title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-D7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-D20

status: Public on Dec 22 2025

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: strain

tag: age

value: 18 months

tag: brain region

value: DHC

tag: gender

value: M


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-D19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-E19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-J19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-I7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-C8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-C20


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-C19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-B7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-B8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-B20


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-A20


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-4-N7-B19


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title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-I1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-H2


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title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-E14


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title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-E1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-E13


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-D2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-D13


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title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-C2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-C14


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title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-D14


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-F14


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-B1


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title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-P11


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-A1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-C1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-O23


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-B13


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-O11


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-A13


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-N12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-P24


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-P12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-N11


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-O24


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-O12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-N23


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-N24


title: AMB_200225_18mo_8E_9H_8J_9J_1_P3-1-C15-A14


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-M23


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-P23


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-L24


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-M12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-L23


title: ATAC_in_WT_Day2

city: Shanghai

first: Feizhen

last: Wu

state: Shanghai

address: Zhangheng Road 825, Pudong

department: Intelligent Medicine Institute

country: China

institute: Fudan Univ, Shanghai, China

description: Library name: Sample 5

data_processing:
Sequencing reads underwent trimming with Trim_galore (v0.6.4_dev).
ChIP seq data were aligned to human genomes using Bowtie2 (v2.2.5)
PCR duplicate reads were eliminated using the rmdup command of samtools (v1.7)
To visualize ChIP signals in the UCSC Genome Browser, genomic coverage bedGraph fileswere generated using the bamCoverage in deeptools (v3.0.2)
Peak identification was performed using the callpeak in macs2
Assembly: hg38

organism: Homo sapiens

source_name: WT-iPSC

growth_protocol: the hiPSCs were dissociated using Accutase and were cultured on Matrigel-coated plates in mTeSRTM Plus medium.

extract_protocol:
7-8 x 10^6 Day 2 differentiated cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature, then quenched with 0.125 M glycine for 5 minutes. Cells were washed three times with cold PBS and harvested in DNA LoBind Tubes (Eppendorf, 0030108035/0030108051). Sonication was performed using a Bioruptor (Diagenode, B01020001) on high setting (30 sec on, 30 sec off) for 30 minutes in high salt lysis buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.05% SDS, 1% Triton X-100) containing a protease inhibitor cocktail. Chromatin samples were precleared with 15 μL each of Dynabeads Protein G and Protein A, and rotated at 4°C for 1 hour. Precleared samples were then incubated with 4 µg of specific antibody at 4°C for 16 hours. After antibody binding, 15 μL each of Dynabeads Protein G and Protein A were added and incubated for an additional 2 hours at 4°C. The chromatin-antibody complexes underwent four washes with high salt buffer, two washes with low salt buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% sodium deoxycholate), and one wash with TE buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 50 mM NaCl).Complexes were eluted in elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) on a Thermal Mixer (Thermo, 13687712) at 65°C for 4 hours, followed by treatment with 10 µg RNase and 10 µg Proteinase K at 55°C for 1 hour on the Thermal Mixer. DNA was purified using a QIAquick PCR Purification Kit (QIAGEN, 28006). For Re-ChIP assays, the starting material was scaled to 2 x 107 cells. Chromatin was first immunoprecipitated with 12 µg of anti-HA antibody and competitively eluted under native conditions using HA peptide (1 mg/mL) (MCE, HY-P0239). Subsequently, 30% of the eluate was retained as the primary ChIP fraction, while the remaining 70% was diluted and subjected to incubation with 12 µg of anti-NONO antibody overnight, and then and captured with Dynabeads. The purified DNA library preparation was constructed using VAHTS Universal Plus DNA Library Prep Kit for Illumina (Vazyme, ND617) in accordance with the manufacturer’s instruction. Libraries were sequenced by the Haplox company (Jiangxi, China) using Illumina NovaSeq 6000.
The purified DNA library preparation was constructed using VAHTS Universal Plus DNA Library Prep Kit for Illumina (Vazyme, ND617) in accordance with the manufacturer’s instruction.

treatment_protocol: the hiPSCs Upon reaching approximately 80% confluence, the cells were split at a ratio of 1:5 using Accutase (Sigma, A6964). We utilized a previously established protocol involving WNT activation and inhibition to differentiate hiPSCs into cardiomyocytes38. Briefly, hiPSCs were seeded and, at 80% confluence, treated with B27 minus insulin (Thermo, A1895601)/RPMI1640 (Thermo, 11875119) plus 7μM CHIR-99021 (Selleck, S1263). Following two days of CHIR99021 treatment, the medium was switched to B27 minus insulin/RPMI1640. After 24 hours, the medium was replaced with B27 minus insulin/RPMI1640 containing 5 μM IWR1 (Selleck, S7086) for two days. Subsequently, IWR1 was removed, and differentiation continued in CDM3 medium containing RPMI640, 50mg/ml BSA (Sigma, A1933), and 213mg/ml ascorbic acid (Sigma, A4544).

tag: cell line

value: WT-iPSC

tag: cell type

value: hiPSCs-derived cardiomyocytes

tag: time

tag: genotype

value: WT

tag: chip antibody

value: HA (Abcam, #ab9110)

tag: treatment


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-M11


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-K23


title: Input_in_WT_Day2

description: Library name: Sample 4

value: Dox induced HOXA1-HA hiPSCs-derived cardiomyocytes

value: Dox induced HOXA1_WT

value: Dox


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-K24


title: ReChIP_in_WT_Day2 overexpressing HOXA1-HA

description: Library name: Sample 3


title: First ChIP_in_WT_Day2 overexpressing HOXA1-HA

description: Library name: Sample 2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-K12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-K11


title: H3K27AC_in_WT_Day2

description: Library name: Sample 1

value: H3K27AC (Active motif, #39133)


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-J12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-I24


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-L12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-J23


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-J11


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-L11


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-I12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-J24


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-I11


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-H24


title: PLAG1_VC_2

city: Kharghar

first: Rukmini

last: Govekar

state: Maharashtra

address: Sector 22, Utsav Chowk-CISF Rd, Owe camp

department: Cancer Research Institute

country: India

institute: Advanced centre for Treatment, Research and Education in Cancer

description: Library name: Sample 2

library_source: transcriptomic

data_processing:
transcript quantification was performed using Salmon v0.8.1
Gene-level counts were derived from Salmon output via tximport
Differential expression analysis was conducted by comparing each cell line to three normal tissue samples through negative binomial generalized linear modelling. Genes were considered differentially expressed based on a Wald test adjusted p-value < 0.05 and an absolute log fold change > 1.5.
Assembly: Transcriptome index building was performed on transcriptome reference index downloaded from UCSC browser followed by quantification of transcripts. #hg19
Supplementary files format and content: tab-delimited table contains transcript-level quantification from RNA-seq.

molecule: total RNA

source_name: K562 cells

extract_protocol:
RNA was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Quigen). 200ng of Total RNA was taken as the input for the assay
NEB Ultra RNA-Seq Library Prep kit  (NEB # E7530L) was used to prepare libraries for total RNA sequencing

value: K562 cells

value: Erythroid cells

value: IM treated

value: Imatinib resistant


title: PLAG1_VC_1

description: Library name: Sample 1


title: PLAG1_KD_1

description: Library name: Sample 3


title: PLAG1_KD_2

description: Library name: Sample 4


title: HAEC, Sample-CL-5

city: Columbus

first: Marios

last: Arvanitis

state: OH

address: 473 W 12th Ave

institute: The Ohio State University

description: Library name: Sample-CL-5

data_processing:
We performed paired-end poly-A enriched RNA sequencing (fragment size 150bp) targeting 50 million reads per sample in HAEC that were transfected with siRNA for REST compared to scramble control, 48 hours after transfection (in 4 biological replicates per group). We followed the DESeq2 pipeline to normalize the gene expression results using a size factor that accounts for library size and gene size. This was followed by a variance stabilizing transformation as implemented in DESeq2, the output of which was used to perform principal components analysis (PCA). Surrogate variable analysis (SVA) was employed to control for unknown confounders and batch effects while preserving the biological differences between groups. Differential expression (DE) was tested based on a Wald test with a two-tailed alternative hypothesis and a corresponding p-value was generated and adjusted for multiple testing using false discovery rate (FDR). Genes were considered significant if their FDR was < 0.05. The gene set enrichment analysis (GSEA) package with the preranked method was used to identify pathways enriched in our DE results24 using the DESeq2 Wald statistic to generate the rank list. P-values for pathway enrichment were estimated based on a permutation approach as implemented in GSEA and were subsequently FDR adjusted with an FDR < 0.05 considered significant
Assembly: Human
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human Aortic Endothelial cells

extract_protocol:
RNA extraction was performed using the RNeasy Plus Micro Kit (Qiagen, # 74034).
RNA-sequencing libraries were prepared according to the manufacter's instructions.

tag: tissue

value: Aorta

value: Endothelial cells

value: siRNA REST

tag: batch


title: HAEC, Sample-CL-8

description: Library name: Sample-CL-8


title: HAEC, Sample-CL-6

description: Library name: Sample-CL-6


title: HAEC, Sample-CL-2

description: Library name: Sample-CL-2

value: Scramble Control


title: HAEC, Sample-CL-7

description: Library name: Sample-CL-7


title: HAEC, Sample-CL-4

description: Library name: Sample-CL-4


title: HAEC, Sample-CL-1

description: Library name: Sample-CL-1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-H11

value: 18 months

value: DHC

value: M


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-G24


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-H12


title: ChIP_BRD4

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

description: Library name: sample7

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg38 using BWA 0.7.12.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg38
Supplementary files format and content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: Cells are cultured with DMEM medium containing 10% FBS (Sigma).

extract_protocol:
DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-seq: ChIP-sequencing libraries were prepared using KAPA HyperPrep Kit (Kapa Biosystems) following manufacturer’s recommendation. In brief, 500ng of input DNA sheared by Covaris LE220 ultrasonicator or 10 ng of immunoprecipitated DNA was end-repaired and 3'-dA tailed. Adapter was then ligated to the DNA, and ligated product was PCR amplified and cleaned up using SPRIselect Reagent (Beckman Coulter). for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit

value: kidney cell

value: WT


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-I23


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-G12


title: RNAseq of 2xBE BFU-E colony, biol rep 3

city: Nicosia

first: Nikoletta

middle: Y.

last: Papaioannou

address: Iroon Avenue

department: Molecular Genetics Thalassemia Department

country: Cyprus

institute: The Cyprus Institute of Neurology and Genetics

description:
Library name: 2xBE-9H
Column name in Differential_expression_analysis_table:2xBE-9H

data_processing:
Raw RNA-seq data in FASTQ format were trimmed to remove adapter sequences and low-quality nucleotides using Trimmomatic v0.36. DESeq2 was performed for comparison gene expression results. The Wald test was applied to generate p-values and log2fold change values.
Assembly: Homo sapiens GRCH38 available on ENSEMBL using STAR aligner v2.5.2b
Supplementary files format and content: xlxc file include differntial expression analysis values of each sample compared to control with the gene name that is differentially expressed

source_name: Bone Marrow

growth_protocol: CD34+ cells were cultured in SFEMII media supplemented with cc100, Dexamethasone, EPO and Pen/Strep

extract_protocol: After the collection of BFU-E colonies and the investigation of editing levels, three colonies from each treatment were selected for RNA sequencing by Genewiz (Germany)

treatment_protocol: DSB-Cas9 sample was nucleofected with PNA-Cas9 nuclease and a gRNA as RNP. The  BE-BCL11A, BE-HBG and 2xBE were nuclefected with BE4max base editor and corresponding gRNAs as mRNAs. The 4D-Nucleofector™ instrument, using the P3 Primary Cell 4D-Nucleofector X Kit (Lonza) and applying the CA-137 program was used for the nucleofection.

value: Bone Marrow


title: RNAseq of 2xBE BFU-E colony, biol rep 2

description:
Library name: 2xBE-8G
Column name in Differential_expression_analysis_table: 2xBE-8G


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-G11


title: RNAseq of 2xBE BFU-E colony, biol rep 1

description:
Library name: 2xBE-7F
Column name in Differential_expression_analysis_table:2xBE-7F


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-F24


title: RNAseq of BE-HBG BFU-E colony, biol rep 3

description:
Library name: HBG-6F
Column name in Differential_expression_analysis_table: HBG-6F


title: HAEC, Sample-CL-3

description: Library name: Sample-CL-3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-H23


title: RNAseq of BE-HBG BFU-E colony, biol rep 2

description:
Library name: HBG-5E
Column name in Differential_expression_analysis_table: HBG-5E


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-F23


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-E24


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-F11


title: RNAseq of BE-BCL11A BFU-E colony, biol rep 2

description:
Library name: BCL11A-11B
Column name in Differential_expression_analysis_table: BCL11A-11B


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-E12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-F12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-E11


title: RNAseq of BE-HBG BFU-E colony, biol rep 1

description:
Library name: HBG-3C
Column name in Differential_expression_analysis_table: HBG-3C


title: RNAseq of DSB-Cas9 BFU-E colony, biol rep 2

description:
Library name: CAS9-8D
Column name in Differential_expression_analysis_table: CAS9-8D


title: RNAseq of BE-BCL11A BFU-E colony, biol rep 3

description:
Library name: BCL11A-11H
Column name in Differential_expression_analysis_table: BCL11A-11H


title: RNAseq of DSB-Cas9 BFU-E colony, biol rep 1

description:
Library name: CAS9-8C
Column name in Differential_expression_analysis_table: CAS9-8C


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-E23


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-D23


title: RNAseq of BE-BCL11A BFU-E colony, biol rep 1

description:
Library name: BCL11A-10G
Column name in Differential_expression_analysis_table: BCL11A-10G


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-G23


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-D12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-D24


title: RNAseq of DSB-Cas9 BFU-E colony, biol rep 3

description:
Library name: CAS9-8G
Column name in Differential_expression_analysis_table: CAS9-8G


title: RNAseq of Control BFU-E colony, biol rep 2

description:
Library name: CONTROL-1D
Column name in Differential_expression_analysis_table: CONTROL-1D


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-C24


title: RNAseq of Control BFU-E colony, biol rep 1

description:
Library name: CONTROL-1C
Column name in Differential_expression_analysis_table: CONTROL-1C


title: RNAseq of Control BFU-E colony, biol rep 3

description:
Library name: CONTROL-1E
Column name in Differential_expression_analysis_table: CONTROL-1E


title: MDA_MB_231_UNC1999_w3d_2

city: PITTSBURGH

first: runzi

last: sun

state: PA

address: 203 Lothrop st

institute: university of pittsburgh

description:
Library name: Sample 34
MDA_MB_231_UNC1999_w3d_2

data_processing:
RNA-Seq raw reads were filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). Clean reads were aligned using STAR (version 2.7.9a) to human reference sequence (Homo_sapiens.GRCh38.dna.primary_assembly). Gene expression values TPM (Transcripts Per Kilobase Million) were quantitated with RSEM (version 1.3.1).
Assembly: GRCh38
Supplementary files format and content: csv files include TPM values for each Sample

molecule: polyA RNA

source_name: Breast

growth_protocol: A375 and MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), and MCF7 cells were maintained in EMEM supplemented with 10% FBS. 1% penicillin-streptomycin was added to all media. Cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA,5067-1511), high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification.
Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). 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 (NEB, cat.m0280, USA) 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.

treatment_protocol: For drug treatments, cells were exposed to the following conditions:A375 cells: untreated control (DMSO), 2 µM I-BET151 for 72 h, and withdrawal treatment (2 µM I-BET151 for 72 h followed by 72 h without drug).MDA-MB-231 cells: untreated control (DMSO), 2 µM OTX-015, 5 µM GSK126, 5 µM UNC1999, 10 µM CCS1477, and 5 µM A485 for 72 h, and withdrawal treatment (drug treatment for 72 h followed by 72 h without drug).MCF7 cells: untreated control (DMSO), 10 µM CCS1477 for 72 h, and withdrawal treatment (drug treatment for 72 h followed by 72 h without drug). After treatment, cells were harvested for RNA extraction following standard protocols for RNA-seq analysis.

value: Breast

value: Triple-negative breast adenocarcinoma cell


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-C23


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-C12


title: MDA_MB_231_UNC1999_2

description:
Library name: Sample 32
MDA_MB_231_UNC1999_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-C11


title: MDA_MB_231_UNC1999_1

description:
Library name: Sample 31
MDA_MB_231_UNC1999_1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-B24


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-B23


title: MDA_MB_231_OTX_015_1

description:
Library name: Sample 27
MDA_MB_231_OTX_015_1


title: MDA_MB_231_OTX_015_w3d_2

description:
Library name: Sample 30
MDA_MB_231_OTX_015_w3d_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-D11


title: MDA_MB_231_OTX_015_w3d_1

description:
Library name: Sample 29
MDA_MB_231_OTX_015_w3d_1


title: MDA_MB_231_CCS_1477_w3d_2

description:
Library name: Sample 22
MDA_MB_231_CCS_1477_w3d_2


title: MDA_MB_231_CCS_1477_2

description:
Library name: Sample 20
MDA_MB_231_CCS_1477_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-B11


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-A11


title: MDA_MB_231_OTX_015_2

description:
Library name: Sample 28
MDA_MB_231_OTX_015_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-B12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-A23


title: MDA_MB_231_GSK126_1

description:
Library name: Sample 23
MDA_MB_231_GSK126_1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-A24


title: MDA_MB_231_UNC1999_w3d_1

description:
Library name: Sample 33
MDA_MB_231_UNC1999_w3d_1


title: MDA_MB_231_GSK126_2

description:
Library name: Sample 24
MDA_MB_231_GSK126_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-P10


title: MDA_MB_231_CCS_1477_w3d_1

description:
Library name: Sample 21
MDA_MB_231_CCS_1477_w3d_1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-A12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-P9


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-P22


title: MDA_MB_231_GSK126_w3d_2

description:
Library name: Sample 26
MDA_MB_231_GSK126_w3d_2


title: MDA_MB_231_CCS_1477_1

description:
Library name: Sample 19
MDA_MB_231_CCS_1477_1


title: MDA_MB_231_GSK126_w3d_1

description:
Library name: Sample 25
MDA_MB_231_GSK126_w3d_1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-O9


title: MDA_MB_231_A485_w3d_2

description:
Library name: Sample 18
MDA_MB_231_A485_w3d_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-O22


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-P21


title: MDA_MB_231_A485_w3d_1

description:
Library name: Sample 17
MDA_MB_231_A485_w3d_1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-O21


title: MDA_MB_231_A485_1

description:
Library name: Sample 15
MDA_MB_231_A485_1


title: MDA_MB_231_DMSO_2

description:
Library name: Sample 14
MDA_MB_231_DMSO_2

value: DMSO


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-N9


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-N10


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-N21


title: MCF_7_CCS_1477_2

description:
Library name: Sample 10
MCF_7_CCS_1477_2

value: Breast adenocarcinoma cell (luminal A)


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-O10


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-M21


title: MCF_7_DMSO_1

description:
Library name: Sample 7
MCF_7_DMSO_1


title: MCF_7_CCS_1477_1

description:
Library name: Sample 9
MCF_7_CCS_1477_1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-M10


title: MDA_MB_231_DMSO_1

description:
Library name: Sample 13
MDA_MB_231_DMSO_1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-N22


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-L9


title: A375_IBET_151_w3d_2

description:
Library name: Sample 6
A375_IBET_151_w3d_2

source_name: Skin

value: Skin

value: Human malignant melanoma cell


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-M9


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-L22


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-M22


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-L21


title: A375_IBET_151_w3d_1

description:
Library name: Sample 5
A375_IBET_151_w3d_1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-L10


title: A375_IBET_151_1

description:
Library name: Sample 3
A375_IBET_151_1


title: MDA_MB_231_A485_2

description:
Library name: Sample 16
MDA_MB_231_A485_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-K9


title: MCF_7_CCS_1477_w3d_1

description:
Library name: Sample 11
MCF_7_CCS_1477_w3d_1


title: MCF_7_CCS_1477_w3d_2

description:
Library name: Sample 12
MCF_7_CCS_1477_w3d_2


title: A375_DMSO_2

description:
Library name: Sample 2
A375_DMSO_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-K22


title: MCF_7_DMSO_2

description:
Library name: Sample 8
MCF_7_DMSO_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-K21


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-K10


title: ChIP_BRD4_ASXL1_645_WT

description: Library name: sample5

value: ASXL1 WT overexpression


title: ChIP_GFP_ASXL1_645_I574D

description: Library name: sample4

value: ASXL1 mutant overexpression overexpression


title: ChIP_ASXL1_FL

description: Library name: sample2


title: ChIP_GFP_ASXL1_645_WT

description: Library name: sample3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-J22


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-J21


title: ChIP_BAP1

description: Library name: sample1


title: A375_IBET_151_2

description:
Library name: Sample 4
A375_IBET_151_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-I22


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-J10


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-I21


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, treated with Deferoxamine for 3 days, biol rep 2

city: Brussels

first: Yue

last: Tong

state: Brussels

address: Route de Lennik, 808

country: Belgium

institute: Université Libre de Bruxelles

description:
Library name: TFRC_IPSCBETA_MACS_DFO_4_2
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads

data_processing:
Raw read quality was assessed using FastQC (v0.12.1)
Low-quality reads and adapter sequences were removed using fastp (v0.23.2)
Filtered reads (processed files) were then aligned to the GRCh38 primary assembly (GENCODE v46) using Salmon (v1.10.3)
Assembly: GRCh38
Supplementary files format and content: Salmon quantification file with .sf extention, tab separated. Headers: Name (of transcripts), Length, EffectiveLength, TPM, NumReads. Each row represents one transcript.

source_name: pancreatic differentiation

growth_protocol: The control iPSC lines 1.023 (PMID: 36060810), HEL115.6 (PMID: 30247717), ESIBIe003-A-10 (PMID: 34619644), and ULBi015.18 were cultured in Matrigel-coated plates (Corning, BDAA356231) in E8 medium as described (PMID: 30247717). The 7-stage differentiation into ß-cells was done as described (PMID: 36060810) (PMID: 30247717). Cells were seeded at 2.5 × 106 cells per 3.5 cm diameter well in E8 medium containing 5 or 10 μM ROCK inhibitor (StemCell Technologies, 72304, Y-27632). Differentiation was started 24 hours later. After reaching the pancreatic progenitor stage (stage 4), cells were plated in microwell plates at 900 cells per microwell (AggreWell400, StemCell Technologies, 34411) to allow islet-like aggregate formation until 1 week into stage 7.

extract_protocol:
Total RNA from MACS-purified iPSC-ß cells was isolated using the RNeasy Plus Micro kit (Qiagen, 74034). RNA concentration and integrity were measured using the Bioanalyzer RNA 6000 Nano assay (Agilent, 5067-1511) on the Agilent 2100 Bioanalyzer.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7760L) for samples sequenced by Illumina NovaSeq6000 and Novogene NGS Stranded RNA Library Prep Set (Novogene, PT044) for samples sequenced by Illlumina NovaSeq X Plus. Paired-end sequencing (2x151bp) was performed at 200 million reads.

treatment_protocol: iPSC aggregates at stage 7 were exposed to 100 μM DFO for 3 days in Ham’s F-10 medium (Gibco, 41550) supplemented with 0.75% fatty acid-free BSA, 0.5% GlutaMAX (Gibco, 35050038), and 1% Pen/Strep (ThermoFisher, 15070063). Medium was renewed every 2 days.

value: pancreatic differentiation

value: ULBi015.18 iPSC

value: human induced pluripotent stem cell derived pancreatic beta-like cell aggregates

value: wildtype

value: Deferoxamine


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-I9

value: 18 months

value: DHC

value: M


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, treated with Vehicle H2O for 3 days, biol rep 3

description:
Library name: TFRC_IPSCBETA_MACS_CTL_5_1
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-I10


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, treated with Deferoxamine for 3 days, biol rep 3

description:
Library name: TFRC_IPSCBETA_MACS_DFO_5_2
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, treated with Vehicle H2O for 3 days, biol rep 2

description:
Library name: TFRC_IPSCBETA_MACS_CTL_4_1
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-H9


title: A375_DMSO_1

description:
Library name: Sample 1
A375_DMSO_1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-H22


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-6-E19-M24


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, treated with Vehicle H2O for 3 days, biol rep 1

description:
Library name: TFRC_IPSCBETA_MACS_CTL_2_1
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads


title: ChIP_BRD4_ASXL1_645_I574D

description: Library name: sample6

value: kidney cell


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-H21


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-J9


title: AD, replicate 6, scRNAseq

city: Tel Aviv

first: Ofer

last: Sarig

address: 6 weitzman street

country: Israel

institute: TASMC

description: Library name: AD17

library_source: transcriptomic single cell

data_processing:
Single-cells libraries were sequenced with pair-ended sequencing using NovaSeq 6000 (Illumina, San Diego, CA, USA) targeting 40,000 reads per cell. ScRNAseq data analysis was processed using a standard computational procedure, using Cellranger V6.0 software to map reads and to quantify gene expression.
Assembly: GRCh38
Supplementary files format and content: For each sample, processed data include Cell Ranger Count filtered outputs: cell barcodes (barcodes.tsv.gz), genes (features.tsv.gz) and count matrix (matrix.mtx.gz).

source_name: skin

extract_protocol:
Skin samples obtained with 4mm punch biopsies were disassociated using the gentleMACS™ Dissociator and the Human Whole Skin Dissociation Kit (130-101-540, Miltenyi BioTec, Gaithersburg, MD, USA) following the manufacture instructions with incubation of 3 hours. The dissociated cell suspension was strained with a 40-mM filter and cell viability was measured using Cellometer ViaStain™ AOPI Staining solution (CS2-0106-5ML, Revvity, Waltham, MA, USA).
Approximately 10,000 cells per sample were loaded on a Chromium controller and library preparation was performed using Chromium Single Cell 3' v3 following the manufacturer protocol(PN-1000120, 10X Genomics, Pleasanton, CA, USA).

value: skin


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-H10


title: control, replicate 6, scRNAseq

description: Library name: AD16


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-G9


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-G22


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-G21


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-G10


title: AD, replicate 5, scRNAseq

description: Library name: AD08


title: control, replicate 5, scRNAseq

description: Library name: AD15


title: AD, replicate 4, scRNAseq

description: Library name: AD07


title: control, replicate 4, scRNAseq

description: Library name: AD12


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-F9


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-F21


title: AD, replicate 3, scRNAseq

description: Library name: AD05


title: control, replicate 3, scRNAseq

description: Library name: AD06


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-F10


title: AD, replicate 2, scRNAseq

description: Library name: AD04


title: AD, replicate 1, scRNAseq

description: Library name: AD03


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-E22


title: control, replicate 2, scRNAseq

description: Library name: AD02


title: MACS-sorted pancreatic iPSC-derived beta-like cell aggregates, treated with Deferoxamine for 3 days, biol rep 1

description:
Library name: TFRC_IPSCBETA_MACS_DFO_2_2
salmon aligned quantification column names: Name (of transcripts) Length EffectiveLength TPM NumReads


title: control, replicate 1, scRNAseq

description: Library name: AD01


title: E2F1 K117R, SETD6 KO, Replicate 3

city: Stuttgart

first: Albert

last: Jeltsch

address: Allmandring 31

department: Institute of Biochemistry and Technical Biochemistry

country: Germany

institute: University Stuttgart

description: Library name: E2F1 K117R SETD6 KO_Replicate 3

data_processing:
Library generation was prefomred with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB), along with NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB). All library preparation steps were conducted according to the manufacturer’s instructions.
The quality and concentration of RNA-seq libraries were determined by Labchip® GX Touch (Perkin Elmer) for fragment size distribution and concentration analysis. Finally, each RNA library was sequenced by Novogene (UK) using an Illumina Novaseq 6000 system in paired-end 2×150 bp-mode.
Assembly: hg38
Supplementary files format and content: readcounts.xlsx: Readcounts of the individual samples and replicates. MS-Excel file.

source_name: Prostate

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (Sigma, D5671) media supplemented with 10% Fetal bovine serum (FBS) (Gibco), 1% Penicillin-Streptomycin (Sigma, P0781), 2 mM L-glutamine (Sigma, G7513) and 1% non-essential amino acids (Sigma, M7145), at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
For the DU145 CRISPR/Cas9 generated SETD6 knock-out, single clones were confirmed by sequencing as described in previously (Kublanovsky et al., 2023)
total RNA was isolated from approximately 1 × 106 cells by using the RNeasy® Mini Kit (Qiagen). The extracted RNA was quantified by NanoDrop1000 and reverse-transcribed into complementary DNA (cDNA) to generate RNA-seq libraries.

value: Prostate

value: Prostate cancer cells

value: SETD6 KO


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-E10


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-E21


title: E2F1 K117R, SETD6 KO, Replicate 1

description: Library name: E2F1 K117R SETD6 KO_Replicate 1


title: E2F1 K117R, SETD6 KO, Replicate 2

description: Library name: E2F1 K117R SETD6 KO_Replicate 2


title: E2F1 K117R, SETD6 WT, Replicate 3

description: Library name: E2F1 K117R SETD6 WT_Replicate 3

value: SETD6 WT


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-D21


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-D22


title: E2F1 K117R, SETD6 WT, Replicate 2

description: Library name: E2F1 K117R SETD6 WT_Replicate 2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-C9


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-F22


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-C21


title: E2F1 WT, SETD6 KO, Replicate 3

description: Library name: E2F1 WT SETD6 KO_Replicate 3

value: E2F1 WT


title: E2F1 K117R, SETD6 WT, Replicate 1

description: Library name: E2F1 K117R SETD6 WT_Replicate 1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-D10


title: E2F1 WT, SETD6 KO, Replicate 1

description: Library name: E2F1 WT SETD6 KO_Replicate 1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-E9


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-C10


title: E2F1 WT, SETD6 WT, Replicate 2

description: Library name: E2F1 WT SETD6 WT_Replicate 2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-B22


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-B9


title: E2F1 WT, SETD6 WT, Replicate 3

description: Library name: E2F1 WT SETD6 WT_Replicate 3


title: E2F1 WT, SETD6 WT, Replicate 1

description: Library name: E2F1 WT SETD6 WT_Replicate 1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-B21


title: Input, SETD6 WT, Rep2

description: Library name: Replica 2, Flag tagged E2F1 WT SETD6 WT, Input

data_processing:
Sequencing data were received in FASTQ format and processed using the Galaxy Europe Server (https://usegalaxy.eu/).
The read quality of FATSQ was analyzed by using FastQC adaptors were trimmed using Trimmomatic.
Next, HISAT2 was used for alignment to the GRCh38/hg38 reference genome.
The resulting BAM file was used to generate a coverage bigWig file using 10 bp bin size and normalized by reads per kilobase per million mapped reads (RPKM).
To investigate differential binding sites of E2F1 in SETD6 WT or KO, E2F1 peaks were determined by using the MACS2 bdgpeakcall tool.
Assembly: hg38
Supplementary files format and content: bigwig file

extract_protocol:
For the DU145 CRISPR/Cas9 generated SETD6 knock-out, single clones were confirmed by sequencing as described in previously (Kublanovsky et al., 2023)
Approximately 2 × 107 cells were washed with 1X PBS buffer (Gibco) and harvested by centrifugation at 500 g for 5 min. Next, formaldehyde was added directly to the cell culture media to a final concentration of 2%. After 10 min of incubation at room temperature, glycine was added to a concentration of 125 mM to quench crosslinking reaction. After that, the Magna ChIP™ HiSens Chromatin Immunoprecipitation Kit (Milipore, MAGNA0025) was used to remove cytosolic proteins. To digest chromatin fraction, the nuclear pellet was sonicated with EpiShear™ Probe Sonicator (Active Motif) at 4°C. In the following, ChIP preparation steps were processed according to the manufacturer’s instructions. For each ChIP, 10 μg Flag antibody (Invitrogen, F1804) was used for enrichment of sample. All library preparation steps were conducted according to manufacturer’s instructions of NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1) (NEB). The ChIP-seq library was send to Novogene (UK) for Next-Generation-Sequencing (Illumina Novaseq 6000 system, paired-end, 2× 150 bp-mode).


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-B10


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-D9


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-A9


title: Input, SETD6 WT, Rep1

description: Library name: Replica 1, Flag tagged E2F1 WT SETD6 WT, Input


title: Input, SETD6 KO, Rep1

description: Library name: Replica 1, Flag tagged E2F1 WT SETD6 KO, Input


title: Input, SETD6 KO, Rep2

description: Library name: Replica 2, Flag tagged E2F1 WT SETD6 KO, Input


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-A21


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-A22


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-C22


title: E2F1, SETD6WT, Rep2

description: Library name: Replica 2, Flag tagged E2F1 WT SETD6 WT, ChIP Flag Antibody

value: Flag (Sigma)


title: E2F1 WT, SETD6 KO, Replicate 2

description: Library name: E2F1 WT SETD6 KO_Replicate 2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-P8


title: E2F1, SETD6KO, Rep2

description: Library name: Replica 2, Flag tagged E2F1 WT SETD6 KO, ChIP Flag Antibody


title: E2F1, SETD6WT, Rep1

description: Library name: Replica 1, Flag tagged E2F1 WT SETD6 WT, ChIP Flag Antibody


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-P20


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-P19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-P7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-O8


title: PPCL-68 EVs, Replicate2

city: Washington

first: Amrita

last: Cheema

state: DC

address: 3900 Reservoir Road NW

department: Oncology

institute: Georgetown University Medical Centre

description:
Library name: Sample8
PPCL-68 Evs - 2

data_processing:
The generated .bam files were used for subsequent analysis using Partek Genomics Suite 6.6 (PGS, Partek Genomics Suite software, version 6.6 beta, Partek Inc., St. Louis, MO, USA).
Assembly: hg38
Supplementary files format and content: comma-delimited text file includes raw counts for each sample

source_name: Epithelial

extract_protocol:
The microRNA was isolated from hTERT-HPNE, PANC-1 and PPCL-68 cell line derived EVs by using Exo-RNA extraction kit ( in vitrogen)
The samples were subjected to library construction and sequencing was performed by Novogene Corporation (Sacramento, CA). RNA quality control (QC) was assessed using Bioanalyzer (Agilent) analysis. Libraries were prepared using small RNA Library Prep kit (New England BioLabs,). Library quality and concentration was assessed with Labchip and qPCR. Libraries were sequenced on a Novaseq6000 (Illumina) platform at a depth of 30 mm reads.

value: Epithelial

tag: sample type

value: exosome


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-O7


title: PANC-1 EVs, Replicate3

description:
Library name: Sample6
PANC-1 Evs - 4


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-O20


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-5-O11-A10


title: PPCL-68 EVs, Replicate1

description:
Library name: Sample7
PPCL-68 Evs - 1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-O19


title: PANC-1 EVs, Replicate2

description:
Library name: Sample5
PANC-1 Evs - 3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-N8


title: PANC-1 EVs, Replicate1

description:
Library name: Sample4
PANC-1 Evs - 1


title: hTERT HPNE EVs, Replicate3

description:
Library name: Sample3
HPNE Evs - 4

value: hTERT HPNE


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-N7


title: hTERT HPNE EVs, Replicate2

description:
Library name: Sample2
HPNE Evs - 3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-N19


title: HPD03 on serum, Exome-Seq, Replicate 2

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

country: Italy

institute: University of Padua

description: Library name: HPD03_serum_Exome_Rep_2

data_processing:
Removal of duplicate reads and variant calling with Sentieon 202308 (Freed et al, 2017).
Annotation with the Ensembl Variant Effect Predictor (VEP) tool3 (v. 104).
Assembly: Human hg38, GCA_000001405.15
Supplementary files format and content: HPD06_Exom-Seq.vcf is a vcf containing read and allelic depths, base and mapping quality, population allele frequencies and ratio score of variants.
Supplementary files format and content: HPD03_Exom-Seq.vcf is a vcf containing read and allelic depths, base and mapping quality, population allele frequencies and ratio score of variants.
Library strategy: Exome-Seq

source_name: human induced pluripotent stem cells

growth_protocol:
Cultured on serum coating (10% Fetal Bovine Serum [Gibco A5256701] in DMEM high glucose [Gibco 41965039]) in PXGL medium (Bredenkamp et al, 2019) at 37°C, 5% CO2, 5% O2. The PXGL medium was prepared as follows: N2B27 (DMEM/F12 [Gibco 11320074], and Neurobasal in 1:1 ratio [Gibco 21103049], with 1:200 N2 Supplement [Gibco 17502048], and 1:100 B27 Supplement [Gibco 17504044], 2 mM L-glutamine [Gibco 25030024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1 µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem 1408), 2 μM Gö6983 (Axon Medchem 2466) and 10 ng/ml human LIF (Qkine Qk036). Cells were passaged as single cells every 3-4 days at a split ratio of 1:3 or 1:4 following dissociation with TrypLE (Gibco 12563029) for 3 minutes at room temperature. 10 μM ROCK inhibitor (ROCKi, Y27632, Axon Medchem 1683) was added to the naive medium for 24 hours after passaging.
Cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs; DR4 ATCC), or  on serum coating (10% Fetal Bovine Serum [Gibco A5256701] in DMEM high glucose [Gibco 41965039]) in PXGL medium (Bredenkamp et al, 2019) at 37°C, 5% CO2, 5% O2. The PXGL medium was prepared as follows: N2B27 (DMEM/F12 [Gibco 11320074], and Neurobasal in 1:1 ratio [Gibco 21103049], with 1:200 N2 Supplement [Gibco 17502048], and 1:100 B27 Supplement [Gibco 17504044], 2 mM L-glutamine [Gibco 25030024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1 µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem 1408), 2 μM Gö6983 (Axon Medchem 2466) and 10 ng/ml human LIF (Qkine Qk036). Cells were passaged as single cells every 3-4 days at a split ratio of 1:3 or 1:4 following dissociation with TrypLE (Gibco 12563029) for 3 minutes at room temperature. 10 μM ROCK inhibitor (ROCKi, Y27632, Axon Medchem 1683) was added to the naive medium for 24 hours after passaging.

extract_protocol:
DNA was extracted with a paramagnetic beads technology using the Negedia DNA extraction service (NEGEDIA srl).
Libraries were prepared from 100 ng of total DNA using the Next Generation Diagnostic s.r.l NEGEDIA Exome sequencing service which included library preparation and target enrichment using Agilent V8 probe set.

value: human induced pluripotent stem cells


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-M8


title: hTERT HPNE EVs, Replicate1

description:
Library name: Sample1
HPNE Evs - 2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-N20


title: PPCL-68 EVs, Replicate3

description:
Library name: Sample9
PPCL-68 Evs - 3


title: HPD03 on serum, Exome-Seq, Replicate 1

description: Library name: HPD03_serum_Exome_Rep_1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-M7


title: E2F1, SETD6KO, Rep1

description: Library name: Replica 1, Flag tagged E2F1 WT SETD6 KO, ChIP Flag Antibody


title: HPD03 on MEFs, Exome-Seq, Replicate 1

description: Library name: HPD03_MEFs_Exome_Rep_1

growth_protocol:
Cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs; DR4 ATCC) in PXGL medium (Bredenkamp et al, 2019) at 37°C, 5% CO2, 5% O2. The PXGL medium was prepared as follows: N2B27 (DMEM/F12 [Gibco 11320074], and Neurobasal in 1:1 ratio [Gibco 21103049], with 1:200 N2 Supplement [Gibco 17502048], and 1:100 B27 Supplement [Gibco 17504044], 2 mM L-glutamine [Gibco 25030024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1 µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem 1408), 2 μM Gö6983 (Axon Medchem 2466) and 10 ng/ml human LIF (Qkine Qk036). Cells were passaged as single cells every 3-4 days at a split ratio of 1:3 or 1:4 following dissociation with TrypLE (Gibco 12563029) for 3 minutes at room temperature. 10 μM ROCK inhibitor (ROCKi, Y27632, Axon Medchem 1683) was added to the naive medium for 24 hours after passaging.
Cultured on mitotically inactivated mouse embryonic fibroblasts (MEFs; DR4 ATCC), or  on serum coating (10% Fetal Bovine Serum [Gibco A5256701] in DMEM high glucose [Gibco 41965039]) in PXGL medium (Bredenkamp et al, 2019) at 37°C, 5% CO2, 5% O2. The PXGL medium was prepared as follows: N2B27 (DMEM/F12 [Gibco 11320074], and Neurobasal in 1:1 ratio [Gibco 21103049], with 1:200 N2 Supplement [Gibco 17502048], and 1:100 B27 Supplement [Gibco 17504044], 2 mM L-glutamine [Gibco 25030024], 0.1 mM 2-mercaptoethanol [Sigma-Aldrich M3148]) supplemented with 1 µM PD0325901 (Axon Medchem), 2 μM XAV939 (Axon Medchem 1408), 2 μM Gö6983 (Axon Medchem 2466) and 10 ng/ml human LIF (Qkine Qk036). Cells were passaged as single cells every 3-4 days at a split ratio of 1:3 or 1:4 following dissociation with TrypLE (Gibco 12563029) for 3 minutes at room temperature. 10 μM ROCK inhibitor (ROCKi, Y27632, Axon Medchem 1683) was added to the naive medium for 24 hours after passaging.


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-M19


title: HPD06 on serum, Exome-Seq, Replicate 1

description: Library name: HPD06_serum_Exome_Rep_1


title: HPD03 on MEFs, Exome-Seq, Replicate 2

description: Library name: HPD03_MEFs_Exome_Rep_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-L8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-L7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-M20


title: HPD06 on serum, Exome-Seq, Replicate 2

description: Library name: HPD06_serum_Exome_Rep_2


title: HPD06 on MEFs, Exome-Seq, Replicate 1

description: Library name: HPD06_MEFs_Exome_Rep_1


title: VIM-AS1+TGFβ_3

city: Uppsala

first: Mohamad

middle: Moustafa

last: Ali

state: Uppsala län

address: husargatan 3, Biomedical Center

department: IMBIM

country: Sweden

institute: Uppsala University

description: Biological replicate 3

data_processing:
Trimmomatic was used to trim sequecning adapters and low-quality reads
STAR Aligner was used to align trimmed reads
Aligned reads were annotated and quantified against the gencode comprehensive gene annotation release 38 (GRCh38.p13) using featureCounts of subread package v2.0.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include quantified reads from Subread package

growth_protocol: A549 cells were cultured in DMEM with 10% FBS and 1% P+S and incubated at 37C in a humified incubator with 5% CO2.

extract_protocol:
RNA was extracted using ReliaPrep RNA Cell miniprep system (Promega). 600 ng of total RNA was used for the construction of sequencing libraries.
Library preparation was constructed using the TruSeq stranded total RNA Gold library preparation kit with RiboZero Gold treatment and unique dual indexes according to the manufacturer’s instructions
whole transcriptome RNA-seq with Ribosomal RNA depletion

treatment_protocol: Cells were either treated or not with TGFβ for 24 hours and transfected with scramble siRNA or specific siRNAs against VIM-AS1

value: Lung Adenocarcinoma

value: WT

value: VIM-AS1 siRNA  + TGFβ


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-L20

value: 18 months

value: DHC


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-L19

value: M


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-K8


title: VIM-AS1+TGFβ_2

description: Biological replicate 2


title: HPD06 on MEFs, Exome-Seq, Replicate 2

description: Library name: HPD06_MEFs_Exome_Rep_2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-K7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-K20


title: VIM-AS1_3

description: Biological replicate 3

value: VIM-AS1 siRNA


title: VIM-AS1_2

description: Biological replicate 2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-J8


title: TGFβ_3

description: Biological replicate 3

value: Control scramble siRNA + TGFβ


title: VIM-AS1_1

description: Biological replicate 1


title: VIM-AS1+TGFβ_1

description: Biological replicate 1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-K19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-J7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-J19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-I8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-J20


title: TGFβ_1

description: Biological replicate 1


title: Ctrl_3

description: Biological replicate 3

value: Control scramble siRNA


title: TGFβ_2

description: Biological replicate 2


title: Ctrl_2

description: Biological replicate 2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-I20


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-I7


title: DIPG6_RNA_Combo_rep3

city: Kensington

first: Holly

last: Holliday

address: Lowy Cancer Research Centre

country: Australia

institute: Children's Cancer Institute

data_processing:
Illumina paired-end fastq files were aligned to the human genome GRCh38 and gencode v41 using STAR (v2.7.8a) in two-pass mode with quantMode set to TranscriptomeSAM.
Transcriptome alignment was quantified using RSEM (v1.3.3) rsem-calculate-expression to obtain raw read counts.
normalized transcripts per million (TPM) and fragments per kilobase million (FPKM) values.
Assembly: hg38
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: TPM counts for each sample

source_name: Diffuse Midline Glioma

growth_protocol: Cells were maintained as neurospheres in Tumour Stem Cell (TSM) media consisting of a 1:1 mixture of DMEM/F12 and Neurobasal medium (Invitrogen) supplemented with Glutamax, Pyruvate, non-essential amino acids, HEPES buffer, antibiotic/antimycotic, B-27 (Invitrogen), Heparin (0.0002%), EGF (20 ng/mL), bFGF (20 ng/mL), PDGF-AA (10 ng/mL) and PDGF-BB (10 ng/mL) (StemCell Technologies).

extract_protocol:
Total RNA was extracted from treated cells using the ISOLATE II RNA Mini Kit from Bioline.
cDNA libraries were prepared using the Illumina Stranded mRNA prep kit

treatment_protocol: Neurospheres were treated with DMSO, or with CBL0137 (1µM for DIPG7 and 2µM for DIPG6) or JQ1 (1µM) as single agents and in combination for 4h. DMSO concentrations were normalised across the 4 treatment groups.

value: Diffuse Midline Glioma

value: SU-DIPGVI


title: Ctrl_1

description: Biological replicate 1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-I19


title: DIPG6_RNA_Combo_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-H8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-H19


title: DIPG6_RNA_JQ1_rep3


title: DIPG6_RNA_Combo_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-H20


title: DIPG6_RNA_JQ1_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-G8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-G20


title: DIPG6_RNA_CBL0137_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-G7


title: DIPG6_RNA_JQ1_rep1


title: DIPG6_RNA_Veh_rep2

value: DMSO


title: DIPG6_RNA_Veh_rep3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-F20


title: DIPG6_RNA_CBL0137_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-G19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-F8


title: DIPG6_RNA_Veh_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-E8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-F7


title: DIPG7_RNA_Combo_rep2


title: DIPG7_RNA_Combo_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-F19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-E19


title: DIPG7_RNA_Combo_rep3


title: DIPG7_RNA_JQ1_rep3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-H7


title: DIPG7_RNA_CBL0137_rep3


title: DIPG6_RNA_CBL0137_rep3


title: DIPG7_RNA_JQ1_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-D7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-D20


title: DIPG7_RNA_CBL0137_rep2


title: DIPG7_RNA_Veh_rep2


title: DIPG7_RNA_Veh_rep3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-D19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-C20


title: DIPG7_RNA_CBL0137_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-C7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-C8


title: DIPG7_RNA_Veh_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-E20


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-C19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-E7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-B8


title: DIPG7_H3K27me3_CBL1

data_processing:
Quality control analysis of CUT&RUN reads was performed using fastQC (v0.11.9).
Adapter trimming was performed using cutadapt (v4.2) with parameters: --error-rate 0.1 --times 1 --overlap 3 --action trim --minimum-length 17 --pair-filter any. Reads were aligned using bowtie2 (v2.5.0) with -k 1 against the GRCh38 human reference genome.
BAM files were sorted, and optical duplicates marked using picard (v2.27.5) with parameters: --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --VALIDATION_STRINGENCY SILENT.
Marked duplicates were filtered and removed using samtools (v1.12).
Peak calling was performed using MACS2 (v2.2.7.1) using IgG as the control. Narrow peaks parameters: --keep-dup all -p 1e-5 and broad peak using parameters: --keep-dup all -q 0.05 --broad --broad-cutoff 0.05. BigWig coverage files were generated using deeptools bamCoverage (v3.5.1) with parameters: --binSize 10 --normalizeUsing BPM --effectiveGenomeSize 2913022398. Broad peak settings were used for H3K27M and H3K27me3, and narrow peaks for SPT16, BRD4, H3K27ac, H3K4me3.
Assembly: hg38
Supplementary files format and content: narrowPeak (all except H3K27me3 and IgG), broadPeak (H3K27me3)
Supplementary files format and content: BigWig
Library strategy: CUT&RUN

growth_protocol: HSJD-DIPG007 cells were maintained as neurospheres in Tumour Stem Cell (TSM) media consisting of a 1:1 mixture of DMEM/F12 and Neurobasal medium (Invitrogen) supplemented with Glutamax, Pyruvate, non-essential amino acids, HEPES buffer, antibiotic/antimycotic, B-27 (Invitrogen), Heparin (0.0002%), EGF (20 ng/mL), bFGF (20 ng/mL), PDGF-AA (10 ng/mL) and PDGF-BB (10 ng/mL) (StemCell Technologies).

extract_protocol:
CUT&RUN was performed using the EpiCypher CUTANA CUT&RUN kit according to the manufacturer’s instructions. Briefly, 500,000 viable cells per reaction were washed and permeabilized with 0.01% Digitonin, which was determined to be the minimum concentration for effective permeabilization. Cells were incubated with 0.5 µg antibody, or a 1:50 dilution for SPT16, on a nutator overnight at 4°C. Following washing, pAG-MNase was added to the reactions and CaCl2 was used to activate antibody-bound MNase for targeted chromatin digestion and release of DNA fragments
The entire volume of purified DNA (ranging from 1-10 ng) was used as input for NGS library preparation, according to the EpiCypher CUTANA Library Prep Kit instructions.

treatment_protocol: for H3K27me3 CUT&RUN, HSJD-DIPG007 cells were treated with 1uM of CBL0137 for 4 hours prior to harvesting cells.

tag: antibody


title: DIPG7_H3K27me3_CBL2


title: DIPG7_H3K27me3_Veh2


title: DIPG7_RNA_JQ1_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-B7


title: DIPG7_H3K27me3_Veh1


title: DIPG7_IgG_rep2

value: EpiCypher 13-0042


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-D8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-B19


title: DIPG7_H3K27M_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-A8


title: DIPG7_BRD4_rep2

value: EpiCypher 13-2003


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-A20


title: DIPG7_SPT16_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-A19


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-P6


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-P18


title: DIPG6_ATAC_Combo_rep2

data_processing:
ATAC-seq reads were trimmed with Trimmomatic (ILLUMINACLIP:Nextera.fa:2:30:10:8:TRUE SLIDINGWINDOW:5:20 LEADING:3 TRAILING:3 MINLEN:20 CROP:130 HEADCROP:150).
Trimmed reads were mapped with bowtie2 using default settings.
Resulting BAM files deduplicated using Sambamba markdup.
Deduplicated BAM files were then filtered to remove reads with fragment sizes greater than 100bp.
CPM BigWigs were generated using the DeepTools bamCoverage and peaks called using MACS2.
Assembly: hg38
Supplementary files format and content: narrowPeak
Supplementary files format and content: BigWig

extract_protocol:
Transposition was performed as described in the OMNI-ATAC-seq protocol (https://doi.org/10.1038/nmeth.4396). Nuclei from 50,000 viable cells were isolated, permeabilized and transposed with 2.1 µL Tn5 (Illumina) for 30 min with mixing (1000 rpm).
DNA was then purified, and PCR amplified (7-14 cycles) with sequencing primers to generate libraries for sequencing.


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-P5

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: DIPG6_ATAC_Combo_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-P17


title: DIPG6_ATAC_JQ1_rep3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-B20


title: DIPG6_ATAC_JQ1_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-O6


title: DIPG6_ATAC_JQ1_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-O5


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-N6


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-O18


title: DIPG6_ATAC_CBL0137_rep2


title: DIPG6_ATAC_CBL0137_rep3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-4-O6-A7


title: DIPG6_ATAC_Veh_rep3


title: DIPG6_ATAC_CBL0137_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-O17


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-N17


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-N5


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-N18


title: DIPG7_ATAC_Combo_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-M6


title: DIPG6_ATAC_Veh_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-M5


title: DIPG6_ATAC_Veh_rep1


title: DIPG6_ATAC_Combo_rep3


title: DIPG7_ATAC_Combo_rep1


title: DIPG7_ATAC_CBL0137_rep2


title: DIPG7_ATAC_JQ1_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-M17


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-L6


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-M18


title: DIPG7_ATAC_JQ1_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-L5


title: DIPG7_ATAC_CBL0137_rep1


title: DIPG7_ATAC_Veh_rep2


title: DIPG7_ATAC_Veh_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-L18


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-L17


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-K6


title: 786O+VHL_EV_rep3

city: Cambridge

first: Niek

last: Wit

state: Not US or Canada

address: Puddicombe Way

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality trimming, to remove adapter sequences and check for low quality base calling, was performed with TrimGalore
Transcript quantification was performed using Salmon
TE analysis was performed with STAR/TEtranscripts
Assembly: hg38
Supplementary files format and content: .sf files contain transcript quantifications generated w. Salmon
Supplementary files format and content: .cntTable files contain (TE) gene quantifications generated w. TEtranscripts

extract_protocol:
PureLink RNA Mini kit including on-column digestion with PureLink DNase
NEBNext Ultra II RNA Library Preparation kit

value: VHL positive


title: 786O+VHL_EV_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-K5


title: 786O+VHL_CBFB-ko_rep3

value: VHL positive CBFB null


title: 786O+VHL_EV_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-K17


title: 786O+VHL_CBFB-ko_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-J5


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-J18


title: 786O_EV_rep2

value: VHL null


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-J17


title: 786O_EV_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-I5


title: 786O_CBFB-ko_rep3

value: VHL null CBFB null


title: 786O_CBFB-ko_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-I18


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-I17


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-H6


title: RCC4_day4_rep1

description: RCC4 CRISPR screen

library_source: other

data_processing:
Vector sequence removed with cutadapt
sgRNA sequences were counted with HISAT2 and sort/uniq Unix commands
Assembly: Toronto KO library v3
Supplementary files format and content: Each line in the txt files has the count and name of an sgRNA

molecule: other

extract_protocol:
QIAGEN Puregene Cell kit
Two-step PCR method


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-H18


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-K18


title: RCC4+VHL_day4_rep1

description: RCC4 CRISPR screen


title: RCC4+VHL_day28_rep1

description: RCC4 CRISPR screen


title: RCC4_day37_rep1

description: RCC4 CRISPR screen


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-H5


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-H17


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-G6


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-G5


title: 786O+VHL_CBFB-ko_rep1


title: 786O_EV_rep3


title: RCC4_day22_rep1

description: RCC4 CRISPR screen


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-J6


title: RCC4+VHL_day16_rep1

description: RCC4 CRISPR screen


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-G17


title: RNA_NELFC-AID_TetGFP_DOX_NT_Rep3.2

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Preprocessing was performed using CETO Toolbox. Sequence quality was assessed using FastQC v 0.11.2, and quality trimming was done using Trimmomatic with parameters TRAILING:30 MINLEN:20. RNA-seq reads were aligned to the GRCh38 genome using STAR v.2.5.2 and only uniquely mapped reads with a two-mismatch threshold were considered for downstream analysis and quantified to the gene level using HTSeq . Output bam files were converted into bigwig track files to display coverage throughout the genome (in rpm).  Gene count tables were constructed following Ensembl GRCh38, release 78 annotation
Assembly: hg38
Supplementary files format and content: bigWig

source_name: colon

growth_protocol: All cells were cultured in Dulbecco's modified Eagle's medium (DMEM) from Thermo Fisher (cat# 11965-118) supplemented with 15% fetal bovine serum (FBS) from Millipore Sigma (cat# F2442), 1x Glutamax from Thermo Fisher (cat# 35050-079) and 100 units/ml penicillin-streptomycin from Thermo Fisher (cat# 15140-163).

extract_protocol:
RNA was extracted from cells using the RNeasy Mini Kit (Qiagen, 74106) using an on column DNaseI digestion step (Qiagen 79256).
RNA was subjected to polyadenylated RNA enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module Kit (New England Biolabs, E7490L), and libraries were synthesized using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, E7760L).

treatment_protocol: ELOA-KO and NELF-C-AID DLD-1 cells were treated with 500 µM Auxin or H2O (duration as indicated in the text) at 37°C to deplete the NELF-C-AID protein. To select lentivirus-infected cells, puromycin (1.5 μg/ml) and hygromycin (250 μg/ml) were used.

value: colon

value: DLD-1 NELFC-AID

value: epithelial cell

value: TetGFP

value: Dox


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-I6

value: 18 months

value: DHC

value: M


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-F6


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-G18


title: RNA_NELFC-AID_TetGFP_DOX_NT_Rep2.2


title: RNA_NELFC-AID_TetGFP_DOX_NT_Rep2.1


title: RNA_NELFC-AID_TetGFP_DOX_NT_Rep3.1


title: 786O_CBFB-ko_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-F18


title: RNA_NELFC-AID_TetGFP_DOX_NT_Rep1.1


title: RNA_NELFC-AID_TetGFP_DOX_Aux6hr_Rep3

value: Dox+Aux


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-E5


title: RNA_NELFC-AID_TetGFP_DOX_Aux6hr_Rep2


title: RNA_NELFC-AID_TetGFP_DOX_Aux6hr_Rep1


title: RNA_NELFC-AID_TetGFP_DOX_Aux3hr_Rep3


title: RNA_NELFC-AID_TetGFP_DOX_Aux3hr_Rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-E6


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-E17


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-D5


title: RNA_NELFC-AID_TetGFP_DMSO_rep2

value: no treatment


title: RNA_NELFC-AID_TetGFP_DOX_Aux3hr_Rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-D18


title: RNA_NELFC-AID_TetELOA3_DOX_NT_Rep3.2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-C5


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-C6


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-D17


title: RNA_NELFC-AID_TetGFP_DMSO_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-F5


title: RNA_NELFC-AID_TetELOA3_DOX_NT_Rep2.2


title: RNA_NELFC-AID_TetELOA3_DOX_NT_Rep2.1


title: RNA_NELFC-AID_TetELOA3_DOX_NT_Rep1.2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-C17


title: RNA_NELFC-AID_TetELOA3_DOX_NT_Rep3.1


title: RNA_NELFC-AID_TetGFP_DOX_NT_Rep1.2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-F17


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-E18


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-A18


title: RNA_NELFC-AID_TetELOA3_DOX_Aux3hr_Rep1


title: RNA_NELFC-AID_TetELOA3_DOX_Aux6hr_Rep3


title: RNA_NELFC-AID_TetELOA3_DOX_Aux6hr_Rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-A17


title: RNA_NELFC-AID_TetELOA3_DOX_Aux3hr_Rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-B5


title: RNA_NELFC-AID_TetELOA3_DOX_NT_Rep1.1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-B18


title: RNA_NELFC-AID_TetELOA_DMSO_rep2

value: TetELOA


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-P4


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-A5


title: RNA_NELFC-AID_Tet_GFP_Aux_rep2

value: Auxin


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-P16


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-B17


title: RNA_NELFC-AID_TetELOA3_DOX_Aux6hr_Rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-P15


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-O4


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-P3


title: RNA_NELFC-AID_TetELOA_DMSO_rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-C18


title: RNA_NELFC-AID_Tet_GFP_Aux_rep1


title: RNA_NELFC-AID_Tet_ELOA_Aux_rep1


title: RNA_NELFC-AID_Tet_ELOA_Aux_rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-O3


title: RNA_NELFC-AID_ELOA-WT_Rep2.2

value: WT


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-A6


title: RNA_NELFC-AID_TetELOA3_DOX_Aux3hr_Rep3


title: RNA_NELFC-AID_ELOA-WT_Rep2.1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-O16


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-O15


title: RNA_NELFC-AID_ELOA-WT_Rep1.2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-N4


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-N3


title: RNA_NELFC-AID_ELOA-WT_Rep1.1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-N15


title: RNA_NELFC-AID_ELOA-WT_Auxin6hr_Rep1.2


title: 0012 CepEV rep4

city: Belfast

first: Clifford

middle: C

last: Taggart

address: 97 Lisburn Road

institute: Queen's University Belfast

description: Library name: 12

data_processing:
Genomics CTU QUB standard processing
Assembly: GRCh38 Genome Reference Consortium Human Build 38
Supplementary files format and content: csv containing raw counts for each sample

source_name: THP-1 cells

extract_protocol:
Extraction was done via the RNeasy Plus using elution columns (Qiagen)
KAPA HyperPrep with Riboerase

value: THP-1 cells

value: Macrophage


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-N16

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-M4


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-M16


title: 0011 CepEV rep3

description: Library name: 11


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-B6


title: RNA_NELFC-AID_ELOA-WT_Auxin6hr_Rep2.1


title: RNA_NELFC-AID_ELOAKO-C2_Rep2

value: ELOA-KO


title: 0009 CepEV rep1

description: Library name: 9


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-M3


title: 0008 HepEV rep4

description: Library name: 8


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-M15


title: 0010 CepEV rep2

description: Library name: 10


title: RNA_NELFC-AID_ELOAKO-C2_Rep1


title: RNA_NELFC-AID_ELOAKO-C2_Auxin6hr_Rep2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-L4


title: 0006 HepEV rep2

description: Library name: 6


title: 0005 HepEV rep1

description: Library name: 5


title: RNA_NELFC-AID_ELOA-WT_Auxin6hr_Rep2.2


title: RNA_NELFC-AID_ELOA-WT_Auxin6hr_Rep1.1


title: 0004 VX765 THP1 rep2

description: Library name: 4


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-L3


title: RNA_NELFC-AID_ELOAKO-C1_Rep2


title: 0003 VX765 THP1 rep1

description: Library name: 3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-3-O2-D6


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-L16


title: 0007 HepEV rep3

description: Library name: 7


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-L15


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-K4


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-K16


title: ChIP_NELFC-AID_TetGFP_NT_SPT6_Rep2

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis,  the nuclei were transferred to 1ml milliTUBEs with AFA fibers (Covaris, 520130) and sonicated in a Covaris E220 focused ultrasonicator (duty factor: 10%, peak intensity pulse: 140, cycles per burst: 200, time: 500 seconds).
Libraries were made using the KAPA HTP Biosystems Library Prep kit (Roche, KK8234) using Perkin Elmer Unique Dual Index Barcodes for NovaSeq 6000.

treatment_protocol: NELF-C-AID DLD-1 cells were treated with 500 µM Auxin or H2O (duration as indicated in the text) at 37°C to deplete the NELF-C-AID protein. To select lentivirus-infected cells, puromycin (1.5 μg/ml) and hygromycin (250 μg/ml) were used.


title: RNA_NELFC-AID_ELOAKO-C1_Rep1


title: RNA_NELFC-AID_ELOAKO-C1_Auxin6hr_Rep2


title: RNA_NELFC-AID_ELOAKO-C1_Auxin6hr_Rep1


title: ChIP_NELFC-AID_TetGFP_NT_SPT6_Rep1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-K3


title: RNA_NELFC-AID_ELOAKO-C2_Auxin6hr_Rep1


title: BAR_H3K27ac_run3

city: Ghent

first: Sarah-Lee

last: Bekaert

state: No state

address: Corneel Heymanslaan 10

institute: UGent

description:
Library name: BAR_H3K27ac_run3
Sequencing _Run3

data_processing:
The raw sequencing data of CUT&RUN was evaluated using FastQC and adapter trimming was done using TrimGalore (v0.6.5).
Mapping to the human reference genome (GRCh37/hg19) was done with bowtie2 (v.2.3.1)
Quality of aligned reads were filtered using min MAPQ 30 and reads with known low sequencing confidence were removed using Encode Blacklist regions. For sample with a percentage duplicated reads higher then 10%, deduplication was performed using MarkDuplicates (Picard, v4.0.11).
Peak calling was performed using MACS2 (v2.1.0) taking a q value of 0.05 as threshold and using the parameter keep-dup auto. NarrowPeak calling was used for transcription factors while broadPeak calling was used for histone marks.
Assembly: GRCh38
Supplementary files format and content: Bigwig files were generated using bamCoverage with binSize 10 and normalizeUsing RPKM.
Supplementary files format and content: Peak calling files from MACS2.
Library strategy: CUT&Run

extract_protocol:
CUT&RUN coupled with high-throughput DNA sequencing was performed on isolated nuclei using Cutana pA/G-MNase (Epicypher, 15-1016) according to the manufacturer’s manual.
Sequencing libraries were prepared with the NEBNext Ultra II kit (Illumina, E7645), followed by paired-end sequencing on a Nextseq2000 using the NextSeq 2000 P2 Reagents 100 Cycles v3 (Illumina, 20046811).

value: CLB-Bar

value: neuroblast


title: BAR_RUVBL2_run3

description:
Library name: BAR_RUVBL2_run3
Sequencing _Run3

value: Novus Biologicals (#NBP2-57593)


title: BAR_H3K27ac_run2

description:
Library name: BAR_H3K27ac_run2
Sequencing_Run2


title: BAR_IgG_run3

description:
Library name: BAR_IgG_run3
Sequencing _Run3


title: BAR_IgG_run2

description:
Library name: BAR_IgG_run2
Sequencing_Run2


title: BAR_RUVBL2_run2

description:
Library name: BAR_RUVBL2_run2
Sequencing_Run2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-K15

city: La Jolla


title: BAR_MYCN_run2

description:
Library name: BAR_MYCN_run2
Sequencing_Run2

value: Santa Cruz (sc53993)


title: BAR_MYCN_run3

description:
Library name: BAR_MYCN_run3
Sequencing _Run3


title: BAR_RUVBL2_run1

description:
Library name: BAR_RUVBL2_run1
Sequencing Run1


title: BAR_RUVBL1_run1

description:
Library name: BAR_RUVBL1_run1
Sequencing Run1

value: CST (#D1L8J)


title: ChIP_NELFC-AID_TetGFP_NT_pSer2

value: colon

value: DLD-1 NELFC-AID

value: epithelial cell

value: TetGFP


title: 0002 Untreated THP1 rep2

description: Library name: 2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-J4

value: 18 months

value: DHC

value: M


title: BAR_MYCN_run1

description:
Library name: BAR_MYCN_run1
Sequencing Run1


title: 0001 Untreated THP1 rep1

description: Library name: 1


title: Naive serum-adapted Shef6 on Geltrex, PXGL d0, Ex2, RNA-Seq, Replicate 2

description: Library name: Shef6_Ex2_PXGLY_d4_R2

data_processing:
The fastq files were processed with the Nextflow 23.04.1.5866/nf-core/rnaseq v3.10.1 pipeline. This included quality control with fastQC (v0.11.9), pseudo-alignment to the human reference genome hg38 with Salmon (v1.9.0) and alignment with STAR (v2.7.10a).
Gene expression levels were estimated with the tximport R package (v1.26.1)
Assembly: human reference genome hg38
Supplementary files format and content: csv file with raw counts per gene from the DESeq2 object for each sample.

growth_protocol: Naive serum-adapted Shef6 were cultured on serum coating (10% Fetal Bovine Serum in DMEM high glucose) or on Geltrex in PXGL medium (Bredenkamp et al, 2019). The same cells were plated for differentiation on Geltrex into N2B27, E8, mTeSR or N2B27 supplemented with XAV or with FGF2, XAV and Activin A (FAX).

extract_protocol:
Total RNA was isolated with the ExtractMe kit (Blirt EM15) following the manufacturer’s instructions.
Quant Seq 3' mRNA-seq Library Prep kit (Lexogen) was used for library construction.

value: human embryonic stem cells

tag: experiment

tag: condition

value: PXGLY

tag: timepoint

tag: condition timepoint


title: Naive serum-adapted Shef6 on Geltrex, PXGL d0, Ex2, RNA-Seq, Replicate 1

description: Library name: Shef6_Ex2_PXGLY_d4_R1


title: BAR_H3K27ac_run1

description:
Library name: BAR_H3K27ac_run1
Sequencing Run1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-J16

tag: strain

tag: age


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-J15

tag: brain region

tag: gender


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-J3


title: ChIP_NELFC-AID_TetGFP_NT_NELFC

tag: cell line

tag: cell type

value: no treatment

value: NELFC


title: ChIP_NELFC-AID_TetGFP_NT_PAF1

tag: genotype


title: BAR_IgG_run1

description:
Library name: BAR_IgG_run1
Sequencing Run1

tag: chip antibody


title: ChIP_NELFC-AID_TetGFP_NT_INPUT

tag: treatment


title: Naive serum-adapted Shef6 on Geltrex, FAX d4, Ex2, RNA-Seq, Replicate 1

description: Library name: Shef6_Ex2_FAX_d4_R1

value: FAX


title: Naive serum-adapted Shef6 on Geltrex, FAX d4, Ex2, RNA-Seq, Replicate 2

description: Library name: Shef6_Ex2_FAX_d4_R2


title: Naive serum-adapted Shef6 on Geltrex, N2B27 d4, Ex2, RNA-Seq, Replicate 2

description: Library name: Shef6_Ex2_N2B27_d4_R2


title: Naive serum-adapted Shef6 on Geltrex, XAV d4, Ex2, RNA-Seq, Replicate 1

description: Library name: Shef6_Ex2_XAV_d4_R1

value: XAV


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-I3


title: Naive serum-adapted Shef6 on Geltrex, mTeSR d8, RNA-Seq, Replicate 1

description: Library name: Shef6_mTeSR_d8_R1

value: mTeSR


title: ChIP_NELFC-AID_TetGFP_NT_HA-ELOA3

tag: tissue


title: Naive serum-adapted Shef6 on Geltrex, N2B27 d4, Ex2, RNA-Seq, Replicate 1

description: Library name: Shef6_Ex2_N2B27_d4_R1


title: Naive serum-adapted Shef6 on Geltrex, XAV d4, Ex2, RNA-Seq, Replicate 2

description: Library name: Shef6_Ex2_XAV_d4_R2


title: ChIP_NELFC-AID_TetGFP_Aux5hr_PAF1

value: Auxin


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-I4


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-I16


title: Naive serum-adapted Shef6 on Geltrex, mTeSR d6, RNA-Seq, Replicate 2

description: Library name: Shef6_mTeSR_d6_R2


title: ChIP_NELFC-AID_TetGFP_Aux4hr_SPT6


title: Naive serum-adapted Shef6 on Geltrex, mTeSR d8, RNA-Seq, Replicate 2

description: Library name: Shef6_mTeSR_d8_R2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-I15


title: ChIP_NELFC-AID_TetGFP_NT_POL2


title: ChIP_NELFC-AID_TetGFP_Aux4hr_pSer2


title: Naive serum-adapted Shef6 on Geltrex, mTeSR d6, RNA-Seq, Replicate 1

description: Library name: Shef6_mTeSR_d6_R1


title: Naive serum-adapted Shef6 on Geltrex, mTeSR d4, RNA-Seq, Replicate 2

description: Library name: Shef6_mTeSR_d4_R2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-H4


title: Naive serum-adapted Shef6 on Geltrex, mTeSR d4, RNA-Seq, Replicate 1

description: Library name: Shef6_mTeSR_d4_R1


title: ChIP_NELFC-AID_TetGFP_Aux4hr_NELFC


title: Naive serum-adapted Shef6 on Geltrex, E8 d8, RNA-Seq, Replicate 1

description: Library name: Shef6_E8_d8_R1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-H16


title: Naive serum-adapted Shef6 on Geltrex, E8 d6, RNA-Seq, Replicate 1

description: Library name: Shef6_E8_d6_R1


title: ChIP_NELFC-AID_TetGFP_Aux4h_POL2


title: Naive serum-adapted Shef6 on Geltrex, E8 d8, RNA-Seq, Replicate 2

description: Library name: Shef6_E8_d8_R2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-H3


title: Naive serum-adapted Shef6 on Geltrex, E8 d6, RNA-Seq, Replicate 2

description: Library name: Shef6_E8_d6_R2


title: ChIP_NELFC-AID_TetGFP_Aux_INPUT


title: Naive serum-adapted Shef6 on Geltrex, E8 d4, RNA-Seq, Replicate 2

description: Library name: Shef6_E8_d4_R2


title: ChIP_NELFC-AID_TetGFP_Aux_HA-ELOA3


title: Naive serum-adapted Shef6 on Geltrex, E8 d2, RNA-Seq, Replicate 1

description: Library name: Shef6_E8_d2_R1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-G4


title: Naive serum-adapted Shef6 on Geltrex, E8 d3, RNA-Seq, Replicate 2

description: Library name: Shef6_E8_d3_R2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-G3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-G16


title: ChIP_NELFC-AID_TetELOA3_NT_SPT6


title: Naive serum-adapted Shef6 on Geltrex, E8 d2, RNA-Seq, Replicate 2

description: Library name: Shef6_E8_d2_R2


title: Naive serum-adapted Shef6 on Geltrex, N2B27 d8, RNA-Seq, Replicate 2

description: Library name: Shef6_N2B27_d8_R2


title: Naive serum-adapted Shef6 on Geltrex, E8 d3, RNA-Seq, Replicate 1

description: Library name: Shef6_E8_d3_R1


title: Naive serum-adapted Shef6 on Geltrex, E8 d4, RNA-Seq, Replicate 1

description: Library name: Shef6_E8_d4_R1


title: Naive serum-adapted Shef6 on Geltrex, N2B27 d8, RNA-Seq, Replicate 1

description: Library name: Shef6_N2B27_d8_R1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-G15


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-H15


title: Naive serum-adapted Shef6 on Geltrex, N2B27 d6, RNA-Seq, Replicate 2

description: Library name: Shef6_N2B27_d6_R2


title: ChIP_NELFC-AID_TetELOA3_NT_POL2


title: Naive serum-adapted Shef6 on Geltrex, N2B27 d6, RNA-Seq, Replicate 1

description: Library name: Shef6_N2B27_d6_R1


title: ChIP_NELFC-AID_TetELOA3_NT_INPUT


title: ChIP_NELFC-AID_TetELOA3_NT_HA-ELOA3


title: Naive serum-adapted Shef6 on Geltrex, N2B27 d4, RNA-Seq, Replicate 2

description: Library name: Shef6_N2B27_d4_R2


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-F4


title: ChIP_NELFC-AID_TetELOA3_Aux4hr_SPT6


title: Naive serum-adapted Shef6 on Geltrex, N2B27 d3, RNA-Seq, Replicate 2

description: Library name: Shef6_N2B27_d3_R2


title: Naive serum-adapted Shef6 on Geltrex, N2B27 d3, RNA-Seq, Replicate 1

description: Library name: Shef6_N2B27_d3_R1


title: ChIP_NELFC-AID_TetELOA3_Aux_POL2


title: Naive serum-adapted Shef6 on Geltrex, N2B27 d2, RNA-Seq, Replicate 2

description: Library name: Shef6_N2B27_d2_R2


title: Naive serum-adapted Shef6 on Geltrex, N2B27 d2, RNA-Seq, Replicate 1

description: Library name: Shef6_N2B27_d2_R1


title: Naive serum-adapted Shef6 on Geltrex, N2B27 d4, RNA-Seq, Replicate 1

description: Library name: Shef6_N2B27_d4_R1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-F3


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-F16


title: Naive serum-adapted Shef6 on Geltrex, PXGL d0, RNA-Seq, Replicate 2

description: Library name: Shef6_PXGLY_Geltrex_R2


title: ChIP_NELFC-AID_TetELOA3_Aux_INPUT


title: Naive serum-adapted Shef6 on Geltrex, PXGL d0, RNA-Seq, Replicate 1

description: Library name: Shef6_PXGLY_Geltrex_R1


title: Naive serum-adapted Shef6 on serum, PXGL d0, RNA-Seq, Replicate 1

description: Library name: Shef6_PXGLY_GelFBS_R1


title: AMB_200225_18mo_8E_9H_8J_9J_1_P2-2-A3-E3


title: ChIP_NELFC-AID_TetELOA_Aux5hr_PAF1

value: TetELOA


title: Naive serum-adapted Shef6 on serum, PXGL d0, RNA-Seq, Replicate 2

description: Library name: Shef6_PXGLY_GelFBS_R2


title: ChIP_NELFC-AID_TetELOA_NT_PAF1