title: Day 0_Lib 1_GEX

description:
Library name: SRTP0006801
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep1.
day0_raw_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad

data_processing:
Basecalling and FASTQ generation with bcl2fastq v2.20.0.422.
Read alignment and gene counting with Cell Ranger v5.0.1 (10x Genomics) using STAR v2.7.0a against GRCh38.
Initial QC for hashed (Days 1–7) data prior to demultiplexing: retain cells with total counts between 5,000 and 80,000 and mitochondrial fraction <20 percent.
Demultiplex hashed libraries using CLR-normalized hashtag counts and a Gaussian mixture model; classify singlets, multiplets, negatives; retain singlets and assign to wells/perturbations.
Additional per-cell QC after demultiplexing: remove cells with <2,500 or >60,000 counts and cells with <1,600 or >9,000 detected genes.
Per-cell normalization to 10,000 counts and natural log transform (Scanpy v1.9.3).
Reference mapping and label transfer: construct a batch-corrected PC space with harmony; project the query time course into the reference time course CITE-seq PC space; integrate in the reference’s harmony-corrected PC space; transfer cell type labels with SymphonyPy v0.2.1 KNN classifier.
Label transfer validation: evaluate weighted Mahalanobis distance to mapped reference clusters, cosine similarity across highly variable genes between matched types, and expression of canonical markers.
Assemble outputs for GEO: Day 0 raw counts (unhashed); Days 1–7 raw counts (hashed, pre-demultiplexing) and demultiplexed counts (singlets with well assignments); normalized counts across Days 0–7 with transferred cell type annotations.
Assembly: GRCh38
Supplementary files format and content: day0_raw_counts.h5ad - Day 0 single-cell raw count matrix (genes x cells), unhashed and untreated; includes basic per-cell QC metrics; no demultiplexing.
Supplementary files format and content: day1-7_raw_counts.h5ad - Days 1, 2, 5, and 7 hashed single-cell raw count matrices combined prior to demultiplexing; pre-demux QC applied (counts 5,000–80,000; mitochondrial fraction <20 percent); includes hashtag count data and per-cell QC metrics.
Supplementary files format and content: day1-7_demuxed_counts.h5ad - Demultiplexed singlet cells for Days 1, 2, 5, and 7; cells assigned to wells/perturbations via Gaussian mixture modeling on CLR-normalized hashtags; additional QC applied (<2,500 or >60,000 counts; <1,600 or >9,000 genes filtered); includes per-cell well/treatment metadata.
Supplementary files format and content: day0-7_normalized_counts_with_celltype_annotations.h5ad - Normalized (10,000 counts per cell; natural log transformed) cell-by-gene matrix spanning Days 0–7 with transferred cell type annotations obtained by mapping to a reference time course using harmony-corrected PCs and SymphonyPy KNN label transfer; includes validation metrics supporting label robustness.

growth_protocol: Dual-mobilized (Neupogen + Mozobil) peripheral blood CD34+ HSPCs (AllCells) were thawed and cultured in StemSpan SFEM supplemented with TPO (100 ng/mL) and CC100 (Stemcell Technologies). On day 0 (48 h post-thaw), cells were plated in 96-well plates: for megakaryocyte differentiation, 60,000 cells per well in round-bottom plates; for erythroid differentiation, 30,000 cells per well in flat-bottom plates. Cells were passaged 1:4 on day 2 and media were refreshed on day 5.

extract_protocol:
Single-cell RNA was captured directly in droplets per the 10x Genomics Single Cell 3’ v3.1 workflow; no separate bulk RNA extraction was performed.
On days 1, 2, 5, and 7, samples were multiplexed with cell multiplexing oligos (CMOs; 10x Genomics) following the manufacturer’s protocol. Briefly, cells were washed in Cell Staining Buffer (BioLegend), counted, incubated with CMOs for 5 min at room temperature, then washed three times with 4% HSA (Grifols). Twelve CMO-tagged samples were pooled per library by combining ~100,000 cells from each well. Pooled cells were washed once in 4% HSA, counted, and resuspended in Cell Staining Buffer at 1.2e6 cells/mL. Each compound was sequenced in duplicate with duplicates distributed across libraries. Each library included positive and negative controls and a mixture of hit and non-hit compounds. Single-cell 3’ libraries were prepared with Chromium Single Cell 3’ Reagent Kit v3.1 (10x Genomics, 1000268) and sequenced on an Illumina NovaSeq 6000 (paired-end).

treatment_protocol: Compounds (Frontier Scientific; 10 mM stocks in DMSO) were arrayed by Hamilton Microlab STAR. For screening, compounds were arrayed at 0.1, 1, or 10 mM in triplicate; for target deconvolution, 10 mM stocks were serially diluted 3-fold for 8 concentrations and duplicated. Plates were stored at −80 C. On treatment days, plates were thawed at 37 C for 10 min, diluted with IMDM, and transferred with an Integra VIAFLO384 to achieve a final 1,000x dilution in culture. Treatments were applied on days 0, 2, and 5. In this dataset, cells from one donor were analyzed at a final concentration of 1 uM per compound or DMSO control.

value: peripheral blood

value: CD34+ HSPCs

tag: time

value: Day 0


title: LG321_NY_65

status: Public on Oct 23 2025

type: SRA

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

country: USA

institute: Weill Cornell Medicine

description: mRNA expression in mouse hippocampus

library_source: transcriptomic single cell

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.3.1.0) (10× Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than two cells, cells with a unique gene count over 8000 or less than 300, and cells with a high fraction of mitochondrial reads (>5%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v3.0.182 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

organism: Mus musculus

source_name: hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

tag: tissue

value: hippocampus

tag: Sex

value: Female

tag: age

tag: genotype

value: DAP12 KO:+/+;PSUK:Tg/Tg

tag: strain


title: LG180_503

description: mRNA expression in mouse hippocampus

value: wildtype


title: LJR0166

city: Shanghai

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

country: China

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: AML_Patient_129
AML_Patient_129

library_source: transcriptomic

data_processing:
Trim-galore was employed to remove the adapter sequences.
The clean reads were aligned with STAR and quantified with HT-Seq using the GRCh38 human assembly.
The differential expression assessment was conducted using the DESeq2 package.
Gene expression levels were normalized to Transcripts Per Kilobase of exon model per Million mapped reads (TPM) using a customed script.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw count values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: Bone. Marrow

extract_protocol:
Bone marrow mononuclear cells from AML patients were isolated after Ficoll–Isopaque density gradient centrifugation. Genomic mRNA were extracted from the patients’ BM using the AllPrep PowerFecal RNA Kit in accordance with the manufacturer’s instructions.
Libraries were prepared using the KAPA RNA HyperPrep kit in accordance with the manufacturer’s instructions (KAPA). High-throughput sequencing was performed on the NovaSeq 6000 platform in accordance with the manufacturer’s protocol (paired-end 2 × 150 bp).

value: Bone. Marrow

tag: cell line

value: Primary patient cells

tag: disease state

value: Acute Myeloid Leukemia

tag: treatment

value: Aza-Ven

tag: batch

value: Cohort 2


title: LJR0160

description:
Library name: AML_Patient_123
AML_Patient_123


title: DrugSEQ03_24well_A375v2_row2_ADT

city: Somerville

first: Mauricio

last: Cortes

state: MA

address: 101 South Street

institute: Cellarity

description:
Library name: ILD1-001_SRAB0000507
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.

library_source: other

data_processing:
Ingest data per plate: load 10x outputs (Gene Expression and Antibody Capture) for all libraries belonging to a plate into a single AnnData object.
Compute per-cell QC metrics: total UMIs (nCount_RNA), genes detected (nFeature_RNA), mitochondrial fraction (percent_mito), and housekeeping gene checks; derive library-specific thresholds for library size and percent_mito.
Filter cells using per-library QC thresholds to retain high-quality cells only.
Filter genes with very low prevalence (genes detected in too few cells are removed).
Normalize and transform (pre-demultiplexing): store raw counts in a “counts” layer; apply library-wise total count normalization (target_sum = 1e6) and log1p transform to produce the filtered_normalized plate-level matrix.
Demultiplex per library using HTO/CMO counts: compute CLR-normalized hashtag counts; apply per-library thresholding to classify cells (singlet/multiplet/negative); assign singlet cells to a specific hashtag/well; merge assignments across libraries to plate level.
Generate demultiplexed plate object: retain singlets with well and treatment mapping; save as demuxed plate-level AnnData.
Pseudobulk by well: sum gene counts across cells within each well (including vehicle control wells and replicate wells); preserve raw summed counts in a “counts” layer; normalize pseudobulk matrices (target_sum = 1e6, exclude_highly_expressed = True) and log1p transform.
Compute v-scores within each plate: for each perturbation vs DMSO (matched within library_id), compute per-gene v-score as [mean(log1p(y)) − mean(log1p(x))] / sqrt(Var(log1p(x)) + Var(log1p(y))); save as vscores.
Differential expression on pseudobulk: run limma within each plate (perturbation vs DMSO) and export moderated statistics (e.g., logFC, t, p-value, FDR).
Create combined files: concatenate plate-level outputs across all plates to produce combined_demuxed.h5ad, combined_pseudobulk.h5ad, combined_vscores.h5ad, and combined_limma.csv; no additional filtering, normalization, or re-analysis performed.
Assembly: hg38
Supplementary files format and content: SRTPXXXX_raw_feature_bc_matrix.h5 – Raw cell × feature count matrix (HDF5 format) generated by 10x Genomics Cell Ranger. Contains unfiltered UMI counts for all detected barcodes across both gene expression and feature barcoding (including antibody/hashtag features).
Supplementary files format and content: SRTPXXXX_filtered_feature_bc_matrix.h5 – Filtered cell × feature count matrix (HDF5 format) generated by 10x Genomics Cell Ranger. Contains UMI counts for barcodes identified as high-quality cells, across gene expression and feature barcoding modalities.
Supplementary files format and content: SRTPXXXX_metrics_summary.csv – Summary file produced by 10x Genomics Cell Ranger with run-level QC metrics, including sequencing depth, reads per cell, mapping statistics, fraction of reads in cells, and other quality control indicators.
Supplementary files format and content: SRTPXXXX_feature_reference.csv – Feature reference file used in Cell Ranger to define the set of non-gene features included in the library. In this dataset, it specifies hashtag oligos (CMOs/HTOs) used for cell multiplexing; does not include gene annotations.
Supplementary files format and content: ILD1/2-XXX_raw.h5ad - Unfiltered cell x gene count matrix for the entire plate (all libraries from that plate concatenated); pre-QC, pre-normalization, pre-demultiplexing.
Supplementary files format and content: ILD1/2-XXX_filtered_normalized.h5ad - QC-filtered high-quality cells (thresholds applied per library), library-wise total-count normalized and log1p-transformed; produced before demultiplexing; stored as a single plate-level matrix.
Supplementary files format and content: ILD1/2-XXX_demuxed.h5ad - Plate-level AnnData with per-cell assignments to well and treatment; demultiplexing performed per library using CLR-normalized hashtag counts and a mixture model, then merged across libraries for the plate.
Supplementary files format and content: ILD1/2-XXX_pseudobulk.h5ad - Well-level expression for the plate: gene counts summed across cells within each well (vehicle controls such as DMSO and any replicate wells kept as separate entries); includes raw summed counts in a layer and a normalized/log representation.
Supplementary files format and content: ILD1/2-XXX_vscores.h5ad - Gene-level differential statistics within the plate (perturbation vs a matched-library DMSO well). For a comparison x->y: v-score = [mean(log1p(y)) - mean(log1p(x))] / sqrt(Var(log1p(x)) + Var(log1p(y))), where means and variances are over single-cell counts in each well (i.e. computed directly downstream of demuxed.h5ad, before pseudobulking).
Supplementary files format and content: ILD1/2-XXX_limma.csv - limma differential expression results against plate-level DMSO replicates, run on the plate’s well-level pseudobulk matrix; per-gene coefficients and moderated statistics (e.g., logFC, t, p-value, FDR). Results for all wells in the plate are concatenated, with the compound used to treat each well annotated in the "compound name" column.
Supplementary files format and content: combined_demuxed.h5ad - Concatenation of all plates’ demuxed AnnData objects; no additional filtering, normalization, or analysis.
Supplementary files format and content: combined_pseudobulk.h5ad - Concatenation of all plates’ well-level pseudobulk profiles; plate and well provenance retained; no recomputation.
Supplementary files format and content: combined_vscores.h5ad - Concatenation of v-score results from all plates; definitions and comparisons unchanged; no recomputation.
Supplementary files format and content: combined_limma.csv - Concatenation of plate-level limma outputs; same columns as plate files; no recomputation.

molecule: protein

growth_protocol: A375, A549, HepG2, PC3, and HEK293T cell lines were purchased from the American Tissue Culture Collection and cultured in either RPMI or DMEM with fetal bovine serum, as per supplier recommendations. The human embryonic kidney cell line HA1E was obtained from the Cancer Cell Line Encyclopedia at the Broad Institute and maintained under the same conditions. Normal human bronchial epithelial cells (HBECs) were obtained from Lonza from two healthy donors; cells were thawed and grown in PneumaCult medium for three days at 37 °C before plating in 24-well dishes for two days. Peripheral blood mononuclear cells (PBMCs) from two healthy donors were isolated from leukopaks (Miltenyi Biotec), frozen at 1×10^8 cells per vial, then thawed and CD8+ cytotoxic T cells isolated using the CD8+ T Cell Isolation Kit (Miltenyi). T cells were cultured in RPMI supplemented with fetal bovine serum and IL-2, and activated for 72 hours at 37 °C with CD3/CD28 Dynabeads (Life Technologies); beads were removed by magnetic separation before plating. Mobilized human peripheral blood CD34+ cells from healthy donors were obtained from StemCell Technologies, thawed into PBS with 1% human serum albumin, and incubated for 48 hours in StemSpan medium containing CC100 and rhTPO at 37 °C, then replated in fresh medium with CC100 and rhTPO. Human preadipocytes from healthy lean donors (Zen-Bio) were thawed into 24-well plates in plating medium; after incubation at 37 °C for 24 hours, the medium was changed to differentiation medium and cells were incubated for an additional 72 hours.

extract_protocol:
For adherent cell lines and preadipocytes, cells were harvested with 0.05% trypsin and collected with serum-containing medium. HBECs were harvested with ACF Enzymatic Dissociation Solution for 7 minutes according to the manufacturer’s protocol and collected with medium. CD8+ T cells and CD34+ hematopoietic stem cells were harvested by centrifugation for 5 minutes at 300 × g.
Single-cell library generation: Harvested cells were washed with PBS and labeled with TotalSeq-B hashtag antibodies from BioLegend according to manufacturer’s protocol. Briefly, cells were incubated with 250ng of TotalSeq-B antibodies (hashtags 1-10) for 30 minutes at room temperature. Cells were washed with PBS a total of three times and then ten samples with different hashtags were pooled and counted on a Luna Cell Counter. Single-cell libraries were then prepared using the Chromium Single Cell 3’ Feature Barcoding Kit targeting 10,000 cells per library, according to manufacturer’s protocols (10x Genomics; CG000317 Rev B). Following cell encapsulation, RNA is released by lysis within droplets and captured by barcoded gel beads.

treatment_protocol: For adherent cell lines (A375, A549, HepG2, PC3, HEK293T, HA1E), cells were seeded into 24-well dishes, incubated for 24 hours at 37 °C, and then treated with compounds for 24 hours at the maximum tolerated dose previously determined for each line. HBECs were treated in PneumaCult medium with compounds and incubated for 24 hours at 37 °C. CD8+ T cells were plated in 96-well plates in medium containing IL-2; compounds were added at 2× concentration and incubated for 24 hours at 37 °C. CD34+ hematopoietic stem cells were plated in 96-well plates in medium containing CC100 and rhTPO; compounds were added at 2× concentration and incubated for 24 hours at 37 °C. Human preadipocytes in differentiation medium were treated with compounds at 2× concentration and incubated for 24 hours at 37 °C.

value: Multiplexed treatment with small molecules, one per hashtag. Processed files contain demultiplexed treatment values


title: DrugSEQ03_24well_A375v2_row1_ADT

description:
Library name: ILD1-001_SRAB0000506
Perturbational single-cell screen with hashtag oligos. for cell line A375, replicate1.


title: LG321_NY_53

description: mRNA expression in mouse hippocampus

value: DAP12 KO:-/-;PSUK:Tg/Tg


title: LJR0158

description:
Library name: AML_Patient_121
AML_Patient_121


title: LJR0159

description:
Library name: AML_Patient_122
AML_Patient_122


title: LJR0157

description:
Library name: AML_Patient_120
AML_Patient_120


title: LJR0156

description:
Library name: AML_Patient_119
AML_Patient_119


title: Day 0_Lib 2_GEX

description:
Library name: SRTP0006802
Perturbational single-cell screen with hashtag oligos. for cell line not applicable, replicaterep2.
day0_raw_counts.h5ad
day0-7_normalized_counts_with_celltype_annotations.h5ad

source_name: peripheral blood

tag: cell type


title: RS-S3 RNA

city: Yinchuan

first: Jin

last: Haoyan

state: NingXia

address: No. 489, West Helanshan Road

department: colllege of animal science and technology

institute: NingXia University

data_processing:
RNA-seq: Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software, and compared the sequencing results with the pig genome reference sequence (Sscrofa11.1)
Assembly: Sscrofa11.1
Supplementary files format and content: Includes information such as gene expression content
Supplementary files format and content: Includes information such as gene expression content; "Un-SG_RNA_S1_R1.clean.fq.gz",  "Un-SG_RNA_S2_R1.clean.fq.gz", "Un-SG_RNA_S3_R1.clean.fq.gz"corresponds to "SSEA4-S3",  "SSEA4-S4","SSEA4-S5"of the processed data; "CL100101120_L1_WHPIGxrsEAAARAAPEI-511_1.fq.gz"corresponds to "RS-S2". The rest corresponds to the labelling.

organism: Sus scrofa

source_name: testis

extract_protocol:
Testicular cells were placed in centrifuge tubes, and total RNA was extracted by A and placed in a -80°C refrigerator, and RNA-seq libraries were created following the protocol provided by the manufacturer
RNA-seq: RNA-seq was constructed according to the instructions of the NEBNest® UltraTM Directional RNA Library Prep Kit for Illumina (NEB), utilizing the Illumina HiSeq 4000 platform for bipartite sequencing, with three biological samples, each containing 74 million paired reads

value: testis

value: testis cell

value: Round spermatids


title: 2057, RFX4+, H3K4me3

city: London

first: Alexander

last: Nott

address: 86 Wood Lane

country: United Kingdom

institute: Imperial College London

description: Library name: 2057_rfx4_k4me3

library_source: genomic

data_processing:
Align reads to genome (hg19) and filter to remove anything below a q-score of 40
Deduplication of reads followed by peak calling with MACS 2.0
Assembly: hg19
Supplementary files format and content: narrowPeak: for H3K27ac CUT&Tag, peaks were called with narrowPeak setting in MACS2
Supplementary files format and content: broadPeak: for H3Kme4 CUT&Tag, peaks were called with broadPeak setting in MACS2
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Postmortem cortical brain

extract_protocol:
Unfixed tissue was dissociated and nuclei were isolated and permeabilised with 0.01% NP-40 and 0.01% digitonin. Chromatin is targeted using histone modification antibodies and tagmented with nano-Tn5.
CUT&Tag libraries were prepared using the Illumina Nextera kit. Extracted DNA underwent linear amplification for 8-10 cycles in a thermocycler. 5 ng of this DNA was tagmented with a Tn5 tagmentase. Tagmented DNA was then amplified for 9-11 cycles. Libraries were quantifed using the Qubit HS DNA Sensitivity Assay and the fragment distribution was determined using the Agilent High Sensitivity DNA kit.

value: Postmortem cortical brain

tag: fans antibody

value: RFX4(Abcam, ab188020) + Anti-rabbit PE(Cell Signaling, #79408)

tag: cut&tag antibody


title: B71

description: mRNA expression in mouse hippocampus


title: C3H10T1-2_TKO_HP1_input

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

description: Library name: ChIPseq_sample_64

data_processing:
Raw ChIP-Seq reads were aligned to a combined reference of mm10 (or to hg38 for HNSCC cells) and dm6 genome assembly using BWA version 0.7.17 with default parameters. Afterwards, they were filtered using a cut-off of MAPQ < 3 using Samtools v.1.18. Samclip v.0.2 (samtools view -h in.bam | samclip --ref ref.fa | samtools sort > out.bam) was used to filter any bacterial sequences.
bigWig files were generated using the bamCoverage function from deepTools v3.3.1 with parameters '-b ${samp}.sorted.bam -o ${samp}.cpm.bw -p $nprocs --normalizeUsing CPM --centerReads -e 200 -bs 10'.
Assembly: mm10 for C3H10T1/2, hg38 for Cal27 and Detroit562
Supplementary files format and content: bigWig

growth_protocol: C3H10T1/2 mouse mesenchymal stem cells (ATCC) were cultured in DMEM with 10% fetal bovine serum (FBS,) and supplemented with 1% GlutaMax. Cal27 and Detroit562 HNSCC cells (ATCC, CRL-2095 and ATCC, CCL-138, respectively) were cultured in DMEM (F12) (Invitrogen) with 10% FBS. Drosophila S2 cells were cultured in Schneider’s Drosophila medium (ThermoFisher) containing 10% FBS. All cell lines tested negative for mycoplasma contamination. Epitope-tagged H3.3 was previously cloned into pCDH-EF1-MCS-Puro lentiviral vector and site-directed mutagenesis techniques were used to generate the H3K36M mutation. To produce lentivirus, 293T cells were transfected with a lentiviral vector containing H3.3K36M (provided by Dr. Chao Lu) and helper plasmids (psPAX2 and pMD2.G). Supernatant containing lentivirus was collected after 48h, filtered and used to infect Cal27 and Detroit562 cells. Transduced cells were grown under puromycin selection (1 μg/ml) for 48 h after transduction.  To establish stable overexpression of human SUV39H1, the pCDH-blast-HA-3XFlag-SUV39H1-WT plasmid was provided by the laboratory of Dr. Scott Rothbart. Lentivirus production, infection and establishment of C3H10T1/2 parental and NSD1/2-SETD2-TKO cells overexpressing SUV39H1 was performed as previously described in Liu et al. Mol Cell (2025). The infected cells were selected using blasticidin (4 µg/ml) for 10 days, and all surviving cells were pooled to generate stable cell lines overexpressing FLAG-tagged SUV39H1.

extract_protocol:
For ChIP-Seq of post-translation modifications (PTMs), approximately 20 million cells per cell line were used. Crosslinking was performed in 150 mm cell culture plates using 1% formaldehyde (Sigma) at room temperature with gentle rocking for 10 minutes. The crosslinking reaction was quenched using 1.25 M Glycine with gentle rocking at room temperature for 5 minutes. Fixed cell preparations were washed with ice-cold PBS, scraped, and then washed twice more with ice-cold PBS. Crosslinked pellets were resuspended in 500 μl cell lysis buffer (5 mM pH 8.5 PIPES, 85 mM KCl, 1% (v/v) IGEPAL CA-630, 50 mM NaF, 1 mM PMSF, 1 mM phenylarsine oxide, 5 mM sodium orthovanadate, EDTA-free protease inhibitor tablet) and incubated for 30 minutes on ice. Samples were centrifuged and pellets were resuspended in 500 μl of nuclei lysis buffer (50 mM pH 8.0 Tris-HCl, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM phenylarsine oxide, 5 mM sodium orthovanadate, EDTA-free protease inhibitor tablet) and incubated for 30 minutes on ice. Sonication of lysed nuclei was performed using the BioRuptor UCS-300 at maximum intensity for 75-90 cycles (10s on, 20s breaks). Sonication efficiency to achieve fragments between 150 - 500 bp was evaluated using gel electrophoresis on a reversed-crosslinked and purified aliquot from each sample. After sonication, chromatin was diluted to reduce SDS levels to 0.1% and concentrated using Nanosep 10K OMEGA (Pall) columns. Prior to the chromatin immunoprecipitation (ChIP) reaction, 2% sonicated Drosophila S2 cell chromatin was spiked into each sample for quantification of total levels of histone marks. The ChIP reactions were performed using the Diagenode SX-8G IP-Star Compact and Diagenode automated iDeal ChIP-seq Kit for Histones. Dynabeads Protein A (Invitrogen) were washed, then incubated with specific antibodies, 1.5 million cells of sonicated cell lysate, and protease inhibitors for 10 hrs, followed by a 20 min wash cycle using the provided wash buffers (Diagenode Immunoprecipitation Buffers, iDeal ChIP-seq Kit for Histones). Reverse cross-linking was then performed using 5M NaCl at 65℃ for 4 hrs. ChIP samples were then treated with 2 μl RNase Cocktail at 65℃ for 30 min followed by 2 μl Proteinase K at 65℃ for 30 min. Samples were then purified with QIAGEN MinElute PCR purification kit (QIAGEN) as per the manufacturer’s protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol. For protein ChIP-Seq (i.e. HP1), Approximately 40 million cells per cell line were used. Crosslinking was performed in 150 mm cell culture plates using 1% formaldehyde (Sigma) at room temperature with gentle rocking for 10 minutes. The crosslinking reaction was quenched using 1.25 M Glycine with gentle rocking at room temperature for 5 minutes. Fixed cell preparations were washed with ice-cold PBS, scraped, and then washed twice more with ice-cold PBS. Crosslinked pellets were resuspended in 500 μl cell lysis buffer (5 mM pH 8.5 PIPES, 85 mM KCl, 1% (v/v) IGEPAL CA-630, 50 mM NaF, 1 mM PMSF, 1 mM phenylarsine oxide, 5 mM sodium orthovanadate, EDTA-free protease inhibitor tablet) and incubated for 30 minutes on ice. Samples were centrifuged and pellets were resuspended in 500 μl of nuclei lysis buffer (50 mM pH 8.0 Tris-HCl, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM phenylarsine oxide, 5 mM sodium orthovanadate, EDTA-free protease inhibitor tablet) and incubated for 30 minutes on ice. Sonication of lysed nuclei was performed using the BioRuptor UCS-300 at maximum intensity for 75-90 cycles (10s on, 20s breaks). Sonication efficiency to achieve fragments between 150 - 500 bp was evaluated using gel electrophoresis on a reversed-crosslinked and purified aliquot from each sample. After sonication, chromatin was diluted to reduce SDS levels to 0.1% and concentrated using Nanosep 10K OMEGA (Pall) columns. Prior to the chromatin immunoprecipitation (ChIP) reaction, 2% sonicated Drosophila S2 cell chromatin was spiked into each sample for quantification. For each IP, Dynabeads Protein A or G (Invitrogen) were washed with RIPA buffer and then resuspended in RIPA buffer. Specific antibodies were added (Supplementary Table 2) and then incubated at 4℃ for at least 3 hours on a rotator. Following antibody conjugation, Dynabeads were washed with RIPA buffer, and then resuspended in RIPA buffer, ~5 million cells of sonicated cell lysate, and protease inhibitors, followed by overnight incubation on a rotator at 4℃. Four successive washes were then performed using 1. RIPA buffer; 2. RIPA buffer with 500 mM NaCl (1% (v/v) Triton X-100, 0.10% SDS, 500 mM NaCl, 20 mM Tris-HCl pH 8.0, 2 mM EDTA, H2O); 3. LiCl buffer (1% NP-40, 250 mM LiCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, H2O); 4. TE buffer (50 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, H2O). Samples were then resuspended in Elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% (v/v) SDS, H2O) and incubated at room temperature for 30 minutes. Reverse cross-linking was then performed using 5M NaCl at 65℃ for 4 hrs. ChIP samples were then treated with 2 μl RNase Cocktail at 65℃ for 30 min followed by 2 μl Proteinase K at 65℃ for 30 min. Samples were then purified with QIAGEN MinElute PCR purification kit (QIAGEN) as per the manufacturer’s protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol. Library preparation was performed using the Kapa Hyper Prep library preparation reagents following the manufacturer’s protocol (Kapa Hyper Prep Kit, Roche 07962363001).
Library preparation was performed using the Kapa Hyper Prep library preparation reagents following the manufacturer’s protocol (Kapa Hyper Prep Kit, Roche 07962363001). ChIP libraries were sequenced by the McGill University Genome Centre using the Illumina HiSeq 4000 at 50 bp single reads.

value: fibroblast

tag: chip antibody


title: C3H10T1-2_TKO_HP1

description: Library name: ChIPseq_sample_63


title: C3H10T1-2_PA_HP1

description: Library name: ChIPseq_sample_61

value: parental


title: LJR0155

description:
Library name: AML_Patient_118
AML_Patient_118


title: 2218, RFX4+, H3K4me3

description: Library name: 2218_rfx4_k4me3


title: LJR0154

description:
Library name: AML_Patient_117
AML_Patient_117


title: RS-S1 RNA


title: C3H10T1-2_PA_HP1_input

description: Library name: ChIPseq_sample_62


title: 1560, RFX4+, H3K4me3

description: Library name: 1560_rfx4_k4me3


title: 1349, RFX4+, H3K4me3

description: Library name: 1349_rfx4_k4me3


title: 2216, RFX4+, H3K4me3

description: Library name: 2216_rfx4_k4me3


title: C3H10T1-2_TKO_SUV39H1_FLAG_input

description: Library name: ChIPseq_sample_60


title: LJR0153

description:
Library name: AML_Patient_116
AML_Patient_116


title: C3H10T1-2_PA_SUV39H1_FLAG_input

description: Library name: ChIPseq_sample_59


title: 2302, RFX4+, H3K4me3

description: Library name: 2302_rfx4_k4me3


title: SPY-S4 RNA

value: Spermatocyte


title: 1560, PU.1+, H3K4me3

description: Library name: 1560_pu1_k4me3

value: H3K4me3 (Sigma-Aldrich, #04-745)


title: 1349, PU.1+, H3K4me3

description: Library name: 1349_pu1_k4me3


title: C3H10T1-2_TKO_SUV39H1_FLAG

description: Library name: ChIPseq_sample_58

value: FLAG M2 (Sigma-Aldrich, F3165)


title: SPY-S3 RNA


title: SPY-S2 RNA


title: C3H10T1-2_PA_SUV39H1_FLAG

description: Library name: ChIPseq_sample_57


title: B70

description: mRNA expression in mouse hippocampus

value: hippocampus

value: Female

value: wildtype


title: LJR0151

description:
Library name: AML_Patient_114
AML_Patient_114

value: Bone. Marrow

value: Primary patient cells

value: Acute Myeloid Leukemia

value: Aza-Ven


title: SPG-S3 RNA

value: testis

value: Spermatogonia


title: RS-S2 RNA

value: testis cell

value: Round spermatids


title: C3H10T1-2_Parental_sgCtrl_RNAseq_rep3

data_processing:
Raw RNA-seq reads were aligned to mm10 using STAR v2.5.3a with default parameters. Afterwards, featureCounts v1.5.3 was used to count exonic reads from the GTF transcript annotation (GENCODE version from UCSC). DESeq2 v1.26.0 was used to generate FPKM for each sample and perform differential gene expression analysis. Adjusted log fold changes (LFC) were calculated using ‘apeglm’ v.1.8.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each sample

growth_protocol: C3H10T1/2 mouse mesenchymal stem cells (ATCC) were cultured in DMEM with 10% fetal bovine serum (FBS,) and supplemented with 1% GlutaMax.

extract_protocol:
Total RNA was extracted from approximately 1 million cells using the AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN) and following the manufacturer’s protocol, including DNase treatment option.
Library preparation was performed using the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) (New England Biolabs) following the manufacturer’s protocol (including RNase H and DNase I digestions). 100-bp paired-end sequencing was performed on the Illumina HiSeq 4000.


title: LJR0146

description:
Library name: AML_Patient_113
AML_Patient_113

value: Cohort 2


title: 2057, PU.1+, H3K4me3

description: Library name: 2057_pu1_k4me3

value: Postmortem cortical brain


title: C3H10T1-2_Parental_sgCtrl_RNAseq_rep2

value: fibroblast


title: LJR0140

description:
Library name: AML_Patient_112
AML_Patient_112


title: LJR0137

description:
Library name: AML_Patient_111
AML_Patient_111


title: SPG-S1 RNA


title: 2216, PU.1+, H3K4me3

description: Library name: 2216_pu1_k4me3


title: 2218, PU.1+, H3K4me3

description: Library name: 2218_pu1_k4me3


title: C3H10T1-2_Parental_sgCtrl_RNAseq_rep1


title: SPG-S2 RNA


title: 1349, OLIG2+, H3K4me3

description: Library name: 1349_olig2_k4me3


title: LJR0113

description:
Library name: AML_Patient_108
AML_Patient_108

value: Cohort 1


title: LJR0152

description:
Library name: AML_Patient_115
AML_Patient_115


title: C3H10T1-2_NSD1-2-SETD2-TKO_RNAseq_rep3


title: LJR0112

description:
Library name: AML_Patient_107
AML_Patient_107


title: f27_4w_WM_rep1

type: genomic

city: Clayton

first: Nir

last: Eynon

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium MethylationEPIC v2.0 following standard protocols.

scan_protocol: Arrays were imaged on a Illumina iScan system using standard protocols.

data_processing:
All processing and analysis were performed using the R statistical computing platform version 4.4.2. Raw IDAT files were processed using the minfi package version 1.50.0. Probes with a detection p-value >0.01, and/or bead count <3 were removed, along with all non-CpG probes, probes located in the sex chromosomes and cross reactive EPICv1 and 450K probes were removed. Furthermore, off-target probes were removed and replicate probes were averaged using the remap functions in DMRcate. Normalisation of type I and type II probes were performed using the Dasen normalisation method as implemented in the wateRmelon R package version 2.11.4.
[processed value definition] Dasen normalised, filtered, beta values (linked as supplementary file on Series record)

label: Cy3 and Cy5

source_name: Vastus lateralis

label_protocol: Between 200-250ng gDNA was bisulfite converted using the EZ-96DNA Methylation™MagPrep (ZYMO Research, California, United States) according to the manufacturer’s instructions.

extract_protocol: DNA was extracted from pooled muscle fibre samples using a phenol-chloroform-isoamyl extraction protocol and whole muscle samples were extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) following manufacturer instructions.

value: Vastus lateralis

value: WM

value: female

tag: timepoint

tag: replicate

value: No


title: f27_pre_WM_rep1

value: Pre


title: LJR0114

description:
Library name: AML_Patient_109
AML_Patient_109

value: Bone. Marrow


title: 1560, OLIG2+, H3K4me3

description: Library name: 1560_olig2_k4me3


title: C3H10T1-2_NSD3-KO_RNAseq_rep3


title: 2057, OLIG2+, H3K4me3

description: Library name: 2057_olig2_k4me3


title: C3H10T1-2_NSD3-KO_RNAseq_rep2


title: C3H10T1-2_NSD1-2-SETD2-TKO_RNAseq_rep2


title: C3H10T1-2_NSD3-KO_RNAseq_rep1


title: C3H10T1-2_NSD1-2-SETD2-TKO_RNAseq_rep1


title: f28_12w_WM_rep1

value: Post


title: LJR0111

description:
Library name: AML_Patient_106
AML_Patient_106

value: Primary patient cells

value: Acute Myeloid Leukemia


title: f27_12w_WM_rep1


title: 2302, PU.1+, H3K4me3

description: Library name: 2302_pu1_k4me3

value: H3K4me3 (Sigma-Aldrich, #04-745)


title: 2216, OLIG2+, H3K4me3, Rep2

description: Library name: 2216_olig2_k4me3_rep2


title: f28_pre_WM_rep1

value: Yes


title: LJR0115

description:
Library name: AML_Patient_110
AML_Patient_110

value: Aza-Ven


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_RNAseq_rep3


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_RNAseq_rep2


title: f28_pre_WM_rep2


title: LJR0108

description:
Library name: AML_Patient_103
AML_Patient_103


title: 2302, OLIG2+, H3K4me3, Rep2

description: Library name: 2302_olig2_k4me3_rep2


title: f28_4w_WM_rep1


title: f29_12w_TI_rep1


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_RNAseq_rep1


title: LJR0106

description:
Library name: AML_Patient_101
AML_Patient_101


title: LJR0110

description:
Library name: AML_Patient_105
AML_Patient_105


title: 2218, OLIG2+, H3K4me3

description: Library name: 2218_olig2_k4me3


title: f29_12w_TII_rep1


title: 2302, OLIG2+, H3K4me3, Rep1

description: Library name: 2302_olig2_k4me3_rep1


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_RNAseq_rep3


title: f29_12w_WM_rep1


title: 1349, NOTCH3+, H3K4me3

description: Library name: 1349_notch3_k4me3

value: NOTCH3-PE (BioLegend, #345405)


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_RNAseq_rep2


title: LJR0104

description:
Library name: AML_Patient_099
AML_Patient_099


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_RNAseq_rep1


title: LJR0105

description:
Library name: AML_Patient_100
AML_Patient_100


title: f29_4w_WM_rep1


title: 2057, NOTCH3+, H3K4me3

description: Library name: 2057_notch3_k4me3


title: f29_pre_TI_rep1


title: LJR0109

description:
Library name: AML_Patient_104
AML_Patient_104


title: 2216, OLIG2+, H3K4me3, Rep1

description: Library name: 2216_olig2_k4me3_rep1


title: C3H10T1-2_ASH1L-KO_RNAseq_rep3


title: LJR0103

description:
Library name: AML_Patient_098
AML_Patient_098


title: LJR0102

description:
Library name: AML_Patient_097
AML_Patient_097


title: f29_pre_TII_rep1


title: 2218, NOTCH3+, H3K4me3

description: Library name: 2218_notch3_k4me3


title: C3H10T1-2_ASH1L-KO_RNAseq_rep2


title: LJR0107

description:
Library name: AML_Patient_102
AML_Patient_102


title: LJR0101

description:
Library name: AML_Patient_096
AML_Patient_096


title: C3H10T1-2_ASH1L-KO_RNAseq_rep1


title: f30_12w_TI_rep1


title: 1560, NOTCH3+, H3K4me3

description: Library name: 1560_notch3_k4me3


title: f30_12w_TII_rep1


title: LJR0100

description:
Library name: AML_Patient_095
AML_Patient_095


title: 1349, NeuN+, H3K4me3

description: Library name: 1349_neun_k4me3

value: NeuN-AF488 (Sigma-Aldrich, MAB377X)


title: C3H10T1-2_SETD2KO_ChIPseq_input_batch1

data_processing:
Raw ChIP-Seq reads were aligned to a combined reference of mm10 (or to hg38 for Cal27 cells) and dm6 genome assembly using BWA version 0.7.17 with default parameters. Afterwards, they were filtered using a cut-off of MAPQ < 3 using Samtools v.1.18. Samclip v.0.2 (samtools view -h in.bam | samclip --ref ref.fa | samtools sort > out.bam) was used to filter any bacterial sequences.
bigWig files were generated using the bamCoverage function from deepTools v3.3.1 with parameters '-b ${samp}.sorted.bam -o ${samp}.cpm.bw -p $nprocs --normalizeUsing CPM --centerReads -e 200'.
Assembly: mm10 for C3H10T1/2, hg38 for Cal27
Supplementary files format and content: bigWig

growth_protocol: C3H10T1/2 mouse mesenchymal stem cells (ATCC) were cultured in DMEM with 10% fetal bovine serum (FBS,) and supplemented with 1% GlutaMax. Cal27 HNSCC cells (ATCC, CRL-2095) were cultured in DMEM (F12) (Invitrogen) with 10% FBS. Drosophila S2 cells were cultured in Schneider’s Drosophila medium (ThermoFisher) containing 10% FBS. All cell lines tested negative for mycoplasma contamination.

extract_protocol:
Approximately 20 million mMSC cells per cell line were used. Crosslinking was performed in 150 mm cell culture plates using 1% formaldehyde (Sigma) at room temperature with gentle rocking for 10 minutes. The crosslinking reaction was quenched using 1.25 M Glycine with gentle rocking at room temperature for 5 minutes. Fixed cell preparations were washed with ice-cold PBS, scraped, and then washed twice more with ice-cold PBS. Crosslinked pellets were resuspended in 500 μl cell lysis buffer (5 mM pH 8.5 PIPES, 85 mM KCl, 1% (v/v) IGEPAL CA-630, 50 mM NaF, 1 mM PMSF, 1 mM phenylarsine oxide, 5 mM sodium orthovanadate, EDTA-free protease inhibitor tablet) and incubated for 30 minutes on ice. Samples were centrifuged and pellets were resuspended in 500 μl of nuclei lysis buffer (50 mM pH 8.0 Tris-HCl, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM phenylarsine oxide, 5 mM sodium orthovanadate, EDTA-free protease inhibitor tablet) and incubated for 30 minutes on ice. Sonication of lysed nuclei was performed using the BioRuptor UCS-300 at maximum intensity for 75-90 cycles (10s on, 20s breaks). Sonication efficiency to achieve fragments between 150 - 500 bp was evaluated using gel electrophoresis on a reversed-crosslinked and purified aliquot from each sample. After sonication, chromatin was diluted to reduce SDS levels to 0.1% and concentrated using Nanosep 10K OMEGA (Pall) columns. Prior to the chromatin immunoprecipitation (ChIP) reaction, 2% sonicated Drosophila S2 cell chromatin was spiked into each sample for quantification of total levels of histone marks. The ChIP reactions were performed using the Diagenode SX-8G IP-Star Compact and Diagenode automated iDeal ChIP-seq Kit for Histones. Dynabeads Protein A (Invitrogen) were washed, then incubated with specific antibodies, 1.5 million cells of sonicated cell lysate, and protease inhibitors for 10 hrs, followed by a 20 min wash cycle using the provided wash buffers (Diagenode Immunoprecipitation Buffers, iDeal ChIP-seq Kit for Histones). Reverse cross-linking was then performed using 5M NaCl at 65℃ for 4 hrs. ChIP samples were then treated with 2 μl RNase Cocktail at 65℃ for 30 min followed by 2 μl Proteinase K at 65℃ for 30 min. Samples were then purified with QIAGEN MinElute PCR purification kit (QIAGEN) as per the manufacturer’s protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was performed using the Kapa Hyper Prep library preparation reagents following the manufacturer’s protocol (Kapa Hyper Prep Kit, Roche 07962363001). ChIP libraries were sequenced by the McGill University Genome Centre using the Illumina HiSeq 4000 at 50 bp single reads.


title: C3H10T1-2_SETD2KO_ChIPseq_H3K27me2_batch1

value: H3K27me2 (Cell Signaling Technology, 9728)


title: LJR0099

description:
Library name: AML_Patient_094
AML_Patient_094


title: 1560, NeuN+, H3K4me3

description: Library name: 1560_neun_k4me3

value: Postmortem cortical brain


title: C3H10T1-2_SETD2KO_ChIPseq_H3K27me1_batch1

value: fibroblast

value: H3K27me1 (Active Motif, 61016)


title: 2057, NeuN+, H3K4me3

description: Library name: 2057_neun_k4me3


title: f30_12w_WM_rep1

value: Vastus lateralis

value: WM


title: f30_4w_WM_rep1

value: female

value: No


title: LJR0098

description:
Library name: AML_Patient_093
AML_Patient_093

value: Bone. Marrow

value: Cohort 1


title: 2216, NOTCH3+, H3K4me3

description: Library name: 2216_notch3_k4me3


title: f30_pre_TI_rep1

value: Pre


title: C3H10T1-2_Parental_ChIPseq_input_rep3_batch2

value: parental


title: LJR0097

description:
Library name: AML_Patient_092
AML_Patient_092

value: Primary patient cells

value: Acute Myeloid Leukemia


title: 2218, NeuN+, H3K4me3

description: Library name: 2218_neun_k4me3

value: H3K4me3 (Sigma-Aldrich, #04-745)


title: C3H10T1-2_Parental_ChIPseq_input_rep1-2_batch2


title: LJR0095

description:
Library name: AML_Patient_090
AML_Patient_090

value: Aza-Ven


title: LJR0096

description:
Library name: AML_Patient_091
AML_Patient_091


title: 2216, NeuN+, H3K4me3

description: Library name: 2216_neun_k4me3

value: NeuN-AF488 (Sigma-Aldrich, MAB377X)


title: f30_pre_TII_rep1


title: f29_pre_WM_rep1


title: C3H10T1-2_Parental_ChIPseq_input_batch1


title: 2302, NeuN+, H3K4me3

description: Library name: 2302_neun_k4me3


title: 2302, NOTCH3+, H3K4me3

description: Library name: 2302_notch3_k4me3

value: NOTCH3-PE (BioLegend, #345405)


title: LJR0094

description:
Library name: AML_Patient_089
AML_Patient_089


title: 1349, ERG+, H3K4me3

description: Library name: 1349_erg_k4me3

value: Postmortem cortical brain


title: LJR0093

description:
Library name: AML_Patient_088
AML_Patient_088


title: f30_pre_WM_rep1


title: C3H10T1-2_Parental_ChIPseq_H3K4me3_rep2_batch2

value: fibroblast

value: H3K4me3 (Diagenode, C15410003)


title: 1560, ERG+, H3K4me3

description: Library name: 1560_erg_k4me3


title: C3H10T1-2_Parental_ChIPseq_H3K4me3_rep3_batch2


title: f31_12w_TI_rep1

value: Vastus lateralis

value: Post


title: f31_12w_TII_rep1

value: female


title: C3H10T1-2_Parental_ChIPseq_H3K4me3_rep1_batch2


title: LJR0091

description:
Library name: AML_Patient_086
AML_Patient_086


title: 2057, ERG+, H3K4me3

description: Library name: 2057_erg_k4me3


title: LJR0092

description:
Library name: AML_Patient_087
AML_Patient_087


title: C3H10T1-2_Parental_ChIPseq_H3K27me2_batch1

value: H3K27me2 (Cell Signaling Technology, 9728)


title: f31_12w_WM_rep1

value: WM

value: No


title: 2218, ERG+, H3K4me3

description: Library name: 2218_erg_k4me3


title: LJR0090

description:
Library name: AML_Patient_085
AML_Patient_085

value: Bone. Marrow

value: Cohort 1


title: f31_pre_TI_rep1

value: Pre


title: f31_4w_WM_rep1


title: LJR0089

description:
Library name: AML_Patient_084
AML_Patient_084

value: Primary patient cells

value: Acute Myeloid Leukemia


title: 2216, ERG+, H3K4me3

description: Library name: 2216_erg_k4me3


title: C3H10T1-2_Parental_ChIPseq_H3K27ac_rep3_batch2

value: parental

value: H3K27ac (Diagenode, C15410196)


title: 2302, ERG+, H3K4me3

description: Library name: 2302_erg_k4me3


title: C3H10T1-2_Parental_ChIPseq_H3K27me1_batch1

value: H3K27me1 (Active Motif, 61016)


title: LJR0087

description:
Library name: AML_Patient_083
AML_Patient_083

value: Aza-Ven


title: C3H10T1-2_Parental_ChIPseq_H3K27ac_rep2_batch2

value: fibroblast


title: f31_pre_TII_rep1


title: 1349, RFX4+, H3K27ac

description: Library name: 1349_rfx4_ac

value: Postmortem cortical brain

value: RFX4(Abcam, ab188020) + Anti-rabbit PE(Cell Signaling, #79408)

value: H3K27ac (Invitrogen, #MA5-23516)


title: f31_pre_WM_rep1

value: Vastus lateralis

value: female


title: C3H10T1-2_Parental_ChIPseq_H3K27ac_rep1_batch2


title: 1560, RFX4+, H3K27ac

description: Library name: 1560_rfx4_ac


title: f32_pre_TI_rep1


title: f32_pre_TII_rep1


title: LJR0084

description:
Library name: AML_Patient_080
AML_Patient_080


title: LJR0085

description:
Library name: AML_Patient_081
AML_Patient_081


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_input_rep1-2_batch2


title: 2057, RFX4+, H3K27ac

description: Library name: 2057_rfx4_ac


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_input_rep3_batch2


title: f32_pre_WM_rep1

value: WM


title: 2218, RFX4+, H3K27ac

description: Library name: 2218_rfx4_ac


title: f33_12w_TI_rep1

value: Post

value: No


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_input_batch1


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_H3K9me3_batch1

value: H3K9me3 (Abcam, ab8898)


title: LJR0082

description:
Library name: AML_Patient_078
AML_Patient_078

value: Bone. Marrow

value: Cohort 1


title: LJR0081

description:
Library name: AML_Patient_077
AML_Patient_077

value: Primary patient cells

value: Acute Myeloid Leukemia


title: f33_12w_TII_rep1


title: 1349, PU.1+, H3K27ac

description: Library name: 1349_pu1_ac

value: H3K27ac (Abcam, #ab4729)


title: 2302, RFX4+, H3K27ac

description: Library name: 2302_rfx4_ac


title: LJR0080

description:
Library name: AML_Patient_076
AML_Patient_076


title: 1560, PU.1+, H3K27ac

description: Library name: 1560_pu1_ac


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_H3K4me3_rep2_batch2

value: H3K4me3 (Diagenode, C15410003)


title: f33_12w_WM_rep1


title: f33_4w_WM_rep1


title: LJR0086

description:
Library name: AML_Patient_082
AML_Patient_082

value: Aza-Ven


title: LJR0078

description:
Library name: AML_Patient_075
AML_Patient_075


title: 2057, PU.1+, H3K27ac

description: Library name: 2057_pu1_ac


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_H3K4me3_rep1_batch2

value: fibroblast


title: f33_pre_TI_rep1

value: Pre


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_H3K27me3_batch1

value: H3K27me3 (Cell Signaling Tech, 9733)


title: LJR0077

description:
Library name: AML_Patient_074
AML_Patient_074


title: LJR0083

description:
Library name: AML_Patient_079
AML_Patient_079


title: LJR0076

description:
Library name: AML_Patient_073
AML_Patient_073


title: 2216, PU.1+, H3K27ac

description: Library name: 2216_pu1_ac

value: Postmortem cortical brain


title: 2216, RFX4+, H3K27ac

description: Library name: 2216_rfx4_ac

value: RFX4(Abcam, ab188020) + Anti-rabbit PE(Cell Signaling, #79408)

value: H3K27ac (Invitrogen, #MA5-23516)


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_H3K27me2_batch1

value: H3K27me2 (Cell Signaling Technology, 9728)


title: 2218, PU.1+, H3K27ac

description: Library name: 2218_pu1_ac


title: f33_pre_TII_rep1

value: Vastus lateralis

value: female


title: f33_pre_WM_rep1

value: WM

value: No


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_H3K27me1_batch1

value: H3K27me1 (Active Motif, 61016)


title: LJR0075

description:
Library name: AML_Patient_072
AML_Patient_072

value: Bone. Marrow

value: Primary patient cells

value: Cohort 1


title: LJR0074

description:
Library name: AML_Patient_071
AML_Patient_071

value: Acute Myeloid Leukemia


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_H3K4me3_rep3_batch2

value: H3K4me3 (Diagenode, C15410003)


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_H3K27ac_rep3_batch2

value: fibroblast

value: H3K27ac (Diagenode, C15410196)


title: 2302, PU.1+, H3K27ac

description: Library name: 2302_pu1_ac

value: H3K27ac (Abcam, #ab4729)


title: 1349, OLIG2+, H3K27ac

description: Library name: 1349_olig2_ac

value: Postmortem cortical brain


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_H3K27ac_rep2_batch2


title: s196_12w_WM_rep1

value: male

value: Post


title: LJR0072

description:
Library name: AML_Patient_069
AML_Patient_069

value: Aza-Ven


title: LJR0073

description:
Library name: AML_Patient_070
AML_Patient_070


title: s196_4w_WM_rep1

value: Vastus lateralis


title: 1560, OLIG2+, H3K27ac

description: Library name: 1560_olig2_ac

value: H3K27ac (Invitrogen, #MA5-23516)


title: 2057, OLIG2+, H3K27ac

description: Library name: 2057_olig2_ac


title: C3H10T1-2_NSD1-2-DKO_ChIPseq_input_batch1


title: LJR0071

description:
Library name: AML_Patient_068
AML_Patient_068


title: 2218, OLIG2+, H3K27ac

description: Library name: 2218_olig2_ac


title: s196_pre_WM_rep1

value: WM

value: Pre


title: LJR0070

description:
Library name: AML_Patient_067
AML_Patient_067


title: s197_12w_TI_rep1

value: No


title: C3H10T1-2_NSD1-2-DKO_ChIPseq_H3K27me2_batch1

value: H3K27me2 (Cell Signaling Technology, 9728)


title: 2216, OLIG2+, H3K27ac

description: Library name: 2216_olig2_ac


title: C3H10T1-2_NSD1-2-DKO_ChIPseq_H3K9me3_batch1

value: H3K9me3 (Abcam, ab8898)


title: s197_12w_TII_rep1


title: 2302, OLIG2+, H3K27ac

description: Library name: 2302_olig2_ac


title: LJR0069

description:
Library name: AML_Patient_066
AML_Patient_066

value: Bone. Marrow

value: Primary patient cells

value: Cohort 1


title: C3H10T1-2_NSD1-2-DKO_ChIPseq_H3K27me1_batch1

value: fibroblast

value: H3K27me1 (Active Motif, 61016)


title: LJR0068

description:
Library name: AML_Patient_065
AML_Patient_065

value: Acute Myeloid Leukemia


title: s197_12w_WM_rep1


title: TI_pre_rep1

value: not provided

value: Mix


title: LJR0067

description:
Library name: AML_Patient_064
AML_Patient_064


title: TII_pre_rep1


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_ChIPseq_input_rep3_batch2


title: C3H10T1-2_NSD1-2-SETD2-TKO_ChIPseq_H3K27ac_rep1_batch2

value: H3K27ac (Diagenode, C15410196)


title: s197_4w_WM_rep1

value: male


title: 1560, NOTCH3+, H3K27ac

description: Library name: 1560_notch3_ac

value: Postmortem cortical brain

value: NOTCH3-PE (BioLegend, #345405)

value: H3K27ac (Abcam, #ab4729)


title: LJR0066

description:
Library name: AML_Patient_063
AML_Patient_063

value: Aza-Ven


title: LJR0065

description:
Library name: AML_Patient_062
AML_Patient_062


title: 2057, NOTCH3+, H3K27ac

description: Library name: 2057_notch3_ac


title: s197_pre_TI_rep1

value: Vastus lateralis

value: Pre

value: No


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_ChIPseq_input_rep1_batch2


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_ChIPseq_input_rep2_batch2


title: 2218, NOTCH3+, H3K27ac

description: Library name: 2218_notch3_ac


title: s197_pre_TII_rep1


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_ChIPseq_H3K4me3_rep3_batch2

value: H3K4me3 (Diagenode, C15410003)


title: LJR0064

description:
Library name: AML_Patient_061
AML_Patient_061

value: Bone. Marrow

value: Primary patient cells


title: s197_pre_WM_rep1

value: WM


title: 2216, NOTCH3+, H3K27ac

description: Library name: 2216_notch3_ac


title: LJR0063

description:
Library name: AML_Patient_060
AML_Patient_060

value: Cohort 1


title: s198_12w_TI_rep1

value: Post


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_ChIPseq_H3K4me3_rep1_batch2

value: fibroblast


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_ChIPseq_H3K4me3_rep2_batch2


title: 2302, NOTCH3+, H3K27ac

description: Library name: 2302_notch3_ac


title: 1349, NOTCH3+, H3K27ac

description: Library name: 1349_notch3_ac


title: LJR0061

description:
Library name: AML_Patient_058
AML_Patient_058

value: Acute Myeloid Leukemia


title: 1349, NeuN+, H3K27ac

description: Library name: 1349_neun_ac

value: NeuN-AF488 (Sigma-Aldrich, MAB377X)


title: s198_12w_WM_rep1

value: male


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_ChIPseq_H3K27ac_rep3_batch2

value: H3K27ac (Diagenode, C15410196)


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_ChIPseq_H3K27ac_rep2_batch2


title: LJR0060

description:
Library name: AML_Patient_057
AML_Patient_057


title: s198_4w_WM_rep1


title: 2057, NeuN+, H3K27ac

description: Library name: 2057_neun_ac

value: Postmortem cortical brain


title: 1560, NeuN+, H3K27ac

description: Library name: 1560_neun_ac

value: H3K27ac (Abcam, #ab4729)


title: C3H10T1-2_NSD1-2-3-SETD2-QKO_ChIPseq_H3K27ac_rep1_batch2


title: LJR0059

description:
Library name: AML_Patient_056
AML_Patient_056

value: Aza-Ven


title: LJR0058

description:
Library name: AML_Patient_055
AML_Patient_055


title: s198_pre_TII_rep1

value: Vastus lateralis


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_ChIPseq_input_rep3_batch2


title: LJR0057

description:
Library name: AML_Patient_054
AML_Patient_054


title: 2302, NeuN+, H3K27ac

description: Library name: 2302_neun_ac


title: 2216, NeuN+, H3K27ac

description: Library name: 2216_neun_ac


title: LJR0062

description:
Library name: AML_Patient_059
AML_Patient_059


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_ChIPseq_input_rep2_batch2


title: LJR0056

description:
Library name: AML_Patient_053
AML_Patient_053


title: s198_pre_WM_rep1

value: Pre


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_ChIPseq_input_rep1_batch2


title: s199_12w_TI_rep1

value: No


title: LJR0055

description:
Library name: AML_Patient_052
AML_Patient_052


title: 1349, ERG+, H3K27ac

description: Library name: 1349_erg_ac

value: H3K27ac (Invitrogen, #MA5-23516)


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_ChIPseq_H3K4me3_rep3_batch2

value: H3K4me3 (Diagenode, C15410003)


title: s198_12w_TII_rep1


title: 1560, ERG+, H3K27ac

description: Library name: 1560_erg_ac


title: s199_12w_TII_rep1


title: LJR0054

description:
Library name: AML_Patient_051
AML_Patient_051

value: Bone. Marrow

value: Primary patient cells


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_ChIPseq_H3K4me3_rep2_batch2


title: s199_12w_WM_rep1

value: WM


title: 2057, ERG+, H3K27ac

description: Library name: 2057_erg_ac


title: LJR0053

description:
Library name: AML_Patient_050
AML_Patient_050

value: Cohort 1


title: 2218, NeuN+, H3K27ac

description: Library name: 2218_neun_ac


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_ChIPseq_H3K4me3_rep1_batch2

value: fibroblast


title: s198_pre_TI_rep1


title: 2218, ERG+, H3K27ac

description: Library name: 2218_erg_ac


title: s199_4w_WM_rep1


title: LJR0052

description:
Library name: AML_Patient_049
AML_Patient_049

value: Acute Myeloid Leukemia


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_ChIPseq_H3K27ac_rep3_batch2


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_ChIPseq_H3K27ac_rep2_batch2


title: 2216, ERG+, H3K27ac

description: Library name: 2216_erg_ac


title: s199_pre_TII_rep1


title: LJR0050

description:
Library name: AML_Patient_047
AML_Patient_047


title: C3H10T1-2_NSD1-2-3-SETD2-ASH1L-QuiKO_ChIPseq_H3K27ac_rep1_batch2


title: 2302, ERG+, H3K27ac

description: Library name: 2302_erg_ac


title: LJR0049

description:
Library name: AML_Patient_046
AML_Patient_046


title: s199_pre_TI_rep1


title: LJR0051

description:
Library name: AML_Patient_048
AML_Patient_048


title: s200_12w_TI_rep1

value: Post


title: Patient 3 – LL6 intrabony and supracrestal granulation tissue

city: Solna

first: Wentao

last: Zhu

address: 17177 Solna

country: Sweden

institute: Karolinska Institutet

description:
Library name: Patient3_LL6_intrabony_supracrestal
Female, 30 years old; collected from a site planned for surgical intervention

data_processing:
Raw sequencing data were demultiplexed, aligned to the human genome, and processed to generate cell-by-gene expression matrices using standard 10x Genomics workflows integrated with Illumina HiSeq processing pipelines.
Assembly: GRCh38/hg38
Supplementary files format and content: The file contains hierarchical data, typically used in single-cell RNA sequencing (scRNA-seq) analysis. It stores processed and filtered gene expression matrices.

source_name: Periodontal granulation tissue

growth_protocol: Tissue collection followed standard clinical protocols at Guy’s Hospital under routine periodontal surgical procedures.

extract_protocol:
Fresh granulation tissue was mechanically minced using a scalpel and enzymatically digested in PBS containing 2% FBS, 2 mg/mL Collagenase Type II, and 1 mg/mL DNAse Type I. The samples were incubated at 37 °C for 20–30 minutes with shaking and intermittent homogenization, filtered through a 40µm strainer, and subsequently centrifuged and cleansed using Miltenyi Biotec Debris Removal Solution.
Single-cell libraries were constructed using the Chromium Single Cell 3’ kit (10x Genomics). A single-cell suspension in PBS + 0.04% BSA was combined with an RT-PCR master mix, Single Cell 3’ Gel Beads, and Partitioning Oil. Barcoded RNA transcripts were generated and the libraries were sequenced on the Nextseq 2000..

treatment_protocol: Samples were obtained from periodontal sites indicated for surgical intervention following completion of step 1 and step 2 periodontal treatments, in accordance with current S3 treatment guidelines.

value: Periodontal granulation tissue

value: granulation cell

value: Wild-type

value: Standard periodontal surgery


title: LJR0048

description:
Library name: AML_Patient_045
AML_Patient_045

value: Aza-Ven


title: C3H10T1-2_H3K36M_ChIPseq_H3K27me2_batch1

value: H3K27me2 (Cell Signaling Technology, 9728)


title: s200_12w_TII_rep1

value: Vastus lateralis

value: male


title: Patient 2 – UR6 supracrestal granulation tissue

description:
Library name: Patient2_UR6_supracrestal
Female, 37 years old; collected from a site planned for surgical intervention


title: C3H10T1-2_H3K36M_ChIPseq_H3K27me1_batch1

value: H3K27me1 (Active Motif, 61016)


title: Patient 1 – UR1 intrabony granulation tissue

description:
Library name: Patient1_UR1_intrabony
Male, 59 years old; collected from a site planned for surgical intervention


title: s199_pre_WM_rep1

value: Pre

value: No


title: s200_12w_WM_rep1


title: LJR0046

description:
Library name: AML_Patient_043
AML_Patient_043

value: Bone. Marrow

value: Primary patient cells


title: Detroit562_PA_RNAseq_rep1

description: Library name: RNAseq_sample_25

data_processing:
Raw RNA-seq reads were aligned to mm10 or hg38 using STAR v2.5.3a with default parameters. Afterwards, featureCounts v1.5.3 was used to count exonic reads from the GTF transcript annotation (GENCODE version from UCSC). DESeq2 v1.26.0 was used to generate FPKM for each sample and perform differential gene expression analysis. Adjusted log fold changes (LFC) were calculated using ‘apeglm’ v.1.8.0.
Assembly: mm10 for C3H10T1/2, hg38 for Cal27 and Detroit562
Supplementary files format and content: tab-separated text files containing FPKM values for each sample

growth_protocol: C3H10T1/2 mouse mesenchymal stem cells (ATCC) were cultured in DMEM with 10% fetal bovine serum (FBS,) and supplemented with 1% GlutaMax. Cal27 (ATCC, CRL-2095) and Detroit562 (ATCC, CCL-138) HNSCC cells were cultured in DMEM (F12) (Invitrogen) with 10% FBS and penicillin-streptomycin. Epitope-tagged H3.3 was previously cloned into pCDH-EF1-MCS-Puro lentiviral vector and site-directed mutagenesis techniques were used to generate the H3K36M mutation. To produce lentivirus, 293T cells were transfected with a lentiviral vector containing H3.3K36M (provided by Dr. Chao Lu) and helper plasmids (psPAX2 and pMD2.G). Supernatant containing lentivirus was collected after 48h, filtered and used to infect Cal27 and Detroit562 cells. Transduced cells were grown under puromycin selection (1 μg/ml) for 48 h after transduction.

value: patient-derived head and neck squamous cell carcinoma cell line

value: parental


title: Detroit562_PA_RNAseq_rep2

description: Library name: RNAseq_sample_26


title: LJR0045

description:
Library name: AML_Patient_042
AML_Patient_042

value: Acute Myeloid Leukemia

value: Cohort 1


title: Fibroblasts treated with ADSC NVs rep3

city: Harbin

first: Tonghao

last: Yao

state: Heilongjiang

address: No. 246 Xuefu Road

department: Second Affiliated Hospital of Harbin Medical University

institute: Harbin Medical University

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM and genecount values for each Sample

source_name: Fibroblasts of abdominal skin

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Fibroblasts of abdominal skin

value: ADSC NVs


title: Fibroblasts treated with ADSC NVs rep4


title: LJR0044

description:
Library name: AML_Patient_041
AML_Patient_041


title: Fibroblasts treated with ADSC NVs rep2


title: s200_4w_WM_rep1

value: WM


title: s200_pre_TI_rep1


title: Detroit562_H3K36M_OE_RNAseq_rep2

description: Library name: RNAseq_sample_24


title: Fibroblasts treated with ADSC NVs rep1


title: C3H10T1-2_H3K36M_ChIPseq_input_batch1

value: fibroblast


title: Detroit562_H3K36M_OE_RNAseq_rep1

description: Library name: RNAseq_sample_23


title: LJR0047

description:
Library name: AML_Patient_044
AML_Patient_044

value: Aza-Ven


title: LJR0043

description:
Library name: AML_Patient_040
AML_Patient_040


title: s200_pre_WM_rep1


title: Cal27_PA_RNAseq_rep2

description: Library name: RNAseq_sample_22


title: Control rep3

value: Control


title: s201_12w_TI_rep1

value: Vastus lateralis

value: Post


title: LJR0042

description:
Library name: AML_Patient_039
AML_Patient_039


title: LJR0041

description:
Library name: AML_Patient_038
AML_Patient_038


title: Control rep4


title: s201_12w_TII_rep1

value: male


title: s200_pre_TII_rep1

value: Pre


title: Control rep2


title: Cal27_H3K36M_OE_RNAseq_rep2

description: Library name: RNAseq_sample_20


title: LJR0040

description:
Library name: AML_Patient_037
AML_Patient_037


title: Cal27_PA_RNAseq_rep1

description: Library name: RNAseq_sample_21


title: s201_12w_WM_rep1

value: No


title: LJR0039

description:
Library name: AML_Patient_036
AML_Patient_036

value: Bone. Marrow


title: CNOT4-AID_12h_rep2_TPL

city: State College

first: Shardul

last: Kulkarni

state: PA

address: 463 North Frear Laboratory

institute: Penn State University

data_processing:
For libraries to caluculate changes in steadystate and RNA halflife  (Triptolide libraries), FASTQ files were further processed as per the Bulk RNA-seq Data Standards and Processing Pipeline (https://www.encodeproject.org/), using STAR [(Dobin et al. 2013), version - STAR_2.5.1b_modified] and RSEM (RNA-Seq by Expectation-Maximization) tool. The reads were mapped to hg38 (GRCh38) using Gencode-v29 comprehensive gene set, predicted tRNA genes, and the ERCC spike-in controls. Read-counts for each gene generated by RSEM were used for differential expression analysis using DESeq2 (Love et al., 2014, PMID: 25516281). Genes with a sum of ≥ 8 across both replicates and conditions were used in DESeq2. The expression data were normalized to ERCC spike in controls using estimateSizeFactors function in DESeq2.
TT-seq data was mapped to a human and S pombe concatenated genome reference sequence using STAR aligner. The alignments were filtered using samtools where alignments with a mapping quality < 7 were skipped and only proper pairs were selected. TT-Seq raw read counts were obtained for gene including exon and intron regions using featureCounts, Differential expression analysis was performed with DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw counts of each sample.

growth_protocol: Cells were maintained in complete media [Dulbecco's Modified Eagle Medium (DMEM) with 10% Fetal Bovine Serum, 1X glutamax and 1X Penicillin and Streptomycin] in 5% CO2 atmosphere at 37 °C in a humidified incubator.

extract_protocol:
To calculate changes in nascent RNA synthesis (TTseq): Parental (untagged), CNOT1AID and CNOT4AID cells were pretreated with 1mM auxin for 2 h, follwed by pulse labelling with 4-thiouridine (4SU) for 15 minutes, followed by total RNA extraction.
Total RNA was extracted from the cells using Trizol (Invitrogen#15596026) and cleaned up using PureLink RNA Mini kit (Invitrogen#12183018A)
For libraries to caluculate changes in steadystate and RNA halflife (Triptolide libraries), 500 ng of Turbo DNase digested RNA was mixed with 2 µl of 1:200 diluted ERCC Spike-in mix (Invitrogen#4456740) which was subjected to library preparation. TT-seq. libraries were prepared as described by Gregersen et al., 2020 (PMID: 31915390). Briefly, following depletion of desired protein, cells were treated with 4-thiouridine (4SU) for 15 minutes. The total RNA was extracted using Trizol and PureLink RNA Mini kit. RNA was mixed with that from S. pombe labelled with 4TU (as a spike in control). The labelled RNA was biotinylated using methanethiosulfonate (MTS)-biotin (Biotium#90065) and enriched using Dynabeads™ MyOne™ Streptavidin C1 (Invitrogen#65001). 300 ng of RNA was subjected to library preparation. All the sequencing libraries were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Plus (Illumina#20040525) according to manufacturer’s instructions. Sequencing was carried out at Genomics Research Incubator, Penn State University, USA using NextSeq™1000/2000 P2 Reagents(100Cycles) on NextSeq 2000.

treatment_protocol:
To calculate changes in steadystate RNA: Parental (untagged), CNOT1AID and CNOT4AID cells were treated with ± 1mM auxin for 8 h and 24 h, followed by total RNA extraction.
To calculate changes in RNA hallives: Parental (untagged), CNOT1AID and CNOT4AID cells were pretreated with 1mM auxin for 2 h, follwed by treatment with 1µM Triptlide for 0, 3, 6 and 12 h, followed by total RNA extraction.

value: Cells were treated with 1mM auxin for 2h; followed by treatment with 1µM Triptolide for 12h


title: s201_4w_WM_rep1


title: Cal27_H3K36M_OE_RNAseq_rep1

description: Library name: RNAseq_sample_19

value: patient-derived head and neck squamous cell carcinoma cell line


title: LJR0038

description:
Library name: AML_Patient_035
AML_Patient_035

value: Primary patient cells


title: s201_pre_TI_rep1


title: LJR0037

description:
Library name: AML_Patient_034
AML_Patient_034

value: Acute Myeloid Leukemia


title: HNSCC_Detroit562_H3K36M_OE_ChIPseq_H3K27ac

description: Library name: ChIPseq_sample_81

value: H3K27ac (Diagenode, C15410196)


title: CNOT4-AID_12h_rep1_TPL


title: s201_pre_TII_rep1


title: CNOT4-AID_6h_rep2_TPL

value: Cells were treated with 1mM auxin for 2h; followed by treatment with 1µM Triptolide for 6h


title: HNSCC_Detroit562_Parental_ChIPseq_H3K27ac

description: Library name: ChIPseq_sample_79

value: parental


title: CNOT4-AID_6h_rep1_TPL


title: s201_pre_WM_rep1

value: WM

value: Yes


title: LJR0035

description:
Library name: AML_Patient_032
AML_Patient_032

value: Aza-Ven

value: Cohort 1


title: LJR0036

description:
Library name: AML_Patient_033
AML_Patient_033


title: CNOT4-AID_3h_rep2_TPL

value: Cells were treated with 1mM auxin for 2h; followed by treatment with 1µM Triptolide for 3h


title: HNSCC_Detroit562_Parental_sgCtrl_ChIPseq_H3K27ac

description: Library name: ChIPseq_sample_78

value: parental-sgCtrl


title: s201_pre_WM_rep2

value: Vastus lateralis

value: male


title: s201_pre_WM_rep3

value: Pre


title: LJR0033

description:
Library name: AML_Patient_030
AML_Patient_030

value: Bone. Marrow


title: LJR0034

description:
Library name: AML_Patient_031
AML_Patient_031


title: CNOT4-AID_0h_rep2_TPL

value: Cells were treated with 1mM auxin for 2h; no Triptolide treatment


title: HNSCC_Detroit562_Parental_sgCtrl_ChIPseq_input

description: Library name: ChIPseq_sample_75

value: patient-derived head and neck squamous cell carcinoma cell line


title: Control rep1

value: Fibroblasts of abdominal skin

value: Control


title: HNSCC_Detroit562_Parental_sgCtrl_ChIPseq_H3K27me3

description: Library name: ChIPseq_sample_76


title: LJR0032

description:
Library name: AML_Patient_029
AML_Patient_029

value: Primary patient cells

value: Acute Myeloid Leukemia


title: CNOT4-AID_0h_rep1_TPL


title: HNSCC_Detroit562_Parental_ChIPseq_input

description: Library name: ChIPseq_sample_80

value: parental


title: s202_12w_TII_rep1

value: Post

value: No


title: s202_12w_WM_rep1

value: WM


title: LJR0031

description:
Library name: AML_Patient_028
AML_Patient_028

value: Aza-Ven

value: Cohort 1


title: CNOT1-AID_12h_rep2_TPL

value: Cells were treated with 1mM auxin for 2h; followed by treatment with 1µM Triptolide for 12h


title: HNSCC_Detroit562_H3K36M_OE_ChIPseq_input

description: Library name: ChIPseq_sample_73


title: HNSCC_Detroit562_Parental_sgCtrl_ChIPseq_H3K9me3

description: Library name: ChIPseq_sample_74

value: parental-sgCtrl

value: H3K9me3 (Abcam, ab8898)


title: LJR0030

description:
Library name: AML_Patient_027
AML_Patient_027


title: CNOT1-AID_12h_rep1_TPL


title: s202_4w_WM_rep1

value: Vastus lateralis

value: male


title: LJR0029

description:
Library name: AML_Patient_026
AML_Patient_026

value: Bone. Marrow


title: HNSCC_Detroit562_H3K36M_OE_ChIPseq_H3K9me3

description: Library name: ChIPseq_sample_72

value: patient-derived head and neck squamous cell carcinoma cell line


title: CNOT4-AID_3h_rep1_TPL

value: Cells were treated with 1mM auxin for 2h; followed by treatment with 1µM Triptolide for 3h


title: s202_pre_TI_rep1

value: Pre


title: CNOT1-AID_6h_rep2_TPL

value: Cells were treated with 1mM auxin for 2h; followed by treatment with 1µM Triptolide for 6h


title: HNSCC_Detroit562_H3K36M_OE_ChIPseq_H3K27me3

description: Library name: ChIPseq_sample_77


title: LJR0028

description:
Library name: AML_Patient_025
AML_Patient_025

value: Primary patient cells

value: Acute Myeloid Leukemia


title: HNSCC_Cal27_H3K36M_OE_ChIPseq_input_batch2

description: Library name: ChIPseq_sample_71


title: HNSCC_Cal27_H3K36M_OE_ChIPseq_H3K27ac_batch2

description: Library name: ChIPseq_sample_70

value: H3K27ac (Diagenode, C15410196)


title: s202_12w_TI_rep1

value: Post

value: No


title: LJR0027

description:
Library name: AML_Patient_024
AML_Patient_024

value: Aza-Ven


title: s202_pre_WM_rep1

value: WM


title: LJR0026

description:
Library name: AML_Patient_023
AML_Patient_023

value: Cohort 1


title: s203_12w_TI_rep1


title: HNSCC_Cal27_Parental_ChIPseq_H3K27ac_rep2_batch2

description: Library name: ChIPseq_sample_69

value: parental


title: LJR0025

description:
Library name: AML_Patient_022
AML_Patient_022


title: s203_12w_TII_rep1


title: HNSCC_Cal27_Parental_ChIPseq_H3K27ac_rep1_batch2

description: Library name: ChIPseq_sample_68


title: LJR0024

description:
Library name: AML_Patient_021
AML_Patient_021


title: s203_12w_WM_rep1


title: CNOT1-AID_0h_rep1_TPL

value: Cells were treated with 1mM auxin for 2h; no Triptolide treatment


title: CNOT1-AID_0h_rep2_TPL


title: LJR0023

description:
Library name: AML_Patient_020
AML_Patient_020


title: s202_pre_TII_rep1

value: Vastus lateralis


title: s203_pre_TI_rep1

value: male


title: CNOT1-AID_3h_rep2_TPL


title: CNOT1-AID_6h_rep1_TPL


title: WT_12h_rep1_TPL

value: Parental

value: Cells were treated with 1mM auxin for 2h; followed by treatment with 1µM Triptolide for 12h


title: LJR0021

description:
Library name: AML_Patient_018
AML_Patient_018

value: Bone. Marrow


title: HNSCC_Cal27_Parental_ChIPseq_input_batch2

description: Library name: ChIPseq_sample_65

value: patient-derived head and neck squamous cell carcinoma cell line


title: HNSCC_Cal27_Parental_sgCtrl_ChIPseq_input

value: parental-sgCtrl NSD1 wild-type


title: LJR0022

description:
Library name: AML_Patient_019
AML_Patient_019

value: Primary patient cells


title: CNOT1-AID_3h_rep1_TPL

value: Cells were treated with 1mM auxin for 2h; followed by treatment with 1µM Triptolide for 3h


title: WT_6h_rep2_TPL

value: Cells were treated with 1mM auxin for 2h; followed by treatment with 1µM Triptolide for 6h


title: WT_6h_rep1_TPL


title: s203_pre_WM_rep1

value: Pre


title: HNSCC_Cal27_Parental_sgCtrl_ChIPseq_H3K9me3

value: H3K9me3 (Abcam, ab8898)


title: LJR0019

description:
Library name: AML_Patient_016
AML_Patient_016

value: Acute Myeloid Leukemia

value: Aza-Ven


title: WT_3h_rep2_TPL


title: LJR0020

description:
Library name: AML_Patient_017
AML_Patient_017

value: Cohort 1


title: s203_pre_TII_rep1

value: No


title: LJR0018

description:
Library name: AML_Patient_015
AML_Patient_015


title: HNSCC_Cal27_H3K36M_ChIPseq_H3K9me3


title: HNSCC_Cal27_Parental_ChIPseq_H3K27me3_batch2

description: Library name: ChIPseq_sample_66

value: parental


title: WT_12h_rep2_TPL


title: TIIx_pre_rep1

value: Vastus lateralis

value: not provided

value: Mix


title: WT_3h_rep1_TPL

value: Parental


title: HNSCC_Cal27_H3K36M_OE_ChIPseq_H3K27me3_batch2

description: Library name: ChIPseq_sample_67


title: s203_4w_WM_rep1

value: WM

value: male


title: O90, JQ1, rep3

city: Baltimore

first: Fernando

last: Zamuner

state: MD

address: 1550 Orleans Street

department: Department of Otolaryngology - Head and Neck Surgery

institute: Johns Hopkins University, School of Medicine

data_processing:
Gene expression values were quantified from RNA sequencing data using RNA-Seq by Salmon (version 0.8.2).
We load results from Salmon and DESeq2 version 1.28.0 was performed for differential gene expression analysis between tumor and normal samples.
Assembly: gencode_v19_ref_index
Supplementary files format and content: JQ1_counts.txt: Tab-delimited file with raw RNA-seq counts from DESeq2. Rows use Ensembl Gene IDs (ENSG format), with columns for each sample. The first column lists gene IDs, and subsequent columns contain raw counts per sample.

growth_protocol: Cells were grown on high-glucose DMEM media (Clontech, Mountain View, CA), supplemented by 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin at 37°C in 5% CO2

extract_protocol:
RNA was harvested using using the mirVana miRNA Isolation Kit (Ambion, Forster City, CA) per manufacturer's recommendations.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq stranded total RNA-seq Gold kit (San Diego, CA) following the manufacturer's recommendations.

treatment_protocol: HPV+ HNSCC cell lines were cultivated in 6-well tissue culture dishes and then treated with 500 nM of JQ1, a bromodomain inhibitor (Selleck Chemicals, Houston, TX, USA) or 0.1% dimethyl sulfoxide (DMSO) as a control. The treated cells were incubated at 37°C for 72 hours.

value: HPV+ HNSCC tumor

value: JQ1 (the treatment)


title: LJR0016

description:
Library name: AML_Patient_014
AML_Patient_014

value: Bone. Marrow

value: Primary patient cells


title: WT_0h_rep2_TPL

value: Cells were treated with 1mM auxin for 2h; no Triptolide treatment


title: LJR0015

description:
Library name: AML_Patient_013
AML_Patient_013


title: KO 24hr 3

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

description:
Library name: Sample 18
KO 24hr 3

data_processing:
Adapter sequences and low quality reads were filtered by Trimmoatic
Surviving reads were aligned to reference genome using STAR aligner
Assembly: mm39
Supplementary files format and content: TAB file for gene count

molecule: polyA RNA

source_name: liver

extract_protocol:
RNA was isolated from individual WT and EGFR-KO mice liver samples at 0, 1,3, 6, 12, and 24hr (n=3) using the TRIzol method.
Following Illumina library prep and RNA-seq protocols.

value: liver

value: KO


title: WT_0h_rep1_TPL


title: LJR0014

description:
Library name: AML_Patient_012
AML_Patient_012

value: Acute Myeloid Leukemia

value: Aza-Ven


title: O90, JQ1, rep1


title: KO 24hr 2

description:
Library name: Sample 17
KO 24hr 2


title: O90, DMSO, rep3

value: DMSO (non-treatment control)


title: WT 24hr 3

description:
Library name: Sample 15
WT 24hr 3

value: WT


title: LJR0013

description:
Library name: AML_Patient_011
AML_Patient_011

value: Cohort 1


title: TIIx_12w_rep1

value: Vastus lateralis

value: not provided

value: Post

value: No


title: CNOT4-AID_Treated_24h_rep2_steady_state

value: Cells were treated with 1mM auxin for 24h


title: KO 24hr 1

description:
Library name: Sample 16
KO 24hr 1


title: HNSCC_Cal27_H3K36M_ChIPseq_input

value: patient-derived head and neck squamous cell carcinoma cell line


title: CNOT4-AID_Treated_24h_rep1_steady_state


title: O90, DMSO, rep1

value: HPV+ HNSCC tumor


title: LJR0012

description:
Library name: AML_Patient_010
AML_Patient_010

value: Bone. Marrow


title: CNOT4-AID_Untreated_24h_rep1_steady_state

value: Cells were left untreated for 24h


title: LJR0011

description:
Library name: AML_Patient_009
AML_Patient_009

value: Primary patient cells


title: O90, DMSO, rep2


title: O47, JQ1, rep3

value: JQ1 (the treatment)


title: LJR0010

description:
Library name: AML_Patient_008
AML_Patient_008


title: CNOT4-AID_Untreated_24h_rep2_steady_state


title: CNOT1-AID_Treated_24h_rep2_steady_state


title: CNOT1-AID_Treated_24h_rep1_steady_state


title: O90, JQ1, rep2


title: WT 24hr 1

description:
Library name: Sample 13
WT 24hr 1

value: liver


title: KO 6hr 3

description:
Library name: Sample 12
KO 6hr 3

value: KO


title: O47, JQ1, rep2


title: LJR0009

description:
Library name: AML_Patient_007
AML_Patient_007

value: Acute Myeloid Leukemia

value: Aza-Ven


title: KO 6hr 2

description:
Library name: Sample 11
KO 6hr 2


title: LJR0007

description:
Library name: AML_Patient_005
AML_Patient_005


title: CNOT1-AID_Untreated_24h_rep1_steady_state


title: O47, JQ1, rep1


title: O47, DMSO, rep2

value: DMSO (non-treatment control)


title: LJR0008

description:
Library name: AML_Patient_006
AML_Patient_006

value: Cohort 1


title: WT 24hr 2

description:
Library name: Sample 14
WT 24hr 2

value: WT


title: CNOT1-AID_Untreated_24h_rep2_steady_state


title: O47, DMSO, rep3


title: KO 6hr 1

description:
Library name: Sample 10
KO 6hr 1


title: WT_Treated_24h_rep1_steady_state

value: Parental


title: WT 6hr 3

description:
Library name: Sample 9
WT 6hr 3


title: LJR0006

description:
Library name: AML_Patient_004
AML_Patient_004


title: WT 6hr 1

description:
Library name: Sample 7
WT 6hr 1


title: WT_Treated_24h_rep2_steady_state


title: O47, DMSO, rep1


title: KO 0hr 3

description:
Library name: Sample 6
KO 0hr 3


title: WT_Untreated_24h_rep2_steady_state


title: LJR0005

description:
Library name: AML_Patient_003
AML_Patient_003


title: LJR0003

description:
Library name: AML_Patient_001
AML_Patient_001


title: WT_Untreated_24h_rep1_steady_state


title: KO 0hr 2

description:
Library name: Sample 5
KO 0hr 2


title: Hi-C S-phase,  WT, replicate 3

city: Lyon

first: Aurele

last: Piazza

address: 46 Allee d'Italie

country: France

institute: ENS Lyon

description: Library name: AD681

data_processing:
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2) pipeline function in cutsite mode with mapping quality set to 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function. Cooler zoomify function was used to generate balanced cooler at 1, 2, 5, 10, and 20 kb resolution.
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz)
Supplementary files format and content: Hi-C in mcool format, containing balanced contact data at 1, 2, 5, 10, and 20 kb resolution.

organism: Saccharomyces cerevisiae

growth_protocol: Cells arrested in G1 with alpha-factor in YPD medium (1% yeast extract, 2% peptone, 2% glucose) at 30°C were washed 3 times with 200 mL of YPD and released in S-phase at 30°C for 20 minutes prior to crosslinking. In all cultures, 2 mM indole-3-acetic acid (aka auxin) was added 2 hours prior to, and in all following wash and culture media post G1 release.

extract_protocol:
Cells were spheroplasted with 0.25 mg/mL Zymolyase 100T at 37°C for 30 minutes, crosslinked with 3 mM EGS (ethylene glycol bis(succinimidyl succinate)) at 30°C for 40 minutes at 100 rpm, and quenched with 400 mM glycine for 5 minutes at 100 rpm.
Hi-C library were generated using the Arima Hi-C+ kit following manufacturer instructions starting from 2-5x10^7 cells. DNA was fragmented in 300-400 bp DNA fragments using Covaris M220 sonicator. Illumina sequencing libraries were prepared using the Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems with UD indexes following manufacturer's instructions.

treatment_protocol: ~1.5x10^9 cells were crosslinked with 3% formaldehyde for 30 minutes at 120 rpm at room temperature, followed by quenching with 330 mM glycine for 30 minutes at 120 rpm.

value: MATa-inc, ura3::LY-HOcs, lys2::LY, can1::HIS3-LY-Pad, trp1::GAL-HO-hphMX, his3::OsTIR1-9Myc::HIS3, ade2-1, leu2-3,112, RAD5

value: Auxin


title: Hi-C S-phase,  Cdc45-depleted, replicate 2

description: Library name: AD680

value: MATa, leu2-3,112, trp1-1, can1-100, ura3-1, ade2-1, his3::ADH1promoter-OsTIR1-9myc::HIS3,  CDC45-Flagx5-aid::KanMX4, RAD5


title: Hi-C S-phase, ctf4

description: Library name: AD641

value: MATa-inc, ura3::LY-HOcs, lys2::LY, can1::HIS3-LY-Pad, trp1::GAL-HO-hphMX, his3::OsTIR1-9Myc::HIS3, ctf4::KanMX, ade2-1, leu2-3,112, RAD5


title: LJR0004

description:
Library name: AML_Patient_002
AML_Patient_002


title: DownstreamTAD2_48h, rep2

city: Copenhagen N

first: Nils

last: Krietenstein

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

description:
Library name: DownstreamTAD2_48h
Processed file derives from the merged of the two sequencing runs of two biological replicates

data_processing:
RCMC paired-end reads were downloaded as .fastq files and processed with Distiller pipeline (https://github.com/mirnylab/distiller-nf). Briefly, read pairs were aligned against the human reference assembly hg38. Aligned reads were parsed, PCR duplicates were removed, and pairs files were generated. Pairs files obtained from the Distiller pipeline were used in further analyses.
Pairs files were shifted by 73 bp relative to the read orientation, and read pairs separated by less than 500 bp were discarded to remove undigested di-nucleosome contaminants. The nucleosomal shift represents the approximate locations of the nucleosome dyad axes.
To retain only those reads that both mates align on the region of interest, the awk bash function was used. A 10-bp bin file of the human reference assembly hg38 was used to convert filtered reads into .cool files using cooler cload pairs of the cooler package (https://github.com/open2c/cooler).
Cool files were then converted into multiresolution cooler files using the cooler zoomify option of the cooler package (https://github.com/open2c/cooler).
RCMC data were visualized with cooltools package (https://github.com/open2c/cooltools) in python.
Assembly: Hg38
Supplementary files format and content: mcool files.  For CTCF and ORF c-Myc samples 500 bp, 1 kb, 2 kb, 5 kb, 10 kb resolutions were generated, for all the other cuts an additional 20 kb resolution was included.

source_name: HeLa Kyoto

growth_protocol: DMEM, 10% heat-inactivated FBS and penicillin-streptomycin antibiotics. Cells were cultured at 37 C, 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at RT. The reaction was quenched with 0.25 M of glycine (final concentration) for 5 min at RT. Cells were then washed and crosslinked for the second time with ethylene glycol bis(succinimidyl succinate) EGS at a final concentration of 3 mM, the reaction was quenched with 0.4 M glycine (final concentration) for 5 min RT. Micro-C libraries were built and a tiled array of probes was used to enrich for the region of interest.
Region Capture Micro-C libraries were prepared using NEBNext UltraII DNA Library Prep Kit for Illumina with NEBNext Multiplex Oligos for Illumina from New England Biolabs (NEB). After library amplification, DNA libraries were size selected at 100-1000 bp in length using SPRIselect size selection beads from Beckman Coulter.

treatment_protocol: To generate site-specific DNA double-strand breaks, cells were transfected with sgRNA–Cas9 ribonucleoprotein complexes (RNPs) using Lipofectamine CRISPRMAX Cas9.

value: HeLa Kyoto

value: immortal human epithelial cell

value: Cas9 cleavage


title: CNOT4-AID_Treated_8h_rep2_steady_state

value: Cells were treated with 1mM auxin for 8h


title: WT 6hr 2

description:
Library name: Sample 8
WT 6hr 2


title: KO 0hr 1

description:
Library name: Sample 4
KO 0hr 1


title: CNOT4-AID_Treated_8h_rep1_steady_state


title: Hi-C S-phase, Scc1-depleted

description: Library name: AD561

value: MATa-inc, ura3::LY-HOcs, lys2::LY, trp1::GAL-HO-hphMX, can1-100, ade2-1, leu2-3,112, his3::OsTIR1-9Myc::HIS3, SCC1-Pk3-AID::KMX, RAD5


title: Hi-C S-phase,  WT, replicate 2

description: Library name: AD560


title: CNOT4-AID_Untreated_8h_rep2_steady_state

value: Cells were left untreated for 8h


title: CNOT4-AID_Untreated_8h_rep1_steady_state


title: WT 0hr 2

description:
Library name: Sample 2
WT 0hr 2

value: liver


title: Hi-C S-phase,  WT, replicate 1

description: Library name: AD436


title: Control_cuts, rep2

description:
Library name: Control_cuts
Processed file derives from the merged of the two sequencing runs of two biological replicates


title: UpstreamTAD1_48h, rep2

description:
Library name: UpstreamTAD1_48h
Processed file derives from the merged of the two sequencing runs of two biological replicates


title: Hi-C S-phase,  Cdc45-depleted, replicate 1

description: Library name: AD559

value: MATa-inc, ura3::LY-Hocs, lys2::LY, trp1::GAL-HO-hphMX,can1::HIS3-L0.6kb, his3::pADH1-OsTIR1-9Myc::HIS3, ade2-1, leu2-3,112, RAD5, CDC45-FlagX5-mini-AID::KanMx4


title: CNOT1-AID_Treated_8h_rep2_steady_state


title: CTCFsite_72h, rep2

description:
Library name: CTCFsite_72h
Processed file derives from the merged of the three sequencing runs of two biological replicates


title: RS-S5 Hi-C

data_processing:
Hi-C reads were aligned to the pig reference genome (Sscrofa 11.1) and contact frequency of genomic loci was calculated by Juicer pipeline (version 1.8.9), Unmapped reads, low-quality (defined as MAPQ<30) and intra-fragment reads were discarded in order to later valid Hi-C contacts analyses. Built contact matrices and then KR-normalized them with Juicer. All matrices from different samples were standardized by R software bnbc (version 1.12.0). The correlation of contact matrices was calculated with QuASAR-Rep, HiCRep (version1.14.0), or GenomeDISCO (Yardımcı et al.2019). We choose 100-kb or 20-kb bin size for construction of global interaction patterns of the whole chromosome, and 20-kb bin size to show local interactions and perform TAD calling. Then the binned matrices were normalized to obtain the KR-normalized contact matrices with the high-resolution of 5-kb.
Assembly: Sscrofa11.1
Supplementary files format and content: Hi-C file format, reflecting genomic interaction patterns

extract_protocol:
2.0×106 cells were fixed with 37% formaldehyde and quenched formaldehyde with glycine for 10min at RT. Cells were washed by PBS for three times and then centrifugal pellet of cells, snap-frozen, and stored at -80℃. Resuspended cell pellets in lysis buffer on ice for 50min and then the nuclei were digested with 200U MboI for 1h at 37℃. Filled restriction fragment overhangs and sheared DNAs to 300-500bp, biotinylated DNAs were pulled down with streptavidin beads.
Hi-C：Submission of DNA reads to Illumina NovaSeq 6000 for sequencing, we generated data from 6 samples (two for SPG, two for SPY and two for RS), totaling approximately 2.7 billion valid interactions, with an average of 448 million valid interactions per sample.

value: testis

value: testis cell

value: Round spermatids


title: DownstreamTAD1_48h, rep2

description:
Library name: DownstreamTAD1_48h
Processed file derives from the merged of the two sequencing runs of two biological replicates


title: CTCFsite_48h, rep2

description:
Library name: CTCFsite_48h
Processed file derives from the merged of the three sequencing runs of two biological replicates


title: CNOT1-AID_Treated_8h_rep1_steady_state


title: KO 12hr 3

description:
Library name: Sample 24
KO 12hr 3

extract_protocol:
RNA was isolated from individual WT and EGFR-KO mice liver samples at 0, 1,3, 6, 12, and 24hr (n=3) using the TRIzol method.
Following AVITI library prep and RNA-seq protocols.

value: KO 12hr 3


title: KO 12hr 2

description:
Library name: Sample 23
KO 12hr 2

value: KO 12hr 2


title: RS-S4 Hi-C


title: CNOT1-AID_Untreated_8h_rep2_steady_state


title: CTCFsite_24h, rep2

description:
Library name: CTCFsite_24h
Processed file derives from the merged of the three sequencing runs of two biological replicates


title: CNOT1-AID_Untreated_8h_rep1_steady_state


title: WT 0hr 3

description:
Library name: Sample 3
WT 0hr 3

value: WT


title: UpstreamTAD2_48h, rep2

description:
Library name: UpstreamTAD2_48h
Processed file derives from the merged of the two sequencing runs of two biological replicates


title: SPY-S4 Hi-C

value: Spermatocyte


title: CTCFsite_6h, rep2

description:
Library name: CTCFsite_6h
Processed file derives from the merged of the three sequencing runs of two biological replicates


title: SPY-S2 Hi-C


title: WT 12hr 2

description:
Library name: Sample 20
WT 12hr 2

value: WT 12hr 2


title: WT_Treated_8h_rep2_steady_state

value: Parental


title: WT 0hr 1

description:
Library name: Sample 1
WT 0hr 1


title: WT_Treated_8h_rep1_steady_state


title: c-mycORF_48h, rep2

description:
Library name: c-mycORF_48h
Processed file derives from the merged of the three sequencing runs of two biological replicates

value: HeLa Kyoto


title: SPG-S1 Hi-C

value: Spermatogonia


title: WT_Untreated_8h_rep2_steady_state


title: SPG-S2 Hi-C


title: KO 3hr 3

description:
Library name: Sample 18
KO 3hr 3

value: KO 3hr 3


title: c-mycORF_72h, rep2

description:
Library name: c-mycORF_72h
Processed file derives from the merged of the three sequencing runs of two biological replicates

value: immortal human epithelial cell

value: Cas9 cleavage


title: WT 12hr 1

description:
Library name: Sample 19
WT 12hr 1

value: WT 12hr 1