title: Input (HSF1)_ChIP-Seq

data_processing:
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8).
Sequence quality was examined using the FastQC software. After passing Solexa CHASTITY quality filter, the clean reads were aligned to Human reference genome UCSC HG19 using BOWTIE (V2.2.7).
Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.2.
Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model, using a p-value threshold of 10-4.
Then the peaks were annotated by the nearest gene using the newest UCSC RefSeq database.
Assembly: HG19
Supplementary files format and content: The signal profile (at 10 bp resolution) with UCSC WIG file format was generated from ChIP-seq data, which can be visualized on UCSC genome browser or IGB browser (Integrated Genome Browser, Java Runtime Environment needed, http://www.bioviz.org/igb/).

extract_protocol:
Lysates were clarified from sonicated HSF1/H3K27ac-DNA complexes were isolated with antibody.
10 ng DNA of each sample was converted to phosphorylated blunt-ended; An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments; Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads.

treatment_protocol: The cells were directly fixed with formalin without any treatment.


title: E8_B008648_B008695

status: Public on Aug 15 2022

type: SRA

city: San Francisco

first: Juliane

last: Winkler

address: 513 Parnassus Avenue

department: Department of Cell and Tissue Biology

country: USA

institute: University of California, San Francisco

library_source: transcriptomic single cell

data_processing:
Sequences from the NovaSeq or NextSeq were de-multiplexed using bcl2fastq v.2.19.0.316. Reads were aligned to the gencode V30 genome using STAR v.2.5.2b with parameters TK. Gene counts were produced using HTSEQ v.0.6.1p1 with default parameters, except ‘stranded’ was set to ‘false’, and ‘mode’ was set to ‘intersection-nonempty’.
Gene count tables were combined with the metadata variables using the Scanpy Python package version 1.8.1. We removed the genes that were not expressed in at least 5 cells. Cells with less than 5000 counts and 500 detected genes were removed. Additionally, we removed cells with more than 50% mitochondrial genes and 20% ERCC reads.  The data were then normalized using size factor normalization such that every cell has 10,000 counts and log-transformed. We selected the top 2000 genes with the highest standardized variance as the highly variable genes by using VST method from Seurat V3, which is also implemented in Scanpy. Cell-cycle regression was performed after calculating the score of S and G2M phases for each cell. The data was then scaled to a maximum value of 10. We then computed principal component (PC) analysis, neighborhood graph and clustered the data using Louvain and Leiden methods. The data was visualized using UMAP projection.
Assembly: genecode V30
Supplementary files format and content: csv
Supplementary files format and content: comma seperated values file for meta data, raw gene count matrix, and normalized and log-transformed gene count matrix

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Live, LIN-/hDC298+ single breast primary tumor and metastatic cells from lung were sorted into 384 well plates followed by cDNA preparation using modified SmartSeq2.
SmartSeq2 for preparation of cDNA followed by library preparation using a homebrew adapted version.

tag: tissue

value: patient-derived-xenograft

tag: cell type

value: tumor

tag: strain

value: NSG


city: Basel

first: Arne

last: Wehling

state: Basel-Stadt

address: Mattenstrasse 24

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118546_HCKFFBGXB_1_H4_Plate1_Seq4_TCCTGAGC_TCTCTCCG_S32_R1_001_MM_1

library_source: transcriptomic

data_processing:
Illumina RTA Version: 2.4.11 used for basecalling.
Sequenced reads were mapped to M21 musmusculus whole genome using star 2.5.3a with --quantMode GeneCounts.
The resulting sam files were converted into bam files with samtools. R
Raw counts were extracted from bam files using  subread version 1.5.0 featureCount with parameters:-t gene -g gene_id
M21 (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M21)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Mus musculus

source_name: HSC daughter cell

extract_protocol:
Single HSC daughter cells were isolated with a micromanipulator and immediately placed into lysis buffer at 4 degree Celsius. Then Smart-Seq2 in adaption from https://www.nature.com/articles/s41467-018-05347-6
Nextera DNA Flex Library Prep
Nextera Illumina IDT

value: bone marrow

tag: age

value: 12 - 19 weeks

tag: genotype

value: wild type


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118561_HCKFFBGXB_1_G6_Plate1_Seq4_TAGGCATG_CGTCTAAT_S47_R1_001_MM_1


title: HSF1_ChIP-Seq

city: Weifang City

first: Jiaqiu

last: Li

state: 省/直辖市

address: No. 2428, Yuhe Road, Kuiwen District

country: China

institute: weifang medical university

library_source: genomic

molecule: genomic DNA

source_name: HCT116 cell

growth_protocol: HCT116 was cultured in McCOY’s 5A medium supplemented with 10% bovine serum at 37ºC with 5% CO2.

tag: cell line

tag: chip antibody


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118553_HCKFFBGXB_1_G5_Plate1_Seq4_GGACTCCT_CGTCTAAT_S39_R1_001_MM_1


title: F13_B008648_B008695


title: F14_B008648_B008695


title: F10_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118545_HCKFFBGXB_1_G4_Plate1_Seq4_TCCTGAGC_CGTCTAAT_S31_R1_001_MM_1


title: Input (H3K27ac)_ChIP-Seq


title: F17_B008648_B008695


title: H21_B008640_B010275


title: Medium donor1

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

data_processing:
fastp -q 15 -n 10 -l 20  -i target_R1.fastq (fastp v0.19.10)
STAR --readFilesIn target_R1.fastq --outSAMtype BAM Unsorted --outFilterMultimapNmax 4 --outFilterType BySJout --outSAMmultNmax 1 --outFilterMismatchNoverReadLmax 0.1 --outSAMstrandField intronMotif --sjdbGTFfile gencode.gtf --outReadsUnmapped Fastx (STAR v2.7.3a)
samtools sort -n target_STAR.Aligned.out.bam | samtools fixmate -rm - - | samtools sort - > target_STAR.Aligned.sortedByCoord.out.bam (samtools v1.9)
featureCounts -p -a gencode.gtf -s 2 -o reverse_stranded.txt target_STAR.Aligned.sortedByCoord.out.bam (featureCounts v2.0.1)
Assembly: hg38
Supplementary files format and content: Tab delimited file containing reads per gene across samples

source_name: blood

extract_protocol:
RNA was extracted using RNA Qiagen extraction kit
Library was prepared using NEB Next single cell/Low input RNA library

value: blood

value: pDCs

tag: disease state

value: healthy

tag: treatment

value: medium


title: H3K27ac_ChIP-Seq


title: F19_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118577_HCKFFBGXB_1_G8_Plate1_Seq4_CGAGGCTG_CGTCTAAT_S63_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118537_HCKFFBGXB_1_G3_Plate1_Seq4_AGGCAGAA_CGTCTAAT_S23_R1_001_MM_1


title: E20_B008648_B008695


title: F1_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118569_HCKFFBGXB_1_G7_Plate1_Seq4_CTCTCTAC_CGTCTAAT_S55_R1_001_MM_1


title: TC71-EFKD-RNAseq 2

city: Columbus

first: Iftekhar

middle: Ahmed

last: Showpnil

state: OH

address: 700 Childrens Drive

department: CCCBD

institute: Nationwide Children's Hospital

description: RNA-seq

data_processing:
Low-quality reads (q<10) were filtered out and adaptor sequences trimmed from raw reads using bbduk (v37.64).
Each sample was aligned to HumanG1Kv37 assembly of the Homo Sapiens reference (hg19) using STAR version 2.6.0c (Dobin et al., 2013)
Differential gene expression performed between EF-Endo and EF-KD in TC71 cells.
RNA-seq bigwig tracks were generated and averaged across biological replicates using bamCompare from deepTools package.
Differential gene expression for EF-Endo vs EF-KD and EF-Rescue vs EF-KD were available from previously published data from the laboratory under GEO accession GSE160898
Genome_build: hg19
Supplementary_files_format_and_content: See file type and description for processed data file below
Supplementary_files_format_and_content: A673_RNAseq_iLuc_197.bw: bigwig file of RNA sequencing track for EF-Endo in A673 cells
Supplementary_files_format_and_content: A673_RNAseq_iEF_197.bw: bigwig file of RNA sequencing track for EF-KD in A673 cells
Supplementary_files_format_and_content: A673_RNAseq_iEF_714.bw: bigwig file  of RNA sequencing track for EF-Rescue in A673 cells
Supplementary_files_format_and_content: TC71_iLuc_RNAseq.bw: bigwig file of RNA sequencing track for EF-Endo in TC71 cells
Supplementary_files_format_and_content: TC71_iEF_RNAseq.bw: bigwig file of RNA sequencing track for EF-KD in TC71 cells
Supplementary_files_format_and_content: A673_RNAseq_iLucempty197vsiEFempty197.complete.txt: Differentially expressed genes in EF-Endo vs EF-KD in A673 cells
Supplementary_files_format_and_content: A673_RNAseq_iEFwtEF714vsiEFempty197.complete.txt: Differentially expressed genes in EF-Rescue vs EF-KD in A673 cells
Supplementary_files_format_and_content: TC71_iLucvsiEF_DEG.txt: Differentially expressed genes in EF-Endo vs EF-KD in TC71 cells
Supplementary_files_format_and_content: EF_direct_upregulated_EndovsKD.txt: Differentially expressed genes in EF-Endo vs EF-KD that are directly upregulated by EWS/FLI
Supplementary_files_format_and_content: EF_direct_downregulated_EndovsKD.txt: Differentially expressed genes in EF-Endo vs EF-KD that are directly downregulated by EWS/FLI
Supplementary_files_format_and_content: GSEA_EF_direct_upregulated_A673_iLuc197vsiEF197_vs_DEGs_TC71_iLucvsiEF.grp.html: Gene set enrichment analysis results for functional enrichment of genes directly upregulated by EWS/FLI (gene set) in TC71 differentially expressed genes (EF-Endo vs EF-KD; rank order)
Supplementary_files_format_and_content: GSEA_EF_direct_downregulated_A673_iLuc197vsiEF197_vs_DEGs_TC71_iLucvsiEF.grp.html: Gene set enrichment analysis results for functional enrichment of genes directly downregulated by EWS/FLI (gene set) in TC71 differentially expressed genes (EF-Endo vs EF-KD; rank order)

source_name: TC71 Ewing sarcoma cells

growth_protocol: A673 cells were cultured in DMEM with L-Glutamine, supplemented with 10% FBS, 1% PSQ, 1% sodium pyruvate for 2-3 days, followed by selection in the same media supplemented with 2μg/mL puromycin, and 150μg/mL hygromycin B at 37ºC and 5% CO2. TC71 cells were cultured in RPMI 1640 without L-Glutamine, supplemented with 10% FBS and 1% PSQ at 37ºC and 5% CO2 for 2 days, followed by selection in the same media supplemented with 2μg/mL puromycin.

extract_protocol:
Total RNA was extracted from frozen cell pellets using RNeasy Extraction Kit (Qiagen 74136)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: EWS/FLI knock-down with RNAi followed by rescue of EWS/FLI expression with a 3XFLAG tagged EWS/FLI cDNA construct in A673. EWS/FLI knock-down with RNAi in TC71 cells

tag: transduced shrna

value: iEF

tag: replicate


title: F8_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118529_HCKFFBGXB_1_G2_Plate1_Seq4_CGTACTAG_CGTCTAAT_S15_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118521_HCKFFBGXB_1_G1_Plate1_Seq4_TAAGGCGA_CGTCTAAT_S7_R1_001_MM_1


title: F6_B008648_B008695


title: C14_B008640_B010275


title: G13_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118576_HCKFFBGXB_1_F8_Plate1_Seq4_CGAGGCTG_CTAAGCCT_S62_R1_001_MM_1


title: G14_B008648_B008695


title: TC71-EFEndo-RNAseq 2

description: RNA-seq

value: iLuc


title: TC71-EFEndo-RNAseq 1

description: RNA-seq


title: G17_B008648_B008695


title: TC71-EFKD-Rabbit-IgG-CUT&Tag 2

description:
TC71-EFKD-Rabbit-IgG-CUT&Tag
CTCF CUT&Tag

data_processing:
Adapter sequences and low quality reads were trimmed using Trim Galore
Reads aligned to human hg19 and E.Coli genomes using Bowtie2
Reads were spike-in normalized using DESeq2 median ratio method
Peaks were called with spike-in normalization using corresponding IgG as controls, and accounting for variation between the biological replicates using MACS2 (v 2.2.7.1; Zhang et al., 2008), DiffBind (v2.14.0; Ross-Innes et al., 2012; Stark R., 2011) and DESeq2
Spike-in normalized bigwig tracks were generated and averaged across biological replicates using deepTools
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files containing CTCF peak calls were generated per peak calling method described above
Supplementary_files_format_and_content: bigwig files for CTCF signals compared to IgG control signals were created using deepTools
Supplementary_files_format_and_content: Overlap of CTCF and TAD boundaries were performed using BEDTools
Supplementary_files_format_and_content: CTCF localization matrix at stable, EF-WT and EF-KD TAD boundaries was generated using deepTools

extract_protocol:
AMPure XP bead extraction
Cleavage Under Target & Tagmentation (CUT&Tag)
CUT&Tag

treatment_protocol: EWS/FLI knock-down with RNAi followed by rescue of EWS/FLI expression with a 3XFLAG tagged EWS/FLI cDNA construct

tag: condition

value: EF-KD


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118560_HCKFFBGXB_1_F6_Plate1_Seq4_TAGGCATG_CTAAGCCT_S46_R1_001_MM_1


title: J17_B008648_B008695


title: G18_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118552_HCKFFBGXB_1_F5_Plate1_Seq4_GGACTCCT_CTAAGCCT_S38_R1_001_MM_1


title: G1_B008648_B008695


title: J18_B008648_B008695


title: TC71-EFKD-Rabbit-IgG-CUT&Tag 1


title: J1_B008648_B008695


title: J20_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118544_HCKFFBGXB_1_F4_Plate1_Seq4_TCCTGAGC_CTAAGCCT_S30_R1_001_MM_1


title: TC71-EFKD-CTCF-CUT&Tag 2

description:
TC71-EFKD-CTCF-CUT&Tag
CTCF CUT&Tag


title: J21_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118536_HCKFFBGXB_1_F3_Plate1_Seq4_AGGCAGAA_CTAAGCCT_S22_R1_001_MM_1


title: TC71-EFKD-RNAseq 1

description: RNA-seq


title: TC71-EFKD-CTCF-CUT&Tag 1

description:
TC71-EFKD-CTCF-CUT&Tag
CTCF CUT&Tag


title: J22_B008648_B008695


title: TC71-EFEndo-Rabbit-IgG-CUT&Tag 2

description:
TC71-EFEndo-Rabbit-IgG-CUT&Tag
CTCF CUT&Tag

value: EF-Endo


title: J4_B008648_B008695


title: J2_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118520_HCKFFBGXB_1_F1_Plate1_Seq4_TAAGGCGA_CTAAGCCT_S6_R1_001_MM_1


title: K10_B008648_B008695


title: C2_B008640_B010275


title: K11_B008648_B008695


title: K12_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118575_HCKFFBGXB_1_E8_Plate1_Seq4_CGAGGCTG_AAGGAGTA_S61_R1_001_MM_1


title: K15_B008648_B008695


title: TC71-EFEndo-CTCF-CUT&Tag 1

description:
TC71-EFEndo-CTCF-CUT&Tag
CTCF CUT&Tag


title: K16_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118567_HCKFFBGXB_1_E7_Plate1_Seq4_CTCTCTAC_AAGGAGTA_S53_R1_001_MM_1


title: K1_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118559_HCKFFBGXB_1_E6_Plate1_Seq4_TAGGCATG_AAGGAGTA_S45_R1_001_MM_1


title: A673-EFRescue-Rabbit-IgG-CUT&Tag 2

description:
A673-EFRescue-Rabbit-IgG-CUT&Tag
CTCF CUT&Tag

source_name: A673 Ewing sarcoma cells

value: iEF + 3XFLAG-EWS/FLI

value: EF-Rescue


title: K21_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118528_HCKFFBGXB_1_F2_Plate1_Seq4_CGTACTAG_CTAAGCCT_S14_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118551_HCKFFBGXB_1_E5_Plate1_Seq4_GGACTCCT_AAGGAGTA_S37_R1_001_MM_1


title: K2_B008648_B008695


title: A21_B008640_B010275


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118543_HCKFFBGXB_1_E4_Plate1_Seq4_TCCTGAGC_AAGGAGTA_S29_R1_001_MM_1


title: A673-EFRescue-Rabbit-IgG-CUT&Tag 1


title: TC71-EFEndo-Rabbit-IgG-CUT&Tag 1


title: TC71-EFEndo-CTCF-CUT&Tag 2

description:
TC71-EFEndo-CTCF-CUT&Tag
CTCF CUT&Tag


title: A673-EFRescue-CTCF-CUT&Tag 1

description:
A673-EFRescue-CTCF-CUT&Tag
CTCF CUT&Tag


title: P10_B008648_B008695


title: O7_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118583_HCKFFBGXB_1_E9_Plate1_Seq4_AAGAGGCA_AAGGAGTA_S69_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118535_HCKFFBGXB_1_E3_Plate1_Seq4_AGGCAGAA_AAGGAGTA_S21_R1_001_MM_1


title: A673-EFRescue-CTCF-CUT&Tag 2

description:
A673-EFRescue-CTCF-CUT&Tag
CTCF CUT&Tag


title: A673-EFKD-Rabbit-IgG-CUT&Tag 2

description:
A673-EFKD-Rabbit-IgG-CUT&Tag
CTCF CUT&Tag

value: iEF + empty cDNA


title: K18_B008648_B008695

value: patient-derived-xenograft


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118527_HCKFFBGXB_1_E2_Plate1_Seq4_CGTACTAG_AAGGAGTA_S13_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118519_HCKFFBGXB_1_E1_Plate1_Seq4_TAAGGCGA_AAGGAGTA_S5_R1_001_MM_1


title: K22_B008648_B008695

value: tumor


title: P18_B008648_B008695

value: NSG


title: A673-EFKD-CTCF-CUT&Tag 2

description:
A673-EFKD-CTCF-CUT&Tag
CTCF CUT&Tag


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118574_HCKFFBGXB_1_D8_Plate1_Seq4_CGAGGCTG_ACTGCATA_S60_R1_001_MM_1

value: bone marrow


title: P19_B008648_B008695


title: A673-EFKD-CTCF-CUT&Tag 1

description:
A673-EFKD-CTCF-CUT&Tag
CTCF CUT&Tag


title: D12_B008640_B010275


title: P21_B008648_B008695


title: P2_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118566_HCKFFBGXB_1_D7_Plate1_Seq4_CTCTCTAC_ACTGCATA_S52_R1_001_MM_1

value: 12 - 19 weeks


title: P5_B008648_B008695


title: P6_B008648_B008695


title: P4_B008648_B008695


title: A14_B008649_B008703


title: A673-EFKD-Rabbit-IgG-CUT&Tag 1


title: D15_B008640_B010275


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118550_HCKFFBGXB_1_D5_Plate1_Seq4_GGACTCCT_ACTGCATA_S36_R1_001_MM_1

value: wild type


title: P11_B008648_B008695


title: P9_B008648_B008695


title: A673-EFEndo-Rabbit-IgG-CUT&Tag 2

description:
A673-EFEndo-Rabbit-IgG-CUT&Tag
CTCF CUT&Tag

value: iLuc + empty cDNA


title: P14_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118534_HCKFFBGXB_1_D3_Plate1_Seq4_AGGCAGAA_ACTGCATA_S20_R1_001_MM_1


title: O6_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118558_HCKFFBGXB_1_D6_Plate1_Seq4_TAGGCATG_ACTGCATA_S44_R1_001_MM_1


title: P12_B008648_B008695


title: A15_B008649_B008703


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118573_HCKFFBGXB_1_C8_Plate1_Seq4_CGAGGCTG_GTAAGGAG_S59_R1_001_MM_1


title: A19_B008649_B008703


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118526_HCKFFBGXB_1_D2_Plate1_Seq4_CGTACTAG_ACTGCATA_S12_R1_001_MM_1


title: D3_B008640_B010275


title: A22_B008640_B010275


title: A1_B008649_B008703


title: D4_B008639_B008701


title: D3_B008649_B008703


title: A673-EFEndo-Rabbit-IgG-CUT&Tag 1


title: A673-EFEndo-CTCF-CUT&Tag 1

description:
A673-EFEndo-CTCF-CUT&Tag
CTCF CUT&Tag


title: TTC466-EWS/ERG-CUT&Tag 2

description:
TTC466-EWS/ERG-CUT&Tag
CUT&Tag

data_processing:
Adapter sequences and low quality reads were trimmed using Trim Galore
Reads aligned to human hg19 and E.Coli genomes using Bowtie2
Reads were spike-in normalized using DESeq2 median ratio method
Peaks were called with spike-in normalization using corresponding IgG as controls, and accounting for variation between the biological replicates using MACS2 (v 2.2.7.1; Zhang et al., 2008), DiffBind (v2.14.0; Ross-Innes et al., 2012; Stark R., 2011) and DESeq2
Spike-in normalized bigwig tracks were generated and averaged across biological replicates using deepTools
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files containing EWS/FLI and EWS/ERG peak calls were generated per peak calling method described above
Supplementary_files_format_and_content: bigwig files for EWS/FLI and EWS/ERG signals compared to IgG control signals were created using deepTools
Supplementary_files_format_and_content: Overlap of EWS/FLI and EWS/ERG peaks were performed using ChIPpeakAnno, VennDiagram, GenomicRanges, and Vennerable R packages. Conserved EWS/FLI peaks were identified in A673 cells from the common overlapping peak regions within 200bps from all 5 cell lines
Supplementary_files_format_and_content: Conserved EWS/FLI peaks intersecting chromatin features like TAD boundaries, Compartment shifts and differential enhancers were identified using BEDTools
Supplementary_files_format_and_content: peaks_A673_FLI_fdr05_idr05_meanT1_FC4.narrowPeak: peak file for EWS/FLI in A673 cells
Supplementary_files_format_and_content: peaks_TC71_FLI_fdr05_idr05_meanT1_FC4.narrowPeak: peak file for EWS/FLI in TC71 cells
Supplementary_files_format_and_content: peaks_EWS_502_FLI_fdr05_idr05_meanT1_FC4.narrowPeak: peak file for EWS/FLI in EWS-502 cells
Supplementary_files_format_and_content: peaks_SK_N_MC_FLI_fdr05_idr05_meanT1_FC4.narrowPeak: peak file for EWS/FLI in SK-N-MC cells
Supplementary_files_format_and_content: peaks_TTC_466_ERG_fdr05_idr05_meanT1_FC4.narrowPeak: peak file for EWS/ERG in TTC-466 cells
Supplementary_files_format_and_content: A673log2FLIvsIgG10.bw: bigwig tracks of EWS/FLI vs. IgG in A673 cells
Supplementary_files_format_and_content: TC71log2FLIvsIgG10.bw: bigwig tracks of EWS/FLI vs. IgG in TC71 cells
Supplementary_files_format_and_content: EWS502log2FLIvsIgG10.bw: bigwig tracks of EWS/FLI vs. IgG in EWS-502 cells
Supplementary_files_format_and_content: SKNMClog2FLIvsIgG10.bw: bigwig tracks of EWS/FLI vs. IgG in SK-N-MC cells
Supplementary_files_format_and_content: TTC466log2ERGvsIgG10.bw: bigwig tracks of EWS/ERG vs. IgG in TTC-466 cells
Supplementary_files_format_and_content: FLI_ERG_overlaps_FC4_T1_IDR0.05_FDR0.05.bed: regions overlapping EWS/FLI and EWS/ERG peak calls in A673, TC71, EWS-502, SK-N-MC, and TTC-466 cells within 200bps
Supplementary_files_format_and_content: A673_EEts_uniq.bed: EWS/FLI peaks in A673 cells underlying the regions overlapping EWS/FLI and EWS/ERG peaks in 5 cell lines
Supplementary_files_format_and_content: A673_EEts_MS_uniq.bed: Conserved EWS/FLI peaks in A673 cells at GGAA-microsatellite sites
Supplementary_files_format_and_content: A673_EEts_nonMS_uniq.bed: Conserved EWS/FLI peaks in A673 cells at non-microsatellite sites
Supplementary_files_format_and_content: homerResults_A673_EEts_uniq.html: Homer motif analysis results for conserved EWS/FLI peaks in A673 cells
Supplementary_files_format_and_content: Stable_endokd_EF_uniq.bed: Conserved EWS/FLI peaks underlying stable compartments in EF-Endo vs EF-KD
Supplementary_files_format_and_content: AB_endokd_EF_uniq.bed: Conserved EWS/FLI peaks underlying B like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: BA_endokd_EF_uniq.bed: Conserved EWS/FLI peaks underlying A like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: Stable_rskd_EF_uniq.bed: Conserved EWS/FLI peaks underlying stable compartments in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: AB_rskd_EF_uniq.bed: Conserved EWS/FLI peaks underlying B like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: BA_rskd_EF_uniq.bed: Conserved EWS/FLI peaks underlying A like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: A673EEts_EndostableEnh_uniq.bed: Conserved EWS/FLI peaks underlying stable enhancers in EF-Endo vs EF-KD
Supplementary_files_format_and_content: A673EEts_EndoGainedEnh_uniq.bed: Conserved EWS/FLI peaks underlying gained enhancers in EF-Endo vs EF-KD
Supplementary_files_format_and_content: A673EEts_EndoLostEnh_uniq.bed: Conserved EWS/FLI peaks underlying lost enhancers in EF-Endo vs EF-KD
Supplementary_files_format_and_content: A673EEts_RescuestableEnh_uniq.bed: Conserved EWS/FLI peaks underlying stable enhancers in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: A673EEts_RescueGainedEnh_uniq.bed: Conserved EWS/FLI peaks underlying gained enhancers in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: A673EEts_RescueLostEnh_uniq.bed: Conserved EWS/FLI peaks underlying lost enhancers in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: EFatstableboundaries_uniq.bed: Conserved EWS/FLI peaks underlying stable TAD boundaries between EF-Endo, EF-KD and EF-Rescue
Supplementary_files_format_and_content: EFatWTboundaries_uniq.bed: Conserved EWS/FLI peaks underlying EF-WT TAD boundaries only (boundaries that are only common to EF-Endo and EF-Rescue but not EF-KD)
Supplementary_files_format_and_content: EFatKDboundaries_uniq.bed: Conserved EWS/FLI peaks underlying EF-KD only TAD boundaries

source_name: TTC-466 Ewing sarcoma cell line

growth_protocol: A673 and SK-N-MC cells were cultured in DMEM with L-Glutamine, supplemented with 10% FBS, 1% PSQ, 1% sodium pyruvate at 37ºC and 5% CO2. TC-71 and TTC-466 cells were cultured in RPMI 1640 without L-Glutamine, supplemented with 10% FBS and 1% PSQ at 37ºC and 5% CO2. EWS-502 cells were cultured in RPMI 1640 without L-Glutamine, supplemented with 15% FBS and 1% PSQ at 37ºC and 5% CO2.

extract_protocol:
AMPure XP bead extraction
CUT&Tag

treatment_protocol: parental cells were harvested and CUT&Tag performed using FLI1, ERG or Rabbit-IgG antiboties

value: parental


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118565_HCKFFBGXB_1_C7_Plate1_Seq4_CTCTCTAC_GTAAGGAG_S51_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118518_HCKFFBGXB_1_D1_Plate1_Seq4_TAAGGCGA_ACTGCATA_S4_R1_001_MM_1


title: D4_B008649_B008703


title: D8_B008649_B008703


title: D6_B008639_B008701


title: TTC466-EWS/ERG-CUT&Tag 1

description:
TTC466-EWS/ERG-CUT&Tag
CUT&Tag


title: D7_B008649_B008703


title: SKNMC-Rb-IgG-CUT&Tag 2

description:
SKNMC-Rb-IgG-CUT&Tag
CUT&Tag

source_name: SK-N-MC Ewing sarcoma cell line


title: TTC466-Rb-IgG-CUT&Tag 2

description:
TTC466-Rb-IgG-CUT&Tag
CUT&Tag


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118549_HCKFFBGXB_1_C5_Plate1_Seq4_GGACTCCT_GTAAGGAG_S35_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118533_HCKFFBGXB_1_C3_Plate1_Seq4_AGGCAGAA_GTAAGGAG_S19_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118557_HCKFFBGXB_1_C6_Plate1_Seq4_TAGGCATG_GTAAGGAG_S43_R1_001_MM_1


title: E14_B008639_B008701


title: E16_B008649_B008703


title: SKNMC-Rb-IgG-CUT&Tag 1

description:
SKNMC-Rb-IgG-CUT&Tag
CUT&Tag


title: A673-EFEndo-CTCF-CUT&Tag 2

description:
A673-EFEndo-CTCF-CUT&Tag
CTCF CUT&Tag


title: D3_B008639_B008701


title: TTC466-Rb-IgG-CUT&Tag 1

description:
TTC466-Rb-IgG-CUT&Tag
CUT&Tag


title: E21_B008639_B008701


title: SKNMC-EWS/FLI-CUT&Tag 2

description:
SKNMC-EWS/FLI-CUT&Tag
CUT&Tag


title: E4_B008639_B008701


title: E11_B008640_B010275


title: E3_B008639_B008701


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118517_HCKFFBGXB_1_C1_Plate1_Seq4_TAAGGCGA_GTAAGGAG_S3_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118525_HCKFFBGXB_1_C2_Plate1_Seq4_CGTACTAG_GTAAGGAG_S11_R1_001_MM_1


title: E4_B008649_B008703


title: E6_B008649_B008703


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118580_HCKFFBGXB_1_B9_Plate1_Seq4_AAGAGGCA_TATCCTCT_S66_R1_001_MM_1


title: EWS502-Rb-IgG-CUT&Tag 2

description:
EWS502-Rb-IgG-CUT&Tag
CUT&Tag

source_name: EWS-502 Ewing sarcoma cell line


title: E6_B008639_B008701


title: E7_B008649_B008703


title: EWS502-Rb-IgG-CUT&Tag 1

description:
EWS502-Rb-IgG-CUT&Tag
CUT&Tag


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118564_HCKFFBGXB_1_B7_Plate1_Seq4_CTCTCTAC_TATCCTCT_S50_R1_001_MM_1


title: E8_B008639_B008701


title: SKNMC-EWS/FLI-CUT&Tag 1

description:
SKNMC-EWS/FLI-CUT&Tag
CUT&Tag


title: N14_B008639_B008701


title: EWS502-EWS/FLI-CUT&Tag 1

description:
EWS502-EWS/FLI-CUT&Tag
CUT&Tag


title: N17_B008649_B008703


title: EWS502-EWS/FLI-CUT&Tag 2

description:
EWS502-EWS/FLI-CUT&Tag
CUT&Tag


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118540_HCKFFBGXB_1_B4_Plate1_Seq4_TCCTGAGC_TATCCTCT_S26_R1_001_MM_1


title: N20_B008639_B008701


title: N2_B008649_B008703


title: TC71-Rb-IgG-CUT&Tag 2

description:
TC71-Rb-IgG-CUT&Tag
CUT&Tag

source_name: TC71 Ewing sarcoma cell line


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118532_HCKFFBGXB_1_B3_Plate1_Seq4_AGGCAGAA_TATCCTCT_S18_R1_001_MM_1


title: F16_B008640_B010275


title: TC71-Rb-IgG-CUT&Tag 1

description:
TC71-Rb-IgG-CUT&Tag
CUT&Tag


title: N3_B008639_B008701


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118524_HCKFFBGXB_1_B2_Plate1_Seq4_CGTACTAG_TATCCTCT_S10_R1_001_MM_1


title: N5_B008649_B008703


title: N5_B008639_B008701


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118516_HCKFFBGXB_1_B1_Plate1_Seq4_TAAGGCGA_TATCCTCT_S2_R1_001_MM_1


title: N8_B008649_B008703


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118571_HCKFFBGXB_1_A8_Plate1_Seq4_CGAGGCTG_CTCTCTAT_S57_R1_001_MM_1


title: N9_B008639_B008701


title: TC71-EWS/FLI-CUT&Tag 2

description:
TC71-EWS/FLI-CUT&Tag
CUT&Tag


title: N7_B008649_B008703


title: TC71-EWS/FLI-CUT&Tag 1

description:
TC71-EWS/FLI-CUT&Tag
CUT&Tag


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118548_HCKFFBGXB_1_B5_Plate1_Seq4_GGACTCCT_TATCCTCT_S34_R1_001_MM_1


title: O14_B008649_B008703


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118555_HCKFFBGXB_1_A6_Plate1_Seq4_TAGGCATG_CTCTCTAT_S41_R1_001_MM_1


title: A673-Rb-IgG-CUT&Tag 2

description:
A673-Rb-IgG-CUT&Tag
CUT&Tag

source_name: A673 Ewing sarcoma cell line


title: N9_B008649_B008703


title: O12_B008649_B008703


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118563_HCKFFBGXB_1_A7_Plate1_Seq4_CTCTCTAC_CTCTCTAT_S49_R1_001_MM_1


title: F18_B008640_B010275


title: O2_B008649_B008703


title: A673-Rb-IgG-CUT&Tag 1

description:
A673-Rb-IgG-CUT&Tag
CUT&Tag


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118539_HCKFFBGXB_1_A4_Plate1_Seq4_TCCTGAGC_CTCTCTAT_S25_R1_001_MM_1


title: N22_B008649_B008703


title: A673-EWS/FLI-CUT&Tag 1

description:
A673-EWS/FLI-CUT&Tag
CUT&Tag


title: O3_B008649_B008703


title: O3_B008639_B008701


title: D18_D088224_B106233_S90


title: A673-EWS/FLI-CUT&Tag 2

description:
A673-EWS/FLI-CUT&Tag
CUT&Tag


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118547_HCKFFBGXB_1_A5_Plate1_Seq4_GGACTCCT_CTCTCTAT_S33_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118531_HCKFFBGXB_1_A3_Plate1_Seq4_AGGCAGAA_CTCTCTAT_S17_R1_001_MM_1


title: A673-EWS/FLI-Rescue-HiC 2

description: in situ Hi-C

data_processing:
Juicer software used to generate .hic files from concatenated fastq.gz files
Read alignment using BWA-MEM
Filter out chimeric reads, filter by map quality, filter out PCR duplicates using Picard Tools
Paired end reads in BAM files were converted to BEDPE format using SAMTools.
BEDPE files were then used to generate Hi-C Summary files (.hicsum) using the iHiC_BEDPE2HiCSummary function
Homer Hi-C analysis pipeline used to generate petag.FreqDistribution_1000.txt files from .hicsum files
DiffHiC R package used to generate differential interactions at 1mb and 20kb resolution (.bedpe files)
Loop lengths were calculated from 1mb lost and gained loops .bedpe files using excel to generate the Interaction_lengths.xlsx file
iHiC and TopDom software were used to call TAD domains and TAD boundaries from aligned and filtered Hi-C data
DiffHiC R package was used to calculate directionality statistic for 20kb regions in the genome from Hi-C data
Homer Hi-C analysis pipeline used to generate compartment eigenvectors (PC1 values) from EF-Endo, EF-KD and EF-Rescue Hi-C data
DeepTools used to convert bedgraph to bigwig and generate comparative bigwigs of ΔPC1 values for EF-Endo vs. EF-KD and EF-Rescue vs. EF-KD
Genome_build: hg19
Supplementary_files_format_and_content: See file type and description below under processed data files
Supplementary_files_format_and_content: A673_iLuc_197_30.hic: HiC contact matrix for EF-Endo
Supplementary_files_format_and_content: A673_iEF_197_30.hic: HiC contact matrix for EF-KD
Supplementary_files_format_and_content: A673_iEF_714_30.hic: HiC contact matrix for EF-Rescue
Supplementary_files_format_and_content: A673_iLuc197_petag.FreqDistribution_1000.txt: Interaction frequency over genomic distance in basepairs for EF-Endo
Supplementary_files_format_and_content: A673_iEF197_petag.FreqDistribution_1000.txt: Interaction frequency over genomic distance in basepairs for EF-KD
Supplementary_files_format_and_content: A673_iEF714_petag.FreqDistribution_1000.txt: Interaction frequency over genomic distance in basepairs for EF-Rescue
Supplementary_files_format_and_content: all_1_tmm.bedpe: all interaction counts for 1mb differential interactions between EF-Endo and EF-KD
Supplementary_files_format_and_content: si_tmm_1_gainedloops_10filt_0.05FDR_FC4_intrachromosomal.bedpe: gained interactions at 1mb resolution between EF-Endo and EF-KD
Supplementary_files_format_and_content: si_tmm_1_lostloops_10filt_0.05FDR_FC4_intrachromosomal.bedpe: lost interactions at 1mb resolution between EF-Endo and EF-KD
Supplementary_files_format_and_content: all_1R_tmm.bedpe: all interaction counts for 1mb differential interactions between EF-Rescue and EF-KD
Supplementary_files_format_and_content: si_tmm_1R_gainedloops_10filt_0.05FDR_FC4_intrachromosomal.bedpe: gained interactions at 1mb resolution between EF-Rescue and EF-KD
Supplementary_files_format_and_content: si_tmm_1R_lostloops_10filt_0.05FDR_FC4_intrachromosomal.bedpe: lost interactions at 1mb resolution between EF-Rescue and EF-KD
Supplementary_files_format_and_content: Interaction_lengths.xlsx: Excel file calculating lengths of gained and lost interactions
Supplementary_files_format_and_content: a673iluctagdir.20x40kb.PC1.bedGraph: PC1 bedgraph track for EF-Endo
Supplementary_files_format_and_content: a673ieftagdir.20x40kb.PC1.bedGraph: PC1 bedgraph track for EF-KD
Supplementary_files_format_and_content: a673714tagdir.20x40kb.PC1.bedGraph: PC1 bedgraph track for EF-Rescue
Supplementary_files_format_and_content: Endo_PC1_20X40.bw: PC1 bigwig track for EF-Endo
Supplementary_files_format_and_content: KD_PC1_20X40.bw: PC1 bigwig track for EF-KD
Supplementary_files_format_and_content: Rescue_PC1_20X40.bw: PC1 bigwig track for EF-Rescue
Supplementary_files_format_and_content: EndovsKD_PC1_subtract.bw: ΔPC1 bigwig track of EF-Endo PC1 minus EF-KD PC1
Supplementary_files_format_and_content: RescuevsKD_PC1_subtract.bw: ΔPC1 bigwig track of EF-Rescue PC1 minus EF-KD PC1
Supplementary_files_format_and_content: a673iluc20x40pc1_endokd_stable.bed: Stable compartments in EF-Endo vs EF-KD
Supplementary_files_format_and_content: a673iluc20x40pc1_endokd_AB.bed: B like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: a673iluc20x40pc1_endokd_BA.bed: A like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: a67371420x40pc1_rskd_stable.bed: Stable compartments in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: a67371420x40pc1_rskd_AB.bed: B like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: a67371420x40pc1_rskd_BA.bed: A like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: Stable_endoKD_DEG.txt: Differential gene expression in EF-Endo vs EF-KD for Stable compartments in EF-Endo vs EF-KD
Supplementary_files_format_and_content: AB_endoKD_DEG.txt: Differential gene expression in EF-Endo vs EF-KD for B like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: BA_endoKD_DEG.txt: Differential gene expression in EF-Endo vs EF-KD for A like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: Stable_RSKD_DEG.txt: Differential gene expression in EF-Rescue vs EF-KD for stable compartments in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: AB_RSKD_DEG.txt: Differential gene expression in EF-Rescue vs EF-KD for B like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: BA_RSKD_DEG.txt: Differential gene expression in EF-Rescue vs EF-KD for A like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: Stable_EndoKD_H3K27ac.txt: Differential H3K27ac enrichment in EF-Endo vs EF-KD for Stable compartments in EF-Endo vs EF-KD
Supplementary_files_format_and_content: AB_EndoKD_H3K27ac.txt: Differential H3K27ac enrichment in EF-Endo vs EF-KD for B like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: BA_EndoKD_H3K27ac.txt: Differential H3K27ac enrichment in EF-Endo vs EF-KD for A like compartment shifts in EF-Endo vs EF-KD
Supplementary_files_format_and_content: Stable_RSKD_H3K27ac.txt: Differential H3K27ac enrichment in EF-Rescue vs EF-KD for stable compartments in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: AB_RSKD_H3K27ac.txt: Differential H3K27ac enrichment in EF-Rescue vs EF-KD for B like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: BA_RSKD_H3K27ac.txt: Differential H3K27ac enrichment in EF-Rescue vs EF-KD for A like compartment shifts in EF-Rescue vs EF-KD
Supplementary_files_format_and_content: A673_EEts_uniq_comps.histogram.txt: Histogram analysis of PC1 values at conserved EWS/FLI sites
Supplementary_files_format_and_content: A673_EEts_MS_comps.histogram.txt: Histogram analysis of PC1 values at GGAA-microsatellite bound EWS/FLI sites
Supplementary_files_format_and_content: A673_EEts_nonMS_comps.histogram.txt: Histogram analysis of PC1 values at non-microsatellite bound EWS/FLI sites
Supplementary_files_format_and_content: a673_endo_EEts_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping conserved EWS/FLI sites for EF-Endo
Supplementary_files_format_and_content: a673_kd_EEts_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping conserved EWS/FLI sites for EF-KD
Supplementary_files_format_and_content: a673_rescue_EEts_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping conserved EWS/FLI sites for EF-Rescue
Supplementary_files_format_and_content: a673_endo_EEts_MS_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping GGAA-microsatellite bound EWS/FLI sites for EF-Endo
Supplementary_files_format_and_content: a673_kd_EEts_MS_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping GGAA-microsatellite bound EWS/FLI sites for EF-KD
Supplementary_files_format_and_content: a673_rescue_EEts_MS_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping GGAA-microsatellite bound EWS/FLI sites for EF-Rescue
Supplementary_files_format_and_content: a673_endo_EEts_nonMS_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping non-microsatellite bound EWS/FLI sites for EF-Endo
Supplementary_files_format_and_content: a673_kd_EEts_nonMS_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping non-microsatellite bound EWS/FLI sites for EF-KD
Supplementary_files_format_and_content: a673_rescue_EEts_nonMS_comp_uniq.bed: PC1 values for 20 kilobase regions directly overlapping non-microsatellite bound EWS/FLI sites for EF-Rescue
Supplementary_files_format_and_content: A673iLuc197.domain: TAD locations in EF-Endo
Supplementary_files_format_and_content: A673iEF197.domain: TAD locations in EF-KD
Supplementary_files_format_and_content: A673iEF714.domain: TAD locations in EF-Rescue
Supplementary_files_format_and_content: A673_iLuc197_p0.05.tadboundary.bedgraph: TAD boundaries in EF-Endo
Supplementary_files_format_and_content: A673_iEF197_p0.05.tadboundary.bedgraph: TAD boundaries in EF-KD
Supplementary_files_format_and_content: A673_iEF714_p0.05.tadboundary.bedgraph: TAD boundaries in EF-Rescue
Supplementary_files_format_and_content: EF-WTBoundaries.bed: TAD boundaries specific to EF-Endo and EF-Rescue only and not EF-KD
Supplementary_files_format_and_content: EF-KDBoundaries.bed: TAD boundaries specific to EF-KD only
Supplementary_files_format_and_content: StableBoundaries.bed: TAD boundaries common to EF-Endo, EF-KD and EF-Rescue
Supplementary_files_format_and_content: Directionality_Statistic_EndovsKD.txt: Directionality statistic calculated for EF-Endo and EF-KD
Supplementary_files_format_and_content: Directionality_Statistic_ResvsKD.txt: Directionality statistic calculated for EF-Rescue and EF-KD
Supplementary_files_format_and_content: EFEndovsEFKD_20kb_diffhicloops_tmmnormalized.bedpe: all interactions at 20kb resolution between EF-Endo and EF-KD
Supplementary_files_format_and_content: EFRescueVSEFKD_20kb_diffhicloops_tmmnormalized.bedpe: all interactions at 20kb resolution between EF-Rescue and EF-KD
Supplementary_files_format_and_content: si_tmm_20kb_EndovsKD_gainedloops_10filt_0.05FDR_FC4.bedpe: gained interactions at 20kb resolution for EF-Endo vs EF-KD
Supplementary_files_format_and_content: si_tmm_20kb_EndovsKD_lostloops_10filt_0.05FDR_FC4.bedpe: lost interactions at 20kb resolution for EF-Endo vs EF-KD
Supplementary_files_format_and_content: si_tmm_20kb_RescuevsKD_gainedloops_10filt_0.05FDR_FC4.bedpe: gained interactions at 20kb resolution for EF-Rescue vs EF-KD
Supplementary_files_format_and_content: si_tmm_20kb_RescuevsKD_lostloops_10filt_0.05FDR_FC4.bedpe: lost interactions at 20kb resolution for EF-Rescue vs EF-KD
Supplementary_files_format_and_content: all20_EndostableEnh_uniq.bedpe: all interactions at 20kb resolution overlapping Stable enhancers for EF-Endo vs EF-KD
Supplementary_files_format_and_content: all20_EndoLostEnh_uniq.bedpe: all interactions at 20kb resolution overlapping lost enhancers for EF-Endo vs EF-KD
Supplementary_files_format_and_content: all20_EndoGainedEnh_uniq.bedpe: all interactions at 20kb resolution overlapping gained enhancers for EF-Endo vs EF-KD
Supplementary_files_format_and_content: all20R_RescuestableEnh_uniq.bedpe: all interactions at 20kb resolution overlapping Stable enhancers for EF-Rescue vs EF-KD
Supplementary_files_format_and_content: all20R_RescueLostEnh_uniq.bedpe: all interactions at 20kb resolution overlapping lost enhancers for EF-Rescue vs EF-KD
Supplementary_files_format_and_content: all20R_RescueGainedEnh_uniq.bedpe: all interactions at 20kb resolution overlapping gained enhancers for EF-Rescue vs EF-KD
Supplementary_files_format_and_content: up20_anchors_DEG.txt: Differential gene expression for genes overlapping gained loop anchors for EF-Endo vs. EF-KD
Supplementary_files_format_and_content: up20R_anchors_DEG.txt: Differential gene expression for genes overlapping gained loop anchors for EF-Rescue vs. EF-KD
Supplementary_files_format_and_content: down20_anchors_DEG.txt: Differential gene expression for genes overlapping lost loop anchors for EF-Endo vs. EF-KD
Supplementary_files_format_and_content: down20R_anchors_DEG.txt: Differential gene expression for genes overlapping lost loop anchors for EF-Rescue vs. EF-KD
Supplementary_files_format_and_content: homerResults_gained20kb_endovskd.html: Homer motif enrichment containing top motifs occupied by gained interactions at 20 kb resolution for EF-Endo vs EF-KD
Supplementary_files_format_and_content: homerResults_gained20kb_rescuevskd.html: Homer motif enrichment containing top motifs occupied by gained interactions at 20 kb resolution for EF-Rescue vs EF-KD
Supplementary_files_format_and_content: all20EF_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD intersecting with a conserved EWS/FLI peak
Supplementary_files_format_and_content: all20REF_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD intersecting with a conserved EWS/FLI peak
Supplementary_files_format_and_content: 1_all20noEF_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD intersecting with no conserved EWS/FLI peak
Supplementary_files_format_and_content: 1_all20RnoEF_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD intersecting with no conserved EWS/FLI peak
Supplementary_files_format_and_content: 2_all20_bothEF_MSNMS_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at one anchor and to an EWS/FLI peak bound to a non-microsatellite binding site at the second anchor of the loop/interaction
Supplementary_files_format_and_content: 2_all20R_bothEF_MSNMS_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at one anchor and to an EWS/FLI peak bound to a non-microsatellite binding site at the second anchor of the loop/interaction
Supplementary_files_format_and_content: 3_all20EF_bothMS_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD intersecting with a conserved EWS/FLI peak bound to GGAA-microsatellite at both loop anchors
Supplementary_files_format_and_content: 3_all20REF_bothMS_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD intersecting with a conserved EWS/FLI peak bound to GGAA-microsatellite at both loop anchors
Supplementary_files_format_and_content: 4_all20_xorEFNMS_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD with one and only one anchor intersecting with a conserved EWS/FLI peak bound to non-microsatellite sites
Supplementary_files_format_and_content: 4_all20R_xorEFNMS_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD with one and only one anchor intersecting with a conserved EWS/FLI peak bound to non-microsatellite sites
Supplementary_files_format_and_content: 5_all20_bothEFNMS_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD with both anchors intersecting with a conserved EWS/FLI peak bound to non-microsatellite sites
Supplementary_files_format_and_content: 5_all20R_bothEFNMS_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD with both anchors intersecting with a conserved EWS/FLI peak bound to non-microsatellite sites
Supplementary_files_format_and_content: 6_all20_EFMSonly_uniq.bedpe: all 20kb interactions between EF-Endo and EF-KD with one and only one anchor intersecting with a conserved EWS/FLI peak bound to GGAA-microsatellite site
Supplementary_files_format_and_content: 6_all20R_EFMSonly_uniq.bedpe: all 20kb interactions between EF-Rescue and EF-KD with one and only one anchor intersecting with a conserved EWS/FLI peak bound to GGAA-microsatellite site
Supplementary_files_format_and_content: 2_all20_bothEF_MSNMS_sig.bedpe: Significant 20kb interactions between EF-Endo and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at one anchor and to an EWS/FLI peak bound to a non-microsatellite binding site at the second anchor of the loop/interaction
Supplementary_files_format_and_content: 2_all20_bothEF_MSNMS_sig_iLucintraTAD.bed: Significant 20kb interaction region between EF-Endo and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at one anchor and to an EWS/FLI peak bound to a non-microsatellite binding site at the second anchor that exist within a TAD region
Supplementary_files_format_and_content: 2_all20R_bothEF_MSNMS_sig.bedpe: Significant 20kb interactions between EF-Rescue and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at one anchor and to an EWS/FLI peak bound to a non-microsatellite binding site at the second anchor of the loop/interaction
Supplementary_files_format_and_content: 2_all20R_bothEF_MSNMS_sig_714intraTAD.bed: Significant 20kb interaction region between EF-Rescue and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at one anchor and to an EWS/FLI peak bound to a non-microsatellite binding site at the second anchor that exist within a TAD region
Supplementary_files_format_and_content: 3_all20EF_bothMS_sig.bedpe: Significant 20kb interactions between EF-Endo and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at both anchors
Supplementary_files_format_and_content: 3_all20EF_bothMS_sig_iLucintraTAD.bed: Significant 20kb interaction regions for EF-Endo vs EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at both anchors that exist within a TAD region
Supplementary_files_format_and_content: 3_all20REF_bothMS_sig.bedpe: Significant 20kb interactions between EF-Rescue and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at both anchors
Supplementary_files_format_and_content: 3_all20REF_bothMS_sig_714intraTAD.bed: Significant 20kb interaction regions between EF-Rescue and EF-KD intersecting with an EWS/FLI peak bound to GGAA-microsatellite at both anchors that exist within a TAD region
Supplementary_files_format_and_content: ggaa0to10_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 0-10 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa0to10_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 0-10 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa11to20_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 11-20 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa11to20_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 11-20 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa21to30_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 21-30 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa21to30_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 21-30 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa31to40_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 31-40 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa31to40_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 31-40 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa41up_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with > 40 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa41up_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with >40 total GGAA repeats (distance between GGAA repeats < 20bp) in the reference genome
Supplementary_files_format_and_content: ggaa1to5_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 1-5 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa1to5_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 1-5 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa6to10_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 6-10 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa6to10_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 6-10 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa11to15_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 11-15 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa11to15_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 11-15 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa16to20_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 16-20 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa16to20_diR_uniq.bedpe: differential interactions for EF-Rescue vs. EF-KD at 20kb resolution overlapping with 16-20 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa21to25_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with 21-25 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome
Supplementary_files_format_and_content: ggaa25up_di_uniq.bedpe: differential interactions for EF-Endo vs. EF-KD at 20kb resolution overlapping with >25 consecutive GGAA repeats (distance between GGAA repeats =0bp ) in the reference genome

growth_protocol: A673 cells were cultured in DMEM with L-Glutamine, supplemented with 10% FBS, 1% PSQ, 1% sodium pyruvate for 2-3 days, followed by selection in the same media supplemented with 2μg/mL puromycin, and 150μg/mL hygromycin B at 37ºC and 5% CO2.

extract_protocol:
AMPure XP bead extraction
in situ Hi-C (high throughput chromatin conformation capture)


title: D20_D088224_B106233_S92


title: D4_D088224_B106233_S76


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118523_HCKFFBGXB_1_A2_Plate1_Seq4_CGTACTAG_CTCTCTAT_S9_R1_001_MM_1


title: D8_D088224_B106233_S80


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118706_HCKFFBGXB_1_H12_Plate2_Seq4_TCGACGTC_TCTCTCCG_S192_R1_001_MM_1


title: E18_D088224_B106233_S114


title: A673-EWS/FLI-Rescue-HiC 1

description: in situ Hi-C


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118698_HCKFFBGXB_1_H11_Plate2_Seq4_TGCAGCTA_TCTCTCCG_S184_R1_001_MM_1


title: A673-EWS/FLI-KD-HiC 2

description: in situ Hi-C


title: O15_B008639_B008701


title: A673-EWS/FLI-Endo-HiC 2

description: in situ Hi-C


title: E11_D088224_B106233_S107


title: A673-EWS/FLI-KD-HiC 1

description: in situ Hi-C


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118602_HCKFFBGXB_1_H11_Plate1_Seq4_GCTCATGA_TCTCTCCG_S88_R1_001_MM_1


title: E20_D088224_B106233_S116


title: E16_D088224_B106233_S112


title: A673-EWS/FLI-Endo-HiC 1

description: in situ Hi-C


title: PTB2539-IAA4H-R4-T1

city: Worcester

first: Anne-Laure

last: Valton

state: MA

address: 368 Plantation St

institute: University of Massachusetts Medical School

description:
Tir1 is inserted. Add AID tag in N term and C term of RPB1
PTB2539-IAA.hg19.mapq_30.1000.mcool
PTB2539-IAA-pool-800000000.mcool

data_processing:
Fastq files were mapped to the hg19 genome using the distiller pipeline (github.com/open2c/distiller-nf ). Hi-C interaction data was stored in the cooler format (Abdennur, N., and Mirny, L. (2019)).
Replicates were combined into multires.cool file
Genome_build: hg19 human genome
Supplementary_files_format_and_content: Multiresolution cooler files (multires.cool) containing pairwise interactions

source_name: HAP1 cells

growth_protocol: HAP1 cells (and the derived cells lines) were cultured at 37C with 5% CO2 in IMDM GlutaMAX™ Supplement (Gibo, 31980097) with 10% FBS (Gibco, 16000069), 1% Penicillin-Streptomycin (Gibco, 15140122).

extract_protocol:
5-10M formaldehyde cross-linked cells were lysed and digested overnight at 37°C with 400 units of DpnII (NEB). Next, the DNA ends were marked with biotin-14-dATP (Thermo Fisher Scientific #19524016) for 4 hours at 23°C and ligated for 4 hours at 16°C. To remove proteins and reverse crosslink, DNA was treated with proteinase K overnight at 65°C. DNA was then purified using phenol:chloroform and biotin was removed from unligated ends. Ligation products were fragmented by sonication to an average size of 200bp and size selected with Ampure XP beads (Beckman Coulter, # A63880) to fragments ranging from 100 to 350 bp.
End repair was performed on the DNA fragments to obtain blunt ends and biotinylated ligation products were purified using streptavidin beads (Thermo Fisher Scientific #65001). dA-tailing was then performed and the TrueSeq DNA LT kits Set A (Illumina, #15041757) was used for adapter ligation and PCR amplification. PCR primers were removed using Ampure XP beads. The Hi-C libraries were sequenced using 50 bp paired end reads on Illumina HiSeq4000.

treatment_protocol: For auxin treatment: 500uM auxin. For siRNA treatment: 40nM for 72H.

value: auxin

tag: enzyme

value: DpnII

value: RPB1-AID, TIR1


title: E6_D088224_B106233_S102


title: E3_D088224_B106233_S99


title: E22_D088224_B106233_S118


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118801_HCKFFBGXB_1_G12_Plate3_Seq4_ATCTCAGG_GAGCCTTA_S287_R1_001_MM_1


title: PTB2539-IAA4H-R3-T1


title: A3_B008640_B010275


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118793_HCKFFBGXB_1_G11_Plate3_Seq4_GCTCATGA_GAGCCTTA_S279_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118705_HCKFFBGXB_1_G12_Plate2_Seq4_TCGACGTC_CGTCTAAT_S191_R1_001_MM_1


title: F2_B008640_B010275


title: E10_D088224_B106233_S106


title: F4_B008640_B010275


title: PTB2539-IAA4H-R2-T1


title: E7_D088224_B106233_S103


title: PTB2539-IAA4H-R1-T1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118697_HCKFFBGXB_1_G11_Plate2_Seq4_TGCAGCTA_CGTCTAAT_S183_R1_001_MM_1


title: E9_D088224_B106233_S105


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118601_HCKFFBGXB_1_G11_Plate1_Seq4_GCTCATGA_CGTCTAAT_S87_R1_001_MM_1


title: F16_D088224_B106233_S136


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118696_HCKFFBGXB_1_F11_Plate2_Seq4_TGCAGCTA_CTAAGCCT_S182_R1_001_MM_1


title: F11_D088224_B106233_S131


title: F15_D088224_B106233_S135


title: PTB2539-NT-R4-T1

description:
Tir1 is inserted. Add AID tag in N term and C term of RPB1
PTB2539-NT.hg19.mapq_30.1000.mcool
PTB2539-NT-pool-800000000.mcool

value: non-treated


title: PTB2539-NT-R3-T1


title: F19_D088224_B106233_S139


title: F13_D088224_B106233_S133


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118792_HCKFFBGXB_1_F11_Plate3_Seq4_GCTCATGA_AAGGCTAT_S278_R1_001_MM_1


title: F21_D088224_B106233_S141


title: F2_D088224_B106233_S122


title: PTB2539-NT-R2-T1


title: F1_D088224_B106233_S121


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118608_HCKFFBGXB_1_F12_Plate1_Seq4_ATCTCAGG_CTAAGCCT_S94_R1_001_MM_1


title: PTB2539-NT-R1-T1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118600_HCKFFBGXB_1_F11_Plate1_Seq4_GCTCATGA_CTAAGCCT_S86_R1_001_MM_1


title: F5_B008640_B010275


title: Hap1-WT-IAA4HW48-R1-T1

description:
Original WT HAP1 cell line from Horizon. Male Chronic Myelogenous Leukemia (CML) cell line KBM-7.
Hap1-WT-combined.mcool

value: wild-type HAP1


title: H3_B008640_B010275


title: H4_B008640_B010275


title: H7_B008640_B010275


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118703_HCKFFBGXB_1_E12_Plate2_Seq4_TCGACGTC_AAGGAGTA_S189_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118695_HCKFFBGXB_1_E11_Plate2_Seq4_TGCAGCTA_AAGGAGTA_S181_R1_001_MM_1


title: Hap1-WT-IAA4HW24-R1-T1


title: Hap1-WT-IAA4HW4-R1-T1


title: A19_B008640_B010275


title: F17_D088224_B106233_S137


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118599_HCKFFBGXB_1_E11_Plate1_Seq4_GCTCATGA_AAGGAGTA_S85_R1_001_MM_1


title: A15_B008640_B010275


title: Hap1-WT-IAA48H-R2-T1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118702_HCKFFBGXB_1_D12_Plate2_Seq4_TCGACGTC_ACTGCATA_S188_R1_001_MM_1


title: A9_B008648_B008695


title: B18_B008648_B008695


title: B15_B008648_B008695


title: B14_B008648_B008695


title: B16_B008648_B008695


title: Hap1-WT-IAA48H


title: Hap1-WT-IAA24H


title: B20_B008648_B008695


title: B22_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118694_HCKFFBGXB_1_D11_Plate2_Seq4_TGCAGCTA_ACTGCATA_S180_R1_001_MM_1


title: B1_B008648_B008695


title: Hap1-WT-IAA4H-R2-T1


title: Hap1-WT-IAA4H


title: Hap1-WT-NT-R2-T1


title: B3_B008640_B010275


title: B3_B008648_B008695


title: B20_B008640_B010275


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118598_HCKFFBGXB_1_D11_Plate1_Seq4_GCTCATGA_ACTGCATA_S84_R1_001_MM_1


title: B6_B008648_B008695


title: B2_B008648_B008695


title: B4_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118797_HCKFFBGXB_1_C12_Plate3_Seq4_ATCTCAGG_CCTAGAGT_S283_R1_001_MM_1


title: C15_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118701_HCKFFBGXB_1_C12_Plate2_Seq4_TCGACGTC_GTAAGGAG_S187_R1_001_MM_1


title: C19_B008648_B008695


title: C18_B008648_B008695


title: C1_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118597_HCKFFBGXB_1_C11_Plate1_Seq4_GCTCATGA_GTAAGGAG_S83_R1_001_MM_1


title: Hap1-WT-NT


title: C22_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118796_HCKFFBGXB_1_B12_Plate3_Seq4_ATCTCAGG_TTCTAGCT_S282_R1_001_MM_1


title: C21_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118606_HCKFFBGXB_1_D12_Plate1_Seq4_ATCTCAGG_ACTGCATA_S92_R1_001_MM_1


title: CkoCT442-TAF5Lsg2-3-IAA-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
TAF5L-clones-IAA.hg19.mapq_30.1000.mcool

value: endogenous CTCF KO, CTCF-AID, TIR1, TAF5L KO


title: CkoCT442-TAF5Lsg2-7-NT-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
TAF5L-clones-NT.hg19.mapq_30.1000.mcool


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118605_HCKFFBGXB_1_C12_Plate1_Seq4_ATCTCAGG_GTAAGGAG_S91_R1_001_MM_1


title: C3_B008648_B008695


title: CkoCT442-DDX55sg2-7-IAA-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
DDX55-clones-IAA.hg19.mapq_30.1000.mcool

value: endogenous CTCF KO, CTCF-AID, TIR1, DDX55 heterozygous KO


title: G22_B008648_B008695


title: CkoCT442-TAF5Lsg2-3-NT-R1-T1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118604_HCKFFBGXB_1_B12_Plate1_Seq4_ATCTCAGG_TATCCTCT_S90_R1_001_MM_1


title: G2_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118788_HCKFFBGXB_1_B11_Plate3_Seq4_GCTCATGA_TTCTAGCT_S274_R1_001_MM_1


title: G3_B008648_B008695


title: C18_B008640_B010275


title: G8_B008648_B008695


title: G9_B008648_B008695


title: CkoCT442-DDX55sg2-B-IAA-R1-T1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118596_HCKFFBGXB_1_B11_Plate1_Seq4_GCTCATGA_TATCCTCT_S82_R1_001_MM_1


title: CkoCT442-DDX55sg2-7-NT-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
DDX55-clones-NT.hg19.mapq_30.1000.mcool


title: CkoCT442-TAF5Lsg2-7-IAA-R1-T1


title: CkoCT442-DDX55sg2-B-NT-R1-T1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118607_HCKFFBGXB_1_E12_Plate1_Seq4_ATCTCAGG_AAGGAGTA_S93_R1_001_MM_1


title: CkoCT442-AAVS1sg2-4-IAA-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
CkoCT442-AAVS1-IAA-pool.mcool

value: endogenous CTCF KO, CTCF-AID, TIR1, AAVS1 locus mutation


title: H14_B008648_B008695


title: H18_B008648_B008695


title: H17_B008648_B008695


title: CkoCT442-AAVS1sg2-4-NT-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
CkoCT442-AAVS1-NT-pool.mcool


title: H11_B008648_B008695


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118603_HCKFFBGXB_1_A12_Plate1_Seq4_ATCTCAGG_CTCTCTAT_S89_R1_001_MM_1


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118699_HCKFFBGXB_1_A12_Plate2_Seq4_TCGACGTC_CTCTCTAT_S185_R1_001_MM_1


title: G6_B008648_B008695


title: H22_B008648_B008695


title: C19_B008640_B010275


title: CkoCT442-IAA-si-TAF5L-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
siTAF5L-IAA.hg19.mapq_30.1000.mcool

value: auxin, siTAF5L

value: endogenous CTCF KO, CTCF-AID, TIR1


title: HFD-fed KO2

city: Shanghai

first: Xing

last: Ming

state: Shanghai

address: Huangpu

department: Department of Endocrine and Metabolic Diseases

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Sequencing was performed using an Illumina NextSeq500 to generate 100 bp paired-end reads.
Quality trimmed reads were mapped onto the mouse genome (mm10) by Tophat2 (Kim D, et al, Genome Biol, 2013).
Ggene expression in terms of Fragments Per Kilobase of transcript per Million mapped reads (FPKM) of genes overlapping with gene annotations in Ensembl release 96 was calculated by Cufflinks (Trapnell C, et al, Nat Biotechnol, 2010).
Differentially expressed transcripts were detected using the R/Bioconductor package DESeq (Anders S and Huber W, Genome Biology, 2010).
Genome_build: mm10

source_name: Pancreatic islets

extract_protocol:
G solution was prepared by adding 0.25% (wt./vol.) BSA into HBSS (Invitrogen, USA). Collagenase P (Roche, Switzerland) was dissolved in G solution to obtain 0.8 mg/ml collagenase solution. Ice cold collagenase solution (around 3 ml) was injected into the pancreas of anesthetized mouse through the joint site of the hepatic duct and the cystic duct of the common bile duct. Pancreas was removed and infused in another 3 ml 0.8 mg/ml ice cold collagenase solution in centrifuge tube. Pancreas was then transferred to a 37 ℃ water bath and gentle shaken (200 rpm) for 8 min. Pancreas was shaken vigorously for 10 s at the end of the digestion. Digested tissues were washed with 10 ml G solution three times and filtered with 500 µm mesh. Tissues were resuspended with G solution and gradient centrifuged with Histopaque 1119, 1083 and 1077 (Sigma-Aldrich, USA). Islet layer was poured into a 70 µm cell strainer. Finally, the strainer was turned upside down and rinsed with RPMI 1640 medium on a petri dish to capture the islets.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The male pancreatic beta cell selective Sirt3 knockout mice and wild type mice were fed with standard diet (6.2% fat, Teklad, USA) or high fat diet (60% cal from fat, Research Diets, USA) for 36-week.

value: Pancreatic islets

tag: gender/age

value: High fat diet feeding

tag: treatment period

value: 5-week standard diet feeding after birth, followed by 36-week high fat diet feeding


title: CkoCT442-NT-si-TAF5L-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
siTAF5L-NT.hg19.mapq_30.1000.mcool

value: non-treated, siTAF5L


title: G7_B008648_B008695

value: patient-derived-xenograft

value: tumor

value: NSG


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118595_HCKFFBGXB_1_A11_Plate1_Seq4_GCTCATGA_CTCTCTAT_S81_R1_001_MM_1

value: bone marrow

value: 12 - 19 weeks

value: wild type


title: HFD-fed KO3

value: 6-week standard diet feeding after birth, followed by 36-week high fat diet feeding


description:
For kinship info see Metadata_Seq4
CountMatrix_Seq4.csv
BSSE_QGF_118787_HCKFFBGXB_1_A11_Plate3_Seq4_GCTCATGA_TCGACTAG_S273_R1_001_MM_1


title: H2_B008648_B008695


title: H19_B008648_B008695


title: CkoCT442-IAA-si-TAF5L-R2-T1

value: DpnII


title: K9_B008648_B008695


title: H4_B008648_B008695


title: HFD-fed WT1

value: 4-week standard diet feeding after birth, followed by 36-week high fat diet feeding


title: CkoCT442-IAA-si-DDX55-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
siDDX55-IAA.hg19.mapq_30.1000.mcool

value: auxin, siDDX55


title: CkoCT442-NT-si-DDX55-R2-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
siDDX55-NT.hg19.mapq_30.1000.mcool

value: non-treated, siDDX55


title: K5_B008648_B008695


title: CkoCT442-NT-si-TAF5L-R2-T1


title: H3_B008648_B008695


title: HFD-fed KO1


title: K3_B008648_B008695


title: H13_B008648_B008695


title: H15_B008648_B008695


title: C3_B008640_B010275


title: L11_B008648_B008695


title: L12_B008648_B008695


title: CkoCT442-IAA-si-DDX55-R2-T1


title: HFD-fed WT3


title: STD-fed KO3

value: Standard diet feeding

value: Continuously fed with standard diet


title: L14_B008648_B008695


title: CkoCT442-NT-si-DDX55-R1-T1

value: endogenous CTCF KO, CTCF-AID, TIR1


title: L16_B008648_B008695


title: L18_B008648_B008695


title: HFD-fed WT2

value: Pancreatic islets

value: High fat diet feeding


title: K4_B008648_B008695


title: L22_B008648_B008695


title: STD-fed KO2


title: STD-fed KO1


title: L4_B008648_B008695


title: CkoCT442-NT-si-ctrl-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
siCTRL-NT.hg19.mapq_30.1000.mcool

value: non-treated, siCTRL


title: STD-fed WT2


title: CkoCT442-IAA-si-ctrl-R2-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
siCTRL-IAA.hg19.mapq_30.1000.mcool

value: auxin, siCTRL


title: STD-fed WT3


title: C4_B008640_B010275

value: patient-derived-xenograft

value: tumor


title: M15_B008648_B008695

value: NSG


title: CkoCT442-IAA-si-ctrl-R1-T1


title: STD-fed WT1


title: Female LPS, biol rep 3

city: Minneapolis

first: Andrew

middle: Traver

last: Rajczewski

state: MN

institute: University of Minnesota

data_processing:
Raw reads were screened for low-quality bases and adapter contamination with FastQC version 0.11.7 and cleaned of low-quality bases and adapter contamination with Trimmomatic version 0.33
Surviving reads were then mapped to the mouse genome build GRCm38.p6, downloaded from Ensembl release 98 with HISAT2
The resulting BAM files were filtered for reads with a mapping quality score of less than 60, keeping only uniquely mapped reads. These filtered BAM files were then sorted by read name and a counts matrix was generated with featureCounts
The scripts for performing the quality control, mapping, filtering, and generation of a counts matrix are available in a suite of scripts called CHURP
The counts matrix was analyzed with edgeR (29) in the R statistical computing environment
Assembly: GRCm38.p6
Supplementary files format and content: counts matrix

source_name: Lung

extract_protocol:
RNA was isolated from harvested Type II pneumpocytes using Qiagen AllPrep kit
RNA samples were converted to Illumina sequencing libraries using SMARTer Stranded Total RNA-Seq Kit

value: Lung

value: Type II  pneumocyte

value: WT

tag: Sex

value: female

value: lipopolysaccharide


title: CkoCT442-G1-IAA-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
G1-IAA.hg19.mapq_30.1000.mcool

value: auxin

value: DpnII


title: CkoCT442-NT-si-ctrl-R2-T1


title: M13_B008648_B008695


title: M20_B008648_B008695


title: Female LPS, biol rep 2


title: Female LPS, biol rep 1


title: L6_B008648_B008695


title: M21_B008648_B008695


title: A20_B008649_B008703


title: M2_B008648_B008695


title: Female Control, biol rep3

value: PBS (control)


title: L8_B008648_B008695


title: CkoCT442-G1-IAA-R2-T1


title: A22_B008649_B008703


title: CkoCT442-G1-NT-R2-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
G1-NT.hg19.mapq_30.1000.mcool

value: non-treated


title: B10_B008639_B008701


title: Female Control, biol rep2


title: A2_B008649_B008703


title: A2_B008639_B008701


title: CkoCT442-G1-NT-R1-T1

value: endogenous CTCF KO, CTCF-AID, TIR1


title: A4_B008649_B008703


title: B17_B008639_B008701


title: B19_B008649_B008703


title: CkoCT442-IAA-R4-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
CkoCT442-IAA-pool.mcool
CkoCT442-IAA-pool-500000000.mcool


title: CkoC442-IAA48H-R2-T1


title: A21_B008639_B008701


title: CkoC442-IAA48H-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
CkoCT442-IAA-pool.mcool
CkoC442-IAA48H-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoCT442-IAA-pool-500000000.mcool


title: B13_B008639_B008701


title: CkoCT442-IAA-R5-T1


title: D18_B008640_B010275


title: CkoCT442-IAA-R3-T1


title: B14_B008649_B008703


title: B7_B008639_B008701


title: C16_B008649_B008703


title: CkoCT442-NT-R5-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
CkoCT442-NT-pool.mcool
CkoCT442-NT-pool-500000000.mcool


title: B15_B008649_B008703


title: Male LPS, biol rep 3

value: male


title: E8_B008649_B008703


title: CkoCT442-NT-R3-T1


title: Male LPS, biol rep 2


title: B22_B008639_B008701


title: B12_B008649_B008703


title: B5_B008639_B008701


title: Male LPS, biol rep 1


title: C15_B008639_B008701


title: Male Control, biol rep 3


title: D19_B008640_B010275


title: F19_B008649_B008703


title: CD69negDP_Rad21_ChIPseq_rep2

city: London

first: Ya

last: Guo

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Basecalls performed using CASAVA-1.82 or CASAVA-1.84
Hi-C Sequenced data (100 bp paired-end) were mapped using the bowtie 2 (version 2.3.2) and then processed by the HiC-Pro (version 2.7.8) with default settings. After converting using the script, HiC-Pro hicpro2juicebox.sh, valid chromatin contacts were normalized and .hic files were created by the Juicer Pre (Juicer tools version 0.7.5).
ChIP-seq raw reads (50 bp single-end) were mapped using the bowtie (version 1.0.0). After alignment and duplicates removal, peaks were identified using MACS2 (version 2.1.0).
Assembly: mm9
Supplementary files format and content: .hic files were created by the Juicer Pre (Juicer tools version 0.7.5)
Supplementary files format and content: Peak files were generated using MACS2 (version 2.1.0)

source_name: primary CD69-CD4+CD8+ cells

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min at room temperature and then the reaction was quenched with 125 mM glycine at room temperature for 5 minutes. [Hi-C] Chromatin was digested with 100 units of MboI overnight at 37 °C while shaking at 900 rpm. After overnight incubation, 100 units of MboI were added for the second-round digestion for 2-4 hours. The DNA polymerase I, large (Klenow) fragment, was used to fill in MboI-digested fragment overhangs in the presence of biotin-labelled dATP. Fragment ends were then ligated with 4000 units of T4 DNA ligase by incubating at room temperature for 4-6 h with rotation at 12 rpm. After ligation, cell nuclei were collected by centrifugation, and chromatin was reverse crosslinked overnight at 65 °C. RNase A was used to remove RNA after decrosslinking. Genomic DNA was isolated and precipitated by sodium acetate-ethanol precipitation, and then purified DNA was sheared for 8 min using a sonicator (Bioruptor) with high power setting, and 30 seconds on and 30 seconds off per minute. DNA fragments in the range of 300–500 bp were then selected using the AMPure XP beads (Beckmann Coulter). [ChIP-seq] Cell nuclei were isolated using a RIPA lysis buffer (10mM Tris pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 0.1% SDS, 0.15M NaCl, 1X Roche protease inhibitors). Following isolation of cell nuclei, genomic DNA was sonicated in a high-salt RIPA buffer (10mM Tris pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1% SDS, 0.8M NaCl, 1X Roche protease inhibitors) for 30 minutes on a sonicator (Bioruptor) with high power setting, and 30 seconds on and 30 seconds off per minute. Immunoprecipitation was performed in a RIPA buffer (10mM Tris pH7.5, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 0.1% SDS, 0.15M NaCl, 1X Roche protease inhibitors), and then antibody-antigen complex was precipitated using Dynabead Protein G (Thermo Fisher). Protein was digested using Proteinase K, and then DNA-protein complex was reverse crosslinked overnight at 65 °C. RNase A was added to remove RNA after decrosslinking.
[Hi-C] After biotin-labelled DNA fragments were captured on Dynabeads MyOne Streptavidin T1 (Thermo Fisher), fragment ends were repaired in a mixture of enzymes containing T4 polynucleotide kinase, T4 DNA polymerase I and DNA polymerase I, large (Klenow) fragment, and then NEBNext adaptors for Illumina sequencing were ligated to the dA-tailed fragment ends. After the USER enzyme digestion, NEBNext oligos for Illumina sequencing were used for PCR for library preparation. A PCR titration was firstly carried out to determine the lowest number of PCR cycles (8-10 cycles in this work). Final Hi-C sequencing libraries were quantified and checked for size distribution using Bioanalyzer (Agilent Technologies), and then sequenced on an HiSeq 2500 sequencer (Illumina). [ChIP-seq] ChIP-seq library preparation were carried out using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (NEB) according to the manufacturer’s protocol.

value: wild type

value: thymus

tag: antibody


title: CkoCT442-NT-R4-T1


title: CD69negDP_Rad21_ChIPseq_rep1

tag: tissue


title: Female Control, biol rep1

tag: cell type


title: F5_B008649_B008703

tag: strain


title: F4_B008649_B008703


title: Male Control, biol rep 2


title: CkoC44-NT-R2-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
CkoC44-NO-TIR1-pool.mcool

value: endogenous CTCF KO, CTCF-AID


title: F13_B008639_B008701

value: patient-derived-xenograft


title: F10_B008649_B008703

value: tumor


title: F17_B008639_B008701

value: NSG


title: Male Control, biol rep 1

value: Lung


title: CD69negDP_CTCF_ChIPseq

value: CTCF


title: E14_B008640_B010275


title: CkoC442-NT-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
CkoCT442-NT-pool.mcool
CkoC442-NT-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoCT442-NT-pool-500000000.mcool


title: F1_B008639_B008701


title: ChIP-442-IAA-TAF5L-R3-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
IAA-TAF5L-narrowPeaks-sort-merge-with-strength.bed

data_processing:
Fastq files were processed using the nf-core/chipseq pipeline, version 1.1.0 : https://github.com/nf-core/chipseq (Ewels, 2020)
BigWig files scaled to 1 million mapped reads were created
Genome_build: hg19 human genome
Supplementary_files_format_and_content: BigWig files using the nf-core/chipseq pipeline, version 1.1.0 : https://github.com/nf-core/chipseq (Ewels, 2020)
Supplementary_files_format_and_content: peak text files

extract_protocol:
Cells were fixed in the plates with 1% formaldehyde. Each 5 million cells were resuspended in 1 mL of hypotonic lysis buffer (20mM TRIS HCl pH8.0, 85mM KCl, 0.5% IGEPAL, 1X HALT protease inhibitor) and incubated 15 min on ice. Cells were then spun down 5 min, 500g, 4C, supernatant was removed and 5 million cells were resuspended in 300 uL of sonication buffer (20mM TRIS HCl pH8.0, 0.2% SDS, 0.5% Sodium Deoxycholate, 1X HALT protease inhibitor). Cells were sonicated using a bioruptor pico, at 4C, following the manufacturer instructions and with the following settings: 30 s on, 30 s off, for 15 cycles. 300 uL of chromatin from 5M cells was diluted with 1 200 uL of dilution IP buffer (20 mM TRIS HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% TRITON, 1X HALT protease inhibitor) and specific antibody was added.
For end repair, 35 μL of sample were transferred to a PCR tube, then 15 μL of the end-repair mix (1X NEB ligation buffer (NEB B0202S), 17.5 mM dNTP mix, 7.5 U T4 DNA polymerase (NEBM0203L), 25 U T4 polynucleotide kinase (NEB M0201S), 2.5 U Klenow polymerase Polymerase I (NEB M0210L)) were added. The reactions were then incubated at 37°C for 30 minutes, followed by incubation at 75°C for 20 minutes to inactivate Klenow polymerase. An ampure beads purification was then performed (1.6X) and DNA was eluted in 41 uL of water. For A-tailing, dATP was added to the 3’ ends by adding 9 μL of A-tailing mix (5 μL NEB buffer 2.1, 1 μL of 1 mM dATP, 5 U Klenow exo (NEB M0212S)) to the 41 μL of DNA sample from the previous step. The reaction was incubated in a PCR machine at 37°C for 30 minutes, then at 65°C for 20 minutes. An ampure beads purification was then performed (1.6X) and DNA was eluted in 40 uL of water. The TrueSeq DNA LT kits Set A (Illumina, #15041757) was used for adapter ligation and PCR amplification. PCR primers were removed using Ampure XP beads.
The ChIP-seq libraries were sequenced using 50 bp paired end reads on Illumina HiSeq4000.

treatment_protocol: For auxin treatment: 500uM auxin.

value: TAF5L (Proteintech, #19274-1-AP)


title: CkoC44-IAA48H-R2-T1


title: G17_B008639_B008701


title: F20_B008639_B008701


title: CkoC44-IAA48H-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
CkoC44-IAA48H-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoC44-NO-TIR1-pool.mcool


title: CD69negDP_Input_ChIPseq_rep1


title: F20_B008649_B008703


title: CD69negDP_H3K27ac_ChIPseq_rep2


title: CD69negDP_DKO_HIC_rep2

description:
in situ Hi-C
CD69negDPDKOR1R2_merged.hic


title: CkoC442-NT-R2-T1


title: G11_B008639_B008701


title: CkoC44-NT-R1-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
CkoC44-NT-R1-T1__hg19.hg19.mapq_30.1000.mcool
CkoC44-NO-TIR1-pool.mcool


title: G15_B008649_B008703


title: G14_B008639_B008701


title: CD69negDP_H3K27ac_ChIPseq_rep1


title: CD69negDP_CTCFKO_HIC_rep1

description:
in situ Hi-C
CD69negDPCTCFKOR1R2_merged.hic

value: CTCF-/-


title: CD69negDP_Input_ChIPseq_rep2


title: J22_B008639_B008701


title: J4_B008639_B008701


title: G19_B008649_B008703


title: G20_B008639_B008701


title: ChIP-442-IAA-TAF5L-R2-T1


title: G20_B008649_B008703


title: J4_B008649_B008703


title: J9_B008649_B008703


title: CD69negDP_DKO_HIC_rep1


title: G21_B008639_B008701


title: ChIP-442-NT-TAF5L-R3-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
NT-TAF5L-narrowPeaks-sort-merge-with-strength.bed


title: K11_B008649_B008703


title: K11_B008639_B008701


title: ChIP-442-NT-TAF5L-R2-T1


title: ChIP-442-IAA-RAD21-R3-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
IAA-RAD21-narrowPeaks-sort-merge-with-strength.bed

value: RAD21 (Abcam, #ab992)


title: CD69negDP_CTCFKO_HIC_rep2


title: J19_B008639_B008701


title: J18_B008639_B008701


title: ChIP-442-NT-RAD21-R4-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
NT-RAD21-narrowPeaks-sort-merge-with-strength.bed


title: E16_B008640_B010275


title: ChIP-442-IAA-DDX55-R3-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
IAA-DDX55-narrowPeaks-sort-merge-with-strength.bed

value: auxin

value: DDX55 (Bethyl Laboratories, #A303-027A)


title: J20_B008639_B008701


title: J21_B008639_B008701


title: ChIP-442-NT-RAD21-R2-T1


title: K13_B008639_B008701


title: ChIP-442-IAA-DDX55-R2-T1


title: J22_B008649_B008703


title: K15_B008639_B008701


city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

description:
FOS overexpressing isolated muscle satellite cells RNA-seq Rep1
FOS_GFP_RNAseq_genecounts.txt

data_processing:
RNA-seq analysis (polyA) was performed by filtering and mapping the reads by Bowtie 2  (mm9), quantifying the transcripts by RSEM v1.2.29 . Differential gene expression was calculated using  DESeq2 by removing  genes with a gene count <10, and by using the mean value of gene-wise dispersion estimates. We defined differentially expressed genes as being changed > 0.5 log2 fold in expression with an adjusted p-value < 0.01 using the DEbrowser package (PMID: 30611200). Gene ontology (GO) analysis was performed using the FuncAssociate software version 3.0 (PMID: 19717575).
The resulting Hi-C sequencing reads were mapped (mm9), filtered, corrected and bined using the HiC-Pro software v2.8 (PMID: 26619908). There was a high eigenvector correlation among all the Hi-C biological replicates (average Pearson’s correlation R2 > 0.9), indicating the high quality and reproducibility of the datasets. Thus, we pooled all biological replicates for each condition and mapped, filtered, corrected and binned them as a single Hi-C dataset for all subsequent analyses. Genomic A/B compartments and TADs (insulation method) were defined and visualized using the cworld, HiGlass, and Juicebox toolkits (cworld toolkit codes available at: https://github.com/dekkerlab/cworld-dekker), (PMID: 27467249, 27467250, 30143029). We generated saddle plots, meta-TAD and meta-loop plots using the cooltools package (PMID: 31290943, 32003791). Compartment switching analysis was performed as previously described (PMID: 25693564). Differentially regulated looping interactions were determined using the hiccups algorithm from the juicer toolkit (PMID: 27467249).
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq gene count file (in tab-delimited txt format)
Supplementary_files_format_and_content: hic chromatin interaction file (that can be opened with juicebox (PMID:27467250)).
Supplementary_files_format_and_content: hic chromatin interaction file (that can be opened with juicebox (PMID:27467250)).

source_name: isolated muscle satellite cells

growth_protocol: Freshly isolated SCs were sorted into pre-coated, 96-well plates containing standard Growth Media (GM) consisting of 20% Donor Horse Serum (DHS), 1% Penicillin/Streptomycin, 1% GlutaMax, and  5 ng/mL of bFGF in F10 media. Plates were pre-coated for 24 hours with a solution containing Collagen Type 1 (1ug/ml final) and Laminin (10 ug/ml) in PBS. GM was refreshed every 48-72 hours, and cells were passaged by removing half the volume of GM and adding back 5 mM EDTA (to achieve a 2.5 mM final concentration), incubating for 20 minutes at 37°C, spinning at 1200 RPM, resuspending in fresh GM, counting, and seeding cells to new wells at desired densities. C2C12 cell lines (C2C12 ATCC CRL-1772) were purchased from ATCC, and cultured according to the manufacturer’s recommendations.

extract_protocol:
Total RNA was extracted from Gfp or Fos-expressing primary muscle progenitor cells using TRIzol followed by RNeasy Mini Qiagen extraction kit according to manufacturer’s protocol. In-situ Hi-C libraries were generated using the HindIII restriction enzyme (PMID: 22652625). Briefly, ~25 million cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Then, the chromatin was extracted, digested with HindIII, end-labelled with biotin-14-dCTP, followed by  in-situ ligation (EL0011, Thermo Fisher). After DNA extraction, biotin was removed from unligated ends, and the sample was sheared using a Covaris S220 instrument (100-500bp range) as previously described (PMID: 22652625). After A-tailing, biotin pull-down, and adapter ligation, we performed paired-end sequencing on Illumina’s HiSeq 2000 instrument.
RNA-seq libraries were generated using the Illumina TruSeq (version 2) kit and sequenced on the Illumina HiSeq2500 instrument.
RNA-seq libraries were prepared with polyA enrichment.

treatment_protocol: Primary muscle satellite cells (SCs) were isolated as previously reported in [12]. Briefly, hind-limb, abdominal, and tricep muscles were isolated from mice and digested in 0.2% collagenase type II (285 U/mg) in Dulbecco’s modified eagle medium (DMEM) for 90 minutes at 37°C. Single fibers were separated from digested muscle by trituration and enriched through several gravitational sedimentation steps at 37°C. Single fibers were digested in 0.0125% Collagenase type II/0.05% Dispase (1.81U/mg) in F10 for 30 minutes at 37°C to release mono-nuclear cells from the basal lamina of individual muscle fibers. The resulting cell suspension was spun (~500 rpm) to remove cellular debris, and then filtered through a 70-micron cell strainer. Cells were incubated on ice for 30 minutes with fluorescently-conjugated antibodies to detect the following antigens: anti-Ly6A/E-APC or anti-Ly6A/E-PE  (Sca-1) (1:200), anti-CD31-APC (1:200), anti-CD45-APC (1:200), CD11b-APC (Mac-1) (1:200), CD29-APC-Cy7 (β1-Integrin) (1:200), CD184-Biotin (CXCR4) (1:100). For CXCR4 detection, a secondary antibody, Streptavidin-PeCy7 (1:200), was incubated with the relevant samples for 20 minutes on ice. Stained cells were analyzed by FACS using the BD FACSAria III cell sorter. After gating on physical parameters and live cells (Propidium Iodide-negative/Calcein Blue-positive) [12], SCs were defined as the Sca1-; CD45-; CD11b-; Ter119- ; CD31- ; CD29+ (β1-Integrin); CD184+ (CXCR4) cell population.

value: FOS overexpression

value: Primary muscle satellite cells


title: K13_B008649_B008703


title: ChIP-442-NT-DDX55-R3-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
NT-DDX55-narrowPeaks-sort-merge-with-strength.bed

value: non-treated

value: endogenous CTCF KO, CTCF-AID, TIR1


title: ChIP-442-IAA-CTCF-R2-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
IAA-CTCF-narrowPeaks-sort-merge-with-strength.bed

value: CTCF (Cell signaling Technology, #2899)


title: F4_D088224_B106233_S124


title: F5_D088224_B106233_S125


title: J1_B008639_B008701


description:
GFP overexpressing isolated muscle satellite cells RNA-seq Rep3
FOS_GFP_RNAseq_genecounts.txt

value: GFP overexpression


title: ChIP-442-NT-DDX55-R2-T1


title: F8_D088224_B106233_S128


description:
GFP overexpressing isolated muscle satellite cells RNA-seq Rep2
FOS_GFP_RNAseq_genecounts.txt


title: ChIP-442-IAA-RAD21-R2-T1


title: J8_B008639_B008701


title: ChIP-442-NT-CTCF-R2-T1

description:
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
NT-CTCF-narrowPeaks-sort-merge-with-strength.bed


title: F6_D088224_B106233_S126


description:
GFP overexpressing isolated muscle satellite cells RNA-seq Rep1
FOS_GFP_RNAseq_genecounts.txt


title: G12_D088224_B106233_S156


title: E2_B008640_B010275


title: G16_D088224_B106233_S160


description:
FOS overexpressing isolated muscle satellite cells RNA-seq Rep3
FOS_GFP_RNAseq_genecounts.txt


title: ChIP-442-IAA-input-R4-T1

description: KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.

value: input


title: HL60_DMSO_R3

city: La Jolla

first: Michael

last: Erb

state: CA

address: 10650 N Torrey Pines Rd

department: Department of Chemistry

institute: The Scripps Research Institute

description: SLAMseq in HL-60 after 2 hour of DMSO treatment.

data_processing:
SLAMdunk (https://t-neumann.github.io/slamdunk/) was used with default settings to align reads, calculate counts per million, and calculate T to C conversion rate for each transcript.
Assembly: hg19
Supplementary files format and content: T-to-C conversion rates and CPM table.

source_name: acute myeloid leukemia

growth_protocol: MOLM-13 cells were cultured in RPMI supplemented with 10% FBS, penicillin, and streptomycin. HL-60 were cultured in RPMI supplemented with 20% FBS, penicillin, and streptomycin.

extract_protocol:
Total RNA was isolated with Qiagen Rneasy Mini Kit. SIRV-Set 3 RNA was spiked into samples.
4SU-labeled transcripts were alkylated by addition of 5 µL 100 mM iodoacetamide, 25 µL DMSO, and 5 µL of sodium phosphate buffer (0.5M, pH 8) and incubating at 50C for 15 minutes. 3' mRNA libraries were prepared with Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Cat. No. 015) according to manufacturer's instructions.

treatment_protocol: Cells were treated with 3 µM A-485 or DMSO for 2 hours. For the last hour of treatment 100 µM 4-thiouracil (4SU) was added to label newly synthesized transcripts.

value: acute myeloid leukemia

value: 0.1% DMSO

tag: time

value: 2 hours


title: K12_B008649_B008703

value: patient-derived-xenograft

value: tumor

value: NSG


title: G20_D088224_B106233_S164


title: G13_D088224_B106233_S157


title: ChIP-442-IAA-input-R3-T1

tag: genotype


title: K12_B008639_B008701


title: G5_D088224_B106233_S149


description:
FOS overexpressing isolated muscle satellite cells RNA-seq Rep2
FOS_GFP_RNAseq_genecounts.txt


title: G6_D088224_B106233_S150


title: K19_B008649_B008703


title: ChIP-442-NT-input-R3-T1


title: ChIP-442-NT-CTCF-R1-T1


title: G9_D088224_B106233_S153


title: H11_D088224_B106233_S179


title: HL60_DMSO_R2

tag: cell line


title: HL60_3uM_A485_R1

description: SLAMseq in HL-60 after 2 hour of 3 µM A-485 treatment.


title: G1_D088224_B106233_S145


title: H15_D088224_B106233_S183


title: MOLM13_DMSO_R3

description: SLAMseq in MOLM-13 after 2 hour of DMSO treatment.


title: HL60_3uM_A485_R3


title: HL60_DMSO_R1


title: ChIP-442-IAA-input-R2-T1

tag: chip antibody


title: ChIP-442-IAA-CTCF-R1-T1


title: G8_D088224_B106233_S152


title: H21_D088224_B106233_S189


title: G18_D088224_B106233_S162


title: ChIP-442-NT-input-R4-T1


title: H22_D088224_B106233_S190


title: H2_D088224_B106233_S170


title: H12_D088224_B106233_S180


title: MOLM13_DMSO_R2


title: ChIP-442-NT-input-R2-T1