1

description: Library name: SIRV_hyperprep_kit_rep_1


title: koA_rep2

description: Library name: FG3706


title: Input_sh2

city: Fort Worth

first: Kejin

last: Hu

state: TX

address: 3400 Camp Bowie Boulevard

department: Microbiology, Immunology and Genetics

institute: UNT Health Science Center

description: Library name: Input_sh2_S2_R1_001

data_processing:
Fastq files were mapped to the human genome GRCh38 with Bowtie2 using single end setting with local alignment. BAM files were filtered to retain reads with a mapping quality >= 20. Peak calling was performed using MACS2 package setting for a fragment size estimate of 200 bp (fragment size selected during library preparation) with default parameters to handle duplicates.
For BAM coverage calculations, BAM files were first sorted and indexed using SAMtools. Indexed BAM files were processed with bamCoverage and BigWig files were used for peak density analysis.
Assembly: GRCH38 (canonical)
Supplementary files format and content: BigWig; peak coverage

source_name: BJ

growth_protocol: Human iPS cells were cultured in standard feeder-free and serum-free chemically defined E8 media. Human fibroblast BJ cells were cultured in fibroblast media: DMEM/F12 media supplemented with 10% FBS and 5 ng/mL human bFGF

extract_protocol:
Samples were sent to Active Motif (Carlsbad, CA) for BRD2 ChIP-Seq. Active Motif prepared chromatin, performed ChIP reactions, generated libraries, sequenced the libraries and performed basic data analysis. In brief, human fibroblast cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by adding lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp with Active Motif’s EpiShear probe sonicator (cat# 53051). Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by SPRI beads clean up (Beckman Coulter) and quantitation by Qubit. Extrapolation to the original chromatin volume allowed determination of the total chromatin yield.  An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against BRD2 (Bethyl Laboratories, cat number A302-582A). For H3K12ac, 3 µg of antibody was used (MA5-23516, Invitrogen). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NovaSeq (75 nt reads, single end).

treatment_protocol: Human fibroblasts BJ were transduced with lentiviral preparation of BRD2 shRNA or Scramble control. For BRD2 ChIP we used BJ cells carrying an inducible Cas9 construct.

value: male

value: BJ

value: foreskin fibroblast

value: with random lentivirus integration of reprogramming factors

value: shRNA BRD2

value: shRNA


title: chip_msl2_wt_rep2

description: Library name: chip_msl2_wt_rep2

data_processing:
Paired-end CUT&RUN and ChIP-MNase sequencing reads were aligned to the Drosophila melanogaster dm6 reference genome (UCSC) using Bowtie2 (v2.2.9, --local --very-sensitive-local --no-unal --no-mixed --no-discordant)( Maximum fragment sizes were set to 700 bp for CUT&RUN and 1000 bp for ChIP-MNase to accommodate the distinct fragment size distributions of each method. SAM files were converted to BAM format retaining high-quality alignments (samtools v1.22.1, samtools view -q 2), name-sorted, and converted to BED format using BEDtools (v2.31.1) bamToBed to extract fragment coordinates. CUT&RUN data were normalized to total read counts. Scaling factors were calculated as 106 divided by the total number of filtered reads per sample (excluding secondary, supplementary, and unmapped reads, and reads with mapping quality < 30). Normalized coverage tracks were generated using deepTools2 (v3.5.0) bamCoverage at 10 bp resolution with target-specific smoothing (20 bp for MSL2/PPI; 80 bp for H4K16ac/IgG). Pairwise target-to-control comparisons were computed using bamCompare to generate ratio tracks with a pseudocount of 1. Pre-immune serum (PPI) and rabbit IgG were used as negative controls for the targets MSL2 and H4K16ac respectively. For ChIP-MNase data, spike-in normalization was performed using reads aligned to the Drosophila virilis droVir3 genome. Scaling factors were calculated as 106 divided by the spike-in read count for each sample. Normalized to Input coverage tracks were generated using BEDtools (v2.31.1) genomecov and converted to bigWig format using bedGraphToBigWig (UCSC utilities, 3.4.1).
Assembly: Drosophila melanogaster dm6
Supplementary files format and content: Normalized coverage tracks in bigwig format.

extract_protocol:
ChIP-seq on MNase-digested chromatin and sonicated chromatin was performed as previously described in (Albig et al., 2019) and (Jayakrishnan et al., 2025).
Libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Strand-specific RNA-seq libraries were prepared from 100 ng of DNase-treated total RNA using the QIAseq FastSelect RNA Library Kit (Qiagen, Cat. No. 334302).

value: S2 cells

value: wild-type


title: SIRV_total_rep2

description: Library name: SIRV_hyperprep_kit_rep_2


title: dpSTR_Hela_RNH_KD_cDNA_Rep1

description:
Library name: dpSTR_Hela_RNH_KD_cDNA_Rep1
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.

value: HeLa


title: Input_sh1

description: Library name: Input_sh1_S1_R1_001

value: with random lentivirus integration of reprogramming factors overexpressing OCT4, SOX2, KLF4 and BRD2 with its ET tail deleted


title: chip_msl2_wt_rep3

description: Library name: chip_msl2_wt_rep3


title: TR DKO tumor 2

description: Library name: Sample 22

data_processing:
All data processing steps were conducted on Galaxy platform. Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic. Trimmed sequence reads were mapped to hg38 for human and mm10 for mouse samples using HISAT2. Read count extraction and normalization were performed using featurecounts/Kallistro counts.
Assembly: hg38 for human, mm10 for mouse
Supplementary files format and content: txt or xls files include raw counts for each sample

extract_protocol:
Total RNA from homogenized tumors was isolated using RNeasy Mini Kit (Qiagen). After quality check with Agilent BioAnalyzer and Qubit, 1 µg RNA per sample was used for poly(A) mRNA isolation.
cDNA libraries were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina, following manufacturer instructions. Barcode-indexed libraries were purified with AMPure XP beads (Beckman Coulter) and checked for library quality using Agilent BioAnalyzer DNA Chip and quantified using KAPA qPCR.

value: small cell lung cancer


title: chip_input_wt_rep2

description: Library name: chip_input_wt_rep2


title: dpSTR_Hela_RNH_KD_cDNA_Rep2

description:
Library name: dpSTR_Hela_RNH_KD_cDNA_Rep2
Library prepared from cDNA by PCR amplification of barcodes using MPRA plasmid adaptors. Sequencing quantifies regulatory activity via barcode abundance.

value: cervical epithelial

value: RNASEH1 KD


title: U30 bleo D18 CD45- scRNAseq

description:
Library name: U30 bleo D18 CD45-
10X Genomics

data_processing:
The demultiplexing, barcodes processing counting and aggregation were made using the Cell ranger software v8.0.1
Assembly: mm10
Supplementary files format and content: tar file includes matrix files for the sample

extract_protocol:
On day 18, CD45+ and CD45- cells were flow-sorted from bleomycin-treated wild-type (WT) and USP30-/- mice for single-cell RNA sequencing (scRNA-seq) analysis.
Library was performed according to the manufacture's instructions(single cell 3' v4 protocol, 10x Genomics）

value: lung

value: non-immune cells

value: bleomycin d18


title: WT bleo D18 CD45- scRNAseq

description:
Library name: WT bleo D18 CD45-
10X Genomics

value: WT


title: chip_msl2_wt_rep1

description: Library name: chip_msl2_wt_rep1


title: H3K27ac_sh2

description: Library name: H3K27ac_sh2_S5_R1_001

value: male


title: chip_input_wt_rep3

description: Library name: chip_input_wt_rep3


title: Input_Ctrl2

description: Library name: Input_Ctrl2_S4_R1_001

value: BJ

value: shRNA Scramble


title: U30 bleo D18 CD45+ scRNAseq

description:
Library name: U30 bleo D18 CD45+
10X Genomics

value: immune cells


title: Input_Ctrl1

description: Library name: Input_Ctrl1_S3_R1_001

value: foreskin fibroblast


title: chip_input_wt_rep1

description: Library name: chip_input_wt_rep1


title: H3K27ac_sh1

description: Library name: H3K27ac_sh1_S4_R1_001

value: shRNA BRD2

value: shRNA


title: WT bleo D18 CD45+ scRNAseq

description:
Library name: WT bleo D18 CD45+
10X Genomics


title: BJ-P7

description:
Library name: BJ_P7_AACGTG_L001
allSamples_NormalizedCounts.xlsx
ESC_BJ_iPSC_normalizedCounts.xlsx

data_processing:
Original image data file from high-throughput sequencing (Illumina) is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
The human reference genome (assembly GRCH38, release 114) was indexed  using STAR (STAR version 2.7.11b) (runMode  genomeGenerate) on Cheaha supercomputer, and the read fragments of each FASTQ file was aligned to human reference genome using the STAR aligner (version 2.7.11b).
The BAM files were sorted and indexed using SAMtools (version 1.12), and the counting was achieved using FeatureCounts in bioocontainer on Texas Advanced Computing Center (TACC).
The statistics and normalization of the RNA-seq were conducted using the DESeq2 software (version 1.48.1) on a Dell PC.
Assembly: GRCH38, release 113
Supplementary files format and content: normalized read counts in Excel xlsx
Supplementary files format and content: allSamples_NormalizedCounts.xlsx

source_name: male

extract_protocol:
BJ fibroblast cells (ATCC, CRL-2522, foreskin fibroblasts) were cultured in six well plates at a density of 2 00000 cells per well. At 24 hrs post seeding, the medium was removed and 2 mL fresh medium containing polybrene (final concentration = 5 µg/mL) was added to the wells. The viruse preparations were then added into respective wells (day 0). At 18 hrs after virus addition, the virus-containing spent media were removed, and fresh fibroblast medium was added. At 72 hrs (or indicated times) after virus removal (on Day 4), the spent medium was removed and 1 mL of TRIzol (Invitrogen; Cat no. 15596018) was added directly to each well. RNA was extracted following manufacturer’s protocol. After extraction, the RNA was further purified using Quick RNA Miniprep kit (Zymo Research; Cat. no. R1055) using manufacturer’s protocol.   RNA for the nontreated BJ was extracted the same way but without virus transduction. RNA from humna iPSCs or ESCs was prepared using the same kits. Human PSCs were grown in E8 medium
Briefly, mRNA from BJ or human PSCs is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented randomly by the addition of fragmentation buffer. The Novogene ENB library protocol was used as briefed below (from Novogene). ENB library: Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization (1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: Human fibroblasts BJ were transduced with lentiviral preparation of the indicated genes, shRNA, CRISPR KO constructs or BRD2 mutants (MOI, OCT4, 8; SOX2, 5, KLF4, 5; and all others are 3). At 18 hours post transduction, virus-containing spent media were removed and RNAs were extracted 72 hours (or as indicated) after virus removal using extraction protocols described.

value: NO


title: chip_input_koB_res_rep3

description: Library name: chip_input_koB_res_rep3

value: S2 cells

value: stable expression of roX2-FL


title: H3K27ac_Ctrl1

description: Library name: H3K27ac_Ctrl1_S6_R1_001

value: with random lentivirus integration of reprogramming factors overexpressing OCT4, SOX2, KLF4 and BRD2 with its ET tail deleted


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_ZSWIM3_KU60019_rep3

city: Haidian District

first: Jiawei

last: Yu

state: Beijing

address: Tsinghua  University

department: School of Pharmaceutical Sciences

institute: Tsinghua University

description:
Library name: 20230830_nih3t3_cas9_ku60019_ZSWIM3_KU60019_rep3
ATAC-seq sample ZSWIM3_KU60019_rep3

data_processing:
ATAC-seq read adaptors were trimmed using cutadapt (version 3.4).
Trimmed reads were aligned to hg38 (human) or mm10 (mouse) using bowtie2 (version 2.4.4) with parameters -X2000 --mm -t -q -N1 -L 25 --no-mixed --no-discordant.
Aligned reads were filtered using samtools (version 1.13) to exclude unmapped reads, unmapped mates, non-primary alignments, vendor/quality-fail reads, and duplicates (SAM flag 1804).
Standard samtools sort and fixmate operations were applied. PCR duplicates were removed using picard MarkDuplicates (version 2.20.4), followed by samtools view filtering (-F1804 -f2). ENCODE blacklist regions were removed in the final alignment set.
For uploaded processed bigWig files, bamCoverage was used with -p 8 --normalizeUsing RPKM --binSize 100.
Assembly: mm10/hg38
Supplementary files format and content: ATAC-seq coverage bigWig

extract_protocol:
Cells were collected and washed with ice-cold PBS. Cell pellets were resuspended in ATAC-seq RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% IGEPAL-630, 0.1% Tween-20, and 0.01% digitonin, and incubated on ice for 10 minutes. ATAC-seq RSB containing 0.1% Tween-20 (without IGEPAL-630 or digitonin) was then added for washing. Nuclei were pelleted in a pre-chilled centrifuge. Nuclei were incubated with Tn5 transposase and tagmentation buffer at 37°C for 30 minutes. Stop buffer and Proteinase K were added, and samples were incubated at 55°C for 30 minutes to terminate tagmentation and remove proteins.
PCR was performed to amplify the ATAC library for 5 cycles using KAPA HiFi PCR kit. To determine additional amplification cycles for each sample, qPCR was performed, and the additional cycle number was determined as the cycle reaching one-third of maximal abundance in the qPCR amplification curve. All samples were then amplified for another N+3 cycles, followed by final extension. Libraries were purified with DNA clean beads and sequenced as paired-end libraries on Illumina platforms.


title: H3K27ac_Ctrl2

description: Library name: H3K27ac_Ctrl2_S7_R1_001


title: chip_input_koB_res_rep2

description: Library name: chip_input_koB_res_rep2


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_ZSWIM3_KU60019_rep2

description:
Library name: 20230830_nih3t3_cas9_ku60019_ZSWIM3_KU60019_rep2
ATAC-seq sample ZSWIM3_KU60019_rep2


title: WT1_24_EP, rep1

city: Suwon-si

first: Minsuk

last: Cha

address: 2066, Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University

description: Library name: SAMPLES 1

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: spleen

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

treatment_protocol: Flt3L-Ig (10 μg) was intraperitoneally administered on days 0 and 3, and CD24⁺ EPs were sorted from the spleen on day 9.

value: spleen

value: in vivo spleen-CD24+ Emergency progenitor


title: D11_B4jian_20220225NA

description: Library name: D11_B4jian

data_processing:
The raw paired end reads were trimmed and quality controlled by Skewer with default parameters
STAR software was used to compare the preprocessed sequecnces with the reference genome sequences of sequenced species
STringTie was used to count the original sequence of known genes
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

value: lung

value: alveolar epithelial cells

value: flu D11


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_ZSWIM3_KU60019_rep1

description:
Library name: 20230830_nih3t3_cas9_ku60019_ZSWIM3_KU60019_rep1
ATAC-seq sample ZSWIM3_KU60019_rep1


title: cKO1_24_EP, rep1

description: Library name: SAMPLES 3

value: cKO


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_ZSWIM3_DMSO_rep1

description:
Library name: 20230830_nih3t3_cas9_ku60019_ZSWIM3_DMSO_rep1
ATAC-seq sample ZSWIM3_DMSO_rep1


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_ZSWIM3_DMSO_rep3

description:
Library name: 20230830_nih3t3_cas9_ku60019_ZSWIM3_DMSO_rep3
ATAC-seq sample ZSWIM3_DMSO_rep3


title: WT2_24_EP, rep2

description: Library name: SAMPLES 2

value: WT


title: cKO2_24_EP, rep2

description: Library name: SAMPLES 4


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_TYR_DMSO_rep3

description:
Library name: 20230830_nih3t3_cas9_ku60019_TYR_DMSO_rep3
ATAC-seq sample TYR_DMSO_rep3


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_TYR_KU60019_rep1

description:
Library name: 20230830_nih3t3_cas9_ku60019_TYR_KU60019_rep1
ATAC-seq sample TYR_KU60019_rep1


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_ZSWIM3_DMSO_rep2

description:
Library name: 20230830_nih3t3_cas9_ku60019_ZSWIM3_DMSO_rep2
ATAC-seq sample ZSWIM3_DMSO_rep2


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_TYR_KU60019_rep3

description:
Library name: 20230830_nih3t3_cas9_ku60019_TYR_KU60019_rep3
ATAC-seq sample TYR_KU60019_rep3


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_TYR_KU60019_rep2

description:
Library name: 20230830_nih3t3_cas9_ku60019_TYR_KU60019_rep2
ATAC-seq sample TYR_KU60019_rep2


title: chip_input_koB_rep3

description: Library name: chip_input_koB_rep3

source_name: S2 cells


title: D6_B4jian_20220225NA

description: Library name: D6_B4jian

value: flu D6


title: chip_input_koB_rep1

description: Library name: chip_input_koB_rep1


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_TYR_DMSO_rep2

description:
Library name: 20230830_nih3t3_cas9_ku60019_TYR_DMSO_rep2
ATAC-seq sample TYR_DMSO_rep2


title: chip_input_koB_res_rep1

description: Library name: chip_input_koB_res_rep1


title: chip_input_koB_rep2

description: Library name: chip_input_koB_rep2


title: koA_rep3

description: Library name: FG3707


title: chip_input_koA_rep2

description: Library name: chip_input_koA_rep2


title: D2_B4jian_20220225NA

description: Library name: D2_B4jian

value: flu D2


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_EMX1_KU60019_rep3

description:
Library name: 20230830_nih3t3_cas9_ku60019_EMX1_KU60019_rep3
ATAC-seq sample EMX1_KU60019_rep3


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_TYR_DMSO_rep1

description:
Library name: 20230830_nih3t3_cas9_ku60019_TYR_DMSO_rep1
ATAC-seq sample TYR_DMSO_rep1


title: WT_B4jian_20220225NA

description: Library name: WT_B4jian

value: PBS


title: chip_input_koA_rep3

description: Library name: chip_input_koA_rep3


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_EMX1_DMSO_rep3

description:
Library name: 20230830_nih3t3_cas9_ku60019_EMX1_DMSO_rep3
ATAC-seq sample EMX1_DMSO_rep3


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_EMX1_DMSO_rep2

description:
Library name: 20230830_nih3t3_cas9_ku60019_EMX1_DMSO_rep2
ATAC-seq sample EMX1_DMSO_rep2


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_EMX1_KU60019_rep1

description:
Library name: 20230830_nih3t3_cas9_ku60019_EMX1_KU60019_rep1
ATAC-seq sample EMX1_KU60019_rep1


title: m4-Sham1

city: Chongqing

first: Dabin

last: Wu

address: No.1 Medical College Road, Yuzhong District, Chongqing

institute: Chongqing medical university

description:
Library name: Sample16
m4_Sham1:fpkm

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis.
Assembly: mm10
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific).
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).

value: Lung

value: Irradiation


title: chip_h4k16ac_wt_rep3

last: Gkountromichos

address: Großhaderner Strasse 9

institute: Biomedical Center, Ludwig-Maximilians-Universität München

description: Library name: chip_h4k16ac_wt_rep3

value: wild-type


title: m4-Sham3

description:
Library name: Sample18
m4_Sham3:fpkm


title: chip_input_koA_rep1

description: Library name: chip_input_koA_rep1


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_EMX1_KU60019_rep2

description:
Library name: 20230830_nih3t3_cas9_ku60019_EMX1_KU60019_rep2
ATAC-seq sample EMX1_KU60019_rep2


title: m4-RT3

description:
Library name: Sample15
m4_RT3:fpkm


title: ATAC-seq 20230825_nih3t3_cas9_atmi_ZSWIM3_MIRIN200MM_rep3

description:
Library name: 20230825_nih3t3_cas9_atmi_ZSWIM3_MIRIN200MM_rep3
ATAC-seq sample ZSWIM3_MIRIN200MM_rep3


title: ATAC-seq 20230825_nih3t3_cas9_atmi_ZSWIM3_MIRIN25MM_rep3

description:
Library name: 20230825_nih3t3_cas9_atmi_ZSWIM3_MIRIN25MM_rep3
ATAC-seq sample ZSWIM3_MIRIN25MM_rep3


title: ATAC-seq 20230830_nih3t3_cas9_ku60019_EMX1_DMSO_rep1

description:
Library name: 20230830_nih3t3_cas9_ku60019_EMX1_DMSO_rep1
ATAC-seq sample EMX1_DMSO_rep1


title: ATAC-seq 20230825_nih3t3_cas9_atmi_ZSWIM3_MIRIN25MM_rep2

description:
Library name: 20230825_nih3t3_cas9_atmi_ZSWIM3_MIRIN25MM_rep2
ATAC-seq sample ZSWIM3_MIRIN25MM_rep2


title: chip_h4k16ac_wt_rep1

description: Library name: chip_h4k16ac_wt_rep1


title: m4-RT1

description:
Library name: Sample13
m4_RT1:fpkm


title: m4-RT2

description:
Library name: Sample14
m4_RT2:fpkm


title: ATAC-seq 20230825_nih3t3_cas9_atmi_ZSWIM3_MIRIN200MM_rep2

description:
Library name: 20230825_nih3t3_cas9_atmi_ZSWIM3_MIRIN200MM_rep2
ATAC-seq sample ZSWIM3_MIRIN200MM_rep2