title: HEK293T_IAA_IP_MBD2_rep1

description:
HEK293T_IAA_IP_MBD2_rep123_treat_pileup.bigwig
HEK293T_IAA_IP_MBD2_rep123_TvsC_peaks.narrowPeak


title: HEK293T_IAA_plus_72h_IP_TET2_rep2

status: Public on May 02 2026

type: SRA

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

country: China

institute: City University of Hong Kong

description: HEK293T_IAA_plus_72h_IP_TET2_rep123_TvsC_peaks.narrowPeak

library_source: genomic

data_processing:
The raw ChIP-Seq data were quality-controlled using FastQC (v0.11.7) with default parameters.
ChIP-seq reads were aligned to human genome (hg19) using bowtie2 (v2.3.4) with default parameters and only the uniquely mapped reads were kept for the subsequent analyses.
Sam files were converted to bam files by using samtools (v1.9) with default parameters.
Binding peaks for each sample were identified by using MACS2 software (v2.1.2) with default parameters.
Peaks were annotated by using bedtools (v2.25.0).
All peaks and reads distribution were visualized by using IGV software (v2.4.14).
Assembly: hg19
Supplementary files format and content: narrowPeak (except for input sample)  were generated by MACS2 (v2.1.2) which include the detail informations for all binding peaks;

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: The HEK293T (ATCC, CRL-3216) and its derived edited cells were cultured with DMEM (Invitrogen) supplemented with 10% FBS and antibiotics (penicillin and streptomycin), under the regular tissue culture condition, i.e. 5% CO2 at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody (CTCF (abcam, Cat. #ab128873), MBD3 (abcam, Cat. #ab157464),TET1 (GeneTex, Cat No. GTX125888),TET2 (GeneTex, Cat No. GTX124205)).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection. The libraries were sequenced with an MGIseq2000 instrument (BGI, Shenzhen) using a paired-end scheme (PE100).

treatment_protocol: For the CTCF-AID experiment, CTCF-edited HEK293T were co-transfected with 1.5 μg of pcDNA3.1-ScFv-miniIAA7-mEGFP plasmid and 1.5 μg of pcDNA3.1-AtAFB2-mCherry constructs using 9 μg of PEI (0.1%, Polysciences). At 48 h post plasmid transfection, the medium was changed to 2 mL of fresh medium without or containing 0.5 mM IAA (Indole-3-acetic acid sodium salt, Santa Cruz, sc-215171). The cells were harvested 72 hours after being treated with 0.5mM IAA for subsequent experiments.

tag: cell line

tag: cell type

value: human embryonic kidney (HEK) 293T cells

tag: time

tag: treatment

tag: chip antibody


title: HEK293T_IAA_IP_MBD3_rep2

description:
HEK293T_IAA_IP_MBD3_rep123_treat_pileup.bigwig
HEK293T_IAA_IP_MBD3_rep123_TvsC_peaks.narrowPeak

data_processing:
The raw ChIP-Seq data were quality-controlled using FastQC (v0.11.7) with default parameters.
ChIP-seq reads were aligned to human genome (hg19) using bowtie2 (v2.3.4) with default parameters and only the uniquely mapped reads were kept for the subsequent analyses.
Sam files were converted to bam files by using samtools (v1.9) with default parameters.
Binding peaks for each sample were identified by using MACS2 software (v2.1.2) with default parameters.
Peaks were annotated by using bedtools (v2.25.0).
The ChIP signal enrichment heat map of the flank of a specific point collection (such as CTCF binding sites) was calculated using deeptools (v3.5.0).
All peaks and reads distribution were visualized by using IGV software (v2.4.14).
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak (except for input sample)  were generated by MACS2 (v2.1.2) which include the detail informations for all binding peaks;

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody (CTCF (abcam, Cat. #ab128873), MBD2 (abcam, Cat. #ab224827), MBD3 (abcam, Cat. #ab157464),TET1 (GeneTex, Cat No. GTX125888).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection.

treatment_protocol: HEK293T cells were treated with DMSO, IAA(0.5mM) or BPK-25 (30 μM) for 72 hr. Chromatin immunoprecipitation was conducted as mentioned above.

value: IAA


title: hESC_H9_d0_WT_input_rep3

growth_protocol: Human embryonic stem (hES) cell line (H9) cells were routinely cultured under feeder-free condition in mTeSR1 medium (Stem cell technologies) on Matrigel (Corning) coated tissue culture dishes, under the regular tissue culture condition, i.e. 5% CO2 at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody (CTCF (abcam, Cat. #ab128873), MBD3 (abcam, Cat. #ab157464) and TET1 (GeneTex 125888)).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection. The libraries were sequenced with an MGIseq2000 instrument (BGI, Shenzhen) using a paired-end scheme (PE100).

treatment_protocol: Human embryonic stem (hES) cell line (H9) were dissociated into single cell suspension using Gentle Cell Dissociation Reagent. Cells were collected by centrifugation at 300×g for 5 min. Careful aspiration of the supernatant was conducted followed  by resuspension of cells in STEMdiff™ Neural Induction Medium supplemented with SMADi and 10 μM Y-27632 (Stem cell technologies, USA), to obtain a final concentration of 1 × 106 cells/mL (i.e. 2 × 105 cells/cm2). Two milliliters of cell suspension (2 x 106 cells/well) were added into one well of a Matrigel-coated 6-well plate. Place the plate in a 37 °C CO2 (5%) incubator. Warm (37°C) STEMdiff™ Neural Induction Medium with SMADi was used to replace the full medium once a day on Days 1-5. On day 6, the medium was aspirated from the wells containing NPCs and 1 mL of ACCUTASE™ (Stem cell technologies, USA) was add and incubated at 37 °C for 10 min. Then the remaining attached cells were removed by pipetting up and down the cell suspension. Five mL of DMEM/F-12 was added to each well to suspend the pellet and transferred to a 15 mL conical tube for centrifuge at 300×g for 5 min. Next, the supernatant was carefully aspirated in which 1 mL of complete STEMdiff™ Neural Induction Medium containing SMADi was added. Cells were plated at the desired density (e.g., 1.5 - 2 x 105 cells/cm2) into a single well of a newly Matrigel-coated 6-well plate containing 2 mL of STEMdiff™ Neural Induction Medium with SMADi. STEMdiff™ Neural Induction Medium containing SMADi was daily replaced with the fresh medium.Human embryonic stem (hES) cell line (H9) cells were treated with 20 μM of BPK-25 and induced to differentiate by STEMdiff Neural Induction Medium at 24 hours. During differentiation, the medium was replaced daily with STEMdiff™ Neural Induction Medium supplemented with SMADi and 20 μM BPK-25.

value: human embryonic stem cells (hESC) H9

value: day 0

value: WT

value: input


title: hESC_H9_d0_WT_IP_CTCF_rep3

description: H9_d0_WT_IP_CTCF_rep123_TvsC_peaks.narrowPeak

value: CTCF


title: HEK293T_IAA_IP_MBD2_rep2


title: HEK293T_IAA_plus_72h_IP_MBD3_rep3

description: HEK293T_IAA_plus_72h_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: HEK293T_IAA_plus_72h_IP_MBD3_rep2


title: HEK293T_IAA_IP_MBD3_rep1


title: HEK293T_IAA_IP_TET1_rep3

description:
HEK293T_IAA_IP_TET1_rep123_treat_pileup.bigwig
HEK293T_IAA_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: HEK293T_IAA_plus_72h_IP_TET1_rep3

description: HEK293T_IAA_plus_72h_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: HEK293T_IAA_IP_MBD2_rep3


title: HEK293T_IAA_plus_72h_IP_MBD3_rep1


title: HEK293T_IAA_IP_CTCF_rep3

description:
HEK293T_IAA_IP_CTCF_rep123_treat_pileup.bigwig
HEK293T_IAA_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: HEK293T_IAA_plus_72h_IP_TET1_rep2


title: HEK293T_IAA_plus_72h_IP_CTCF_rep3

description: HEK293T_IAA_plus_72h_IP_CTCF_rep123_TvsC_peaks.narrowPeak

value: Anti-CTCF


title: HEK293T_IAA_IP_CTCF_rep2


title: HEK293T_IAA_plus_72h_IP_CTCF_rep2


title: HEK293T_IAA_plus_72h_IP_TET1_rep1


title: HEK293T_IAA_plus_72h_IP_TET2_rep1


title: HEK293T_IAA_input_rep3

description: HEK293T_IAA_input_rep123_control_lambda.bigwig


title: HEK293T_IAA_plus_72h_input_rep2

value: Input


title: HEK293T_IAA_plus_72h_IP_CTCF_rep1


title: HEK293T_IAA_IP_CTCF_rep1


title: HEK293T_IAA_input_rep1


title: HEK293T_IAA_plus_72h_input_rep3


title: HEK293T_IAA_input_rep2


title: HEK293 vehicle replicate 3 ATAC-seq

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

country: USA

institute: UNC Chapel Hill

description:
Library name: YAPP_ATAC_HEK_wt_Control_0h_S_2p1p1_S3
ATAC-seq in HEK293 cells with vehicle treatment

data_processing:
ATAC-seq reads were processed using the bagPipes Snakemake workflow (ATACpipe.snakefile; https://github.com/PhanstielLab/bagPipes). Reads were trimmed with Trim Galore (v0.6.10) and quality assessed with FastQC (v0.12.1) and MultiQC (v1.28). Trimmed reads were aligned to the hg38 reference genome using bwa mem (v0.7.17) and sorted with samtools (v1.22). PCR duplicates were removed using Picard MarkDuplicates (REMOVE_DUPLICATES=true) and mitochondrial reads were excluded with samtools idxstats and view. Per-replicate peaks were called using MACS2 (v2.2.9.1; callpeak -f BAM -q 0.01 -g hs --nomodel --shift 100 --extsize 200 --keep-dup all -B --SPMR). Peaks from all replicates were merged using bedtools merge (v2.31.1) to generate a unified peak set, and fragment counts per peak per sample were quantified using bedtools multicov. Signal tracks were generated using deepTools bamCoverage (v3.5.4). Genome build: hg38 (GRCh38).
ATAC-seq reads were processed using the bagPipes Snakemake workflow (ATACpipe.snakefile). Reads were trimmed with Trim Galore (v0.6.10) and quality assessed with FastQC (v0.12.1) and MultiQC (v1.28). Trimmed reads were aligned to the hg38 reference genome using bwa mem (v0.7.17) and sorted with samtools (v1.22). PCR duplicates were removed using Picard MarkDuplicates (REMOVE_DUPLICATES=true) and mitochondrial reads were excluded using samtools idxstats and view. Per-replicate peaks were called using MACS2 (v2.2.9.1; callpeak -f BAM -q 0.01 -g hs --nomodel --shift 100 --extsize 200 --keep-dup all -B --SPMR). Peaks from all replicates were merged using bedtools merge (v2.31.1) to generate a unified peak set, and fragment counts per peak per sample were quantified using bedtools multicov. Signal tracks were generated using deepTools bamCoverage (v3.5.4). Genome build: hg38 (GRCh38).
Assembly: hg38 (GRCh38) human reference genome.
Supplementary files format and content: bigWig (.bw) files contain per-replicate and merged ATAC-seq chromatin accessibility signal tracks for untreated (0h) and 1-hour sorbitol-treated eGFP-YAP HEK293 cells, generated with deepTools bamCoverage. Values represent normalized read coverage across the genome at hg38 coordinates.
Supplementary files format and content: TSV file (YAPP_HEK_1_peakCounts.tsv) contains the merged peak-by-sample fragment count matrix across all ATAC-seq replicates and conditions (untreated and 1h sorbitol), where rows are merged peak coordinates (chr, start, stop) and columns are individual replicate BAM-derived counts. Used as input for differential accessibility analysis with DESeq2.

growth_protocol: HEK293 cells were cultured in standard conditions (37 °C, 5% CO₂) in DMEM supplemented with 10% fetal bovine serum and penicillin/streptomycin. Cells were regularly monitored for mycoplasma contamination and maintained at 30–80% confluence prior to experimental treatments.

extract_protocol:
Cells were detached, counted, and pelleted at 4 °C. For RNA-seq, total RNA was extracted using a column-based RNA purification kit following the manufacturer’s instructions. For CUT&Tag and Hi-C, nuclei were isolated by gentle lysis in detergent-containing buffer prior to downstream processing. For ATAC-seq, 50,000 cells per sample were used. Nuclei were isolated using Omni-ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin) on ice for 3 minutes, followed by a wash with 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Tween-20. Isolated nuclei were used immediately for tagmentation.
ATAC-seq libraries were prepared following the Omni-ATAC protocol (Corces et al., 2017). 50,000 cells per sample were lysed in ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin) on ice for 3 minutes. Nuclei were pelleted, washed once with wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% Tween-20), and resuspended in transposition mix containing Nextera XT transposase (Illumina) for 30 minutes at 37 °C with gentle shaking. Transposed DNA was purified using the Zymo DNA Clean and Concentrator kit. Libraries were amplified by PCR for 5 initial cycles; a qPCR side reaction on 5% of the amplified material was used to determine the number of additional cycles required (typically 4–7 additional cycles). Libraries were size-selected using a two-sided AMPure XP bead cleanup (0.5× then 1.3×), quantified by Qubit (dsDNA HS Assay) and the KAPA Library Quantification kit, and sequenced in paired-end 75 bp mode on an Illumina NextSeq 500.

treatment_protocol: Hyperosmotic stress was induced by adding sorbitol to a final concentration of 200 mM for the indicated timepoints. Untreated samples were collected in parallel as controls. Cells were harvested at the specified time after treatment and processed immediately for downstream library preparation.

tag: genotype

value: eGFP-YAP

value: vehicle


title: HEK293T_BPK25_IP_MBD2_rep3

description:
HEK293T_BPK25_IP_MBD2_rep123_treat_pileup.bigwig
HEK293T_BPK25_IP_MBD2_rep123_TvsC_peaks.narrowPeak


title: HEK293T_IAA_plus_72h_input_rep1


title: HEK293T_BPK25_IP_TET1_rep1

description:
HEK293T_BPK25_IP_TET1_rep123_treat_pileup.bigwig
HEK293T_BPK25_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: HEK293T_BPK25_IP_MBD3_rep2

description:
HEK293T_BPK25_IP_MBD3_rep123_treat_pileup.bigwig
HEK293T_BPK25_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: HEK293T_IAA_minus_72h_IP_TET1_rep1

description: HEK293T_IAA_minus_72h_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: hESC_H9_d0_DMSO_IP_MBD3_rep1

description: H9_d0_DMSO_IP_MBD3_rep123_TvsC_peaks.narrowPeak

value: DMSO


title: HEK293T_IAA_minus_72h_IP_TET2_rep2

description: HEK293T_IAA_minus_72h_IP_TET2_rep123_TvsC_peaks.narrowPeak


title: HEK293T_BPK25_IP_TET1_rep3


title: HEK293T_BPK25_IP_TET1_rep2


title: HEK293T_IAA_minus_72h_IP_TET2_rep1


title: HEK293T_BPK25_IP_MBD3_rep1


title: HEK293T_IAA_minus_72h_IP_MBD3_rep3

description: HEK293T_IAA_minus_72h_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: HEK293T_IAA_minus_72h_IP_MBD3_rep2


title: HEK293T_IAA_minus_72h_IP_TET2_rep3


title: HEK293T_IAA_minus_72h_IP_TET1_rep2


title: HEK293T_BPK25_IP_MBD2_rep1


title: HEK293T_BPK25_IP_CTCF_rep3

description:
HEK293T_BPK25_IP_CTCF_rep123_treat_pileup.bigwig
HEK293T_BPK25_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: HEK293T_IAA_minus_72h_IP_TET1_rep3


title: HEK293T_BPK25_IP_MBD2_rep2


title: HEK293T_BPK25_IP_CTCF_rep2


title: HEK293T_IAA_minus_72h_IP_CTCF_rep3

description: HEK293T_IAA_minus_72h_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: HEK293T_IAA_minus_72h_IP_MBD3_rep1


title: HEK293T_BPK25_input_rep3

description: HEK293T_BPK25_input_rep123_control_lambda.bigwig


title: HEK293T_IAA_minus_72h_IP_CTCF_rep2


title: HEK293T_BPK25_IP_CTCF_rep1


title: HEK293T_IAA_minus_72h_IP_CTCF_rep1


title: HEK293T_BPK25_input_rep2


title: HEK293T_IAA_minus_72h_input_rep3


title: HEK293T_IAA_minus_72h_input_rep1


title: HEK293T_BPK25_input_rep1


title: HEK293T_TET3_Flag_DMSO_IP_TET3_rep3

description: HEK293T_TET3_Flag_DMSO_IP_TET3_rep123_TvsC_peaks.narrowPeak

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody (CTCF (abcam, Cat. #ab128873), MBD3 (abcam, Cat. #ab157464),Flag (Origene, Cat#: TA50011-100)).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection. The libraries were sequenced with an MGIseq2000 instrument (BGI, Shenzhen) using a paired-end scheme (PE100).

treatment_protocol: HEK293T cells were treated with DMSO or BPK-25 (30 μM) for 72 hr. Chromatin immunoprecipitation was conducted as mentioned above.

value: Anti-Flag


title: HEK293T_DMSO_IP_MBD3_rep1

description:
HEK293T_DMSO_IP_MBD3_rep123_treat_pileup.bigwig
HEK293T_DMSO_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: HEK293T_IAA_minus_72h_input_rep2


title: HEK293T_DMSO_IP_TET1_rep1

description:
HEK293T_DMSO_IP_TET1_rep123_treat_pileup.bigwig
HEK293T_DMSO_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: HEK293T_TET3_Flag_DMSO_IP_TET3_rep1


title: HEK293T_DMSO_IP_TET1_rep3


title: HEK293T_TET3_Flag_DMSO_input_rep2


title: HEK293T_TET3_Flag_DMSO_input_rep1


title: HEK293T_DMSO_IP_TET1_rep2


title: HEK293T_TET3_Flag_BPK25_IP_TET3_rep3

description: HEK293T_TET3_Flag_BPK25_IP_TET3_rep123_TvsC_peaks.narrowPeak


title: HEK293T_DMSO_IP_MBD2_rep1

description:
HEK293T_DMSO_IP_MBD2_rep123_treat_pileup.bigwig
HEK293T_DMSO_IP_MBD2_rep123_TvsC_peaks.narrowPeak


title: HEK293T_TET3_Flag_BPK25_IP_TET3_rep1


title: HEK293T_TET3_Flag_DMSO_input_rep3


title: HEK293T_DMSO_IP_MBD3_rep3


title: HEK293T_TET3_Flag_BPK25_input_rep3


title: HEK293T_DMSO_IP_MBD3_rep2


title: HEK293T_TET3_Flag_DMSO_IP_TET3_rep2


title: HEK293T_TET3_Flag_BPK25_IP_TET3_rep2


title: HEK293T_DMSO_IP_MBD2_rep2


title: HEK293T_DMSO_IP_MBD2_rep3


title: HEK293T_DMSO_IP_CTCF_rep1

description:
HEK293T_DMSO_IP_CTCF_rep123_treat_pileup.bigwig
HEK293T_DMSO_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: HEK293T_DMSO_IP_CTCF_rep3


title: HEK293T_DMSO_IP_CTCF_rep2


title: HEK293T_DMSO_input_rep3

description: HEK293T_DMSO_input_rep123_control_lambda.bigwig


title: HEK293T_DMSO_input_rep2


title: HEK293T_TET3_Flag_BPK25_input_rep1


title: HEK293T_TET3_Flag_BPK25_input_rep2


title: HEK293T_TET2_Flag_DMSO_IP_TET2_rep3

description: HEK293T_TET2_Flag_DMSO_IP_TET2_rep123_TvsC_peaks.narrowPeak


title: HEK293T_TET2_Flag_DMSO_IP_TET2_rep1


title: HEK293T_DMSO_input_rep1


title: HEK293T_TET2_Flag_DMSO_input_rep2


title: HEK293T_TET2_Flag_DMSO_input_rep3


title: HEK293T_TET2_Flag_BPK25_IP_TET2_rep3

description: HEK293T_TET2_Flag_BPK25_IP_TET2_rep123_TvsC_peaks.narrowPeak


title: Human_CTCF-MBD2-random_CAP-Methyl-SELEX_cycle4_rep2

library_source: other

data_processing:
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 40-nt target region without bases annotated as N were extracted using custom script.
Then the dinucleotide frequencies at target region of oligos were generated using custom script.
Assembly: NA
Supplementary files format and content: tab-delimited text file include the statistical results of dinucleotide frequencies for each sample.

molecule: other

organism: Escherichia coli

source_name: E. coli

growth_protocol: The E. coli strains for protein purification were grown at 37 ℃ in LB (Luria-Bertani) broth with shaking at 220 rpm or on LB agar plates until OD600=0.6.

extract_protocol:
The pellet was suspended in 10 ml buffer A (0.5 mg/ml Lysozyme, 50 mM tris-HCl pH 7.5, 300 mM NaCl, 10 mM Imidazole, 1 mM DTT, 1 mM PMSF) and lysed by sonication at ten seconds interval for 10 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA beads was set at 4 ℃ for 30min before being eluted with Buffer A containing 300 mM imidazole
The CAP-SELEX experiments were carried out using a previously established protocol. Briefly, dilute 10–200 ng of purified Flag and SBP-tagged proteins into a 25 µl volume of binding  buffer (140 mM KCl, 5 mM NaCl, 2 mM MgSO4, 3 μM ZnSO4, 100 μM EGTA, 1 mM K2HPO4, in a solution containing approximately 10 μmol DNA select ligand in 20mM HEPES, pH 7.0, and incubate at room temperature for 20 minutes. Subsequently, add two volumes of 0.2% BSA, 0.1% Tween 20 in binding buffer to the preblocked streptavidin-coated magnetic Sepharose beads (1.25 μl; GE Healthcare Streptavidin Mag Sepharose) and the mixture was incubated with strong  medium for 2 h at room temperature. The beads were washed 5 times with binding buffer. Protein_x0002_DNA complexes were eluted from the beads using 50 μl of 10 mM biotin (Sigma) in binding buffer. Transfer the eluate to M2 containing 50 μl of binding buffer. Add 1.25 μl anti-Flag magnetic beads (Sigma) to a fresh plate and shake at 800 r.p.m. Leave at room temperature for 20 minutes. The beads are washed ten times with binding buffer and suspended in 0.1% Tween 20, 0.5mM EDTA, 10mM Tris-Cl, pH 8.0, and transferred to a PCR plate. DNA was then eluted from the beads by incubation at 95 °C for 10 min. A 10 μl aliquot of the bead suspension was transferred to a new PCR plate and amplified by PCR Amplify DNA. The amplified selected ligands are then subjected to sequencing and new cycles of CAP-SELEX (up to 3 cycles in total). After each cycle, purified PCR products were pooled and sequenced using an Illumina HiSeq Xten sequencer.

treatment_protocol: 1 mM IPTG (Isopropyl β-D-1-Thiogalactopyranoside) was added into the bacterial culture to induce protein expression at 16 °C for 16 h.

tag: tissue

value: E. coli

value: Rosetta (DE3)

value: no treatment


title: HEK293T_TET2_Flag_DMSO_input_rep1


title: Human_CTCF-MBD2-random_CAP-Methyl-SELEX_cycle4_rep3


title: HEK293T_TET2_Flag_BPK25_IP_TET2_rep1


title: Human_CTCF-MBD2-random_CAP-Methyl-SELEX_cycle4_rep1


title: Human_CTCF-MBD2-random_CAP-Methyl-SELEX_cycle3_rep2


title: Human_CTCF-MBD2-random_CAP-Methyl-SELEX_cycle3_rep3


title: HEK293T_TET2_Flag_BPK25_input_rep2


title: HEK293T_TET2_Flag_BPK25_IP_TET2_rep2


title: HEK293T_TET1_Flag_DMSO_IP_TET1_rep3

description: HEK293T_TET1_Flag_DMSO_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: Human_CTCF-MBD2-random_CAP-Methyl-SELEX_cycle2_rep1


title: Human_CTCF-MBD2-random_CAP-Methyl-SELEX_cycle2_rep2


title: Human_CTCF-MBD2-random_CAP-Methyl-SELEX_cycle2_rep3


title: HEK293T_TET2_Flag_BPK25_input_rep3


title: Human_CTCF-MBD2-random_CAP-Methyl-SELEX_cycle1_rep3


title: Human_CTCF-MBD2-random_CAP-Methyl-SELEX_cycle1_rep2


title: HEK293T_TET2_Flag_BPK25_input_rep1


title: HEK293T_TET1_Flag_DMSO_input_rep3


title: Human_CTCF-MBD2-random_CAP-Methyl-SELEX_cycle1_rep1


title: HEK293T_TET1_Flag_DMSO_IP_TET1_rep2


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle4_rep2


title: HEK293T_TET1_Flag_DMSO_input_rep2


title: HEK293T_TET1_Flag_DMSO_IP_TET1_rep1


title: HEK293T_TET1_Flag_DMSO_input_rep1


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle4_rep3


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle3_rep3


title: Human_CTCF-MBD2-random_CAP-Methyl-SELEX_cycle3_rep1


title: HEK293T_TET1_Flag_BPK25_IP_TET1_rep3

description: HEK293T_TET1_Flag_BPK25_IP_TET1_rep123_TvsC_peaks.narrowPeak


title: HEK293T_TET1_Flag_BPK25_IP_TET1_rep2


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle3_rep1


title: HEK293T_TET1_Flag_BPK25_input_rep3


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle3_rep2


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle4_rep1


title: HEK293T_ChIP_Seq_DMSO_IP_MBD3_rep3

description: HEK293T_DMSO_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle1_rep3


title: HEK293T_ChIP_Seq_DMSO_IP_MBD3_rep2


title: HEK293T_ChIP_Seq_DMSO_IP_MBD3_rep1


title: HEK293T_BPK25_IP_MBD3_rep3

description:
HEK293T_BPK25_IP_MBD3_rep123_treat_pileup.bigwig
HEK293T_BPK25_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: HEK293T_TET1_Flag_BPK25_IP_TET1_rep1


title: HEK293T_TET1_Flag_BPK25_input_rep2


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle2_rep2


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle1_rep1


title: HEK293T_TET1_Flag_BPK25_input_rep1


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle0_rep3


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle2_rep3


title: HEK293T_ChIP_Seq_DMSO_IP_CTCF_rep2

description: HEK293T_DMSO_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle2_rep1


title: HEK293T_ChIP_Seq_DMSO_IP_CTCF_rep3


title: HEK293T_ChIP_Seq_DMSO_IP_CTCF_rep1


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle1_rep2


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle0_rep2


title: HEK293T_ChIP_Seq_DMSO_INPUT_rep2


title: Human_MBD2_Me-SELEX_cycle4_rep2


title: HEK293T_ChIP_Seq_DMSO_INPUT_rep1


title: Human_CTCF-MBD2-random_CAP-HT-SELEX_cycle0_rep1


title: Human_MBD2_Me-SELEX_cycle4_rep3


title: HEK293T_ChIP_Seq_DMSO_INPUT_rep3


title: Human_MBD2_Me-SELEX_cycle3_rep3


title: HEK293T_ChIP_Seq_BPK25_IP_MBD3_rep2

description: HEK293T_BPK25_IP_MBD3_rep123_TvsC_peaks.narrowPeak


title: Human_MBD2_Me-SELEX_cycle4_rep1


title: HEK293T_ChIP_Seq_BPK25_IP_MBD3_rep3


title: Human_MBD2_Me-SELEX_cycle3_rep1


title: Human_MBD2_Me-SELEX_cycle3_rep2


title: Human_MBD2_Me-SELEX_cycle2_rep3


title: Human_MBD2_Me-SELEX_cycle2_rep2


title: HEK293T_ChIP_Seq_BPK25_INPUT_rep3


title: HEK293T_ChIP_Seq_BPK25_IP_CTCF_rep3

description: HEK293T_BPK25_IP_CTCF_rep123_TvsC_peaks.narrowPeak


title: Human_MBD2_Me-SELEX_cycle2_rep1


title: Human_MBD2_Me-SELEX_cycle1_rep1


title: Human_MBD2_Me-SELEX_cycle1_rep2


title: HEK293T_ChIP_Seq_BPK25_IP_CTCF_rep2


title: HEK293T_ChIP_Seq_BPK25_IP_CTCF_rep1


title: HEK293T_ChIP_Seq_BPK25_INPUT_rep1


title: HEK293T_BPK25_48h_BS_Seq_rep1

description: HEK293T_BPK25_BS_Seq_rep123.all_CpG_methylation_stat_result.txt.gz

data_processing:
The raw bisulfite-sequencing (BS-Seq) data were quality-controlled using FastQC (v0.11.7) and sequencing adapter were removed by cutadapt (v2.7).
The preprocessed sequence data were mapped to human genome (hg19) by using Bismark (v0.22.3). Only the uniquely mapped reads were kept for the subsequent analyses.
PCR duplicates were removed by 'deduplicate_bismark' (a command in the Bismark software package).
Genome-wide m5C sites information was extracted using 'bismark_methylation_extractor' (key parameters: --no_header --comprehensive  --cytosine_report --CX --zero_based).
The genome-wide CpG m5C methylation were extracted based on the 'bismark_methylation_extractor' result by using custom script.
Assembly: hg19
Supplementary files format and content: tab-delimited text files (bed6 plus 4 column with additional important values) include CpG methylation results.

extract_protocol:
The genomic DNA was extracted with Blood & Cell Culture DNA Kits (Thermo Fisher, Cat. #13323). Concentration of the DNA was measured with NanoDrop 2000 Spectrophotometers (Thermo Fisher).
To prepare the bisulfite-seq sample, 5 μg of genomic DNA was sonicated into 250-550bp fragments with Covaris M220 ultrasonicator with the manufacturer’s instructed setting. The fragmented DNA was directly applied for illumina Tru-seq library preparation. The library was quantified with Qubit and sequenced with illumina Hiseq 4000 sequencer with at least 20% Spike-in PhiX.

treatment_protocol: HEK293T cells were treated with DMSO or BPK-25 (30 μM) for 48 hr. Chromatin immunoprecipitation was conducted as mentioned above.


title: Human_MBD2_Me-SELEX_cycle1_rep3


title: HEK293T_ChIP_Seq_BPK25_INPUT_rep2


title: HEK293T_BPK25_48h_BS_Seq_rep2


title: HEK293T_ChIP_Seq_BPK25_IP_MBD3_rep1


title: Human_MBD2_HT-SELEX_cycle4_rep2


title: HEK293T_BPK25_48h_BS_Seq_rep3


title: Human_MBD2_HT-SELEX_cycle4_rep1


title: Human_MBD2_HT-SELEX_cycle3_rep3


title: HEK293T_DMSO_48h_BS_Seq_rep2

description: HEK293T_DMSO_BS_Seq_rep123.all_CpG_methylation_stat_result.txt.gz


title: Human_MBD2_HT-SELEX_cycle3_rep1


title: Human_MBD2_HT-SELEX_cycle2_rep3


title: HEK293T_CTCF_GCN4_IAA_plus_BS_Seq_rep3

description: HEK293T_CTCF_GCN4_IAA_plus_BS_Seq_rep123.bismark_bt2_pe.dedup.bme.all_CpG_result.txt.gz

data_processing:
The raw bisulfite-sequencing (BS-Seq) data were quality-controlled using FastQC (v0.11.7) and sequencing adapter were removed by cutadapt (v2.7).
The preprocessed sequence data were mapped to human genome (hg19) by using Bismark (v0.22.3). Only the uniquely mapped reads were kept for the subsequent analyses.
PCR duplicates were removed by 'deduplicate_bismark' (a command in the Bismark software package).
Genome-wide m5C sites information was extracted using 'bismark_methylation_extractor' (key parameters: --no_header --comprehensive  --cytosine_report --CX --zero_based).
The genome-wide CpG m5C methylation were extracted based on the 'bismark_methylation_extractor' result by using custom script.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files (bed6 plus 4 column with additional important values) include CpG methylation results.

extract_protocol:
The genomic DNA was extracted with Blood & Cell Culture DNA Kits (Thermo Fisher, Cat. #13323). Concentration of the DNA was measured with NanoDrop 2000 Spectrophotometers (Thermo Fisher).
To prepare the bisulfite-seq sample, 5 μg of genomic DNA was sonicated into 250-550bp fragments with Covaris M220 ultrasonicator with the manufacturer’s instructed setting. The fragmented DNA was directly applied for MGIseq library preparation. The libraries were sequenced with an MGIseq instrument (BGI, Shenzhen) using a paired-end scheme (PE100).

treatment_protocol: Before transfection, the cells were cultured in fresh culture medium for at least 1 hour. For siRNA (si-NC,si-MBD2,si-MBD3) transfection into HEK293T cells, 100pmol of siRNA were mixed with 5 μL of lipo 3000 (invitrogen) in serum-free Opti-MEM (Invitrogen) by vortexing and incubation at Room Temperature (RT) for 15 min to allow formation of stable transfection complex. The mixture was evenly applied to ~300,000 cells cultured in a single well of a 6-well plate. For CTCF-AID, Before transfection, the cells were cultured in fresh culture medium for at least 1 hour. For  plasmid transfection into HEK293T cells, 1.5ug of plasmid were mixed with 5 μL of PEI  in serum-free Opti-MEM (Invitrogen) by vortexing and incubation at Room Temperature (RT) for 15 min to allow formation of stable transfection complex. 48 hours after transfection, IAA was added to induce CTCF degradation. After 12 hours of IAA treatment, the cells were collected for subsequent experiments.

value: IAA(plus)


title: HEK293T_CTCF_GCN4_IAA_plus_BS_Seq_rep2

value: human embryonic kidney (HEK) 293T cells


title: HEK293T_DMSO_48h_BS_Seq_rep1


title: Human_MBD2_HT-SELEX_cycle2_rep2


title: Human_MBD2_HT-SELEX_cycle1_rep2


title: Human_MBD2_HT-SELEX_cycle1_rep3


title: HEK293T_CTCF_GCN4_IAA_minus_BS_Seq_rep2

description: HEK293T_CTCF_GCN4_IAA_minus_BS_Seq_rep123.bismark_bt2_pe.dedup.bme.all_CpG_result.txt.gz

value: IAA(minus)


title: Human_MBD2_HT-SELEX_cycle2_rep1


title: HEK293T_CTCF_GCN4_IAA_minus_BS_Seq_rep3


title: HEK293T_CTCF_GCN4_IAA_plus_BS_Seq_rep1


title: HEK293T_DMSO_48h_BS_Seq_rep3


title: Six-d-old flu1-5/ex1 were kept in the dark for 4 h and light for 1 h, 1st replicate

city: Beijing

first: Liangsheng

last: Wang

address: No. 2 Yuanmingyuan West Road

institute: China Agricultural University

description: Library name: flu1-5 ex1 4hD 1hL Rep1

library_source: transcriptomic

data_processing:
Transcript quantification for Arabidopsis genes was conducted using Kallisto_0.46.2, and transcripts per million (TPM) values were computed.
Differentially expressed genes were identified using an R script, Sleuth_0.30.0, with criteria set at fold change (FC) > 2 or < 0.5  and a p-value < 0.05.
Assembly: The Arabidopsis TAIR10 genome
Supplementary files format and content: Excel file includes TPM in each sample

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Surface-sterilized Arabidopsis seeds were stratified at 4°C for 2 days, and grown on half MS medium under continues light at 22°C for 6 days.

extract_protocol:
Total RNA was isolated using the HiPure Universal RNA Mini Kit (R4130-02, Magen, Beijing, China) according to the manufacturer’s instructions.
RNA libraries were constructed following the standard BGI RNA project workflow and sequenced on a DNBSEQ-T7 platform.

treatment_protocol: 4 hour in the dark, or 4 hour in the dark followed by 1 hour in the light.

value: Seedlings

value: Tissue

value: 4 h in the dark, 1 h in the light

tag: batch


title: Six-d-old flu1-5/ex1 were kept in the dark for 4 h and light for 1 h, 2nd replicate

description: Library name: flu1-5 ex1 4hD 1hL Rep2


title: Six-d-old flu1-5/ex1 were kept in the dark for 4 h and light for 1 h, 3rd replicate

description: Library name: flu1-5 ex1 4hD 1hL Rep3


title: Human_MBD2_HT-SELEX_cycle1_rep1

value: WT


title: Six-d-old flu1-5/ex1 were kept in the dark for 4 h, 3rd replicate

description: Library name: flu1-5 ex1 4hD Rep3

value: 4 h in the dark


title: HEK293T_CTCF_GCN4_IAA_minus_BS_Seq_rep1


title: HEK293T_CTCF_GCN4_siMBD3_BS_Seq_rep3

description: HEK293T_BS_Seq_CTCF_GCN4_siMBD3_merge_rep123.bismark_bt2_pe.dedup.bme.all_CpG_result.txt.gz


title: Six-d-old flu1-5/ex1 were kept in the dark for 4 h, 1st replicate

description: Library name: flu1-5 ex1 4hD Rep1


title: Six-d-old flu1/ex1 were kept in the dark for 4 h and light for 1 h, 3rd replicate

description: Library name: flu1-1 ex1 4hD 1hL Rep3


title: Six-d-old flu1/ex1 were kept in the dark for 4 h and light for 1 h, 1st replicate

description: Library name: flu1-1 ex1 4hD 1hL Rep1


title: Human_MBD2_HT-SELEX_cycle3_rep2


title: Human_MBD2_HT-SELEX_cycle0_rep2


title: Human_MBD2_HT-SELEX_cycle0_rep3


title: HEK293T_CTCF_GCN4_siMBD3_BS_Seq_rep2


title: Six-d-old flu1-5/ex1 were kept in the dark for 4 h, 2nd replicate

description: Library name: flu1-5 ex1 4hD Rep2


title: Six-d-old flu1/ex1 were kept in the dark for 4 h, 3rd replicate

description: Library name: flu1-1 ex1 4hD Rep3


title: HEK293T_CTCF_GCN4_siMBD3_BS_Seq_rep1


title: Human_MBD2_HT-SELEX_cycle4_rep3


title: Six-d-old flu1/ex1 were kept in the dark for 4 h, 2nd replicate

description: Library name: flu1-1 ex1 4hD Rep2


title: Six-d-old flu1/ex1 were kept in the dark for 4 h, 1st replicate

description: Library name: flu1-1 ex1 4hD Rep1


title: Human_CTCF_Me-SELEX_cycle4_rep3


title: HEK293T_IAA_IP_TET1_rep2

description:
HEK293T_IAA_IP_TET1_rep123_treat_pileup.bigwig
HEK293T_IAA_IP_TET1_rep123_TvsC_peaks.narrowPeak

value: IAA


title: HEK293T_siNC_input-TET1_rep3

data_processing:
The raw ChIP-Seq data were quality-controlled using FastQC (v0.11.7) with default parameters.
ChIP-seq reads were aligned to human genome (hg19) using bowtie2 (v2.3.4) with default parameters and only the uniquely mapped reads were kept for the subsequent analyses.
Sam files were converted to bam files by using samtools (v1.9) with default parameters.
Binding peaks for each sample were identified by using MACS2 software (v2.1.2) with default parameters.
Peaks were annotated by using bedtools (v2.25.0).
All peaks and reads distribution were visualized by using IGV software (v2.4.14).
Reads enrichment heat maps were calculated and plotted using deeptools (v3.5.0).
Assembly: hg19
Supplementary files format and content: narrowPeak (except for input sample)  were generated by MACS2 (v2.1.2) which include the detail informations for all binding peaks;

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody TET1 (GeneTex, Cat No. GTX125888).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection. The libraries were sequenced with an MGIseq2000 instrument (BGI, Shenzhen) using a paired-end scheme (PE100).

treatment_protocol: For the ChIP-seq,HEK293T were co-transfected with 50 mmol of si-NC,si-CHD3,si-CHD4,si-CHD5,si-MBD2,si-MBD3.

value: siNC

value: Input


title: HEK293T_siNC_input-TET1_rep1


title: HEK293T_CTCF_GCN4_siMBD2_BS_Seq_rep3

description: HEK293T_BS_Seq_CTCF_GCN4_siMBD2_merge_rep123.bismark_bt2_pe.dedup.bme.all_CpG_result.txt.gz


title: Human_CTCF_Me-SELEX_cycle4_rep2


title: HEK293T_CTCF_GCN4_siMBD2_BS_Seq_rep1


title: HEK293T_siNC_IP_TET1_rep2


title: HEK293T_CTCF_GCN4_siMBD2_BS_Seq_rep2


title: HEK293T_siNC_IP_TET1_rep3


title: HEK293T_siNC_input-TET1_rep2


title: Human_CTCF_Me-SELEX_cycle3_rep2


title: Human_CTCF_Me-SELEX_cycle3_rep3


title: HEK293T_siNC_IP_TET1_rep1


title: HEK293T_CTCF_GCN4_siNC_BS_Seq_rep2

description: HEK293T_BS_Seq_CTCF_GCN4_siNC_merge_rep123.bismark_bt2_pe.dedup.bme.all_CpG_result.txt.gz

value: si-NC


title: HEK293T_siMBD3_IP_TET1_rep3


title: HEK293T_siMBD3_input-TET1_rep2


title: Human_CTCF_Me-SELEX_cycle3_rep1


title: HEK293T_siMBD3_input-TET1_rep1


title: HEK293T_siMBD3_IP_TET1_rep2


title: Human_CTCF_Me-SELEX_cycle4_rep1


title: HEK293T_siMBD2_input-TET1_rep3


title: HEK293T_CTCF_GCN4_siNC_BS_Seq_rep1


title: HEK293T_siMBD3_IP_TET1_rep1


title: HEK293T_CTCF_GCN4_siNC_BS_Seq_rep3


title: Human_CTCF_Me-SELEX_cycle2_rep3


title: HEK293T_siMBD2_input-TET1_rep2


title: Human_CTCF_Me-SELEX_cycle2_rep2


title: HEK293T_CTCF_GCN4_IAA_plus_input

description:
processed data file:
HEK293T_CTCF_GCN4_IAA_plus_MBD3_IP_vs_input_peaks.narrowPeak.gz

data_processing:
The raw ChIP-Seq data were quality-controlled using FastQC (v0.11.7) with default parameters.
ChIP-seq reads were aligned to human genome (hg19) using bowtie2 (v2.3.4) with default parameters and only the uniquely mapped reads were kept for the subsequent analyses.
Sam files were converted to bam files by using samtools (v1.9) with default parameters.
Binding peaks for each repeat were identified by using MACS2 software (v2.1.2) with default parameters.
Peaks were annotated by using bedtools (v2.25.0).
All peaks and reads distribution were visualized by using IGV software (v2.4.14).
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files were generated by MACS2 (v2.1.2) which include the detail informations for all binding peaks;

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody (ab224827,ab157464,ab188408,Abcam).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection. The libraries were sequenced with an MGIseq2000 instrument (BGI, Shenzhen) using a paired-end scheme (PE100).

tag: antibody


title: HEK293T_CTCF_GCN4_IAA_plus_MBD3_IP


title: HEK293T_CTCF_GCN4_IAA_minus_MBD3_IP

description:
processed data file:
HEK293T_CTCF_GCN4_IAA_minus_MBD3_IP_vs_input_peaks.narrowPeak.gz


title: HEK293T_siMBD2_IP_TET1_rep3


title: HEK293T_siMBD2_input-TET1_rep1


title: HEK293T_siMBD2_IP_TET1_rep2


title: HEK293T_siCHD5_input-TET1_rep3


title: HEK293T_CTCF_GCN4_IAA_minus_input


title: Human_CTCF_Me-SELEX_cycle1_rep3


title: HEK293T_siCHD5_IP_TET1_rep2


title: Human_CTCF_Me-SELEX_cycle2_rep1


title: HEK293T_CTCF_GCN4_siMBD3_IP_CTCF_rep2

description:
processed data file:
HEK293T_CTCF_GCN4_siMBD3_IP_vs_input_peaks.narrowPeak.gz

value: Anti-CTCF


title: HEK293T_siCHD5_IP_TET1_rep3


title: HEK293T_siCHD5_input-TET1_rep1


title: HEK293T_siCHD5_IP_TET1_rep1


title: HEK293T_siCHD5_input-TET1_rep2


title: Human_CTCF_Me-SELEX_cycle1_rep1


title: HEK293T_siMBD2_IP_TET1_rep1


title: HEK293T_CTCF_GCN4_siMBD3_IP_CTCF_rep1


title: HEK293T_CTCF_GCN4_siMBD3_IP_CTCF_rep3


title: HEK293T_siCHD4_input-TET1_rep2


title: Human_CTCF_HT-SELEX_cycle4_rep3


title: Human_CTCF_HT-SELEX_cycle4_rep2


title: HEK293T_CTCF_GCN4_siMBD3_Input_rep3


title: HEK293T_siCHD4_IP_TET1_rep3


title: Human_CTCF_HT-SELEX_cycle4_rep1


title: HEK293T_siCHD4_input-TET1_rep1


title: HEK293T_siCHD4_input-TET1_rep3


title: HEK293T_siCHD4_IP_TET1_rep1


title: HEK293T_CTCF_GCN4_siMBD3_Input_rep2


title: HEK293T_siCHD4_IP_TET1_rep2


title: HEK293T_siCHD3_input-TET1_rep2


title: HEK293T_siCHD3_input-TET1_rep3


title: HEK293T_siCHD3_input-TET1_rep1


title: Human_CTCF_HT-SELEX_cycle3_rep1


title: HEK293T_CTCF_GCN4_siNC3_IP_CTCF_rep2

description:
processed data file:
HEK293T_CTCF_GCN4_siNC3_IP_vs_input_peaks.narrowPeak.gz


title: Human_CTCF_HT-SELEX_cycle2_rep3


title: HEK293T_siNC_input_rep3

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody CTCF (abcam, Cat. #ab128873).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection. The libraries were sequenced with an MGIseq2000 instrument (BGI, Shenzhen) using a paired-end scheme (PE100).


title: HEK293T_siCHD3_IP_TET1_rep2


title: HEK293T_siCHD3_IP_TET1_rep3


title: HEK293T_CTCF_GCN4_siNC3_IP_CTCF_rep3


title: Human_CTCF_HT-SELEX_cycle3_rep2


title: HEK293T_CTCF_GCN4_siMBD3_Input_rep1


title: Human_CTCF_HT-SELEX_cycle3_rep3


title: HEK293T_CTCF_GCN4_siNC3_IP_CTCF_rep1


title: HEK293T_CTCF_GCN4_siNC3_Input_rep3


title: Human_MBD2_HT-SELEX_cycle0_rep1


title: HEK293T_siNC_input_rep1


title: HEK293T_CTCF_GCN4_siNC3_Input_rep2


title: HEK293T_siCHD3_IP_TET1_rep1


title: HEK293T_siNC_IP_CTCF_rep3


title: Human_CTCF_HT-SELEX_cycle2_rep1


title: HEK293T_siMBD3_input_rep2


title: HEK293T_siMBD3_input_rep3


title: HEK293T_siNC_IP_CTCF_rep1


title: HEK293T_CTCF_GCN4_siMBD2_IP_CTCF_rep3

description:
processed data file:
HEK293T_CTCF_GCN4_siMBD2_IP_vs_input_peaks.narrowPeak.gz


title: HEK293T_CTCF_GCN4_siNC3_Input_rep1


title: HEK293T_siMBD3_IP_CTCF_rep2


title: HEK293T_CTCF_GCN4_siMBD2_IP_CTCF_rep2


title: HEK293T_siMBD3_IP_CTCF_rep1


title: HEK293T_siMBD3_IP_CTCF_rep3


title: Human_CTCF_HT-SELEX_cycle1_rep3


title: Six-d-old flu1/ex1 were kept in the dark for 4 h and light for 1 h, 2nd replicate

description: Library name: flu1-1 ex1 4hD 1hL Rep2


title: Human_CTCF_HT-SELEX_cycle1_rep1


title: Human_CTCF_HT-SELEX_cycle1_rep2


title: HEK293T_CTCF_GCN4_siMBD2_IP_CTCF_rep1


title: Human_CTCF_HT-SELEX_cycle2_rep2


title: HEK293T_siMBD3_input_rep1


title: HEK293T_siMBD2_input_rep3


title: Human_CTCF_HT-SELEX_cycle0_rep3


title: Human_CTCF_HT-SELEX_cycle0_rep2


title: HEK293T_siNC_input_rep2


title: HEK293T_CTCF_GCN4_siMBD2_input_rep3


title: HEK293T_siMBD2_input_rep1


title: HEK293T_siMBD2_IP_CTCF_rep2


title: HEK293T_siMBD2_input_rep2


title: HEK293T_siMBD2_IP_CTCF_rep3


title: Human_CTCF_HT-SELEX_cycle0_rep1


title: HEK293T_siCHD5_input_rep2


title: HEK293T_siCHD5_input_rep3


title: HEK293T_siMBD2_IP_CTCF_rep1


title: HEK293T_CTCF_GCN4_siNC2_IP_CTCF_rep3

description:
processed data file:
HEK293T_CTCF_GCN4_siNC2_IP_vs_input_peaks.narrowPeak.gz


description: PCR products from CTCF-Mouse_oligoLib3_Methyl-SELEX_cycle4_rep1

data_processing:
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 41-nt target region without bases annotated as N were extracted using custom script.
Then the CG dinucleotide frequencies at each position on target region of oligos were generated using custom script.
Assembly: NA
Supplementary files format and content: tab-delimited text file include the statistical results of CG dinucleotide frequencies at each position on oligos for each sample.
Library strategy: SELEX

source_name: Rosetta (DE3)

extract_protocol:
The pellet was suspended in 10 ml buffer A (0.5 mg/ml Lysozyme, 50 mM tris-HCl pH 7.5, 300 mM NaCl, 10 mM Imidazole, 1 mM DTT, 1 mM PMSF) and lysed by sonication at ten seconds interval for 10 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA beads was set at 4 ℃ for 30min before being eluted with Buffer A containing 300 mM imidazole
The HT-SELEX experiments were carried out using a previously established protocol12. Briefly, selection ligands consisted of 41 bp (with a 19 bp core CTCF motif sequence flanked by 11 bp random sequences on each side) adapted to Illumina HiSeq Xten sequencing system with multiplexing indices. Ligand libraries were then generated by PCR amplification using primers in Extended Data Table 6 and 41-bp SELEX ligands as templates. The input library was amplified for 16 cycles using Q5® High-Fidelity DNA Polymerase (NEB). All PCR reactions were performed according to the manufacturer's manual. Libraries were sequenced using an Illumina HiSeq Xten sequencer to analyze the identity of each base (A, T, C, G). Then, 150 ng protein and 5 μL of selection ligand were added to Promega binding buffer (10 mM Tris, pH 7.5, 50 mM NaCl, 1 mM DTT, 1 mM MgCl2, 4% glycerol, 0.5 mM EDTA, 5 μg/ml poly -dIdC (Sigma P4929)) until the total volume reaches 25 μL. After a 30-minute incubation at room temperature, 150-µL Promega buffer (without poly-dIdC) containing 10-µL Nickel Sepharose 6 Fast Flow resin (GE) equilibrated in binding buffer was added to the mixture, followed by incubation for 60 minutes with gentle shaking. After binding, the Nickel Sepharose beads were washed for 12 consecutive times with 200 μl Promega Binding Buffer (without poly-dIdC) with gentle shaking. Each wash took 5 min. Subsequently, the residual water was carefully removed from the beads by centrifugation at 500×g for 30 seconds. Then, beads with bound DNA were resuspended in 200 μL of mili-Q water. Finally, approximately 20 μL of beads was PCR amplified for 18 cycles using Phusion DNA polymerase (NEB), and the resulting PCR product was used as the selection ligand for the next cycle of SELEX. This process was repeated four times. After each cycle, purified PCR products were pooled and sequenced using an Illumina HiSeq Xten sequencer.The methylation sensitive-SELEX experiments were carried out using a previously established protocol13. CpG methylation is modified by the CpG-specific methyltransferase M.SssI. The methylation protocol was adapted from13 as follows: 2.5 μL (10U, for initial library) or 1.25 μL (5U, for cycles 1 to 3) CpG methyltransferase M.SssI (NEB; twofold excess units in input and SELEX cycle beyond), with 0.4 μL (for initial library) or 0.2 μL (for cycles 1 to 3) S-adenosylmethionine (SAM), 3.4 μL of 50 mM MgCl2, and 0.2 μL of 100 mM DTT to DNA ligand in a total volume of 20 μL. The mixture was incubated at 37°C for 3 hours to methylate CpG dinucleotides in double-stranded DNA ligands, then at 65°C for 20 minutes to inactivate the M.SssI enzyme before each selection cycle. The methylation status of the ligands was examined by the methylation-specific restriction enzyme BstBI digestion (Extended Data Fig. 5a). CpG methylated DNA ligands and unmethylated DNA ligands SELEX assays were performed in parallel for each protein in separate tubes, and the selection process was repeated for up to 4 cycles to enrich for binding sequences. After each cycle, purified PCR products from each cycle of methyl-SELEX and HT-SELEX were pooled separately and sequenced using an Illumina HiSeq Xten sequencer.


title: HEK293T_CTCF_GCN4_siMBD2_input_rep2


title: HEK293T_siCHD5_IP_CTCF_rep2


description: PCR products from CTCF-Mouse_oligoLib3_HT-SELEX_cycle4_rep1


description: PCR products from CTCF-Mouse_oligoLib3_Methyl-SELEX_cycle3_rep1


title: HEK293T_CTCF_GCN4_siNC2_IP_CTCF_rep2


title: HEK293T_CTCF_GCN4_siNC2_input_rep3


title: HEK293T_siCHD5_IP_CTCF_rep1


title: HEK293T_CTCF_GCN4_siMBD2_input_rep1


title: ZLToFV3

city: Baoding

first: jun

last: Zhang

address: No. 437 Dongguan Street, Baoding City, Hebei Province, China

institute: Plant Protection Institute, Hebei Academy of Agriculture and Forestry Sciences

description: Library name: Sample_4

data_processing:
Samples are sequenced on the platform to getimage files, which are transformed by thesoftware of the sequencing platform, and theoriginal data in FASTQ format (Raw Data) isgenerated. Sequencing data contains a numberof connectors, low-quality Reads, so we usefastp(0.22.0) software to filter the sequencingdata to get high quality sequence (Clean Data)for further analysis.
Assembly: GCF_000188115.2 (SL2.40)
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Solanum lycopersicum

source_name: leaves

extract_protocol:
Total RNA was extracted from mock and the ToBRFV-infected tomato leaves using Invitrogen TRIzol reagent (Thermo Fisher Scientific, Inc.), according to the manufacturer's protocol.
RNA libraries for RNA-seq Were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols.

value: leaves

value: CK

value: Grind with a sterile mortar


title: ZLCK3

description: Library name: Sample_2


title: HEK293T_siCHD5_IP_CTCF_rep3


title: CTCF-Mouse_oligoLib3_input_cycle0_rep1

description: PCR products from CTCF-Mouse_oligoLib3_input_cycle0_rep1

value: Rosetta (DE3)

value: no treatment


description: PCR products from CTCF-Mouse_oligoLib3_HT-SELEX_cycle3_rep1


title: HEK293T_siCHD5_input_rep1

value: human embryonic kidney (HEK) 293T cells


title: ZLToFV1

description: Library name: Sample_3


title: HEK293T_siCHD4_input_rep3


title: ZLCK1

description: Library name: Sample_1


title: HEK293T_siCHD4_input_rep2


title: HEK293T_CTCF_GCN4_siNC2_input_rep2


title: HEK293T_CTCF_GCN4_siNC2_IP_CTCF_rep1


title: Human_CTCF_Me-SELEX_cycle1_rep2

value: E. coli


description: PCR products from CTCF-Mouse_oligoLib2_Methyl-SELEX_cycle4_rep1


title: HEK293T_siCHD4_input_rep1


title: Mammary fat pad, Virgin, pooled from 5+ mice

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University

description:
Library name: GEX_Virgin_S1
10x genomics

library_source: transcriptomic single cell

data_processing:
Single-cell RNA sequencing data was processed using the Cell Ranger pipeline  (v7.0.0, 10x Genomics).
Briefly, raw base call files (BCLs) were demultiplexed into FASTQ files using cellranger mkfastq, followed by alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting using cellranger multi against the mm10 reference genome for both gene expression and Feature Barcode libraries.
The resulting count matrices were imported into R (v4.4.2) and converted into a Seurat object. Initial quality control filtering involved the removal of mitochondrial and ribosomal genes, as well as genes not expressed (≥1 UMI) in at least 10 cells across any sample.
Cells with fewer than 500 or more than 5000 detected genes, or having mitochondrial content >20%, were also excluded. Data normalisation was performed using Seurat's "LogNormalize" method, applying a scale factor of 10,000. Highly variable genes were identified using the FindVariableFeatures function, and the normalised data was subsequently scaled using ScaleData to prepare for dimensionality reduction. Cell cycle phase scores were calculated based on canonical markers using CellCycleScoring and regressed out during scaling.
Principal component analysis (PCA) was performed using the identified variable genes. The optimal number of principal components (PCs) was determined using the JackStraw function, and the first 15 PCs were selected for downstream clustering. Clustering was performed using the Seurat pipeline with a resolution of 0.3, and the resulting clusters were visualised using Uniform Manifold Approximation and Projection (UMAP).
Assembly: mm10
Supplementary files format and content: Matrix (.mtx), barcodes (.barcode.tsv), and features (.features.tsv) files.

organism: Mus musculus

source_name: Mammary adipose tissue

growth_protocol: Primary cells were sorted, no culture conditions are applicable.

extract_protocol:
Chromium Next GEM Chip K Single Cell Kit, Chromium Next GEM Single Cell 5ʹ GEM Kit v2 manufacturer protocols were followed.
Library Construction Kit and TCR Amplification Kit from 10X genomics were used for library construction, manufacturer protocols were followed.

treatment_protocol: Untreated cells.

value: Mammary adipose tissue

value: CD8 T cells

tag: strain

tag: parity

value: Virgin


title: HEK293T_CTCF_GCN4_siNC2_input_rep1


title: CTCF-Mouse_oligoLib2_input_cycle0_rep1

description: PCR products from CTCF-Mouse_oligoLib2_input_cycle0_rep1

value: WT


description: PCR products from CTCF-Mouse_oligoLib2_Methyl-SELEX_cycle3_rep1


title: HEK293T_siCHD4_IP_CTCF_rep3


title: HEK293T_siCHD4_IP_CTCF_rep2


title: CapC_EBd7_dTAG_R2_rep2

city: Oxford

first: Felice

middle: Hoching

last: Tsang

state: Oxfordshire

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Library name: Sample 23
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

data_processing:
Based on Telenius et al. 2020 (bioRxiv)
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Assembly: mm9 or mm9 based custom genome
Supplementary files format and content: "custom format (.gff)"

source_name: EB day 7

growth_protocol: Proliferating ES cells were cultured in IMDM-ES media (Iscove’s Modified Dulbecco Medium (IMDM) (Gibco) supplemented with 15% FBS, 100 U/ml penicillin/streptomycin, 1000 U/ml LIF, and 1.5 x 10-4 M monothioglycerol (MTG; Sigma-Aldrich: M6145)) for 24 to 48 hours prior to primary plating. Subsequently, cells were plated in 10 ml differentiation media on bacterial petri dishes (15000-50000 cells/plate) and cultured for 7 days. Differentiation medium consisted of IMDM media supplemented with 15% heat-inactivated FBS (1 hour at 56 °C), 2 mM L-Glutamine, 0.3 mg/ml transferrin (Roche), 0.05 mg/ml ascorbic acid, MTG and 5% Protein-Free Hybridoma Media II (Gibco). At day 7, EBs were disaggregated and selected for CD71 surface marker.

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016) or the NuCapture-C protocol (Downes et al., 2020). A total of 3 - 10 x 106 ¬¬EB-derived CD71+ were processed per biological replicate and libraries of sufficient quality were used to capture .
5-10ug of each library was sheared using a Covaris S2. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a a Tapestation (Agilent Technologies). Libraries were prepared using NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs). Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each  library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation . The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)

treatment_protocol: For dTAG treatment, CD71+ cells were plated in differentiation media, as described above, supplemented with 1U/ml Epo (Janssen, PL 00242/029), and 500 nM dTAG-13 for up to 6 hours for the treated cells. Control cells were incubated with DMSO for the same amount of time as the treated cells.

value: EB day 7

value: Erythroid


title: CapC_EBd7_dTAG_R2_rep3

description:
Library name: Sample 24
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


description: PCR products from CTCF-Mouse_oligoLib2_HT-SELEX_cycle3_rep1


title: HEK293T_siCHD4_IP_CTCF_rep1


title: CapC_EBd7_dTAG_R2_rep1

description:
Library name: Sample 22
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


description: PCR products from CTCF-Mouse_oligoLib2_HT-SELEX_cycle4_rep1


title: anti-IgM+anti-CD40, 48h, DKO1

city: shenzhen

first: Zhijian

last: Zhu

state: guangdong

address: 1088 Xueyuan Blvd, Nanshan

institute: southern university of science and technology

description: Library name: Sample 9

data_processing:
The sequencing data analysis was conducted by Suzhou Genewiz Biotechnology Co., Ltd. Briefly, FastQC (v0.10.1) was used for sequencing quality assessment; Cutadapt (version 1.9.1) was used for filtering sequencing data; short reads were aligned to the reference genome using Hisat2 (v2.2.1) with default parameters; differential alternative splicing analysis was performed using rMATS (v4.1.0); and gene expression quantification was carried out using HTSeq (v0.6.1).
Assembly: GRCm39.107
Supplementary files format and content: xls files include FPKM and counts values for each sample
Supplementary files format and content: xls files include FPKM and counts values for each sample

source_name: spleen

growth_protocol: For unstimulated B cells: B cells were isolated by negative selection using CD43 magnetic beads, washed with PBS, and total RNA was extracted using Trizol. For stimulated B cells: After isolation, B cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS) and antibiotics, and stimulated with anti-CD40 (1 μg/mL) and anti-IgM (10 μg/mL) for 48 hours at 37°C

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit, and poly(A) mRNA was enriched using the poly(A) mRNA Magnetic Isolation Module. All procedures were performed by Suzhou Genewiz Biological Technology Co., Ltd.
cDNA libraries were constructed using the NEBNext Ultra RNA Library Prep Kit

value: spleen

value: B cell

value: DKO


title: HEK293T_siCHD3_input_rep3

value: Input


title: anti-IgM+anti-CD40, 48h, DKO2

description: Library name: Sample 10


title: Splenic_B_cell_1

description: Library name: Sample11

value: untreated


title: CapC_EBd7_dTAG_Hba1_rep2

description:
Library name: Sample 20
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


title: HEK293T_siMBD3_input-TET1_rep3


description: PCR products from CTCF-Mouse_oligoLib1_Methyl-SELEX_cycle4_rep1


description: PCR products from CTCF-Mouse_oligoLib1_Methyl-SELEX_cycle3_rep1


title: HEK293T_siCHD3_input_rep2


title: Splenic_B_cell_2

description: Library name: Sample12


title: Splenic B cell, DKO3

description: Library name: Sample 6


description: PCR products from CTCF-Mouse_oligoLib1_HT-SELEX_cycle3_rep1


title: anti-IgM+anti-CD40, 48h, WT1

description: Library name: Sample 7


title: HEK293T_siCHD3_input_rep1


title: CapC_EBd7_dTAG_Hba1_rep1

description:
Library name: Sample 19
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


title: anti-IgM+anti-CD40, 48h, WT2

description: Library name: Sample 8


title: CapC_EBd7_dTAG_Hba1_rep3

description:
Library name: Sample 21
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


title: HEK293T_siCHD3_IP_CTCF_rep3

value: Anti-CTCF


description: PCR products from CTCF-Mouse_oligoLib1_HT-SELEX_cycle4_rep1


title: CTCF-Human_oligoLib4_input_cycle0_rep1

description: PCR products from CTCF-Human_oligoLib4_input_cycle0_rep1


title: Splenic B cell, DKO2

description: Library name: Sample 5


title: CapC_EBd7_DMSO_R2_rep3

description:
Library name: Sample 18
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


title: HEK293T_siCHD3_IP_CTCF_rep2


description: PCR products from CTCF-Human_oligoLib4_Methyl-SELEX_cycle3_rep1


title: HEK293T_siCHD3_IP_CTCF_rep1


description: PCR products from CTCF-Human_oligoLib4_HT-SELEX_cycle4_rep1


title: Splenic B cell, DKO1

description: Library name: Sample 4


description: PCR products from CTCF-Human_oligoLib4_Methyl-SELEX_cycle4_rep1


title: Mammary fat pad, parous, pooled from 5+ mice

description:
Library name: GEX_Multiparous_S2
10x genomics

value: Multiparous


title: CapC_EBd7_DMSO_R2_rep2

description:
Library name: Sample 17
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


title: CapC_EBd7_DMSO_Hba1_rep3

description:
Library name: Sample 15
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


title: CapC_EBd7_DMSO_Hba1_rep2

description:
Library name: Sample 14
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


title: mESC_TKO_BS_Seq_rep3

data_processing:
The raw bisulfite-sequencing (BS-Seq) data were quality-controlled using FastQC (v0.11.7) and sequencing adapter were removed by cutadapt (v2.7).
The preprocessed sequence data were mapped to mouse genome (mm10) by using Bismark (v0.22.3).
PCR duplicates were removed by 'deduplicate_bismark' (a command in the Bismark software package). Only the uniquely mapped reads were kept for the subsequent analyses.
Genome-wide m5C sites information was extracted using 'bismark_methylation_extractor' (key parameters: --no_header --comprehensive  --cytosine_report --CX --zero_based).
The genome-wide CpG m5C methylation were extracted based on the 'bismark_methylation_extractor' result by using custom script.
Histograms and cumulative distribution curves of methylation levels at all CpG sites were plotted using python matplotlib and seaborn. Changes of genome-wide methylation levels were visualized by circos(v0.69.9).
Assembly: mm10
Supplementary files format and content: tab-delimited text files (bed6 plus 4 column with additional important values) include CpG methylation results.
Supplementary files format and content: bigwig, methylation ratio results of CpG sites with coverage greater than or equal to 5 are stored in bigwig format for genome browser viewing

source_name: mESC

growth_protocol: Mouse embryonic stem (mES) cells were cultured in mouse ES cell medium containing KnockOut Serum Replacement: DMEM 85%, 15% KnockOut Serum Replacement (Gibco), penicillin–streptomycin (Gibco), 1× non-essential amino acids (Gibco), 1× GlutaMax (Gibco), 1000 U ml–1 LIF (Millipore), 0.4 mM β-mercaptoethanol (Gibco). The cells were typically grown  on 0.1% gelatin-coated plates with irradiated mouse embryonic fibroblasts (MEFs) (Thermo Fisher).

extract_protocol:
The genomic DNA was extracted with Blood & Cell Culture DNA Kits (Thermo Fisher, Cat. #13323). Concentration of the DNA was measured with NanoDrop 2000 Spectrophotometers (Thermo Fisher).
To prepare the bisulfite-seq sample, 5 μg of genomic DNA was sonicated into 250-550bp fragments with Covaris M220 ultrasonicator with the manufacturer’s instructed setting. The fragmented DNA was directly applied for illumina Tru-seq library preparation. The library was quantified with Qubit and sequenced with illumina NovaSeq 6000 sequencer with at least 20% Spike-in PhiX.

value: mESC

value: mouse embryonic stem cells (mESC)

value: TKO (Tet1/2/3 triple knockout)


title: Splenic B cell, WT2

description: Library name: Sample 2


title: CapC_EBd7_DMSO_Hba1_rep1

description:
Library name: Sample 13
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


description: PCR products from CTCF-Human_oligoLib3_Methyl-SELEX_cycle4_rep1

value: Rosetta (DE3)

value: no treatment


title: Splenic B cell, WT1

description: Library name: Sample 1


description: PCR products from CTCF-Human_oligoLib4_HT-SELEX_cycle3_rep1


title: mESC_TKO_BS_Seq_rep1


title: Agrp MFF KO Input 4

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

country: Germany

institute: Max Planck Institute for Metabolism Research

description: Library name: agrp_mffko_fed_input_4

data_processing:
After validation (Agilent 2200 TapeStation) and quantification (Invitrogen Qubit System), transcriptome libraries were pooled. The pool was quantified using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection and sequenced on an Illumina HiSeq 4000 sequencing instrument with a 2 × 100-bp paired-end read length protocol.
We applied the community-curated nfcore rnaseq analysis pipeline (version 1.4) (https://nf-co.re/ rnaseq).
The gene-level quantification was carried out using Salmon (version 0.14.1) using the reference genome GRCm38
Assembly: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012
Supplementary files format and content: Excel sheet of Salmon counts

source_name: 3 mice pooled

extract_protocol:
Mice were sacrificed at 11-12 weeks of age in a random-fed or overnight fasting state by decapitation. Brains were rapidly removed from the skull and placed in a brain slicer blocker (World Precision Instruments) with the inferior view upwards. A 3 mm coronal slice was obtained using two blades. The first blade was located at the intersection between the brainstem and the midbrain, and the second one was placed 3 mm forward, containing the ARC. Then, the brain slice was placed on a plate covered with aluminum foil on ice. Two parasagittal cuts were made at 1 mm distance from the 3V, followed by a horizontal cut just above the ARC. Once the ARC was isolated, it was frozen in liquid nitrogen and stored at -80ºC until further processing. For the Translating Ribosome Affinity Purification (TRAP) protocol 3 bacTRAP control (Mffwt/wt;AgRP-IRES-Cretg/wt;RpL10a-GFPfl/wt) and 3 experimental (Mfffl/fl;AgRP-IRES-Cretg/wt;RpL10a-GFPfl/wt) mice (mixed genders) were pooled for each replicate, accounting for three to four replicates per group. Protein A Dynabeads (Thermo Fischer Scientific) were washed three times in 0.15 M KCl IP wash buffer (20 mM HEPES pH 7.4; 5 mM MgCl2; 150 mM KCl; 1% NP40; 0.5 mM DTT and 100 mg/ml cycloheximide). Beads were resuspended in 275 µl 0.15M KCl IP wash buffer, loaded with 50 µg of 19C8 and 50 µg of 19F7 (Memorial Sloan Kettering Monoclonal Antibody Facility) and incubated with slow end-over-end mixing at 4ºC overnight. Pooled hypothalamic tissue was homogenized in 1 ml of lysis buffer (20 mM HEPES pH 7.4; 5 mM MgCl2; 150 mM KCl; 0.5 mM DTT; 40 U/ml RNasin; 100mg/ml cyclo-heximide; protease and phosphatase inhibitor cocktails containing 1 tablet of cOmplete mini EDTA-free protease inhibitor cocktail/7 ml and 2 tablets of PhosSTOP/10 ml) two times at 250 rpm, and nine times at 750 rpm on a rotating glass/teflon potter homogenizer at 4ºC. Homogenates were transferred to low-binding microcentrifuge tubes (Nonstick, RNase-free microfuge tubes, 1.5 ml; Ambion; Thermo Fischer Scientific) and centrifuged at 2000g for 10 min at 4ºC. The supernatant was transferred to a new tube on ice, and 1/9 sample volume 10% NP-40 (final concentration: 1%) and 1/9 sample volume 300 mM DHPC (final concentration: 30 mM) were added. This solution was mixed, incubated on ice for 5 min, and then centrifuged at 20000g for 10 min at 4ºC. Next, the resulting supernatant was transferred to a new tube, and a 30 µl aliquot was removed, transferred to a new tube, frozen in liquid nitrogen and stored at -80ºC for purification as input RNA. The remaining supernatant was incubated with 200 µl of antibody-bound beads (800 – 1000 µl SN) at 4ºC for 1 h with end-over-end mixing. Then, beads were collected with a magnet in an ice bucket and resuspended in 1000 µl of 0.35 M KCl IP wash buffer (20 mM HEPES pH 7.4; 5 mM MgCl2; 350 mM KCl; 1% NP40; 0.5 mM DTT; 100 mg/ml cycloheximide). This step was repeated three more times in order to wash the beads. After the final wash, the beads were collected with a magnet, and the SN was removed. In order to elute the RNA, RLT buffer (350 µl) (RNeasy Micro Kit, Qiagen) was added to the beads and incubated at RT for 5 min. Finally, RNA was purified using the RNeasy Micro Kit (Qiagen), and its integrity was assessed using an Agilent 2100 bioanalyzer.
Pre-amplification was performed using the Ovation RNA-seq system (V2). Total RNA was used for first-strand cDNA synthesis, using both poly(T) and random primers, followed by second-strand synthesis and isothermal strand-displacement amplification. For library preparation, the Illumina Nextera XT DNA sample preparation protocol was used, with 1 ng cDNA input.

value: Hypothalamus

value: Hypothalamic cells

value: random-fed state Mff KO


title: Agrp MFF KO IP 2

description: Library name: agrp_mffko_fed_ip_2

value: Hypothalamic cells expressing Agrp


title: Agrp MFF KO IP 1

description: Library name: agrp_mffko_fed_ip_1


title: Agrp MFF KO IP 4

description: Library name: agrp_mffko_fed_ip_4


title: Agrp MFF KO IP 3

description: Library name: agrp_mffko_fed_ip_3


title: CapC_EBd5_dTAG_R2_rep2

description:
Library name: Sample 11
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

source_name: EB day 5

value: EB day 5

value: Erythroid


title: CTCF-Human_oligoLib3_input_cycle0_rep1

description: PCR products from CTCF-Human_oligoLib3_input_cycle0_rep1

value: WT


title: mESC_SKO_BS_Seq_rep3

value: SKO (Dnmt1/3a/3b and Tet1/2/3 sextuple knockout)


title: mESC_TKO_BS_Seq_rep2


title: Splenic B cell, WT3

description: Library name: Sample 3

value: spleen

value: B cell


title: CapC_EBd5_dTAG_R2_rep3

description:
Library name: Sample 12
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


title: CapC_EBd5_dTAG_Hba1_rep3

description:
Library name: Sample 9
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


description: PCR products from CTCF-Human_oligoLib3_HT-SELEX_cycle3_rep1


title: Agrp MFF KO Input 3

description: Library name: agrp_mffko_fed_input_3


title: CTCF-Mouse_oligoLib1_input_cycle0_rep1

description: PCR products from CTCF-Mouse_oligoLib1_input_cycle0_rep1


title: CTCF-Human_oligoLib2_input_cycle0_rep1

description: PCR products from CTCF-Human_oligoLib2_input_cycle0_rep1


title: CapC_EBd5_dTAG_Hba1_rep1

description:
Library name: Sample 7
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


description: PCR products from CTCF-Human_oligoLib3_Methyl-SELEX_cycle3_rep1


title: CapC_EBd5_DMSO_R2_rep3

description:
Library name: Sample 6
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


title: mESC_SKO_BS_Seq_rep2


title: mESC_WT_BS_Seq_rep2


description: PCR products from CTCF-Human_oligoLib2_Methyl-SELEX_cycle3_rep1


title: Agrp MFF KO Input 2

description: Library name: agrp_mffko_fed_input_2


title: CapC_EBd5_DMSO_R2_rep2

description:
Library name: Sample 5
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


description: PCR products from CTCF-Human_oligoLib2_HT-SELEX_cycle4_rep1


title: CapC_EBd5_dTAG_R2_rep1

description:
Library name: Sample 10
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


description: PCR products from CTCF-Human_oligoLib2_HT-SELEX_cycle3_rep1


description: PCR products from CTCF-Human_oligoLib3_HT-SELEX_cycle4_rep1


title: Agrp MFF KO Input 1

description: Library name: agrp_mffko_fed_input_1


title: CapC_EBd5_DMSO_Hba1_rep3

description:
Library name: Sample 3
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


title: mESC_SKO_BS_Seq_rep1


title: CapC_EBd5_dTAG_Hba1_rep2

description:
Library name: Sample 8
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


description: PCR products from CTCF-Human_oligoLib1_Methyl-SELEX_cycle4_rep1


title: CTCF-Human_oligoLib1_input_cycle0_rep1

description: PCR products from CTCF-Human_oligoLib1_input_cycle0_rep1


title: mESC_TKO_IP_CTCF_rep3

description:
mESC_TKO_IP_CTCF_rep123_treat_pileup.bigwig
mESC_TKO_IP_CTCF_rep123_TvsC_peaks.narrowPeak.gz

data_processing:
The raw ChIP-Seq data were quality-controlled using FastQC (v0.11.7) with default parameters.
ChIP-seq reads were aligned to mouse genome (mm10) using bowtie2 (v2.3.4) with default parameters and only the uniquely mapped reads were kept for the subsequent analyses.
Sam files were converted to bam files by using samtools (v1.9) with default parameters.
Binding peaks for each sample were identified by using MACS2 software (v2.1.2) with default parameters.
Peaks were annotated by using bedtools (v2.25.0).
The ChIP signal enrichment heat map of the flank of a specific point collection (such as CTCF binding sites) was calculated using deeptools (v3.5.0).
All peaks and reads distribution were visualized by using IGV software (v2.4.14).
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak (except for input sample)  were generated by MACS2 (v2.1.2) which include the detail informations for all binding peaks;

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody (CTCF (abcam, Cat. #ab128873).
Sequencing libraries were made following the protocol of NEB Next ChIP-Seq DNA Sample Prep Kit with minor modifications. To perform end repair of DNA fragments, 12 μL mixture (5µL NEB T4 DNA ligase buffer with 10mM ATP, 2µL dNTPs mix 10mM each, 2µL T4 DNA polymerase 3u/µL, 1µL Klenow DNA polymerase 5u/µL, 2µL T4 PNK 10u/µL) was added to 38 μL of IP DNA and input DNA (20 ng in 38 μL) and incubated for 30 min at 20 °C. The DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 41 μL H2O, following the manufacturer’s instructions. To prepare the DNA fragments for ligation to adapters by adding an “A” base to the 3' end, 9 μL mix (5µL NEB Buffer 2, 1µL dATP 100mM, 3µL Klenow 3'-5' exo minus 5u/µL) was added to 41 μL DNA from previous step and incubated for 30 min at 37 °C. After “A” base addition, the DNA was then purified using VAHTS® DNA Clean Beads (N411-01, Vazyme) and eluted in 42 μL H2O. To ligate adapters to DNA fragments, 8 µL reaction mixture (1µL adapter mix (1uM) (1000005282, MGI), 5µL NEB T4 DNA ligase buffer, 2µL NEB T4 DNA ligase) was added to 42 μL DNA from the previous step and incubated at 16 °C overnight. Size selection (200–500 bp) was achieved using a 1.5% agarose gel and NEB Monarch DNA Gel Extraction Kit (T1020S), and the DNA was eluted in 20 μL H2O. Finally, the libraries were amplified by 18 PCR cycles using Phusion High-Fidelity DNA Polymerases (M0530L, NEB) with the DNA from size selection and purified as size selection.

value: Anti-CTCF


title: mESC_TKO_IP_CTCF_rep2


description: PCR products from CTCF-Human_oligoLib1_Methyl-SELEX_cycle3_rep1


title: 7-d-old flu/toc33-1 seedlings were kept in the dark for 4 hours, 1st replicate

description: flu toc33 4hD-1

data_processing:
Transcript quantification for Arabidopsis genes was conducted using Kallisto_0.46.2, and transcripts per million (TPM) values were computed.
Differentially expressed genes were identified using an R script, Sleuth_0.30.0, with criteria set at fold change (FC) > 1.5 and a p-value < 0.05.
Assembly: The Arabidopsis TAIR10 genome
Supplementary files format and content: Excel file includes TPM in each sample

organism: Arabidopsis

source_name: Leaf

growth_protocol: Surface-sterilized Arabidopsis seeds were stratified at 4°C for 2 days, and grown on half MS medium under continues light at 22°C for 7 days.

extract_protocol:
Total RNA from 7-d-old flu and flu/toc33-1 mutants was isolated using the HiPure Universal RNA Mini Kit (R4130-02, Magen, Beijing, China) according to the manufacturer’s instructions.
RNA libraries were constructed following the standard BGI RNA project workflow and sequenced on a DNBSEQ-T7 platform.

value: Leaf

value: Total leaf cells

value: 4 h dark


title: 7-d-old flu seedlings were kept in the dark for 4 hours and transferred to the light for 1 hour, 3rd replicate

description: flu 4 hD 1hL-3

value: flu

value: 4 h dark, 1 h light


title: mESC_TKO_IP_CTCF_rep1

value: mESC

value: mouse embryonic stem cells (mESC)

value: TKO (Tet1/2/3 triple knockout)


title: 7-d-old flu/toc33-1 seedlings were kept in the dark for 4 hours and transferred to the light for 1 hour, 3rd replicate

description: flu toc33 4hD 1hL-3


title: mESC_WT_BS_Seq_rep3


title: 7-d-old flu/toc33-1 seedlings were kept in the dark for 4 hours and transferred to the light for 1 hour, 2nd replicate

description: flu toc33 4hD 1hL-2


title: HEK293T_siNC_IP_CTCF_rep2

value: human embryonic kidney (HEK) 293T cells

value: siNC


description: PCR products from CTCF-Human_oligoLib2_Methyl-SELEX_cycle4_rep1

value: Rosetta (DE3)

value: no treatment


title: mESC_TKO_INPUT_rep2

description: mESC_TKO_INPUT_rep123_control_lambda.bigwig

value: INPUT


title: 7-d-old flu/toc33-1 seedlings were kept in the dark for 4 hours and transferred to the light for 1 hour, 1st replicate

description: flu toc33 4hD 1hL-1


title: mESC_WT_BS_Seq_rep1

value: WT


title: CTCF-DBD_oligoLib3_input_cycle0_rep1

description: PCR products from CTCF-DBD_oligoLib3_input_cycle0_rep1


title: 7-d-old flu/toc33-1 seedlings were kept in the dark for 4 hours, 3rd replicate

description: flu toc33 4hD-3


title: Stag2_Spleen_Fwd_rep3

description:
Library name: Sample 15
Genome-wide library of Immunoprecipitated fragments

data_processing:
Trimming: trimgalore --stringency 2
Mapping : bowtie2
samtools view chr11
Removing duplicates : samtools rmdup
Generating bigwig tracks: deeptools -bs 20 --normalizeUsingRPKM
Assembly: mm9 or mm9 based custom genome
Supplementary files format and content: bigWig : (deeptools) bamCoverage converison of filtered fragments (duplicate-filtered fragments) from bam to bigwig,  (--binSize 20 --normalizeUsingRPKM)

source_name: mouse spleen cells

growth_protocol: EB: Proliferating ES cells were cultured in IMDM-ES media (Iscove’s Modified Dulbecco Medium (IMDM) (Gibco) supplemented with 15% FBS, 100 U/ml penicillin/streptomycin, 1000 U/ml LIF, and 1.5 x 10-4 M monothioglycerol (MTG; Sigma-Aldrich: M6145)) for 24 to 48 hours prior to primary plating. Subsequently, cells were plated in 10 ml differentiation media on bacterial petri dishes (15000-50000 cells/plate) and cultured for 7 days. Differentiation medium consisted of IMDM media supplemented with 15% heat-inactivated FBS (1 hour at 56 °C), 2 mM L-Glutamine, 0.3 mg/ml transferrin (Roche), 0.05 mg/ml ascorbic acid, MTG and 5% Protein-Free Hybridoma Media II (Gibco). At day 7, EBs were disaggregated and selected for CD71 surface marker. FL: E12.5 mouse fetal liver were dissected and cultured in StemPro medium (Invitrogen) supplemented with Epo (1 U/mL; Janssen, PL 00242/029), SCF (50 ng/mL; Peprotech, 250-03), dexamethasone (1 μM; Hameln, DEXA3.3) and 1× L-Glutamine (Invitrogen) for 6–7d to expand the erythroid progenitor population. If necessary cells were frozen at day 4 and after thawing expanded for a further 2-4 days. Cells were selected for Ter119.

extract_protocol:
DNA was purified by phenol-chloroform extraction and ethanol precipitation with NaOAc, and 1 µl GlycoBlue (Invitrogen). ChIP enrichment was determined by RT-qPCR.
NEBNext Ultra II DNA Library Prep kit for Illumina (New England Biolabs).

treatment_protocol: For ChIP-seq, chromatin was crosslinked with 1 % formaldehyde (Sigma) at room temperature for 10 minutes. Crosslinking was quenched with 130 mM glycine, and cells were washed with cold PBS before snap freezing pelleted cells. Fixed material was stored at -80 ºC. Chromatin immunoprecipitation was performed using Agarose ChIP Assay Kit (Merck Millipore). Briefly, 5-107 cells were lysed by incubation on ice in lysis buffer for 10 minutes. Chromatin was sonicated using the Bioruptor or Bioruptor pico to generate 200-400 bp fragments. Insoluble material was removed by centrifugation (15,000 rcf, 10 min, 4 ºC) and soluble material was diluted to 2 ml with dilution buffer. Immunoprecipitation was performed by incubation of diluted chromatin with antibodies for CTCF (10 µl 07-729; Millipore); RAD21 (5 µg ab154769; Abcam); STAG2 (5 µg A302-580A; Bethyl) overnight. Chromatin incubation with Protein A/agarose slurry, washes and elution were performed according to the manufacturer’s instructions.

value: mouse spleen cells

value: Erythroid


description: PCR products from CTCF-DBD_oligoLib3_Methyl-SELEX_cycle4_rep1


title: CapC_EBd5_DMSO_R2_rep1

description:
Library name: Sample 4
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

value: EB day 5


title: 7-d-old flu/toc33-1 seedlings were kept in the dark for 4 hours, 2nd replicate

description: flu toc33 4hD-2

value: Leaf


title: mESC_BPK25_HiC_rep2_batch2

data_processing:
The raw Hi-C data were quality-controlled using FastQC (v0.11.7).
The sequence reads were mapped to mouse genome (mm10) by using bwa-mem2 (v2.2.1), with parameters '-SP -L 0'.
Then we refer to pairtools walkthrough tutorials using pairtools (v1.1.0) 'parse', 'sort' and 'dedup' to generate interaction pairs results.
The interaction matrices in cool format was created by using 'cload pairs' from cooler(v0.9.3) under 1k resolution. Then two replicates were merged by using 'cooler merge'. The individual and merged contact matrices were zoomified to produce multiresolution cooler (.mcool) files by using 'cooler zoomify'.
The visualization of specific regions of the interaction matrix, insulation boundaries, TADs and dots (loops) analysis are all done using cooltools(v0.7.0).
All pileup analysis, including TAD boundaries, CTCF/MBD3 binding sites, and Dots (loops ancher), were created under 10kb resolution using coolpup.py (v1.1.0) python API.
Assembly: mm10
Supplementary files format and content: mcool, Contact matrices of multiresolutions are stored.

growth_protocol: Mouse embryonic stem (mES) cells were cultured in mouse ES cell medium containing KnockOut Serum Replacement: DMEM 85%, 15% KnockOut Serum Replacement (Gibco), penicillin–streptomycin (Gibco), 1× non-essential amino acids (Gibco), 1× GlutaMax (Gibco), 1000 U ml–1 LIF (Millipore), 0.4 mM β-mercaptoethanol (Gibco). The cells were typically grown on 0.1% gelatin-coated plates with irradiated mouse embryonic fibroblasts (MEFs) (Thermo Fisher).

extract_protocol:
Genomic DNA were extracted.
Four to five million cells were fixed for 5 min with 2 % formaldehyde in PBS and then the reaction was quenched for another 5 min in 0.125 M glycine. Nuclei were then extracted by incubating cells on ice for 30 min (inverting every 10 min) in 10 mM Tris pH 8.0, 10 mM NaCl, 0.2 % NP-40 (IGEPAL CA-630) and protease inhibitor cocktail (Roche).Hi-C libraries were prepared using an adaptor ligation method. Briefly, biotinylated junctions were captured on streptavidin M-280 dynabeads and digested with DpNII enzyme to generate blunt ends. The blunt ends were A-tailed with Klenow (3'→5' exo-) before ligation with adaptor sequences containing unique barcode. After adaptor ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of ~300-1000 bp (insert plus adaptor and PCR primer sequences) were isolated using AMPure beads (Beckman). The purified DNA was captured on an Illumina flow cell for cluster generation.


title: Stag2_Spleen_Fwd_rep2

description:
Library name: Sample 14
Genome-wide library of Immunoprecipitated fragments


title: CTCF-DBD_oligoLib3_HT-SELEX_cycle4_rep1

description: PCR products from CTCF-DBD_oligoLib3_HT-SELEX_cycle4_rep1


title: Rad21_Spleen_Rev_rep3

description:
Library name: Sample 12
Genome-wide library of Immunoprecipitated fragments


title: osteoclast, IFN-γ2, day3

city: Hangzhou

first: Yani

last: Chen

state: Zhejiang

address: No. 268, Kaixuan Rd.

institute: Zhejiang University

description: Library name: IFN2

data_processing:
Raw reads were quality-filtered using KneadData (v0.7.2) and host DNA (GRCh37/C57BL) and rRNA (SILVA v128) were removed with Bowtie2 (v2.4.4). Trimmed reads were assembled with MEGAHIT (v1.2.9), and coding sequences were predicted with Prodigal (v2.6.3). A non-redundant gene catalog was generated using CD-HIT (v4.8.1; 95% identity, 90% coverage).
Assembly: GRCm39.112
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: osteoclast

extract_protocol:
RNA was harvested using a total RNA extraction kit (Tiangen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Total RNA was extracted using the appropriate kit based on sample type (Tiangen DP411, Tiangen DP762-T1C, Aidlab RN40 with CLB or CTAB, or TRIzol, etc.). RNA quality and integrity were assessed using a NanoDrop2000 and an Agilent 2100 Bioanalyzer / LabChip GX, with the following criteria: total amount ≥ 2 μg, concentration ≥ 40 ng/μl, OD260/280 1.7-2.5, OD260/230 0.5-2.5, RIN ≥ 7 (non-plant) or ≥ 6.5 (plant) (or RIN 6.0-6.4 with 28S/18S ≥ 1 and no baseline elevation). mRNA Capture Beads were equilibrated for 30 min on a four-dimensional rotator. mRNA was enriched by two rounds of binding: total RNA was mixed with the beads, denatured at 65°C, held at room temperature for 5 min, and magnetically separated; after washing, mRNA was eluted in Tris Buffer at 80°C. For the second binding, Beads Binding Buffer was added, incubated for 5 min at room temperature, washed, and then Frag/Prime Buffer was added. mRNA fragmentation was performed in a thermal cycler according to sample quality. First-strand cDNA was synthesized using reverse transcriptase in a thermal cycler, and second-strand cDNA synthesis was carried out in a metal bath, followed by purification with 1.8X VAHTS™ DNA Clean Beads and elution in Nuclease-free Water. After end repair and A-tailing, adapters containing index sequences were ligated. The ligation products were purified and size-selected by sequential bead-based steps: 0.9X beads, then 0.6X beads (supernatant retained), and finally 0.1X beads (beads retained), with 80% ethanol washes. PCR amplification was performed, and the PCR products were purified using beads. Library quality was checked on a Qsep-400 system, and only libraries rated A (or B with negligible effect) were used. Libraries were constructed with the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR604-02) and purified with VAHTS™ DNA Clean Beads (Vazyme, N411-03). The qualified libraries were sequenced on an Illumina NovaSeq X Plus platform using paired-end 150 bp reads.

value: osteoclast

value: wildtype


title: osteoclast, IFN-γ1, day3

description: Library name: IFN1


title: mESC_BPK25_HiC_rep1_batch2


title: Rad21_Spleen_Rev_rep2

description:
Library name: Sample 11
Genome-wide library of Immunoprecipitated fragments


title: Rad21_Spleen_Rev_rep1

description:
Library name: Sample 10
Genome-wide library of Immunoprecipitated fragments


title: mESC_SKO_INPUT_rep2

description: mESC_SKO_INPUT_rep123_control_lambda.bigwig

value: SKO (Dnmt1/3a/3b and Tet1/2/3 sextuple knockout)


title: osteoclast, ctrl2, day3

description: Library name: BLANK2


title: CapC_EBd5_DMSO_Hba1_rep2

description:
Library name: Sample 2
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


title: Rad21_Spleen_Fwd_rep3

description:
Library name: Sample 9
Genome-wide library of Immunoprecipitated fragments


title: CapC_EBd7_DMSO_R2_rep1

description:
Library name: Sample 16
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

value: EB day 7


title: 7-d-old flu seedlings were kept in the dark for 4 hours, 2nd replicate

description: flu 4hD-2

value: Total leaf cells

value: flu

value: 4 h dark


title: CapC_EBd5_DMSO_Hba1_rep1

description:
Library name: Sample 1
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown


title: mESC_TKO_INPUT_rep1

value: mESC

value: mouse embryonic stem cells (mESC)

value: TKO (Tet1/2/3 triple knockout)


title: 7-d-old flu seedlings were kept in the dark for 4 hours and transferred to the light for 1 hour, 2nd replicate

description: flu 4 hD 1hL-2

value: 4 h dark, 1 h light


title: Stag2_Spleen_Rev_rep3

description:
Library name: Sample 18
Genome-wide library of Immunoprecipitated fragments


title: mESC_SKO_INPUT_rep1

value: INPUT


title: 7-d-old flu seedlings were kept in the dark for 4 hours and transferred to the light for 1 hour, 1st replicate

description: flu 4 hD 1hL-1


description: PCR products from CTCF-Human_oligoLib1_HT-SELEX_cycle4_rep1

value: Rosetta (DE3)

value: WT

value: no treatment


title: Stag2_Spleen_Rev_rep2

description:
Library name: Sample 17
Genome-wide library of Immunoprecipitated fragments

value: mouse spleen cells

value: Erythroid


title: mESC_TKO_INPUT_rep3

description: mESC_TKO_INPUT_rep123_control_lambda.bigwig


title: 7-d-old flu seedlings were kept in the dark for 4 hours, 3rd replicate

description: flu 4hD-3

value: Leaf


description: PCR products from CTCF-Human_oligoLib1_HT-SELEX_cycle3_rep1


title: Stag2_Spleen_Rev_rep1

description:
Library name: Sample 16
Genome-wide library of Immunoprecipitated fragments


title: 7-d-old flu seedlings were kept in the dark for 4 hours, 1st replicate

description: flu 4hD-1


title: mESC_SKO_IP_CTCF_rep3

description:
mESC_SKO_IP_CTCF_rep123_treat_pileup.bigwig
mESC_SKO_IP_CTCF_rep123_TvsC_peaks.narrowPeak.gz

value: Anti-CTCF


title: osteoclast, IFN-γ3, day3

description: Library name: IFN3

value: osteoclast

value: wildtype