Keyword >> Genome DNA
| Accession | File (86) | Cell/Tissue | Keywords |
|---|---|---|---|
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GMS-122-1 Small sample chromatin analysis using ChIL-seq |
1071
N/A Day5_H3K27ac_L_3_cpm_bs100sm1000.bigwig (34.42 MB) 2025-05-19 14:52:34 1047 JBrowse N/A Day14_H3K27ac_L_3_cpm_bs100sm1000.bigwig (53.44 MB) 2025-05-19 14:30:38 mm39 ChIP-Seq 1048 N/A Day3_H3K27ac_L_5_cpm_bs100sm1000.bigwig (39.38 MB) 2025-05-19 14:52:17 1049 N/A Day5_H3K27ac_L_5_cpm_bs100sm1000.bigwig (43.49 MB) 2025-05-19 14:52:17 1050 N/A Day7_H3K27ac_L_1_cpm_bs100sm1000.bigwig (44.85 MB) 2025-05-19 14:52:17 1051 N/A Day5_H3K27ac_L_4_cpm_bs100sm1000.bigwig (43.78 MB) 2025-05-19 14:52:17 1052 N/A Day7_H3K27ac_L_3_cpm_bs100sm1000.bigwig (45.99 MB) 2025-05-19 14:52:18 1053 N/A Day3_H3K27ac_L_1_cpm_bs100sm1000.bigwig (46.46 MB) 2025-05-19 14:52:18 1054 N/A Day3_H3K27ac_L_4_cpm_bs100sm1000.bigwig (38.99 MB) 2025-05-19 14:52:18 1055 N/A Day7_H3K27ac_L_5_cpm_bs100sm1000.bigwig (43.18 MB) 2025-05-19 14:52:18 1056 N/A Day3_H3K27ac_L_3_cpm_bs100sm1000.bigwig (36.74 MB) 2025-05-19 14:52:18 1057 N/A Day14_H3K27ac_L_4_cpm_bs100sm1000.bigwig (42.03 MB) 2025-05-19 14:52:18 1058 N/A Day7_H3K27ac_L_4_cpm_bs100sm1000.bigwig (42.95 MB) 2025-05-19 14:52:18 1060 N/A Day14_H3K27ac_L_1_cpm_bs100sm1000.bigwig (36.58 MB) 2025-05-19 14:52:18 1059 N/A Day5_H3K27ac_L_2_cpm_bs100sm1000.bigwig (41.18 MB) 2025-05-19 14:52:18 1070 N/A Day5_H3K27ac_L_1_cpm_bs100sm1000.bigwig (31.71 MB) 2025-05-19 14:52:34 1069 N/A Day0_H3K27ac_L_3_cpm_bs100sm1000.bigwig (24.06 MB) 2025-05-19 14:52:34 1068 N/A Day7_H3K27ac_L_2_cpm_bs100sm1000.bigwig (14.66 MB) 2025-05-19 14:52:34 1067 N/A Day0_H3K27ac_L_4_cpm_bs100sm1000.bigwig (37.63 MB) 2025-05-19 14:52:31 1066 N/A Day0_H3K27ac_L_1_cpm_bs100sm1000.bigwig (595.70 KB) 2025-05-19 14:52:19 1065 N/A Day14_H3K27ac_L_2_cpm_bs100sm1000.bigwig (1.35 MB) 2025-05-19 14:52:19 1064 N/A Day0_H3K27ac_L_2_cpm_bs100sm1000.bigwig (30.22 MB) 2025-05-19 14:52:19 1063 N/A Day3_H3K27ac_L_2_cpm_bs100sm1000.bigwig (36.04 MB) 2025-05-19 14:52:19 1062 N/A Day0_H3K27ac_L_5_cpm_bs100sm1000.bigwig (31.93 MB) 2025-05-19 14:52:18 1061 N/A Day14_H3K27ac_L_5_cpm_bs100sm1000.bigwig (37.81 MB) 2025-05-19 14:52:18 |
Skeletal muscle | Genome DNA Nuclear-scale |
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GMS-175-2 Smc-mediated genome organization in the archaeon Thermococcus kodakarensis |
992
Genomic contact map data from a trmBL2 deletion mutant of T. kodakarensis T_kodakarensis_trmBL2.mcool (85.47 MB) 2025-05-14 11:47:12 Others Hi-C 994 Genomic contact map data from a T. kodakarensis wild-type strain T_kodakarensis_WT.mcool (85.56 MB) 2025-05-14 11:47:19 Others Hi-C 995 Genomic contact map data from an smc deletion mutant of T. kodakarensis T_kodakarensis_smc.mcool (83.28 MB) 2025-05-14 11:47:24 Others Hi-C 996 Genomic contact map data from an scpB deletion mutant of T. kodakarensis T_kodakarensis_scpB.mcool (85.65 MB) 2025-05-14 11:47:29 Others Hi-C 997 Genomic contact map data from an scpA deletion mutant of T. kodakarensis T_kodakarensis_scpA.mcool (85.79 MB) 2025-05-14 11:47:34 Others Hi-C 998 Genomic contact map data from a dif deletion mutant of T. kodakarensis T_kodakarensis_dif.mcool (85.50 MB) 2025-05-14 12:02:58 Others Hi-C 999 Genomic contact map data from an smc scpA double deletion mutant of T. kodakarensis T_kodakarensis_smc_scpA.mcool (85.59 MB) 2025-05-14 12:03:03 Others Hi-C 1000 Genomic contact map data from an smc scpB double deletion mutant of T. kodakarensis T_kodakarensis_smc_scpB.mcool (85.44 MB) 2025-05-14 12:03:08 Others Hi-C 1001 Genomic contact map data from a TK0795 deletion mutant of T. kodakarensis T_kodakarensis_TK0795.mcool (85.35 MB) 2025-05-14 12:03:17 Others Hi-C 1002 Genomic contact map data from a xerA deletion mutant of T. kodakarensis T_kodakarensis_xerA.mcool (85.34 MB) 2025-05-14 12:03:25 Others Hi-C 1041 3C-seq analysis on the genome of the T. kodakarensis strain KU216 3C-seq_fig1.png (1.58 MB) 2025-05-16 17:39:34 |
not applicable | Nuclear-scale SMC Archaea Stiffness Asynchronous Cell culture 3C-seq Genome DNA |
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GMS-175-3 Localization of genome-organizing proteins in the archaeon Thermococcus kodakare... |
1003
Smc enrichment in a trmBL2 deletion mutant of T. kodakarensis T_kodakarensis_trmBL2_Smc_enrichment.txt (1.81 MB) 2025-05-14 12:12:06 Others 1004 Smc enrichment in a wild-type strain of T. kodakarensis T_kodakarensis_WT_Smc_enrichment.txt (1.82 MB) 2025-05-14 12:12:07 Others 1005 TrmBL2 enrichment in a wild-type strain of T. kodakarensis T_kodakarensis_WT_TrmBL2_enrichment.txt (1.82 MB) 2025-05-14 12:12:08 Others 1042 TrmBL2-mediated regulation of Smc-ScpAB dynamics in T. kodakarensis TrmBL2_fig8.png (657.07 KB) 2025-05-16 17:44:09 |
not applicable | Nuclear-scale SMC Archaea Stiffness Asynchronous Cell culture ChIP-seq Genome DNA |
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GMS-65-1 Intra-chromosomal Hi-C contacts (mESC Rep1) |
172
JBrowse
H1 cell line (SRR2977621) H1_human_RNA.bam (429.08 MB) 2022-03-02 18:51:57 hg38 RNA-Seq 171 JBrowse Mouse ESC RNA-seq (GSM4647545) ESC1_RNA.bam (1.65 GB) 2022-03-02 18:42:53 mm10 RNA-Seq 190 JBrowse Transcriptome at E16.5 E16.5_Rep1.bam (558.05 MB) 2022-03-12 16:36:08 mm10 RNA-Seq 228 Domains PHiC JBrowse Intra-chromosomal Hi-C contacts (mESC Rep1) mESC1.intra.hic (1.69 GB) 2022-03-14 18:33:29 mm10 Hi-C 393 Chr8 Model Image Chr8_PhiC.png (455.24 KB) 2023-06-04 13:02:42 |
embryonic stem cell | Chromatin Hi-C PHi-C2 Genome DNA Nuclear-scale |
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GMS-65-112 A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes |
747
JBrowse
NIPBL in NIPBL-mutated cells GSM8529575_NIPBL_ChIP_NIPBLmut.100.bigwig (153.26 MB) 2025-04-02 10:09:29 hg38 ChIP-Seq 744 JBrowse RAD21 in NIPBL-mutated cells GSM8529573_RAD21_ChIP_NIPBLmut.100.bigwig (151.69 MB) 2025-04-01 18:26:35 hg38 ChIP-Seq 745 JBrowse RAD21 in wild-type cells GSM8529572_RAD21_ChIP_FT_control.100.bigwig (151.95 MB) 2025-04-01 18:31:09 hg38 ChIP-Seq 746 JBrowse NIPBL in wild-type cells GSM8529574_NIPBL_ChIP_FT_control.100.bigwig (153.77 MB) 2025-04-02 10:09:05 hg38 ChIP-Seq 748 JBrowse BRD4 in wild-type cells GSM8529576_BRD4_ChIP_FT_control.100.bigwig (149.17 MB) 2025-04-02 10:10:13 hg38 ChIP-Seq 749 JBrowse BRD4 in NIPBL-mutated cells GSM8529577_BRD4_ChIP_NIPBLmut.100.bigwig (148.86 MB) 2025-04-02 10:10:34 hg38 ChIP-Seq 750 JBrowse H3K27ac in wild-type cells GSM8529578_H3K27ac_ChIP_FT_control.100.bigwig (137.23 MB) 2025-04-02 10:46:38 hg38 ChIP-Seq 751 JBrowse H3K27ac in NIPBL-mutated cells GSM8529579_H3K27ac_ChIP_NIPBLmut.100.bigwig (135.98 MB) 2025-04-02 10:46:55 hg38 ChIP-Seq 752 JBrowse NELFC in wild-type cells GSM8529584_NELFC_ChIP_FT_control.100.bigwig (153.47 MB) 2025-04-02 11:44:51 hg38 ChIP-Seq 753 JBrowse NELFC in NIPBL-mutated cells GSM8529585_NELFC_ChIP_NIPBLmut.100.bigwig (149.35 MB) 2025-04-02 11:45:33 hg38 ChIP-Seq 755 JBrowse AFF4 in NIPBL-mutated cells GSM8529583_AFF4_ChIP_NIPBLmut.100.bigwig (154.75 MB) 2025-04-02 12:23:42 hg38 ChIP-Seq 756 JBrowse Input in wild-type cells (replicate 1) GSM8529580_input_1_FT_control.100.bigwig (153.15 MB) 2025-04-02 12:38:37 hg38 ChIP-Seq 757 JBrowse Input in NIPBL-mutated cells (replicate 1) GSM8529581_input_1_NIPBLmut.100.bigwig (148.66 MB) 2025-04-02 12:39:05 hg38 ChIP-Seq 758 JBrowse Input in wild-type cells (replicate 2) GSM8529586_input_2_FT_control.100.bigwig (150.44 MB) 2025-04-02 12:40:35 hg38 ChIP-Seq 754 JBrowse AFF4 in wild-type cells GSM8529582_AFF4_ChIP_FT_control.100.bigwig (157.90 MB) 2025-04-02 12:23:14 hg38 ChIP-Seq 759 JBrowse Input in NIPBL-mutated cells (replicate 2) GSM8529587_input_2_NIPBLmut.100.bigwig (148.85 MB) 2025-04-02 12:41:28 hg38 ChIP-Seq 760 Graphical Abstract GraphicalAbstract.png (303.18 KB) 2025-04-02 15:14:23 |
293FT | Disease CHOPS CdLS Nuclear-scale AFF4 NELFC RAD21 NIPBL BRD4 Genome DNA |
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GMS-65-113 Intra-chromosomal Hi-C contacts in mESC |
765
PHiC: Stiffness
JBrowse
Intra-chromosomal Hi-C contacts (Rep1) Merge1.intra.MQ30.ValidPairs.hic (1.69 GB) 2025-04-10 09:49:35 mm10 Hi-C 766 Domains PHiC JBrowse Intra-chromosomal Hi-C contacts (Rep 2) Merge2.intra.MQ30.ValidPairs.hic (1.79 GB) 2025-04-10 14:27:30 mm10 Hi-C 1043 Flexibility and Viscoelasticity PHiC_FlexVisco.png (1.13 MB) 2025-05-16 18:37:18 |
embryonic stem cell | PHi-C2 Nanog Flexibility Viscoelasiticity Genome DNA Stiffness Nuclear-scale |
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GMS-65-2 Degradation of RAD21 in HCT-116 |
385
JBrowse
H3K27ac narrow peaks (control) H3K27ac_np1_peaks.narrowPeak.scaled.bigwig (5.42 MB) 2023-05-29 17:59:08 hg38 ChIP-Seq 346 human cohesin subunit STAG1 in complex with RAD21 peptide 6RRC.png (237.36 KB) 2023-05-29 14:25:36 347 JBrowse AFF4 narrow peaks (control) AFF4_np1_peaks.narrowPeak.scaled.bigwig (992.08 KB) 2023-05-29 14:37:38 hg38 ChIP-Seq 350 JBrowse BRD4 narrow peaks (control) BRD4_np1_peaks.narrowPeak.scaled.bigwig (3.30 MB) 2023-05-29 14:53:19 hg38 ChIP-Seq 353 JBrowse CBP narrow peaks (control) CBP_np1_peaks.narrowPeak.scaled.bigwig (2.90 MB) 2023-05-29 15:47:45 hg38 ChIP-Seq 367 JBrowse NELFCD narrow peaks (control) NELFCD_np1_peaks.narrowPeak.scaled.bigwig (2.35 MB) 2023-05-29 16:57:08 hg38 ChIP-Seq 368 JBrowse CDK9 narrow peaks (control) CDK9_np1_peaks.narrowPeak.scaled.bigwig (1.94 MB) 2023-05-29 16:57:08 hg38 ChIP-Seq 369 JBrowse MED1 narrow peaks (control, rep2) MED1_np2_peaks.narrowPeak.scaled.bigwig (2.66 MB) 2023-05-29 16:57:08 hg38 ChIP-Seq 370 JBrowse NCBP1 narrow peaks (control) NCBP1_np1_peaks.narrowPeak.scaled.bigwig (1.81 MB) 2023-05-29 16:57:08 hg38 ChIP-Seq 371 JBrowse MAU2 narrow peaks (control) MAU2_np1_peaks.narrowPeak.scaled.bigwig (3.23 MB) 2023-05-29 16:57:08 hg38 ChIP-Seq 372 JBrowse MED1 narrow peaks (control, rep1) MED1_np1_peaks.narrowPeak.scaled.bigwig (1.68 MB) 2023-05-29 16:57:08 hg38 ChIP-Seq 373 JBrowse P300 narrow peaks (control) P300_np1_peaks.narrowPeak.scaled.bigwig (2.63 MB) 2023-05-29 16:57:08 hg38 ChIP-Seq 374 JBrowse RAD21 narrow peaks (control) RAD21_np1_peaks.narrowPeak.scaled.bigwig (6.32 MB) 2023-05-29 16:57:08 hg38 ChIP-Seq 386 JBrowse H3K4me1 narrow peaks (control) H3K4me1_np1_peaks.narrowPeak.scaled.bigwig (7.56 MB) 2023-05-29 17:59:08 hg38 ChIP-Seq 389 JBrowse EU-seq (control, Rep1) accepted_hits.bam.sorted.bam (1.87 GB) 2023-05-29 18:12:53 hg38 RNA-Seq |
HCT116 | Cohesin Micro-C Disease CdLS Nuclear-scale AFF4 BRD4 MAU2 RAD21 Genome DNA |
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GMS-97-1 PHi-C2: interpreting Hi-C data as the dynamic 3D genome state |
979
Rheology analysis figureS5.png (717.12 KB) 2025-05-13 14:47:45 978 Rheology analysis figureS5.pdf (2.11 MB) 2025-05-13 14:43:43 |
embryonic stem cell | PHi-C2 Genome DNA Mesoscale Rheology Modeling Viscoelasticity |
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GMS-97-2 Transcription-coupled changes in genomic region proximities during transcription... |
980
Genome dynamics in Nanog inactive state simulated by PHi-C adn0020_movie_s3.mp4 (6.01 MB) 2025-05-13 14:55:46 981 Genome dynamics in Nanog active state simulated by PHi-C adn0020_movie_s2.mp4 (5.37 MB) 2025-05-13 14:55:47 |
embryonic stem cell | PHi-C2 Genome DNA Modeling Mesoscale Brownian dynamics Nanog |
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GMS-97-3 4D Genome Analysis Using PHi-C2 |
983
A 4D genome analysis of PHi-C2 for mESCs (chr1: 130–135 Mb, 25-kb bins) fig3.png (449.23 KB) 2025-05-13 15:08:49 982 A 4D genome analysis of PHi-C2 for mESCs (chr1: 130–135 Mb, 25-kb bins) fig3.pdf (363.37 KB) 2025-05-13 15:08:16 |
embryonic stem cell | PHi-C2 Genome DNA Mesoscale MSD analysis Viscoelasticity Rheology |
