Welcome to ChromOS

NGS Samples

Tissues (Cells)

Registered Users

Example: [OLP-1-608] 
HiC collection 
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ChromOS services online access to the data resources from Chromosome Orchestration System (OS) , a research project supported by MEXT Japan.

Chromosomes play a fundamental role in many biological processes. Previous research efforts have advanced our understanding of specific chromosomal events, such as DNA transcription, replication, recombination, partitioning, and epigenetic modification. One of the major future challenges in chromosome biology will be to provide an overall framework of how these individual activities are orchestrated and coordinated to maximize their effects in a variety of biological processes that evolve over time. The main goal of this project is to describe the mechanisms that regulate the functional unity of the chromosomes (chromosome OS) by thoroughly examining the structural relationship between, and the hierarchy of, individual chromosomal functions.

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Accession Cell Organism Restriction enzyme Condition Run ID
OLP-2-620 RPEhumanMboIESCO1, 2 KD (siRNA transfection 48 h), No Sync1809JNHX-0004_si11-19_res
OLP-2-614 RPEhumanMboIRAD21 KD (siRNA transfection 72 h), No Sync1809JNHX-0003_si621_res
OLP-2-628 RPEhumanMboIPDS5B KD (siRNA transfection 48 h), No SyncHN00102383_si91_res
OLP-2-621 RPEhumanMboIMAU2 KD (siRNA transfection 72 h), No Sync1809JNHX-0004_si251_res
OLP-2-613 RPEhumanMboIRAD21 KD (siRNA transfection 72 h), No Sync1809JNHX-0003_si7-621_res
OLP-2-623 RPEhumanMboICTCF KD (siRNA transfection 72 h), No Sync1811KHX-0110_R_626_628_d3_res
OLP-2-624 RPEhumanMboIWAPL KD (siRNA transfection 48 h), No SyncHN00102380_si31_res
OLP-2-625 RPEhumanMboIPDS5A KD (siRNA transfection 72 h), No SyncHN00102380_si88_d3_res
OLP-2-619 RPEhumanMboIESCO1 KD (siRNA transfection 48 h), No Sync1809JNHX-0004_si11_res
OLP-2-626 RPEhumanMboIJQ1 (BRD Inhibitor), No SyncHN00102383_JQ1_plus_res
OLP-2-615 RPEhumanMboIControl, No Sync1807JNHX-0018_Ctrl_res
OLP-2-627 RPEhumanMboIPDS5A,B KD (siRNA transfection 48 h), No SyncHN00102383_si88_91_res
OLP-2-616 RPEhumanMboIControl, No Sync1809JNHX-0003_Ctrl_res
OLP-2-618 RPEhumanMboICTCF KD (siRNA transfection 72 h), No Sync1811KHX-0109_FT_WT_res
OLP-2-617 RPEhumanMboICTCF KD (siRNA transfection 72 h), No Sync1809JNHX-0003_si628_res
OLP-2-622 RPEhumanMboIControl, No Sync1811KHX-0109_R_Ctrl_res
OLP-2-629 LCLhumanMboIWT, No Sync1904JNHX-0009_GIA_res
OLP-2-630 LCLhumanMboIHP1beta mutation, No Sync1904JNHX-0009_RIM_res
OLP-2-631 HCT116/Rad21-mAD/TIR1humanMboINIPBL, exon3 frame-shift, No Sync1903JNHX-0034_B3_res
OLP-2-633 HCT116/ESCO1-mAD/TIR1humanMboIDox 12 h -> IAA 3 h (ESCO1 depletion), No Sync1907JNHX-0026_E1_dox_iaa_res
OLP-2-632 HCT116/ESCO1-mAD/TIR1humanMboIDox 16 h -> (control), No Sync1908JNHX-0025_E1_dox_res
OLP-2-634 HCT116humanMboINIPBL, exon 3 single allele mutation, No sync1807JNHX-0018_HCT_3-3_res
OLP-2-635 HCT116humanMboIWild Type, No Sync1807JNHX-0018_HCT_Wt_res
OLP-2-641 fibroblasthumanMboIWT, female, No Sync1807JNHX-0018_GM2036_res
OLP-2-640 fibroblasthumanMboIWT, female, No Sync1904JNHX-0009_2036_res
OLP-2-639 fibroblasthumanMboICdLS, NIPBL:2479_2480delAG; R827GfsX2, No Sync1807JNHX-0018_CdLS304_res
OLP-2-636 fibroblasthumanMboICdLS, NIPBL: 1372C>T;Q458X / Nonsense, female, No Sync1807JNHX-0018_CdLS510_res
OLP-2-642 fibroblasthumanMboIWT, male, No Sync1807JNHX-0018_GM3348_res
OLP-2-638 fibroblasthumanMboICdLS, NIPBL:2479_2480delAG; R827GfsX2, No Sync1807JNHX-0018_CdLS087_res
OLP-2-637 fibroblasthumanMboIWT, male, No Sync1807JNHX-0018_CdLS006_res
OLP-2-643 Blood Cell Stem CellmouseMboISTAG2 conditional KO1811KHX-0110_KO_561_res
OLP-2-646 Blood Cell Stem CellmouseMboISTAG2 conditional KO1811KHX-0110_KO_544_res
OLP-2-645 Blood Cell Stem CellmouseMboIWT1811KHX-0110_WT_546_res
OLP-2-644 Blood Cell Stem CellmouseMboIWT1811KHX-0110_WT_563_res
OLP-2-654 293FThumanMboIWT, No Sync1905JNHX-0006_FT_res
OLP-2-648 293FThumanMboIlentiviral vector Infection, Control, No Sync1903JNHX-0034_FT-vi24_res
OLP-2-649 293FThumanMboIlentiviral vector Infection, Control, No Sync1903JNHX-0035_FT-Wt_res
OLP-2-651 293FThumanMboIlentiviral vector Infection, Control, No Sync1908JNHX-0026_vi24_res
OLP-2-652 293FThumanMboIWild AFF4 lentiviral vector Infection, No Sync1908JNHX-0026_vi27_res
OLP-2-647 293FThumanMboIMutant AFF4 lentiviral vector Infection, No Sync1903JNHX-0035_FT-vi28_res
OLP-2-653 293FThumanMboIMutant AFF4 lentiviral vector Infection, No Sync1908JNHX-0026_vi28_res
OLP-2-650 293FThumanMboINIPBL, exon 3 bi-allele mutation, No Sync1811KHX-0109_FT_ND1_res
  1. ChromOS manages the data from the project "Chromosome OS".
  2. ChromOS provides the analytic pipeline for Hi-C data by collaborating with OpenLooper (OLP).
  3. Registration via OpenLooper is required. Thereby, users can manage the data and submit jobs to analyze. Learn more..
  4. Anyone can freely access the data opened by the registered users.
Run_Hi-C
To reduce BAM filesize, prepare one chromosome per BAM.
"Samtools view" command will be helpful to do it.

Data Sharing (OpenLooper)

OpenLooper (OLP) collects genome-wide data on chromatin structures investigated by various high-throughput experimental assays. Simultaneously, OLP provides a platform that supports opening and sharing the data.

Get started »

Genome Browser

A web-based genome browser displays multiple processed NGS data in interactive multi-tracks. The users can access it directly or through the data browser that provides selectable individual assay .

Get started »

Hi-C

Hi-C Analysis

ChromOS runs a pipeline for Hi-C data analysis with user-uploaded BAM files via OpenLooper. This pipeline is now in service (2020.06).

Example: [OLP-1-608]
HiC collection: [RPE, HCT116, LCL,...]


 In Focus Articles (last modified: 2020-10-28 19:43:16)

Three-dimensional nuclear organization in Arabidopsis thaliana.


Pontvianne F, Grob S (J Plant Res. 2020 Jul;133(4):479-488)
In recent years, the study of plant three-dimensional nuclear architecture received increasing attention. Enabled by technological advances, our knowledge on nuclear architecture has greatly increased and we can now access large data sets describing its manifold aspects. The principles of nuclear organization in plants do not significantly differ from those in animals. Plant nuclear organization comprises various scales, ranging from gene loops to topologically associating domains to nuclear compartmentalization. However, whether plant three-dimensional chromosomal features also exert similar functions as in animals is less clear. This review discusses recent advances in the fields of three-dimensional chromosome folding and nuclear compartmentalization and describes a novel silencing mechanism, which is closely linked to nuclear architecture....
PubMed:32240449

Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome.


Li Y, Gao G, Lin Y, Hu S, Luo Y, Wang G, Jin L, Wang Q, Wang J, Tang Q, Li M (Gigascience. 2020 Oct 24;9(10):)
BACKGROUND: The domestic goose is an economically important and scientifically valuable waterfowl; however, a lack of high-quality genomic data has hindered research concerning its genome, genetics, and breeding. As domestic geese breeds derive from both the swan goose (Anser cygnoides) and the graylag goose (Anser anser), we selected a female Tianfu goose for genome sequencing. We generated a chromosome-level goose genome assembly by adopting a hybrid de novo assembly approach that combined Pacific Biosciences single-molecule real-time sequencing, high-throughput chromatin conformation capture mapping, and Illumina short-read sequencing....
PubMed:33099628

Revisiting the organization of Polycomb-repressed domains: 3D chromatin models from Hi-C compared with super-resolution imaging.


Liu L, Hyeon C (Nucleic Acids Res. 2020 Oct 23;:)
The accessibility of target gene, a factor critical for gene regulation, is controlled by epigenetic fine-tuning of chromatin organization. While there are multiple experimental techniques to study change of chromatin architecture with its epigenetic state, measurements from them are not always complementary. A qualitative discrepancy is noted between recent super-resolution imaging studies, particularly on Polycomb-group protein repressed domains in Drosophila cell. One of the studies shows that Polycomb-repressed domains are more compact than inactive domains and are segregated from neighboring active domains, whereas Hi-C and chromatin accessibility assay as well as the other super-resolution imaging studies paint a different picture. To examine this issue in detail, we analyzed Hi-C libraries of Drosophila chromosomes as well as distance constraints from one of the imaging studies, and modeled different epigenetic domains by employing a polymer-based approach. According to our chromosome models, both Polycomb-repressed and inactive domains are featured with a similar degree of intra-domain packaging and significant intermixing with adjacent active domains. The epigenetic domain......
PubMed:33095877

High-resolution three-dimensional chromatin profiling of the Chinese hamster ovary cell genome.


Bevan S, Schoenfelder S, Young RJ, Zhang L, Andrews S, Fraser P, O'Callaghan PM (Biotechnol Bioeng. 2020 Oct 23;:)
Chinese hamster ovary (CHO) cell lines are the pillars of a multi-billion dollar biopharmaceutical industry producing recombinant therapeutic proteins. The effects of local chromatin organisation and epigenetic repression within these cell lines result in unpredictable and unstable transgene expression following random integration. Limited knowledge of the CHO genome and its higher-order chromatin organisation has thus far impeded functional genomics approaches required to tackle these issues. Here, we present an integrative three-dimensional (3D) map of genome organisation within the CHOK1SV® 10E9 cell line in conjunction with an improved, less fragmented CHOK1SV® 10E9 genome assembly. Using our high-resolution chromatin conformation datasets, we have assigned ≈ 90% of sequence to a chromosome-scale genome assembly. Our genome-wide 3D map identifies higher-order chromatin structures such as topologically associated domains, incorporates our chromatin accessibility data to enhance the identification of active cis-regulatory elements and importantly links these cis-regulatory elements to target promoters in a 3D promoter interactome. We demonstrate the power of our improved func......
PubMed:33095445

ASHIC: hierarchical Bayesian modeling of diploid chromatin contacts and structures.


Ye T, Ma W (Nucleic Acids Res. 2020 Oct 19;:)
The recently developed Hi-C technique has been widely applied to map genome-wide chromatin interactions. However, current methods for analyzing diploid Hi-C data cannot fully distinguish between homologous chromosomes. Consequently, the existing diploid Hi-C analyses are based on sparse and inaccurate allele-specific contact matrices, which might lead to incorrect modeling of diploid genome architecture. Here we present ASHIC, a hierarchical Bayesian framework to model allele-specific chromatin organizations in diploid genomes. We developed two models under the Bayesian framework: the Poisson-multinomial (ASHIC-PM) model and the zero-inflated Poisson-multinomial (ASHIC-ZIPM) model. The proposed ASHIC methods impute allele-specific contact maps from diploid Hi-C data and simultaneously infer allelic 3D structures. Through simulation studies, we demonstrated that ASHIC methods outperformed existing approaches, especially under low coverage and low SNP density conditions. Additionally, in the analyses of diploid Hi-C datasets in mouse and human, our ASHIC-ZIPM method produced fine-resolution diploid chromatin maps and 3D structures and provided insights into the allelic chromatin orga......
PubMed:33074315