rearrangement_ID rearrangement_type cell_type capture_WT_data_archive capture_Mut_data_archive capture_WT_data capture_Mut_data cite cHi-C_raw_wt_data cHi-C_raw_mut_data genome_assembly chr start_prediction end_prediction start_capture end_capture start1 end1 start2 end2 start3 end3 start4 end4 start5 end5 CTCF_data CTCF_paper CTCF_raw_data CTCF_input_raw_data delattP-Rel5d9lac_1 deletion_deletion Distal Forelimb E12 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5855094-SRR5855095.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5855102-SRR5855103.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5855094-SRR5855095 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5855102-SRR5855103 "Rodriguez-Carballo Eddie et al. ""The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes."" Genes & development 31.22 (2017): 2264-2281." SRR5855094-SRR5855095 SRR5855102-SRR5855103 mm10 chr2 70945000 81015000 70945000 81015000 74422050 74693922 74701834 7468746 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_DFL_E12.oriented.narrowPeak.gz "Rodr?guez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, Huynh THN, Ozadam H, Dekker J, Duboule D. The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes Dev. 2017 Nov 15;31(22):2264-2281. doi: 10.1101/gad.307769.117. Epub 2017 Dec 22. PMID: 29273679; PMCID: PMC5769770." SRX3024492 SRX4096951 del1-13d9lac_1 deletion_deletion Distal Forelimb E12 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5855094-SRR5855095.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5855098-SRR5855099.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5855094-SRR5855095 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5855098-SRR5855099 "Rodriguez-Carballo Eddie et al. ""The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes."" Genes & development 31.22 (2017): 2264-2281." SRR5855094-SRR5855095 SRR5855098-SRR5855099 mm10 chr2 70945000 81015000 70945000 81015000 74663890 74693921 74701834 74764314 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_DFL_E12.oriented.narrowPeak.gz "Rodr?guez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, Huynh THN, Ozadam H, Dekker J, Duboule D. The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes Dev. 2017 Nov 15;31(22):2264-2281. doi: 10.1101/gad.307769.117. Epub 2017 Dec 22. PMID: 29273679; PMCID: PMC5769770." SRX3024492 SRX4096951 DelBs deletion E11.5 distal limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5099908.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5099910.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5099908 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5099910 "Bianco Simona et al. ""Polymer physics predicts the effects of structural variants on chromatin architecture."" Nature genetics 50.5 (2018): 662-667." SRR5099908 SRR5099910 mm10 chr1 70945000 81010000 70945000 81010000 76392403 77862399 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_HL-E115.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX1975285-SRX1975286 SRX4096939 InvF inversion E11.5 distal limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5099908.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5099911.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5099908 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5099911 "Bianco Simona et al. ""Polymer physics predicts the effects of structural variants on chromatin architecture."" Nature genetics 50.5 (2018): 662-667." SRR5099908 SRR5099911 mm10 chr1 70945000 81010000 70945000 81010000 74786262 75902132 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_HL-E115.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX1975285-SRX1975286 SRX4096939 MusDelB deletion E11.5 distal limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5099908.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5099909.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5099908 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5099909 "Bianco Simona et al. ""Polymer physics predicts the effects of structural variants on chromatin architecture."" Nature genetics 50.5 (2018): 662-667." SRR5099908 SRR5099909 mm10 chr1 70945000 81010000 70945000 81010000 76395828 78067689 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_HL-E115.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX1975285-SRX1975286 SRX4096939 Bor deletion E12.5 limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179588.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179590.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179588 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179590 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." SRR3179588 SRR3179590 mm10 chr11 109140001 115015000 109140001 115015000 111522545 111540886 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_E125.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX5259427-SRX5259428 SRX4096941 BorC1 deletion_deletion E12.5 limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179588.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8453401-SRR8453402.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179588 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8453401-SRR8453402 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." SRR3179588 SRR8453401-SRR8453402 mm10 chr11 109140001 115015000 109140001 115015000 111904229 111904329 111522535 111540879 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_E125.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX5259427-SRX5259428 SRX4096941 BorC1-2 deletion_deletion_deletion E12.5 limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179588.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8453403-SRR8453404.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179588 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8453403-SRR8453404 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." SRR3179588 SRR8453403-SRR8453404 mm10 chr11 109140001 115015000 109140001 115015000 112209542 112209642 111522535 111540879 111653006 111653106 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_E125.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX5259427-SRX5259428 SRX4096941 BorC1-4 deletion_deletion_deletion_deletion_deletion E12.5 limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179588.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8453405.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179588 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8453405 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." SRR3179588 SRR8453405 mm10 chr11 109140001 115015000 109140001 115015000 111522535 111540879 111514320 111653006 111653106 111904229 111904329 111964807 112103393 112103493 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_E125.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX5259427-SRX5259428 SRX4096941 dup-C duplication E12.5 limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179588.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3733921.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179588 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3733921 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." SRR3179588 SRR3733921 mm10 chr11 109140001 115015000 109140001 115015000 110910796 112653378 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_E125.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX5259427-SRX5259428 SRX4096941 dup-L duplication E12.5 limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179588.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179589.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179588 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179589 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." SRR3179588 SRR3179589 mm10 chr11 109140001 115015000 109140001 115015000 111098275 112653378 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_E125.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX5259427-SRX5259428 SRX4096941 Dup-LBor duplication_deletion E12.5 limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179588.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179591.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179588 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179591 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." SRR3179588 SRR3179591 mm10 chr11 109140001 115015000 109140001 115015000 111098275 112653378 111522545 111540886 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_E125.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX5259427-SRX5259428 SRX4096941 dup-S duplication E12.5 limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179588.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3733922.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179588 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3733922 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." SRR3179588 SRR3733922 mm10 chr11 109140001 115015000 109140001 115015000 111891303 112311622 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_E125.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX5259427-SRX5259428 SRX4096941 InvC inversion E12.5 limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179588.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8453396-SRR8453397.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179588 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8453396-SRR8453397 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." SRR3179588 SRR8453396-SRR8453397 mm10 chr11 109140001 115015000 109140001 115015000 111522535 112653434 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_E125.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX5259427-SRX5259428 SRX4096941 InvIntra inversion E12.5 limb buds https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR3179588.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8453398-SRR8453399.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR3179588 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8453398-SRR8453399 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." SRR3179588 SRR8453398-SRR8453399 mm10 chr11 109140001 115015000 109140001 115015000 111540879 112653434 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_E125.oriented.narrowPeak.gz "Wiehle L, Thorn GJ, Raddatz G, Clarkson CT, Rippe K, Lyko F, Breiling A, Teif VB. DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries. Genome Res. 2019 May;29(5):750-761. doi: 10.1101/gr.239707.118. Epub 2019 Apr 4. PMID: 30948436; PMCID: PMC6499307." SRX5259427-SRX5259428 SRX4096941 D3839 deletion_deletion erythroid cells https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5453529-SRR5453530-SRR5453531-SRR5453514-SRR5453515-SRR5453516-SRR5453505-SRR5453506-SRR5453507.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5453532-SRR5453533-SRR5453534.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5453529-SRR5453530-SRR5453531-SRR5453514-SRR5453515-SRR5453516-SRR5453505-SRR5453506-SRR5453507 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5453532-SRR5453533-SRR5453534 Hanssen LLP, et al. Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. Nat Cell Biol. 2017 SRR5453529-SRR5453530-SRR5453531-SRR5453514-SRR5453515-SRR5453516-SRR5453505-SRR5453506-SRR5453507 SRR5453532-SRR5453533-SRR5453534 mm10 chr11 32190000 32335000 32190000 32335000 32238646 32238667 32237202 32237228 _ Pdgfra_KO_fibr deletion fibroblasts https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/CapF1-CapF2.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/CapF3-CapF4.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/CapF1-CapF2/ https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/CapF3-CapF4/ unpublished data unpublished data unpublished data mm10 chr5 74150000 76400000 74150000 76400000 _ Pdgfra_left deletion fibroblasts https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/CapF1-CapF2.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/CapF5-CapF6.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/CapF5-CapF6/ https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/CapF3-CapF4/ unpublished data unpublished data unpublished data mm10 chr5 74150000 76400000 74150000 76400000 _ i4i5 deletion_deletion FLHL https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8284500-SRR8284501-SRR8984911.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8284495-SRR8284496.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8284500-SRR8284501-SRR8984911 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8284495-SRR8284496 "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." SRR8284500-SRR8284501-SRR8984911 SRR8284495-SRR8284496 mm10 chr5 27460000 30345000 27460000 30345000 29293392 29293421 29336029 29336056 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FLHL-E105.oriented.narrowPeak.gz "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." "SRX5099280;SRX5099281" SRX4096949 i4i5ZRS_1 deletion_deletion_deletion FLHL https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8284500-SRR8284501-SRR8984911.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8284497-SRR8284498.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8284500-SRR8284501-SRR8984911 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8284497-SRR8284498 "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." SRR8284500-SRR8284501-SRR8984911 SRR8284497-SRR8284498 mm10 chr5 27460000 30345000 27460000 30345000 29293392 29293421 29336029 29336056 29314814 29314832 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FLHL-E105.oriented.narrowPeak.gz "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." "SRX5099280;SRX5099281" SRX4096949 i4i5ZRSreg deletion_deletion_deletion FLHL https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8284500-SRR8284501-SRR8984911.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8984915-SRR8984916.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8284500-SRR8284501-SRR8984911 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8984915-SRR8984916 "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." SRR8284500-SRR8284501-SRR8984911 SRR8984915-SRR8984916 mm10 chr5 27460000 30345000 27460000 30345000 29293392 29293421 29336029 29336056 29314818 29315227 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FLHL-E105.oriented.narrowPeak.gz "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." "SRX5099280;SRX5099281" SRX4096949 Lprom deletion FLHL https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8284500-SRR8284501-SRR8984911.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8284499-SRR8984910.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8284500-SRR8284501-SRR8984911 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8284499-SRR8984910 "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." SRR8284500-SRR8284501-SRR8984911 SRR8284499-SRR8984910 mm10 chr5 27460000 30345000 27460000 30345000 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FLHL-E105.oriented.narrowPeak.gz "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." "SRX5099280;SRX5099281" SRX4096949 ZRSreg deletion FLHL https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8284500-SRR8284501-SRR8984911.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8984912.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8284500-SRR8284501-SRR8984911 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8984912 "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." SRR8284500-SRR8284501-SRR8984911 SRR8984912 mm10 chr5 27460000 30345000 27460000 30345000 29314818 29315227 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FLHL-E105.oriented.narrowPeak.gz "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." "SRX5099280;SRX5099281" SRX4096949 DelL-Mm deletion Forelimb E11.5 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6024957-SRR6024958-SRR6024959-SRR6024960.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6024981-SRR6024982.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6024957-SRR6024958-SRR6024959-SRR6024960 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6024981-SRR6024982 "Kragesteen Bjort K. et al. ""Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis."" Nature genetics 50.10 (2018): 1463-1473." SRR6024957-SRR6024958-SRR6024959-SRR6024960 SRR6024981-SRR6024982 mm10 chr13 53895001 57200000 53895001 57200000 56048376 56147390 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FL-E115.oriented.narrowPeak.gz "Andrey G, Sch?pflin R, Jerkovi? I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S. Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. Genome Res. 2017 Feb;27(2):223-233. doi: 10.1101/gr.213066.116. Epub 2016 Dec 6. PMID: 27923844; PMCID: PMC5287228." SRX1975279 SRX4096942 Inv1 inversion forelimb E11.5 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR7500315.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR7500316.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR7500315 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR7500316 "Kraft Katerina et al. ""Serial genomic inversions induce tissue-specific architectural stripes gene misexpression and congenital malformations."" Nature cell biology 21.3 (2019): 305-310." SRR7500315 SRR7500316 mm10 chr1 70945000 81015000 70945000 81015000 75279391 75902131 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FL-E115.oriented.narrowPeak.gz "Andrey G, Sch?pflin R, Jerkovi? I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S. Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. Genome Res. 2017 Feb;27(2):223-233. doi: 10.1101/gr.213066.116. Epub 2016 Dec 6. PMID: 27923844; PMCID: PMC5287228." SRX1975279 SRX4096942 Inv1-Mm_2 inversion Forelimb E11.5 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6024957-SRR6024958-SRR6024959-SRR6024960.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6024979-SRR6024980.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6024957-SRR6024958-SRR6024959-SRR6024960 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6024979-SRR6024980 "Kragesteen Bjort K. et al. ""Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis."" Nature genetics 50.10 (2018): 1463-1473." SRR6024957-SRR6024958-SRR6024959-SRR6024960 SRR6024979-SRR6024980 mm10 chr13 53895001 57200000 53895001 57200000 56048376 56160753 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_HL-E115.oriented.narrowPeak.gz "Andrey G, Sch?pflin R, Jerkovi? I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S. Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. Genome Res. 2017 Feb;27(2):223-233. doi: 10.1101/gr.213066.116. Epub 2016 Dec 6. PMID: 27923844; PMCID: PMC5287228." SRX1975279 SRX4096942 Inv1d inversion forelimb E11.5 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR7500315.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR7500320.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR7500315 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR7500320 "Kraft Katerina et al. ""Serial genomic inversions induce tissue-specific architectural stripes gene misexpression and congenital malformations."" Nature cell biology 21.3 (2019): 305-310." SRR7500315 SRR7500320 mm10 chr1 70945000 81015000 70945000 81015000 75650966 75655176 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FL-E115.oriented.narrowPeak.gz "Andrey G, Sch?pflin R, Jerkovi? I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S. Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. Genome Res. 2017 Feb;27(2):223-233. doi: 10.1101/gr.213066.116. Epub 2016 Dec 6. PMID: 27923844; PMCID: PMC5287228." SRX1975279 SRX4096942 Inv2 inversion forelimb E11.5 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR7500315.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR7500317.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR7500315 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR7500317 "Kraft Katerina et al. ""Serial genomic inversions induce tissue-specific architectural stripes gene misexpression and congenital malformations."" Nature cell biology 21.3 (2019): 305-310." SRR7500315 SRR7500317 mm10 chr1 70945000 81015000 70945000 81015000 75135035 75902131 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FL-E115.oriented.narrowPeak.gz "Andrey G, Sch?pflin R, Jerkovi? I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S. Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. Genome Res. 2017 Feb;27(2):223-233. doi: 10.1101/gr.213066.116. Epub 2016 Dec 6. PMID: 27923844; PMCID: PMC5287228." SRX1975279 SRX4096942 Inv3 inversion forelimb E11.5 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR7500315.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR7500318.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR7500315 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR7500318 "Kraft Katerina et al. ""Serial genomic inversions induce tissue-specific architectural stripes gene misexpression and congenital malformations."" Nature cell biology 21.3 (2019): 305-310." SRR7500315 SRR7500318 mm10 chr1 70945000 81015000 70945000 81015000 74887741 75902131 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FL-E115.oriented.narrowPeak.gz "Andrey G, Sch?pflin R, Jerkovi? I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S. Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. Genome Res. 2017 Feb;27(2):223-233. doi: 10.1101/gr.213066.116. Epub 2016 Dec 6. PMID: 27923844; PMCID: PMC5287228." SRX1975279 SRX4096942 Inv4 inversion forelimb E11.5 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR7500315.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR7500319.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR7500315 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR7500319 "Kraft Katerina et al. ""Serial genomic inversions induce tissue-specific architectural stripes gene misexpression and congenital malformations."" Nature cell biology 21.3 (2019): 305-310." SRR7500315 SRR7500319 mm10 chr1 70945000 81015000 70945000 81015000 7489655 78902131 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FL-E115.oriented.narrowPeak.gz "Andrey G, Sch?pflin R, Jerkovi? I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S. Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. Genome Res. 2017 Feb;27(2):223-233. doi: 10.1101/gr.213066.116. Epub 2016 Dec 6. PMID: 27923844; PMCID: PMC5287228." SRX1975279 SRX4096942 Neur1-Mm deletion Forelimb E11.5 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6024957-SRR6024958-SRR6024959-SRR6024960.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6024987-SRR6024988.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6024957-SRR6024958-SRR6024959-SRR6024960 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6024987-SRR6024988 "Kragesteen Bjort K. et al. ""Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis."" Nature genetics 50.10 (2018): 1463-1473." SRR6024957-SRR6024958-SRR6024959-SRR6024960 SRR6024987-SRR6024988 mm10 chr13 53895001 57200000 53895001 57200000 56219601 56264136 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FL-E115.oriented.narrowPeak.gz "Andrey G, Sch?pflin R, Jerkovi? I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S. Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. Genome Res. 2017 Feb;27(2):223-233. doi: 10.1101/gr.213066.116. Epub 2016 Dec 6. PMID: 27923844; PMCID: PMC5287228." SRX1975279 SRX4096942 Inv1-Mm_1 inversion Hindlimb E11.5 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6024961-SRR6024962-SRR6024963-SRR6024964.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6451287-SRR7203995.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6024961-SRR6024962-SRR6024963-SRR6024964 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6451287-SRR7203995 "Kragesteen Bjort K. et al. ""Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis."" Nature genetics 50.10 (2018): 1463-1473." SRR6024961-SRR6024962-SRR6024963-SRR6024964 SRR6451287-SRR7203995 mm10 chr13 53895001 57200000 53895001 57200000 56048376 56160753 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_HL-E115.oriented.narrowPeak.gz "Andrey G, Sch?pflin R, Jerkovi? I, Heinrich V, Ibrahim DM, Paliou C, Hochradel M, Timmermann B, Haas S, Vingron M, Mundlos S. Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding. Genome Res. 2017 Feb;27(2):223-233. doi: 10.1101/gr.213066.116. Epub 2016 Dec 6. PMID: 27923844; PMCID: PMC5287228." SRX1975285-SRX1975286 SRX4096967 DelB deletion human fibroblasts https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5099904.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5099905.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5099904 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5099905 "Bianco Simona et al. ""Polymer physics predicts the effects of structural variants on chromatin architecture."" Nature genetics 50.5 (2018): 662-667." SRR5099904 SRR5099905 hg38 chr2 217445000 223235000 217445000 223235000 220413511 222149613 _ kit30_mast deletion mast cells https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/VLA2-VLA5-CapM1-CapM2.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/VLA4-VLA6.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/VLA2-VLA5-CapM1-CapM2/ https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/VLA4-VLA6/ unpublished data unpublished data unpublished data mm10 chr5 74130000 76415000 74130000 76415000 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/mast_cells.oriented.narrowPeak.gz unpublished data unpublished data unpublished data kit30plus deletion mast cells https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/VLA2-VLA5-CapM1-CapM2.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/VLA7-VLA12.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/VLA2-VLA5-CapM1-CapM2/ https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/VLA7-VLA12/ unpublished data unpublished data unpublished data mm10 chr5 74130000 76415000 74130000 76415000 75852780 75881218 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/mast_cells.oriented.narrowPeak.gz unpublished data unpublished data unpublished data Pdgfra_KO_mast deletion mast cells https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/VLA2-VLA5-CapM1-CapM2.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/VLA16-VLA19.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/VLA2-VLA5-CapM1-CapM2/ https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/VLA16-VLA19/ unpublished data unpublished data unpublished data mm10 chr5 74130000 76415000 74130000 76415000 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_MEF.oriented.narrowPeak.gz unpublished data unpublished data unpublished data FirreKO_1 deletion MEF female https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6129090-SRR6129091-SRR6129092-SRR6129093-SRR6129094-SRR6129095-SRR6129096-SRR6129097.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6129090-SRR6129091-SRR6129092-SRR6129093-SRR6129094-SRR6129095-SRR6129096-SRR6129097 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104 "Barutcu A. Rasim et al. ""A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus."" Nature communications 9.1 (2018): 1-11." SRR6129090-SRR6129091-SRR6129092-SRR6129093-SRR6129094-SRR6129095-SRR6129096-SRR6129097 SRR6129098-SRR6129099-SRR6129100-SRR6129101-SRR6129102-SRR6129103-SRR6129104 mm10 chrX 50550000 50675000 50550000 50675000 50555286 50637116 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_MEF.oriented.narrowPeak.gz "Barutcu A. Rasim et al. ""A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus."" Nature communications 9.1 (2018): 1-11." SRX3230671-SRX3230678 SRX3230694-SRX3230695 FirreKO_2 deletion MEF male https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6129105-SRR6129106-SRR6129107-SRR6129108.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6129105-SRR6129106-SRR6129107-SRR6129108 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114 "Barutcu A. Rasim et al. ""A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus."" Nature communications 9.1 (2018): 1-11." SRR6129105-SRR6129106-SRR6129107-SRR6129108 SRR6129109-SRR6129110-SRR6129111-SRR6129112-SRR6129113-SRR6129114 mm10 chrX 50550000 50675000 50550000 50675000 50555286 50637116 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_MEF.oriented.narrowPeak.gz "Barutcu A. Rasim et al. ""A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus."" Nature communications 9.1 (2018): 1-11." SRX3230671-SRX3230678 SRX3230694-SRX3230695 kit30_mel deletion melanocytes https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/CapM3-CapM4.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/CapM5-CapM6.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/CapM3-CapM4/ https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/CapM5-CapM6/ unpublished data unpublished data unpublished data mm10 chr5 74130000 76415000 74130000 76415000 _ FirreKO_3 deletion mESC male https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6158160-SRR6158161.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR6158158-SRR6158159.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6158160-SRR6158161 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR6158158-SRR6158159 "Barutcu A. Rasim et al. ""A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus."" Nature communications 9.1 (2018): 1-11." SRR6158160-SRR6158161 SRR6158158-SRR6158159 mm10 chrX 50550000 50675000 50550000 50675000 50555286 50637116 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_MEF.oriented.narrowPeak.gz "Barutcu A. Rasim et al. ""A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus."" Nature communications 9.1 (2018): 1-11." SRX3230671-SRX3230678 SRX4096948 i4i5ZRS_2 deletion_deletion_deletion midbrain https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8284503-SRR8284504.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR8984913-SRR8984914.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8284503-SRR8284504 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR8984913-SRR8984914 "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." SRR8284503-SRR8284504 SRR8984913-SRR8984914 mm10 chr5 27460000 30345000 27460000 30345000 29293392 29293421 29336029 29336056 29314814 29314832 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_FLHL-E105.oriented.narrowPeak.gz "Paliou Christina et al. ""Preformed chromatin topology assists transcriptional robustness of Shh during limb development."" Proceedings of the National Academy of Sciences 116.25 (2019): 12390-12399." "SRX5099280;SRX5099281" SRX4096953 del1-13d9lac_2 deletion_deletion Proximal Forelimb E12 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5855104-SRR5855105.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5855100-SRR5855101.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5855104-SRR5855105 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5855100-SRR5855101 "Rodriguez-Carballo Eddie et al. ""The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes."" Genes & development 31.22 (2017): 2264-2281." SRR5855104-SRR5855105 SRR5855100-SRR5855101 mm10 chr2 70945000 81015000 70945000 81015000 74663890 74693921 74701834 74764314 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_PFL_E12.oriented.narrowPeak.gz "Rodr?guez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, Huynh THN, Ozadam H, Dekker J, Duboule D. The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes Dev. 2017 Nov 15;31(22):2264-2281. doi: 10.1101/gad.307769.117. Epub 2017 Dec 22. PMID: 29273679; PMCID: PMC5769770." SRX3024493 SRX4096950 delattP-Rel5d9lac_2 deletion_deletion Proximal Forelimb E12 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5855104-SRR5855105.tar.gz https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/hic_dataset_zipped/SRR5855104-SRR5855105.tar.gz https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5855104-SRR5855105 https://genedev.bionet.nsc.ru/hic_out/Unordered/INC_COST_3DBenchmark_%5bremake%5d/SRR5855104-SRR5855105 "Rodriguez-Carballo Eddie et al. ""The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes."" Genes & development 31.22 (2017): 2264-2281." SRR5855104-SRR5855105 SRR5855104-SRR5855105 mm10 chr2 70945000 81015000 70945000 81015000 74422050 74693922 74701834 7468746 https://genedev.bionet.nsc.ru/hic_out/by_Project/INC_COST_3DBenchmark/CTCF_data/CTCF_PFL_E12.oriented.narrowPeak.gz "Rodr?guez-Carballo E, Lopez-Delisle L, Zhan Y, Fabre PJ, Beccari L, El-Idrissi I, Huynh THN, Ozadam H, Dekker J, Duboule D. The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes. Genes Dev. 2017 Nov 15;31(22):2264-2281. doi: 10.1101/gad.307769.117. Epub 2017 Dec 22. PMID: 29273679; PMCID: PMC5769770." SRX3024493 SRX4096952