title: D7 ES RNA-seq, rep1

description: Library name: d7 RNA-seq R1

data_processing:
!Sample_data_processing = RNA-seq: RNA-seq reads were processed for adaptor sequence trimming and PCR duplicate removal using Trim Galore (v0.4.1; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with a stringency of 12 allowed error rate 0.2. Prior to genome alignment, a preliminary alignment step was conducted using STAR aligner80 (v2.7.3) to remove reads aligning to rDNA sequences. The unmapped reads from this rDNA alignment were then aligned to the mouse genome (GRCm38/mm10) using STAR with the parameters ?--outSAMprimaryFlag AllBestScore --outMultimapperOrder Random --outSAMtype BAM Unsorted --outFilterMultimapNmax 200 --outFilterMismatchNoverLmax 0.3 --seedSearchStartLmax 50 --outSAMattributes NH HI NM MD --outSAMunmapped Within --outReadsUnmapped Fastx.? All unmapped reads were subsequently filtered out. Allele parsing was performed using SNPsplit (https://www.bioinformatics.babraham.ac.uk/projects/SNPsplit) with SNP VCF file (mgp.v5.merged.snps_all.dbSNP142.vcf.gz) obtained from ftp://ftp-mouse.sanger.ac.uk/current_snps/. Reads aligned to either cas (CAST/EiJ) or mus (129S1/SvImJ) alleles were distinguished based on known SNP positions. To prepare RNA-seq data for generating signal summaries over genes, we utilized the HOMER (v4.10)76 toolkit with the parameters ?makeTagDirectory -removeSpikes 10000 8 -sspe -flip?. To obtain the counts of reads mapped to exons, we employed the Homer script ?analyzeRepeats.pl? with the parameters ?rna mm10 -count genes -dfile OrderSet1 -noadj -norm 0 -condenseGenes -strand +?. Gene expression counts from HOMER-processed BAM files were imported into R and organized into a DGEList object using the edgeR package. Genes were filtered using the filterByExpr function with default parameters, retaining 15,333 out of 24,940 genes based on sufficient raw count expression across samples, as determined by the experimental groups (d0, d4, d7, each with two replicates). Library sizes were recalculated from filtered counts, and normalization was performed using the Trimmed Mean of M-values (TMM) method (calcNormFactors, method="TMM") to adjust for differences in library composition, yielding a normalized DGEList object. Dispersions were estimated in three sequential steps: common dispersion (estimateCommonDisp), trended dispersion (estimateGLMTrendedDisp), and tagwise dispersion (estimateTagwiseDisp), capturing gene-specific variability and generating pseudo-counts that reflect normalized expression adjusted for dispersion.  A design matrix was constructed without an intercept to model the three conditions (d0, d4, d7), each with two replicates.To further account for potential batch effects and unmodeled sources of variation, surrogate variable analysis (SVA) was applied using the sva package. The normalized counts were used as input, with the design matrix defined by the experimental group labels. Surrogate variables estimated by SVA were appended to the design matrix and incorporated into the linear modeling framework. Precision weights were calculated using the voom function from the limma package, and the resulting expression matrix was further adjusted using removeBatchEffect to regress out the surrogate variables while preserving the primary group structure. For downstream analysis and visualization, these values were transformed to transcripts per million (TPM). We selected 372 X-linked genes based on exonic allelic read counts with a minimum of 45 (sum of Castaneus and Musculus reads > 45) in at least one of the libraries across all libraries. Allelic ratios were calculated by computing the Xi proportion [mus/(mus+cas)] of read counts between mus and cas alleles for each replicate at each time point.
Assembly: mm10
Supplementary files format and content: Allelic read counts, allelic proportions, and gene expression levels in TPM (xlsx)

growth_protocol: Undifferentiated female mouse embryonic stem cells were grown on the irradiated MEF feeders in regular DMEM medium (high-glucose) with 15% FBS and LIF. For differentiation, cells were trypsinizied and incubated in the medium at 37 °C for at least 40 min. After separation of ES cells from attached feeders, ES cells were re-plated on non-gelatinized petri dishes in the complete DMEM medium without LIF. Embryoid bodies (EB) formed from ES cells were transferred to the gelatinized cell culture plates on day 4 of differentiation. Cells were harvested on indicated days.

extract_protocol:
Total RNA was extracted using TRIzol, depleted of ribosomal RNA and then treated with DNase. The rRNA-depleted RNA was selected by size greater than 200nt, fragmented to a mediam size of about 200nt and then subjected to RT reaction. The subsequent first-strand cDNA was subjected to second strand cDNA synthesis using NEBNext Ultra Directional RNA Second Strand Synthesis Module (NEB, #E7550S).
After second strand cDNA synthesis, the resulting double-stranded DNA was subjected to library construction using  NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S) for Illumina.

value: WT


title: D7 ES RNA-seq, rep2

status: Public on Jun 11 2025

type: SRA

city: Boston

first: Hyun Jung

last: Oh

state: MA

address: 185 Cambridge St.

country: USA

institute: MGH

description: Library name: d7 RNA-seq R2

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: cell type

value: Differentiating mESC (day 7)

tag: genotype


title: RNA-seq in primary mouse cortical neurons after control GapmeRs uptake, replicate 1

status: Public on Jun 12 2025

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

data_processing:
RNA-seq: RNA-seq reads were mapped to the mouse genome (mm10 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. RSEM (Li and Dewey, 2011) or STAR -quant with RefSeq annotations were used to call differential expression between samples
CUT&RUN: CUT&RUN reads were mapped to the mouse genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008) or epic2 (Stovner and Sætrom, 2019). HOMER (Heinz et al., 2011) was used to call differential expression between samples.
Assembly: mm10
Supplementary files format and content: bigWig read coverage files are provided for all samples. RSEM/STAR quantification is provided for the RNA-seq samples, and MACS2/epic2-called peaks are provided for the CUT&RUN data.

molecule: polyA RNA

growth_protocol:
Neuro2a (N2a) cells were cultured in DMEM supplemented with 4.5 g/L of glucose, 4 mM L-Glutamine, 10% FBS, 1% PenStrep solution, grown in incubators maintained at 37°C with 5% CO2, and were routinely passaged by gentle dissociation using a Trypsin (0.05%) – EDTA (0.02%) solution. DNA plasmid transfections were performed by using Lipofectamine 3000 (ThermoFisher Scientific), according to the respective protocols. For each transfection, the optimal DNA concentration and amount of transfection reagents were empirically determined to minimize cellular stress and maximize efficiency, to eventually ensure clean readouts. SiRNAs were transfected using DharmaFECT reagents (DharmaFECT 2), at a final concentration of 25 µM concordantly to the manufacturer’s protocol. GapmeRs were transfected at the final concentration of 50 µM with Lipofectamine 3000, following the manufacturer’s guidelines. In all cases, cells were plated the day before the transfection in an antibiotic-free medium which was subsequently changed prior to adding the transfection mix, and again after 24h to minimize cell death. Finally, transfections were carried out for 72h, unless stated otherwise.
Primary neuronal culture Embryonic cortices (embryonic day 16.5–17) were dissected from 5–6 embryos of mixed sex and pooled for a single replicate culture. Trypsin (0.25%) was used to dissociate tissue through a 10 minutes incubation at 37°C. Digestion was terminated with the addition of ovomucoid (trypsin inhibitor, Worthington). Digested tissue was gently triturated through a P1000 pipette to release cells and passed through a 40 µm filter. After trituration, the cell suspension was transferred to a 15 mL Falcon tube and centrifuged for 5 minutes at RT / 154×g. After centrifugation, the cloudy supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 10 mL DMEM medium and added to uncoated 90 mm Petri dishes. The plates were incubated at 37°C, 5% CO2 humidified incubator for 30 minutes. During this incubation, glial cells and other unwanted debris adhere to the bottom of the plate while cortical cells are retained in the media and recover from the trituration. The supernatant was carefully removed, without disturbing attached glial cells and unwanted cell debris at the bottom of the plate, and moved into a new 15 mL Falcon tube using a pipette. The collected supernatant was then centrifuged for 5 minutes at RT / 154×g. Neurons were plated onto cell culture dishes pre-coated overnight with poly-d-lysine (20 µg/mL) and laminin (4 µg/mL) and were grown in neurobasal medium (Gibco) containing B27 supplement (2%), 1% PenStrep solution and glutaMAX (1 mM). Neurons were grown in incubators maintained at 37°C with a CO2 concentration of 5%. GapmeRs for unassisted uptake were added directly to the culture medium at a final concentration of 500 nM.

extract_protocol:
CUT&RUN reactions were performed as previously described (Meers et al., 2019), with the addition of 20mM sodium butyrate when profiling BAHCC1, SIN3A and H3K27ac
RNA-seq libraries were prepared using the CORALL mRNA-Seq Kit V2 (Lexogen), following the manufacturer’s instructions. CUT&RUN libraries were prepared as described previously (Meers et al., 2019)

treatment_protocol: Sodium Butyrate (Sigma) was diluted in sterile H2O at a stock concentration of 1M and added to the cell culture media at a final concentration of 5µM. As a control, cells were supplemented with an equal volume of H2O. All treatments were performed for 24h in order to minimize indirect effects due to the extensive inhibition of deacetylation. Retinoic Acid (Sigma) was diluted in DMSO at a stock concentration of 0.01M, and added to a complete media with reduced (1%) serum concentration at a final concentration of 10µM, with equal volumes of DMSO serving as vehicle controls. After three days of treatment, cells were transfected with GapmeRs as previously described, and incubated for three additional days in the retinoic acid medium.

tag: tissue

value: Primary Mouse Cortical Neurons

tag: treatment

value: untreated


title: D7 ES Control Hi-C^2, rep1

description: Processed data: d7.comp.matrix.txt, d7.control.cas.combined.matrix.txt, d7.control.mus.combined.matrix.txt

library_source: genomic

data_processing:
Hi-C^2 reads were trimmed using cutadapt (v1.2.1) with the options --adapter=GATCGATC (MboI ligation junction) and --minimum-length=20. Reads of each pair were individually mapped to the mus and cas genomes using Novoalign (v3.00.02) and merged into Hi-C summary files and filtered using HOMER(v4.8) as previously described (Minajigi et al. Science 2015). To avoid computational complexities arising from normalization of sparse or non-enriched regions in the Hi-C contact map, we considered only Hi-C interactions falling within the capture region for further analysis. For each capture, the filtered Hi-C interactions falling within the target region (chrX:100,153,712-101,269,503) were pulled out from HOMER tag directories. Hi-C2 data of the capture regions in hic format were generated using the command  “pre” of Juicer tools (v1.5.3) and then converted into the matrices with “square root vanilla coverage” normalization using the command “dump” of Juicer tools and a custom script. The average interaction values of each library were obtained from the Juicebox tool (v1.9.8) and then used to normalize the interaction values among different libraries. The resulting Hi-C2 matrix values were used to generate the heatmaps. To generate allelic Hi-C^2 contact matrices for control and Jpx KD cells, allele-specific reads were combined from two biological replicates and converted into HOMER tag directories.
Assembly: mm9
Supplementary files format and content: Hi-C^2 probes (Xic_capture_probes.bed). Normalized Hi-C^2 contact matrices (*.txt).

molecule: genomic DNA

source_name: Day 7 ES cells

growth_protocol: Undifferentiated female mouse embryonic stem cells were grown on the irradiated MEF feeders in regular DMEM medium (high-glucose) with 15% FBS and LIF. For differentiation, cells were trypsinizied and incubated in the medium at 37 °C for at least 40 min. After separation of ES cells from attached feeders, ES cells were re-plated on non-gelatinized petri dishes in the complete DMEM medium without LIF. Embryonic bodies (EB) formed from ES cells were transferred to the gelatinized cell culture plates on day 4 of differentiation. Cells were harvested on indicated days.

extract_protocol: Hi-C libraries were generated essentially based on the in-situ Hi-C protocol (Rao et al. Cell 2014; Oh et al. Cell 2021).  MboI (200U) was used for digestion of nuclei collected from 3 million cells.  The subsequent Hi-C^2 experiment was performed as descried previously (Sanborn et al.PNAS 2015). Briefly, 120 bp probes were designed around the MboI restriction sites in the region of interest: chrX:100,153,712-101,269,503 (mm9). Single stranded DNA oligos were amplified and biotinylated in a MAXIScript T7 transcription reaction (Ambion). The resulting biotinylated RNA probes were hybridized to 500 ng of in situ Hi-C libraries for 24 hours at 65°C. DNA hybridized to the RNA probes was pulled down by streptavidin beads, washed, and eluted as described (Sanborn et al. PNAS 2015). The resulting DNA was desalted with a cleanup using 1X AMPure beads and amplified with Illumina primers for 12 cycles of PCR to prepare for sequencing (paired-end 50bp).

treatment_protocol: LNA transfection: D7 ES cells were trypsinized, transfected with scrambled LNA or Jpx LNA using Mouse ES cell Nucleofector Kit (Lonza), transferred to the gelatinized plates and harvested after incubation at 37°C for 8 hr.

tag: strain

value: CAST/EiJ x 129S1

tag: transfection

value: Scramble LNA-transfected

tag: library strategy


title: D0 ES Hi-C^2

description: Processed data: d0.comp.matrix.txt

source_name: Day 0 ES cells

value: Undifferentiated mESC (day 0)

value: Untransfected


title: D7 ES Control Hi-C^2, rep2

description: Processed data: d7.control.cas.combined.matrix.txt, d7.control.mus.combined.matrix.txt


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 65

type: genomic

city: toulouse ou paris si j'ai une salle

first: Emmanuelle

last: URO-COSTE

state: occitanie

address: 1 avenue Irène Joliot Curie, IUC-T oncopole

country: France

institute: CHU de Toulouse

description: PA

hyb_protocol: bissulfite converted DNA was restored, amplified, fragmented and hybridized to human methylationEPIC beadchip v1 850 000 CpG (illumina) using standard illumina FFPE protocol

scan_protocol: array were imaged using bead array HiScan and standard remmanded illumina scanner setting

data_processing:
QC, functional normalization, feature selection (pval > 0.01, sexual chromosome, SNP) with minfi package (v1.50.0) in R (v4.4.3)
Beta values

label: Cy3 and Cy5

organism: Homo sapiens

source_name: tumor

label_protocol: standard illumina protocol FFPE

extract_protocol: DNA was isolated using the Maxwell 16 FFPE Plus LEV DNA Purification Kit (Promega)

tag: Sex

value: Female

tag: diagnosis

value: Pleomorphic adenoma

tag: localisation

value: salivary gland; Parotid

value: No mutation

value: NR


title: Tumor DNA from peri-mandibular pleomorphic adenoma FFPE patient 66

description: PA

label: Cy3 and Cy6

value: salivary gland; Peri-mandibular


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 62

description: PA


title: D4 ES Hi-C^2

description: Processed data: d4.comp.matrix.txt

source_name: Day 4 ES cells

value: Differentiating mESC (day 4)


title: Tumor DNA from pleomorphic adenoma FFPE patient 63

description: PA

value: salivary gland; Unknown


title: 3T3, GFP-dHP1, induced

city: Toulouse

first: Fabian

last: Erdel

address: 169 Avenue Grunberg-Manago

department: MCD

institute: CNRS, CBI Toulouse

data_processing:
After sequencing, the raw reads were filtered. Data filtering includes removing adapter sequences, contamination and low-quality reads from raw reads.
Reads were mapped to the mouse genome (GRCm39) using STAR
Count tables (considering genes and repetitive elements) were generated with TEtranscripts
Differential expression analysis was carried out using DESeq2
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file, containing counts for each gene or repetitive element

growth_protocol: 3T3 cells were cultured in DMEM supplemented with 10% fetal bovine serum, 1% Penicillin/Streptomycin and 1×GlutaMAX at 37°C in a humidified atmosphere with 5% CO2

extract_protocol:
Total RNA was purified using the MasterPure Complete DNA and RNA Purification Kit (Biosearch Technologies).
Libraries were prepared by BGI (rRNA Depletion stranded Library)

treatment_protocol: Expression of GFP-tagged HP1 variants was induced by addition of 500 ng/ml doxycycline

value: fibroblast

value: with dox


title: Tumor DNA from peri-mandibular pleomorphic adenoma FFPE patient 61

description: PA

value: Male


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 57

description: PA

value: No mutation; PLAG1 Fusion


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 59

description: PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 58

description: PA


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 50

description: epithelial/myoepithelial carcinoma ex PA

value: Carcinoma Ex PA

value: HRAS; PI3KCA


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 54

description: myoepithelial carcinoma ex PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 55

description: PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 51

description: PA

value: PLAG1 Fusion


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 47

description: salivary duct carcinoma ex PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 53

description: PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 52

description: PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 45

description: PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 49

description: PA


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 44

description: Carcinoma NOS ex PA


title: Tumor DNA from para-pharyngeal pleomorphic adenoma FFPE patient 48

description: PA

value: salivary gland; Para-pharyngeal


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 42

description: PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 46

description: PA


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 39

description: myoepithelial carcinoma ex PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 64

description: PA

value: VUS


title: Tumor DNA from cervical tumor pleomorphic adenoma FFPE  patient 40

description: PA

value: Female

value: salivary gland; Cervical


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 38

description: salivary duct carcinoma ex PA

value: salivary gland; Parotid


title: Tumor DNA from tumor pleomorphic adenoma FFPE  patient 41

description: PA

value: Pleomorphic adenoma


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 35

description: myoepithelial carcinoma ex PA

value: NR


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 34

description: PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 37

description: PA

value: No mutation


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 36

description: PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 60

description: PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 32

description: PA


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 33

description: myoepithelial carcinoma ex PA


title: Tumor DNA from para-pharyngeal tumor carcinoma FFPE  patient 31

description: Carcinoma NOS ex PA

value: PTEN p.L182V


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 29


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 56

description: PA


title: Tumor DNA from sub-maxillary tumor carcinoma FFPE  patient 28

description: salivary duct carcinoma ex PA

value: salivary gland; Sub-maxillary


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 30

description: PA


title: Tumor DNA from pleomorphic adenoma FFPE patient 27

description: PA

value: salivary gland; Unknown


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 25

description: salivary duct carcinoma ex PA


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 24

value: HRAS p.Q61L; PLAG1 Fusion


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 43

description: PA

value: Male


title: Tumor DNA from pleomorphic adenoma FFPE patient 26

description: PA


title: Tumor DNA from parotid pleomorphic adenoma FFPE patient 22

description: PA


title: Tumor DNA from Sub-mandibular pleomorphic adenoma FFPE patient 21

description: PA

value: salivary gland; Sub-mandibular

value: No mutation; PLAG1 Fusion


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 19

description: Carcinoma NOS ex PA

value: Carcinoma Ex PA


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 17

value: HRAS p.G13R


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 23

value: HRAS p.Q61K


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 18

value: VUS


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 14

description: salivary duct carcinoma ex PA


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 15

description: salivary duct carcinoma ex PA


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 11

description: salivary duct carcinoma ex PA

value: TP53 p.C141Y; PLAG1 Fusion


title: Tumor DNA from Cervical tumor carcinoma FFPE  patient 16

value: Female

value: salivary gland; Cervical

value: HRAS p.Q61R, PIK3CA p.C420R, PIK3CA p.H1047R


title: Tumor DNA from Sub-mandibular tumor carcinoma FFPE  patient 12

description: myoepithelial carcinoma ex PA

value: NR


title: Tumor DNA from Sub-maxillary tumor carcinoma FFPE  patient 10

description: adenoid cystic carcinoma ex PA

value: MYB Fusion


title: Tumor DNA from Sub-maxillary tumor carcinoma FFPE  patient 13

description: salivary duct carcinoma ex PA

value: TP53 p.G244D; NCOA2 Fusion


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 9

value: salivary gland; Parotid

value: CTNNB1 p.I35T


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 8

description: myoepithelial carcinoma ex PA

value: No mutation


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 4

value: Male


title: Tumor DNA from Sub-maxillary tumor carcinoma FFPE  patient 6

value: salivary gland; Sub-maxillary


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 5


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 2

description: Carcinoma NOS ex PA


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 1

description: myoepithelial carcinoma ex PA


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 7

value: TP53 p.V73Gfs*50; PLAG1 Fusion


title: Tumor DNA from parotid tumor carcinoma FFPE  patient 3

description: myoepithelial carcinoma ex PA

value: Carcinoma Ex PA

value: TERT promoter region, PTEN p.T277Sfs*13


title: Tumor DNA from sub-maxillary pleomorphic adenoma FFPE patient 20

description: PA

value: Pleomorphic adenoma


title: Bulk CUT&TAG of IgG control in H1, rep3

city: Hong Kong

first: Jingchun

last: Ma

state: Hong Kong

address: Sassoon Rd 21, Laboratory Block L3-53

department: School of Biomedical Sciences, LSK Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

description: Library name: CUTTag-H1-IgG-Rep3

data_processing:
mammary gland scRNA-seq: Raw sequencing data were processed using Cell Ranger (v6.0, 10x Genomics) with default parameters. Reads were aligned to the mm10 mouse genome. Filtered UMI count matrices were used for downstream analysis in Seurat (v4). Cells with >10% mitochondrial transcripts or fewer than 500 detected genes were excluded. Gene expression matrices were normalized using SCTransform, followed by dimensionality reduction and clustering. Marker genes were identified using the Wilcoxon rank-sum test implemented in Seurat.
IT-scC&T-seq libraries: Reads were trimmed with Cutadapt v4.5 to remove adapters and extract H5XX, H7XX, Q5XX, and Q7XX barcodes, which were concatenated and added to read headers. Reads were aligned to mm10, hg38, or hg38+mm10 using Bowtie2 v2.5.3 with sensitive settings. BAM files were sorted and demultiplexed by cell barcode using SAMtools v1.17, and duplicates were removed with Picard v3.1.0. Fragment file was generated by Sinto 0.1 and was imported into ArchR 1.0.3 (R 4.3.1) for downstream analysis. MACS2
Assembly: mouse mm10, human hg38
Supplementary files format and content: bw, bigWig file showing genome-wide H3K4me3 signal aggregated from mouse (mm10) or human (hg38) cells using IT-scCUT&Tag.
Supplementary files format and content: bed, BED file of deduplicated and sorted CUT&Tag fragments from replicate 1-2 of multiplexed single-cell experiment generated via sinto from BAM.
Supplementary files format and content: bw, bigWig file showing RPKM-normalized H3K4me3/H3K27me3/CTCF/RNA-PolII CUT&Tag signal aggregated from K562 single cell libraries.
Supplementary files format and content: broadPeak, broadPeak file with H3K4me3 or H3K27me3-enriched regions in K562 cells identified from aggregated CUT&Tag signal.
Supplementary files format and content: narrowPeak, narrowPeak file showing CTCF or RNA-PolII-enriched regions in K562 cells from CUT&Tag profiling.
Supplementary files format and content: bed, BED file showing LADs (lamina-associated domains) identified by epic2 (`--keep-duplicates`, `--bin 8000`, `-g 6`) from LMNB1 CUT&Tag in H1 cells (replicate 1-3) with IgG controls, sorted and filtered black-list regions.
Supplementary files format and content: h5, 10X Genomics filtered feature-barcode matrix in HDF5 format from scRNA-seq of mouse mammary gland.
Library strategy: CUT&Tag

source_name: cell line

extract_protocol:
Mammary gland tissues were isolated from 10-week-old female C57BL/6J mice. Tissues were enzymatically digested overnight in complete EpiCult-B medium supplemented with 5% FBS and 10× collagenase/hyaluronidase. After red blood cell lysis using NH₄Cl, tissue fragments were further dissociated sequentially with 0.25% trypsin, Dispase (5 mg/ml), and DNase I (1 mg/ml), then filtered through a 40-μm strainer to obtain a single-cell suspension. Cells were washed in HBSS with 2% FBS and then in DPBS. For IT-scC&T-seq, cells were fixed in 0.1% formaldehyde, quenched with glycine, and stored in DPBS with 0.5% BSA prior to single-cell CUT&Tag profiling. For scRNA-seq, unfixed cells were resuspended in PBS with 0.04% BSA.
IT-scC&T-seq: For each sample, native or 0.1%–0.2% formaldehyde crosslinked cells (see Table S2 for detailed conditions) were lysed in antibody buffer to isolate nuclei. Nuclei were incubated overnight with primary antibodies, followed by secondary antibody incubation and washes in Dig-300 buffer. Indexed pA-Tn5 complexes were added to nuclei in Dig-300 buffer (0.02 μM final) and incubated at room temperature for 1 h. Tagmentation was performed in Mg²⁺-containing buffer at 37 °C for 1 h, followed by quenching and single-nucleus FACS sorting into 384-well plates. After lysis and SDS quenching, indexed primers (H5XX, H7XX) and PCR master mix were dispensed using an acoustic liquid handler. First-round PCR was performed with 15–17 cycles. Products were pooled, purified, Exo I–treated, and bead-cleaned. A second PCR added Truseq P5/P7 adapters, followed by double-sided size selection. Libraries were QC-checked and sequenced by ANOROAD GENOME. scRNA-seq: libraries were constructed using the 10x Genomics Chromium Single Cell 3′ v3.1 platform according to the manufacturer’s protocol.

value: cell line

tag: chip antibody

value: IgG

value: WT

value: No


title: Bulk CUT&TAG of IgG control in H1, rep1

description: Library name: CUTTag-H1-IgG-Rep1


title: IT-scC&T-seq of LMNB1 in a mix of H1, K562, HEK293T and MSCs

description: Library name: 4cell-LMNB1

value: H1, HEK293T, MSCs, K562


title: Bulk CUT&TAG of LMNB1 in H1, rep2

description: Library name: CUTTag-H1-LMNB1-Rep2


title: IT-scC&T-seq of H3K4me3 in K562

description: Library name: K562-K4me3


title: Young exercise-trained male Fischer-344; biol rep 1

city: Tallahassee

first: Cynthia

last: Vied

state: Florida

address: 1115 W. Call St

department: Translational Science Laboratory

institute: Florida State University

description:
Library name: YE_1
Column name in processed file: YE_1

data_processing:
Quality control analysis of each sequenced library was performed using fastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter trimming was performed with Trimmomatic using the TruSeq3-SE.fa adapter sequence file provided alongside the program. A minimum length of 50 bases was chosen as the cutoff. The trimmed sequencing reads were aligned and mapped to the rat genome (genome release RGSC Rnor_6.0: GCA_000001895.4) using Tophat 2.1.1. Six mismatches were allowed due to the variation between the reference genome – based on the inbred brown Norway rat – and inbred rats in the current study. Reads were then filtered with Samtools and only unique reads that mapped to a single gene were incorporated in further analyses. These unique reads were used to generate counts for each gene using HTSeq. The DESeq2 package in R was used to determine statistically significant differentially expressed genes (DEGs) (Love et al., 2014).
Assembly: RGSC Rnor_6.0: GCA_000001895.4
Supplementary files format and content: tab delimited text file (.txt) with raw counts

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
Two days following the final behavioral tests, rats (n = 4 per group) were euthanized, and brains were immediately removed for isolation of hippocampal tissue. Total cellular RNA from the bulk hippocampal tissue was extracted using the Trizol method (Life Technologies).
RNA-seq samples were prepared from messenger RNA isolated with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, catalog no. E7490S) and libraries were generated using the NEBNext Ultra RNA library kit for Illumina sequencers (New England Biolabs, catalog no. E7530S). Five libraries were created for each condition, and 12 pM of each multiplexed library (10 per flow cell lane) were sequenced on an Illumina HiSeq 2500.

treatment_protocol: Young (6-mo old; n = 20) and old (20-mo old; n = 20) male Fischer-344 rats were obtained from the National Institute on Aging colony. Rats were housed under a 12:12-hour light:dark cycle and given food and water ad libitum. After acclimation, rats were randomized to either a control sedentary group (SED; young, n = 10; old, n = 10) or an exercise trained group (ET; young, n = 10; old, n = 10) that was trained using the same protocol as described in Protocol 1. This resulted in the same 4 group conditions described in protocol 1, i.e., young SED, young ET, old SED and old ET. Efficacy of the training was determined with soleus citrate synthase activity (Srere, 1969). Behavioral tests and isolation of hippocampal tissue for RNA sequencing (RNA-Seq) were performed after the sedentary or exercise training 10-week periods.

value: hippocampus

value: male

tag: age

value: 6 months

value: exercise training


title: Old exercise-trained male Fischer-344; biol rep 4

description:
Library name: OE_4
Column name in processed file: OE_4

value: 20 months


title: Old exercise-trained male Fischer-344; biol rep 1

description:
Library name: OE_1
Column name in processed file: OE_1


title: Young sedentary male Fischer-344; biol rep 1

description:
Library name: YS_1
Column name in processed file: YS_1

value: sedentary


title: Young exercise-trained male Fischer-344; biol rep 4

description:
Library name: YE_4
Column name in processed file: YE_4


title: Young sedentary male Fischer-344; biol rep 2

description:
Library name: YS_2
Column name in processed file: YS_2


title: Young sedentary male Fischer-344; biol rep 3

description:
Library name: YS_3
Column name in processed file: YS_3


title: Young exercise-trained male Fischer-344; biol rep 2

description:
Library name: YE_2
Column name in processed file: YE_2


title: Bulk CUT&TAG of IgG control in H1, rep2

description: Library name: CUTTag-H1-IgG-Rep2


title: Young exercise-trained male Fischer-344; biol rep 3

description:
Library name: YE_3
Column name in processed file: YE_3


title: Old sedentary male Fischer-344; biol rep 3

description:
Library name: OS_3
Column name in processed file: OS_3


title: Old exercise-trained male Fischer-344; biol rep 2

description:
Library name: OE_2
Column name in processed file: OE_2


title: Old exercise-trained male Fischer-344; biol rep 3

description:
Library name: OE_3
Column name in processed file: OE_3


title: Bulk CUT&TAG of LMNB1 in H1, rep1

description: Library name: CUTTag-H1-LMNB1-Rep1


title: Young sedentary male Fischer-344; biol rep 4

description:
Library name: YS_4
Column name in processed file: YS_4


title: Old sedentary male Fischer-344; biol rep 1

description:
Library name: OS_1
Column name in processed file: OS_1


title: Old sedentary male Fischer-344; biol rep 2

description:
Library name: OS_2
Column name in processed file: OS_2


title: IT-scC&T-seq of H3K27me3 in K562

description: Library name: K562-K27me3


title: IT-scC&T-seq of RNA-PolII in K562

description: Library name: K562-RNAPolII

value: RNA-PolII


title: Bulk CUT&TAG of LMNB1 in H1, rep3

description: Library name: CUTTag-H1-LMNB1-Rep3


title: IT-scC&T-seq of multiple histone marks in multiple cell lines, rep1

description: Library name: MHT-Rep1

value: H1, HEK293T, MSCs

value: H3K4me3, H3K27me3, H3K36me3, CTCF


title: IT-scC&T-seq of CTCF in K562

description: Library name: K562-CTCF

value: CTCF


title: Old sedentary male Fischer-344; biol rep 4

description:
Library name: OS_4
Column name in processed file: OS_4


title: Soma_OPTN RGCs_4

city: Portland

first: Chi

last: Zhang

state: Oregon

address: 3303 S.W. Bond Avenue

department: Biomedical Engineering

institute: Oregon Health & Science University

description: Library name: Sample 16

data_processing:
Data is mapping to genome GRCH38 using STAR software
Assembly: GRCH38
Supplementary files format and content: txt; counts

source_name: OPTN RGC soma

extract_protocol:
At 4 weeks after plating, RNA was collected from soma and axon compartments of microfluidic devices using the PicoPureTM RNA Isolation Kit (KIT0204, Applied Biosystems), following manufacturer’s instructions. Due to the low RNA concentration obtained from the axon compartment, samples were then pre-amplified using the SuperScript™ IV Single Cell/Low Input cDNA PreAmp Kit (Invitrogen, 11752048), following manufacturer’s instructions. After pre-amplification, cDNA samples were purified using the Agencourt AMPure XP beads (Beckman Coulter, A63880) and the DynaMag-2 Magnet (Invitrogen, 12321D). The cDNA products were next checked on Agilent Bioanalyzer.
The Nextera XT DNA Library Preparation Kit (Illumina) was used for subsequent library preparation. The resulting libraries were quantified, and quality accessed by Qubit and Agilent TapeStation. The libraries were pooled in equal molarity and sequenced with 2×150bp paired-end configuration on an Illumina NovaSeq 6000 sequencer.

value: OPTN RGC soma

value: hPSC-derived Retinal Ganglion Cells


title: IT-scC&T-seq of multiple histone marks in multiple cell lines, rep2

description: Library name: MHT-Rep2

value: cell line


title: S3

city: 广州

first: li

last: xiaobai

address: 381 Wushan Road, Tianhe District, Guangzhou

country: China

institute: south china university of technology

description: Library name: S3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 3 or fold change <0.5.
Assembly: GRCh38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: CAF

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: CAF

value: Human pancreatic cancer-associated fibroblasts

value: circKLHL24 knockdown


title: Soma_OPTN RGCs_1

description: Library name: Sample 13


title: Soma_OPTN RGCs_3

description: Library name: Sample 15


title: Soma_OPTN RGCs_2

description: Library name: Sample 14


title: KC06A, scRNAseq

city: Wuhan

first: Tanzeel

last: Yousaf

state: Hubei

address: 185 Donghu Road

department: Taikang Medical School (School of Basic Medical Sciences)

institute: Wuhan University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The Cell Ranger(v3.1.0) was used from 10× Genomics for initial data demultiplexing, read alignment, UMI counting, and annotation on the raw read data. Cell Ranger filtered the low-quality reads with default parameters. Then, the clean reads were aligned to the human reference genome GRCh38 to quantify the gene expression in single cells.
Assembly: hg38
Supplementary files format and content: SCRNA.counts.txt.gz : tab-delimited text file containing single-cell gene expression data in raw counts.
Supplementary files format and content: SCRNA.normalized.txt.gz : tab-delimited text file that contains single-cell gene expression data in normalized counts.
Supplementary files format and content: ScRNA.metadata.txt : tab-separated  text file containing metadata for each cell, typically including information like cell barcodes, cell type annotations, experimental conditions, or batch identifiers.

source_name: Primary HCC

extract_protocol:
Following surgical resection, ~1g of tissue was dissociated, with the remaining fixed in formalin for immunohistochemistry. Fresh tissues were transferred to pre-cooled MACS Tissue Storage Solution (Miltenyi Biotech, Germany) and shipped at 4°C.Tissue dissociation was performed in RPMI 1640 medium (Thermo Fisher) with 0.5 mg/ml collagenase II and 0.02 mg/ml DNase I (Sigma-Aldrich) at 37°C for 25 minutes on a shaker. The process was terminated with 15 mL RPMI 1640, followed by centrifugation through a 70μm cell strainer.The cell suspension was treated with 1X Red Blood Cell Lysis Solution (Miltenyi Biotech) on ice for 10 minutes. Cells were washed with PBS containing 0.04% BSA, passed through a 30μm strainer, and centrifuged twice at 4°C, first at 300g and then at 400g. The final pellet was resuspended in PBS with 0.04% BSA.
The viable singlet cell suspension was prepared at a concentration range of 700-1200 cells/µl, as recommended by the user protocol of 10× Genomics. It was then subjected to single-cell capture using the Chromium platform. Pooled and barcoded single cells were subjected to subsequent manipulation procedures, including complete cell lysis, mRNA capture, reverse transcription, cDNA amplification, and Illumina sequencing library preparation.

value: Primary HCC


title: KC03A, scRNAseq

description: 10x Genomics


title: NC3

description: Library name: NC3

value: control


title: NC1

description: Library name: NC1


title: NC2

description: Library name: NC2


title: UXGL_ULIX_3

city: Cambridge

first: Loke CTR

last: Bioinformatics

address: Downing Street

department: Physiology building

country: United Kingdom

institute: Loke Centre for Trophoblast Research

description:
Library name: Sample10
day 6.5 (36hrs treatment)

data_processing:
Raw sequencing was processed according to a modified nf-core/scrnaseq pipeline
Technical replicate fastq files were merged and preprocessed using the nf-core/rnaseq pipeline 3.10.1 with Nextflow 22.10.1. Briefly, reads were trimmed for adaptors and quality using Trimgalore 0.6.7 and cutadapt 3.4. Trimmed reads were pseudoaligned to GRCh38 with salmon 1.9.0.
Assembly: Human GRCh38
Supplementary files format and content: geo_tpm.tsv
Supplementary files format and content: geo_counts.tsv

source_name: human embryo

growth_protocol: PXGL or UXGL medium was made from N2B27 medium (Takara, Y40002), supplemented with 1 µM PD0325901 ("P", Cambridge Bioscience; 13034-1mg-CAY) or with 5uM Ulixertinib ("U", Cambridge Bioscience) plus: 2 µM XAV939 (Cambridge bioscience, CAY13596-1mg), 2 µM Gö6983 (Bio-Techne; 2285/1), 10 ng/ml hLIF (PeproTech; 300-05), and Pen/Strep (Gibco). Embryo outgrowths were left undisturbed for 48 hours at 5%O2 5%CO2 37°C, then fed with pre-equilibrated half medium changes every 2 days. After 7-10 days, outgrowths were manually picked under a dissecting microscope. Outgrowths were dissociated by washing, and then incubated in microdrops of Accutase under mineral-oil for 5 min at 37°C before trituration into single cells with 290 µm and 100 µm STRIPPER tips (CooperSurgical). Dissociated single cells were then washed in PXGL or UXGL medium, and plated onto MEF feeder plates with PXGL or UXGL medium supplemented with ROCK inhibitor 10 µM Y27632 (Tocris), and then re-fed with PXGL or UXGL medium every 2 days. Clones were passaged manually every 5-7 days until sufficient numbers for bulk passaging, initially in a 1:1 split ratio, then 1:2 – 1:3 split ratio every 3-5 days.

extract_protocol:
Stable naive hESC lines were used for the bulk RNA-seq experiments. Human naïve ESCs were dissociated to single cells. 6x10^5 cells were resuspended in 600 µl RLT buffer (Qiagen) and snap frozen on dry ice for later processing. RNA was isolated using the RNAeasy Mini Kit (Qiagen, 74104) , QIAShredder DNase digest (Qiagen, 79654), automated on a QIAcube (Qiagen) according to the manufacturer’s instructions.
The RNA library prep was performed using the mRNA polyA (NEB) kit, before paired-end 100 bp sequencing on a NovaSeq2.

treatment_protocol: Human Day 5 embryos were cultured for 36 hours in 5uM Ulixertinib (Cambridge Bioscience) or in DMSO control medium, or thawed on Day 6 and cultured for 2 hours in Global medium. Embryos that had not yet hatched had the zona pellucida removed by a brief wash in Acidic Tyrode’s pre-warmed at 37°C . Whole intact embryos, or laser dissected embryos to remove mural trophectoderm, were then plated on MEF coated 4-well plates (Nunc) in pre-equilibrated PXGL or UXGL medium.

value: human embryo

value: hESC

value: Naive hESC

value: wildtype


title: KC07A, scRNAseq

description: 10x Genomics


title: KC09A, scRNAseq

description: 10x Genomics


title: S1

description: Library name: S1


title: S2

description: Library name: S2


title: KC10A, scRNAseq

description: 10x Genomics


title: KC08A, scRNAseq

description: 10x Genomics


title: Keratinocytes, HN285,sub-confluent, rep2

city: Philadelphia

first: Andrew

last: South

state: PA

address: 233 S 10th St

department: Cancer Biology

institute: Thomas Jefferson University

data_processing:
Raw FASTQ files were preprocessed to remove adapter sequences using cutadapt version 4.6 with appropriate adapter sequences for forward and reverse reads.
Post-trimming, the quality of the processed reads was assessed using FastQC version 0.12.1 and the results were aggregated with MultiQC version 1.19.
Trimmed and quality-controlled reads were aligned to the reference genome using STAR version 2.7.11b. Transcript abundance quantification was performed using Salmon version 1.10.1
Assembly: STAR version 2.7.11b, reference Gencode Release 42 (GRCh38.p13)
Supplementary files format and content: Text file - Normalized counts using Median of Ratios in DESeq2

source_name: Alveolar ridge

extract_protocol:
RNA was extracted from subconfluent HNSCC keratinocytes using RNA stat 60 and chloroform
cDNA was made using SuperScript™ III Reverse Transcriptase.

value: Alveolar ridge

value: Keratinocytes


title: UXGL_ULIX_2

description:
Library name: Sample9
day 6.5 (36hrs treatment)


title: ExpLBM-derived chodro-plate rep2

city: Okayama

first: Takeshi

last: Takarada

country: Japan

institute: Okayama University

description: Library name: ExpLBM-derived chodro-plate rep2

data_processing:
Sequencing was performed using NovaSeq 6000 (Illumina) with a pair-read sequencing length of 150 bp. All sequence reads were extracted in FASTQ format using the CASAVA 1.8.4 pipeline. Fastp (v0.23.4) was used to remove adapters and filter raw reads with < 60 bases in addition to leading and trailing bases with a read quality of less than 30. For pseudoalignment of the filtered reads to GRCh38, Kallisto (v0.48.0) was used. GeTMM normalization was performed using edgeR (v4.0.3) to account for sample variation. Differentially expressed genes were identified by NOISeq (v2.46.0) analysis with a threshold of p > 0.8 and abs(Log2FC) > 1.
Assembly: GRCh38
Supplementary files format and content: tsv of normalized counts

source_name: chondro-plate from chondroprogenitor cells (ExpLBM cells)

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (QIAGEN)
Sequencing libraries were prepared using a KAPA RNA HyperPrep Kit with RiboErase (HMR) (Nippon Genetics) and a SeqCap Adapter Kit (Set A or Set B) (Roche) following the manufacturers’ instructions.


title: KC02A, scRNAseq

description: 10x Genomics


title: Keratinocytes, HN20,sub-confluent, rep2

source_name: Hard palate

value: Hard palate


title: UXGL_DMSO_2

description:
Library name: Sample8
day 6.5 (36hrs treatment)


title: ExpLBM-derived chodro-plate rep1

description: Library name: ExpLBM-derived chodro-plate rep1

value: chondro-plate from chondroprogenitor cells (ExpLBM cells)


title: KC05A, scRNAseq

description: 10x Genomics


title: Keratinocytes, HN379,sub-confluent, rep2

source_name: Skin

value: Skin


title: Keratinocytes, HN8,sub-confluent, rep2

source_name: Larynx

value: Larynx


title: Keratinocytes, HN65,sub-confluent, rep2

source_name: Oropharynx

value: Oropharynx


title: Keratinocytes, HN9,sub-confluent, rep2

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2FastQ v2.20.0.422.
Reads were aligned to the Nothobranchius furzeri reference genome ((Nfu_20150522, annotation nfurzeri_genebuild_v1.150922) using STAR 2.7.10a (parameters: --alignIntronMax 100000, --outSJfilterReads Unique, --outSAMmultNmax 1, --outFilterMismatchNoverLmax 0.04) (PMID: 23104886).
For each gene, all reads that map uniquely to one genomic position were counted with FeatureCounts 2.0.3 (-p -B --countReadPairs -s 2) (PMID: 24227677).
Assembly: Nfu_20150522, annotation nfurzeri_genebuild_v1.150922
Supplementary files format and content: Counts of each gene from different samples

source_name: Tongue

extract_protocol:
Total RNA was extracted from Nothobranchius furzeri (strain MZCS-08/122) ventricles using Trizol.
Preparation of libraries was done using NEBNext Ultra II directional RNA library preparation kit including enrichment of polyA RNAs using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer‘s description.
Libraries were pooled and sequenced using a HiSeq 2500 system (San Diego, CA, USA) in 51 cycle/single-end/high-output mode.

value: Tongue


title: 1868B_OV_HGSC_ovary

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

data_processing:
Initial QC on the raw FASTQ files were done using FastQC (v0.11.8). Reads were trimmed for low quality bases, adapters, N content and poly-A tails using fastq-mcf (v1.05). Contamination was checked using FastQ Screen (v0.11.4).
Reads were mapped to the human reference GRCh37.92 using the STAR two pass method (v2.6.0b).
Mapped reads were sorted using Picard Tools (v2.17.3). Additional QC after mapping was performed using Picard Tools CollectRnaSeqMetrics (v2.17.3) and RSeQC (v 2.6.4).
Counts were generated on the ensemble release GRCh37.92 GTF annotation using HTSeq (v0.10.0). Counts were done on the exons only using the "intersection-nonempty" mode.
Assembly: Human reference GRCh37.92
Supplementary files format and content: Excel, Transcripts per million, (tpm)

source_name: High Grade Serous Ovarian Cancer_ovary

extract_protocol:
DNA and RNA was simultaneously isolated using the AllPrep DNA/RNA/miRNA Universal kit (Qiagen) as per manufacturer’s protocol.
RNA from FF ovarian and omentum HGSC tissues (RIN >9) were used for library preparation using TruSeq Stranded mRNA (Illumina, San Diego, CA) as per manufacturer’s instructions.

value: High Grade Serous Ovarian Cancer_ovary


title: 1859B_OM_HGSCS_omentum

source_name: High Grade Serous Ovarian Cancer_omentum


title: 1861B_OV_HGSC_ovary


title: 1859A_OV_HGSC_ovary


title: 1868A_OM_HGSC_omentum

value: High Grade Serous Ovarian Cancer_omentum


title: 1855B_OV_HGSC_ovary


title: 842A_OM_HGSC_omentum


title: 1855A_OM_HGSC_omentum


title: 676A_OV_HGSC_ovary


title: 676B_OM_HGSC_omentum


title: 842B_OV_HGSC_ovary


title: 387B_OV_HGSC_ovary


title: 156C_OM_HGSC_omentum


title: 587B_OM_HGSC_omentum


title: 587A_OV_HGSC_ovary


title: HFFs, 1.9-4.9krpsL HCMV, 24 hpi, replicate 1

city: Seoul

first: Dohoon

last: Lee

address: 1, Gwanak-ro, Gwanak-gu

department: Bioinformatics Institute

country: South Korea

institute: Seoul National University

data_processing:
RNA-seq reads were mapped to hg38 reference genome with STAR v2.7.8a.
RNA expression levels were quantified using RSEM v1.3.1, and gene annotations from GENCODE v32 release were used to build RSEM reference.
Assembly: hg38
Supplementary files format and content: TSV for gene expression TPM, FPKM table

source_name: Skin; Foreskin

growth_protocol: HFFs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was extracted by TRIzol (Invitrogen)
Libraries were prepared by TruSeq stranded mRNA library kit (Illumina) through manafacturer's instrument.

treatment_protocol: HFFs with 90% confluency were infected with HCMV (1 MOI)

value: Skin; Foreskin

value: HFF-1 (Primary cell)

value: Fibroblast

value: Primary cell (WT)

value: 1.9-4.9krpsL HCMV infection, 24 hpi


title: 433B_OM_HGSC_omentum


title: 433A_OV_HGSC_ovary


title: 580A_OM_HGSC_omentum


title: HFFs, 1.9-4.9krpsL HCMV, 24 hpi, replicate 2

value: HFF-11 (Primary cell)


title: HFFs, 1.9-4.9krpsL HCMV, 6 hpi, replicate 1

value: 1.9-4.9krpsL HCMV infection, 6 hpi


title: 387A_OM_HGSC_omentum


title: HFFs, WT HCMV, 6 hpi, replicate 2

value: WT HCMV infection, 6 hpi


title: HFFs, 1.9-4.9krpsL HCMV, 6 hpi, replicate 2


title: HFFs, WT HCMV, 24 hpi, replicate 2

value: WT HCMV infection, 24 hpi


title: 156A_OV_HGSC_ovary


title: HFFs, WT HCMV, 6 hpi, replicate 1


title: HFFs, WT HCMV, 24 hpi, replicate 1


title: 1861A_OM_HGSC_omentum


title: PXGL_ULIX_13

description:
Library name: SIM5761A7
day 6.5 (36hrs treatment)

value: human embryo

value: hESC

value: Naive hESC

value: wildtype


title: PXGL_ULIX_4

description:
Library name: SIM5761A5
day 6.5 (36hrs treatment)


title: PXGL_ULIX_7

description:
Library name: SIM5761A6
day 6.5 (36hrs treatment)


title: PXGL_ULIX_1

description:
Library name: SIM5761A3
day 6.5 (36hrs treatment)


title: 580B_OV_HGSC_ovary


title: Human_DMSO_4_12

data_processing:
Technical replicate fastq files were merged and preprocessed using the nf-core/rnaseq pipeline 3.10.1 with Nextflow 22.10.1. Briefly, reads were trimmed for adaptors and quality using Trimgalore 0.6.7 and cutadapt 3.4. Trimmed reads were pseudoaligned to GRCh38 with salmon 1.9.0.
Assembly: GRCh38
Supplementary files format and content: all_tpm.tsv: TPM normalised counts
Supplementary files format and content: all_counts.tsv: salmon raw count output

extract_protocol:
Human and mouse embryos were subject to immunosurgery to remove outer trophectoderm cells and isolate the inner cell mass (ICM), as reported previously(Strawbridge et al., 2002: PMID 34870826;Solter and Knowles 1975 PMID 1108013). The zona pellucida was removed by washing embryos through drops of acid Tyrode’s solution pre-warmed to 37°C. Embryos were then washed briefly and incubated at 37°C for 30min in 20% anti-mouse serum (Sigma) or 20% anti-human serum (Sigma), depending on the species, in Global media + 10% HSA. Embryos were then washed briefly in Global medium + 10% HSA, before incubation with 20% Guinea Pig Serum Complement (Merk) at 37°C for 10-15min until trophectoderm began to lyse. Embryos were then moved to a drop of medium and triturated with 100µm STRIPPER tip (Cooper Surgical) to remove lysed trophectoderm and isolate the inner cell mass.Isolated ICMs were then briefly washed, then incubated at 37°C for 3 min in 0.5% Trypsin, 1mM EDTA in PBS. Then, ICMs were transferred to 4% BSA, 0.5mM EDTA in PBS for fine manual dissociation into single cells with pulled (Sutter Instruments) glass capillaries (World Precision Instruments). Cells were then picked manually with pulled glass capillaries for downstream single-cell RNA-seq. cDNA kit lot number 2109360A
Single-cell cDNA synthesis was performed using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) according to the manufacturers protocol with some modifications as previously described(Blakeley et al., PMID 26293300). Briefly, single-cells were manually picked after dissociation and snap frozen on dry ice in 5µl 10x Reaction Buffer in low-bind 0.2ml PCR tubes and stored at -80°C until processing. Samples were subject to first strand cDNA synthesis, then cDNA was amplified by LD PCR for 23 cycles. Amplified cDNA was purified on AMPure XP beads, using a 96-well magnetic stand (ThermoFisher), and eluted in 17µl of elution buffer. Single-cell RNA-seq libraries were prepared using a Nextera XT DNA Library Preparation Kit (Illumina) using according to the manufacturers protocol. Sequencing was carried out as paired-end 50bp read on Novaseq 6000 to a depth of 12 million reads.

treatment_protocol: Human blastocysts were cultured in Global media (Cooper Surgical) supplemented with 10% Human Serum Albumin (HSA, Cooper Surgical) in Embryo+ slide dishes (Vitrolife) overlaid with Mineral oil (Cooper Surgical). Embryos were incubated at 37°C 5% CO2 in an EmbryoScope time-lapse imaging system (Vitrolife). For treatments, immediately after thawing embryos were incubated in Global media, 10% HSA supplemented with; 250 FGF: 250ng/ml FGF4 (R&D) and 250ng/ml Heparin (Sigma); 500 FGF: 500ng/ml FGF4 and 500ng/ml Heparin; 750 FGF: 750ng/ml FGF4 and 750ng/ml Heparin; 1000 FGF: 1000ng/ml FGF4 and 1000ng/ml Heparin; 5µM Ulixertinib (Cambridge Bioscience); 1% DMSO. Day 5 embryos were treated with cytokines and inhibitors for 36 hours to Day 6.5.

tag: sample collection

tag: cdna prep

tag: embryo stage

value: DMSO


title: PXGL_DMSO_1

description:
Library name: SIM5761A1
day 6.5 (36hrs treatment)


title: Human_DMSO_4_11


title: PXGL_DMSO_2

description:
Library name: SIM5761A2
day 6.5 (36hrs treatment)


title: Human_DMSO_4_10


title: Human_DMSO_4_9


title: Human_DMSO_4_6


title: Human_DMSO_4_8


title: Human_DMSO_4_4


title: Human_DMSO_4_5


title: hiPSC-FBs day 2 incubation negative control rep 3

city: Pamplona

first: Asier

last: Ullate-Agote

state: Navarra

address: Av. de Pío XII, 55

department: Hemato-Oncology

country: Spain

institute: CIMA

description:
Library name: FB_p6_neg
ips_p6_neg

data_processing:
Samples were demultiplexed using Illumina bcl2fastq software (v.2.2.0), reads trimmed and quality filtered with Trim Galore (v0.6.10) and aligned to the human genome (GRCh38) with STAR (V2.7.11b) using default parameters. Gene expression quantification was performed using the featureCounts function implemented in the R package Rsubread (v2.20.0) counting uniquely mapped reads with reverse strandness. The Ensembl v112 gene annotation was considered as the reference
Normalization, processing and differential expression analyses were performed using DEseq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was isolated from cells using the RNeasy® Plus Mini Kit (Qiagen, #74134), following the manufacturer´s instructions
RNA-seq libraries were prepared using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus according to the manufacturer’s instructions

value: hiPSC-derived FBs

value: negative control


title: hiPSC-FBs day 2 incubation V122I TTR Fibril rep 2

description:
Library name: FB_p3_V122I_Fibril
ips_p3_V122I

value: V122I TTR Fibrils


title: hiPSC-FBs day 2 incubation WT TTR Fibril rep 3

description:
Library name: FB_p6_WT_Fibril
ips_p6_WT

value: WT TTR Fibrils


title: hiPSC-FBs day 2 incubation V30M TTR Fibril rep 3

description:
Library name: FB_p6_V30M_Fibril
ips_p6_V30M

value: V30M TTR Fibrils


title: Human_DMSO_4_3


title: hiPSC-FBs day 2 incubation V30M TTR Fibril rep 2

description:
Library name: FB_p3_V30M_Fibril
ips_p3_V30M


title: Human_DMSO_4_2


title: hiPSC-FBs day 2 incubation V122I TTR Fibril rep 3

description:
Library name: FB_p6_V122I_Fibril
ips_p6_V122I


title: hiPSC-FBs day 2 incubation negative control rep 2

description:
Library name: FB_p3_neg
ips_p3_neg


title: hiPSC-FBs day 2 incubation WT TTR Fibril rep 1

description:
Library name: FB_p4_WT_Fibril
ips_p4_WT


title: Human_DMSO_4_1


title: Human_Ulix_5_24

value: Ulixertinib


title: Human_DMSO_4_7


title: hiPSC-FBs day 2 incubation V30M TTR Fibril rep 1

description:
Library name: FB_p4_V30M_Fibril
ips_p4_V30M


title: PXGL_ULIX_2

description:
Library name: SIM5761A4
day 6.5 (36hrs treatment)


title: Human_Ulix_5_22


title: hiPSC-FBs day 2 incubation V122I TTR Fibril rep 1

description:
Library name: FB_p4_V122I_Fibril
ips_p4_V122I


title: Human_Ulix_5_23


title: Human_Ulix_5_21


title: hiPSC-FBs day 2 incubation negative control rep 1

description:
Library name: FB_p4_neg
ips_p4_neg


title: HUVEC ECs day 2 incubation WT TTR Fibril rep 3

description:
Library name: Huvec_p4_WT_Fibril
Huvec_p4_WT

source_name: HUVEC

value: HUVEC

value: Ecs


title: Human_Ulix_5_20


title: HUVEC ECs day 2 incubation V30M TTR Fibril rep 3

description:
Library name: Huvec_p4_V30M_Fibril
Huvec_p4_V30M


title: Human_Ulix_5_19


title: Human_Ulix_5_18


title: hiPSC-FBs day 2 incubation WT TTR Fibril rep 2

description:
Library name: FB_p3_WT_Fibril
ips_p3_WT


title: HUVEC ECs day 2 incubation WT TTR Fibril rep 2

description:
Library name: Huvec_p3_WT_Fibril
Huvec_p3_WT


title: Human_Ulix_5_17


title: Human_Ulix_5_15


title: Human_Ulix_5_16


title: HUVEC ECs day 2 incubation negative control rep 2

description:
Library name: Huvec_p3_neg
Huvec_p3_neg


title: Human_Ulix_5_12


title: Human_Ulix_5_11


title: HUVEC ECs day 2 incubation V122I TTR Fibril rep 1

description:
Library name: Huvec_p2_V122I_Fibril
Huvec_p2_V122I


title: Human_Ulix_5_9


title: Human_Ulix_5_8


title: hiPSC-CMs day 4 incubation WT TTR Fibril rep 3

description:
Library name: CM_p34_WT_Fibril
CM_p34_WT

value: hiPSC-derived CMs


title: HUVEC ECs day 2 incubation negative control rep 1

description:
Library name: Huvec_p2_neg
Huvec_p2_neg


title: Human_Ulix_5_6


title: hiPSC-CMs day 4 incubation negative control rep 3

description:
Library name: CM_p34_neg
CM_p34_neg


title: Human_Ulix_5_5


title: HUVEC ECs day 2 incubation V122I TTR Fibril rep 3

description:
Library name: Huvec_p4_V122I_Fibril
Huvec_p4_V122I


title: hiPSC-CMs day 4 incubation V122I TTR Fibril rep 3

description:
Library name: CM_p34_V122I_Fibril
CM_p34_V122I


title: HUVEC ECs day 2 incubation negative control rep 3

description:
Library name: Huvec_p4_neg
Huvec_p4_neg


title: Human_Ulix_5_7


title: hiPSC-CMs day 4 incubation V30M TTR Fibril rep 3

description:
Library name: CM_p34_V30M_Fibril
CM_p34_V30M


title: Human_Ulix_5_4


title: HUVEC ECs day 2 incubation V30M TTR Fibril rep 2

description:
Library name: Huvec_p3_V30M_Fibril
Huvec_p3_V30M


title: HUVEC ECs day 2 incubation V122I TTR Fibril rep 2

description:
Library name: Huvec_p3_V122I_Fibril
Huvec_p3_V122I


title: hiPSC-CMs day 4 incubation V30M TTR Fibril rep 2

description:
Library name: CM_p36_V30M_Fibril
CM_p36_V30M


title: Human_Ulix_5_3


title: Human_Ulix_5_2


title: Human_Ulix_5_14


title: HUVEC ECs day 2 incubation WT TTR Fibril rep 1

description:
Library name: Huvec_p2_WT_Fibril
Huvec_p2_WT


title: hiPSC-CMs day 4 incubation negative control rep 2

description:
Library name: CM_p36_neg
CM_p36_neg


title: HUVEC ECs day 2 incubation V30M TTR Fibril rep 1

description:
Library name: Huvec_p2_V30M_Fibril
Huvec_p2_V30M


title: hiPSC-CMs day 4 incubation V122I TTR Fibril rep 2

description:
Library name: CM_p36_V122I_Fibril
CM_p36_V122I


title: Human_Ulix_5_13


title: hiPSC-CMs day 4 incubation WT TTR Fibril rep 1

description:
Library name: CM_p35_WT_Fibril
CM_p35_WT


title: Human_Ulix_4_40


title: Human_Ulix_5_10


title: Human_Ulix_5_1


title: Human_Ulix_4_39


title: hiPSC-CMs day 4 incubation V30M TTR Fibril rep 1

description:
Library name: CM_p35_V30M_Fibril
CM_p35_V30M


title: Human_Ulix_4_38


title: Human_Ulix_4_36


title: hiPSC-CMs day 4 incubation negative control rep 1

description:
Library name: CM_p35_neg
CM_p35_neg


title: hiPSC-CMs day 4 incubation WT TTR Fibril rep 2

description:
Library name: CM_p36_WT_Fibril
CM_p36_WT


title: 9:1 hiPSCs CMs:CFs at day 30 in 3D engineered human cardiac tissues rep 3

data_processing:
Samples were demultiplexed using Illumina bcl2fastq software (v.2.2.0) and aligned to the human genome (GRCh38) with STAR (V2.7.0d) using default parameters. Gene expression quantification was performed using the featureCounts function implemented in the R package Rsubread (v2.4.3) counting uniquely mapped reads with reverse strandness. The Ensembl v103 gene annotation was considered as the reference.
Normalization, processing and differential expression analyses were performed using DEseq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was extracted using Trizol reagent
RNA-seq libraries were prepared using Illumina Stranded mRNA Prep Ligation according to the manufacturer’s instructions

value: hiPSCs-derived CMs (90%) and CFs (10%)

value: XY

tag: time

value: day 30


title: Human_Ulix_4_37

value: human embryo


title: 9:1 hiPSCs CMs:CFs at day 30 in 3D engineered human cardiac tissues rep 1

tag: cell line


title: Human_Ulix_4_34


title: 9:1 hiPSCs CMs:CFs at day 30 in 3D engineered human cardiac tissues rep 2

tag: cell type


title: Human_Ulix_4_33


title: Human_Ulix_4_35


title: 9:1 hiPSCs CMs:CFs at day 0 rep 3

tag: genotype

value: day 0


title: Human_Ulix_4_32

tag: tissue


title: Human_Ulix_4_31

tag: treatment


title: 9:1 hiPSCs CMs:CFs at day 0 rep 2


title: 9:1 hiPSCs CMs:CFs at day 0 rep 1


title: Human_Ulix_4_29


title: Human_Ulix_4_28


title: 9:1 hiPSCs CMs:CFs at day 30 in 2D rep 1


title: Human_Ulix_4_27


title: Human_Ulix_4_30


title: siCtIP_R8h_ENDseq_R2

city: Bethesda

first: Ajith

last: Viswanathan Asari Pankajam

address: Building 37

institute: National Institutes of Health

description: Related to Fig S13

data_processing:
For the END-seq, raw reads from Illumina NextSeq 2000/550 were aligned to the human genome (hg19) or mouse (mm10) using Bowtie (v1.3.1)  with -n 3 -l 50 -k 1. For ChIP-seq, Illumina adapter and low-quality reads were trimmed using trimmomatics (v0.39) . Processed reads were aligned to the human genome (hg19) using Bowtie2 (v2.2.5.1) with the default parameter. Samtools (v1.5.1) functions “view” and “sort” were used to convert and sort the aligned sam files to sorted bam files. Reads from the mitochondria and blacklisted regions were removed for further downstream analysis. Bam files were converted to bed files using the bedtools (v2.3.0) bamTobed command. Aligned-reads bed files were first converted to BedGraph files using bedtools genomecov. The BedGraph files were then converted to BigWig files using BedGraphToBigWig. Genome browser profiles were normalized to the library size (RPM). Visualization of genomic profiles was done by UCSC genome browser
Assembly: hg19
Supplementary files format and content: BigWig file for the Positive strand
Supplementary files format and content: BigWig file for the Negative strand
Supplementary files format and content: BigWig file for the Replication fork direction
Library strategy: ENDseq

extract_protocol:
For END-seq, Live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing.
For ChIP-seq, Live cells were fixed using 1% Formaldehyde. After cell lysis, DNA was sonicated and captured using specific antibodies.
For TrAEL-seq, Live cells were harvested and embedded into agarose plugs (Bio-Rad cat#1703591). Cells were lysed in agarose using proteinase K, follwed by Rnase treatment. DNA was later precipitated after plug melting and shearing.
For EdU-seq, Live cells were fixed with methanol 90%. Genomic DNA was extracted after Click-IT reaction.
Libraries were constructed and sequenced following Illumina standard protocols and were quantified using with the KAPA Library Quantification Kit (Kapa Biosciences)
END-seq, EdU-seq, Amplicon-seq, ChIP-seq, TrAEL-seq

value: retinal pigment epithelial cells

value: p53-/- CtIP KD by siRNA

value: siCtIP for 48h


title: RPE1_WT_RAD51_ChIPseq_Rep3

description: Related to Fig 4D 5E replicate

data_processing:
For the END-seq, raw reads from Illumina NextSeq 2000/550 were aligned to the human genome (hg19) or mouse (mm10) using Bowtie (v1.3.1)  with -n 3 -l 50 -k 1. For ChIP-seq, Illumina adapter and low-quality reads were trimmed using trimmomatics (v0.39) . Processed reads were aligned to the human genome (hg19) using Bowtie2 (v2.2.5.1) with the default parameter. Samtools (v1.5.1) functions “view” and “sort” were used to convert and sort the aligned sam files to sorted bam files. Reads from the mitochondria and blacklisted regions were removed for further downstream analysis. Bam files were converted to bed files using the bedtools (v2.3.0) bamTobed command. Aligned-reads bed files were first converted to BedGraph files using bedtools genomecov. The BedGraph files were then converted to BigWig files using BedGraphToBigWig. Genome browser profiles were normalized to the library size (RPM). Visualization of genomic profiles was done by UCSC genome browser
Assembly: hg19
Supplementary files format and content: BigWig file for the Positive strand
Supplementary files format and content: BigWig file for the Negative strand
Supplementary files format and content: BigWig file for the Replication fork direction


title: RPE1_BRCA1KO_RAD51_ChIPseq_Rep3

description: Related to Fig 4D 5E replicate


title: hiPSC-CMs day 4 incubation V122I TTR Fibril rep 1

description:
Library name: CM_p35_V122I_Fibril
CM_p35_V122I


title: Human_Ulix_4_26


title: siCtIP_R8h_ENDseq

description: Related to Fig S13


title: Human_Ulix_4_25


title: Control_R8h_ENDseq

description: Related to Fig S13


title: Human_Ulix_4_24


title: RPE-1_WT_regular_Cas9_sg1_END-seq

description: Related to Fig S12


title: RPE-1_BRCA1KO_regular_Cas9_sg1_END-seq

description: Related to Fig S12


title: Human_Ulix_4_22


title: Human_Ulix_4_23


title: 9:1 hiPSCs CMs:CFs at day 30 in 2D rep 2


title: Human_Ulix_4_21


title: Human_Ulix_4_20


title: RPE-1_BRCA1KO_R12h_Leading_END-seq

description: Related to Fig S12


title: Human_Ulix_4_19


title: Human_Ulix_4_17


title: Human_Ulix_4_16


title: RPE-1_WT_R8h_Leading_END-seq

description: Related to Fig S12


title: RPE-1_BRCA1KO_R8h_Leading_END-seq

description: Related to Fig S12


title: RPE1_WT_R16h_Leading_END-seq

description: Related to Fig S12


title: Human_Ulix_4_14


title: Human_Ulix_4_13


title: MCF10A_siBRCA2_R12h_RPA-ChIP_nCas9DFKBP_control

description: Related to Fig S11

value: mammary epithelial cells

value: WT BRCA2KD by siRNA

value: siBRCA2 for 48h


title: RPE-1_WT_R12h_Leading_END-seq

description: Related to Fig S12


title: MCF10A_siBRCA2_R12h_RPA-ChIP_nCas9DFKBP_dTAG

description: Related to Fig S11


title: Human_Ulix_4_18


title: RPA_ChIP_siPOLD3_sg1_sgblocking_rep3

description: Related to Fig S10

value: WT POLD3KD by siRNA

value: siPOLD3 for 24h


title: RPA_ChIP_siPOLD3_sg1_sgblocking_rep2

description: Related to Fig S10

value: siPOLD3for 24h


title: Human_Ulix_4_15

value: Ulixertinib


title: MCF10A_siBRCA2_R6h_RPA-ChIP_nCas9DFKBP_control

description: Related to Fig S11


title: RPA_ChIP_siPOLD3_sg1_sgblocking_rep1

description: Related to Fig S10


title: Mycn conditional knockout, P4 ATAC

city: Minneapolis

first: Daniel

last: Garry

state: MN

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

institute: University of Minnesota

description:
Library name: AB-UMGC-10X-scA-Gar-118-P4-MycnCKO
10X Genomics Chromium Single-Cell Multiome ATAC+Gene Expression kit

library_source: genomic single cell

data_processing:
Single nucleus RNA-seq and  Single nucleus ATAC-seq was quantified using unique molecular identifiers (UMIs) by 10x Genomics’ “CellRanger ARC” software.
Assembly: Mus musculus reference genome mm10 (GRCm38)
Supplementary files format and content: The processed data file is in HDF5 format and was generated using the CellRanger Arc pipeline (10x Genomics). It contains filtered gene expression matrices for high-quality nuclei, including cell barcodes, gene annotations, and UMI count matrices in sparse format. Only nuclei that passed quality control filtering are included. For ATAC-Seq the fragment files in provided in the TSV format

source_name: ventricles

extract_protocol:
Nuclei were isolated using 10X Genomics Chromium Nuclei Isolation kit from 2-3 P4 ventricles per sample.
Library construction was performed according to the manufacturers instructions using the 10X Genomics Chromium Single-Cell Multiome ATAC+Gene Expression kit.

treatment_protocol: 80 ug/g 4-hydroxy tamoxifen (Sigma) or corn oil control vehicle was delivered subcutaneously to neonatal mice on P0, P1, and P2.

value: ventricles

value: mixed

tag: strain

value: Mycn f/f, Myh6-MerCreMer (+)

tag: library type

value: ATAC


title: Control, P4 ATAC

description:
Library name: AB-UMGC-10X-scA-Gar-118-P4-Ctrl
10X Genomics Chromium Single-Cell Multiome ATAC+Gene Expression kit

value: Corn oil


title: RPE-1_BRCA1KO_R16h_Leading_END-seq

description: Related to Fig S12


title: Human_Ulix_4_11

value: human embryo


title: Mycn conditional knockout, P4 GEX

description:
Library name: AB-UMGC-10X-2s-GAR-118-P4-My
10X Genomics Chromium Single-Cell Multiome ATAC+Gene Expression kit

molecule: nuclear RNA

value: mRNA


title: Human_Ulix_4_10


title: RPA_ChIP_control_sg1_sgblocking_rep2

description: Related to Fig S10

value: WT


title: RPA_ChIP_control_sg1_sgblocking_rep1

description: Related to Fig S10


title: Human_Ulix_4_9


title: Control, P4 GEX

description:
Library name: AB-UMGC-10X-2s-GAR-118-P4-Ctrl
10X Genomics Chromium Single-Cell Multiome ATAC+Gene Expression kit


title: MCF10A_siBRCA2_R6h_RPA-ChIP_nCas9DFKBP_dTAG

description: Related to Fig S11


title: RPA_ChIP_siPOLD3_sg1_rep2

description: Related to Fig S10


title: Human_Ulix_4_12


title: Human_Ulix_4_8


title: RPA_ChIP_control_sg1_rep2

description: Related to Fig S10


title: Human_Ulix_4_7


title: RPA_ChIP_siPOLD3_sg1_rep1

description: Related to Fig S10


title: RPA_ChIP_WT_sg1_sgblocking_rep3

description: Related to Fig S10


title: Human_Ulix_4_6


title: RPA_ChIP_control_sg1_rep3

description: Related to Fig S10


title: RPA_ChIP_WT_sg1_R3

description: Related to Fig S10


title: Human_Ulix_4_5


title: RPA_ChIP_control_sg1_sgblocking_rep3

description: Related to Fig S10


title: RPA_ChIP_WT_sg1_sgblocking_R2

description: Related to Fig S10


title: Input sample of 72-hour-old female embryos

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

description: Library name: Input

data_processing:
The libraries were sequenced using MiSeq System (paired end, 75 bp). The reads were mapped to S. coprophila genome assembly using MOSAIK software {Lee, 2014 #678} with following parameters: -m all -mmp 0.1 -act 20 -a single, paired reads were combined. Only uniquely aligned reads were used to generate profiles. For each genomic position, the RPM (reads per million) value was calculated for ChIP sample and input sample.
Assembly: Scop2025
Supplementary files format and content: Log2 of the ChIP to input ratio was used as a measure of local methylation enrichment. To build the whole-genome profile, the data were smoothed using a 1-kb sliding window, step 100 bp.

organism: Bradysia coprophila

source_name: embryo

extract_protocol:
Formaldehyde-fixed chromatin from approximately 20ml of 72-hour-old female embryos was used for each ChIP experiments. Anti-H3K9me3 antibodies (Active Motif, Cat.No. 39161), anti-H4K20me3 antibodies (Active Motif, Cat.No. 39671) and anti-H3K4me3 antibodies (Diagenode, Cat.No. C15410003) were used with the True MicroChIP & MicroPlex Library Preparation™ Package (Diagenode), according to manufacturer’s recommendations. Formaldehyde-fixed chromatin was sheared using BioRuptor instrument (Diagenode). Three biological replicates were processed. DNA from precipitated material and input were used for library preparation using Illumina Nextera protocol.
Illumina TruSeq Nano

value: embryo


title: RPA_ChIP_control_sg1_rep1

description: Related to Fig S10


title: RPA_ChIP_WT_sg1_R2

description: Related to Fig S10


title: melb-a cells, lenti- shLuciferase

city: La Jolla

first: Xue

last: Lei

state: CA

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

data_processing:
Reads were trimmed using Cutadapt v2.3 and then aligned against chrM mm10 using Bowtie2.
Duplicate reads were removed using Picard MarkDuplicates v2.22.0.
MACS2 v2.2.9.1 was used to call peaks.
Reproducible peaks for replicates (n=2) were determined using IDR v2.0.4.2.
Differential accessibility of peaks were tested using edgeR v3.38.4
Assembly: mm10
Supplementary files format and content: Differential peaks with tag count, p-value and fold change.

source_name: melb-a cells

growth_protocol: melb-a cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 10ng/ml SCF, 40 pM Fgf2, 25U/ml penicillin, and 25 μg/ml streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
DNA was extracted from cells using the ATAC-seq kit (Active Motif, 53150)
ATAC libraries were prepared using the ATAC-seq kit (Active Motif, 53150) following the manufacturer's protocol.

treatment_protocol: melb-a cells were splitted to a confluency of ~50%. Lentivirus was diluted in 1 ml growth medium per 3.5 cm well and incubated with 8 μg/ml polybrene for 16 hours. The infected cells were selected using 1 μg/ml puromycin.

value: melb-a cells

value: melanoblasts

value: wt

value: lenti- shLuciferase


title: RPA_ChIP_siPOLD3_sg1_rep3

description: Related to Fig S10

value: mammary epithelial cells

value: WT POLD3KD by siRNA


title: RPA_ChIP_WT_sg1_sgblocking

description: Related to Fig S10


title: MeDIP-Seq sample of 72-hour-old female embryos with anti-5mC antibodies

description: Library name: MeDIP


title: MCF10A_TrAELseq_sg1_blocking

description: Related to Fig S10

data_processing:
For the END-seq, raw reads from Illumina NextSeq 2000/550 were aligned to the human genome (hg19) or mouse (mm10) using Bowtie (v1.3.1)  with -n 3 -l 50 -k 1. For ChIP-seq, Illumina adapter and low-quality reads were trimmed using trimmomatics (v0.39) . Processed reads were aligned to the human genome (hg19) using Bowtie2 (v2.2.5.1) with the default parameter. Samtools (v1.5.1) functions “view” and “sort” were used to convert and sort the aligned sam files to sorted bam files. Reads from the mitochondria and blacklisted regions were removed for further downstream analysis. Bam files were converted to bed files using the bedtools (v2.3.0) bamTobed command. Aligned-reads bed files were first converted to BedGraph files using bedtools genomecov. The BedGraph files were then converted to BigWig files using BedGraphToBigWig. Genome browser profiles were normalized to the library size (RPM). Visualization of genomic profiles was done by UCSC genome browser
Assembly: hg19
Supplementary files format and content: BigWig file for the Positive strand
Supplementary files format and content: BigWig file for the Negative strand
Supplementary files format and content: BigWig file for the Replication fork direction
Library strategy: TrAEL-seq


title: RPA_ChIP_WT_sg1

description: Related to Fig S10


title: Human_Ulix_4_3


title: melb-a cells, lenti- shHIRA II

value: lenti- shHIRA II


title: ChIP-Seq sample of 72-hour-old female embryos with anti-H4K20me3 antibodies

description: Library name: ChIPH4-20AB


title: Leading_RPE-1_siRAD52_16h_ENDseq

description: Related to Figure S7

value: retinal pigment epithelial cells

value: p53-/- RAD52KD by siRNA

value: siRAD52 for 24h


title: MCF10A_TrAELseq_NT

description: Related to Fig S10


title: Leading_RPE-1_siRAD52_8h_ENDseq

description: Related to Figure S7


title: melb-a cells, lenti- shScramble

value: lenti- shScramble


title: Human_Ulix_4_1

value: Ulixertinib


title: Leading_RPE-1_siPOLD3_8h_ENDseq

description: Related to Figure S7

value: p53-/- POLD3KD by siRNA

value: siPOLD3 for 24h


title: Leading_RPE-1_siPOLD3_16h_ENDseq

description: Related to Figure S7

value: siPOLD3for 24h


title: ChIP-Seq sample of 72-hour-old female embryos with anti-H3K4me3 antibodies

description: Library name: ChIP-H3K4me3


title: Leading_RPE-1_WT_16h_ENDseq

description: Related to Figure S7


title: melb-a cells, lenti- shHIRA I

value: lenti- shHIRA I


title: Human_Ulix_3_14

value: human embryo


title: Human_Ulix_4_4


title: MCF10A_END-seq_WT_9h_Leading

description: Related to Figure S5

value: WT


title: Human_Ulix_3_13


title: Leading_RPE-1_WT_8h_ENDseq

description: Related to Figure S7


title: MCF10A_END-seq_WT_3h_Leading

description: Related to Figure S5


title: Human_Ulix_3_12


title: Human_Ulix_3_11


title: MCF10A_ENDseq_sg4_sgblocking

description: Related to Fig S4


title: MCF10A_END-seq_WT_3h_Lagging

description: Related to Figure S5


title: HEK293, rs11607019_3

city: San Diego

first: Chengyu

last: Liu

address: 10949 Barbados Way

institute: University of California San Diego

description: Library name: HEK293-01-E3A

data_processing:
Raw sequencing reads were aligned to the hg38 reference genome using HISAT2
The aligned reads were then sorted and indexed using SAMtools
Read counts were generated with HTSeq-count
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma delimited text file includes raw counts for each Sample, genes with counts less than 3 in all samples are removed

extract_protocol:
Total RNA was extracted from tissues or cells using TRIzol reagent (Invitrogen) following manufacturer's instructions.
RNA-seq was performed by BGI (Shenzhen, China) using the DNBseq platform with read length of SE50 and DNBSEQ Eukaryotic Strand-specific mRNA library.


title: MCF10A_END-seq_WT_9h_Lagging

description: Related to Figure S5


title: HEK293, Control_2

description: Library name: 01-G8A


title: HEK293, rs11607019_1

description: Library name: 01-D3A


title: HEK293, Control_1

description: Library name: 01-F4A


title: Human_Ulix_3_10


title: Human_Ulix_4_2


title: ChIP-Seq sample of 72-hour-old female embryos with anti-H3K9me3 antibodies

description: Library name: H3K9me2

value: embryo


title: MCF10A_S1_ENDseq_sg4_blocking_guides

description: Related to Fig S4

data_processing:
For the END-seq, raw reads from Illumina NextSeq 2000/550 were aligned to the human genome (hg19) or mouse (mm10) using Bowtie (v1.3.1)  with -n 3 -l 50 -k 1. For ChIP-seq, Illumina adapter and low-quality reads were trimmed using trimmomatics (v0.39) . Processed reads were aligned to the human genome (hg19) using Bowtie2 (v2.2.5.1) with the default parameter. Samtools (v1.5.1) functions “view” and “sort” were used to convert and sort the aligned sam files to sorted bam files. Reads from the mitochondria and blacklisted regions were removed for further downstream analysis. Bam files were converted to bed files using the bedtools (v2.3.0) bamTobed command. Aligned-reads bed files were first converted to BedGraph files using bedtools genomecov. The BedGraph files were then converted to BigWig files using BedGraphToBigWig. Genome browser profiles were normalized to the library size (RPM). Visualization of genomic profiles was done by UCSC genome browser
Assembly: hg19
Supplementary files format and content: BigWig file for the Positive strand
Supplementary files format and content: BigWig file for the Negative strand
Supplementary files format and content: BigWig file for the Replication fork direction
Library strategy: S1-ENDseq


title: MCF10A_siHLTF_nickase_D10A_lagging_END-seq

description: Related to Fig S2D

value: WT HLTFKD by siRNA

value: siHLTF for 48h


title: Human_Ulix_3_9


title: MCF10A_siHLTF_nickase_H840A_Leading_END-seq

description: Related to Fig S2C

value: mammary epithelial cells


title: MCF10A_WT_nickase_D10A_lagging_END-seq

description: Related to Fig S2D


title: Human_Ulix_3_8


title: Donor 3, Islet, thapsigargin

city: Boston

first: Jonathan

middle: M

last: Dreyfuss

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Fastq files were trimmed & filtered using SOAPnuke, reads were aligned to the human transcriptome (Ensembl version 111) using kallisto, transcript counts were converted to gene counts using tximport, lowly expressed genes were filtered out, counts were normalized using TMM, and normalized counts were transformed to log2 counts-per-million (logCPM) using Limma Voom.
Assembly: Ensembl version 111
Supplementary files format and content: CSV of logCPM

source_name: Pancreatic islets

extract_protocol:
RNA was extracted using Rneasy kit (Qiagen)
DNBSEQ RNA-Seq PolyA-Stranded index

treatment_protocol: T1D islets, pre-stained with DTZ, were selectively treated with thapsigargin (TG) and/or taurodeoxycolic acid (TUDCA). A total of 100 islets for each experimental condition were meticulously selected, excluding any cluster-like structures indicative of acinar cells, and subjected to RNA sequencing. The treatment regimen included inducing ER stress using TG (250 nM) and mitigating it in T1D islets with TUDCA (100 ng/ml), TG, or their combination. These treatments were administered for 24 hours prior to RNA-seq analysis to evaluate the changes in ER stress response.

value: Pancreatic islets

value: Male

tag: disease

value: thapsigargin


title: MCF10A_WT_nickase_H840A_Lagging_END-seq

description: Related to Fig S2B


title: MCF10A_siHLTF_nickase_H840A_Lagging_END-seq

description: Related to Fig S2B


title: HEK293, rs11607019_2

description: Library name: 01-E4A


title: Human_Ulix_3_7


title: Donor 3, Islet, untreated

tag: Sex

value: untreated


title: MCF10A_dead_Cas9_sg1_sg2_END-seq

description: Related to Fig S1F


title: MCF10A_WT_nickase_H840A_Leading_END-seq

description: Related to Fig S2C


title: Human_Ulix_3_6


title: MCF10A_G1_arrest_D10A_lagging_guides_END-seq

description: Related to Fig S1F


title: Human_Ulix_3_5


title: MCF10A_TrAELseq_deep_seq

description: Related to Fig S1

value: retinal pigment epithelial cells


title: MCF10A_ENDseq_sg4_control_no_blocking

description: Related to Fig S4


title: Donor 2, Islet, thapsigargin

value: Female


title: Donor 3, Islet, taurodeoxycolic acid

value: taurodeoxycolic acid


title: MCF10A_G1_arrest_D10A_leading_guides_END-seq

description: Related to Fig S1F


title: MCF10A_dead_Cas9_sg4_sg5_END-seq

description: Related to Fig S1F


title: RPE1_WT_sgAluGG_nD10A

description: Related to Fig 6


title: Donor 2, Islet, taurodeoxycolic acid


title: RPE-1_BRCA1KO_sgAluGG_nD10A

description: Related to Fig 6


title: Human_Ulix_3_3

value: Ulixertinib


title: Human_Ulix_3_4


title: MCF10A_gRAlu_nD10A

description: Related to Fig 6


title: RPE-1_BRCA1_53BP1_R8h_END-seq_Rep2

description: Related to Fig 5A and S14


title: RPE-1_BRCA1_53BP1_R16h_END-seq_Rep2

description: Related to Fig 5A and S14


title: Donor 2, Islet, thapsigargin + taurodeoxycolic acid

value: thapsigargin + taurodeoxycolic acid


title: RPE-1_BRCA1KO_R16h_END-seq_Rep2

description: Related to Fig 5A and S14


title: RPE-1_BRCA1KO_R8h_END-seq_Rep2

description: Related to Fig 5A and S14


title: Donor 2, Islet, untreated


title: RPE-1_WT_control_R16h_END-seq_Rep2

description: Related to Fig 5A and S14


title: Human_DMSO_3_6

value: DMSO


title: Human_Ulix_3_1


title: Donor 3, Islet, thapsigargin + taurodeoxycolic acid


title: Donor 1, Islet, thapsigargin


title: Donor 1, Islet, taurodeoxycolic acid


title: RPE-1_WT_control_R8h_END-seq_Rep2

description: Related to Fig 5A and S14


title: RPE-1_BRCA1KO_R8h_END-seq_Rep1

description: Related to Fig 5A and S14


title: Human_DMSO_3_4


title: RPE-1_BRCA1KO_R16h_END-seq_Rep1

description: Related to Fig 5A and S14


title: RPE-1_BRCA1_53BP1_R8h_END-seq_Rep1

description: Related to Fig 5A and S14


title: RPE-1_BRCA1_53BP1_R16h_END-seq_Rep1

description: Related to Fig 5A and S14


title: RPE-1_WT_control_R8h_END-seq_Rep1

description: Related to Fig 5A and S14


title: RPE-1_WT_control_R16h_END-seq_Rep1

description: Related to Fig 5A and S14


title: Donor 1, Islet, untreated


title: BRCA153BP1KO_RAD51_ChIP_siRNF168_rep3

description: Related to Fig S14


title: Human_DMSO_3_2


title: BRCA153BP1KO_RAD51_ChIP_siRNF168_rep2

description: Related to Fig S14


title: BRCA153BP1KO_RAD51_ChIP_siRNF168_rep1

description: Related to Fig S14


title: Human_Ulix_3_2


title: Human_DMSO_3_3


title: Human_DMSO_3_5


title: IT-scC&T-seq of H3K4me3 and H3K27ac in 10-week female mouse mammary gland, rep 2

city: Hong Kong

first: Jingchun

last: Ma

institute: The University of Hong Kong

description: Library name: 10wkMmMG-K4me3_K27ac_Rep2

data_processing:
mammary gland scRNA-seq: Raw sequencing data were processed using Cell Ranger (v6.0, 10x Genomics) with default parameters. Reads were aligned to the mm10 mouse genome. Filtered UMI count matrices were used for downstream analysis in Seurat (v4). Cells with >10% mitochondrial transcripts or fewer than 500 detected genes were excluded. Gene expression matrices were normalized using SCTransform, followed by dimensionality reduction and clustering. Marker genes were identified using the Wilcoxon rank-sum test implemented in Seurat.
IT-scC&T-seq libraries: Reads were trimmed with Cutadapt v4.5 to remove adapters and extract H5XX, H7XX, Q5XX, and Q7XX barcodes, which were concatenated and added to read headers. Reads were aligned to mm10, hg38, or hg38+mm10 using Bowtie2 v2.5.3 with sensitive settings. BAM files were sorted and demultiplexed by cell barcode using SAMtools v1.17, and duplicates were removed with Picard v3.1.0. Fragment file was generated by Sinto 0.1 and was imported into ArchR 1.0.3 (R 4.3.1) for downstream analysis. MACS2
Assembly: mouse mm10, human hg38
Supplementary files format and content: bw, bigWig file showing genome-wide H3K4me3 signal aggregated from mouse (mm10) or human (hg38) cells using IT-scCUT&Tag.
Supplementary files format and content: bed, BED file of deduplicated and sorted CUT&Tag fragments from replicate 1-2 of multiplexed single-cell experiment generated via sinto from BAM.
Supplementary files format and content: bw, bigWig file showing RPKM-normalized H3K4me3/H3K27me3/CTCF/RNA-PolII CUT&Tag signal aggregated from K562 single cell libraries.
Supplementary files format and content: broadPeak, broadPeak file with H3K4me3 or H3K27me3-enriched regions in K562 cells identified from aggregated CUT&Tag signal.
Supplementary files format and content: narrowPeak, narrowPeak file showing CTCF or RNA-PolII-enriched regions in K562 cells from CUT&Tag profiling.
Supplementary files format and content: bed, BED file showing LADs (lamina-associated domains) identified by epic2 (`--keep-duplicates`, `--bin 8000`, `-g 6`) from LMNB1 CUT&Tag in H1 cells (replicate 1-3) with IgG controls, sorted and filtered black-list regions.
Supplementary files format and content: h5, 10X Genomics filtered feature-barcode matrix in HDF5 format from scRNA-seq of mouse mammary gland.
Library strategy: CUT&Tag

source_name: mammary gland

extract_protocol:
Mammary gland tissues were isolated from 10-week-old female C57BL/6J mice. Tissues were enzymatically digested overnight in complete EpiCult-B medium supplemented with 5% FBS and 10× collagenase/hyaluronidase. After red blood cell lysis using NH₄Cl, tissue fragments were further dissociated sequentially with 0.25% trypsin, Dispase (5 mg/ml), and DNase I (1 mg/ml), then filtered through a 40-μm strainer to obtain a single-cell suspension. Cells were washed in HBSS with 2% FBS and then in DPBS. For IT-scC&T-seq, cells were fixed in 0.1% formaldehyde, quenched with glycine, and stored in DPBS with 0.5% BSA prior to single-cell CUT&Tag profiling. For scRNA-seq, unfixed cells were resuspended in PBS with 0.04% BSA.
IT-scC&T-seq: For each sample, native or 0.1%–0.2% formaldehyde crosslinked cells (see Table S2 for detailed conditions) were lysed in antibody buffer to isolate nuclei. Nuclei were incubated overnight with primary antibodies, followed by secondary antibody incubation and washes in Dig-300 buffer. Indexed pA-Tn5 complexes were added to nuclei in Dig-300 buffer (0.02 μM final) and incubated at room temperature for 1 h. Tagmentation was performed in Mg²⁺-containing buffer at 37 °C for 1 h, followed by quenching and single-nucleus FACS sorting into 384-well plates. After lysis and SDS quenching, indexed primers (H5XX, H7XX) and PCR master mix were dispensed using an acoustic liquid handler. First-round PCR was performed with 15–17 cycles. Products were pooled, purified, Exo I–treated, and bead-cleaned. A second PCR added Truseq P5/P7 adapters, followed by double-sided size selection. Libraries were QC-checked and sequenced by ANOROAD GENOME. scRNA-seq: libraries were constructed using the 10x Genomics Chromium Single Cell 3′ v3.1 platform according to the manufacturer’s protocol.

value: mammary gland

value: not applicable

value: H3K4me3, H3K27ac

value: No


title: BRCA153BP1KO_RAD51_ChIP_control_rep3

description: Related to Fig S14


title: scRNA-seq of 10-week female mouse mammary gland

description: Library name: 10wkMmMG-scRNA

data_processing:
mammary gland scRNA-seq: Raw sequencing data were processed using Cell Ranger (v6.0, 10x Genomics) with default parameters. Reads were aligned to the mm10 mouse genome. Filtered UMI count matrices were used for downstream analysis in Seurat (v4). Cells with >10% mitochondrial transcripts or fewer than 500 detected genes were excluded. Gene expression matrices were normalized using SCTransform, followed by dimensionality reduction and clustering. Marker genes were identified using the Wilcoxon rank-sum test implemented in Seurat.
IT-scC&T-seq libraries: Reads were trimmed with Cutadapt v4.5 to remove adapters and extract H5XX, H7XX, Q5XX, and Q7XX barcodes, which were concatenated and added to read headers. Reads were aligned to mm10, hg38, or hg38+mm10 using Bowtie2 v2.5.3 with sensitive settings. BAM files were sorted and demultiplexed by cell barcode using SAMtools v1.17, and duplicates were removed with Picard v3.1.0. Fragment file was generated by Sinto 0.1 and was imported into ArchR 1.0.3 (R 4.3.1) for downstream analysis. MACS2
Assembly: mouse mm10, human hg38
Supplementary files format and content: bw, bigWig file showing genome-wide H3K4me3 signal aggregated from mouse (mm10) or human (hg38) cells using IT-scCUT&Tag.
Supplementary files format and content: bed, BED file of deduplicated and sorted CUT&Tag fragments from replicate 1-2 of multiplexed single-cell experiment generated via sinto from BAM.
Supplementary files format and content: bw, bigWig file showing RPKM-normalized H3K4me3/H3K27me3/CTCF/RNA-PolII CUT&Tag signal aggregated from K562 single cell libraries.
Supplementary files format and content: broadPeak, broadPeak file with H3K4me3 or H3K27me3-enriched regions in K562 cells identified from aggregated CUT&Tag signal.
Supplementary files format and content: narrowPeak, narrowPeak file showing CTCF or RNA-PolII-enriched regions in K562 cells from CUT&Tag profiling.
Supplementary files format and content: bed, BED file showing LADs (lamina-associated domains) identified by epic2 (`--keep-duplicates`, `--bin 8000`, `-g 6`) from LMNB1 CUT&Tag in H1 cells (replicate 1-3) with IgG controls, sorted and filtered black-list regions.
Supplementary files format and content: h5, 10X Genomics filtered feature-barcode matrix in HDF5 format from scRNA-seq of mouse mammary gland.

value: WT


title: Human_DMSO_3_1

source_name: human embryo

value: human embryo


title: IT-scC&T-seq of H3K4me3 and H3K27ac in 10-week female mouse mammary gland, rep 1

description: Library name: 10wkMmMG-K4me3_K27ac_Rep1


title: BRCA153BP1KO_RAD51_ChIP_control_rep2

description: Related to Fig S14


title: BRCA153BP1KO_RAD51_ChIP_control_rep1

description: Related to Fig 5D and S14


title: Human_Ulix_2_1


title: Donor 1, Islet, thapsigargin + taurodeoxycolic acid


title: IT-scC&T-seq of H3K4me3 in a mix of HEK293T and mESCs

description: Library name: MixSpecies-K4me3

source_name: cell line

value: cell line

value: HEK293T, B6


title: RPE-1_WT_RAD51_ChIPseq_2

description: Related to Fig 5D


title: RPE-1_BRCA1_53BP1KO_RAD51_ChIPseq_2

description: Related to Fig 5D


title: Human_Ulix_1_8


title: RPE-1_BRCA1KO_RAD51_ChIPseq_2

description: Related to Fig 5D


title: 30uM replicate 4

city: Memphis

first: Douglas

middle: R

last: Green

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St. Jude Children's Research Hospital

description: Library name: Sample 8

data_processing:
The reads were trimmed with Trim Galore (version 0.5.0) with default parameters.
Then reads were aligned to the reference mouse mm10 assembly plus ERCC spike-in sequences using STAR (version 2.7.5a).
The resulting alignments, recorded in BAM file, were sorted, indexed, and marked for duplicates with Picard MarkDuplicates function (version 2.19.0).
Transcript quantification was calculated using RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: CD8+ T cells

growth_protocol: Tumor infiltrating CD8+ T cells were isolated from tumors at D9 post T-cell injection.

extract_protocol:
Total-RNA was isolated using RNAqueous-Micro Total RNA isolation kit (Catalog-AM1931, Thermo).
Libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (HMR) (08098131702, Roche) and purified by AMPure SPRI beads (B23318, Beckman-Coulter).

value: CD8+ T cells

value: Wild type

value: 0.03mM Methionine


title: Human_Ulix_1_7


title: RPE-1_BRCA1_53BP1KO_RAD51_ChIPseq_1

description: Related to Fig 5D Replicate

value: retinal pigment epithelial cells


title: RPE1_WT_RAD51_ChIPseq_1

description: Related to Fig 4E


title: Human_Ulix_1_6


title: RPE1_BRCA1KO_RAD51_ChIPseq_1

description: Related to Fig 4E


title: RPE-1_BRCA1KO_regular_Cas9_sg4_END-seq

description: Related to Fig 4D


title: 30uM replicate 3

description: Library name: Sample 7


title: Human_Ulix_1_5


title: 30uM replicate 2

description: Library name: Sample 6


title: 30uM replicate 1

description: Library name: Sample 5


title: Human_Ulix_1_4


title: RPE-1_WT_regular_Cas9_sg4_END-seq

description: Related to Fig 4D


title: RPE-1_BRCA1KO_R12h_Lagging_END-seq

description: Related to Fig 4A


title: RPE-1_BRCA1KO_R8h_Lagging_END-seq

description: Related to Fig 4 A,B,C


title: RPE-1_BRCA1KO_R16h_Lagging_END-seq

description: Related to Fig 4 A,B,C


title: Control replicate 4

description: Library name: Sample 4

value: 0.1mM Methionine


title: RPE-1_WT_R16h_Lagging_END-seq

description: Related to Fig 4 A,B,C


title: Human_Ulix_1_3


title: RPE-1_WT_R12h_Lagging_END-seq

description: Related to Fig 4A


title: Control replicate 3

description: Library name: Sample 3


title: RPE-1_WT_R8h_Lagging_END-seq

description: Related to Fig 4 A,B,C


title: Human_Ulix_1_2


title: Control replicate 2

description: Library name: Sample 2


title: RPA_ChIP_siRAD51_sg1_rep3

description: Related to Fig 3D

value: mammary epithelial cells

value: WT RAD51KD by siRNA

value: siRAD51 for 24h


title: RPA_siRAD51_sg1_sgblocking_rep3

description: Related to Fig 3D


title: RPA_siRAD51_sg1_sgblocking_rep2

description: Related to Fig 3D


title: MCF10A_RPA_ChIP_siRAD51_sg1_sgblocking_R1

description: Related to Fig 3D


title: Human_DMSO_2_11

value: DMSO