Key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifier | Additional Information |
| Antibody | CTCF(rabbit polyclonal) | Abcam | AB70303 | WB(1:1000) |
| Antibody | BCL11A(rabbit polyclonal) | Abcam | AB191401 | WB(1:1000) |
| Antibody | β-Actin(rabbit polyclonal) | Proteintech | 20536-1-AP | WB(1:2000) |
| Antibody | β-Globin(mouse monoclonal) | Santa Cruz Biotechnology | SC-21757 | WB(1:2000) |
| Antibody | γ-Globin(mouse monoclonal) | Santa Cruz Biotechnology | SC-21756 | WB(1:500) |
| Antibody | ZBTB7A(mouse monoclonal) | R&D systems | MAB3496 | WB(1:1000) |
| Antibody | Human HbF-FITC(recombinant) | Miltenyl Biotec | 130-108-241 | FC(1:100) |
| Antibody | Human CD71-PE(mouse monoclonal) | BioLegend | 334105 | FC(1:100) |
| Antibody | Human CD235a-APC(mouse monoclonal) | BD Biosciences | 561775 | FC(1:100) |
| Antibody | Starbright B700-conjugated goat α-rabbit IgG(goat polyclonal) | Bio-Rad | 12004161 | WB(1:2000-1:5000) |
| Antibody | DyLight 800 goat α-mouse IgG(goat polyclonal) | Bio-Rad | STAR117D800GA | WB(1:2000-1:10,000) |
| Antibody | Acetyl-histone H3 (Lys27)(rabbit polyclonal) | Cell Signaling | 8173S | 2 µg per ChIP |
| Peptide, recombinant protein | SCF | Peprotech | 300-07 | |
| Peptide, recombinant protein | FLT3L | Peprotech | 300-19 | |
| Peptide, recombinant protein | TPO | Peprotech | 300-18 | |
| Peptide, recombinant protein | EPO | Amgen | EPOGEN | |
| Peptide, recombinant protein | IL-3 | Peprotech | 200-03 | |
| Other | SFEM II | STEMCELL Technologies | 09655 | |
| Chemical compound, drug | Dexamethasone | Sigma | D2915 | |
| Chemical compound, drug | Doxycycline | Sigma | D9891 | |
| Peptide, recombinant protein | Recombinant human insulin | Sigma | I2643 | |
| Peptide, recombinant protein | Holo-transferrin | Sigma | T4132 | |
| Chemical compound, drug | Heparin | Sigma | H3393 | |
| Other | Human AB serum | Sigma | H6914 | |
| Peptide, recombinant protein | Cas9 Protein | IDT | 1081058 | |
| Commercial assay or kit | Concanavalin A Beads | Bangs Laboratories, Inc | BP531 | |
| Peptide, recombinant protein | pA-MNase | Gift from Steven Henikoff | ||
| Commercial assay or kit | Dynabeads protein A | Thermo Fisher Scientific | 1002D | |
| Commercial assay or kit | Dynabeads MyOne Streptavidin T1 | Thermo Fisher Scientific | 65601 | |
| Chemical compound, drug | Protease Inhibitor Cocktail | GenDEPOT | 50-101-5486 | |
| Cell line (Homo sapiens) | HUDEP-2 cells | Riken Cell Bank | RCB4557 | |
| Cell line (Homo sapiens) | K562 cells | ATCC | CCL-243 | |
| Biological sample (primary cells Homo sapiens) | Human peripheral blood CD34+ HSPCs | STEMCELL Technologies | 70060.1 | CD34+ HSPC isolated from individual donor. Sex is mixed. |
| Commercial assay or kit | Rapid RNA library kit | Swift Biosciences | R2096 | |
| Commercial assay or kit | Nextera XT library preparation kit | Illumina | FC-131-1024 | |
| Commercial assay or kit | MinElute PCR purification kit | Qiagen | 28004 | |
| Commercial assay or kit | Accel-NGS 2S Plus DNA library kit | Swift Biosciences | 21096 | |
| Commercial assay or kit | 2S Combinatorial Dual Indexing Kit | Swift Biosciences | 28096 | |
| Commercial assay or kit | HiC Next Generation Sequencing Kit | Arima Genomics | ||
| Commercial assay or kit | KAPA library quantification kit | KAPA Biosystems | KK4844 | |
| Commercial assay or kit | RNA clean & concentrator | Zymo Research | R1013 | |
| Other | Raw and processed NGS sequencing data | This paper | GSE160425 | Raw and processed data could be obtained from the link : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE160425 |
| Other | HUDEP-2 GATA1 CUT&RUN | GEO: GSE104676 | GSM2805376 | |
| Other | HUDEP-2 CTCF ChIP-seq | GEO: GSE104676 | GSM3671075 | |
| Other | HUDEP-2 BCL11A ChIP-seq | GEO: GSE103445 | GSM2771529 | |
| Other | Hematopoietic cells differentiation ATAC-seq | Corces et al., 2016 | GSE74912 | |
| Sequence-based reagent | sg3’HS1-3′ | Synthego | Synthesized guide RNA | GAGUCUUGGGAUGGCUGAAG |
| Sequence-based reagent | sg3’HS1-5′ | Synthego | Synthesized guide RNA | GUCCAAGGCAGGACAUGUGU |
| Sequence-based reagent | sgHS5-5′ | Synthego | Synthesized guide RNA | GGCACCCACCUUCAAUCAAA |
| Sequence-based reagent | sgHS5-3' | Synthego | Synthesized guide RNA | AGUCCUGCCAGAUAUAGGUC |
| Sequence-based reagent | sgOR52A1-GATA1-5′ | Synthego | Synthesized guide RNA | AUGUCUUAGUGGAUAACAGA |
| Sequence-based reagent | sgOR52A1-GATA1-3′ | Synthego | Synthesized guide RNA | CAUAUGCUCACAGUAGGAGU |
| Sequence-based reagent | sgHPFH-enhancer-5′ | Synthego | Synthesized guide RNA | GGGCAUGUAGACUGUGAUGU |
| Sequence-based reagent | sgHPFH-enhancer-3′: | Synthego | Synthesized guide RNA | CAUAUGCUCACAGUAGGAGU |
| Sequence-based reagent | sgBCL11A- + 58-5′: | Synthego | Synthesized guide RNA | GGACUGGCAGACCUCUCCAU |
| Sequence-based reagent | sgBCL11A- + 58-3’: | Synthego | Synthesized guide RNA | CUCUUACUUAUGCACACCUG |
| Sequence-based reagent | 3'HS1-deletion-genotyping forward | Eurofins Genomics | PCR primer | TCCCTGTGTGATTACTTGCTTAC |
| Sequence-based reagent | 3'HS1-deletion-genotyping reverse | Eurofins Genomics | PCR primer | AGGTCATAACCATTCAGGTAAACT |
| Sequence-based reagent | 3'HS1-inversion-genotyping forward | Eurofins Genomics | PCR primer | TCCCTGTGTGATTACTTGCTTAC |
| Sequence-based reagent | 3'HS1-inversion-genotyping reverse | Eurofins Genomics | PCR primer | GATGAACTACTTACCACTAGGGGTC |
| Sequence-based reagent | 3'HS1-WT-genotyping forward | Eurofins Genomics | PCR primer | TCCCTGTGTGATTACTTGCTTAC |
| Sequence-based reagent | 3'HS1-WT-genotyping reverse | Eurofins Genomics | PCR primer | CTTCTGACCCCTAGTGGTGTC |
| Sequence-based reagent | HPFH enhancer-deletion-genotyping forward | Eurofins Genomics | PCR primer | ACAATGGCCATATGCTCACA |
| Sequence-based reagent | HPFH enhancer-deletion-genotyping reverse | Eurofins Genomics | PCR primer | GTCCAGGTGATTTTGCTGGT |
| Sequence-based reagent | BCL11A_58 enhancer-deletion forward | Eurofins Genomics | PCR primer | GAACAGAGACCACTACTGGCAAT |
| Sequence-based reagent | BCL11A_58 enhancer-deletion forward | Eurofins Genomics | PCR primer | CTCAGAAAAATGACAGCACCA |
| Sequence-based reagent | HBB-qPCR forward | Eurofins Genomics | PCR primer | CTGAGGAGAAGTCTGCCGTTA |
| Sequence-based reagent | HBB-qPCR reverse | Eurofins Genomics | PCR primer | AGCATCAGGAGTGGACAGAT |
| Sequence-based reagent | HBD-qPCR forward | Eurofins Genomics | PCR primer | GAGGAGAAGACTGCTGTCAATG |
| Sequence-based reagent | HBD-qPCR reverse | Eurofins Genomics | PCR primer | AGGGTAGACCACCAGTAATCTG |
| Sequence-based reagent | HBE-qPCR forward | Eurofins Genomics | PCR primer | GCAAGAAGGTGCTGACTTC |
| Sequence-based reagent | HBE-qPCR reverse | Eurofins Genomics | PCR primer | ACCATCACGTTACCCAGGAG |
| Sequence-based reagent | HBG1/2-qPCR forward | Eurofins Genomics | PCR primer | TGGATGATCTCAAGGGCAC |
| Sequence-based reagent | HBG1/2-qPCR reverse | Eurofins Genomics | PCR primer | TCAGTGGTATCTGGAGGACA |
| Sequence-based reagent | ActB-qPCR forward | Eurofins Genomics | PCR primer | CCTGGCACCCAGCACAATGAAG |
| Sequence-based reagent | ActB-qPCR reverse | Eurofins Genomics | PCR primer | AAGTCATAGTCCGCCTAGAAGC |
| Sequence-based reagent | BCL11A-qPCR forward | Eurofins Genomics | PCR primer | AACCCCAGCACTTAAGCAAA |
| Sequence-based reagent | BCL11A-qPCR reverse | Eurofins Genomics | PCR primer | GGAGGTCATGATCCCCTTCT |
| Sequence-based reagent | 3'HS1 HDR template | Gene Universal | CRISPR/Cas9 knock-in HDR template | AGACATAGAGAAAGTATATT GTGTTTAAAAGACAGCTTC TTTATAATTCTATAGAACTAA AACATTCCTATTTGCCAAGG CAGTGGAGTTTTTGCTGTT CTTAGAACATAATTACTGAA AGACACGCACACATGTCCT GCCTTGGACAAAAAATTGT ATGTCCATCCTTTAAAGGT CATTCCTTTAATGGTCTTTT CTGGACCTGACCCCTAGTG GTAAGTAGTTCATCAAACTT TCTTCCCTCCCTACTTCAGT GATGCATAAGGCAGATCTG CTTTAGTGTAAGCGAGGTC AGGCCCTCAAGAGTCTTG GGATGGCTGAAGATGTAA GAACATTCTATAAGACTTG TCCAAAGAACTGACTGTT TAATGATTCTGAATATGCT AGTTCAGAGAGAATCTAT TTACCACAAACCTGAAG |
| Software, algorithm | HiC-Pro | Servant et al., 2015 | https://github.com/nservant/HiC-Pro | |
| Software, algorithm | Juicer | Durand et al., 2016b | https://github.com/theaidenlab/juicer/wiki | |
| Software, algorithm | Juicebox | Durand et al., 2016a; Durand et al., 2016b | http://aidenlab.org/juicebox/ | |
| Software, algorithm | HiNT | Wang et al., 2020 | https://github.com/parklab/HiNT | |
| Software, algorithm | STAR | Dobin et al., 2013 | https://github.com/alexdobin/STAR | |
| Software, algorithm | edgeR | Robinson et al., 2010 | https://bioconductor.org/packages/edgeR/ | |
| Software, algorithm | Bowtie2 | Langmead and Salzberg, 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | |
| Software, algorithm | BWA-MEM | Bauer et al., 2013 | http://bio-bwa.sourceforge.net/ | |
| Software, algorithm | SAMtools | Sankaran et al., 2009 | http://samtools.sourceforge.net/ | |
| Software, algorithm | Picard Tools | http://broadinstitute.github.io/picard/ | ||
| Software, algorithm | deepTools | Ramírez et al., 2014 | https://deeptools.readthedocs.io/en/develop/ | |
| Software, algorithm | Trim Galore | http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ | ||
| Software, algorithm | Trimmomatic | Bolger et al., 2014 | http://www.usadellab.org/cms/?page=trimmomatic |