title: 16day, ncRNA-seq, rep2

city: weifang

first: yongqi

last: liu

state: shandong

address: 699 Binhu Road, Xiashan District

institute: Peking University Institute of Advanced Agricultural Sciences

description: Library name: S16d-rep2

data_processing:
Raw sequencing data quality was assessed using fastp to evaluate read quality.
Cleaned reads were aligned to the Solanum lycopersicum reference genome (S_lycopersicum_chromosomes.4.00) using bowtie with default parameters.
Count matrices were imported into DESeq2 in R to identify differentially expressed genes.
Assembly: S_lycopersicum_chromosomes.4.00
Supplementary files format and content: Txt files include TPM values for each sample, the log2(FoldChange) value and the according p-value of pair-comparisons
Supplementary files format and content: csv file includes log2(FoldChange) values and the according p-value of pair-comparisons
Supplementary files format and content: gene_count.csv (raw counts table ranging from 18nt to 26nt for each sample)

organism: Solanum lycopersicum

source_name: callus

growth_protocol: All cultures were incubated under 70% relative humidity and light at approximately 50 µmol m-2 s-1 (light/dark regime of 16/8 h) at 25°C.

extract_protocol:
The purity, concentration, and integrity of RNA samples were assessed using advanced molecular biological equipment to ensure the quality of samples used in transcriptome sequencing.
Libraries were constructed using the Small RNA Sample Prep Kit with total RNA as the starting material.
After samples passed the quality check, total RNA was used as the starting material for library construction with the small RNA Sample Pre Kit. Given that small RNAs have a phosphate group at the 5' end and a hydroxyl group at the 3' end, T4 RNA Ligase 1 and T4 RNA Ligase 2 (truncated) were used to ligate adapters to the 5' and 3' ends of small RNAs, respectively. This was followed by reverse transcription to synthesize cDNA, PCR amplification, and the use of PAGE gel electrophoresis to select the target fragments. The excised and purified fragments from the gel constituted the small RNA library.

treatment_protocol: Fresh samples were frozen immediately in liquid nitrogen and stored in a refrigerator at -80°C.

value: callus


title: PHC2 KO PHC2 CUT&RUN (HCT116), rep02

status: Public on Mar 27 2026

type: SRA

city: Boston

first: Philipp

last: Schneider

state: Massachusetts

address: 185 Cambridge Street

country: USA

institute: Massachusetts General Hospital

description:
Library name: CR_KO_PHC2_02
KO_PHC2.bw
featureCounts_peak_coverage_PHC2.tsv
PHC2_merged_peaks.bed

library_source: genomic

data_processing:
The raw reads were initially trimmed using Trimmomatic with the empirically determined parameters “HEADCROP:0 ILLUMINACLIP:adapters.fa:2:22:9:2:True LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20”. Quality control of the sequencing data was performed with FastQC and MultiQC. Subsequently, the trimmed reads were aligned to the ribosomal DNA references, retrieved from NCBI with bowtie2 using the -N 1 option to allow single mismatches in the alignment. Reads identified as non-ribosomal were subjected to splicing-aware alignment with the STAR aligner using the settings “--bamRemoveDuplicatesType UniqueIdenticalNotMulti --outMultimapperOrder Random”. For this step, we employed the hg38 genome and RefSeq annotations for introns and exons. Unaligned reads were removed for further processing and a subset of the unaligned reads was used with BLAST to confirm the absence of any contamination. Picard's markDuplicate function was used on the aligned read set to identify duplicate reads. Using the Bedtools' genomecov function, we generated bedgraph files from BAM files with single-base-pair resolution. These files were normalized to 1x genome coverage and converted to bigwigs. In parallel to this, BAM files were processed by featureCounts to determine gene-and-exon-wise coverage in all RNA-Seq samples.
Raw CUT&RUN reads were trimmed with Trimmomatic and empirically determined parameters “HEADCROP:5 ILLUMINACLIP:adapters.fa:2:22:9:2:True LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20”. Quality control of the CUT&RUN sequencing experiment was performed with FastQC and MultiQC. Mitochondrial reads were removed by alignment to the mitochondrial DNA sequence reference from the hg38 genome using Bowtie2. The remaining non-mitochondrial reads were further aligned to the human genome hg38 using Bowtie 2, allowing for single-base mismatches (parameter -N 1). Poor alignments in the produced BAM alignment file, as determined by score fields AS, YS and MAPQ, multi-aligners, as determined by fields AS and XS, large fragments (TLEN>3500) and flagged singletons were subsequently filtered out with samtools. Replicate marking and removal were accomplished using Picard’s MarkDuplicates. Sample- and antibody-specific CUT&RUN peaks were called with macs3, employing multiple replicates for each experiment and using respective IgG CUT&RUNs as controls with a q-value of 0.01 (-q 0.01). For normalizing CUT&RUN tracks, a "background-interval-set" was generated using the complement of a union peak set derived from all samples and antibodies, extending each peak interval by 10 kbp. Bedgraph files, prepared for each sample with BedTools genomecov, were normalized to a standard 1x coverage on the background intervals.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: bigWig files are normalized to 1x background genome coverage

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: We grew wild-type and PHC2 L307R HCT116 cells in 6-well plates. The day before harvesting the cells, we plated 2.5×10⁵ cells per well. Cells were harvested by adding 0.5 ml of TRI Reagent (Molecular Research Center, TR118) and transferred to a 1.5 ml tube. Then 0.1 ml of chloroform was added to the tube and vigorously mixed. Afterwards, the sample was incubated at room temperature for 3 minutes and centrifuged at 16,000 RCF for 15 minutes at 4°C. We then carefully transferred the upper aqueous phase to a new tube and added 1 volume of 100% ethanol to 1 volume of sample (1:1 ratio). Then, the RNA was purified using the RNA clean & concentrator kit (Zymo Research, R1016) following the manufacturer’s manual. To remove the DNA we performed the “In-column DNase treatment” and used 5 units of TURBO DNAase (Thermo Fisher Scientific, AM2238) as described in the appendix of the manufacturer manual. The quality and concentration was accessed by nanodrop and Agilent Tapestation. Subsequently, the RNA library was prepared using the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research, R3000) following the manufacturer’s manual exactly. We started out with 250 ng of RNA. For the final library amplification we ran 12 PCR cycles. Afterwards library quality was assessed using the Agilent Tapestation. The library concentrations were measured using the NEBNext Library Quant Kit for Illumina (New England Biolabs, E7630L) following the manufacturer’s manual exactly. For PHC2 KO and PHC2 KO with PHC2 overexpression through lentivirus, the NEBnext PolyA mRNA magnetic isolation module (New England Biolabs, E7490L) was used instead of the Zymo-Seq RiboFree Total RNA Library Kit.

extract_protocol:
We followed the CUT&RUN protocol from Skene et al. with some minor modifications. First, Concanavalin A (Polysciences, 86057-10) beads were prepared by taking 20 µl per sample and washing the beads three times with 1 ml of Bead Activation Buffer (20 mM HEPES with pH 7.9, 10 mM KCl, 1 mM CaCl₂ 1 mM MnCl₂), incubating for ~15 minutes on a rotator each time. After washing, tubes were placed on a magnetic stand, supernatant was removed, and beads were resuspended in 200 µl Bead Activation Buffer. For each CUT&RUN sample, 1×10⁶ cells were harvested by trypsinization, quenched, and counted. Then cells were spun down at 500 RCF for 5 minutes and washed with 10 ml of PBS with pH 7.4. Then, we resuspend cells in 0.5% formaldehyde in PBS with pH 7.4. Cells were fixed for 5 minutes, then quenched with 1:1 volume of 1 M Tris pH 8.0 for 10 minutes at room temperature. Afterwards, we washed cells twice with 5 ml PBS with pH 7.4 in 15 ml Falcon tubes by spinning at 500 ×g for 3 minutes. Then cells were resuspended in 100 µl of PBS per library. Afterwards, we added 100 µl Wash Buffer (20 mM HEPES with pH 7.5, 150 mM NaCl, 2 mM EDTA with pH 8.0, 0.5% BSA, 0.1% Triton, Protease Inhibitor Tablet Roche cOmplete EDTA-free) and 40 µl of washed ConA beads. This mixture was incubated for 10 minutes on a rotator to bind cells to beads. Then, samples were spun at 50 RCF for 1 minute, moved to a magnetic stand, and cleared for 1 minute. Afterwards, the supernatant was removed and beads were resuspended in 100 µl Wash Buffer and transferred to PCR strip tubes. We then prepared the corresponding antibody solutions (all antibodies were used at 1:400) in 150 µl Wash Buffer. PCR tubes with beads were moved to a magnetic stand, incubated for 1 minute, and then the supernatant was removed. We then added the antibody solution and resuspended the beads. Finally, the tubes were placed on a nutator overnight at 4°C. The next day, the samples were washed twice with 100 µl Wash Buffer. After removing the Wash Buffer, we added 50 µl of proteinA MNase at 700 ng/ml final in Wash Buffer and incubated for 1 hour at room temperature. Then, the beads were washed three times with 100 µl Wash Buffer. Afterwards, the samples were chilled on ice. We then added 100 µl of ice cold Wash Buffer with 10 mM CaCl₂ to each sample and digested for 1 hour at 4°C. During the incubation, we prepared RNase-containing 2× STOP buffer by mixing 4 µl of 100 mg/ml RNase A with 3996 µl 2× STOP buffer (340 mM NaCl, 20 mM EDTA with pH 8.0, 4 mM EGTA with pH 8.0). After the 1 hour incubation, we added 100 µl of STOP/RNase buffer per sample and incubated at 37°C for 15 minutes. Then, samples were placed on the magnet, allowed to clear for 1 minute, and then the supernatant was transferred to new tubes. We then added 2 µl of 10% SDS and 2 µl of 19 mg/mL proteinase K to each tube and mixed gently. With this, reverse crosslink was performed at 50°C overnight. The next day, we performed the DNA Clean-Up using Ampure XP beads (Beckman Coulter, A63881) at 0.9x beads to sample ratio (e.g. 180 µl of beads with 200 µl of DNA sample). Beads and samples were mixed and incubated at room temperature for 10 minutes. Afterwards, we moved the tubes to the magnet, discarded the supernatant, and washed with 200 µl of freshly prepared 90% ethanol without resuspending. This wash was repeated and then the beads were allowed to air dry just until no visible liquid remained. We then removed the tubes from the magnet, added 52 µl of 0.1× TE, resuspended beads by pipetting, and incubated for 2 minutes at room temperature. Then, the tubes were returned to the magnet and we transferred 50 µl of supernatant to new PCR tubes.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®,New England Biolabs, E7645S

tag: cell line

tag: genotype

value: PHC2 KO


title: Human_CellLines_UFM1_NUCL_DOX_ANS_rep1

city: Vienna

first: Yasin

last: Dagdas

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

description: Library name: Human_CellLines_UFM1_NUCL_DOX_ANS_rep1

library_source: transcriptomic

data_processing:
Raw FASTQ files were preprocessed using Trim Galore with default settings to remove adapter sequences and low-quality bases. Trimmed reads were aligned using STAR in two-pass mode to improve splice junction detection. Transcript-level quantification was performed using Salmon with strand-specific settings, using the aligned BAM files as input.   Aligned BAM files were sorted and indexed using samtools75, and splice junction files from STAR were used as input for rMATS to identify differential alternative splicing events between control and anisomycin-treated samples. rMATS was run in paired-end mode for Arabidopsis and human samples and in single-end mode for mouse samples, with strand-specific orientation and the variable read length option enabled.
Assembly: For Arabidopsis, alignments were performed against a genome index generated using the TAIR10 primary assembly and the Ensembl Plants Release 56 GTF annotation. For human RKO, reads were aligned to the GRCh38 primary assembly using the GENCODE v45 annotation. For mouse, reads were aligned to the GRCm39 primary assembly using the Ensembl Release 112 annotation.
Supplementary files format and content: Bigwigs , normalised Bins per million  obtained from deeptools bamCoverage function with binsize set to 5 (similar to Transcripts per million)

molecule: total RNA

source_name: RKO cell lines

extract_protocol:
Cytosolic and nuclear fractions from Arabidopsis and human RKO cells were homogenized and stored in TRIzol at −80 °C until further processing. RNA was extracted using the Direct-zol RNA Microprep Kit (Zymo Research) according to the manufacturer’s instructions. Neuronal cell samples stored in 300 µL of DNA/RNA Shield were also kept at −80 °C until use. RNA from total cells of these samples was extracted using the Quick-RNA Miniprep Plus Kit (Zymo Research), following the recommended protocol. DNase I (NEB) treatment was performed during RNA isolation.
Polyadenylated mRNA was enriched from total RNA using oligo(dT) magnetic beads (NEBNext Poly(A) mRNA Magnetic Isolation Module), followed by strand-specific library preparation using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina. All steps, including mRNA capture, first- and second-strand synthesis, end repair, adaptor ligation, and library amplification, were performed according to the manufacturer’s instructions. Library quality and fragment size distribution were assessed using an Agilent Fragment Analyzer.

tag: tissue

value: RKO cell lines

value: ufm1 KO

tag: treatment

value: Anisomycin


title: Human_CellLines_UFM1_NUCL_DOX_ANS_rep2

description: Library name: Human_CellLines_UFM1_NUCL_DOX_ANS_rep2


title: 14day, ncRNA-seq, rep3

country: China

description: Library name: S14d-rep3


title: PHC2 KO IgG CUT&RUN (HCT116), rep03

description:
Library name: CR_KO_IgG_03
KO_IgG.bw
featureCounts_peak_coverage_EED.tsv
featureCounts_peak_coverage_PHC2.tsv
featureCounts_peak_coverage_PHC3.tsv
featureCounts_peak_coverage_SMARCC1.tsv


title: PHC2 KO PHC2 CUT&RUN (HCT116), rep01

description:
Library name: CR_KO_PHC2_01
KO_PHC2.bw
featureCounts_peak_coverage_PHC2.tsv
PHC2_merged_peaks.bed


title: 16day, ncRNA-seq, rep1

description: Library name: S16d-rep1


title: Lung metastses from a MMTV-PyMT female mouse

type: RNA

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

hyb_protocol: NanoString® ISH probes were prepared by incubation at 95°C for 2 min and placed on ice, and the ISH probe mix (1nM 980 plex ISH probe, 1nM SMI-0006 custom, 1X Buffer R, 0.1 U/μL SUPERase•In™ [Thermo Fisher Scientific] in DEPC H2O) was pipetted into the hybridization chamber. The chamber was sealed to prevent evaporation, and hybridization was performed at 37°C overnight. Tissue sections were rinsed of excess probes in 2X SSCT for 1 min and were washed twice in 50% formamide (VWR) in 2X SSC at 37°C for 25 min, washed twice with 2X SSC for 2 min at room temperature, and blocked with 100 mM NHS-acetate in the dark for 15 min. In preparation for loading onto the CosMx SMI instrument, a custom-made flow cell was affixed to the slide.

scan_protocol: RNA target readout on the CosMx SMI instrument was performed. Briefly, the assembled flow cell was loaded onto the instrument and Reporter Wash Buffer was flowed to remove air bubbles. A preview scan of the entire flow cell was taken, and 15-25 fields of view (FoVs) were placed on the tissue to match regions of interest identified by H&E staining of an adjacent serial section. RNA readout began by flowing 100 μl of Reporter Pool 1 into the flow cell and incubation for 15 min. Reporter Wash Buffer (1 mL) was flowed to wash unbound reporter probes, and Imaging Buffer was added to the flow cell for imaging. Nine Z-stack images (0.8 μm step size) for each FoV were acquired, and photocleavable linkers on the fluorophores of the reporter probes were released by UV illumination and washed with Strip Wash buffer. The fluidic and imaging procedure was repeated for the 16 reporter pools, and the 16 rounds of reporter hybridization-imaging were repeated multiple times to increase RNA detection sensitivity. After RNA readout, the tissue samples were incubated with a 4-fluorophore-conjugated antibody cocktail against CD298/B2M (488 nm), PanCK (532 nm), CD45 (594 nm), and CD3 (647 nm) proteins and DAPI stain in the CosMxTM SMI instrument for 2 h. After unbound antibodies and DAPI stain were washed with Reporter Wash Buffer, Imaging Buffer was added to the flow cell and nine Z-stack images for the 5 channels (4 antibodies and DAPI) were captured.

data_processing: Data preprocessing was conducted using the AtoMx Spatial Informatics Platform. Images were segmented to extract the transcript count matrix, cell boundaries (polygons), and corresponding cell metadata. The expression matrices, polygon coordinates, field of view (FOV) coordinates, and cell metadata were exported and loaded into R using LoadNanostring function of Seurat (version 5.0.3) in R 4.3.2. Each sample's raw data was normalized individually using the regularized negative binomial regression model implemented in Seurat SCTransform function. Before normalization, cells with low total transcript counts - based on the distribution of total counts across the dataset - were removed. Cell typing was performed in supervised mode using the insitutypeML function from the InSituType R package (v1.0.0; https://github.com/Nanostring-Biostats/InSituType; Danaher et al., 2022). As inputs, we used reference data from scRNA-seq, expression profiles, spatial context, and morphological features (e.g., cell size, shape, and immunofluorescence intensity for PanCK and CD45) of individual spatial transcriptomic samples. The cell types identified by insitutypeML were then manually refined, incorporating prior knowledge of marker genes specific to certain cell types.

organism: Mus musculus

source_name: MMTV-PyMT (C57BL/6J) mouse

label_protocol: After HIER, tissue sections were digested with 3 µg/ml Proteinase K diluted in ACD Protease Plus at 40°C for 30 minutes. Tissue sections were then washed twice with diethyl pyrocarbonate (DEPC)-treated water (DEPC H2O) and incubated in 1:2,000 fiducials (Bangs Laboratory) in 2X saline sodium citrate, 0.001% Tween-20 (SSCT solution) for 5 min at room temperature in the dark. Excess fiducials were rinsed from the slides with 1X PBS, then tissue sections were fixed with 10% neutral buffered formalin (NBF) for 5 min at room temperature. Fixed samples were rinsed twice with Tris-glycine buffer (0.1M glycine, 0.1M Tris-base in DEPC H2O) and once with 1X PBS for 5 min each before blocking with 100 mM N-succinimidyl (acetylthio) acetate (NHS-acetate, Thermo Fisher Scientific) in NHS-acetate buffer (0.1M NaP, 0.1% Tween pH 8 in DEPC H2O) for 15 min at room temperature. The sections were then rinsed with 2X saline sodium citrate (SSC) for 5 min and an Adhesive SecureSeal Hybridization Chamber (Grace Bio-Labs) was placed over the tissue.

extract_protocol: FFPE tissue sections were prepared for CosMxTM SMI profiling. Briefly, five-micron tissue sections mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked overnight at 60°C, followed by preparation for in-situ hybridization (ISH) on the Leica Bond RXm system by deparaffinization and heat-induced epitope retrieval (HIER) at 100°C for 15 minutes using ER1 epitope retrieval buffer (Leica Biosystems product, Tris/EDTA-based, pH 9.0).

treatment_protocol: Surgical samples were fixed in formalin and paraffin embedded (FFPE) for CosMxTM SMI and tissue staining (IHC IF, ISH).

value: Lung

tag: Sex

value: Female

tag: age

value: 5.5 months

tag: strain

value: MMTV-PyMT (C57BL/6J )


title: PHC2 KO IgG CUT&RUN (HCT116), rep02

description:
Library name: CR_KO_IgG_02
KO_IgG.bw
featureCounts_peak_coverage_EED.tsv
featureCounts_peak_coverage_PHC2.tsv
featureCounts_peak_coverage_PHC3.tsv
featureCounts_peak_coverage_SMARCC1.tsv


description: Library name: Human_CellLines_UFM1_NUCL_DMSO_CTRL_rep3

value: Wild type

value: DMSO


title: PHC2 KO with PHC2 lentivirus overexpression IgG CUT&RUN (HCT116), rep03

description:
Library name: CR_Lenti_IgG_03
Lenti_IgG.bw
featureCounts_peak_coverage_EED.tsv
featureCounts_peak_coverage_PHC2.tsv
featureCounts_peak_coverage_PHC3.tsv
featureCounts_peak_coverage_SMARCC1.tsv


title: 16day, ncRNA-seq, rep3

description: Library name: S16d-rep3


title: PHC2 KO with PHC2 lentivirus overexpression IgG CUT&RUN (HCT116), rep01

description:
Library name: CR_Lenti_IgG_01
Lenti_IgG.bw
featureCounts_peak_coverage_EED.tsv
featureCounts_peak_coverage_PHC2.tsv
featureCounts_peak_coverage_PHC3.tsv
featureCounts_peak_coverage_SMARCC1.tsv


title: PHC2 KO EED CUT&RUN (HCT116), rep02

description:
Library name: CR_KO_EED_02
KO_EED.bw
featureCounts_peak_coverage_EED.tsv
EED_merged_peaks.bed


title: Human_CellLines_UFM1_NUCL_DOX_ANS_rep3

description: Library name: Human_CellLines_UFM1_NUCL_DOX_ANS_rep3


title: 14day, ncRNA-seq, rep2

description: Library name: S14d-rep2


title: PHC2 KO EED CUT&RUN (HCT116), rep03

description:
Library name: CR_KO_EED_03
KO_EED.bw
featureCounts_peak_coverage_EED.tsv
EED_merged_peaks.bed


title: Human_CellLines_UFM1_NUCL_DOX_CTRL_rep2

description: Library name: Human_CellLines_UFM1_NUCL_DOX_CTRL_rep2


description: Library name: Human_CellLines_UFM1_NUCL_DMSO_CTRL_rep1


title: WT treated with BRM014 SMARCC1 CUT&RUN (HCT116), rep03

description:
Library name: CR_BRM014_SMARCC1_03
BRM014_SMARCC1.bw
featureCounts_peak_coverage_SMARCC1.tsv
SMARCC1_merged_peaks.bed

value: wild type


title: PHC2 KO IgG CUT&RUN (HCT116), rep01

description:
Library name: CR_KO_IgG_01
KO_IgG.bw
featureCounts_peak_coverage_EED.tsv
featureCounts_peak_coverage_PHC2.tsv
featureCounts_peak_coverage_PHC3.tsv
featureCounts_peak_coverage_SMARCC1.tsv


title: PHC2 KO EED CUT&RUN (HCT116), rep01

description:
Library name: CR_KO_EED_01
KO_EED.bw
featureCounts_peak_coverage_EED.tsv
EED_merged_peaks.bed


title: WT treated with BRM014 SMARCC1 CUT&RUN (HCT116), rep01

description:
Library name: CR_BRM014_SMARCC1_01
BRM014_SMARCC1.bw
featureCounts_peak_coverage_SMARCC1.tsv
SMARCC1_merged_peaks.bed


title: 12day, ncRNA-seq, rep2

description: Library name: S12d-rep2


title: 14day, ncRNA-seq, rep1

description: Library name: S14d-rep1


title: WT treated with BRM014 SMARCC1 CUT&RUN (HCT116), rep02

description:
Library name: CR_BRM014_SMARCC1_02
BRM014_SMARCC1.bw
featureCounts_peak_coverage_SMARCC1.tsv
SMARCC1_merged_peaks.bed


title: WT treated with BRM014 PHC2 CUT&RUN (HCT116), rep03

description:
Library name: CR_BRM014_PHC2_03
BRM014_PHC2.bw
featureCounts_peak_coverage_PHC2.tsv
PHC2_merged_peaks.bed


title: Human_CellLines_UFM1_NUCL_DMSO_ANS_rep2

description: Library name: Human_CellLines_UFM1_NUCL_DMSO_ANS_rep2


description: Library name: Human_CellLines_UFM1_NUCL_DMSO_CTRL_rep2


title: WT treated with BRM014 PHC2 CUT&RUN (HCT116), rep02

description:
Library name: CR_BRM014_PHC2_02
BRM014_PHC2.bw
featureCounts_peak_coverage_PHC2.tsv
PHC2_merged_peaks.bed


title: WT treated with BRM014 PHC2 CUT&RUN (HCT116), rep01

description:
Library name: CR_BRM014_PHC2_01
BRM014_PHC2.bw
featureCounts_peak_coverage_PHC2.tsv
PHC2_merged_peaks.bed


title: WT treated with BRM014 IgG CUT&RUN (HCT116), rep02

description:
Library name: CR_BRM014_IgG_02
BRM014_IgG.bw
featureCounts_peak_coverage_EED.tsv
featureCounts_peak_coverage_PHC2.tsv
featureCounts_peak_coverage_PHC3.tsv
featureCounts_peak_coverage_SMARCC1.tsv


title: Human_CellLines_UFM1_NUCL_DMSO_ANS_rep1

description: Library name: Human_CellLines_UFM1_NUCL_DMSO_ANS_rep1


title: WT treated with BRM014 IgG CUT&RUN (HCT116), rep01

description:
Library name: CR_BRM014_IgG_01
BRM014_IgG.bw
featureCounts_peak_coverage_EED.tsv
featureCounts_peak_coverage_PHC2.tsv
featureCounts_peak_coverage_PHC3.tsv
featureCounts_peak_coverage_SMARCC1.tsv


title: WT treated with BRM014 IgG CUT&RUN (HCT116), rep03

description:
Library name: CR_BRM014_IgG_03
BRM014_IgG.bw
featureCounts_peak_coverage_EED.tsv
featureCounts_peak_coverage_PHC2.tsv
featureCounts_peak_coverage_PHC3.tsv
featureCounts_peak_coverage_SMARCC1.tsv


title: 0day, ncRNA-seq, rep2

description: Library name: S0d-rep2

source_name: cotyledon

value: cotyledon


title: 12day, ncRNA-seq, rep1

description: Library name: S12d-rep1


title: 0day, ncRNA-seq, rep3

description: Library name: S0d-rep3


title: 0day, ncRNA-seq, rep1

description: Library name: S0d-rep1


title: Human_CellLines_UFM1_CYTO_DOX_CTRL_rep1

description: Library name: Human_CellLines_UFM1_CYTO_DOX_CTRL_rep1


title: wild type RING1B CUT&RUN (HCT116) rep08

description:
Library name: CR_WT_RING1B_08
CUT&RUN with RING1B antibody (CST 5694) - not used in the analysis

data_processing:
The raw reads were initially trimmed using Trimmomatic with the empirically determined parameters “HEADCROP:0 ILLUMINACLIP:adapters.fa:2:22:9:2:True LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20”. Quality control of the sequencing data was performed with FastQC and MultiQC. Subsequently, the trimmed reads were aligned to the ribosomal DNA references, retrieved from NCBI with bowtie2 using the -N 1 option to allow single mismatches in the alignment. Reads identified as non-ribosomal were subjected to splicing-aware alignment with the STAR aligner using the settings “--bamRemoveDuplicatesType UniqueIdenticalNotMulti --outMultimapperOrder Random”. For this step, we employed the hg38 genome and RefSeq annotations for introns and exons. Unaligned reads were removed for further processing and a subset of the unaligned reads was used with BLAST to confirm the absence of any contamination. Picard's markDuplicate function was used on the aligned read set to identify duplicate reads. Using the Bedtools' genomecov function, we generated bedgraph files from BAM files with single-base-pair resolution. These files were normalized to 1x genome coverage and converted to bigwigs. In parallel to this, BAM files were processed by featureCounts to determine gene-and-exon-wise coverage in all RNA-Seq samples.
Raw CUT&RUN reads were trimmed with Trimmomatic and empirically determined parameters “HEADCROP:5 ILLUMINACLIP:adapters.fa:2:22:9:2:True LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20”. Quality control of the CUT&RUN sequencing experiment was performed with FastQC and MultiQC. Mitochondrial reads were removed by alignment to the mitochondrial DNA sequence reference from the hg38 genome using Bowtie2. The remaining non-mitochondrial reads were further aligned to the human genome hg38 using Bowtie 2, allowing for single-base mismatches (parameter -N 1). Poor alignments in the produced BAM alignment file, as determined by score fields AS, YS and MAPQ, multi-aligners, as determined by fields AS and XS, large fragments (TLEN>3500) and flagged singletons were subsequently filtered out with samtools. Replicate marking and removal were accomplished using Picard’s MarkDuplicates. Sample- and antibody-specific CUT&RUN peaks were called with macs3, employing multiple replicates for each experiment and using respective IgG CUT&RUNs as controls with a q-value of 0.01 (-q 0.01). For normalizing CUT&RUN tracks, a "background-interval-set" was generated using the complement of a union peak set derived from all samples and antibodies, extending each peak interval by 10 kbp. Bedgraph files, prepared for each sample with BedTools genomecov, were normalized to a standard 1x coverage on the background intervals.
Assembly: hg38
Supplementary files format and content: raw counts per gene (RNA-Seq) for part 1 and part 2 of the analysis - tab-separated
Supplementary files format and content: raw counts per antibody-wise merged peak set (CUT&RUN) for part 1 and part 2 of the analysis - tab-separated
Supplementary files format and content: bigwigs (merged replicates)

extract_protocol:
We followed the CUT&RUN protocol from Skene et al. with some minor modifications. First, Concanavalin A (Polysciences, 86057-10) beads were prepared by taking 20 µl per sample and washing the beads three times with 1 ml of Bead Activation Buffer (20 mM HEPES with pH 7.9, 10 mM KCl, 1 mM CaCl₂ 1 mM MnCl₂), incubating for ~15 minutes on a rotator each time. After washing, tubes were placed on a magnetic stand, supernatant was removed, and beads were resuspended in 200 µl Bead Activation Buffer. For each CUT&RUN sample, 1×10⁶ cells were harvested by trypsinization, quenched, and counted. Then cells were spun down at 500 RCF for 5 minutes and washed with 10 ml of PBS with pH 7.4. Then, we resuspend cells in 0.5% formaldehyde in PBS with pH 7.4. Cells were fixed for 5 minutes, then quenched with 1:1 volume of 1 M Tris pH 8.0 for 10 minutes at room temperature. Afterwards, we washed cells twice with 5 ml PBS with pH 7.4 in 15 ml Falcon tubes by spinning at 500 ×g for 3 minutes. Then cells were resuspended in 100 µl of PBS per library. Afterwards, we added 100 µl Wash Buffer (20 mM HEPES with pH 7.5, 150 mM NaCl, 2 mM EDTA with pH 8.0, 0.5% BSA, 0.1% Triton, Protease Inhibitor Tablet Roche cOmplete EDTA-free) and 40 µl of washed ConA beads. This mixture was incubated for 10 minutes on a rotator to bind cells to beads. Then, samples were spun at 50  RCF for 1 minute, moved to a magnetic stand, and cleared for 1 minute. Afterwards, the supernatant was removed and beads were resuspended in 100 µl Wash Buffer and transferred to PCR strip tubes. We then prepared the corresponding antibody solutions (all antibodies were used at 1:400) in 150 µl Wash Buffer. PCR tubes with beads were moved to a magnetic stand, incubated for 1 minute, and then the supernatant was removed. We then added the antibody solution and resuspended the beads. Finally, the tubes were placed on a nutator overnight at 4°C. The next day, the samples were washed twice with 100 µl Wash Buffer. After removing the Wash Buffer, we added 50 µl of proteinA MNase at 700 ng/ml final in Wash Buffer and incubated for 1 hour at room temperature. Then, the beads were washed three times with 100 µl Wash Buffer. Afterwards, the samples were chilled on ice. We then added 100 µl of ice cold Wash Buffer with 10 mM CaCl₂ to each sample and digested for 1 hour at 4°C. During the incubation, we prepared RNase-containing 2× STOP buffer by mixing 4 µl of 100 mg/ml RNase A with 3996 µl 2× STOP buffer (340 mM NaCl, 20 mM EDTA with pH 8.0, 4 mM EGTA with pH 8.0). After the 1 hour incubation, we added 100 µl of STOP/RNase buffer per sample and incubated at 37°C for 15 minutes. Then, samples were placed on the magnet, allowed to clear for 1 minute, and then the supernatant was transferred to new tubes. We then added 2 µl of 10% SDS and 2 µl of 19 mg/mL proteinase K to each tube and mixed gently. With this, reverse crosslink was performed at 50°C overnight. The next day, we performed the DNA Clean-Up using Ampure XP beads (Beckman Coulter, A63881) at 0.9x beads to sample ratio (e.g. 180 µl of beads with 200 µl of DNA sample). Beads and samples were mixed and incubated at room temperature for 10 minutes. Afterwards, we moved the tubes to the magnet, discarded the supernatant, and washed with 200 µl of freshly prepared 90% ethanol without resuspending. This wash was repeated and then the beads were allowed to air dry just until no visible liquid remained. We then removed the tubes from the magnet, added 52 µl of 0.1× TE, resuspended beads by pipetting, and incubated for 2 minutes at room temperature. Then, the tubes were returned to the magnet and we transferred 50 µl of supernatant to new PCR tubes.
We grew wild-type and PHC2 L307R HCT116 cells in 6-well plates. The day before harvesting the cells, we plated 2.5×10⁵ cells per well. Cells were harvested by adding 0.5 ml of TRI Reagent (Molecular Research Center, TR118) and transferred to a 1.5 ml tube. Then 0.1 ml of chloroform was added to the tube and vigorously mixed. Afterwards, the sample was incubated at room temperature for 3 minutes and centrifuged at 16,000 RCF for 15 minutes at 4°C. We then carefully transferred the upper aqueous phase to a new tube and added 1 volume of 100% ethanol to 1 volume of sample (1:1 ratio). Then, the RNA was purified using the RNA clean & concentrator kit (Zymo Research, R1016) following the manufacturer’s manual. To remove the DNA we performed the “In-column DNase treatment” and used 5 units of TURBO DNAase (Thermo Fisher Scientific, AM2238) as described in the appendix of the manufacturer manual. The quality and concentration was accessed by nanodrop and Agilent Tapestation. Subsequently, the RNA library was prepared using the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research, R3000) following the manufacturer’s manual exactly. We started out with 250 ng of RNA. For the final library amplification we ran 12 PCR cycles. Afterwards library quality was assessed using the Agilent Tapestation. The library concentrations were measured using the NEBNext Library Quant Kit for Illumina (New England Biolabs, E7630L) following the manufacturer’s manual exactly. For PHC2 KO and PHC2 KO with PHC2 overexpression through lentivirus, the NEBnext PolyA mRNA magnetic isolation module (New England Biolabs, E7490L) was used instead of the Zymo-Seq RiboFree Total RNA Library Kit.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®,New England Biolabs, E7645S

tag: batch


title: wild type RING1B CUT&RUN (HCT116) rep06

description:
Library name: CR_WT_RING1B_06
CUT&RUN with RING1B antibody (CST 5694) - not used in the analysis


title: Bat, Putamen, rep 3

city: Dallas

first: Jane

middle: E

last: Johnson

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

description: Library name: Bat_put_3

library_source: transcriptomic single cell

data_processing:
Raw base call (BCL) files were analyzed using CellRanger (v6.0.0)
Gene annotation files of non-human primates were generated using Liftoff tool (v1) using the human gene annotation file as reference. Then the genome files were generated using "CellRanger mkref" using the genome fasta files given below with the newly generated gene anniotation files for these species.
The “mkfastq” command was used to generate FASTQ files and the "CellRanger count" command was used to generate raw gene-cell expression matrices.
Ambient RNA contamination was inferred and removed using CellBender (v0.2.0) with standard parameters
Data were filtered, normalized, integrated, clustered, annotated, and visualized using a Seurat v3 pipeline
Assembly: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10), Marmoset: calJac3, Bat:GCF_004126475.2_mPhyDis1.pri.v3, Mouse: mm10, Ferret: GCF_011764305.1_ASM1176430v1.1
Supplementary files format and content: barcodes.tsv.gz' contains cell barcodes, 'features.tsv.gz' containts gene symbols, 'matrix.mtx.gz' contains raw counts. 'meta.tsv.gz' contains the meta data.
Supplementary files format and content: In addition to raw data generated in-house, publicly available raw data for mouse and ferrets from publications were used to process the data for this project. Processed data is also included with this dataset.

molecule: nuclear RNA

organism: Phyllostomus discolor

source_name: Putamen

extract_protocol:
Nuclei for snRNA-seq were isolated from bat putamen and caudate brain tissue. Briefly, the tissue was homogenized in 500 µL of ice-cold Nuclei EZ lysis buffer (EZ PREP NUC-101, Sigma) using a pre-chilled glass Dounce homogenizer. Debris was removed via density gradient centrifugation using Nuclei PURE 2 M sucrose cushion solution and Nuclei PURE sucrose cushion buffer (Nuclei PURE prep isolation kit, no. NUC201-1KT, Sigma Aldrich). These two solutions were mixed in a 9:1 ratio, and 500 µL of the sucrose solution was added to a 2-ml Eppendorf tube. The homogenized nuclei suspension was mixed with 900 µL of sucrose cushion solution by pipetting 10 times, resulting in a 1,400 µL volume, which was carefully layered over the sucrose buffer without mixing. The samples were centrifuged at 13,000 x g for 45 min at 4 °C, and all but 100 µL of supernatant was discarded. Nuclei were resuspended in 300 µL of nucleus suspension buffer (NSB), consisting of 1× PBS, 2% BSA (no. AM2618, Thermo Fisher Scientific), and 0.4 U µL −1 RNAse inhibitor (no. AM2694, Thermo Fisher Scientific). Samples were then centrifuged at 550 x g for 5 min at 4 °C, and all but 50 µL of supernatant was discarded. The nuclear pellet was resuspended in NSB and filtered through a 40-μm Flowmi cell strainer (Bel-Art Products, #H13680-0040) into a new tube. The nuclei concentration was measured using Hoechst and decreased to 1,000 nuclei per µL with NSB if necessary. Cellular nuclei for snRNA-seq were isolated from the putamen and caudate nuclei of human, chimpanzee, and rhesus macaque tissues. Briefly, the tissue was homogenized in 750 µL of ice-cold NP40 lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Nonidet P40 Substitute, 1 mM DTT, 0.2 U/µL RNAse inhibitor) using a pre-chilled glass Dounce homogenizer. An additional 750 µL of ice-cold NP40 lysis buffer was added, and the mixture was pipette-mixed during a 5-minute incubation on ice. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, resuspended in 1 mL of ice-cold lysis buffer, and incubated on ice for 5 minutes with gentle pipette mixing throughout. The nuclei were then centrifuged again at 500 x g for 5 minutes at 4°C, and all but 50 µL of supernatant was discarded. Next, 500 µL of nucleus suspension buffer (NSB) containing 1× PBS, 1% Ultrapure BSA (no. AM2618, Thermo Fisher Scientific), and 0.2 U/µL RNAse inhibitor (no. AM2694, Thermo Fisher Scientific) was added, and the sample was incubated for 5 minutes on ice without mixing. The pellet was resuspended, centrifuged again at 500 x g for 5 minutes at 4°C, and all but 50 µL of supernatant was discarded. The nuclei were then resuspended in 500 µL of NSB and filtered through a 70-μm Flowmi cell strainer (no. H13680-0070, Bel-Art) into a 1.5 mL tube.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3′ v3.1 (10x Genomics) kit, following the manufacturer's protocol. Libraries were sequenced on an Illumina NovaSeq 6000.

tag: sample id

value: male

value: Putamen


title: Human_CellLines_UFM1_CYTO_DOX_CTRL_rep2

description: Library name: Human_CellLines_UFM1_CYTO_DOX_CTRL_rep2


title: wild type RING1B CUT&RUN (HCT116) rep05

description:
Library name: CR_WT_RING1B_05
CUT&RUN with RING1B antibody (CST 5694) - not used in the analysis


title: Human_CellLines_UFM1_NUCL_DMSO_ANS_rep3

description: Library name: Human_CellLines_UFM1_NUCL_DMSO_ANS_rep3


title: wild type RING1B CUT&RUN (HCT116) rep04

description:
Library name: CR_WT_RING1B_04
CUT&RUN with RING1B antibody (CST 5694) - used in part 2 of the analysis


title: Human_CellLines_UFM1_CYTO_DOX_ANS_rep3

description: Library name: Human_CellLines_UFM1_CYTO_DOX_ANS_rep3


title: Human_CellLines_UFM1_CYTO_DOX_ANS_rep2

description: Library name: Human_CellLines_UFM1_CYTO_DOX_ANS_rep2


title: wild type RING1B CUT&RUN (HCT116) rep07

description:
Library name: CR_WT_RING1B_07
CUT&RUN with RING1B antibody (CST 5694) - not used in the analysis


title: 12day, ncRNA-seq, rep3

description: Library name: S12d-rep3


title: Bat, Putamen, rep 2

description: Library name: Bat_put_2


title: Bat, Putamen, rep 4

description: Library name: Bat_put_4


title: wild type RING1B CUT&RUN (HCT116) rep01

description:
Library name: CR_WT_RING1B_01
CUT&RUN with RING1B antibody (CST 5694) - used in part 1 of the analysis


title: Human_CellLines_UFM1_CYTO_DOX_CTRL_rep3

description: Library name: Human_CellLines_UFM1_CYTO_DOX_CTRL_rep3


title: Human_CellLines_UFM1_CYTO_DOX_ANS_rep1

description: Library name: Human_CellLines_UFM1_CYTO_DOX_ANS_rep1


title: wild type PHC2 CUT&RUN (HCT116) rep07

description:
Library name: CR_WT_PHC2_07
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - not used in the analysis


title: Bat, Putamen, rep 1

description: Library name: Bat_put_1


title: wild type RING1B CUT&RUN (HCT116) rep02

description:
Library name: CR_WT_RING1B_02
CUT&RUN with RING1B antibody (CST 5694) - used in part 1 of the analysis


title: wild type PHC2 CUT&RUN (HCT116) rep06

description:
Library name: CR_WT_PHC2_06
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - not used in the analysis


title: wild type PHC2 CUT&RUN (HCT116) rep08

description:
Library name: CR_WT_PHC2_08
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - not used in the analysis


title: wild type PHC2 CUT&RUN (HCT116) rep05

description:
Library name: CR_WT_PHC2_05
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - not used in the analysis


description: Library name: Human_CellLines_UFM1_CYTO_DMSO_CTRL_rep3


title: Bat, Caudate Nucleus, rep 4

description: Library name: Bat_caud_4

source_name: Caudate Nucleus

value: Caudate Nucleus


description: Library name: Human_CellLines_UFM1_CYTO_DMSO_CTRL_rep2


title: wild type PHC2 CUT&RUN (HCT116) rep04

description:
Library name: CR_WT_PHC2_04
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - used in part 2 of the analysis


title: Bat, Caudate Nucleus, rep 3

description: Library name: Bat_caud_3


description: Library name: Human_CellLines_UFM1_CYTO_DMSO_CTRL_rep1


title: wild type PHC2 CUT&RUN (HCT116) rep02

description:
Library name: CR_WT_PHC2_02
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - used in part 1 of the analysis


title: wild type RING1B CUT&RUN (HCT116) rep03

description:
Library name: CR_WT_RING1B_03
CUT&RUN with RING1B antibody (CST 5694) - used in part 2 of the analysis


title: wild type PHC2 CUT&RUN (HCT116) rep03

description:
Library name: CR_WT_PHC2_03
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - used in part 2 of the analysis


title: Bat, Caudate Nucleus, rep 1

description: Library name: Bat_caud_1


title: wild type IgG CUT&RUN (HCT116) rep06

description:
Library name: CR_WT_IgG_06
CUT&RUN with IgG antibody (CST 2729) - not used in the analysis


title: wild type IgG CUT&RUN (HCT116) rep08

description:
Library name: CR_WT_IgG_08
CUT&RUN with IgG antibody (CST 2729) - not used in the analysis


title: Human_CellLines_UFM1_CYTO_DMSO_ANS_rep2

description: Library name: Human_CellLines_UFM1_CYTO_DMSO_ANS_rep2


title: wild type PHC2 CUT&RUN (HCT116) rep01

description:
Library name: CR_WT_PHC2_01
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - used in part 1 of the analysis


title: wild type IgG CUT&RUN (HCT116) rep05

description:
Library name: CR_WT_IgG_05
CUT&RUN with IgG antibody (CST 2729) - not used in the analysis


title: Human_CellLines_UFM1_CYTO_DMSO_ANS_rep3

description: Library name: Human_CellLines_UFM1_CYTO_DMSO_ANS_rep3


title: wild type IgG CUT&RUN (HCT116) rep07

description:
Library name: CR_WT_IgG_07
CUT&RUN with IgG antibody (CST 2729) - not used in the analysis


title: Human_CellLines_UFM1_CYTO_DMSO_ANS_rep1

description: Library name: Human_CellLines_UFM1_CYTO_DMSO_ANS_rep1


title: wild type IgG CUT&RUN (HCT116) rep02

description:
Library name: CR_WT_IgG_02
CUT&RUN with IgG antibody (CST 2729) - used in part 1 of the analysis


title: Bat, Caudate Nucleus, rep 2

description: Library name: Bat_caud_2


title: wild type IgG CUT&RUN (HCT116) rep04

description:
Library name: CR_WT_IgG_04
CUT&RUN with IgG antibody (CST 2729) - used in part 2 of the analysis


title: wild type IgG CUT&RUN (HCT116) rep03

description:
Library name: CR_WT_IgG_03
CUT&RUN with IgG antibody (CST 2729) - used in part 2 of the analysis


description: Library name: Arabidopsis_Seedlings_ufm1_DMSO_Nuclear_Rep3

organism: Arabidopsis thaliana

source_name: 10-days old seedlings

value: 10-days old seedlings

value: ufm1 mutant


description: Library name: Arabidopsis_Seedlings_ufm1_DMSO_Cytosol_Rep3


title: wild type H3K27me3 CUT&RUN (HCT116) rep08

description:
Library name: CR_WT_H3K27me3_08
CUT&RUN with H3K27me3 antibody (CST 9733) - not used in the analysis


title: wild type H3K27me3 CUT&RUN (HCT116) rep06

description:
Library name: CR_WT_H3K27me3_06
CUT&RUN with H3K27me3 antibody (CST 9733) - not used in the analysis


description: Library name: Arabidopsis_Seedlings_ufm1_DMSO_Nuclear_Rep2


title: wild type H3K27me3 CUT&RUN (HCT116) rep04

description:
Library name: CR_WT_H3K27me3_04
CUT&RUN with H3K27me3 antibody (CST 9733) - used in part 2 of the analysis


title: Human_CellLines_AAVS1_NUCL_DOX_ANS_rep1

description: Library name: Human_CellLines_AAVS1_NUCL_DOX_ANS_rep1

value: AAVS1 control


description: Library name: Human_CellLines_AAVS1_NUCL_DOX_CTRL_rep2

value: RKO cell lines


title: wild type H3K27me3 CUT&RUN (HCT116) rep02

description:
Library name: CR_WT_H3K27me3_02
CUT&RUN with H3K27me3 antibody (CST 9733) - used in part 1 of the analysis


description: Library name: Arabidopsis_Seedlings_ufm1_DMSO_Nuclear_Rep1


description: Library name: Arabidopsis_Seedlings_ufm1_ANS_Nuclear_Rep3


description: Library name: Human_CellLines_AAVS1_NUCL_DOX_CTRL_rep3


description: Library name: Arabidopsis_Seedlings_ufm1_DMSO_Cytosol_Rep1


title: wild type H3K27me3 CUT&RUN (HCT116) rep07

description:
Library name: CR_WT_H3K27me3_07
CUT&RUN with H3K27me3 antibody (CST 9733) - not used in the analysis


description: Library name: Human_CellLines_AAVS1_NUCL_DMSO_CTRL_rep2


title: wild type H3K27me3 CUT&RUN (HCT116) rep03

description:
Library name: CR_WT_H3K27me3_03
CUT&RUN with H3K27me3 antibody (CST 9733) - used in part 2 of the analysis


title: wild type H3K27ac CUT&RUN (HCT116) rep07

description:
Library name: CR_WT_H3K27ac_07
CUT&RUN with H3K27ac antibody (CST 8173) - not used in the analysis


title: wild type H3K27ac CUT&RUN (HCT116) rep06

description:
Library name: CR_WT_H3K27ac_06
CUT&RUN with H3K27ac antibody (CST 8173) - not used in the analysis


title: wild type IgG CUT&RUN (HCT116) rep01

description:
Library name: CR_WT_IgG_01
CUT&RUN with IgG antibody (CST 2729) - used in part 1 of the analysis


description: Library name: Arabidopsis_Seedlings_ufm1_DMSO_Cytosol_Rep2


description: Library name: Human_CellLines_AAVS1_NUCL_DOX_CTRL_rep1


title: wild type H3K27ac CUT&RUN (HCT116) rep04

description:
Library name: CR_WT_H3K27ac_04
CUT&RUN with H3K27ac antibody (CST 8173) - used in part 2 of the analysis


description: Library name: Arabidopsis_Seedlings_ufm1_ANS_Cytosol_Rep3


title: wild type H3K27me3 CUT&RUN (HCT116) rep01

description:
Library name: CR_WT_H3K27me3_01
CUT&RUN with H3K27me3 antibody (CST 9733) - used in part 1 of the analysis


description: Library name: Arabidopsis_Seedlings_ufm1_ANS_Nuclear_Rep2


title: wild type H3K27ac CUT&RUN (HCT116) rep08

description:
Library name: CR_WT_H3K27ac_08
CUT&RUN with H3K27ac antibody (CST 8173) - not used in the analysis


description: Library name: Human_CellLines_AAVS1_NUCL_DMSO_ANS_rep1


description: Library name: Human_CellLines_AAVS1_CYTO_DOX_CTRL_rep1


title: wild type H3K27ac CUT&RUN (HCT116) rep05

description:
Library name: CR_WT_H3K27ac_05
CUT&RUN with H3K27ac antibody (CST 8173) - not used in the analysis


title: wild type H3K27me3 CUT&RUN (HCT116) rep05

description:
Library name: CR_WT_H3K27me3_05
CUT&RUN with H3K27me3 antibody (CST 9733) - not used in the analysis


title: wild type H3K27ac CUT&RUN (HCT116) rep03

description:
Library name: CR_WT_H3K27ac_03
CUT&RUN with H3K27ac antibody (CST 8173) - used in part 2 of the analysis


description: Library name: Human_CellLines_AAVS1_NUCL_DMSO_CTRL_rep1


title: wild type H3K27ac CUT&RUN (HCT116) rep01

description:
Library name: CR_WT_H3K27ac_01
CUT&RUN with H3K27ac antibody (CST 8173) - used in part 1 of the analysis


title: wild type H3K27ac CUT&RUN (HCT116) rep02

description:
Library name: CR_WT_H3K27ac_02
CUT&RUN with H3K27ac antibody (CST 8173) - used in part 1 of the analysis


description: Library name: Arabidopsis_Seedlings_ufm1_ANS_Cytosol_Rep2


title: Human_CellLines_AAVS1_CYTO_DOX_ANS_rep1

description: Library name: Human_CellLines_AAVS1_CYTO_DOX_ANS_rep1


description: Library name: Human_CellLines_AAVS1_NUCL_DMSO_CTRL_rep3


title: wild type EZH2 CUT&RUN (HCT116) rep04

description:
Library name: CR_WT_EZH2_04
CUT&RUN with EZH2 antibody (CST D2C9) - not used in the analysis


title: wild type EZH2 CUT&RUN (HCT116) rep03

description:
Library name: CR_WT_EZH2_03
CUT&RUN with EZH2 antibody (CST D2C9) - not used in the analysis


title: wild type BAF155 CUT&RUN (HCT116) rep07

description:
Library name: CR_WT_BAF155_07
CUT&RUN with BAF155 antibody (CST 11956) - not used in the analysis


description: Library name: Arabidopsis_Seedlings_Col0_DMSO_Nuclear_Rep2


title: wild type EZH2 CUT&RUN (HCT116) rep02

description:
Library name: CR_WT_EZH2_02
CUT&RUN with EZH2 antibody (CST D2C9) - used in part 2 of the analysis


description: Library name: Human_CellLines_AAVS1_CYTO_DMSO_ANS_rep1


title: wild type EZH2 CUT&RUN (HCT116) rep01

description:
Library name: CR_WT_EZH2_01
CUT&RUN with EZH2 antibody (CST D2C9) - used in part 2 of the analysis


title: wild type BAF155 CUT&RUN (HCT116) rep06

description:
Library name: CR_WT_BAF155_06
CUT&RUN with BAF155 antibody (CST 11956) - not used in the analysis


description: Library name: Arabidopsis_Seedlings_Col0_DMSO_Nuclear_Rep3


description: Library name: Human_CellLines_AAVS1_CYTO_DMSO_CTRL_rep1


title: wild type BAF155 CUT&RUN (HCT116) rep08

description:
Library name: CR_WT_BAF155_08
CUT&RUN with BAF155 antibody (CST 11956) - not used in the analysis


description: Library name: Arabidopsis_Seedlings_ufm1_ANS_Cytosol_Rep1


description: Library name: Arabidopsis_Seedlings_Col0_DMSO_Nuclear_Rep1


title: wild type BAF155 CUT&RUN (HCT116) rep05

description:
Library name: CR_WT_BAF155_05
CUT&RUN with BAF155 antibody (CST 11956) - not used in the analysis


title: pcDNA:VLDL, Rep5

city: St. John's

first: Lourdes

last: Peña-Castillo

state: Newfoundland and Labrador

address: 9 Arctic Ave

country: Canada

institute: Memorial University of Newfoundland

description:
Library name: P6
Column name in processed data file is the library name

data_processing:
Adapter removal and read filtering/trimming were performed using fastp version 0.24.0
Reads were mapped using STAR version 2.7.11b with the following aligning parameters “--outFilterMismatchNmax 1 --alignEndsType EndToEnd --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 16 --alignSJDBoverhangMin 1000 --alignIntronMax 1 --outFilterMultimapScoreRange 0”
Read counts were obtained using featureCounts
The read count matrix generated by featureCounts for the five biological replicates per condition was read into R version 4.4.2. As small RNA libraries were sequenced,  read counts corresponding to miRNAs, snRNAs, snoRNAs and tRNAs as per the NCBI genome annotation (gtf) file were  selected for further analysis. Differential expression analysis was separately performed using edgeR version 4.4.2 and DESeq2 version 1.46.
Assembly: hg38
Supplementary files format and content: tab-delimited text file with raw counts per sample

source_name: cell line

growth_protocol: HEK-293 cells were maintained at 37°C with 5% CO2 (gas) in T75 flasks with Dulbecco's Modified Eagle Medium (DMEM) (cat. #SH30022.01, Cytiva, Marlborough, MA, USA) containing 1% v/v antibiotic/antimycotic (A/A) (cat. #15240062, Gibco™, Thermo Fisher Scientific, Waltham, MA, USA) and 10% v/v fetal bovine serum (FBS) (cat. #16000044, Gibco™, Thermo Fisher Scientific).

extract_protocol:
Following 18 hours of incubation without or with HP, in the absence or presence of NOX inhibitors, media were removed and the cells were washed with 1X PBS, then 1 mL of TRIzol® Reagent (cat. #15596018, Invitrogen, Thermo Fisher Scientific) was pipetted into each well. RNA was extracted as described by the manufacturer. Isolated RNA was resuspended in 40 μL of nuclease-free water. Genomic DNA contamination was removed by treating the isolated RNA with the TURBO DNA-free™ Kit (cat. #AM1907, Invitrogen, Thermo Fisher Scientific) per the manufacturer’s instructions. The RNA concentration and purity were measured after DNase treatment. The RNA quality was examined using a 1% agarose gel electrophoresis.
Small RNA libraries were prepared at The Centre for Applied Genomics (Toronto, ON, Canada) using the NEBNext® Multiplex Small RNA Library Prep Kit for Illumina® (Index Primers 1-48) (cat. #E7560, New England Biolabs, Whitby, ON, Canada) following the manufacturer's protocol. Pooled libraries of equimolar quantities were sequenced on the Illumina NovaSeq X Series platform using a partial lane of a 25B flow cell.

value: cell line

tag: cell type

value: Human Embryonic Kidney cells

value: WT

value: Cells treated with very low-density lipoprotein (VLDL)


title: wild type BAF155 CUT&RUN (HCT116) rep02

description:
Library name: CR_WT_BAF155_02
CUT&RUN with BAF155 antibody (CST 11956) - used in part 1 of the analysis


title: wild type BAF155 CUT&RUN (HCT116) rep03

description:
Library name: CR_WT_BAF155_03
CUT&RUN with BAF155 antibody (CST 11956) - used in part 2 of the analysis


description: Library name: Arabidopsis_Seedlings_ufm1_ANS_Nuclear_Rep1

value: Anisomycin


title: pcDNA:VLDL, Rep3

description:
Library name: P4
Column name in processed data file is the library name


title: wild type BAF155 CUT&RUN (HCT116) rep04

description:
Library name: CR_WT_BAF155_04
CUT&RUN with BAF155 antibody (CST 11956) - used in part 2 of the analysis


title: pcDNA:VLDL, Rep4

description:
Library name: P5
Column name in processed data file is the library name


title: pcDNA:VLDL, Rep2

description:
Library name: P3
Column name in processed data file is the library name


title: wild type RNA-Seq (HCT116) rep10

description:
Library name: RNA_WT_10
RNA-Seq - not used in the analysis


title: wild type BAF155 CUT&RUN (HCT116) rep01

description:
Library name: CR_WT_BAF155_01
CUT&RUN with BAF155 antibody (CST 11956) - used in part 1 of the analysis


description: Library name: Arabidopsis_Seedlings_Col0_DMSO_Cytosol_Rep2


title: pcDNA:VLDL, Rep1

description:
Library name: P2
Column name in processed data file is the library name


title: wild type RNA-Seq (HCT116) rep08

description:
Library name: RNA_WT_08
RNA-Seq - used in part 2 of the analysis

molecule: polyA RNA


description: Library name: Arabidopsis_Seedlings_Col0_DMSO_Cytosol_Rep3


description: Library name: Arabidopsis_Seedlings_Col0_DMSO_Cytosol_Rep1


title: wild type RNA-Seq (HCT116) rep09

description:
Library name: RNA_WT_09
RNA-Seq - not used in the analysis


title: wild type RNA-Seq (HCT116) rep07

description:
Library name: RNA_WT_07
RNA-Seq - used in part 2 of the analysis


description: Library name: Arabidopsis_Seedlings_Col0_ANS_Nuclear_Rep3


title: wild type RNA-Seq (HCT116) rep06

description:
Library name: RNA_WT_06
RNA-Seq - used in part 1 of the analysis


title: wild type RNA-Seq (HCT116) rep05

description:
Library name: RNA_WT_05
RNA-Seq - used in part 1 of the analysis


title: LPL:VLDL, Rep5

description:
Library name: L6
Column name in processed data file is the library name

value: Cells treated with VLDL lipid hydrolysis products generated by LPL


description: Library name: Arabidopsis_Seedlings_Col0_ANS_Nuclear_Rep2

value: Wild type


title: LPL:VLDL, Rep4

description:
Library name: L5
Column name in processed data file is the library name


title: wild type RNA-Seq (HCT116) rep03

description:
Library name: RNA_WT_03
RNA-Seq - used in part 1 of the analysis


title: LPL:VLDL, Rep3

description:
Library name: L4
Column name in processed data file is the library name


title: wild type RNA-Seq (HCT116) rep02

description:
Library name: RNA_WT_02
RNA-Seq - used in part 1 of the analysis


title: wild type RNA-Seq (HCT116) rep04

description:
Library name: RNA_WT_04
RNA-Seq - used in part 1 of the analysis


title: wild type RNA-Seq (HCT116) rep01

description:
Library name: RNA_WT_01
RNA-Seq - used in part 1 of the analysis


description: Library name: Arabidopsis_Seedlings_Col0_ANS_Nuclear_Rep1


description: Library name: Arabidopsis_Seedlings_Col0_ANS_Cytosol_Rep1


title: LPL:VLDL, Rep2

description:
Library name: L3
Column name in processed data file is the library name


description: Library name: Arabidopsis_Seedlings_Col0_ANS_Cytosol_Rep3


title: LPL:VLDL, Rep1

description:
Library name: L2
Column name in processed data file is the library name


title: PHC2 KO with PHC2 lentivirus overexpression PHC2 CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-Lenti_PHC2_04
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - not used in the analysis


title: PHC2 KO with PHC2 lentivirus overexpression RING1B CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-Lenti_RING1B_01
CUT&RUN with RING1B antibody (CST 5694) - used in part 2 of the analysis


title: PHC2 KO with PHC2 lentivirus overexpression RING1B CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-Lenti_RING1B_02
CUT&RUN with RING1B antibody (CST 5694) - used in part 2 of the analysis


title: 20 µM GKT136901 + LPL:VLDL, Rep5

description:
Library name: G6
Column name in processed data file is the library name

value: “L” + the NOX1/4 inhibitor GKT136901


description: Library name: Arabidopsis_Seedlings_Col0_ANS_Cytosol_Rep2


title: PHC2 KO with PHC2 lentivirus overexpression PHC2 CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-Lenti_PHC2_03
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - not used in the analysis


title: REI_POWR510_GC_DNA

type: genomic

city: Atlanta

first: Alicia

middle: K

last: Smith

state: GA

address: 101 Woodruff Circle NE

institute: Emory University

hyb_protocol: Bisulfite conveted DNA was fragmented and hybridized according to MethylationEPICv2 (Illumina) standard protocol

scan_protocol: Array was imaged with HiScan and standard Illumina settings

data_processing: Enmix package

label: Cy3 and Cy48

source_name: Granulosa Cells

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from blood using the DNeasy Blood and Tissue kit (Qiagen) using standard protocol

value: Granulosa Cells

value: Female


title: PHC2 KO with PHC2 lentivirus overexpression RING1B CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-Lenti_RING1B_03
CUT&RUN with RING1B antibody (CST 5694) - not used in the analysis


title: PHC2 KO with PHC2 lentivirus overexpression PHC2 CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-Lenti_PHC2_01
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - used in part 2 of the analysis


title: PHC2 KO with PHC2 lentivirus overexpression PHC2 CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-Lenti_PHC2_02
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - used in part 2 of the analysis


title: 20 µM GKT136901 + LPL:VLDL, Rep3

description:
Library name: G4
Column name in processed data file is the library name


title: PHC2 KO with PHC2 lentivirus overexpression IgG CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-Lenti_IgG_03
CUT&RUN with IgG antibody (CST 2729) - not used in the analysis


title: REI_POWR193_GC_DNA

label: Cy3 and Cy46


title: 20 µM GKT136901 + LPL:VLDL, Rep4

description:
Library name: G5
Column name in processed data file is the library name


title: PHC2 KO with PHC2 lentivirus overexpression IgG CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-Lenti_IgG_04
CUT&RUN with IgG antibody (CST 2729) - not used in the analysis


title: REI_POWR600_GC_DNA

label: Cy3 and Cy47


title: PHC2 KO with PHC2 lentivirus overexpression RING1B CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-Lenti_RING1B_04
CUT&RUN with RING1B antibody (CST 5694) - not used in the analysis


title: REI_POWR526_GC_DNA

label: Cy3 and Cy45


title: PHC2 KO with PHC2 lentivirus overexpression RNA-Seq H3K27me3 CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-Lenti_H3K27me3_01
CUT&RUN with H3K27me3 antibody (CST 9733) - used in part 2 of the analysis


title: 20 µM GKT136901 + LPL:VLDL, Rep2

description:
Library name: G3
Column name in processed data file is the library name


title: 20 µM GKT136901 + LPL:VLDL, Rep1

description:
Library name: G2
Column name in processed data file is the library name


title: PHC2 KO with PHC2 lentivirus overexpression IgG CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-Lenti_IgG_01
CUT&RUN with IgG antibody (CST 2729) - used in part 2 of the analysis


title: Hepatoblastoma, pediatric sample, merge

city: Shanghai

first: rui

last: Dong

address: 399 Wan Yuan Road

institute: Department of Pediatric Surgery, Children’s Hospital of Fudan University, and Shanghai Key Laboratory of Birth Defect

description: Library name: Hepatoblastoma, pediatric sample, merge

data_processing:
Raw sequencing data were converted to FASTQ files using Illumina bcl2fastq and aligned to the human reference genome GRCh38. Sample demultiplexing, barcode processing, and single-cell 3′ gene counting were performed using the Cell Ranger analysis pipeline to generate digital gene-by-cell expression matrices. Downstream processing and analysis were performed using Seurat. Cells with 250–6000 detected genes and less than 7.5% mitochondrial gene content were retained. Potential doublets were identified using Scrublet with default parameters and an expected doublet rate of 0.02. Additional doublet-enriched clusters were removed based on co-expression of lineage-specific markers, including T-myeloid doublets expressing both myeloid markers (CD14, CD68, TYROBP) and T cell markers (CD2, CD3D, CD3E). Mitochondrial genes were then removed from the expression matrix.
Assembly: GRCh38
Supplementary files format and content: Processed data files include a sparse gene-cell count matrix in Matrix Market format, gene feature annotation, cell barcode identifiers, and a cell-level metadata/annotation table.

source_name: Liver

extract_protocol:
Tumor biopsies were kept in MACS Tissue Storage Solution until processing. Samples were washed with phosphate-buffered saline, minced into small pieces (approximately 1 mm3) on ice, and enzymatically digested in DMEM containing 300 U/mL collagenase II for 30 min at 37°C with agitation. After digestion, samples were filtered through a 70 µm cell strainer and centrifuged at 400 × g for 5 min. Cell pellets were resuspended in red blood cell lysis buffer to remove red blood cells. Dissociated single cells were stained with AO/PI for viability assessment using a Countstar Fluorescence Cell Analyzer. Where necessary, dead cells were further removed using a MACS Dead Cell Removal Kit.
Single-cell 3′ gene expression libraries were generated using the 10x Genomics Chromium workflow according to the manufacturer’s instructions. Briefly, viable dissociated single cells were loaded into the Chromium system for barcoding and library preparation, and single-cell 3′ RNA libraries were constructed for downstream sequencing.

treatment_protocol: Patients classified as post-chemotherapy received 2–4 cycles of neoadjuvant chemotherapy with cisplatin, vincristine, and 5-fluorouracil according to Pediatric Oncology Group treatment protocols. Treatment-naive samples were collected before chemotherapy.

value: Liver


title: PHC2 KO with PHC2 lentivirus overexpression RNA-Seq H3K27me3 CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-Lenti_H3K27me3_03
CUT&RUN with H3K27me3 antibody (CST 9733) - not used in the analysis


title: PHC2 KO with PHC2 lentivirus overexpression IgG CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-Lenti_IgG_02
CUT&RUN with IgG antibody (CST 2729) - used in part 2 of the analysis


title: PHC2 KO with PHC2 lentivirus overexpression RNA-Seq H3K27me3 CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-Lenti_H3K27me3_02
CUT&RUN with H3K27me3 antibody (CST 9733) - used in part 2 of the analysis


title: PHC2 KO with PHC2 lentivirus overexpression RNA-Seq H3K27me3 CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-Lenti_H3K27me3_04
CUT&RUN with H3K27me3 antibody (CST 9733) - not used in the analysis


title: PHC2 KO with PHC2 lentivirus overexpression H3K27ac CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-Lenti_H3K27ac_04
CUT&RUN with H3K27ac antibody (CST 8173) - not used in the analysis


title: REI_POWR710_GC_DNA

label: Cy3 and Cy42


title: REI_POWR521_GC_DNA

label: Cy3 and Cy44


title: REI_POWR884_GC_DNA

label: Cy3 and Cy41


title: Jurkat, BCL11B-dTAG, dTAGV-1, rep2, ATAC

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

description: Library name: ATAC_Jurkat_BCL11BdTAG_dTAG_rep2

data_processing:
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1) and converted to paired-end fragment intervals (BEDPE). For coverage calculation, fragments with inferred insert size < 2000 bp were counted and used to compute a library-size scaling factor to normalize signal to a fixed library size. The center 80 bp of these fragments were used to generate genome-wide coverage tracks using bedtools genomecov in bedGraph format (-bg), applying the scaling factor for depth normalization (-scale). BedGraph files were converted to BigWig format using UCSC tools (bedGraphToBigWig) for visualization in IGV and for creating heatmaps. To increase detection of BCL11BdTAG and RUNX1 binding events in CD34+ HSPCs without DMSO or dTAGV-1 treatment, the mapped bam files from both replicates were merged prior to downstream processing.
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. The first 15 bp of each read were clipped to reduce the GC bias introduced by the Tn5 enzyme. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1). The center 80 bp of nucleosome-free fragments (fragment size < 109 bp) were extracted using bedtools and converted to scaled genome coverage tracks for visualization on IGV and in heatmaps. The scaling factor was computed from the total number of nucleosome-free fragments to normalize signal to a fixed library size. Peaks were called with MACS2 (v2.1.1.20160309) using nucleosome-free fragments with parameters -f BEDPE --keep-dup all -q 0.01
For CD34+ HSPCs: Paired-end RNA-seq reads were adapter and quality trimmed using Trim Galore (v0.4.4), and read quality was assessed with FastQC. Reads were aligned to the GRCh38 reference genome with STAR (v2.7) in two-pass mode. Coordinate-sorted BAM files, transcriptome alignments, gene counts, and strand-specific RPM-normalized coverage tracks were generated during alignment, and wiggle files were converted to BigWig format using wigToBigWig. Duplicate reads were marked with GATK MarkDuplicates, alignments were indexed with SAMtools, and RNA-seq quality metrics were collected using Picard CollectRnaSeqMetrics. Gene- and isoform-level expression was quantified with RSEM. Differential expression analysis was performed using the edgeR/limma-voom workflow. Genes with counts per million (CPM) ≥ 1 in at least 3 samples were retained using edgeR, and normalized expression values were generated by voom as log2-counts per million. Differentially expressed genes between treatment groups and transduction conditions were identified using linear models with empirical Bayes moderation implemented in limma.
For Jurkat BRU-seq: Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2. Unaligned reads were subsequently mapped strand-specifically to human genome build hg38/GRCh38 using STAR and GENCODE annotation version 27. Gene expression was quantified as previously described (Magnuson et al., 2022) and differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: .bw files contain coverage files in bigwig format
Supplementary files format and content: .narrowPeak files contain MACS2 called peaks
Supplementary files format and content: .txt file contains transcripts per million (TPM) values

source_name: Jurkat

growth_protocol: CD34+ HSPCs were expanded in Stemspan media supplemented with 1X penicillin-streptomycin-glutamine, 100ng/mL SCF, TPO, IL-6 and FLT3-L, and 1 µM stemregenin-1. Jurkat cells were cultured in RPMI-1640 supplemented with 1X penicillin-streptomycin-glutamine and 10% FBS.

extract_protocol:
CUT&RUN was performed on 0.1 – 0.5 million CD34+ HSPCs using the CUTANA ChIC/CUT&RUN kit from EpiCypher (#14-1048-24) following manufacturer’s instructions.
ATAC-seq was performed with 50,000 cells using the Omni-ATAC protocol as described (Corces et al., 2017). Cells were washed once with 1X PBS and then lysed in 50µl cold Cell Lysis Buffer containing 0.01% digitonin for 3 minutes on ice. After cell lysis, 1mL cold Resuspension Buffer was added and cells were immediately spun at 600xg for 10 minutes at 4°C. After removing the supernatant, the nuclei were transposed in 50µl Transposition reaction using the Tn5 enzyme from Illumina for 30 minutes at 37°C. Transposed DNA was purified using a Qiagen MinElute PCR clean-up kit and DNA was eluted in 10µl Elution Buffer.
CD34+ HSPCs were harvested following DMSO or dTAGV-1 treatment and resuspended in TRI Reagent (Sigma). RNA was isolated using the Direct-zol RNA miniprep kit (Zymo Research #R2050). For BRU-seq, cells were lysed directly in Trizol followed by isolation of total RNA and treatment with DNAse (TURBO DNA-free Kit; Invitrogen). The Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences).
Libraries were constructed using library prep kits from EpiCypher (#14-1001) following manufacturer’s instructions.
Libraries were constructed by amplifying eluted DNA with barcoded primers described in Corces et al., 2017 for 10-12 cycles. The optimal number of cycles was determined by performing a quantitative PCR analysis after the initial 5 PCR cycles. Amplified libraries were purified using AMPure beads to remove fragments less than 200bp and larger than 700 bp. Final barcoded libraries were pooled and sequenced in paired-end mode.
CD34+ HSPCs: RNA was quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation. Libraries were prepared from total RNA with the Illumina Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20040529). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina). Paired end 100 cycle sequencing was performed on a NovaSeq X Plus (Illumina).
Jurkat (BRU-seq): Strand-specific libraries were prepared from a modified protocol using the TruSeq Kit (Illumina) as previously described (Paulsen et al., 2013)

treatment_protocol: Cells were treated with 500nM dTAGV-1 or an equivalent volume of DMSO(1ul/mL media) for 6 hours and then immediately harvested for downstream processing.

value: Jurkat

value: T cell acute lymphoblastic leukemia

tag: genetic modifiction

value: BCL11B-dTAG (CRISPR knockin)


title: Jurkat, BCL11B-dTAG, DMSO, rep2, ATAC

description: Library name: ATAC_Jurkat_BCL11BdTAG_DMSO_rep2

value: DMSO


title: PHC2 KO with PHC2 lentivirus overexpression H3K27ac CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-Lenti_H3K27ac_03
CUT&RUN with H3K27ac antibody (CST 8173) - not used in the analysis


title: Jurkat, BCL11B-dTAG, dTAGV-1, rep1, ATAC

description: Library name: ATAC_Jurkat_BCL11BdTAG_dTAG_rep1


title: PHC2 KO with PHC2 lentivirus overexpression EZH2 CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-Lenti_EZH2_04
CUT&RUN with EZH2 antibody (CST D2C9) - not used in the analysis


title: PHC2 KO with PHC2 lentivirus overexpression H3K27ac CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-Lenti_H3K27ac_02
CUT&RUN with H3K27ac antibody (CST 8173) - used in part 2 of the analysis


title: Jurkat, BCL11B-dTAG, DMSO, rep1, ATAC

description: Library name: ATAC_Jurkat_BCL11BdTAG_DMSO_rep1


title: REI_POWR250_GC_DNA

label: Cy3 and Cy39


title: PHC2 KO with PHC2 lentivirus overexpression BAF155 CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-Lenti_BAF155_04
CUT&RUN with BAF155 antibody (CST 11956) - not used in the analysis


title: PHC2 KO with PHC2 lentivirus overexpression H3K27ac CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-Lenti_H3K27ac_01
CUT&RUN with H3K27ac antibody (CST 8173) - used in part 2 of the analysis


title: REI_POWR573_GC_DNA

label: Cy3 and Cy38


title: Jurkat, BCL11B-WT, dTAGV-1, rep2, ATAC

description: Library name: ATAC_Jurkat_BCL11Bwt_dTAG_rep2


title: PHC2 KO with PHC2 lentivirus overexpression BAF155 CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-Lenti_BAF155_02
CUT&RUN with BAF155 antibody (CST 11956) - used in part 2 of the analysis


title: REI_POWR622_GC_DNA

label: Cy3 and Cy40


title: PHC2 KO with PHC2 lentivirus overexpression EZH2 CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-Lenti_EZH2_03
CUT&RUN with EZH2 antibody (CST D2C9) - not used in the analysis


title: REI_POWR858_GC_DNA

label: Cy3 and Cy36


title: REI_POWR395_GC_DNA

label: Cy3 and Cy43


title: PHC2 KO with PHC2 lentivirus overexpression BAF155 CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-Lenti_BAF155_03
CUT&RUN with BAF155 antibody (CST 11956) - not used in the analysis


title: Jurkat, BCL11B-WT, DMSO, rep1, ATAC

description: Library name: ATAC_Jurkat_BCL11Bwt_DMSO_rep1


title: PHC2 KO with PHC2 lentivirus overexpression EZH2 CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-Lenti_EZH2_02
CUT&RUN with EZH2 antibody (CST D2C9) - used in part 2 of the analysis


title: PHC2 KO RING1B CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-KO_RING1B_03
CUT&RUN with RING1B antibody (CST 5694) - not used in the analysis

value: PHC2 KO


title: PHC2 KO RING1B CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-KO_RING1B_04
CUT&RUN with RING1B antibody (CST 5694) - not used in the analysis


title: PHC2 KO RING1B CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-KO_RING1B_01
CUT&RUN with RING1B antibody (CST 5694) - used in part 2 of the analysis


title: PHC2 KO with PHC2 lentivirus overexpression EZH2 CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-Lenti_EZH2_01
CUT&RUN with EZH2 antibody (CST D2C9) - used in part 2 of the analysis


title: PHC2 KO PHC2 CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-KO_PHC2_03
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - not used in the analysis


title: PHC2 KO with PHC2 lentivirus overexpression BAF155 CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-Lenti_BAF155_01
CUT&RUN with BAF155 antibody (CST 11956) - used in part 2 of the analysis


title: REI_POWR305_GC_DNA

label: Cy3 and Cy37


title: Jurkat, BCL11B-WT, dTAGV-1, rep1, ATAC

description: Library name: ATAC_Jurkat_BCL11Bwt_dTAG_rep1


title: PHC2 KO PHC2 CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-KO_PHC2_04
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - not used in the analysis


title: CD34, BCL11B-dTAG, DMSO, rep2, ATAC

description: Library name: CD34_BCL11BdTAG_DMSO_rep2

source_name: Cord Blood

value: Cord Blood

value: CD34+ HSPC


title: Jurkat, BCL11B-WT, DMSO, rep2, ATAC

description: Library name: ATAC_Jurkat_BCL11Bwt_DMSO_rep2


title: PHC2 KO with PHC2 lentivirus overexpression RNA-Seq (HCT116) rep04

description:
Library name: RNA_PHC2-Lenti_04
RNA-Seq - used in part 2 of the analysis


title: PHC2 KO PHC2 CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-KO_PHC2_02
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - used in part 2 of the analysis


title: PHC2 KO IgG CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-KO_IgG_04
CUT&RUN with IgG antibody (CST 2729) - not used in the analysis


title: CD34, empty vector, dTAGV-1, rep2, ATAC

description: Library name: CD34_Empty_dTAG_rep2

value: Empty vector


title: PHC2 KO with PHC2 lentivirus overexpression RNA-Seq (HCT116) rep02

description:
Library name: RNA_PHC2-Lenti_02
RNA-Seq - used in part 2 of the analysis


title: REI_POWR200_GC_DNA

label: Cy3 and Cy35


title: CD34, empty vector, dTAGV-1, rep1, ATAC

description: Library name: CD34_Empty_dTAG_rep1


title: PHC2 KO IgG CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-KO_IgG_01
CUT&RUN with IgG antibody (CST 2729) - used in part 2 of the analysis


title: REI_POWR386_GC_DNA

label: Cy3 and Cy34


title: PHC2 KO with PHC2 lentivirus overexpression RNA-Seq (HCT116) rep03

description:
Library name: RNA_PHC2-Lenti_03
RNA-Seq - used in part 2 of the analysis


title: REI_POWR425_GC_DNA

label: Cy3 and Cy31


title: REI_POWR418_GC_DNA

label: Cy3 and Cy30


title: CD34, BCL11B-dTAG, dTAGV-1, rep1, ATAC

description: Library name: CD34_BCL11BdTAG_dTAG_rep1


title: CD34, empty vector, DMSO, rep1, ATAC

description: Library name: CD34_Empty_DMSO_rep1


title: REI_POWR804_GC_DNA

label: Cy3 and Cy32


title: CD34, BCL11B-dTAG, dTAGV-1, rep2, ATAC

description: Library name: CD34_BCL11BdTAG_dTAG_rep2


title: PHC2 KO with PHC2 lentivirus overexpression RNA-Seq (HCT116) rep01

description:
Library name: RNA_PHC2-Lenti_01
RNA-Seq - used in part 2 of the analysis


title: CD34, BCL11B-dTAG, DMSO, rep1, ATAC

description: Library name: CD34_BCL11BdTAG_DMSO_rep1


title: PHC2 KO H3K27ac CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-KO_H3K27ac_04
CUT&RUN with H3K27ac antibody (CST 8173) - not used in the analysis


title: PHC2 KO RING1B CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-KO_RING1B_02
CUT&RUN with RING1B antibody (CST 5694) - used in part 2 of the analysis


title: PHC2 KO PHC2 CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-KO_PHC2_01
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - used in part 2 of the analysis


title: REI_POWR548_GC_DNA

label: Cy3 and Cy33


title: PHC2 KO IgG CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-KO_IgG_03
CUT&RUN with IgG antibody (CST 2729) - not used in the analysis


title: PHC2 KO H3K27ac CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-KO_H3K27ac_02
CUT&RUN with H3K27ac antibody (CST 8173) - used in part 2 of the analysis


title: REI_POWR394_GC_DNA

label: Cy3 and Cy26


title: PHC2 KO H3K27ac CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-KO_H3K27ac_03
CUT&RUN with H3K27ac antibody (CST 8173) - not used in the analysis


title: PHC2 KO IgG CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-KO_IgG_02
CUT&RUN with IgG antibody (CST 2729) - used in part 2 of the analysis


title: PHC2 KO H3K27me3 CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-KO_H3K27me3_02
CUT&RUN with H3K27me3 antibody (CST 9733) - used in part 2 of the analysis


title: CD34, empty vector, DMSO, rep2, ATAC

description: Library name: CD34_Empty_DMSO_rep2


title: PHC2 KO EZH2 CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-KO_EZH2_04
CUT&RUN with EZH2 antibody (CST D2C9) - not used in the analysis


title: REI_POWR335_GC_DNA

label: Cy3 and Cy25


title: REI_POWR601_GC_DNA

label: Cy3 and Cy28


title: PHC2 KO H3K27me3 CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-KO_H3K27me3_01
CUT&RUN with H3K27me3 antibody (CST 9733) - used in part 2 of the analysis


title: PHC2 KO EZH2 CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-KO_EZH2_01
CUT&RUN with EZH2 antibody (CST D2C9) - used in part 2 of the analysis


title: REI_POWR555_GC_DNA

label: Cy3 and Cy29


title: CD34, empty vector, rep1, ATAC

description: Library name: CD34_Empty_rep1


title: PHC2 KO H3K27me3 CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-KO_H3K27me3_04
CUT&RUN with H3K27me3 antibody (CST 9733) - not used in the analysis


title: PHC2 KO BAF155 CUT&RUN (HCT116) rep04

description:
Library name: CR_PHC2-KO_BAF155_04
CUT&RUN with BAF155 antibody (CST 11956) - not used in the analysis


title: PHC2 KO H3K27me3 CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-KO_H3K27me3_03
CUT&RUN with H3K27me3 antibody (CST 9733) - not used in the analysis


title: REI_POWR400_GC_DNA

label: Cy3 and Cy27


title: REI_POWR236_GC_DNA

label: Cy3 and Cy23


title: CD34, BCL11B, rep2, ATAC

description: Library name: CD34_BCL11B_rep2


title: PHC2 KO BAF155 CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-KO_BAF155_03
CUT&RUN with BAF155 antibody (CST 11956) - not used in the analysis


title: CD34-018, empty vector, RUNX1

description:
Library name: CUTRUN_CD34_018_Empty_RUNX1.bw
Experiment to test if untagged BCL11B induces similar decrease in RUNX1 chromatin occupancy as BCL11B-dTAG

data_processing:
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1) and converted to paired-end fragment intervals (BEDPE). For coverage calculation, fragments with inferred insert size < 2000 bp were counted and used to compute a library-size scaling factor to normalize signal to a fixed library size. The center 80 bp of these fragments were used to generate genome-wide coverage tracks using bedtools genomecov in bedGraph format (-bg), applying the scaling factor for depth normalization (-scale). BedGraph files were converted to BigWig format using UCSC tools (bedGraphToBigWig) for visualization in IGV and for creating heatmaps. To increase detection of BCL11BdTAG and RUNX1 binding events in CD34+ HSPCs without DMSO or dTAGV-1 treatment, the mapped bam files from both replicates were merged prior to downstream processing.
Raw paired-end reads were quality trimmed and adapter trimmed using TrimGalore (v0.4.4) with a quality score cutoff of Q20. The first 15 bp of each read were clipped to reduce the GC bias introduced by the Tn5 enzyme. Quality trimmed reads were mapped to the GRCh38 reference genome with BWA (v0.7.12-r1039) and converted to bam format using samtools64 (v1.2). Duplicate reads were marked using biobambam2 (v2.0.87). Properly paired and uniquely mapped reads were extracted by samtools (-F 1804 -b -q 1). The center 80 bp of nucleosome-free fragments (fragment size < 109 bp) were extracted using bedtools and converted to scaled genome coverage tracks for visualization on IGV and in heatmaps. The scaling factor was computed from the total number of nucleosome-free fragments to normalize signal to a fixed library size. Peaks were called with MACS2 (v2.1.1.20160309) using nucleosome-free fragments with parameters -f BEDPE --keep-dup all -q 0.01
For CD34+ HSPCs: Paired-end RNA-seq reads were adapter and quality trimmed using Trim Galore (v0.4.4), and read quality was assessed with FastQC. Reads were aligned to the GRCh38 reference genome with STAR (v2.7) in two-pass mode. Coordinate-sorted BAM files, transcriptome alignments, gene counts, and strand-specific RPM-normalized coverage tracks were generated during alignment, and wiggle files were converted to BigWig format using wigToBigWig. Duplicate reads were marked with GATK MarkDuplicates, alignments were indexed with SAMtools, and RNA-seq quality metrics were collected using Picard CollectRnaSeqMetrics. Gene- and isoform-level expression was quantified with RSEM. Differential expression analysis was performed using the edgeR/limma-voom workflow. Genes with counts per million (CPM) ≥ 1 in at least 3 samples were retained using edgeR, and normalized expression values were generated by voom as log2-counts per million. Differentially expressed genes between treatment groups and transduction conditions were identified using linear models with empirical Bayes moderation implemented in limma.
For Jurkat BRU-seq: Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2. Unaligned reads were subsequently mapped strand-specifically to human genome build hg38/GRCh38 using STAR and GENCODE annotation version 27. Gene expression was quantified as previously described (Magnuson et al., 2022) and differential gene expression was performed using DESeq2.
Assembly: hg38
Supplementary files format and content: .bw files contain coverage files in bigwig format
Supplementary files format and content: .narrowPeak files contain MACS2 called peaks
Supplementary files format and content: .txt file contains transcripts per million (TPM) values
Library strategy: CUT&Run

tag: antibody


title: REI_POWR409_GC_DNA

label: Cy3 and Cy21


title: PHC2 KO EZH2 CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-KO_EZH2_02
CUT&RUN with EZH2 antibody (CST D2C9) - used in part 2 of the analysis


title: PHC2 KO H3K27ac CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-KO_H3K27ac_01
CUT&RUN with H3K27ac antibody (CST 8173) - used in part 2 of the analysis


title: CD34, BCL11B, rep1, ATAC

description: Library name: CD34_BCL11B_rep1


title: PHC2 KO BAF155 CUT&RUN (HCT116) rep01

description:
Library name: CR_PHC2-KO_BAF155_01
CUT&RUN with BAF155 antibody (CST 11956) - used in part 2 of the analysis


title: CD34, empty vector, rep2, ATAC

description: Library name: CD34_Empty_rep2


title: FFPE breast cancer patient (B1) sample (1) profiled with the Xenium human breast gene panel

city: Lausanne

first: Raphael

last: Gottardo

state: Vaud

address: Rue du Bugnon 21

department: Biomedical Data Science Center

country: Switzerland

institute: Lausanne University Hospital

description: Breast cancer tissues analyzed with Xenium human breast gene panel

label: Xenium probe set

source_name: primary breast cancer

label_protocol: Xenium probe set

growth_protocol: Not applicable

treatment_protocol: Not applicable

value: primary breast cancer

tag: tissue preservation method

value: FFPE


title: PHC2 KO EZH2 CUT&RUN (HCT116) rep03

description:
Library name: CR_PHC2-KO_EZH2_03
CUT&RUN with EZH2 antibody (CST D2C9) - not used in the analysis


title: PHC2 KO RNA-Seq (HCT116) rep04

description:
Library name: RNA_PHC2-KO_04
RNA-Seq - used in part 2 of the analysis


title: REI_POWR401_GC_DNA

label: Cy3 and Cy24


title: CD34, BCL11B-dTAG, RUNX1, DMSO, rep1

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_DMSO_rep1


title: REI_POWR279_GC_DNA

label: Cy3 and Cy18


title: REI_POWR624_GC_DNA

label: Cy3 and Cy17


title: PHC2 KO BAF155 CUT&RUN (HCT116) rep02

description:
Library name: CR_PHC2-KO_BAF155_02
CUT&RUN with BAF155 antibody (CST 11956) - used in part 2 of the analysis


title: FFPE breast cancer patient (B1) sample (3) profiled with the Xenium human breast gene panel


title: CD34, BCL11B-dTAG, RUNX1, dTAGV-1, rep2

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_dTAG_rep2


title: FFPE breast cancer patient (B7) sample profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B1) sample (2) profiled with the Xenium human breast gene panel


title: CD34, empty vector, RUNX1, DMSO, rep2

description: Library name: CUTRUN_CD34_Empty_RUNX1_DMSO_rep2


title: FFPE breast cancer patient (B8) sample profiled with the Xenium human breast gene panel


title: CD34, BCL11B-dTAG, RUNX1, dTAGV-1, rep1

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_dTAG_rep1


title: REI_POWR131_GC_DNA

label: Cy3 and Cy20


title: FFPE breast cancer patient (B9) sample profiled with the Xenium human breast gene panel


title: PHC2 L307R mutant RING1B CUT&RUN (HCT116) rep02

description:
Library name: CR_L307R_RING1B_02
CUT&RUN with RING1B antibody (CST 5694) - used in part 1 of the analysis

value: PHC2 L307R mutant


title: REI_POWR566_GC_DNA2

label: Cy3 and Cy13


title: REI_POWR286_GC_DNA

label: Cy3 and Cy22


title: CD34, BCL11B-dTAG, RUNX1, rep2

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_rep2


title: FFPE breast cancer patient (B4) sample profiled with the Xenium human breast gene panel


title: PHC2 L307R mutant RING1B CUT&RUN (HCT116) rep01

description:
Library name: CR_L307R_RING1B_01
CUT&RUN with RING1B antibody (CST 5694) - used in part 1 of the analysis


title: CD34, BCL11B-dTAG, RUNX1, DMSO, rep2

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_DMSO_rep2


title: CD34, BCL11B-dTAG, RUNX1, rep1

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_rep1


title: FFPE breast cancer patient (B5) sample profiled with the Xenium human breast gene panel


title: REI_POWR238_GC_DNA2

label: Cy3 and Cy19


title: FFPE breast cancer patient (B3) sample profiled with the Xenium human breast gene panel


title: CD34, empty vector, RUNX1, dTAGV-1, rep2

description: Library name: CUTRUN_CD34_Empty_RUNX1_dTAG_rep2


title: PHC2 KO RNA-Seq (HCT116) rep03

description:
Library name: RNA_PHC2-KO_03
RNA-Seq - used in part 2 of the analysis


title: REI_POWR194_GC_DNA2

label: Cy3 and Cy10


title: CD34, empty vector, RUNX1, merged

description: Library name: CUTRUN_CD34_Empty_RUNX1_merge


title: FFPE breast cancer patient (B12) sample profiled with the Xenium human breast gene panel


title: CD34, empty vector, RUNX1, rep2

description: Library name: CUTRUN_CD34_Empty_RUNX1_rep2


title: FFPE breast cancer patient (B6) sample profiled with the Xenium human breast gene panel

description: Breast cancer tissues analyzed with Xenium human breast gene panel


title: CD34, empty vector, RUNX1, dTAGV-1, rep1

description: Library name: CUTRUN_CD34_Empty_RUNX1_dTAG_rep1


title: FFPE breast cancer patient (B13) sample profiled with the Xenium human breast gene panel


title: REI_POWR626_GC_DNA

label: Cy3 and Cy16


title: PHC2 L307R mutant RING1B CUT&RUN (HCT116) rep04

description:
Library name: CR_L307R_RING1B_04
CUT&RUN with RING1B antibody (CST 5694) - not used in the analysis


title: PHC2 L307R mutant PHC2 CUT&RUN (HCT116) rep01

description:
Library name: CR_L307R_PHC2_01
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - used in part 1 of the analysis


title: FFPE breast cancer patient (B2) sample profiled with the Xenium human breast gene panel


title: PHC2 KO RNA-Seq (HCT116) rep02

description:
Library name: RNA_PHC2-KO_02
RNA-Seq - used in part 2 of the analysis


title: CD34, empty vector, RUNX1, DMSO, rep1

description: Library name: CUTRUN_CD34_Empty_RUNX1_DMSO_rep1


title: PHC2 L307R mutant RING1B CUT&RUN (HCT116) rep03

description:
Library name: CR_L307R_RING1B_03
CUT&RUN with RING1B antibody (CST 5694) - not used in the analysis


title: CD34, BCL11B-dTAG, HA, rep2

description: Library name: CUTRUN_CD34_BCL11BdTAG_HA_rep2

value: HA (CST3724S)


title: REI_POWR163_GC_DNA

label: Cy3 and Cy7


title: REI_POWR651_GC_DNA

label: Cy3 and Cy6


title: PHC2 KO RNA-Seq (HCT116) rep01

description:
Library name: RNA_PHC2-KO_01
RNA-Seq - used in part 2 of the analysis


title: FFPE breast cancer patient (B15) sample profiled with the Xenium human breast gene panel


title: REI_POWR299_GC_DNA

label: Cy3 and Cy14


title: CD34, BCL11B-dTAG, RUNX1, merged

description: Library name: CUTRUN_CD34_BCL11BdTAG_RUNX1_merge


title: REI_POWR426_GC_DNA

label: Cy3 and Cy12


title: FFPE breast cancer patient (B16) sample profiled with the Xenium human breast gene panel


title: REI_POWR157_GC_DNA

label: Cy3 and Cy15


title: CD34, BCL11B-dTAG, IgG

description: Library name: CUTRUN_CD34_BCL11BdTAG_IgG

value: IgG (Epicypher)


title: FFPE breast cancer patient (B10) sample profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B14) sample profiled with the Xenium human breast gene panel


title: PHC2 L307R mutant IgG CUT&RUN (HCT116) rep01

description:
Library name: CR_L307R_IgG_01
CUT&RUN with IgG antibody (CST 2729) - used in part 1 of the analysis


title: PHC2 L307R mutant PHC2 CUT&RUN (HCT116) rep04

description:
Library name: CR_L307R_PHC2_04
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - not used in the analysis


title: FFPE breast cancer patient (B17) sample profiled with the Xenium human breast gene panel


title: FFPE breast cancer patient (B11) sample profiled with the Xenium human breast gene panel


title: REI_POWR154_GC_DNA

label: Cy3 and Cy11


title: PHC2 L307R mutant H3K27me3 CUT&RUN (HCT116) rep04

description:
Library name: CR_L307R_H3K27me3_04
CUT&RUN with H3K27me3 antibody (CST 9733) - not used in the analysis


title: REI_POWR301_GC_DNA

label: Cy3 and Cy9


title: PHC2 L307R mutant PHC2 CUT&RUN (HCT116) rep03

description:
Library name: CR_L307R_PHC2_03
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - not used in the analysis


title: PHC2 L307R mutant IgG CUT&RUN (HCT116) rep02

description:
Library name: CR_L307R_IgG_02
CUT&RUN with IgG antibody (CST 2729) - used in part 1 of the analysis


title: CD34, empty vector, RUNX1, rep1

description: Library name: CUTRUN_CD34_Empty_RUNX1_rep1


title: CD34, empty vector, HA, rep2

description: Library name: CUTRUN_CD34_Empty_HA_rep2


title: PHC2 L307R mutant PHC2 CUT&RUN (HCT116) rep02

description:
Library name: CR_L307R_PHC2_02
CUT&RUN with PHC2 antibody (Proteintech 12867-1-AP) - used in part 1 of the analysis


title: LLC-Thy1.1 P2 tumour-bearing lung 1

type: other

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

data_processing: Raw data were processed using MERSCOPE Vizualizer software v2.3 (Vizgen Technologies). The processed data files include detected.transcripts.csv file with the spatial coordinates of the detected transcripts, cell_by_gene.csv file, containing the gene expression matrix, and cell_metadata.csv, containing the field of view index and the spatial coordinates of the centroids and cell segmentation boundaries.

molecule: other

source_name: LLC-Thy1.1 P2 tumour-bearing lung

extract_protocol: All methods listed in Bardet et al. Multiomics immune profiling of a patient-relevant orthotopic lung cancer model using SEPARATE-Seq.

value: tumour-bearing lung


title: REI_POWR413_GC_DNA

label: Cy3 and Cy8

value: Granulosa Cells


title: FFPE NSCLC patient (L8) sample profiled with the Xenium human lung gene panel

description: Lung cancer tissues analyzed with Xenium human lung gene panel

label: Xenium probe set

source_name: primary NSCLC

value: primary NSCLC


title: REI_POWR381_GC_DNA

label: Cy3 and Cy5

value: Female


title: PHC2 L307R mutant IgG CUT&RUN (HCT116) rep04

description:
Library name: CR_L307R_IgG_04
CUT&RUN with IgG antibody (CST 2729) - not used in the analysis


title: PHC2 L307R mutant IgG CUT&RUN (HCT116) rep03

description:
Library name: CR_L307R_IgG_03
CUT&RUN with IgG antibody (CST 2729) - not used in the analysis


title: CD34, empty vector, HA, rep1

description: Library name: CUTRUN_CD34_Empty_HA_rep1


title: CD34, BCL11B-dTAG, HA, rep1

description: Library name: CUTRUN_CD34_BCL11BdTAG_HA_rep1


title: CD34, empty vector, IgG

description: Library name: CUTRUN_CD34_Empty_IgG


title: FFPE NSCLC patient (L10) sample profiled with the Xenium human lung gene panel