|
| Status |
Public on Mar 14, 2022 |
| Title |
DeepLoop enables robust mapping of DNA loops from low-depth single cell or allele-resolved Hi-C data at high resolution |
| Platform organism |
Homo sapiens |
| Sample organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
Third-party reanalysis
|
| Summary |
High-resolution mapping of the gene regulatory chromatin interactions from noisy Hi-C contact heatmaps remains a major challenge in 3D genome research due to the complex bias structure and severe data sparsity. Here we present DeepLoop, which addresses this problem by combining a rigorous bias correction strategy (HiCorr) and deep learning-based signal enhancement techniques. We demonstrated that DeepLoop can robustly identify high-resolution chromatin interactions from low-depth and single cell Hi-C data. With DeepLoop, we for the first-time mapped the genetic and epigenetic determinants of human homolog-specific chromatin loops in GM12878 cells at 5kb-resolution. We nominated two new imprinting loci with unbalanced DNA folding in additional to the well-known H19/IGF2 locus. Interestingly, we also found that the sub-TAD loops at the DXZ4 “megadomain” boundary escapes X-inactivation, but the loops at the FIRRE “superloop” locus do not escape. Unexpectedly, DeepLoop detected four previously unknown Mb-sized heterozygous structure variants in the GM12878 genome, including two large inversions causing allele-specific gene expression via enhancer rewiring. Finally, DeepLoop also pinpointed dozens of loop regulatory SNPs that often have transcriptional consequences. Taken together, DeepLoop expands the use of Hi-C to provide genome-wide insights into the genetics of 3D genome at loop resolution.
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| Overall design |
DeepLoop robustly identify high-resolution chromatin loops regardless of noise and depth. Each text file (300K) contains a chromatin loop calling list from Hi-C data for one cell type.
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| Contributor(s) |
Zhang S, Plummer D, Lu L, Cui J, Jin F, Li J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Feb 22, 2021 |
| Last update date |
Mar 17, 2022 |
| Contact name |
Shanshan Zhang |
| Organization name |
Case Western Reserve University
|
| Department |
Department of Genome and Genetics
|
| Lab |
Jin lab
|
| Street address |
10900 Euclid Avenue
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL20795 |
HiSeq X Ten (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (15)
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|
| Relations |
| Reanalysis of |
GSM1267196 |
| Reanalysis of |
GSM1267197 |
| Reanalysis of |
GSM3177700 |
| Reanalysis of |
GSM3177701 |
| Reanalysis of |
GSM3177702 |
| Reanalysis of |
GSM3177703 |
| Reanalysis of |
GSM1055800 |
| Reanalysis of |
GSM1055801 |
| Reanalysis of |
GSM1154021 |
| Reanalysis of |
GSM1154022 |
| Reanalysis of |
GSM1154023 |
| Reanalysis of |
GSM1154024 |
| Reanalysis of |
GSM1181867 |
| Reanalysis of |
GSM1181868 |
| Reanalysis of |
GSM1551583 |
| Reanalysis of |
GSM1551584 |
| Reanalysis of |
GSM1551586 |
| Reanalysis of |
GSM2054564 |
| Reanalysis of |
GSM2054565 |
| Reanalysis of |
GSM2054566 |
| Reanalysis of |
GSM2054567 |
| Reanalysis of |
GSM2054568 |
| Reanalysis of |
GSM2054569 |
| Reanalysis of |
GSM1551551 |
| Reanalysis of |
GSM1551552 |
| Reanalysis of |
GSM1551553 |
| Reanalysis of |
GSM1551554 |
| Reanalysis of |
GSM1551555 |
| Reanalysis of |
GSM1551556 |
| Reanalysis of |
GSM1551557 |
| Reanalysis of |
GSM1551558 |
| Reanalysis of |
GSM1551559 |
| Reanalysis of |
GSM1551560 |
| Reanalysis of |
GSM1551561 |
| Reanalysis of |
GSM1551562 |
| Reanalysis of |
GSM1551563 |
| Reanalysis of |
GSM1551564 |
| Reanalysis of |
GSM1551565 |
| Reanalysis of |
GSM1551566 |
| Reanalysis of |
GSM1551567 |
| Reanalysis of |
GSM1551568 |
| Reanalysis of |
GSM1551569 |
| Reanalysis of |
GSM1551570 |
| Reanalysis of |
GSM1551571 |
| Reanalysis of |
GSM1551572 |
| Reanalysis of |
GSM1551573 |
| Reanalysis of |
GSM1551574 |
| Reanalysis of |
GSM1551575 |
| Reanalysis of |
GSM1551576 |
| Reanalysis of |
GSM1551577 |
| Reanalysis of |
GSM1551578 |
| Reanalysis of |
GSM2322539 |
| Reanalysis of |
GSM2322540 |
| Reanalysis of |
GSM2322541 |
| Reanalysis of |
GSM2322542 |
| Reanalysis of |
GSM2322543 |
| Reanalysis of |
GSM2322544 |
| Reanalysis of |
GSM2322545 |
| Reanalysis of |
GSM2322546 |
| Reanalysis of |
GSM2322547 |
| Reanalysis of |
GSM2322548 |
| Reanalysis of |
GSM2322549 |
| Reanalysis of |
GSM2322550 |
| Reanalysis of |
GSM2322551 |
| Reanalysis of |
GSM2322552 |
| Reanalysis of |
GSM2322553 |
| Reanalysis of |
GSM2322554 |
| Reanalysis of |
GSM2322555 |
| Reanalysis of |
GSM2322556 |
| Reanalysis of |
GSM2322557 |
| Reanalysis of |
GSM1419084 |
| Reanalysis of |
GSM1419086 |
| Reanalysis of |
GSM1419085 |
| Reanalysis of |
GSM862720 |
| Reanalysis of |
GSM862721 |
| Reanalysis of |
GSM1181865 |
| Reanalysis of |
GSM1181866 |
| BioProject |
PRJNA757550 |
| SRA |
SRP334570 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE167200_14.tissue.LoopEnhance.txt.gz |
12.1 Gb |
(ftp)(http) |
TXT |
| GSE167200_39cool.tar.gz |
14.8 Gb |
(ftp)(http) |
TAR |
| GSE167200_Adrenal.top300K.txt.gz |
9.3 Mb |
(ftp)(http) |
TXT |
| GSE167200_Aorta.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Astro.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Bladder.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_CP.raw_HiCorr_LoopDenoise.txt.gz |
2.3 Gb |
(ftp)(http) |
TXT |
| GSE167200_CP_GZ.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Cortex.top300K.txt.gz |
9.3 Mb |
(ftp)(http) |
TXT |
| GSE167200_Endo.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_GM12878.HindIII.raw_HiCorr_LoopDenoise.txt.gz |
2.4 Gb |
(ftp)(http) |
TXT |
| GSE167200_GM12878.in_situ.maternal.raw_HiCorr_LoopEnhance.txt.gz |
8.9 Gb |
(ftp)(http) |
TXT |
| GSE167200_GM12878.in_situ.paternal.raw_HiCorr_LoopEnhance.txt.gz |
9.0 Gb |
(ftp)(http) |
TXT |
| GSE167200_GM12878.in_situ.raw_HiCorr_LoopDenoise.txt.gz |
7.4 Gb |
(ftp)(http) |
TXT |
| GSE167200_GM12878_HindIII.top300K.txt.gz |
9.1 Mb |
(ftp)(http) |
TXT |
| GSE167200_GM12878_insitu.maternal.top300K.txt.gz |
9.0 Mb |
(ftp)(http) |
TXT |
| GSE167200_GM12878_insitu.paternal.top300K.txt.gz |
9.0 Mb |
(ftp)(http) |
TXT |
| GSE167200_GM12878_insitu.top300K.txt.gz |
9.1 Mb |
(ftp)(http) |
TXT |
| GSE167200_GZ.raw_HiCorr_LoopDenoise.txt.gz |
2.3 Gb |
(ftp)(http) |
TXT |
| GSE167200_H1.raw_HiCorr_LoopDenoise.txt.gz |
2.3 Gb |
(ftp)(http) |
TXT |
| GSE167200_H1_HindIII.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_H1_insitu.top300K.txt.gz |
9.1 Mb |
(ftp)(http) |
TXT |
| GSE167200_H9.cool.gz |
342.1 Mb |
(ftp)(http) |
COOL |
| GSE167200_H9.top300K.txt.gz |
9.1 Mb |
(ftp)(http) |
TXT |
| GSE167200_Hippocampus.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_IMR90.raw_HiCorr_LoopDenoise.txt.gz |
2.3 Gb |
(ftp)(http) |
TXT |
| GSE167200_IMR90.top300K.txt.gz |
9.1 Mb |
(ftp)(http) |
TXT |
| GSE167200_L2_3.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_L4.top300K.txt.gz |
9.3 Mb |
(ftp)(http) |
TXT |
| GSE167200_L5.top300K.txt.gz |
9.3 Mb |
(ftp)(http) |
TXT |
| GSE167200_L6.top300K.txt.gz |
9.3 Mb |
(ftp)(http) |
TXT |
| GSE167200_LeftVentricle.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Liver.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Lung.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_MG.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_MP.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Metadata.spreadsheet.xlsx |
53.0 Kb |
(ftp)(http) |
XLSX |
| GSE167200_Ndnf.top300K.txt.gz |
9.3 Mb |
(ftp)(http) |
TXT |
| GSE167200_ODC.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_OPC.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Ovary.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Pancreas.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Psoas_Muscle.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Pvalb.top300K.txt.gz |
9.3 Mb |
(ftp)(http) |
TXT |
| GSE167200_RAW.tar |
7.3 Mb |
(http)(custom) |
TAR (of WIG) |
| GSE167200_README.txt |
338 b |
(ftp)(http) |
TXT |
| GSE167200_Readme_39cool.txt |
2.9 Kb |
(ftp)(http) |
TXT |
| GSE167200_RightVentricle.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Small_Intenstine.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Spleen.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_Sst.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
| GSE167200_VPinfo.txt.gz |
307 b |
(ftp)(http) |
TXT |
| GSE167200_Vip.top300K.txt.gz |
9.3 Mb |
(ftp)(http) |
TXT |
| GSE167200_mESC.raw_HiCorr_LoopDenoise.txt.gz |
2.4 Gb |
(ftp)(http) |
TXT |
| GSE167200_mESC.top300K.txt.gz |
9.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data not applicable for this record |
| Processed data are available on Series record |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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