rearrangement_ID number of replices zigotness path_to_processed_data rearrangement_type cell_type capture_WT_raw_data capture_Mut_raw_data cite genome_assembly chr start_capture end_capture start1 end1 start2 end2 start3 end3 start4 end4 start5 end5 start6 end6 Kit30 2 homozygous  ./deletion/mast_cell/Kit30 deletion mast_cell mm10 chr5 74130000 76415000 75852780 75881218 Kit30plus 2 homozygous  ./deletion/mast_cell/Kit30plus deletion mast_cell mm10 chr5 74130000 76415000 75736367 757336679 75852780 75881218 Pdgfra_KO 2 heterozygous  ./deletion/mast_cell/Pdgfra_KO deletion mast_cell mm10 chr5 74130000 76415000 75155624 75852780 MusDelB 1 homozygous  ./deletion/E11.5 distal limb buds/MusDelB deletion E11.5 distal limb buds SRR5099908 SRR5099909 "Bianco Simona et al. ""Polymer physics predicts the effects of structural variants on chromatin architecture."" Nature genetics 50.5 (2018): 662-667." mm10 chr1 70945000 81010000 76395828 78067689 DelBs 1 homozygous  ./deletion/E11.5 distal limb buds/DelBs deletion E11.5 distal limb buds SRR5099908 SRR5099910 mm10 chr1 70945000 81010000 76395828 77865824 InvF 1 homozygous  ./inversion/E11.5 distal limb buds/InvF inversion E11.5 distal limb buds SRR5099908 SRR5099911 mm10 chr1 70945000 81010000 74786262 75902132 DelB 1 homozygous  ./deletion/human fibroblasts/DelB deletion human fibroblasts SRX2416656 SRX2416657 hg38 chr2 217445000 223235000 220413511 222149613 Inv1 1 homozygous  ./inversion/forelimb E11.5/Inv1 inversion forelimb E11.5 SRX4369709 SRX4369710 "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." mm10 chr1 70945000 81015000 75279391 75902131 Inv2 1 heterozygous  ./inversion/forelimb E11.5/Inv2 inversion forelimb E11.5 SRX4369709 SRX4369711 mm10 chr1 70945000 81015000 75135035 75902131 Inv3 1 heterozygous  ./inversion/forelimb E11.5/Inv3 inversion forelimb E11.5 SRX4369709 SRX4369712 mm10 chr1 70945000 81015000 74887741 75902131 Inv4 1 heterozygous  ./inversion/forelimb E11.5/Inv4 inversion forelimb E11.5 SRX4369709 SRX4369713 mm10 chr1 70945000 81015000 7489655 78902131 Inv1d 1 homozygous  ./inversion/forelimb E11.5/Inv1d inversion forelimb E11.5 SRX4369709 SRX4369714 mm10 chr1 70945000 81015000 75650966 75655176 del1-13d9lac 1 homozygous  ./2deletion/Distal Forelimb E12/del1-13d9lac deletion/deletion Distal Forelimb E12 SRX3024410 SRX3024412 "Rodríguez-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." mm10 chr2 70945000 81015000 74663890 74693921 74701834 74764314 del1-13d9lac 1 homozygous  ./2deletion/Proximal Forelimb E12/del1-13d9lac deletion/deletion Proximal Forelimb E12 SRX3024415 SRX3024413 mm10 chr2 70945000 81015000 74663890 74693921 74701834 74764314 delattP-Rel5d9lac 1 homozygous  ./2deletion/Distal Forelimb E12/delattP-Rel5d9lac deletion/deletion Distal Forelimb E12 SRX3024410 SRX3024414 mm10 chr2 70945000 81015000 74422050 74693922 74701834 7468746 delattP-Rel5d9lac 1 homozygous  ./2deletion/Proximal Forelimb E12/delattP-Rel5d9lac deletion/deletion Proximal Forelimb E12 SRX3024415 SRX3024415 mm10 chr2 70945000 81015000 74422050 74693922 74701834 7468746 dup-S 1 heterozygous  ./duplication/E12.5 limb buds/dup-S duplication E12.5 limb buds SRX1593831 SRX1889696 "Franke Martin et al. ""Formation of new chromatin domains determines pathogenicity of genomic duplications."" Nature 538.7624 (2016): 265-269." mm10 chr11 109140001 115015000 111891303 112311622 dup-L 1 homozygous  ./duplication/E12.5 limb buds/dup-L duplication E12.5 limb buds SRX1593831 SRX1593832 mm10 chr11 109140001 115015000 111098275 112653378 dup-C 1 homozygous  ./duplication/E12.5 limb buds/dup-C duplication E12.5 limb buds SRX1593831 SRX1889695 mm10 chr11 109140001 115015000 110910796 112653378 Bor 1 homozygous  ./deletion/E12.5 limb buds/Bor deletion E12.5 limb buds SRX1593831 SRX1593833 mm10 chr11 109140001 115015000 111522545 111540886 Dup-LBor 1 homozygous  ./duplication&deletoin/E12.5 limb buds/Dup-LBor duplication/deletoin E12.5 limb buds SRX1593831 SRX1593834 mm10 chr11 109140001 115015000 111098275 112653378 111522545 111540886 InvC 1 homozygous  ./inversion/E12.5 limb buds/ InvC inversion E12.5 limb buds SRX1593831 SRX5260108 mm10 chr11 109140001 115015000 111522535 112653434 InvIntra 1 homozygous  ./inversion/E12.5 limb buds/InvIntra inversion E12.5 limb buds SRX1593831 SRX5260109 mm10 chr11 109140001 115015000 111540879 112653434 BorC1-4 1 homozygous  ./5deletion/E12.5 limb buds/BorC1-4 deletion/deletion/deletion/deletion/deletion E12.5 limb buds SRX5260105 mm10 chr11 109140001 115015000 111522535 111540879 111514320 111653006 111653106 111904229 111904329 111964807 112103393 112103493 BorC1-2 1 homozygous  ./3deletion/BorC1-2 deletion/deletion/deletion E12.5 limb buds SRX1593831 SRX5260104 mm10 chr11 109140001 115015000 112209542 112209642 111522535 111540879 111653006 111653106 BorC1 1 homozygous  ./2deletion/E12.5 limb buds/BorC1 deletion/deletion E12.5 limb buds SRX1593831 SRX5260103 mm10 chr11 109140001 115015000 111904229 111904329 111522535 111540879 Inv1-Mm "2 (Mut) 4 (WT)" homozygous  ./inversion/Hindlimb E11.5/Inv1-Mm inversion Hindlimb E11.5 SRX3175636; SRX3175637; SRX3175638; SRX3175639; SRX3542185; SRX4112993 "Kragesteen Bjørt K. et al. ""Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis."" Nature genetics 50.10 (2018): 1463-1473." mm10 chr13 53895001 57200000 56048376 56160753 Inv1-Mm "2 (Mut) 4 (WT)" homozygous  ./inversion/Forelimb E11.5/Inv1-Mm inversion Forelimb E11.5 SRX3175632; SRX3175633; SRX3175634; SRX3175635 SRX3175654-SRX3175655 mm10 chr13 53895001 57200000 56048376 56160753 DelL-Mm "2 (Mut) 4 (WT)" homozygous  ./deletion/Forelimb E11.5/DelL-Mm deletion Forelimb E11.5 SRX3175632; SRX3175633; SRX3175634; SRX3175635 SRX3175656-SRX3175657 mm10 chr13 53895001 57200000 56048376 56147390 Neur1-Mm "2 (Mut) 4 (WT)" homozygous  ./deletion/Forelimb E11.5/Neur1-Mm deletion Forelimb E11.5 SRX3175632; SRX3175633; SRX3175634; SRX3175635 SRX3175662-SRX3175663 mm10 chr13 53895001 57200000 56219601 56264136 D3839 "2 (Mut) 4 (WT)" homozygous  ./2deletion/erythroid cells/D3839 deletion/deletion erythroid cells SRX2741786-SRX2741788; SRX2741771-SRX2741773; SRX2741762-SRX2741764 SRX2741789-SRX2741791; mm10 chr11 32190000 32335000 32238646 32238667 32237202 32237228 i4i5 2 homozygous  ./2deletion/FLHL/i4i5 deletion/deletion FLHL SRX5099269; SRX5099270; SRX5764173 SRX5099264; SRX5099265 "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." mm10 chr5 27465001 30345000 29293392 29293421 29336029 29336056 ZRSreg 2 homozygous  ./deletion/FLHL/ZRSreg deletion FLHL SRX5099269; SRX5099270; SRX5764173 SRX5764174; mm10 chr5 27460000 30345000 29314818 29315227 i4i5ZRSreg 2 homozygous  ./3deletion/FLHL/i4i5ZRSreg deletion/deletion/deletion FLHL SRX5099269; SRX5099270; SRX5764173 SRX5764177; SRX5764178 mm10 chr5 27460000 30345000 29293392 29293421 29336029 29336056 29314818 29315227 i4i5ZRS 2 homozygous  ./3deletion/FLHL/i4i5ZRS deletion/deletion/deletion FLHL SRX5099269; SRX5099270; SRX5764173 SRX5099266; SRX5099267 mm10 chr5 27460000 30345000 29293392 29293421 29336029 29336056 29314814 29314832 i4i5ZRS 2 homozygous  ./3deletion/midbrain/i4i5ZRS deletion/deletion/deletion midbrain SRX5099272; SRX5099273 SRX5764175; SRX5764176 mm10 chr5 27460000 30345000 29293392 29293421 29336029 29336056 29314814 29314832 Lprom 2 homozygous  ./deletion/FLHL/Lprom deletion FLHL SRX5099269; SRX5099270; SRX5764173 SRX5099268; SRX5764172 mm10 chr5 27460000 30345000 FirreKO 3 ./deletion/MEF female/FirreKO deletion MEF female SRX3241571-SRX3241578 SRX3241579-SRX3241585 "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." mm10 chrX 50550000 50675000 50555286 50637116 FirreKO 3 hemizygos ./deletion/MEF male/FirreKO deletion MEF male SRX3241586-SRX3241589 SRX3241590-SRX3241595 mm10 chrX 50550000 50675000 50555286 50637116 FirreKO 3 ./deletion/mESC male/FirreKO deletion mESC male SRX3269798-SRX3269799 SRX3269796-SRX3269797 mm10 chrX 50550000 50675000 50555286 50637116