title: RANKL_2

city: Hefei

first: sijie

last: bian

address: Huaihai Avenue

department: Department of Orthopaedics

institute: The First Affiliated Hospital of Anhui Medical Universit

description:
Library name: RANKL_2
RANKL Group, replicate biosample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: DEseq_result_anno.xlsx

source_name: cell culture

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

value: cell culture

tag: sample group

value: RANKL

tag: batch


title: Sample 4 single cell for microglia sequenced with novaseq

status: Public on Apr 09 2026

type: SRA

city: Cambridge

first: Joshua

last: Levin

state: MA

address: 75 Ames St

department: Stanley Center

country: USA

institute: Broad Institute

description:
Library name: samp4_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed with Cell Ranger v6.1.2, with the refdata-gex-mm10-2020-A Cell Ranger reference (10x Genomics) and with the expected number of cells set based on estimated loading
The downsampleReads command in DropletUtils v1.14.2 was used to downsample all samples to the same number of reads per cell, then the emptyDropsCellRanger command was used to remove empty droplets.
This count matrix was then loaded in R v4.0.3. A Seurat v4.0.0 object was created, cells with less than 200 genes were removed, and the data was LogNormalized with NormalizeData
Variable genes were extracted with FindVariableFeatures, data was scaled with ScaleData, and PCA was run with RunPCA with npcs=60. Dimensionality reduction was performed on the count data with scGBM v0.1.0, using the gbm.sc command with M=25 and subset=50,000, using just the variable genes
Clusters were calculated with the FindNeighbors and FindClusters commands using dims=1:25 and the scGBM reduction
Assembly: mm10
Supplementary files format and content: h5ad containing clustered object

molecule: polyA RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
For single nuclei data: Hippocampal tissue was dissociated in ice-cold HBSS and mechanically homogenized. Nuclei were filtered, washed, and purified through sequential centrifugation steps. The final nuclei suspension was resuspended in RNase inhibitor-containing buffer, filtered, and counted prior to loading for single-nucleus RNA-seq. For single cell data: Hippocampal tissue was dissociated in ice-cold HBSS and mechanically homogenized. Cell suspensions were filtered, subjected to debris removal, and microglia were enriched using CD11b magnetic bead-based isolation. Purified cells were resuspended in RNase inhibitor-containing buffer and assessed for viability prior to scRNA-seq.
Single-nucleus and single-cell RNA-seq libraries were generated using the Chromium™ Single Cell 3′ Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000121) following the manufacturer’s instructions, targeting recovery of up to 10,000 nuclei per sample. For single nucleus data, twenty-four libraries were pooled and sequenced on one NextSeq 500 flow cell and four NovaSeq 6000 SP flow cells (Illumina) with 28 bases for read 1, 55 bases for read 2, and 8 bases for index read 1. For single cell data, twenty-four libraries from different animals were pooled based on molar concentrations and sequenced on one NextSeq 500 flow cell and two NovaSeq 6000 SP flow cells (Illumina) with 28 bases for read 1, 55 bases for read 2, and 8 bases for index read 1.

tag: tissue

value: Hippocampus

tag: cell type

value: Microglia

tag: genotype


title: HCT116_5FU_2

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

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

description: Library name: GA37706

library_source: transcriptomic

data_processing:
Sequencing was performed on DNBSEQ-G400 platform in a 100+100 base paired-end mode.
The DNBSEQ-G400 control software operated base calling analysis software and delivered raw sequencing data.
Generated reads were mapped to the human (hg19) reference genome using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.8 and SAMtools ver. 0.1.18.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: The human CRC cell lines HCT116, SW480, DLD-1 were maintained using Low-Glucose DMEM (Sigma-Aldrich) supplemented with 10% FBS (Thermo Fisher Scientific) at 37°C 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Micro kit (Qiagen) following the manufacturer’s instruction.
According to the manufacturer's instructions, library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA). Libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).

treatment_protocol: CRC cell lines were seeded at a density of 2 × 10⁵ cells/well in 6-well plates. Cells with cell viability >90% and 60-80% confluency were used.

tag: cell line

value: colorectal cancer cell


title: LaminB1 GO-CaRT on WTC11-iPSC-derived NPCs treated with DMSO for one week

city: San Francisco

first: Mitchel

last: Cole

state: CA

address: 35 Medical Center Way

department: Neurological Surgery

institute: UCSF

description: Library name: WTCNPC_DMSO_LMNB

library_source: genomic

data_processing:
Adapter trimming was performed on raw FASTQ files prior to alignment with trim galore (v0.6.10) using default parameters.
Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.5.1)  and parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 for GO-CaRT/C&R. Trimmed reads were aligned with STAR and parameter --outFilterMatchNmin 50 (v2.7.11b) for RNA
Reads were coordinate sorted and filtered for quality score > 30  with samtools sort and view respectively. For GOCaRT/CnR PCR duplicates were removed with picard tools markDupliates. For RNA reads were separated into forward strand reads and reverse strand reads with samtools view --samFlagExclude 16 or --samFlagInclude 16 resepctively
For LaminB1, filtered bam files were downsampled to match IgG read depth. For visualization and further analysis, downsampled bam files of LaminB1 were converted to log2-normalized bigwig files using the deepTools   Cut&RUN bigwigs were generated from bam files with bamCoverage and RPGC normalization. RNA bigwigs were generated from bam files with bamCoverage and BPM normalization.
Lamina associated domains were called using a two-state Hidden Markov Model (pomegranate v1.1.2) on the median of two biological replicate IgG-normalized BigWig files with a 30 kb bin size. Regions overlapping ENCODE blacklisted regions were discarded.
Assembly: hg38
Supplementary files format and content: bigwig files - LMNB1 log 2 enrichment over IgG controls; Histone enrichment normalized by regions per genomic context (deeptools). RNA shows bins per million enrichment by strand.
Supplementary files format and content: Bed files - lamina associated domains

molecule: genomic DNA

source_name: iPSC-derived NPCs

growth_protocol: Human iPSC line WTC11 was maintained in StemFlex medium (Gibco) on plates coated with Matrigel (Corning) and passaged as clumps with ReLeSR (StemCell Technologies).

extract_protocol:
NPCs were harvested using Accutase. The cell pellet was resuspended in 1 mL ice cold PBS (Gibco). The cells were centrifuged at 500g for 3 min at 4 °C and the cell pellet was resuspended in 1 ml of nuclei isolation buffer (NIB: 10 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.1% NP40, 0.5 mM spermidine and 1× Halt protease inhibitor cocktail) and incubated for 10 min on ice. Nuclear pellet was collected by centrifuging at 600g for 3 min at 4°C and again resuspended in 1 ml of NIB to wash. Nuclei were fixed in 0.1% formaldehyde for 2 minutes and washed in NIB. Fixed nuclei were bound to concanavalin A beads and ~100,000 nuclei were subjected to GO-CaRT/CUT&RUN.
Sequencing libraries for GO-CaRT/CUT&RUN were generated using KAPA HyperPrep Kit (KAPA, KK8504) following the manufacturer’s instructions. The libraries were amplified for 12–14 PCR cycles. DNA fragments were quantified by Tapestation D1000 (Agilent) and Qubit high sensitivity dsDNA (Invitrogen) assays, pooled, and sequenced by 150-bp paired-end sequencing on NovaSeq X Plus systems (Illumina).

treatment_protocol: On day 10, iPSC-derived NPCs were passaged using Accutase and plated onto Matrigel-coated 6-well plates in NPC maturation medium supplemented with 10 µM ROCKi. On days 11-12, cells were fed with NPC maturation medium. On day 13, the media was removed and fresh media containing EZH2 inhibitor Tazemetostat (EPZ-6438, Selleckchem, 1 μM) or DMSO was added to the cells. Cells were fed fresh media containing the inhibitor (or DMSO) every day for one week at which point they were harvested for downstream experimental analyses.

value: iPSC-derived NPCs


title: H3K4me3 CUT&RUN on WTC11-iPSC-derived NPCs treated with 1uM EPZ-6438 (EZH2i) for one week

description: Library name: WTCNPC_EPZ1uM_H3K4me3

data_processing:
Adapter trimming was performed on raw FASTQ files prior to alignment with trim galore (v0.6.10) using default parameters.
Trimmed reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.5.1)  and parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 for GO-CaRT/C&R. Trimmed reads were aligned with STAR and parameter --outFilterMatchNmin 50 (v2.7.11b) for RNA
Reads were coordinate sorted and filtered for quality score > 30  with samtools sort and view respectively. For GOCaRT/CnR PCR duplicates were removed with picard tools markDupliates. For RNA reads were separated into forward strand reads and reverse strand reads with samtools view --samFlagExclude 16 or --samFlagInclude 16 resepctively
For LaminB1, filtered bam files were downsampled to match IgG read depth. For visualization and further analysis, downsampled bam files of LaminB1 were converted to log2-normalized bigwig files using the deepTools   Cut&RUN bigwigs were generated from bam files with bamCoverage and RPGC normalization. RNA bigwigs were generated from bam files with bamCoverage and BPM normalization.
Lamina associated domains were called using a two-state Hidden Markov Model (pomegranate v1.1.2) on the median of two biological replicate IgG-normalized BigWig files with a 30 kb bin size. Regions overlapping ENCODE blacklisted regions were discarded.
Assembly: hg38
Supplementary files format and content: bigwig files - LMNB1 log 2 enrichment over IgG controls; Histone enrichment normalized by regions per genomic context (deeptools). RNA shows bins per million enrichment by strand.
Supplementary files format and content: Bed files - lamina associated domains
Library strategy: CUT&RUN


title: RANKL_1

country: China

description:
Library name: RANKL_1
RANKL Group, replicate biosample 1


title: S-27-C

city: Pittsburgh

first: Kathryn

last: Torok

email: TRH107@pitt.edu, kst7@pitt.edu

state: PA

address: 4401  Penn Ave

institute: University of Pittsburgh

description: Library name: Sample 2

data_processing:
CellRanger
samtools bam2fq
Assembly: GRCh38
Supplementary files format and content: 9v9_Fibro_Macro_Seurat_objs.RData contains two Seurat objects used in this paper: A subsetted macrophage seurat object and a subsetted fibroblast seurat object.

source_name: Skin

extract_protocol:
Cells are isolated from up to six 25um sections cut from rehydrated FFPE blocks using the xylene and GentleMACS OctoDissociator section of the Sample Preparation from FFPE Tissue Sections for GEM-X Flex Gene Expression protocol. Cell yield and quality is checked using NucSpot 470 stain on a Revvity Cellometer Ascend automated cell counter. If cells will not be barcoded immediately, they are stored in Long Term Storage Buffer at -80C.
Fixed cells are first hybridized with Probe Barcodes. Using a microfluidic chip, the hybridized samples are then partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs). A pool of ~737,000 10x GEM Barcodes (also referred to as 10x Barcodes) is sampled separately to index the contents of each partition. Up to 16 samples may be equally pooled in each GEM reaction using uniquely barcoded probe sets for generation of one library.

value: Skin

tag: disease state

value: SSc

tag: onset

value: Pediatric


title: H3K27me3 CUT&RUN on WTC11-iPSC-derived NPCs treated with 1uM EPZ-6438 (EZH2i) for one week

description: Library name: WTCNPC_EPZ1uM_H3K27me3


title: SW480_WT_1

description: Library name: GA37711

value: negative control


title: Sample 8 single cell for microglia sequenced with novaseq

description:
Library name: samp8_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: Sample 2 single cell for microglia sequenced with novaseq

description:
Library name: samp2_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: LDE1

city: Shanghai

first: Juanjuan

last: Shi

address: 160 Pujian Rd Shanghai 200127 P. R. China

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

description: Library name: LDE1

data_processing:
scRNAseq reads were trimmed by fastp to remove adaptor sequences. The trimmed reads were aligned to mm10 CellRanger v3.0.0. Seraut package was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.
Assembly: mm10
Supplementary files format and content: txt

source_name: pancreas

extract_protocol:
Single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of NovelBio Co.,Ltd. The tissues were surgically removed and kept in MACS Tissue Storage Solution until processing. The tissue samples were processed as described below. Briefly, samples were first washed with PBS, minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase I  and  for 45 min at 37°C, with agitation . After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells.  After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer. The single-cell suspension was further enriched with a MACS dead cell removal kit
The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA).

value: pancreas

value: primary cells


title: HCT116_OX_3

description: Library name: GA37710


title: Sample 24 single cell for microglia sequenced with novaseq

description:
Library name: samp24_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: MESO-MOK20138-WT2, WT

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: MSX1_MESO_WT2_GT25-11015_TGACTTCGNNNNNNNNN-CTTAGGAC_S29_L001
KOLF2.2J differentiated to mesoderm

data_processing:
GRCh38 gencode.v44.primary assembly- Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon.
Assembly: GRCh38 gencode.v44.primary assembly
Supplementary files format and content: study13_featureCounts.csv study13_genesCounts.csv study13_genesRawCounts.csv study13_genesTPM.csv study13_stats.csv study13_txCounts.csv study13_txRawCounts.csv study13_txTPM.csv

extract_protocol:
RNeasy Mini Kit QIAGEN NucleoSpin RNA Plus MACHEREY-NAGEL
Watchmaker RNA Library Prep Kit with Polaris™ Depletion Illumina NovaSeq X

value: iPSC

tag: editing strategy

value: Not applicable

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 5

tag: model system

value: mesoderm

tag: parental cell_line


title: LaminB1 GO-CaRT on WTC11-iPSC-derived NPCs treated with 1uM EPZ-6438 (EZH2i) for one week

description: Library name: WTCNPC_EPZ1uM_LMNB


title: Sample 7 single cell for microglia sequenced with novaseq

description:
Library name: samp7_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: HCT116_OX_2

description: Library name: GA37709


title: UDRANKL_3

description:
Library name: UDRANKL_3
UD+RANKL Group, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM counts and fpkm for each sample

value: UDRANKL


title: Sample 22 single cell for microglia sequenced with novaseq

description:
Library name: samp22_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: IgG control for WTC11-iPSC-derived NPCs treated with DMSO for one week

description: Library name: WTCNPC_DMSO_IgG


title: HCT116_OX_1

description: Library name: GA37708


title: H3K4me3 CUT&RUN on WTC11-iPSC-derived NPCs treated with DMSO for one week

description: Library name: WTCNPC_DMSO_H3K4me3


title: RANKL_3

description:
Library name: RANKL_3
RANKL Group, replicate biosample 3

value: cell culture


title: UDRANKL_2

description:
Library name: UDRANKL_2
UD+RANKL Group, replicate biosample 2


title: Sample 5 single cell for microglia sequenced with novaseq

description:
Library name: samp5_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: PC9 oeAGR2_72hrGef_rep3

city: Taipei

first: Kang-Yi

last: Su

address: Rm507, Bldg.Lab.Med., NTU Hospital, No.1, Chang-Te St., Taipei 10048, Taiwan

department: Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine

country: Taiwan

institute: National Taiwan University

description: Library name: Sample 12

data_processing:
Reads aligned using STAR v2.7.8a; quantification based on Ensembl transcripts (v113).
Assembly: hg38 (GRCh38), Ensembl release 113.
Supplementary files format and content: excel (.xlsx) file includes TPM (normalized counts) for each sample.

extract_protocol:
RNA was isolated by using NucleoZOL.
The standard procedure for Illumina library preparation.

treatment_protocol: Cells were treated with 300nM Gefitinib for 24 hours or 72 hours.

value: Non-small cell lung cancer cells

tag: treatment

value: 300nM Gefitinib, 72hours


title: MESO-MOK20138W-A05, KO

description:
Library name: MSX1_KO_A5_GT25-11011_GTTGCGATNNNNNNNNN-GACTTGTG_S25_L001
KOLF2.2J derived knockout cell line, MSX1 KO, differentiated to mesoderm

value: full coding length


title: LDE2

description: Library name: LDE2


title: PC9 oeAGR2_72hrGef_rep2

description: Library name: Sample 11


title: HCT116_5FU_3

description: Library name: GA37707

value: colorectal cancer cell


title: H3K27me3 CUT&RUN on WTC11-iPSC-derived NPCs treated with DMSO for one week

description: Library name: WTCNPC_DMSO_H3K27me3

value: iPSC-derived NPCs


title: PC9 oeAGR2_72hrGef_rep1

description: Library name: Sample 10


title: Sample 3 single cell for microglia sequenced with novaseq

description:
Library name: samp3_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus

value: Hippocampus

value: Microglia


title: MESO-MOK20138-WT3, WT

description:
Library name: MSX1_MESO_WT3_GT25-11016_GTGCTTACNNNNNNNNN-TTCCTCCT_S10_L001
KOLF2.2J differentiated to mesoderm


title: UDRANKL_1

description:
Library name: UDRANKL_1
UD+RANKL Group, replicate biosample 1


title: S-32-C

description: Library name: Sample 1

value: Skin

value: SSc

value: Pediatric


title: MESO-MOK20138-WT1, WT

description:
Library name: MSX1_MESO_WT1_GT25-11014_TAGACGTGNNNNNNNNN-CTCACCAA_S11_L001
KOLF2.2J differentiated to mesoderm


title: Sample 23 single cell for microglia sequenced with novaseq

description:
Library name: samp23_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: Ctrl_1

description:
Library name: Ctrl_1
Control Group, replicate biosample 1

value: Ctrl


title: Ctrl_3

description:
Library name: Ctrl_3
Control Group, replicate biosample 3


title: MESO-MOK20138W-B04, KO

description:
Library name: MSX1_KO_B4_GT25-11013_AAGTCGAGNNNNNNNNN-CGCAATGT_S28_L001
KOLF2.2J derived knockout cell line, MSX1 KO, differentiated to mesoderm

value: iPSC


title: Sample 18 single cell for microglia sequenced with novaseq

description:
Library name: samp18_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: phNPC treated with DMSO IP for IGG (aggregated)

city: Chapel Hill

first: Jason

middle: L

last: Stein

state: NC

address: 116 Manning Drive, CB# 7250 Room 7202A, Mary Ellen Jones Building

department: Genetics

institute: UNC Chapel Hill

description:
Library name: x3-6_3_phNPC_IGG_Veh_1
The raw data will be deposited in dbGaP.

data_processing:
raw fastq files were aggregated per condition
trim_galore version 0.6.7 --paired
bowtie2 version 2.5.4 --very-sensitive-local -X 800
picard version 2.26.11 MarkDuplicates
macs version 2.2.9.1 macs2 callpeak -g 2701495761 --call-summits -q .05
samtools version 1.22 view -b -q 30
deeptools version 3.5.4 bamCoverage --binSize 30 --smoothLength 60 --extendReads --ignoreDuplicates --efectiveGenomeSize 2701495761
all data processing steps are implemented as Nextflow pipeline at github.com/raab-lab/cut-n-run using the --mode cnr
Assembly: hg38
Supplementary files format and content: peak files produced from macs2 and bigwig files
Library strategy: CUT&Run

source_name: primary human neural progenitors

growth_protocol: phNPCs were cultivated as previously described. 6-well plates were coated overnight with Poly-L-Ornithine (10 mg/mL; Sigma-Aldrich, cat#P3655-100MG) and fibronectin (5 mg/mL; Sigma-Aldrich, cat#F1141-5MG) overnight the following day. phNPCs were plated for at 500K cells/well in a 6-well plate. The cells were fed with Neurobasal -A media (Thermo Fisher, cat#10888022) supplemented with BIT 9500 (10%; STEMCELL, cat#09500), Primocin (100 mg/mL; Invitrogen, cat#ant-pm-2), Glutamax 100X (1%; Fisher Scientific, cat#5112367), heparin (1 mg/mL; Sigma-Aldrich, cat#H3393100KU), and growth factors: EGF (20 ng/mL; PeproTech, cat#AF-100-15), FGF (20 ng/mL; PeproTech, cat#AF-100-15), PDGF (20 ng/mL; PeproTech, cat#100-00AB), and LIF (2 ng/mL; PeproTech, cat# 300-05).

extract_protocol:
CUT&RUN was performed as adapted from PMID: PMC6598765
Kapa Hyperprep DNA kit

treatment_protocol: 5uL DMSO for 48 hours

value: primary human neural progenitors

tag: chip antibody

value: IgG (Cell Signaling Technologies 3900S Lot 53)

value: Vehicle (DMSO)


title: Ctrl_2

description:
Library name: Ctrl_2
Control Group, replicate biosample 2


title: PC9 control_72hrGef_rep1

description: Library name: Sample 7


title: ENDO-MOK20141P-D07, KO

description:
Library name: SOX17_PTC_D07_GT25-03639_CGTGATCANNNNNNNNN-GAATGGCA_S214_L007
KOLF2.2J derived knockout cell line, SOX17 PTC, differentiated to endoderm

value: Termination codon

value: day 5

value: endoderm


title: Sample 21 single cell for microglia sequenced with novaseq

description:
Library name: samp21_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: Sample 20 single cell for microglia sequenced with novaseq

description:
Library name: samp20_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: ENDO-MOK20141P-A07, KO

description:
Library name: SOX17_PTC_A07_GT25-03638_TGCGAACTNNNNNNNNN-CAACCGTA_S145_L005
KOLF2.2J derived knockout cell line, SOX17 PTC, differentiated to endoderm


title: ENDO-MOK20136P-H04, KO

description:
Library name: LHX1_PTC_H04_GT25-03637_ATCTCGCTNNNNNNNNN-AACAAGGC_S146_L005
KOLF2.2J derived knockout cell line, LHX1 PTC, differentiated to endoderm


title: Sample 16 single cell for microglia sequenced with novaseq

description:
Library name: samp16_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: MESO-MOK20138W-B01, KO

description:
Library name: MSX1_KO_B1_GT25-11012_GCCACTTANNNNNNNNN-GAGTAGAG_S14_L001
KOLF2.2J derived knockout cell line, MSX1 KO, differentiated to mesoderm

value: mesoderm


title: ENDO-MOK20136-141-WT4, WT

description:
Library name: LHX1_SOX17_WT4_GT25-03643_CTCATCAGNNNNNNNNN-TACTAGCG_S30_L002
KOLF2.2J differentiated to endoderm

value: Not applicable


title: RANKL3

description:
Library name: RANKL3
RANKL Group, replicate biosample 3

value: cell culture

value: RANKL


title: Sample 15 single cell for microglia sequenced with novaseq

description:
Library name: samp15_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus

value: Hippocampus


title: phNPC treated with DMSO IP for TF3C (aggregated)

description:
Library name: x1-9_1_phNPC_TF3C_Veh_1
The raw data will be deposited in dbGaP.

value: TF3C (Bethyl Labs A301-291A, Lot 1)


title: ENDO-MOK20136-141-WT2, WT

description:
Library name: LHX1_SOX17_WT2_GT25-03642_GATCCATGNNNNNNNNN-CAACTCCA_S217_L007
KOLF2.2J differentiated to endoderm


title: Sample 19 single cell for microglia sequenced with novaseq

description:
Library name: samp19_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus

value: Microglia


title: Sample 14 single cell for microglia sequenced with novaseq

description:
Library name: samp14_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: Sample 1 single cell for microglia sequenced with novaseq

description:
Library name: samp1_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: RANKL2

description:
Library name: RANKL2
RANKL Group, replicate biosample 2


title: PC9 control_72hrGef_rep3

description: Library name: Sample 9

value: Non-small cell lung cancer cells

value: 300nM Gefitinib, 72hours


title: PC9 control_72hrGef_rep2

description: Library name: Sample 8


title: ENDO-MOK20136-141-WT1, WT

description:
Library name: LHX1_SOX17_WT1_GT25-03641_CTGTGTTGNNNNNNNNN-TAGGAGCT_S216_L007
KOLF2.2J differentiated to endoderm


title: MESO-MOK20134_142_145-WT3, WT

description:
Library name: HES6_SP5_TBXT_WT3_GT25-03655_TGACGCATNNNNNNNNN-TCAGTAGG_S40_L002
KOLF2.2J differentiated to mesoderm


title: Sample 13 single cell for microglia sequenced with novaseq

description:
Library name: samp13_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: Sample 12 single cell for microglia sequenced with novaseq

description:
Library name: samp12_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: BAT SVF shAsh2l,Ash2l(ChIP)

first: Yajie

last: Hu

state: Shanghai

address: 825 Zhangheng Road, Pudong New District, Shanghai, China.

department: Human Phenome Institute

institute: Fudan University

description: Library name: BAT SVF shAsh2l,ChIP

data_processing:
Raw reads of fastq format were processed using fastp software(V0.20.1).
ChIP-seq reads were mapped to the genome using bowtie2(version 2.4.2).
MACS2(version 2.2.7.1) was used to call peaks.
Assembly: GRCm39
Supplementary files format and content: bigWig, narrowPeak(except for Input sample)

source_name: BAT

extract_protocol:
Add final concentration of 1% Formaldehyde solution for Cross-Linking of DNA and Protein. Then stoped the cross-linking reaction by adding final concentration of 125mM glycine. Extract chromatin from cross-linked cells by adding Lysis Buffer
The sequencing libraries of immunoprecipitated chromatin DNA were generated with varied index label by NEBNext® UltraTM DNA Library Prep Kit for Illumina (NEB, USA, cat. E7645L). Libraries were amplified using 8-10 cycles on the thermocycler. Post amplification libraries size was selected and then purified with AMPure XP Beads. Qubit was used for library quantification and High-sensitivity DNA chip was used for test of library insert size.

value: BAT

value: BAT adipocytes


title: ENDO-MOK20141P-H07, KO

description:
Library name: SOX17_PTC_H07_GT25-03640_TAACGAGGNNNNNNNNN-TAGTCTCG_S215_L007
KOLF2.2J derived knockout cell line, SOX17 PTC, differentiated to endoderm

value: iPSC


title: MESO-MOK20134_142_145-WT2, WT

description:
Library name: HES6_SP5_TBXT_WT2_GT25-03654_GTGGTGTTNNNNNNNNN-GCTGTAAG_S31_L002
KOLF2.2J differentiated to mesoderm


title: Sample 11 single cell for microglia sequenced with novaseq

description:
Library name: samp11_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: BAT SVF shControl,Ash2l(ChIP)

description: Library name: BAT SVF shControl,ChIP

value: shControl


title: RANKL1

description:
Library name: RANKL1
RANKL Group, replicate biosample 1


title: Sample 10 single cell for microglia sequenced with novaseq

description:
Library name: samp10_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: Ctrl3

description:
Library name: Ctrl3
Control Group, replicate biosample 3

value: Ctrl


title: Sample 17 single cell for microglia sequenced with novaseq

description:
Library name: samp17_SingleCell_novaseq
Single cell sequencing of microglia from the hippocampus


title: Ctrl2

description:
Library name: Ctrl2
Control Group, replicate biosample 2


title: Ctrl1

description:
Library name: Ctrl1
Control Group, replicate biosample 1


title: Sample 9 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s9_SingleNuc_novaseq
Single nucleus sequencing of hippocampus

value: Mixed


title: proB_53BP1_KO_JH1-4bait_8

city: Beijing

first: Xuefei

last: Zhang

address: No.5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

description:
Library name: Sample 200
53BP1 knockout

data_processing:
Standard basecalling formats for Novaseq reads
Novaseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
We removed potential duplicates by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt and bait sequences shorter than 50nt.
Assembly: mm9
Supplementary files format and content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); the entire stitched paired end read sequence (Seq); the sequence in the + orientation at the junction (J_seq); and the experiment associated with the read (Library)

source_name: ProB cell from bone marrow

extract_protocol:
DNA was extracted overnight at 56 degree in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH8.0, 200ug/mL proteinase K, prior to DNA fragmentation
Translocation libraries were prepared using VDJ-HTGTS-Seq (Hu et al., 2016)

treatment_protocol: v-Abl transformed pro-B cell lines were cultured in R15 medium and stimulated with 3 uM STI-571 treated for 4 days.

value: ProB cell from bone marrow

value: 53BP1 knockout

value: Pro-B (B220+IgM-CD43+)were sorted by FACS Aria SORP


title: AC16 cells, WT, rep 2

city: Houston

first: Isaac

middle: B

last: Hilton

state: TX

address: 6500 Main St

department: Bioengineering

institute: Rice University

description: Library name: Sample 2

data_processing:
Reads were trimmed using Trim Galore (0.6.10)
Trimmed reads were alligned using STAR (2.5.2b)
Reads were then quantified using RSEM (1.3.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing gene level expression estimates

growth_protocol: AC16 cells were cultured in DMEM/F12 supplemented with 2 mM L-Glutamine, 12.5% FBS, and 1% Pen/Step at 37ºC in 5% CO2.

extract_protocol:
RNA isolation was performed on cells with the RNeasy Plus Mini Kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. All library preparation steps were carried out by Novogene

treatment_protocol: Cells were seeded in a 24-well plate with 1E5 cells per well and corresponding lentivirus at a multiplicity of infection (MOI) of ~10

value: cardiomyocytes

value: WT

value: No Treatment


title: PC9 shAGR2_24hrGef_rep2

description: Library name: Sample 5

value: 300nM Gefitinib, 24hours


title: proB_53BP1_KO_JH1-4bait_5

description:
Library name: Sample 197
53BP1 knockout


title: proB_53BP1_KO_JH1-4bait_4

description:
Library name: Sample 196
53BP1 knockout


title: AC16 cells, WT, rep 1

description: Library name: Sample 1


title: PC9 shAGR2_24hrGef_rep1

description: Library name: Sample 4


title: MESO-MOK20145P-C09, KO

description:
Library name: TBXT_PTC_C09_GT25-03651_TGTACCGTNNNNNNNNN-CCTAGAGA_S39_L002
KOLF2.2J derived knockout cell line, TBXT PTC, differentiated to mesoderm

value: Termination codon

value: TBXT

value: day 5

value: mesoderm


title: Sample 6 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s6_SingleNuc_novaseq
Single nucleus sequencing of hippocampus

value: Hippocampus


title: ASXL1_LTR_KI_ATAC_2

city: Guangzhou

first: Xiao

last: Fang

address: No. 1 Panfu Road, Yuexiu District

institute: Guangzhou First People's Hospital

description: Library name: Sample 27

data_processing:
ChIP-seq: Adapter contamination was trimmed using Trimmomatic (v0.39). Reads were aligned to the human reference genome (GRCh38) using Bowtie 2 (v2.5.4) under default parameters. Peak calling was performed with MACS2 (v2.2.9.1) using the input control data and default parameters. SAM files were converted to BAM format with Samtools (v1.7).  BAM files were also converted to BigWig coverage files with deepTools (v3.5.5).
CUT&Tag: Adapters were trimmed using Trim_Galore (v0.6.10). Reads were mapped to GRCh38 with Bowtie 2 (v2.5.4) under default setting. SAM files were converted to BAM format via Samtools (v1.7). PCR duplicates were removed with Picard tools, and unmapped, low-quality, or mitochondrial reads were excluded. BAM files were next converted to BigWig coverage files using DeepTools (v3.5.5).
ATAC-seq: Adapter were trimmed using Trim_Galore (v0.6.10).24 Reads were aligned to GRCh38 with Bowtie 2 (v2.5.4) under default parameters. SAM files were converted to BAM format using Samtools (v1.7), and PCR duplicates were removed with Picard tools. Unmapped, low-quality, and mitochondrial reads were excluded. Strand-specific read offsets were applied: +4 bp for forward reads and -5 bp for reverse reads. BAM files were then converted to BigWig coverage tracks with DeepTools (v3.5.5).
Assembly: GRCh38
Supplementary files format and content: BigWig

source_name: Bone

growth_protocol: U2OS cells were maintained in DMEM supplemented with GlutaMAX and 10% FBS.

extract_protocol:
ChIP-seq: Cells were washed with PBS and crosslinked in 1% formaldehyde (Thermo Scientific #28908) for 10 minutes, then quenched with 125 mM glycine and 0.5% BSA for 5 minutes. Cells were washed twice with cold 0.5%BSA/PBS and resuspended in Resuspension buffer (9 mM HEPES-KOH pH7.9, 76.4 mM KCl, 0.9 mM EDTA, 0.5% Igepal CA-630). The isolated nuclei were pelleted and resuspended in Lysis Buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% Sodium deoxycholate, 0.1% SDS, 1% Igepal CA-630, 0.5 mM DTT, 1 mM PMSF and 1  protease inhibitor cocktail), then sonicated for 12 cycles (30 seconds on/30 seconds off) using a Bioruptor (Diagenode).The lysates were clarified by centrifugation (20,000g, 10 minutes, 4 °C), and the supernatants were incubated with the magnetic beads: Pierce™ Anti-HA Magnetic Beads (Invitrogen #88836) for ASXL1 or Protein A Mag Sepharose (Cytiva #28951378) with BRD2 antibody (Abcam ab13960). Following a series of washes, chromatin–protein complexes were eluted and reverse-crosslinked, followed by RNase A and protease K digestion. DNA was purified using AMPure XP (Beckman, A63881), alongside 1% input control.
ChIP-seq libraries were prepared using the NEBNext Ultra II kit (NEB #E7645S) following the manufacturer’s instructions.CUT&Tag was performed in ASXL1-HA U2OS knock-in cells using the NovoNGS® CUT&Tag 4.0 High-Sensitivity Kit (N259-YH01) according to the manufacturer’s protocol.ATAC-seq in U2OS knock-in cells was performed using High-Sensitivity Open Chromatin Profile Kit 2.0 (N248), according to the manufacturer’s instructions.

value: Bone

value: Osteosarcoma


title: ENDO-MOK20136P-D05, KO

description:
Library name: LHX1_PTC_D05_GT25-03636_TCCGTGAANNNNNNNNN-CACGATTC_S147_L005
KOLF2.2J derived knockout cell line, LHX1 PTC, differentiated to endoderm

value: iPSC

value: endoderm


title: BAT SVF shAsh2l, Ash2l(INPUT)

description: Library name: BAT SVF shAsh2l,INPUT

value: BAT

value: BAT adipocytes


title: PC9 control_24hrGef_rep3

description: Library name: Sample 3

value: Non-small cell lung cancer cells


title: ENDO-MOK20136P-C05, KO

description:
Library name: LHX1_PTC_C05_GT25-03635_AGTCTCACNNNNNNNNN-CGTCCATT_S144_L005
KOLF2.2J derived knockout cell line, LHX1 PTC, differentiated to endoderm


title: MESO-MOK20142P-H10, KO

description:
Library name: SP5_PTC_H10_GT25-03649_AACGTGGANNNNNNNNN-CCGATGTA_S27_L002
KOLF2.2J derived knockout cell line, SP5 PTC, differentiated to mesoderm


title: BAT SVF shControl, Ash2l(INPUT)

description: Library name: BAT SVF shControl, INPUT

value: shControl


title: PC9 control_24hrGef_rep2

description: Library name: Sample 2


title: ASXL1_LTR_KI_ATAC_1

description: Library name: Sample 26


title: proB_53BP1_KO_JH1-4bait_3

description:
Library name: Sample 195
53BP1 knockout

value: ProB cell from bone marrow

value: 53BP1 knockout

value: Pro-B (B220+IgM-CD43+)were sorted by FACS Aria SORP


title: PC9 control_24hrGef_rep1

description: Library name: Sample 1

value: 300nM Gefitinib, 24hours


title: proB_53BP1_KO_JH1-4bait_2

description:
Library name: Sample 194
53BP1 knockout


title: Sample 4 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s4_SingleNuc_novaseq
Single nucleus sequencing of hippocampus

value: Mixed


title: MESO-MOK20142P-A10, KO

description:
Library name: SP5_PTC_A10_GT25-03647_TCGCATTGNNNNNNNNN-ACAGCAAG_S7_L002
KOLF2.2J derived knockout cell line, SP5 PTC, differentiated to mesoderm

value: Termination codon


title: ASXL1_TR_KI_ATAC_2

description: Library name: Sample 25


title: ASXL1_TR_KI_ATAC_1

description: Library name: Sample 24


title: AC16 cells, CRISPRa, rep 1

description: Library name: Sample 3

value: cardiomyocytes

value: WT

value: CRISPRa targeting PPARGC1A


title: MESO-MOK20145P-E06, KO

description:
Library name: TBXT_PTC_E06_GT25-03652_TGACTGACNNNNNNNNN-CAGAACTG_S28_L002
KOLF2.2J derived knockout cell line, TBXT PTC, differentiated to mesoderm

value: TBXT

value: day 5

value: mesoderm


title: AC16 cells, CRISPRa, rep 2

description: Library name: Sample 4


title: MESO-MOK20134W-G04, KO

description:
Library name: HES6_KO_G04_GT25-03646_GCTGACTANNNNNNNNN-GACATCTC_S29_L002
KOLF2.2J derived knockout cell line, HES6 KO, differentiated to mesoderm

value: iPSC

value: full coding length


title: ASXL1_FL_KI_ATAC_2

description: Library name: Sample 23

value: Bone

value: Osteosarcoma


title: proB_53BP1_KO_JH1-4bait_6

description:
Library name: Sample 198
53BP1 knockout


title: proB_JH1-4bait_4

description:
Library name: Sample 191
WT


title: MESO-MOK20134_142_145-WT1, WT

description:
Library name: HES6_SP5_TBXT_WT1_GT25-03653_GTGTCTGANNNNNNNNN-ATAGTCGG_S8_L002
KOLF2.2J differentiated to mesoderm

value: Not applicable


title: proB_53BP1_KO_JH1-4bait_7

description:
Library name: Sample 199
53BP1 knockout

value: ProB cell from bone marrow


title: proB_53BP1_KO_JH1-4bait_1

description:
Library name: Sample 193
53BP1 knockout

value: 53BP1 knockout


title: MESO-MOK20134W-F04, KO

description:
Library name: HES6_KO_F04_GT25-03645_AGTTACGGNNNNNNNNN-GAGACCAA_S44_L002
KOLF2.2J derived knockout cell line, HES6 KO, differentiated to mesoderm


title: PC9 shAGR2_24hrGef_rep3

description: Library name: Sample 6

value: Non-small cell lung cancer cells


title: ASXL1_FL_KI_ATAC_1

description: Library name: Sample 22


title: Sample 3 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s3_SingleNuc_novaseq
Single nucleus sequencing of hippocampus

value: Hippocampus


title: U2OS_WT_ATAC_2

description: Library name: Sample 21


title: Sample 8 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s8_SingleNuc_novaseq
Single nucleus sequencing of hippocampus

value: Mixed


title: proB_JH1-4bait_3

description:
Library name: Sample 190
WT

value: Pro-B (B220+IgM-CD43+)were sorted by FACS Aria SORP


title: ENDO-MOK20132_133-WT4, WT

description:
Library name: GATA6_GSC_WT4_GT25-03664_CGTTGAGTNNNNNNNNN-GCATAGTC_S5_L002
KOLF2.2J differentiated to endoderm

value: endoderm


title: U2OS_WT_ATAC_1

description: Library name: Sample 20

value: WT


title: MESO-MOK20145P-C01, KO

description:
Library name: TBXT_PTC_C01_GT25-03650_ACCTCTGTNNNNNNNNN-ATGCCTAG_S37_L002
KOLF2.2J derived knockout cell line, TBXT PTC, differentiated to mesoderm

value: Termination codon


title: Sample 23 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s23_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: proB_JH1-4bait_2

description:
Library name: Sample 189
WT


title: Sample 7 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s7_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: ASXL1_LTR_KI_ASXL1_CUT&Tag_2

description: Library name: Sample 19

data_processing:
ChIP-seq: Adapter contamination was trimmed using Trimmomatic (v0.39). Reads were aligned to the human reference genome (GRCh38) using Bowtie 2 (v2.5.4) under default parameters. Peak calling was performed with MACS2 (v2.2.9.1) using the input control data and default parameters. SAM files were converted to BAM format with Samtools (v1.7).  BAM files were also converted to BigWig coverage files with deepTools (v3.5.5).
CUT&Tag: Adapters were trimmed using Trim_Galore (v0.6.10). Reads were mapped to GRCh38 with Bowtie 2 (v2.5.4) under default setting. SAM files were converted to BAM format via Samtools (v1.7). PCR duplicates were removed with Picard tools, and unmapped, low-quality, or mitochondrial reads were excluded. BAM files were next converted to BigWig coverage files using DeepTools (v3.5.5).
ATAC-seq: Adapter were trimmed using Trim_Galore (v0.6.10).24 Reads were aligned to GRCh38 with Bowtie 2 (v2.5.4) under default parameters. SAM files were converted to BAM format using Samtools (v1.7), and PCR duplicates were removed with Picard tools. Unmapped, low-quality, and mitochondrial reads were excluded. Strand-specific read offsets were applied: +4 bp for forward reads and -5 bp for reverse reads. BAM files were then converted to BigWig coverage tracks with DeepTools (v3.5.5).
Assembly: GRCh38
Supplementary files format and content: BigWig
Library strategy: CUT&Tag


title: Sample 20 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s20_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: ASXL1_TR_KI_ASXL1_CUT&Tag_2

description: Library name: Sample 17


title: Sample 21 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s21_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: MESO-MOK20142P-D11, KO

description:
Library name: SP5_PTC_D11_GT25-03648_TCGTCTCANNNNNNNNN-AACGCACA_S18_L002
KOLF2.2J derived knockout cell line, SP5 PTC, differentiated to mesoderm


title: Sample 1 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s1_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: Sample 5 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s5_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: Sample 22 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s22_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: ENDO-MOK20133P-H07, KO

description:
Library name: GSC_PTC_H07_GT25-03661_TGACTTCGNNNNNNNNN-CTTAGGAC_S10_L002
KOLF2.2J derived knockout cell line, GSC PTC, differentiated to endoderm

value: GSC


title: ENDO-MOK20133P-C08, KO

description:
Library name: GSC_PTC_C08_GT25-03660_TAGACGTGNNNNNNNNN-CTCACCAA_S32_L002
KOLF2.2J derived knockout cell line, GSC PTC, differentiated to endoderm

value: day 5


title: ENDO-MOK20133P-A07, KO

description:
Library name: GSC_PTC_A07_GT25-03659_AAGTCGAGNNNNNNNNN-CGCAATGT_S23_L002
KOLF2.2J derived knockout cell line, GSC PTC, differentiated to endoderm


title: Sample 2 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s2_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: Sample 18 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s18_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: ASXL1_LTR_KI_BRD2_ChIP_1

description: Library name: Sample 14


title: Sample 24 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s24_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: ENDO-MOK20132P-C10, KO

description:
Library name: GATA6_PTC_C10_GT25-03657_GTTGCGATNNNNNNNNN-GACTTGTG_S34_L002
KOLF2.2J derived knockout cell line, GATA6 PTC, differentiated to endoderm


title: MESO-MOK20134W-B04, KO

description:
Library name: HES6_KO_B04_GT25-03644_TAGAGCTCNNNNNNNNN-AGAAGCCT_S43_L002
KOLF2.2J derived knockout cell line, HES6 KO, differentiated to mesoderm

value: mesoderm


title: ASXL1_TR_KI_BRD2_ChIP_2

description: Library name: Sample 13


title: preB_JKbait_3

description:
Library name: Sample 181
WT

source_name: PreB cell from bone marrow

value: PreB cell from bone marrow

value: Pre-B cells (B220+IgM-CD43-) were sorted by FACS Aria SORP


title: preB_JKbait_4

description:
Library name: Sample 182
WT


title: ASXL1_LTR_KI_input

description: Library name: Sample 11

value: Bone


title: Sample 15 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s15_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: proB_JH1-4bait_1

description:
Library name: Sample 188
WT


title: ENDO-MOK20132_133-WT3, WT

description:
Library name: GATA6_GSC_WT3_GT25-03663_CCGATGTANNNNNNNNN-CAACTTGG_S36_L002
KOLF2.2J differentiated to endoderm

value: iPSC


title: MESO-MOK20131_135-WT4, WT

description:
Library name: CITED_HOXB8_WT4_GT25-03673_CGTATTCGNNNNNNNNN-TGTCGACT_S41_L002
KOLF2.2J differentiated to mesoderm

value: Not applicable


title: ENDO-MOK20132_133-WT1, WT

description:
Library name: GATA6_GSC_WT1_GT25-03662_GTGCTTACNNNNNNNNN-TTCCTCCT_S24_L002
KOLF2.2J differentiated to endoderm


title: preB_53BP1_KO_JKbait_5

description:
Library name: Sample 187
53BP1 knockout


title: ASXL1_LTR_KI_ASXL1_CUT&Tag_1

description: Library name: Sample 18

value: Osteosarcoma


title: MESO-MOK20131_135-WT3, WT

description:
Library name: CITED_HOXB8_WT3_GT25-03672_AGTCGCTTNNNNNNNNN-TCGAACCT_S13_L002
KOLF2.2J differentiated to mesoderm


title: Sample 19 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s19_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: preB_53BP1_KO_JKbait_3

description:
Library name: Sample 185
53BP1 knockout

value: 53BP1 knockout


title: preB_53BP1_KO_JKbait_4

description:
Library name: Sample 186
53BP1 knockout


title: ASXL1_LTR_KI_BRD2_ChIP_2

description: Library name: Sample 15


title: proB_JH1-4bait_5

description:
Library name: Sample 192
WT

value: ProB cell from bone marrow


title: ENDO-MOK20132P-H10, KO

description:
Library name: GATA6_PTC_H10_GT25-03658_GCCACTTANNNNNNNNN-GAGTAGAG_S9_L002
KOLF2.2J derived knockout cell line, GATA6 PTC, differentiated to endoderm


title: preB_53BP1_KO_JKbait_2

description:
Library name: Sample 184
53BP1 knockout


title: ASXL1_TR_KI_ASXL1_CUT&Tag_1

description: Library name: Sample 16


title: ENDO-MOK20132P-B11, KO

description:
Library name: GATA6_PTC_B11_GT25-03656_TTCCTGTGNNNNNNNNN-CTCCTGAA_S19_L002
KOLF2.2J derived knockout cell line, GATA6 PTC, differentiated to endoderm


title: Sample 11 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s11_SingleNuc_novaseq
Single nucleus sequencing of hippocampus

value: Hippocampus


title: ASXL1_TR_KI_BRD2_ChIP_1

description: Library name: Sample 12


title: 53BP1_HMGB1_DKO_Iubait_5

description:
Library name: Sample 177
53BP1 knockout\, HMGB1 knockout\, non-coding IgH VH-3'BCEs deletion

value: aCD40/IL4/TGFb stimulation for 72h


title: MESO-MOK20135P-F02, KO

description:
Library name: HOXB8_PTC_F02_GT25-03670_TCAAGGACNNNNNNNNN-CATTCGTC_S22_L002
KOLF2.2J derived knockout cell line, HOXB8 PTC, differentiated to mesoderm


title: Sample 17 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s17_SingleNuc_novaseq
Single nucleus sequencing of hippocampus

value: Mixed


title: Sample 16 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s16_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: preB_53BP1_KO_JKbait_1

description:
Library name: Sample 183
53BP1 knockout


title: 53BP1_HMGB1_DKO_Iubait_4

description:
Library name: Sample 176
53BP1 knockout\, HMGB1 knockout\, non-coding IgH VH-3'BCEs deletion


title: ASXL1_LTR_OE_BRD2_ChIP_2

description: Library name: Sample 9


title: Sample 14 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s14_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: preB_JKbait_2

description:
Library name: Sample 180
WT


title: preB_JKbait_1

description:
Library name: Sample 179
WT


title: ASXL1_TR_OE_BRD2_ChIP_2

description: Library name: Sample 7


title: ASXL1_TR_KI_input

description: Library name: Sample 10


title: Sample 10 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s10_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: Sample 12 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s12_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: 53BP1_HMGB1_DKO_Iubait_2

description:
Library name: Sample 174
53BP1 knockout\, HMGB1 knockout\, non-coding IgH VH-3'BCEs deletion


title: MESO-MOK20131_135-WT1, WT

description:
Library name: CITED_HOXB8_WT1_GT25-03671_TTCGCAGTNNNNNNNNN-TCCGATCA_S35_L002
KOLF2.2J differentiated to mesoderm


title: Sample 13 single nuclei from hippocampus sequenced with novaseq

description:
Library name: s13_SingleNuc_novaseq
Single nucleus sequencing of hippocampus


title: ASXL1_LTR_OE_ASXL1_ChIP_2

description: Library name: Sample 5


title: P. australis, invasive

city: Helsinki

first: Cui

last: Wang

address: PL 65 (Viikinkaari 1)

country: Finland

institute: University of Helsinki

description:
Library name: NAint61_spatial
Fresh frozen spatial transcriptomics

data_processing:
The raw reads were demultiplexed and preprocessed through BSTMatrix (v1.0).
Assembly: ASM4037322v1, with fragmented contigs replaced by organelle circular sequences and gene models lifted over from the original assembly
Supplementary files format and content: Tab separated values files and matrix files
Library strategy: Spatial Transcriptomics

organism: Phragmites australis

growth_protocol: common garden at 25 ℃

extract_protocol:
Shoot tissues were snap-frozen in isopentane pre-chilled with liquid nitrogen and optimum cutting temperature (OCT) compound (SAKURA,Cat#: 4583) and stored at −80℃ until use.
Spatial transcriptome sequencing libraries were prepared with BMK S3000 gene expression capturing system according to the manufacture's instructions.

treatment_protocol: No treatment.

value: Shoot

value: meristems, vascular cells, epidermis, parenchyma

value: invasive

value: No treatment


title: MESO-MOK20131P-B09, KO

description:
Library name: CITED_PTC_B09_GT25-03667_CACGTTGTNNNNNNNNN-ACACCTCA_S15_L002
KOLF2.2J derived knockout cell line, CITED1 PTC, differentiated to mesoderm

value: Termination codon

value: day 5


title: ASXL1_LTR_OE_BRD2_ChIP_1

description: Library name: Sample 8


title: 53BP1_HMGB1_DKO_Iubait_6

description:
Library name: Sample 178
53BP1 knockout\, HMGB1 knockout\, non-coding IgH VH-3'BCEs deletion


title: ASXL1_TR_OE_BRD2_ChIP_1

description: Library name: Sample 6


title: MESO-MOK20135P-E02, KO

description:
Library name: HOXB8_PTC_E02_GT25-03669_TGGATCACNNNNNNNNN-GCATTGGT_S11_L002
KOLF2.2J derived knockout cell line, HOXB8 PTC, differentiated to mesoderm

value: mesoderm


title: MESO-MOK20135P-B01, KO

description:
Library name: HOXB8_PTC_B01_GT25-03668_CCGGAATTNNNNNNNNN-ACCGAATG_S6_L002
KOLF2.2J derived knockout cell line, HOXB8 PTC, differentiated to mesoderm


title: 53BP1_KO_Iubait_4

description:
Library name: Sample 172
53BP1 knockout\, non-coding IgH VH-3'BCEs deletion


title: MM.1S cells LenR biol rep 2

city: Yantai

first: Xinlong

last: Guo

state: Shandong province

address: No. 198, Binhai East Road, Muping District, Yantai City, Shandong Province, China

department: Shandong Laboratory of Yantai Drug Discovery

institute: Bohai Rim Advanced Research Institute for Drug Discovery

description: Library name: Sample 4

data_processing:
Raw FASTQ files were quality checked using FastQC (v0.11.9) Alignment to hg38 was performed using Bowtie2 (v2.4.4). Peaks were called using MACS3 (v3.0.0b1). Peaks were annotated to nearest genes (ChIPseeker v1.34.1).
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: MM.1S cells were maintained in RPMI 1640 supplemented containing 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in an incubator containing 5% CO2 at 37 oC with suitable humidity.

extract_protocol:
Cells were harvested for genomic DNA extract using a NovoNGS® CUT&Tag 4.0 High-Sensitivity Kit (for Illumina®) (Novoprotein, N259-YH01)
CUT&tag libraries were were prepared using a NovoNGS® CUT&Tag 4.0 High-Sensitivity Kit (for Illumina®) (Novoprotein, N259-YH01) following manufacturer's protocols.

treatment_protocol: To establish a lenalidomide-resistant (LenR) MM cell line, MM.1S cells were subjected to continuous treatment with 10 nM lenalidomide, with the dosage increased 10-fold each month over a period of 3 months. Concurrently, another group of MM cells received continuous treatment with dimethyl sulfoxide (DMSO) as solvent control (WT).

tag: cut&tag antibody

value: H4K8la (PTM BIO, PTM-1415RM)

value: Tumor cells

value: WT

value: lenalidomide


title: 53BP1_HMGB1_DKO_Iubait_3

description:
Library name: Sample 175
53BP1 knockout\, HMGB1 knockout\, non-coding IgH VH-3'BCEs deletion


title: 53BP1_KO_Iubait_1

description:
Library name: Sample 169
53BP1 knockout\, non-coding IgH VH-3'BCEs deletion


title: P. australis, EU, rep2

description:
Library name: EU78
10x Genomics

data_processing:
We first demultiplexed the raw reads of scRNA and removed the barcodes of six individuals (EU60, EU78, EU620, NAint61, NAint113, and NAint191). Then the clean reads were mapped to the chromosome level genome assembly(15) using cellranger pipeline v8.0. The mkref function with default settings in CellRanger was used to build the reference for this species, and count function was used to assess the number of unique molecular identifiers (UMIs) for each gene and barcode. The count matrices were then used for quality control using scanpy. We only kept genes that are expressed in at least 20 cells, and cells that have at least 500 genes expressed. Cells with mitochondrial genes higher than 10% and chloroplast genes higher than 30% may indicate dead cells thus were removed from the analysis. Doublets were removed using DoubleFinder.
Assembly: ASM4037322v1, with fragmented contigs replaced by organelle circular sequences and gene models lifted over from the original assembly
Supplementary files format and content: Tab separated values files and matrix files

source_name: Shoot

extract_protocol:
The Rhizome tip was cut into 1-2 mm strips and added to tubes containing 10ml enzyme solution consisting of 2% cellulase R10, 0.8% macerozyme R-10, 0.5% pectinase Y-23, 0.1% BSA, 20mM MES,20mM KCl,10mMCaCL2 and 0.55M mannitol with shaking at 60rpm for 1 hour at 28℃. Cells were then filtered with a 40 um cell strainer. Cell activity was detected by trypan blue staining and cell concentration was measured using a hemocytometer and a light microscope. Lastly, protoplasts were resuspended in 8% (w/v) mannitol solution in preparation for loading onto the chromium controller of the 10xGenomics platform.
Cells were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 700-1200cells/ul (Single Cell 3′ library and Gel Bead Kit v.3) as described in the manufacturer’s protocol. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were all performed as per the manufacturer’s protocol.

treatment_protocol: No treatment

value: EU

value: European population


title: 53BP1_KO_Iubait_2

description:
Library name: Sample 170
53BP1 knockout\, non-coding IgH VH-3'BCEs deletion


title: MM.1S cells LenR biol rep 1

description: Library name: Sample 3


title: 53BP1_KO_Iubait_3

description:
Library name: Sample 171
53BP1 knockout\, non-coding IgH VH-3'BCEs deletion


title: P. australis, EU, rep1

description:
Library name: EU60
10x Genomics


title: PrS-MOK20126_46-WT1, WT

description:
Library name: TFEB_ZNF175_WT1_GT25-03680_TAGGTAGGNNNNNNNNN-CACAGACT_S21_L002
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

data_processing:
GRCh38 gencode.v44.primary assembly- Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon.
Assembly: GRCh38 gencode.v44.primary assembly
Supplementary files format and content: study12_featureCounts.csv study12_genesCounts.csv study12_genesRawCounts.csv study12_genesTPM.csv study12_stats.csv study12_txCounts.csv study12_txRawCounts.csv study12_txTPM.csv

extract_protocol:
RNeasy Mini Kit QIAGEN NucleoSpin RNA Plus MACHEREY-NAGEL
KAPA RNA HyperPrep Kit with RiboErase (HMR) and Watchmaker RNA Library Prep Kit with Polaris™ Depletion Illumina NovaSeq X

value: iPSC

value: Not applicable

value: day 6

value: primitive syncytium


title: PrS-MOK20126_46-WT2, WT

description:
Library name: TFEB_ZNF175_WT2_GT25-03681_AGCAAGCANNNNNNNNN-AAGGAGAC_S26_L002
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv


title: No6

description: Library name: GB00267

data_processing:
Sequencing was performed on DNBSEQ-G400 platform in 43+100 base paired-end mode.
Raw sequencing data were converted to matrices of expression using Space Ranger (version spaceranger-4.0.1, 10X Genomics).
Assembly: mm10-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5 format file including filtered counts data for each gene and spot-position (barcode) combination
Supplementary files format and content: raw_feature_bc_matrix.h5:  HDF5 format file including raw counts data for each gene and spot-position (barcode) combination
Supplementary files format and content: spatial.tar.gz: tar.gz compressed file of Space Ranger output folder "spatial"
Library strategy: Spatial Transcriptomics

source_name: lung

extract_protocol:
At 6 days post-injection, the mice were sacrificed 30 minutes after the final procedure. Immediately after euthanasia, thoracic tissues were collected from the left lung parenchyma adjacent to the chest wall. The samples were fixed in 4% paraformaldehyde for 24 hours. For spatial transcriptomic analysis, tissues were sectioned at 5 μm thickness. Visium Mouse Transcriptome Probe Set and Visium V4 Slide - Probe-based v2 chemistry were used to extract total RNA and hybridize transcriptomic probes to the Visium slide.
Sequencing library preparation were performed according to standard protocol of the Visium CytAssist Spatial Gene Expression Reagent Kits User Guide.

treatment_protocol: After the mice were sedated, 200 μL of a saline-based talc solution (2.0 g/kg) was administered into the left thoracic cavity through the diaphragm with a 24-gauge needle.

value: lung

tag: strain

value: Saline-based talc solution was administered into the left thoracic cavity.


title: HMGB1_KO_Iubait_6

description:
Library name: Sample 168
HMGB1 knockout\, non-coding IgH VH-3'BCEs deletion

value: HMGB1 knockout

value: aCD40/IL4/TGFb stimulation for 72h


title: MESO-MOK20131P-B08, KO

description:
Library name: CITED_PTC_B08_GT25-03666_CTGAGATCNNNNNNNNN-AGGCAATG_S11_L001
KOLF2.2J derived knockout cell line, CITED1 PTC, differentiated to mesoderm

value: Termination codon


title: P. australis, invasive, rep3

description:
Library name: NAint191
10x Genomics

value: Shoot

value: invasive

value: meristems, vascular cells, epidermis, parenchyma

value: North American invasive population

value: No treatment

tag: batch


title: MESO-MOK20131P-A07, KO

description:
Library name: CITED_PTC_A07_GT25-03665_AACGACGTNNNNNNNNN-TCAATCCG_S14_L002
KOLF2.2J derived knockout cell line, CITED1 PTC, differentiated to mesoderm

value: day 5

value: mesoderm


title: ASXL1_TR_OE_ASXL1_ChIP_2

description: Library name: Sample 3

tag: tissue

value: Bone

value: Osteosarcoma


title: ASXL1_LTR_OE_ASXL1_ChIP_1

description: Library name: Sample 4

tag: cell type


title: PrS-MOK20146P-A08, KO

description:
Library name: TFEB_PTC_A08_GT25-03674_GTTAAGGCNNNNNNNNN-ACCTTCGA_S20_L002
KOLF2.2J derived knockout cell line, TFEB PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

value: iPSC

value: TFEB


title: P. australis, invasive, rep2

description:
Library name: NAint113
10x Genomics

tag: genotype


title: P. australis, invasive, rep1

description:
Library name: NAint61
10x Genomics

tag: cell line


title: HMGB1_KO_Iubait_4

description:
Library name: Sample 166
HMGB1 knockout\, non-coding IgH VH-3'BCEs deletion


title: 53BP1_HMGB1_DKO_Iubait_1

description:
Library name: Sample 173
53BP1 knockout\, HMGB1 knockout\, non-coding IgH VH-3'BCEs deletion


title: RNAseq_UTYKO_rep1

city: Yokohama

first: Tomohiko

last: Akiyama

state: Kanagawa

address: 3-9 Fuku-ura

department: School of medicine

institute: Yokohama city university

description:
Library name: RNAseq_UTYKO_rep1
Counts data from WT and UTYKO samples were combined and submitted as a single matrix table

data_processing:
Sequence reads were aligned to the human genome (GRCh38) using STAR
TPM and FPKM values were estimated using RSEM
Gene-level expression was also quantified using featureCounts based on the annotation file Homo_sapiens.GRCh38.105.gtf
For differential expression analysis, raw counts obtained by featureCounts were analyzed using the TCC-GUI pipeline in R
Normalization was performed using the TMM method, and differentially expressed genes were identified using edgeR
Assembly: hg38
Supplementary files format and content: text files include counts for each sample

source_name: Embryonic cells

extract_protocol:
Total RNA was extracted using TRIzol solution according to the manufacturer's instructions
The cDNA library was prepared from 500 ng of each total RNA sample for massive parallel sequencing using an NEBNext Poly(A) mRNA Magnetic Isolation Module and an Ultra Directional RNA Library Prep Kit for Illumina (NEB). The cDNA library produced ranged from 400 to 1000 bp, including the adaptor sequences

value: Embryonic cells

value: ES cells (SEES3)

value: Pluripotent stem cells


title: RNAseq_UTYKO_ctrl_rep1

description:
Library name: RNAseq_UTYKO_ctrl_rep1
Counts data from WT and UTYKO samples were combined and submitted as a single matrix table


title: MDA-MB-468 with AdipoRON non-treatment No2

first: Shinya

last: Sato

address: 2-3-2, Nakao, Asahi-Ku

institute: Kanagawa Cancer Center Research Institute

description:
Library name: MDA-MB-468-C2
Takarabio

data_processing:
For data cleaning, missing values were checked for each sample, and genes with high missing values were excluded. Data normalization was performed using the TPM (Transcripts Per Million) method. For filtering, genes with very low average expression levels (genes with expression levels less than 1 TPM) were excluded from the analysis. Differential gene expression analysis between conditions was performed using the DESeq2 package. Analysis was performed using the Takara analysis package to compare treated and untreated cases using heat maps.
Assembly: GRCh38.p14
Supplementary files format and content: Processed data files are provided in excel file containing count data normalized with TPM. Each row represents a unique gene, and each column corresponds to a sample.

growth_protocol: All cell lines were incubated in RPMI1640 with 10%FBS and antibiotics

extract_protocol:
All RNAs of all samples were extracted using RNeasy mini (Qiagen) following their protocol.
Adapter sequences were added to both ends of the first strand cDNA using the SMART (Switching Mechanism At 5'End of RNA Template) method. PCR amplification was performed using a primer that recognized the added adapter sequence, and the PCR product obtained was purified using AMPure XP (Beckman Coulter) to obtain a double-stranded cDNA amplified product. Then, double-stranded cDNA was fragmented and adapter sequences were added to both ends by a tagmentation reaction using a transposon. PCR amplification was performed using indexed primers that recognized the adapter sequence and had a tag sequence that differed for each sample, and an indexed sequence library was created. The quality of the created sequence library was tested using an electrophoresis device. The reagents used for library creation are listed in the datasheet. The procedure was performed according to the manual that came with the reagent.

treatment_protocol: All cell lines were treated with AdipoRON or DMSO for 24 hours

value: breast cancer cell line

value: WT

value: DMSO treatment


title: MDA-MB-468 with AdipoRON non-treatment No1

description:
Library name: MDA-MB-468-C1
Takarabio


title: PrS-MOK20126P-B05, KO

description:
Library name: ZNF175_PTC_B05_GT25-03677_ACACCAGTNNNNNNNNN-AGTGCATC_S17_L002
KOLF2.2J derived knockout cell line, ZNF175 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

value: Termination codon

value: day 6

value: primitive syncytium


title: MDA-MB-468 with AdipoRON non-treatment No3

description:
Library name: MDA-MB-468-C3
Takarabio


title: CH12F3PO_Iubait_4

description:
Library name: Sample 162
non-coding IgH VH-3'BCEs deletion

value: aCD40/IL4/TGFb stimulation for 72h


title: PrS-MOK20146P-B06, KO

description:
Library name: TFEB_PTC_B06_GT25-03676_CTCCTAGANNNNNNNNN-GCTTCACA_S42_L002
KOLF2.2J derived knockout cell line, TFEB PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv


title: P. australis, EU, rep3

description:
Library name: EU620
10x Genomics

value: Shoot

value: EU

value: meristems, vascular cells, epidermis, parenchyma

value: European population

value: No treatment


title: MDA-MB-468 with AdipoRON treatment No3

description:
Library name: MDA-MB-468-A3
Takarabio

value: AdipoRON treatment


title: ASXL1_TR_OE_input

description: Library name: Sample 1

value: Bone

value: Osteosarcoma


title: ASXL1_TR_OE_ASXL1_ChIP_1

description: Library name: Sample 2


title: RNAseq_DKO_rep1

description:
Library name: RNAseq_DKO_rep1
Counts data from WT and DKO samples were combined and submitted as a single matrix table

value: Embryonic cells

value: ES cells (SEES3)


title: HMGB1_KO_Iubait_1

description:
Library name: Sample 163
HMGB1 knockout\, non-coding IgH VH-3'BCEs deletion

value: HMGB1 knockout


title: PrS-MOK20146P-A10, KO

description:
Library name: TFEB_PTC_A10_GT25-03675_TCACAGCANNNNNNNNN-GAGGCATT_S16_L002
KOLF2.2J derived knockout cell line, TFEB PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

value: iPSC

value: TFEB


title: PrS-MOK20126_46-WT3, WT

description:
Library name: TFEB_ZNF175_WT3_GT25-03682_ATGCCAACNNNNNNNNN-TTACCGAC_S38_L002
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

value: Not applicable


title: HMGB1_KO_Iubait_5

description:
Library name: Sample 167
HMGB1 knockout\, non-coding IgH VH-3'BCEs deletion


title: MM.1S cells WT biol rep 2

description: Library name: Sample 2

value: H4K8la (PTM BIO, PTM-1415RM)

value: Tumor cells

value: WT

value: DMSO


title: RNAseq_UTXKO_rep2

description:
Library name: RNAseq_UTXKO_rep2
Counts data from WT and UTXKO samples were combined and submitted as a single matrix table

value: Pluripotent stem cells


title: MDA-MB-468 with AdipoRON treatment No1

description:
Library name: MDA-MB-468-A1
Takarabio

value: breast cancer cell line


title: HMGB1_KO_Iubait_3

description:
Library name: Sample 165
HMGB1 knockout\, non-coding IgH VH-3'BCEs deletion

value: aCD40/IL4/TGFb stimulation for 72h


title: ExM-MOK20091P-F12, KO

description:
Library name: SOX7_PTC_F12_NEW_GT25-02688_ACTAAGAT-CCGCGGTT_S145_L007
KOLF2.2J derived knockout cell line,SOX7 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

value: Termination codon

value: day 6

value: fibroblast of villous mesenchyme (CL:0002558)


title: MDA-MB-231 with AdipoRON non-treatment No3

description:
Library name: MDA-MB-231-C3
Takarabio

value: DMSO treatment


title: PrS-MOK20126P-E02, KO

description:
Library name: ZNF175_PTC_E02_GT25-03679_ACGACAGANNNNNNNNN-CGCAACTA_S33_L002
KOLF2.2J derived knockout cell line, ZNF175 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

value: primitive syncytium


title: HMGB1_KO_Iubait_2

description:
Library name: Sample 164
HMGB1 knockout\, non-coding IgH VH-3'BCEs deletion


title: MM.1S cells WT biol rep 1

description: Library name: Sample 1


title: JH1O_T1083del_53BP1_HMGB1_DKO_JH1bait_3

description:
Library name: Sample 158
JH1 bait\, 53BP1 and HMGB1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

source_name: v-Abl transformed pro-B cell line

value: v-Abl transformed pro-B cell line

value: 53BP1 and HMGB1 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient

value: T1083del retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: PrS-MOK20126P-D05, KO

description:
Library name: ZNF175_PTC_D05_GT25-03678_TGAACCTGNNNNNNNNN-ACCTCTTC_S12_L002
KOLF2.2J derived knockout cell line, ZNF175 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

value: iPSC


title: RNAseq_DKO_rep2

description:
Library name: RNAseq_DKO_rep2
Counts data from WT and DKO samples were combined and submitted as a single matrix table

value: Embryonic cells

value: ES cells (SEES3)


title: ExM-MOK20063_68_91-WT3, WT

description:
Library name: WT_SNAI_ELK3_SOX7_3_GT25-02691_TCCAACGC-AAGTCCAA_S141_L007
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

value: Not applicable


title: ATAC-seq_DKO_rep_2

description:
Library name: ATAC-seq_DKO_rep_2
rep_1 and rep_2 were merged and visualized as a single bigWig file.

data_processing:
Raw sequencing reads were quality-controlled and trimmed using Fastp
Sequence reads were aligned using bowtie2
Aligned reads were processed using SAMtools to generate BAM and index files
bamCoverage was used to generate BigWig files with counts per million normalization
Heatmaps and aggregation plots were created using deepTools computeMatrix, followed by visualization with plotHeatmap and plotProfile.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol (Corces et al., 2017) with minor modifications. Briefly, viable cells were lysed in cold ATAC resuspension buffer containing NP-40, Tween-20, and digitonin. After incubation on ice, cells were washed with resuspension buffer containing Tween-20, and nuclei were pelleted by centrifugation. Nuclei were resuspended in transposition mix containing Tn5 transposase and incubated at 37°C for 30 minutes with agitation. Transposed DNA was purified using AMPure XP beads and eluted.
Libraries were pre-amplified for 5 PCR cycles, and the optimal number of additional cycles was determined by qPCR using a 10% side reaction. Final amplification was performed, followed by a two-step AMPure XP cleanup. Libraries were eluted and quality-checked using a Bioanalyzer to assess fragment size distribution.

value: UTX/UTY-KO


title: RNAseq_UTYKO_rep2

description:
Library name: RNAseq_UTYKO_rep2
Counts data from WT and UTYKO samples were combined and submitted as a single matrix table


title: RNAseq_UTYKO_ctrl_rep2

description:
Library name: RNAseq_UTYKO_ctrl_rep2
Counts data from WT and UTYKO samples were combined and submitted as a single matrix table


title: RNAseq_WT_rep2

description:
Library name: RNAseq_WT_rep2
Counts data from WT and UTXKO samples were combined and submitted as a single matrix table


title: CH12F3PO_Iubait_1

description:
Library name: Sample 159
non-coding IgH VH-3'BCEs deletion


title: ExM-MOK20091P-E10, KO

description:
Library name: SOX7_PTC_E10_NEW_GT25-02687_ATGAGGCC-CAATTAAC_S137_L007
KOLF2.2J derived knockout cell line,SOX7 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv


title: RNAseq_WT_rep1

description:
Library name: RNAseq_WT_rep1
Counts data from WT and UTXKO samples were combined and submitted as a single matrix table


title: CH12F3PO_Iubait_2

description:
Library name: Sample 160
non-coding IgH VH-3'BCEs deletion


title: ExM-MOK20091P-B11, KO

description:
Library name: SOX7_PTC_B11_NEW_GT25-02686_GCAGAATT-TGGCCGGT_S143_L007
KOLF2.2J derived knockout cell line,SOX7 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv


title: CH12F3PO_Iubait_3

description:
Library name: Sample 161
non-coding IgH VH-3'BCEs deletion


title: ATAC-seq_DKO_rep_1

description:
Library name: ATAC-seq_DKO_rep_1
rep_1 and rep_2 were merged and visualized as a single bigWig file.


title: MDA-MB-468 with AdipoRON treatment No2

description:
Library name: MDA-MB-468-A2
Takarabio

value: WT

value: AdipoRON treatment


title: ATAC-seq_hES_rep_1

description:
Library name: ATAC-seq_hES_rep_1
rep_1 and rep_2 were merged and visualized as a single bigWig file.

value: Pluripotent stem cells


title: RNAseq_UTXKO_rep1

description:
Library name: RNAseq_UTXKO_rep1
Counts data from WT and UTXKO samples were combined and submitted as a single matrix table


title: JH1O_T1083del_53BP1_HMGB1_DKO_JH1bait_2

description:
Library name: Sample 157
JH1 bait\, 53BP1 and HMGB1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: ExM-MOK20063_68_91-WT2, WT

description:
Library name: WT_SNAI_ELK3_SOX7_2_GT25-02690_CTTGGTAT-GGACTTGG_S136_L007
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv


title: MDA-MB-231 with AdipoRON non-treatment No2

description:
Library name: MDA-MB-231-C2
Takarabio

value: breast cancer cell line


title: JH1O_T1083del_53BP1_KO_JH1bait_3

description:
Library name: Sample 155
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: 53BP1 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient


title: MDA-MB-231 with AdipoRON treatment No3

description:
Library name: MDA-MB-231-A3
Takarabio


title: ExM-MOK20068P-C05, KO

description:
Library name: ELK3_PTC_C05_NEW_GT25-02684_GGTACCTT-GACGTCTT_S139_L007
KOLF2.2J derived knockout cell line,ELK3 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

value: Termination codon

value: day 6


title: ExM-MOK20063_68_91-WT1, WT

description:
Library name: WT_SNAI_ELK3_SOX7_1_GT25-02689_GTCGGAGC-TTATAACC_S140_L007
KOLF2.2J differentiated to the trophoblast lineage and favoring mesenchymal cell formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

value: fibroblast of villous mesenchyme (CL:0002558)


title: MDA-MB-231 with AdipoRON treatment No1

description:
Library name: MDA-MB-231-A1
Takarabio


title: JH1O_T1083del_53BP1_KO_JH1bait_2

description:
Library name: Sample 154
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: MDA-MB-231 with AdipoRON non-treatment No1

description:
Library name: MDA-MB-231-C1
Takarabio

value: DMSO treatment


title: ExM-MOK20063P-E12, KO

description:
Library name: SNA1_PTC_E12_NEW_GT25-02681_CGGCGTGA-ACAGGCGC_S135_L007
KOLF2.2J derived knockout cell line, SNAI2 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv


title: JH1O_T1083del_53BP1_HMGB1_DKO_JH1bait_1

description:
Library name: Sample 156
JH1 bait\, 53BP1 and HMGB1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line


title: T47D with AdipoRON non-treatment No2

description:
Library name: T47D-C2
Takarabio


title: PolII_Ser5_WT_rep_1

description: Library name: PolII_Ser5_WT_rep_1

data_processing:
Raw sequencing reads were quality-controlled and trimmed using Fastp
Sequence reads were aligned using bowtie2
Aligned reads were processed using SAMtools to generate BAM and index files
Peak calling was performed with MACS2 in narrowPeak mode using a q-value cutoff of < 0.05
MAnorm was used for comparison of ChIP peaks
For visualization, bamCoverage was used to generate BigWig files with counts per million normalization
ChIP tracks were visualized using the Integrative Genomics Viewer.
Heatmaps and aggregation plots were created using deepTools computeMatrix, followed by visualization with plotHeatmap and plotProfile.
De novo and known motif enrichment analyses were performed using HOMER
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Cells were cross-linked with 2 mM disuccinimidyl glutarate in PBS/1 mM MgCl2 for 40 min at room temperature followed by 1% formaldehyde in PBS for 15 min at room temperature. The reaction was stopped by 125 mM glycine. The cells were washed with PBS and stored at –80°C prior to use. The cells were lysed in Lysis buffer (10 mM Tris-HCl, pH8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroyl sarcosine) containing proteinase inhibitor cocktail (Roche). Sonication was conducted with the Handy sonicator UR-21P (Tomy) to generate DNA fragments of approximately 150-450 bp. The sonicated lysates from approximately 2 x 106 cells were diluted in ChIP dilution buffer (10 mM HEPES, pH 7.4, 50 mM NaCl, 1% IGEPAL-CA-630, 10% glycerol) containing proteinase inhibitor cocktail and incubated overnight at 4°C with 50 µl of protein G magnetic beads (Invitrogen) that were preincubated with ~2 µg of mouse Zscan4 antibodies. The precipitants were washed once with high salt wash buffer (20 mM Tris-HCl, pH8.0, 400 mM NaCl, 2 mM EDTA, 0.1% SDS, 0.2% Triton-X), three times with LiCl wash buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% NP40, 1% Na-deoxycholate) and once with 10 mM Tris-HCl, pH 8.0, 5 mM EDTA, 10 mM NaCl. Bound chromatin was eluted in elution buffer (90 mM NaHCO3, 1% SDS), followed by RNase treatment at 37°C for 30 min and crosslink reversal with decross-linking mixture (2 M NaCl, 0.1 M EDTA, 0.4 M Tris-HCl, pH 6.8) containing proteinase K at 65°C for 3 h. DNA was purified by a phenol-chloroform-isoamylalcohol extraction and ethanol precipitation.
ChIP DNA libraries were prepared with the NEBNext ChIP-Seq Library Prep Kit for Illumina (NEB)


title: JH1O_T1083del_53BP1_KO_JH1bait_1

description:
Library name: Sample 153
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: MDA-MB-231 with AdipoRON treatment No2

description:
Library name: MDA-MB-231-A2
Takarabio


title: ExM-MOK20063P-G11, KO

description:
Library name: SNA1_PTC_G11_NEW_GT25-02682_ATGTAAGT-CATAGAGT_S146_L007
KOLF2.2J derived knockout cell line, SNAI2 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv


title: ATAC-seq_hES_rep_2

description:
Library name: ATAC-seq_hES_rep_2
rep_1 and rep_2 were merged and visualized as a single bigWig file.


title: T47D with AdipoRON non-treatment No3

description:
Library name: T47D-C3
Takarabio


title: T47D with AdipoRON treatment No2

description:
Library name: T47D-A2
Takarabio


title: EM-seq with KAPAU, 100 pg input

city: Wuhan City

first: Zhiyuan

address: No. 115 East Lake Road (Donghu Road), Wuchang District

department: Medical Research Institute

institute: Wuhan University

description: Library name: KAPAU_PCR_100pg

data_processing:
Adapter and quality filtering were performed with Trim Galore (v0.6.10). Parameters were applied specifically for each sample group: Converted HeLa were trimmed with default parameters, while methylc and fish samples were trimmed with -paired --length 35 --clip_R1 10 --clip_R2 15 --three_prime_clip_R 10 --three_prime_clip_R2 10. Trimmed reads were aligned to the human reference genome (GRCh38) or the zebrafish reference genome (GRCz11.114) with spike-in sequences included. Converted DNA libraries were aligned using Bismark (v0.24.2) with default parameters. Zebrafish samples were aligned using Bismark (v0.24.2) with --maxins 1000. PCR duplicates were removed using deduplicated_bismark. Methylation information was extracted from deduplicated BAM files using bismark_methylation_extractor with default settings.
Assembly: GRCh38, GRCz11.114
Supplementary files format and content: Supplementary_files_format_and_content: CpG modification bismark report in the bedGraph format
Library strategy: EM-seq

source_name: HeLa cell

growth_protocol: HeLa cells were cultured in a humidified incubator at 37°C with 5% CO₂. The cells were maintained in the DMEM supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin. Cells were seeded at a density of approximately 50,000 cells/cm² in T25 flasks and passaged upon reaching 80-90% confluency. Zebrafish were raised and maintained under standard conditions.

extract_protocol:
HeLa cells were detached, collected, and pelleted by centrifugation at 300 × g for 5 min. Genomic DNA was subsequently extracted using the FastPure Blood/Cell/Tissue/Bacteria DNA Isolation Mini Kit (Vazyme) according to the manufacturer’s protocol. Genomic DNA was fragmented to an average size of ~300  bp using a Covaris M220 Focused-ultrasonicator. Embryos of zebrafish were collected at four developmental stages: 64-cell, 128-cell, 1k-cell, and Germ ring. Before DNA extraction, embryos were bleached with bleach solution (0.1 ml 5% NaClO in 170 ml system water) for 5 min and rinsed thoroughly with 1× PBS. Genomic DNA was isolated using the FastPure Blood/Cell/Tissue/Bacteria DNA Isolation Mini Kit (Vazyme), according to the manufacturer’s protocol. Genomic DNA from the embryos was fragmented to an average size of around 300 bp using the Bioruptor Pico sonication device (Diagenode). For the 128-cell, 1K-cell, and Germ-ring samples, an optimised sonication program was used, i.e., 15 s ON/30 s OFF, 4 cycles for the 50-μl sample volume. For the 64-cell-stage gDNA, 3 cycles of 15 s ON/30 s OFF were used instead.
End repair and A-tailing were performed for fragmented DNA using the VANTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) with EM-seq adapters (NEB) according to the manufacturer’s protocol. After adapter ligation, unmethylated cytosines in the DNA were enzymatically converted to uracil using the EpiArt DNA Enzymatic Methylation Kit (Vazyme), following the manufacturer’s protocol. For FINE-EM-seq libraries, FINE amplification was applied on converted DNA(including 1 ng, 100 pg, 1 pg HeLa gDNA and 1 ng of each stage's zebrafish gDNA), followed by a 3-cycle PCR to add full-length adapters for Illumina sequencing. For PCR methylation libraries, converted DNA was amplified using 2× Synthesis Mix (ABclonal) or HiFi V3 (Vazyme). PCR thermal cycling consisted of an initial denaturation at 98°C for 45 s; followed by 16 cycles (for 1 ng), 20 cycles (for 100 pg), or 23 cycles (for 10 pg) of 98°C for 15 s, 60°C for 30 s, and 72°C for 20 s; followed by a final extension at 72°C for 1 min and then hold at 12°C. The amplified DNA was purified twice using 0.8× VANTS DNA Clean Beads (Vazyme).

value: HeLa cell

tag: input amount


title: PolII_Ser5_DKO_rep_1

description: Library name: PolII_Ser5_DKO_rep_1


title: ExM-MOK20068P-A05, KO

description:
Library name: ELK3_PTC_A05_NEW_GT25-02683_GCACGGAC-TGCGAGAC_S144_L007
KOLF2.2J derived knockout cell line,ELK3 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv


title: JH1O_T1083del_HMGB1_KO_JH1bait_3

description:
Library name: Sample 152
JH1 bait\, HMGB1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: HMGB1 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient

value: T1083del retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: JH1O_T1083del_JH1bait_3

description:
Library name: Sample 149
JH1 bait\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: T47D with AdipoRON treatment No1

description:
Library name: T47D-A1
Takarabio


title: ExM-MOK20063P-D12, KO

description:
Library name: SNA1_PTC_D12_NEW_GT25-02680_TAATACAG-GTGAATAT_S138_L007
KOLF2.2J derived knockout cell line, SNAI2 PTC, differentiated to the trophoblast lineage and favoring mesenchymal cell formation
study12_featureCounts.csv
study12_genesCounts.csv
study12_genesRawCounts.csv
study12_genesTPM.csv
study12_stats.csv
study12_txCounts.csv
study12_txRawCounts.csv
study12_txTPM.csv

value: iPSC


title: EM-seq with KAPAU, 1 ng input

description: Library name: KAPAU_PCR_1ng


title: T47D with AdipoRON non-treatment No1

description:
Library name: T47D-C1
Takarabio


title: JH1O_T1083del_HMGB1_KO_JH1bait_2

description:
Library name: Sample 151
JH1 bait\, HMGB1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_T1083del_HMGB1_KO_JH1bait_1

description:
Library name: Sample 150
JH1 bait\, HMGB1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: EM-seq with KAPAU, 10 pg input

description: Library name: KAPAU_PCR_10pg


title: BRG1_DKO_rep_2

description:
Library name: BRG1_DKO_rep_2
Replicates were merged and visualized as a single bigWig file.

value: Embryonic cells

value: ES cells (SEES3)


title: CHD7_DKO_rep_1

description:
Library name: CHD7_DKO_rep_1
Replicates were merged and visualized as a single bigWig file.


title: T47D with AdipoRON treatment No3

description:
Library name: T47D-A3
Takarabio

value: WT


title: CHD7_DKO_rep_2

description:
Library name: CHD7_DKO_rep_2
Replicates were merged and visualized as a single bigWig file.


title: JH1O_T1083del_JH1bait_1

description:
Library name: Sample 147
JH1 bait\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_53BP1_HMGB1_DKO_JH1bait_3

description:
Library name: Sample 146
JH1 bait\, 53BP1 and HMGB1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: 53BP1 and HMGB1 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient

value: RAG2 retrovirally complemented\, 3 uM STI-571 treated for 4 days


title: CHD7_hES_rep_2

description:
Library name: CHD7_hES_rep_2
Replicates were merged and visualized as a single bigWig file.

value: Pluripotent stem cells


title: BRG1_DKO_rep_1

description:
Library name: BRG1_DKO_rep_1
Replicates were merged and visualized as a single bigWig file.


title: JH1O_T1083del_JH1bait_2

description:
Library name: Sample 148
JH1 bait\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: JH1O_53BP1_HMGB1_DKO_JH1bait_2

description:
Library name: Sample 145
JH1 bait\, 53BP1 and HMGB1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: CHD7_hES_rep_1

description:
Library name: CHD7_hES_rep_1
Replicates were merged and visualized as a single bigWig file.


title: WT_Input

first: Di

last: Zhao

state: Tx

address: Zayed Building Z7. 4018

institute: MD Anderson Cancer Center

description: Library name: WT_Input

data_processing:
Adapter sequences were removed from the 3' ends of reads using Trim Galore (version 0.6.7) and cutadapt (version 4.1).
The reads were then mapped to the human genome (hg38) using Bowtie (version 1.1.2) with the following parameters: ""--allow-contain --maxins 2000 -v 2 -m 1 --best --strata".
To avoid PCR bias, only one copy of multiple fragments mapped to the same genomic position was retained for further analysis. Fragments longer than 500 bp (less than 1% of the total) were excluded from subsequent analysis.
For bigWig files, each fragment was resized to a length of 151 bp, spanning from -75 bp to +75 bp around its midpoint. The count of fragments covering each genomic position was normalized to 10M total number of fragments. These values were then averaged over a 10 bp resolution.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Prostate

growth_protocol: RPMI 1640 medium containing 10% (v/v) fetal bovine serum (FBS) and 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature. Cross-linking was quenched by glycine, followed by cell lysis. Chromatin was fragmented by sonication using ultrasonicator to obtain DNA fragments of appropriate size for downstream applications.
KAPA Hyper Prep Kit

value: Prostate

value: LNCaP

value: Human prostate cancer


title: MCF7 with AdipoRON non-treatment No2

description:
Library name: MCF7-C2
Takarabio

value: breast cancer cell line


title: FINE-EM-seq, 100 pg input, biol rep 2

description: Library name: 2xsyn_FINE-2_100pg


title: FINE-EM-seq, 10 pg input, biol rep 2

description: Library name: 2xsyn_FINE-2_10pg


title: FINE-EM-seq, 1 ng input, biol rep 2

description: Library name: 2xsyn_FINE-2_1ng


title: MCF7 with AdipoRON treatment No3

description:
Library name: MCF7-A3
Takarabio

value: AdipoRON treatment


title: BRG1_hES_rep_2

description:
Library name: BRG1_hES_rep_2
Replicates were merged and visualized as a single bigWig file.


title: JH1O_53BP1_KO_JH1bait_14

description:
Library name: Sample 143
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient

value: v-Abl transformed pro-B cell line

value: 53BP1 knockout\, JH2-4-/-, Emu-Bcl2\, RAG2 deficient


title: BRG1_hES_rep_1

description:
Library name: BRG1_hES_rep_1
Replicates were merged and visualized as a single bigWig file.


title: MCF7 with AdipoRON non-treatment No1

description:
Library name: MCF7-C1
Takarabio

value: DMSO treatment


title: JH1O_53BP1_HMGB1_DKO_JH1bait_1

description:
Library name: Sample 144
JH1 bait\, 53BP1 and HMGB1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient


title: MCF7 with AdipoRON treatment No2

description:
Library name: MCF7-A2
Takarabio


title: MCF7 with AdipoRON non-treatment No3

description:
Library name: MCF7-C3
Takarabio


title: WT_CHD1_CHIP_2

description: Library name: WT_CHD1_CHIP_2

value: CHD1 (4351S, Cell Signaling Technology)


title: JH1O_53BP1_KO_JH1bait_13

description:
Library name: Sample 142
JH1 bait\, 53BP1 knockout\, JH2-4-/-\, Emu-Bcl2\, RAG2 deficient